biomedical named entities: Topics by WorldWideScience.org

Sample records for biomedical named entities

Character-level neural network for biomedical named entity recognition.

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

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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
Deep learning with word embeddings improves biomedical named entity recognition.

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Habibi, Maryam; Weber, Leon; Neves, Mariana; Wiegandt, David Luis; Leser, Ulf

2017-07-15

Text mining has become an important tool for biomedical research. The most fundamental text-mining task is the recognition of biomedical named entities (NER), such as genes, chemicals and diseases. Current NER methods rely on pre-defined features which try to capture the specific surface properties of entity types, properties of the typical local context, background knowledge, and linguistic information. State-of-the-art tools are entity-specific, as dictionaries and empirically optimal feature sets differ between entity types, which makes their development costly. Furthermore, features are often optimized for a specific gold standard corpus, which makes extrapolation of quality measures difficult. We show that a completely generic method based on deep learning and statistical word embeddings [called long short-term memory network-conditional random field (LSTM-CRF)] outperforms state-of-the-art entity-specific NER tools, and often by a large margin. To this end, we compared the performance of LSTM-CRF on 33 data sets covering five different entity classes with that of best-of-class NER tools and an entity-agnostic CRF implementation. On average, F1-score of LSTM-CRF is 5% above that of the baselines, mostly due to a sharp increase in recall. The source code for LSTM-CRF is available at https://github.com/glample/tagger and the links to the corpora are available at https://corposaurus.github.io/corpora/ . habibima@informatik.hu-berlin.de. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
NAMED ENTITY RECOGNITION FROM BIOMEDICAL TEXT -AN INFORMATION EXTRACTION TASK

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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.
Named entity normalization in user generated content

NARCIS (Netherlands)

Jijkoun, V.; Khalid, M.A.; Marx, M.; de Rijke, M.

2008-01-01

Named entity recognition is important for semantically oriented retrieval tasks, such as question answering, entity retrieval, biomedical retrieval, trend detection, and event and entity tracking. In many of these tasks it is important to be able to accurately normalize the recognized entities,
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition.

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Tsai, Richard Tzong-Han; Sung, Cheng-Lung; Dai, Hong-Jie; Hung, Hsieh-Chuan; Sung, Ting-Yi; Hsu, Wen-Lian

2006-12-18

Biomedical named entity recognition (Bio-NER) is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes) do not follow one standard nomenclature. They have many irregularities and sometimes appear in ambiguous contexts. In recent years, machine-learning (ML) approaches have become increasingly common and now represent the cutting edge of Bio-NER technology. This paper addresses three problems faced by ML-based Bio-NER systems. First, most ML approaches usually employ singleton features that comprise one linguistic property (e.g., the current word is capitalized) and at least one class tag (e.g., B-protein, the beginning of a protein name). However, such features may be insufficient in cases where multiple properties must be considered. Adding conjunction features that contain multiple properties can be beneficial, but it would be infeasible to include all conjunction features in an NER model since memory resources are limited and some features are ineffective. To resolve the problem, we use a sequential forward search algorithm to select an effective set of features. Second, variations in the numerical parts of biomedical terms (e.g., "2" in the biomedical term IL2) cause data sparseness and generate many redundant features. In this case, we apply numerical normalization, which solves the problem by replacing all numerals in a term with one representative numeral to help classify named entities. Third, the assignment of NE tags does not depend solely on the target word's closest neighbors, but may depend on words outside the context window (e.g., a context window of five consists of the current word plus two preceding and two subsequent words). We use global patterns generated by the Smith-Waterman local alignment algorithm to identify such structures and modify the results of our ML-based tagger. This is called pattern-based post-processing. To develop our ML-based Bio-NER system, we employ conditional
NERBio: using selected word conjunctions, term normalization, and global patterns to improve biomedical named entity recognition

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Hung Hsieh-Chuan

2006-12-01

Full Text Available Abstract Background Biomedical named entity recognition (Bio-NER is a challenging problem because, in general, biomedical named entities of the same category (e.g., proteins and genes do not follow one standard nomenclature. They have many irregularities and sometimes appear in ambiguous contexts. In recent years, machine-learning (ML approaches have become increasingly common and now represent the cutting edge of Bio-NER technology. This paper addresses three problems faced by ML-based Bio-NER systems. First, most ML approaches usually employ singleton features that comprise one linguistic property (e.g., the current word is capitalized and at least one class tag (e.g., B-protein, the beginning of a protein name. However, such features may be insufficient in cases where multiple properties must be considered. Adding conjunction features that contain multiple properties can be beneficial, but it would be infeasible to include all conjunction features in an NER model since memory resources are limited and some features are ineffective. To resolve the problem, we use a sequential forward search algorithm to select an effective set of features. Second, variations in the numerical parts of biomedical terms (e.g., "2" in the biomedical term IL2 cause data sparseness and generate many redundant features. In this case, we apply numerical normalization, which solves the problem by replacing all numerals in a term with one representative numeral to help classify named entities. Third, the assignment of NE tags does not depend solely on the target word's closest neighbors, but may depend on words outside the context window (e.g., a context window of five consists of the current word plus two preceding and two subsequent words. We use global patterns generated by the Smith-Waterman local alignment algorithm to identify such structures and modify the results of our ML-based tagger. This is called pattern-based post-processing. Results To develop our ML
GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text.

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Zhu, Qile; Li, Xiaolin; Conesa, Ana; Pereira, Cécile

2018-05-01

Best performing named entity recognition (NER) methods for biomedical literature are based on hand-crafted features or task-specific rules, which are costly to produce and difficult to generalize to other corpora. End-to-end neural networks achieve state-of-the-art performance without hand-crafted features and task-specific knowledge in non-biomedical NER tasks. However, in the biomedical domain, using the same architecture does not yield competitive performance compared with conventional machine learning models. We propose a novel end-to-end deep learning approach for biomedical NER tasks that leverages the local contexts based on n-gram character and word embeddings via Convolutional Neural Network (CNN). We call this approach GRAM-CNN. To automatically label a word, this method uses the local information around a word. Therefore, the GRAM-CNN method does not require any specific knowledge or feature engineering and can be theoretically applied to a wide range of existing NER problems. The GRAM-CNN approach was evaluated on three well-known biomedical datasets containing different BioNER entities. It obtained an F1-score of 87.26% on the Biocreative II dataset, 87.26% on the NCBI dataset and 72.57% on the JNLPBA dataset. Those results put GRAM-CNN in the lead of the biological NER methods. To the best of our knowledge, we are the first to apply CNN based structures to BioNER problems. The GRAM-CNN source code, datasets and pre-trained model are available online at: https://github.com/valdersoul/GRAM-CNN. andyli@ece.ufl.edu or aconesa@ufl.edu. Supplementary data are available at Bioinformatics online.
CNN-based ranking for biomedical entity normalization.

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

2017-10-03

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

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Pino Buizza

2011-12-01

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A partire da un punto di vista semantico più che morfologico, l'articolo è focalizzato il problema del significato dei nomi propri, con contributi della filosofia del linguaggio e della linguistica semantica. Sono indagate le entità individuali: il loro isolamento all’interno della rete di soggetti e la relazione esemplificativa, il trattamento nelle classificazioni. Le profonde diversità rilevate fra concetti e entità denominate suggeriscono di dichiararle esplicitamente da un punto di vista teorico e di adottare dispositivi che diano risultati unitari ma chiaramente distinguibili nei sistemi di recupero dell’informazione.
Questo contributo è stato presentato col titolo Indexing concepts and/or named entities all'11th ISKO Conference, Paradigms and conceptual systems in knowledge organization, Roma, 23-26 febbraio 2010, non pubblicato negli atti, e qui leggermente ampliato.
Starting from a semantic rather than form a morphological point of view, the essay examines the problem of the meaning of proper names, with contributions coming from the philosophy of language and the semantic linguistics. Individual entities are explored: the way they are isolated in the thread of subjects, the illustrative relation, and the classification treatment. The deep differences between concepts and called entities suggest to declare them specifically in a theoretical way, and to adopt devices that lead to uniform but noticeable results in information retrieval systems.
This article has been discussed as "Indexing concepts and/or named entities" to the 11th ISKO Conference, Paradigms and conceptual systems in knowledge organization, Rome, 23-26 February 2010, here extended since it is not published in the conference proceedings.
Named Entity Linking Algorithm

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M. F. Panteleev

2017-01-01

Full Text Available In the tasks of processing text in natural language, Named Entity Linking (NEL represents the task to define and link some entity, which is found in the text, with some entity in the knowledge base (for example, Dbpedia. Currently, there is a diversity of approaches to solve this problem, but two main classes can be identified: graph-based approaches and machine learning-based ones. Graph and Machine Learning approaches-based algorithm is proposed accordingly to the stated assumptions about the interrelations of named entities in a sentence and in general.In the case of graph-based approaches, it is necessary to solve the problem of identifying an optimal set of the related entities according to some metric that characterizes the distance between these entities in a graph built on some knowledge base. Due to limitations in processing power, to solve this task directly is impossible. Therefore, its modification is proposed. Based on the algorithms of machine learning, an independent solution cannot be built due to small volumes of training datasets relevant to NEL task. However, their use can contribute to improving the quality of the algorithm. The adaptation of the Latent Dirichlet Allocation model is proposed in order to obtain a measure of the compatibility of attributes of various entities encountered in one context.The efficiency of the proposed algorithm was experimentally tested. A test dataset was independently generated. On its basis the performance of the model was compared using the proposed algorithm with the open source product DBpedia Spotlight, which solves the NEL problem.The mockup, based on the proposed algorithm, showed a low speed as compared to DBpedia Spotlight. However, the fact that it has shown higher accuracy, stipulates the prospects for work in this direction.The main directions of development were proposed in order to increase the accuracy of the system and its productivity.
Tagging Named Entities in Croatian Tweets

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Krešimir Baksa

2017-01-01

Full Text Available Named entity extraction tools designed for recognizing named entities in texts written in standard language (e.g., news stories or legal texts have been shown to be inadequate for user-generated textual content (e.g., tweets, forum posts. In this work, we propose a supervised approach to named entity recognition and classification for Croatian tweets. We compare two sequence labelling models: a hidden Markov model (HMM and conditional random fields (CRF. Our experiments reveal that CRF is the best model for the task, achieving a very good performance of over 87% micro-averaged F1 score. We analyse the contributions of different feature groups and influence of the training set size on the performance of the CRF model.
Entity recognition in the biomedical domain using a hybrid approach.

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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.
Named entity recognition in a South African context

CSIR Research Space (South Africa)

De Waal, AJ

2006-10-01

Full Text Available Named Entity Recognition (NER) is the process of identifying occurrences of words or expressions as belonging to a particular category of a Named Entity (NE).The aim of the project was to test the feasibility of a probabilistic NER system using...
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

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Bachman, John A; Gyori, Benjamin M; Sorger, Peter K

2018-06-28

For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers, a process known as named entity linking or "grounding." Correct grounding is essential for resolving relationships among mined information, curated interaction databases, and biological datasets. The accuracy of this process is largely dependent on the availability of machine-readable resources associating synonyms and abbreviations commonly found in biomedical literature with uniform identifiers. In a task involving automated reading of ∼215,000 articles using the REACH event extraction software we found that grounding was disproportionately inaccurate for multi-protein families (e.g., "AKT") and complexes with multiple subunits (e.g."NF- κB"). To address this problem we constructed FamPlex, a manually curated resource defining protein families and complexes as they are commonly encountered in biomedical text. In FamPlex the gene-level constituents of families and complexes are defined in a flexible format allowing for multi-level, hierarchical membership. To create FamPlex, text strings corresponding to entities were identified empirically from literature and linked manually to uniform identifiers; these identifiers were also mapped to equivalent entries in multiple related databases. FamPlex also includes curated prefix and suffix patterns that improve named entity recognition and event extraction. Evaluation of REACH extractions on a test corpus of ∼54,000 articles showed that FamPlex significantly increased grounding accuracy for families and complexes (from 15 to 71%). The hierarchical organization of entities in FamPlex also made it possible to integrate otherwise unconnected mechanistic information across families, subfamilies, and individual proteins. Applications of FamPlex to the TRIPS/DRUM reading system and the Biocreative VI Bioentity
Active learning for ontological event extraction incorporating named entity recognition and unknown word handling.

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Han, Xu; Kim, Jung-jae; Kwoh, Chee Keong

2016-01-01

Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled data, which are required for state-of-the-art supervised learning systems. Active learning is to choose the most informative documents for the supervised learning in order to reduce the amount of required manual annotations. Previous works of active learning, however, focused on the tasks of entity recognition and protein-protein interactions, but not on event extraction tasks for multiple event types. They also did not consider the evidence of event participants, which might be a clue for the presence of events in unlabeled documents. Moreover, the confidence scores of events produced by event extraction systems are not reliable for ranking documents in terms of informativity for supervised learning. We here propose a novel committee-based active learning method that supports multi-event extraction tasks and employs a new statistical method for informativity estimation instead of using the confidence scores from event extraction systems. Our method is based on a committee of two systems as follows: We first employ an event extraction system to filter potential false negatives among unlabeled documents, from which the system does not extract any event. We then develop a statistical method to rank the potential false negatives of unlabeled documents 1) by using a language model that measures the probabilities of the expression of multiple events in documents and 2) by using a named entity recognition system that locates the named entities that can be event arguments (e.g. proteins). The proposed method further deals with unknown words in test data by using word similarity measures. We also apply our active learning method for the task of named entity recognition. We evaluate the proposed method against the BioNLP Shared Tasks datasets, and show that our method
BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature.

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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.
Incorporating rich background knowledge for gene named entity classification and recognition

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Yang Zhihao

2009-07-01

Full Text Available Abstract Background Gene named entity classification and recognition are crucial preliminary steps of text mining in biomedical literature. Machine learning based methods have been used in this area with great success. In most state-of-the-art systems, elaborately designed lexical features, such as words, n-grams, and morphology patterns, have played a central part. However, this type of feature tends to cause extreme sparseness in feature space. As a result, out-of-vocabulary (OOV terms in the training data are not modeled well due to lack of information. Results We propose a general framework for gene named entity representation, called feature coupling generalization (FCG. The basic idea is to generate higher level features using term frequency and co-occurrence information of highly indicative features in huge amount of unlabeled data. We examine its performance in a named entity classification task, which is designed to remove non-gene entries in a large dictionary derived from online resources. The results show that new features generated by FCG outperform lexical features by 5.97 F-score and 10.85 for OOV terms. Also in this framework each extension yields significant improvements and the sparse lexical features can be transformed into both a lower dimensional and more informative representation. A forward maximum match method based on the refined dictionary produces an F-score of 86.2 on BioCreative 2 GM test set. Then we combined the dictionary with a conditional random field (CRF based gene mention tagger, achieving an F-score of 89.05, which improves the performance of the CRF-based tagger by 4.46 with little impact on the efficiency of the recognition system. A demo of the NER system is available at http://202.118.75.18:8080/bioner.
Supporting inter-topic entity search for biomedical Linked Data based on heterogeneous relationships.

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Zong, Nansu; Lee, Sungin; Ahn, Jinhyun; Kim, Hong-Gee

2017-08-01

The keyword-based entity search restricts search space based on the preference of search. When given keywords and preferences are not related to the same biomedical topic, existing biomedical Linked Data search engines fail to deliver satisfactory results. This research aims to tackle this issue by supporting an inter-topic search-improving search with inputs, keywords and preferences, under different topics. This study developed an effective algorithm in which the relations between biomedical entities were used in tandem with a keyword-based entity search, Siren. The algorithm, PERank, which is an adaptation of Personalized PageRank (PPR), uses a pair of input: (1) search preferences, and (2) entities from a keyword-based entity search with a keyword query, to formalize the search results on-the-fly based on the index of the precomputed Individual Personalized PageRank Vectors (IPPVs). Our experiments were performed over ten linked life datasets for two query sets, one with keyword-preference topic correspondence (intra-topic search), and the other without (inter-topic search). The experiments showed that the proposed method achieved better search results, for example a 14% increase in precision for the inter-topic search than the baseline keyword-based search engine. The proposed method improved the keyword-based biomedical entity search by supporting the inter-topic search without affecting the intra-topic search based on the relations between different entities. Copyright © 2017 Elsevier Ltd. All rights reserved.
Cross domains Arabic named entity recognition system

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Al-Ahmari, S. Saad; Abdullatif Al-Johar, B.

2016-07-01

Named Entity Recognition (NER) plays an important role in many Natural Language Processing (NLP) applications such as; Information Extraction (IE), Question Answering (QA), Text Clustering, Text Summarization and Word Sense Disambiguation. This paper presents the development and implementation of domain independent system to recognize three types of Arabic named entities. The system works based on a set of domain independent grammar-rules along with Arabic part of speech tagger in addition to gazetteers and lists of trigger words. The experimental results shown, that the system performed as good as other systems with better results in some cases of cross-domains corpora.

A generic open world named entity disambiguation approach for tweets

NARCIS (Netherlands)

Habib, Mena Badieh; van Keulen, Maurice

Social media is a rich source of information. To make use of this information, it is sometimes required to extract and disambiguate named entities. In this paper we focus on named entity disambiguation (NED) in twitter messages. NED in tweets is challenging in two ways. First, the limited length of
Cross domains Arabic named entity recognition system

KAUST Repository

Al-Ahmari, S. Saad

2016-07-11

Named Entity Recognition (NER) plays an important role in many Natural Language Processing (NLP) applications such as; Information Extraction (IE), Question Answering (QA), Text Clustering, Text Summarization and Word Sense Disambiguation. This paper presents the development and implementation of domain independent system to recognize three types of Arabic named entities. The system works based on a set of domain independent grammar-rules along with Arabic part of speech tagger in addition to gazetteers and lists of trigger words. The experimental results shown, that the system performed as good as other systems with better results in some cases of cross-domains corpora. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Cross domains Arabic named entity recognition system

KAUST Repository

Al-Ahmari, S. Saad; Abdullatif Al-Johar, B.

2016-01-01

Named Entity Recognition (NER) plays an important role in many Natural Language Processing (NLP) applications such as; Information Extraction (IE), Question Answering (QA), Text Clustering, Text Summarization and Word Sense Disambiguation. This paper presents the development and implementation of domain independent system to recognize three types of Arabic named entities. The system works based on a set of domain independent grammar-rules along with Arabic part of speech tagger in addition to gazetteers and lists of trigger words. The experimental results shown, that the system performed as good as other systems with better results in some cases of cross-domains corpora. © (2016) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.
Enhanced Named Entity Extraction via Error-Driven Aggregation

Energy Technology Data Exchange (ETDEWEB)

Lemmond, T D; Perry, N C; Guensche, J W; Nitao, J J; Glaser, R E; Kidwell, P; Hanley, W G

2010-02-22

Despite recent advances in named entity extraction technologies, state-of-the-art extraction tools achieve insufficient accuracy rates for practical use in many operational settings. However, they are not generally prone to the same types of error, suggesting that substantial improvements may be achieved via appropriate combinations of existing tools, provided their behavior can be accurately characterized and quantified. In this paper, we present an inference methodology for the aggregation of named entity extraction technologies that is founded upon a black-box analysis of their respective error processes. This method has been shown to produce statistically significant improvements in extraction relative to standard performance metrics and to mitigate the weak performance of entity extractors operating under suboptimal conditions. Moreover, this approach provides a framework for quantifying uncertainty and has demonstrated the ability to reconstruct the truth when majority voting fails.
Proper Names and Named Entities Recognition in the Automatic Text Processing. Review of the book: Nouvel, D., Ehrmann, M., & Rosset, S. (2016. Named Entities for Computational Linguistics. London; Hoboken: ISTE Ltd; John Wiley & Sons, Inc., 2016.

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Daria M. Golikova

2018-03-01

Full Text Available The reviewed book by Damien Nouvel, Maud Ehrmann, and Sophie Rosset Named Entities for Computational Linguistics deals with automatic processing of texts, written in a natural language, and with named entities recognition, aimed at extracting most important information in these texts. The notion of named entities here extends to the entire set of linguistic units referring to an object. The researchers minutely consider the concept of named entities, juxtaposing this category to that of proper names and comparing their definitions, and describe all the stages of creation and implementation of automatic text annotation algorithms, as well as different ways of evaluating their performance quality. Proper names, in this context, are seen as a particular instance of named entities, one of the typical sources of reference to real objects to be electronically recognized in the text. The book provides a detailed overview and analysis of previous studies in the same field, based mainly on the English language data. It presents instruments and resources required to create and implement the algorithms in question, these may include typologies, knowledge or databases, and various types of corpora. Theoretical considerations, proposed by the authors, are supported by a significant number of exemplary cases, with algorithms operation principles presented in charts. The reviewed book gives quite a comprehensive picture of modern computational linguistic studies focused on named entities recognition and indicates some problems which are unresolved as yet.
Named Entity Recognition for Novel Types by Transfer Learning

OpenAIRE

Qu, Lizhen; Ferraro, Gabriela; Zhou, Liyuan; Hou, Weiwei; Baldwin, Timothy

2016-01-01

In named entity recognition, we often don't have a large in-domain training corpus or a knowledge base with adequate coverage to train a model directly. In this paper, we propose a method where, given training data in a related domain with similar (but not identical) named entity (NE) types and a small amount of in-domain training data, we use transfer learning to learn a domain-specific NE model. That is, the novelty in the task setup is that we assume not just domain mismatch, but also labe...
Assessment of disease named entity recognition on a corpus of annotated sentences.

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Jimeno, Antonio; Jimenez-Ruiz, Ernesto; Lee, Vivian; Gaudan, Sylvain; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich

2008-04-11

In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named entities in the scientific literature. While matching the terminology with language patterns suffers from low recall (e.g., Whatizit) other solutions make use of morpho-syntactic features to better cover the full scope of terminological variability (e.g., MetaMap). Currently, MetaMap that is provided from the National Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus. In addition, little effort has been invested so far to generate an annotated dataset that links disease entities in text to disease entries in a database, thesaurus or ontology and that could serve as a gold standard to benchmark text mining solutions. As part of our research work, we have taken a corpus that has been delivered in the past for the identification of associations of genes to diseases based on the UMLS Metathesaurus and we have reprocessed and re-annotated the corpus. We have gathered annotations for disease entities from two curators, analyzed their disagreement (0.51 in the kappa-statistic) and composed a single annotated corpus for public use. Thereafter, three solutions for disease named entity recognition including MetaMap have been applied to the corpus to automatically annotate it with UMLS Metathesaurus concepts. The resulting annotations have been benchmarked to compare their performance. The annotated corpus is publicly available at ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases and can serve as a benchmark to other systems. In addition, we found
Untangling the brand name from the branded entity

OpenAIRE

Round, Griff; Roper, Stuart

2015-01-01

Purpose\\ud – The purpose of this study is to investigate the value to consumers of the brand name element for established brands, given that the focus in the literature has been on new brands. To accomplish this, conceptual development was initially undertaken to illuminate the links between the brand name element and the brand entity and to provide a theoretical framework for looking at changes in value of the brand name element to consumers over time.\\ud \\ud Design/methodology/approach\\ud –...
Medical Named Entity Recognition for Indonesian Language Using Word Representations

Science.gov (United States)

Rahman, Arief

2018-03-01

Nowadays, Named Entity Recognition (NER) system is used in medical texts to obtain important medical information, like diseases, symptoms, and drugs. While most NER systems are applied to formal medical texts, informal ones like those from social media (also called semi-formal texts) are starting to get recognition as a gold mine for medical information. We propose a theoretical Named Entity Recognition (NER) model for semi-formal medical texts in our medical knowledge management system by comparing two kinds of word representations: cluster-based word representation and distributed representation.
Named entity extraction and disambiguation: the missing link

NARCIS (Netherlands)

Habib, Mena Badieh; van Keulen, Maurice

2013-01-01

Named entity extraction (NEE) and disambiguation (NED) are two areas of research that are well covered in literature. Typical fields addressing these topics are information retrieval, natural language processing, and semantic web. Although these topics are highly dependent, almost no existing works
TwitterNEED: a hybrid approach for named entity extraction and disambiguation for tweets

NARCIS (Netherlands)

Habib, Mena Badieh; van Keulen, Maurice

Twitter is a rich source of continuously and instantly updated information. Shortness and informality of tweets are challenges for Natural Language Processing tasks. In this paper, we present TwitterNEED, a hybrid approach for Named Entity Extraction and Named Entity Disambiguation for tweets. We
LINNAEUS: A species name identification system for biomedical literature

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Nenadic Goran

2010-02-01

Full Text Available Abstract Background The task of recognizing and identifying species names in biomedical literature has recently been regarded as critical for a number of applications in text and data mining, including gene name recognition, species-specific document retrieval, and semantic enrichment of biomedical articles. Results In this paper we describe an open-source species name recognition and normalization software system, LINNAEUS, and evaluate its performance relative to several automatically generated biomedical corpora, as well as a novel corpus of full-text documents manually annotated for species mentions. LINNAEUS uses a dictionary-based approach (implemented as an efficient deterministic finite-state automaton to identify species names and a set of heuristics to resolve ambiguous mentions. When compared against our manually annotated corpus, LINNAEUS performs with 94% recall and 97% precision at the mention level, and 98% recall and 90% precision at the document level. Our system successfully solves the problem of disambiguating uncertain species mentions, with 97% of all mentions in PubMed Central full-text documents resolved to unambiguous NCBI taxonomy identifiers. Conclusions LINNAEUS is an open source, stand-alone software system capable of recognizing and normalizing species name mentions with speed and accuracy, and can therefore be integrated into a range of bioinformatics and text-mining applications. The software and manually annotated corpus can be downloaded freely at http://linnaeus.sourceforge.net/.
Disease named entity recognition from biomedical literature using a novel convolutional neural network.

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Zhao, Zhehuan; Yang, Zhihao; Luo, Ling; Wang, Lei; Zhang, Yin; Lin, Hongfei; Wang, Jian

2017-12-28

Automatic disease named entity recognition (DNER) is of utmost importance for development of more sophisticated BioNLP tools. However, most conventional CRF based DNER systems rely on well-designed features whose selection is labor intensive and time-consuming. Though most deep learning methods can solve NER problems with little feature engineering, they employ additional CRF layer to capture the correlation information between labels in neighborhoods which makes them much complicated. In this paper, we propose a novel multiple label convolutional neural network (MCNN) based disease NER approach. In this approach, instead of the CRF layer, a multiple label strategy (MLS) first introduced by us, is employed. First, the character-level embedding, word-level embedding and lexicon feature embedding are concatenated. Then several convolutional layers are stacked over the concatenated embedding. Finally, MLS strategy is applied to the output layer to capture the correlation information between neighboring labels. As shown by the experimental results, MCNN can achieve the state-of-the-art performance on both NCBI and CDR corpora. The proposed MCNN based disease NER method achieves the state-of-the-art performance with little feature engineering. And the experimental results show the MLS strategy's effectiveness of capturing the correlation information between labels in the neighborhood.
Using workflows to explore and optimise named entity recognition for chemistry.

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Balakrishna Kolluru

Full Text Available Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain, OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM and pattern recognition based classifiers. Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR.
Citizen Science for Mining the Biomedical Literature

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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.
Named-Entity Tagging a Very Large Unbalanced Corpus. Training and Evaluating NE classifiers

DEFF Research Database (Denmark)

Bingel, Joachim; Haider, Thomas

2014-01-01

We describe a systematic and application-oriented approach to training and evaluating named entity recognition and classification (NERC) systems, the purpose of which is to identify an optimal system and to train an optimal model for named entity tagging DeReKo, a very large general-purpose corpus...... when evaluated on more uniform and less diverse data. We create and manually annotate such a representative sample as evaluation data for three different NERC systems, for each of which various models are learnt on multiple training data. The proposed sampling method can be viewed as a generally...
Chemical Entity Recognition and Resolution to ChEBI

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Grego, Tiago; Pesquita, Catia; Bastos, Hugo P.; Couto, Francisco M.

2012-01-01

Chemical entities are ubiquitous through the biomedical literature and the development of text-mining systems that can efficiently identify those entities are required. Due to the lack of available corpora and data resources, the community has focused its efforts in the development of gene and protein named entity recognition systems, but with the release of ChEBI and the availability of an annotated corpus, this task can be addressed. We developed a machine-learning-based method for chemical entity recognition and a lexical-similarity-based method for chemical entity resolution and compared them with Whatizit, a popular-dictionary-based method. Our methods outperformed the dictionary-based method in all tasks, yielding an improvement in F-measure of 20% for the entity recognition task, 2–5% for the entity-resolution task, and 15% for combined entity recognition and resolution tasks. PMID:25937941
BioCause: Annotating and analysing causality in the biomedical domain.

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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
Low-Cost Implementation of a Named Entity Recognition System for Voice-Activated Human-Appliance Interfaces in a Smart Home

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Geonwoo Park

2018-02-01

Full Text Available When we develop voice-activated human-appliance interface systems in smart homes, named entity recognition (NER is an essential tool for extracting execution targets from natural language commands. Previous studies on NER systems generally include supervised machine-learning methods that require a substantial amount of human-annotated training corpus. In the smart home environment, categories of named entities should be defined according to voice-activated devices (e.g., food names for refrigerators and song titles for music players. The previous machine-learning methods make it difficult to change categories of named entities because a large amount of the training corpus should be newly constructed by hand. To address this problem, we present a semi-supervised NER system to minimize the time-consuming and labor-intensive task of constructing the training corpus. Our system uses distant supervision methods with two kinds of auto-labeling processes: auto-labeling based on heuristic rules for single-class named entity corpus generation and auto-labeling based on a pre-trained single-class NER model for multi-class named entity corpus generation. Then, our system improves NER accuracy by using a bagging-based active learning method. In our experiments that included a generic domain that featured 11 named entity classes and a context-specific domain about baseball that featured 21 named entity classes, our system demonstrated good performances in both domains, with F1-measures of 0.777 and 0.958, respectively. Since our system was built from a relatively small human-annotated training corpus, we believe it is a viable alternative to current NER systems in smart home environments.
NEED4Tweet: A Twitterbot for Tweets Named Entity Extraction and Disambiguation

NARCIS (Netherlands)

Habib, Mena Badieh; van Keulen, Maurice

In this demo paper, we present NEED4Tweet, a Twitterbot for named entity extraction (NEE) and disambiguation (NED) for Tweets. The straightforward application of state-of-the-art extraction and disambiguation approaches on informal text widely used in Tweets, typically results in significantly

Named Entity Extraction and Linking Challenge: University of Twente at #Microposts2014

NARCIS (Netherlands)

Habib, Mena Badieh; van Keulen, Maurice; Zhu, Zhemin; Rowe, Matthew; Stankovic, Milan; Dadzie, Aba-Sah

Twitter is a potentially rich source of continuously and instantly updated information. Shortness and informality of tweets are challenges for Natural Language Processing (NLP) tasks. In this paper, we present a hybrid approach for Named Entity Extraction (NEE)and Linking (NEL) for tweets. Although
Using Local Grammar for Entity Extraction from Clinical Reports

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Aicha Ghoulam

2015-06-01

Full Text Available Information Extraction (IE is a natural language processing (NLP task whose aim is to analyze texts written in natural language to extract structured and useful information such as named entities and semantic relations linking these entities. Information extraction is an important task for many applications such as bio-medical literature mining, customer care, community websites, and personal information management. The increasing information available in patient clinical reports is difficult to access. As it is often in an unstructured text form, doctors need tools to enable them access to this information and the ability to search it. Hence, a system for extracting this information in a structured form can benefits healthcare professionals. The work presented in this paper uses a local grammar approach to extract medical named entities from French patient clinical reports. Experimental results show that the proposed approach achieved an F-Measure of 90. 06%.
A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

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Meijing Li

2015-01-01

Full Text Available Many researchers focus on developing protein-named entity recognition (Protein-NER or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM and parsing tree. PPIMiner consists of three main models: natural language processing (NLP model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.
The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text

DEFF Research Database (Denmark)

Pafilis, Evangelos; Pletscher-Frankild, Sune; Fanini, Lucia

2013-01-01

The exponential growth of the biomedical literature is making the need for efficient, accurate text-mining tools increasingly clear. The identification of named biological entities in text is a central and difficult task. We have developed an efficient algorithm and implementation of a dictionary......-based approach to named entity recognition, which we here use to identify names of species and other taxa in text. The tool, SPECIES, is more than an order of magnitude faster and as accurate as existing tools. The precision and recall was assessed both on an existing gold-standard corpus and on a new corpus...
Network analysis of named entity co-occurrences in written texts

Science.gov (United States)

Amancio, Diego Raphael

2016-06-01

The use of methods borrowed from statistics and physics to analyze written texts has allowed the discovery of unprecedent patterns of human behavior and cognition by establishing links between models features and language structure. While current models have been useful to unveil patterns via analysis of syntactical and semantical networks, only a few works have probed the relevance of investigating the structure arising from the relationship between relevant entities such as characters, locations and organizations. In this study, we represent entities appearing in the same context as a co-occurrence network, where links are established according to a null model based on random, shuffled texts. Computational simulations performed in novels revealed that the proposed model displays interesting topological features, such as the small world feature, characterized by high values of clustering coefficient. The effectiveness of our model was verified in a practical pattern recognition task in real networks. When compared with traditional word adjacency networks, our model displayed optimized results in identifying unknown references in texts. Because the proposed representation plays a complementary role in characterizing unstructured documents via topological analysis of named entities, we believe that it could be useful to improve the characterization of written texts (and related systems), specially if combined with traditional approaches based on statistical and deeper paradigms.
Gene name ambiguity of eukaryotic nomenclatures.

Science.gov (United States)

Chen, Lifeng; Liu, Hongfang; Friedman, Carol

2005-01-15

With more and more scientific literature published online, the effective management and reuse of this knowledge has become problematic. Natural language processing (NLP) may be a potential solution by extracting, structuring and organizing biomedical information in online literature in a timely manner. One essential task is to recognize and identify genomic entities in text. 'Recognition' can be accomplished using pattern matching and machine learning. But for 'identification' these techniques are not adequate. In order to identify genomic entities, NLP needs a comprehensive resource that specifies and classifies genomic entities as they occur in text and that associates them with normalized terms and also unique identifiers so that the extracted entities are well defined. Online organism databases are an excellent resource to create such a lexical resource. However, gene name ambiguity is a serious problem because it affects the appropriate identification of gene entities. In this paper, we explore the extent of the problem and suggest ways to address it. We obtained gene information from 21 organisms and quantified naming ambiguities within species, across species, with English words and with medical terms. When the case (of letters) was retained, official symbols displayed negligible intra-species ambiguity (0.02%) and modest ambiguities with general English words (0.57%) and medical terms (1.01%). In contrast, the across-species ambiguity was high (14.20%). The inclusion of gene synonyms increased intra-species ambiguity substantially and full names contributed greatly to gene-medical-term ambiguity. A comprehensive lexical resource that covers gene information for the 21 organisms was then created and used to identify gene names by using a straightforward string matching program to process 45,000 abstracts associated with the mouse model organism while ignoring case and gene names that were also English words. We found that 85.1% of correctly retrieved mouse
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.
"That thing in New York": Impaired naming vs. preserved recognition of unique entities following an anterior temporal lobe lesion

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Daniel Roberts

2014-04-01

Full Text Available Background Anterior temporal lobe (aTL damage often results in semantic impairment. As such, the contribution of this region to semantic processing has received considerable attention. Two theories exist to explain aTL function based on conflicting neuropsychological investigations. The first proposes bilateral aTLs form a “hub” implicated in multimodal semantics (for review see: Jefferies, 2013. The second assumes distinct functions. The left is thought to function as a repertoire for knowledge of entities with unique lexical-conceptual associations (for review: Ross & Olson, 2012. These items represent an extreme end of a continuum of semantic specificity spanning unique (e.g., Eiffel Tower over less specific (e.g., tower to nonspecific (e.g., landmark – often denoted by famous faces, landmarks and proper names. LaTL function, therefore, is to link semantics to language systems for naming, whilst RaTL is involved in familiarity and recognition (e.g., Eiffel Tower -> a building in Paris; Drane et al., 2013. Evidence for each theory has proceeded in parallel but there has been no attempt to directly test them in a patient (Simmons & Martin, 2009. The novelty of this study, therefore, was to determine whether LaTL lesions disproportionately affect unique entity naming vs. recognition. Method WRP, a 51year old right-handed male, three year post-HSVE has a LaTL lesion with destruction of the temporal pole, extending to medial temporal, amygdala and hippocampus and atypical connectivity particularly involving the uncinate fasciculas. There is no evidence of either cortical or white matter damage in the right hemisphere. Previous work with WRP revealed a mild/moderate category-specific semantic deficit (Roberts et al., 2012. This new study focuses on unique entity picture naming, recognition and word-to-picture matching (WPM. Results & Discussion As predicted, results (Table 1 show that WRP was severely impaired in naming different categories
Developing a hybrid dictionary-based bio-entity recognition technique

Science.gov (United States)

2015-01-01

Background Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. Methods This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. Results The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. Conclusions The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall. PMID:26043907
Developing a hybrid dictionary-based bio-entity recognition technique.

Science.gov (United States)

Song, Min; Yu, Hwanjo; Han, Wook-Shin

2015-01-01

Bio-entity extraction is a pivotal component for information extraction from biomedical literature. The dictionary-based bio-entity extraction is the first generation of Named Entity Recognition (NER) techniques. This paper presents a hybrid dictionary-based bio-entity extraction technique. The approach expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues to further improve the performance. The experimental results show that the proposed technique achieves the best or at least equivalent performance among compared techniques, GENIA, MESH, UMLS, and combinations of these three resources in F-measure. The results imply that the performance of dictionary-based extraction techniques is largely influenced by information resources used to build the dictionary. In addition, the edit distance algorithm shows steady performance with three different dictionaries in precision whereas the context-only technique achieves a high-end performance with three difference dictionaries in recall.
REDEN: Named Entity Linking in Digital Literary Editions Using Linked Data Sets

Directory of Open Access Journals (Sweden)

Carmen Brando

2016-07-01

Full Text Available This paper proposes a graph-based Named Entity Linking (NEL algorithm named REDEN for the disambiguation of authors’ names in French literary criticism texts and scientific essays from the 19th and early 20th centuries. The algorithm is described and evaluated according to the two phases of NEL as reported in current state of the art, namely, candidate retrieval and candidate selection. REDEN leverages knowledge from different Linked Data sources in order to select candidates for each author mention, subsequently crawls data from other Linked Data sets using equivalence links (e.g., owl:sameAs, and, finally, fuses graphs of homologous individuals into a non-redundant graph well-suited for graph centrality calculation; the resulting graph is used for choosing the best referent. The REDEN algorithm is distributed in open-source and follows current standards in digital editions (TEI and semantic Web (RDF. Its integration into an editorial workflow of digital editions in Digital humanities and cultural heritage projects is entirely plausible. Experiments are conducted along with the corresponding error analysis in order to test our approach and to help us to study the weaknesses and strengths of our algorithm, thereby to further improvements of REDEN.
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.
Sortal anaphora resolution to enhance relation extraction from biomedical literature.

Science.gov (United States)

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

2016-04-14

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

Directory of Open Access Journals (Sweden)

Raúl Gutiérrez

2015-12-01

Full Text Available Named Entity Recognition (NER is a main task into Natural Language Processing. On the one hand, supporting the extraction of the information on unstructured data. On the other hand, The NER is a probabilistic graphical model that allows us to represent the conditional independency assumptions into the sequential labelling. In this paper, we propose a discriminative graphical model by using linear-chain Conditional Random Fields (CRFs. We present the experiments based on the Conll-2002 shared task and Ancora corpus according to the following criteria: recall, precision and F-score. Our contributions in this work are the following: first, we tested our baseline on the CoNLL-2002 shared task obtaining 80% F1-measure, and 59% F1-measure on AnCora corpus respectively. Finally, the application Vigtech allow us to identify information and patterns in the cancer topic, we discuss the results according to the model performance and the useful information to support the forecasting process
Liberal Entity Extraction: Rapid Construction of Fine-Grained Entity Typing Systems.

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Huang, Lifu; May, Jonathan; Pan, Xiaoman; Ji, Heng; Ren, Xiang; Han, Jiawei; Zhao, Lin; Hendler, James A

2017-03-01

The ability of automatically recognizing and typing entities in natural language without prior knowledge (e.g., predefined entity types) is a major challenge in processing such data. Most existing entity typing systems are limited to certain domains, genres, and languages. In this article, we propose a novel unsupervised entity-typing framework by combining symbolic and distributional semantics. We start from learning three types of representations for each entity mention: general semantic representation, specific context representation, and knowledge representation based on knowledge bases. Then we develop a novel joint hierarchical clustering and linking algorithm to type all mentions using these representations. This framework does not rely on any annotated data, predefined typing schema, or handcrafted features; therefore, it can be quickly adapted to a new domain, genre, and/or language. Experiments on genres (news and discussion forum) show comparable performance with state-of-the-art supervised typing systems trained from a large amount of labeled data. Results on various languages (English, Chinese, Japanese, Hausa, and Yoruba) and domains (general and biomedical) demonstrate the portability of our framework.
Mining heart disease risk factors in clinical text with named entity recognition and distributional semantic models.

Science.gov (United States)

Urbain, Jay

2015-12-01

We present the design, and analyze the performance of a multi-stage natural language processing system employing named entity recognition, Bayesian statistics, and rule logic to identify and characterize heart disease risk factor events in diabetic patients over time. The system was originally developed for the 2014 i2b2 Challenges in Natural Language in Clinical Data. The system's strengths included a high level of accuracy for identifying named entities associated with heart disease risk factor events. The system's primary weakness was due to inaccuracies when characterizing the attributes of some events. For example, determining the relative time of an event with respect to the record date, whether an event is attributable to the patient's history or the patient's family history, and differentiating between current and prior smoking status. We believe these inaccuracies were due in large part to the lack of an effective approach for integrating context into our event detection model. To address these inaccuracies, we explore the addition of a distributional semantic model for characterizing contextual evidence of heart disease risk factor events. Using this semantic model, we raise our initial 2014 i2b2 Challenges in Natural Language of Clinical data F1 score of 0.838 to 0.890 and increased precision by 10.3% without use of any lexicons that might bias our results. Copyright © 2015 Elsevier Inc. All rights reserved.
Semantic representation of scientific literature: bringing claims, contributions and named entities onto the Linked Open Data cloud

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Bahar Sateli

2015-12-01

Full Text Available Motivation. Finding relevant scientific literature is one of the essential tasks researchers are facing on a daily basis. Digital libraries and web information retrieval techniques provide rapid access to a vast amount of scientific literature. However, no further automated support is available that would enable fine-grained access to the knowledge ‘stored’ in these documents. The emerging domain of Semantic Publishing aims at making scientific knowledge accessible to both humans and machines, by adding semantic annotations to content, such as a publication’s contributions, methods, or application domains. However, despite the promises of better knowledge access, the manual annotation of existing research literature is prohibitively expensive for wide-spread adoption. We argue that a novel combination of three distinct methods can significantly advance this vision in a fully-automated way: (i Natural Language Processing (NLP for Rhetorical Entity (RE detection; (ii Named Entity (NE recognition based on the Linked Open Data (LOD cloud; and (iii automatic knowledge base construction for both NEs and REs using semantic web ontologies that interconnect entities in documents with the machine-readable LOD cloud.Results. We present a complete workflow to transform scientific literature into a semantic knowledge base, based on the W3C standards RDF and RDFS. A text mining pipeline, implemented based on the GATE framework, automatically extracts rhetorical entities of type Claims and Contributions from full-text scientific literature. These REs are further enriched with named entities, represented as URIs to the linked open data cloud, by integrating the DBpedia Spotlight tool into our workflow. Text mining results are stored in a knowledge base through a flexible export process that provides for a dynamic mapping of semantic annotations to LOD vocabularies through rules stored in the knowledge base. We created a gold standard corpus from computer
Annotating patient clinical records with syntactic chunks and named entities: the Harvey Corpus.

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Savkov, Aleksandar; Carroll, John; Koeling, Rob; Cassell, Jackie

The free text notes typed by physicians during patient consultations contain valuable information for the study of disease and treatment. These notes are difficult to process by existing natural language analysis tools since they are highly telegraphic (omitting many words), and contain many spelling mistakes, inconsistencies in punctuation, and non-standard word order. To support information extraction and classification tasks over such text, we describe a de-identified corpus of free text notes, a shallow syntactic and named entity annotation scheme for this kind of text, and an approach to training domain specialists with no linguistic background to annotate the text. Finally, we present a statistical chunking system for such clinical text with a stable learning rate and good accuracy, indicating that the manual annotation is consistent and that the annotation scheme is tractable for machine learning.
Text mining patents for biomedical knowledge.

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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.
Commercializing biomedical research through securitization techniques.

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Fernandez, Jose-Maria; Stein, Roger M; Lo, Andrew W

2012-10-01

Biomedical innovation has become riskier, more expensive and more difficult to finance with traditional sources such as private and public equity. Here we propose a financial structure in which a large number of biomedical programs at various stages of development are funded by a single entity to substantially reduce the portfolio's risk. The portfolio entity can finance its activities by issuing debt, a critical advantage because a much larger pool of capital is available for investment in debt versus equity. By employing financial engineering techniques such as securitization, it can raise even greater amounts of more-patient capital. In a simulation using historical data for new molecular entities in oncology from 1990 to 2011, we find that megafunds of $5–15 billion may yield average investment returns of 8.9–11.4% for equity holders and 5–8% for 'research-backed obligation' holders, which are lower than typical venture-capital hurdle rates but attractive to pension funds, insurance companies and other large institutional investors.

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

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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.
Normalizing biomedical terms by minimizing ambiguity and variability

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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.
Moving beyond the Name: Defining Corporate Entities to Support Provenance-Based Access

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Light, Michelle

2007-01-01

The second edition of the "International Standard Archival Authority Records for Corporate Bodies, Persons, and Families (ISAAR(CPF)2)" focuses on describing entities as they exist in reality, rather than on establishing authorized terms. This change allows authority records to include multiple authorized terms representing an entity as it changed…
Physical properties of biological entities: an introduction to the ontology of physics for biology.

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Daniel L Cook

Full Text Available As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB, a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration.
Physical properties of biological entities: an introduction to the ontology of physics for biology.

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Cook, Daniel L; Bookstein, Fred L; Gennari, John H

2011-01-01

As biomedical investigators strive to integrate data and analyses across spatiotemporal scales and biomedical domains, they have recognized the benefits of formalizing languages and terminologies via computational ontologies. Although ontologies for biological entities-molecules, cells, organs-are well-established, there are no principled ontologies of physical properties-energies, volumes, flow rates-of those entities. In this paper, we introduce the Ontology of Physics for Biology (OPB), a reference ontology of classical physics designed for annotating biophysical content of growing repositories of biomedical datasets and analytical models. The OPB's semantic framework, traceable to James Clerk Maxwell, encompasses modern theories of system dynamics and thermodynamics, and is implemented as a computational ontology that references available upper ontologies. In this paper we focus on the OPB classes that are designed for annotating physical properties encoded in biomedical datasets and computational models, and we discuss how the OPB framework will facilitate biomedical knowledge integration. © 2011 Cook et al.
Encoding of Fundamental Chemical Entities of Organic Reactivity Interest using chemical ontology and XML.

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Durairaj, Vijayasarathi; Punnaivanam, Sankar

2015-09-01

Fundamental chemical entities are identified in the context of organic reactivity and classified as appropriate concept classes namely ElectronEntity, AtomEntity, AtomGroupEntity, FunctionalGroupEntity and MolecularEntity. The entity classes and their subclasses are organized into a chemical ontology named "ChemEnt" for the purpose of assertion, restriction and modification of properties through entity relations. Individual instances of entity classes are defined and encoded as a library of chemical entities in XML. The instances of entity classes are distinguished with a unique notation and identification values in order to map them with the ontology definitions. A model GUI named Entity Table is created to view graphical representations of all the entity instances. The detection of chemical entities in chemical structures is achieved through suitable algorithms. The possibility of asserting properties to the entities at different levels and the mechanism of property flow within the hierarchical entity levels is outlined. Copyright © 2015 Elsevier Inc. All rights reserved.
Context and Domain Knowledge Enhanced Entity Spotting in Informal Text

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Gruhl, Daniel; Nagarajan, Meena; Pieper, Jan; Robson, Christine; Sheth, Amit

This paper explores the application of restricted relationship graphs (RDF) and statistical NLP techniques to improve named entity annotation in challenging Informal English domains. We validate our approach using on-line forums discussing popular music. Named entity annotation is particularly difficult in this domain because it is characterized by a large number of ambiguous entities, such as the Madonna album "Music" or Lilly Allen's pop hit "Smile".
ParaBTM: A Parallel Processing Framework for Biomedical Text Mining on Supercomputers.

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Xing, Yuting; Wu, Chengkun; Yang, Xi; Wang, Wei; Zhu, En; Yin, Jianping

2018-04-27

A prevailing way of extracting valuable information from biomedical literature is to apply text mining methods on unstructured texts. However, the massive amount of literature that needs to be analyzed poses a big data challenge to the processing efficiency of text mining. In this paper, we address this challenge by introducing parallel processing on a supercomputer. We developed paraBTM, a runnable framework that enables parallel text mining on the Tianhe-2 supercomputer. It employs a low-cost yet effective load balancing strategy to maximize the efficiency of parallel processing. We evaluated the performance of paraBTM on several datasets, utilizing three types of named entity recognition tasks as demonstration. Results show that, in most cases, the processing efficiency can be greatly improved with parallel processing, and the proposed load balancing strategy is simple and effective. In addition, our framework can be readily applied to other tasks of biomedical text mining besides NER.
A document processing pipeline for annotating chemical entities in scientific documents.

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Campos, David; Matos, Sérgio; Oliveira, José L

2015-01-01

The recognition of drugs and chemical entities in text is a very important task within the field of biomedical information extraction, given the rapid growth in the amount of published texts (scientific papers, patents, patient records) and the relevance of these and other related concepts. If done effectively, this could allow exploiting such textual resources to automatically extract or infer relevant information, such as drug profiles, relations and similarities between drugs, or associations between drugs and potential drug targets. The objective of this work was to develop and validate a document processing and information extraction pipeline for the identification of chemical entity mentions in text. We used the BioCreative IV CHEMDNER task data to train and evaluate a machine-learning based entity recognition system. Using a combination of two conditional random field models, a selected set of features, and a post-processing stage, we achieved F-measure results of 87.48% in the chemical entity mention recognition task and 87.75% in the chemical document indexing task. We present a machine learning-based solution for automatic recognition of chemical and drug names in scientific documents. The proposed approach applies a rich feature set, including linguistic, orthographic, morphological, dictionary matching and local context features. Post-processing modules are also integrated, performing parentheses correction, abbreviation resolution and filtering erroneous mentions using an exclusion list derived from the training data. The developed methods were implemented as a document annotation tool and web service, freely available at http://bioinformatics.ua.pt/becas-chemicals/.
A controlled vocabulary for pathway entities and events.

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Jupe, Steve; Jassal, Bijay; Williams, Mark; Wu, Guanming

2014-01-01

Entities involved in pathways and the events they participate in require descriptive and unambiguous names that are often not available in the literature or elsewhere. Reactome is a manually curated open-source resource of human pathways. It is accessible via a website, available as downloads in standard reusable formats and via Representational State Transfer (REST)-ful and Simple Object Access Protocol (SOAP) application programming interfaces (APIs). We have devised a controlled vocabulary (CV) that creates concise, unambiguous and unique names for reactions (pathway events) and all the molecular entities they involve. The CV could be reapplied in any situation where names are used for pathway entities and events. Adoption of this CV would significantly improve naming consistency and readability, with consequent benefits for searching and data mining within and between databases. Database URL: http://www.reactome.org. © The Author(s) 2014. Published by Oxford University Press.
The Ontology for Biomedical Investigations.

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

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

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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.
Adapting Web content for low-literacy readers by using lexical elaboration and named entities labeling

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Watanabe, W. M.; Candido, A.; Amâncio, M. A.; De Oliveira, M.; Pardo, T. A. S.; Fortes, R. P. M.; Aluísio, S. M.

2010-12-01

This paper presents an approach for assisting low-literacy readers in accessing Web online information. The "Educational FACILITA" tool is a Web content adaptation tool that provides innovative features and follows more intuitive interaction models regarding accessibility concerns. Especially, we propose an interaction model and a Web application that explore the natural language processing tasks of lexical elaboration and named entity labeling for improving Web accessibility. We report on the results obtained from a pilot study on usability analysis carried out with low-literacy users. The preliminary results show that "Educational FACILITA" improves the comprehension of text elements, although the assistance mechanisms might also confuse users when word sense ambiguity is introduced, by gathering, for a complex word, a list of synonyms with multiple meanings. This fact evokes a future solution in which the correct sense for a complex word in a sentence is identified, solving this pervasive characteristic of natural languages. The pilot study also identified that experienced computer users find the tool to be more useful than novice computer users do.
The CALBC Silver Standard Corpus for Biomedical Named Entities - A Study in Harmonizing the Contributions from Four Independent Named Entity Taggers

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D. Rebholz-Schuhmann (Dietrich); A.J. Jimeno-Yepes (Antonio José); E.M. van Mulligen (Erik); N. Kang (Ning); J.A. Kors (Jan); D. Milward (David); P. Corbett (Peter); E. Buyko (Ekaterina); Tomanek (Katrin); E. Beisswanger (Elena); U. Hahn (Udo)

2010-01-01

textabstractThe production of gold standard corpora is time-consuming and costly. We propose an alternative: the 'silver standard corpus' (SSC), a corpus that has been generated by the harmonisation of the annotations that have been delivered from a selection of annotation systems. The systems have
Use of global context for handling noisy names in discussion texts of a homeopathy discussion forum

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Mukta Majumder

2014-03-01

Full Text Available The task of identifying named entities from the discussion texts in Web forums faces the challenge of noisy names. As the names are often misspelled or abbreviated, the conventional techniques have failed to detect the noisy names properly. In this paper we propose a global context based framework for handling the noisy names. The framework is tested on a named entity recognition system designed to identify the names from the discussion texts in a homeopathy diagnosis discussion forum. The proposed global context-based framework is found to be effective in improving the accuracy of the named entity recognition system.
Named Entity Recognition in a Hungarian NL Based QA System

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Tikkl, Domonkos; Szidarovszky, P. Ferenc; Kardkovacs, Zsolt T.; Magyar, Gábor

In WoW project our purpose is to create a complex search interface with the following features: search in the deep web content of contracted partners' databases, processing Hungarian natural language (NL) questions and transforming them to SQL queries for database access, image search supported by a visual thesaurus that describes in a structural form the visual content of images (also in Hungarian). This paper primarily focuses on a particular problem of question processing task: the entity recognition. Before going into details we give a short overview of the project's aims.
The strength of co-authorship in gene name disambiguation

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Farkas Richárd

2008-01-01

Full Text Available Abstract Background A biomedical entity mention in articles and other free texts is often ambiguous. For example, 13% of the gene names (aliases might refer to more than one gene. The task of Gene Symbol Disambiguation (GSD – a special case of Word Sense Disambiguation (WSD – is to assign a unique gene identifier for all identified gene name aliases in biology-related articles. Supervised and unsupervised machine learning WSD techniques have been applied in the biomedical field with promising results. We examine here the utilisation potential of the fact – one of the special features of biological articles – that the authors of the documents are known through graph-based semi-supervised methods for the GSD task. Results Our key hypothesis is that a biologist refers to each particular gene by a fixed gene alias and this holds for the co-authors as well. To make use of the co-authorship information we decided to build the inverse co-author graph on MedLine abstracts. The nodes of the inverse co-author graph are articles and there is an edge between two nodes if and only if the two articles have a mutual author. We introduce here two methods using distances (based on the graph of abstracts for the GSD task. We found that a disambiguation decision can be made in 85% of cases with an extremely high (99.5% precision rate just by using information obtained from the inverse co-author graph. We incorporated the co-authorship information into two GSD systems in order to attain full coverage and in experiments our procedure achieved precision of 94.3%, 98.85%, 96.05% and 99.63% on the human, mouse, fly and yeast GSD evaluation sets, respectively. Conclusion Based on the promising results obtained so far we suggest that the co-authorship information and the circumstances of the articles' release (like the title of the journal, the year of publication can be a crucial building block of any sophisticated similarity measure among biological articles
Top-level categories of constitutively organized material entities--suggestions for a formal top-level ontology.

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Lars Vogt

2011-04-01

Full Text Available Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., 'object', 'fiat object part', 'object aggregate' must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them.By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: 'fiat object part aggregate' and 'object with fiat object part aggregate'. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity.We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools.

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Verspoor, Karin; Cohen, Kevin Bretonnel; Lanfranchi, Arrick; Warner, Colin; Johnson, Helen L; Roeder, Christophe; Choi, Jinho D; Funk, Christopher; Malenkiy, Yuriy; Eckert, Miriam; Xue, Nianwen; Baumgartner, William A; Bada, Michael; Palmer, Martha; Hunter, Lawrence E

2012-08-17

We introduce the linguistic annotation of a corpus of 97 full-text biomedical publications, known as the Colorado Richly Annotated Full Text (CRAFT) corpus. We further assess the performance of existing tools for performing sentence splitting, tokenization, syntactic parsing, and named entity recognition on this corpus. Many biomedical natural language processing systems demonstrated large differences between their previously published results and their performance on the CRAFT corpus when tested with the publicly available models or rule sets. Trainable systems differed widely with respect to their ability to build high-performing models based on this data. The finding that some systems were able to train high-performing models based on this corpus is additional evidence, beyond high inter-annotator agreement, that the quality of the CRAFT corpus is high. The overall poor performance of various systems indicates that considerable work needs to be done to enable natural language processing systems to work well when the input is full-text journal articles. The CRAFT corpus provides a valuable resource to the biomedical natural language processing community for evaluation and training of new models for biomedical full text publications.

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

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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.
Anatomical entity recognition with a hierarchical framework augmented by external resources.

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Yan Xu

Full Text Available References to anatomical entities in medical records consist not only of explicit references to anatomical locations, but also other diverse types of expressions, such as specific diseases, clinical tests, clinical treatments, which constitute implicit references to anatomical entities. In order to identify these implicit anatomical entities, we propose a hierarchical framework, in which two layers of named entity recognizers (NERs work in a cooperative manner. Each of the NERs is implemented using the Conditional Random Fields (CRF model, which use a range of external resources to generate features. We constructed a dictionary of anatomical entity expressions by exploiting four existing resources, i.e., UMLS, MeSH, RadLex and BodyPart3D, and supplemented information from two external knowledge bases, i.e., Wikipedia and WordNet, to improve inference of anatomical entities from implicit expressions. Experiments conducted on 300 discharge summaries showed a micro-averaged performance of 0.8509 Precision, 0.7796 Recall and 0.8137 F1 for explicit anatomical entity recognition, and 0.8695 Precision, 0.6893 Recall and 0.7690 F1 for implicit anatomical entity recognition. The use of the hierarchical framework, which combines the recognition of named entities of various types (diseases, clinical tests, treatments with information embedded in external knowledge bases, resulted in a 5.08% increment in F1. The resources constructed for this research will be made publicly available.
ClusType: Effective Entity Recognition and Typing by Relation Phrase-Based Clustering

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Ren, Xiang; El-Kishky, Ahmed; Wang, Chi; Tao, Fangbo; Voss, Clare R.; Ji, Heng; Han, Jiawei

2015-01-01

Entity recognition is an important but challenging research problem. In reality, many text collections are from specific, dynamic, or emerging domains, which poses significant new challenges for entity recognition with increase in name ambiguity and context sparsity, requiring entity detection without domain restriction. In this paper, we investigate entity recognition (ER) with distant-supervision and propose a novel relation phrase-based ER framework, called ClusType, that runs data-driven phrase mining to generate entity mention candidates and relation phrases, and enforces the principle that relation phrases should be softly clustered when propagating type information between their argument entities. Then we predict the type of each entity mention based on the type signatures of its co-occurring relation phrases and the type indicators of its surface name, as computed over the corpus. Specifically, we formulate a joint optimization problem for two tasks, type propagation with relation phrases and multi-view relation phrase clustering. Our experiments on multiple genres—news, Yelp reviews and tweets—demonstrate the effectiveness and robustness of ClusType, with an average of 37% improvement in F1 score over the best compared method. PMID:26705503
Integrating Naming and Addressing of Persistent data in Programming Language and Operating System Contexts

NARCIS (Netherlands)

van der Valk, M.; van der Valk, M.

1993-01-01

There exist a number of desirable transparencies in distributed computing, viz., name transparency: having a uniform way of naming entities in the system, regardless of their type or physical make up; location transparency: having a uniform way of addressing entities, regardless of their physical
NOMINAL MARKING SYSTEM OF BAHASA MANGGARAI AND ITS INTERRELATION TO NAMING SYSTEM OF ENTITIES: A CULTURAL LINGUISTIC STUDY

Directory of Open Access Journals (Sweden)

Kletus Erom

2012-11-01

Full Text Available This study analyzes the cultural imagery of the Manggaraian SpeechCommunities (MSC in “Nominal Marking System (NMS of Bahasa Manggaraiand Its Interrelation with Naming Systems of Entity (NSE: A CulturalLinguistic Study”. The result of the analysis is useful for both the academic worldand the life of the society, especially the MSC.The study conducted in Manggarai Regency, Flores, East Nusa TenggaraProvince, is qualitative. The data were obtained through observation, elicitation,interview, documentation study, listening, and note taking. For this reason, a numberof questions were prepared in a written form. The data obtained were analyzedthrough steps of selection, listing, translation, and interpretation of the formallinguistic meaning and cultural imagery of the MSC. The result of the data analysisis informally reported and verbally described.To analyze the data, the Cultural Linguistic Theory was applied andsupported by the structural and the dynamic theories. To know the chance and toinspire the study, a number of previous studies were reviewed. To easily understand,direct, and limit the discussion of the study, a number of basic concepts weredefined.Syntactically and semantically, there are four kinds of nominal markers(NMs of BM. NMs in the forms of personal pronouns (PP: hau ‘you SG’, hia/hi‘he/she’, meu ‘you-PLUR’, and ise ‘they’ mark proper nouns (PN as theSubject/Agent or Object/Patient in a clause bearing the meaning of subject or objectposition of a clause and not common nouns (CN. NMs in the forms of de/ di/ disemark the noun (CN/pronoun or PN as the possessor of the possessed noun in aclause bearing the meaning of possession. NMs in the forms of le/ li/ lise mark thenoun (CN/pronoun or PN as the agent diathesis of an action targeted to a noun asthe patient diathesis in a clause bearing the meaning of addition or the target/localityof an action. And NMs in the forms of ge/ gi/ gise mark the noun (CN/pronoun or
Network and Ensemble Enabled Entity Extraction in Informal Text (NEEEEIT) final report

Energy Technology Data Exchange (ETDEWEB)

Kegelmeyer, Philip W. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Shead, Timothy M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Dunlavy, Daniel M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2013-09-01

This SAND report summarizes the activities and outcomes of the Network and Ensemble Enabled Entity Extraction in Information Text (NEEEEIT) LDRD project, which addressed improving the accuracy of conditional random fields for named entity recognition through the use of ensemble methods.
Life Sciences—Life Writing: PTSD as a Transdisciplinary Entity between Biomedical Explanation and Lived Experience

Directory of Open Access Journals (Sweden)

Norbert W. Paul

2015-12-01

Full Text Available Since the second half of the 20th century, the life sciences have become one of the dominant explanatory models for almost every aspect of human life. Hand in hand with biomedical developments and technologies, the life sciences are constantly shaping and reshaping human lives and changing human biographies in manifold ways. The orientation towards life sciences and biomedicine from the very beginning to the end of human life is driven by the utopian notion that all forms of contingency could be technologically and medically controlled. This paper addresses the interrelatedness of life sciences and human biographies in a field where contingency and risk become essential and existential parts of lived experience: post-traumatic stress disorder (PTSD. On the one hand, this diagnostic entity is related to (neuro-biological underpinnings of (a lack of psychic resilience as well as to those of contemporary pharmacotherapy. On the other hand, PTSD is also understood as based on a traumatic life event, which can be accessed through and addressed by talk therapy, particularly narrative exposure therapy (NET. We argue that a novel focus on concepts of narrativity will generate pathways for an interdisciplinary understanding of PTSD by linking biological underpinnings from neurobiological findings, to brain metabolism and pharmacotherapy via the interface of psychotherapy and the specific role of narratives to the lived experience of patients and vice versa. The goal of our study is to demonstrate why therapies such as psychotherapy or pharmacotherapy are successful in controlling the disease burden of PTSD to some extent, but the restitutio ad integrum, the reestablishing of the bodily and psychic integrity remains out of reach for most PTSD patients. As a test case, we discuss the complementary methods of Traditional Chinese Medicine (TCM and the established procedures of talk therapy (NET to show how a methodological focus on narratives enhanced by
Robust hybrid name disambiguation framework for large databases

KAUST Repository

Zhu, Jia

2013-10-26

In many databases, science bibliography database for example, name attribute is the most commonly chosen identifier to identify entities. However, names are often ambiguous and not always unique which cause problems in many fields. Name disambiguation is a non-trivial task in data management that aims to properly distinguish different entities which share the same name, particularly for large databases like digital libraries, as only limited information can be used to identify authors\\' name. In digital libraries, ambiguous author names occur due to the existence of multiple authors with the same name or different name variations for the same person. Also known as name disambiguation, most of the previous works to solve this issue often employ hierarchical clustering approaches based on information inside the citation records, e.g. co-authors and publication titles. In this paper, we focus on proposing a robust hybrid name disambiguation framework that is not only applicable for digital libraries but also can be easily extended to other application based on different data sources. We propose a web pages genre identification component to identify the genre of a web page, e.g. whether the page is a personal homepage. In addition, we propose a re-clustering model based on multidimensional scaling that can further improve the performance of name disambiguation. We evaluated our approach on known corpora, and the favorable experiment results indicated that our proposed framework is feasible. © 2013 Akadémiai Kiadó, Budapest, Hungary.
Robust hybrid name disambiguation framework for large databases

KAUST Repository

Zhu, Jia; Yang, Yi; Xie, Qing; Wang, Liwei; Hassan, Saeed-Ul

2013-01-01

In many databases, science bibliography database for example, name attribute is the most commonly chosen identifier to identify entities. However, names are often ambiguous and not always unique which cause problems in many fields. Name disambiguation is a non-trivial task in data management that aims to properly distinguish different entities which share the same name, particularly for large databases like digital libraries, as only limited information can be used to identify authors' name. In digital libraries, ambiguous author names occur due to the existence of multiple authors with the same name or different name variations for the same person. Also known as name disambiguation, most of the previous works to solve this issue often employ hierarchical clustering approaches based on information inside the citation records, e.g. co-authors and publication titles. In this paper, we focus on proposing a robust hybrid name disambiguation framework that is not only applicable for digital libraries but also can be easily extended to other application based on different data sources. We propose a web pages genre identification component to identify the genre of a web page, e.g. whether the page is a personal homepage. In addition, we propose a re-clustering model based on multidimensional scaling that can further improve the performance of name disambiguation. We evaluated our approach on known corpora, and the favorable experiment results indicated that our proposed framework is feasible. © 2013 Akadémiai Kiadó, Budapest, Hungary.
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.
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
Does the name really matter? The importance of botanical nomenclature and plant taxonomy in biomedical research.

Science.gov (United States)

Bennett, Bradley C; Balick, Michael J

2014-03-28

Medical research on plant-derived compounds requires a breadth of expertise from field to laboratory and clinical skills. Too often basic botanical skills are evidently lacking, especially with respect to plant taxonomy and botanical nomenclature. Binomial and familial names, synonyms and author citations are often misconstrued. The correct botanical name, linked to a vouchered specimen, is the sine qua non of phytomedical research. Without the unique identifier of a proper binomial, research cannot accurately be linked to the existing literature. Perhaps more significant, is the ambiguity of species determinations that ensues of from poor taxonomic practices. This uncertainty, not surprisingly, obstructs reproducibility of results-the cornerstone of science. Based on our combined six decades of experience with medicinal plants, we discuss the problems of inaccurate taxonomy and botanical nomenclature in biomedical research. This problems appear all too frequently in manuscripts and grant applications that we review and they extend to the published literature. We also review the literature on the importance of taxonomy in other disciplines that relate to medicinal plant research. In most cases, questions regarding orthography, synonymy, author citations, and current family designations of most plant binomials can be resolved using widely-available online databases and other electronic resources. Some complex problems require consultation with a professional plant taxonomist, which also is important for accurate identification of voucher specimens. Researchers should provide the currently accepted binomial and complete author citation, provide relevant synonyms, and employ the Angiosperm Phylogeny Group III family name. Taxonomy is a vital adjunct not only to plant-medicine research but to virtually every field of science. Medicinal plant researchers can increase the precision and utility of their investigations by following sound practices with respect to botanical
LeadMine: a grammar and dictionary driven approach to entity recognition

Science.gov (United States)

2015-01-01

Background Chemical entity recognition has traditionally been performed by machine learning approaches. Here we describe an approach using grammars and dictionaries. This approach has the advantage that the entities found can be directly related to a given grammar or dictionary, which allows the type of an entity to be known and, if an entity is misannotated, indicates which resource should be corrected. As recognition is driven by what is expected, if spelling errors occur, they can be corrected. Correcting such errors is highly useful when attempting to lookup an entity in a database or, in the case of chemical names, converting them to structures. Results Our system uses a mixture of expertly curated grammars and dictionaries, as well as dictionaries automatically derived from public resources. We show that the heuristics developed to filter our dictionary of trivial chemical names (from PubChem) yields a better performing dictionary than the previously published Jochem dictionary. Our final system performs post-processing steps to modify the boundaries of entities and to detect abbreviations. These steps are shown to significantly improve performance (2.6% and 4.0% F1-score respectively). Our complete system, with incremental post-BioCreative workshop improvements, achieves 89.9% precision and 85.4% recall (87.6% F1-score) on the CHEMDNER test set. Conclusions Grammar and dictionary approaches can produce results at least as good as the current state of the art in machine learning approaches. While machine learning approaches are commonly thought of as "black box" systems, our approach directly links the output entities to the input dictionaries and grammars. Our approach also allows correction of errors in detected entities, which can assist with entity resolution. PMID:25810776
Building a protein name dictionary from full text: a machine learning term extraction approach

Directory of Open Access Journals (Sweden)

Campagne Fabien

2005-04-01

Full Text Available Abstract Background The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. Results We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. Conclusion This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt.
The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

Science.gov (United States)

Malone, James; Brown, Andy; Lister, Allyson L; Ison, Jon; Hull, Duncan; Parkinson, Helen; Stevens, Robert

2014-01-01

Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility. The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications. The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's needs. The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.
One tagger, many uses

DEFF Research Database (Denmark)

Jensen, Lars Juhl

2016-01-01

Automatic annotation of text is an important complement to manual annotation, because the latter is highly labour intensive. We have developed a fast dictionary-based named entity recognition (NER) system and addressed a wide variety of biomedical problems by applied it to text from many differen....... Despite the simplicity of the approach, it typically achieves 80-90% precision and 70-80% recall. Many of the underlying dictionaries were built from open biomedical ontologies, which further facilitate integration of the text-mining results with evidence from other sources.......Automatic annotation of text is an important complement to manual annotation, because the latter is highly labour intensive. We have developed a fast dictionary-based named entity recognition (NER) system and addressed a wide variety of biomedical problems by applied it to text from many different...
NEMO: Extraction and normalization of organization names from PubMed affiliations.

Science.gov (United States)

Jonnalagadda, Siddhartha Reddy; Topham, Philip

2010-10-04

Today, there are more than 18 million articles related to biomedical research indexed in MEDLINE, and information derived from them could be used effectively to save the great amount of time and resources spent by government agencies in understanding the scientific landscape, including key opinion leaders and centers of excellence. Associating biomedical articles with organization names could significantly benefit the pharmaceutical marketing industry, health care funding agencies and public health officials and be useful for other scientists in normalizing author names, automatically creating citations, indexing articles and identifying potential resources or collaborators. Large amount of extracted information helps in disambiguating organization names using machine-learning algorithms. We propose NEMO, a system for extracting organization names in the affiliation and normalizing them to a canonical organization name. Our parsing process involves multi-layered rule matching with multiple dictionaries. The system achieves more than 98% f-score in extracting organization names. Our process of normalization that involves clustering based on local sequence alignment metrics and local learning based on finding connected components. A high precision was also observed in normalization. NEMO is the missing link in associating each biomedical paper and its authors to an organization name in its canonical form and the Geopolitical location of the organization. This research could potentially help in analyzing large social networks of organizations for landscaping a particular topic, improving performance of author disambiguation, adding weak links in the co-author network of authors, augmenting NLM's MARS system for correcting errors in OCR output of affiliation field, and automatically indexing the PubMed citations with the normalized organization name and country. Our system is available as a graphical user interface available for download along with this paper.
Dynamic collective entity representations for entity ranking

NARCIS (Netherlands)

Graus, D.; Tsagkias, M.; Weerkamp, W.; Meij, E.; de Rijke, M.

2016-01-01

Entity ranking, i.e., successfully positioning a relevant entity at the top of the ranking for a given query, is inherently difficult due to the potential mismatch between the entity's description in a knowledge base, and the way people refer to the entity when searching for it. To counter this
Camera systems in human motion analysis for biomedical applications

Science.gov (United States)

Chin, Lim Chee; Basah, Shafriza Nisha; Yaacob, Sazali; Juan, Yeap Ewe; Kadir, Aida Khairunnisaa Ab.

2015-05-01

Human Motion Analysis (HMA) system has been one of the major interests among researchers in the field of computer vision, artificial intelligence and biomedical engineering and sciences. This is due to its wide and promising biomedical applications, namely, bio-instrumentation for human computer interfacing and surveillance system for monitoring human behaviour as well as analysis of biomedical signal and image processing for diagnosis and rehabilitation applications. This paper provides an extensive review of the camera system of HMA, its taxonomy, including camera types, camera calibration and camera configuration. The review focused on evaluating the camera system consideration of the HMA system specifically for biomedical applications. This review is important as it provides guidelines and recommendation for researchers and practitioners in selecting a camera system of the HMA system for biomedical applications.
Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

KAUST Repository

Smaili, Fatima Z.; Gao, Xin; Hoehndorf, Robert

2018-01-01

We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised learning, or clustering.

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

KAUST Repository

Smaili, Fatima Zohra

2018-01-31

We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised learning, or clustering.
The National Geographic Names Data Base: Phase II instructions

Science.gov (United States)

Orth, Donald J.; Payne, Roger L.

1987-01-01

The Geographic Names Information System is a computer-based information system developed to meet major national needs by providing information for named entities in the United States, its territories, and outlying areas. The National Geographic Names Data Base, a component of the Geographic Names Information System, currently contains most names and associated information recorded on the 1:24,000-scale (or largest scale available) topographic maps of the U.S. Geological Survey. The work involved in this initial compilation of names shown on the topographic-map series, and the development and editing of the National Geographic Names Data Base, is referred to as Phase I. Optimal use and effectiveness of an automated names system require that the names of features
Facilitating biomedical researchers' interrogation of electronic health record data: Ideas from outside of biomedical informatics.

Science.gov (United States)

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

2016-04-01

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

Science.gov (United States)

Choi, Wonjun; Kim, Baeksoo; Cho, Hyejin; Lee, Doheon; Lee, Hyunju

2016-09-20

Plants are natural products that humans consume in various ways including food and medicine. They have a long empirical history of treating diseases with relatively few side effects. Based on these strengths, many studies have been performed to verify the effectiveness of plants in treating diseases. It is crucial to understand the chemicals contained in plants because these chemicals can regulate activities of proteins that are key factors in causing diseases. With the accumulation of a large volume of biomedical literature in various databases such as PubMed, it is possible to automatically extract relationships between plants and chemicals in a large-scale way if we apply a text mining approach. A cornerstone of achieving this task is a corpus of relationships between plants and chemicals. In this study, we first constructed a corpus for plant and chemical entities and for the relationships between them. The corpus contains 267 plant entities, 475 chemical entities, and 1,007 plant-chemical relationships (550 and 457 positive and negative relationships, respectively), which are drawn from 377 sentences in 245 PubMed abstracts. Inter-annotator agreement scores for the corpus among three annotators were measured. The simple percent agreement scores for entities and trigger words for the relationships were 99.6 and 94.8 %, respectively, and the overall kappa score for the classification of positive and negative relationships was 79.8 %. We also developed a rule-based model to automatically extract such plant-chemical relationships. When we evaluated the rule-based model using the corpus and randomly selected biomedical articles, overall F-scores of 68.0 and 61.8 % were achieved, respectively. We expect that the corpus for plant-chemical relationships will be a useful resource for enhancing plant research. The corpus is available at http://combio.gist.ac.kr/plantchemicalcorpus .
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.
An analysis on the entity annotations in biological corpora [v1; ref status: indexed, http://f1000r.es/2o0

Directory of Open Access Journals (Sweden)

Mariana Neves

2014-04-01

Full Text Available Collection of documents annotated with semantic entities and relationships are crucial resources to support development and evaluation of text mining solutions for the biomedical domain. Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain. Annotations for entity types were classified into six semantic groups and an overview on the semantic entities which can be found in each corpus is shown. Results show that while some semantic entities, such as genes, proteins and chemicals are consistently annotated in many collections, corpora available for diseases, variations and mutations are still few, in spite of their importance in the biological domain.
Biomedical engineering - A means to add new dimension to medicine and research

Science.gov (United States)

Doerr, D. F.

1992-01-01

Biomedical engineering is an evolving science that seeks to insert technically oriented and trained personnel to assist medical professionals in solving technological problems in the pursuit of innovations in the delivery of health care. Consequently, engineering solutions are brought to bear on problems that previously were outside the training of physicians and beyond the understanding or appreciation of the conventionally educated electrical or mechanical engineers. This physician/scientist/engineer team has a capability to extend medicine and research far beyond the capability of a single entity operating alone. How biomedical engineering has added a new dimension to medical science at the Kennedy Space Center is described.
Rational engineering of physicochemical properties of nanomaterials for biomedical applications with nanotoxicological perspectives.

Science.gov (United States)

Navya, P N; Daima, Hemant Kumar

2016-01-01

Innovative engineered nanomaterials are at the leading edge of rapidly emerging fields of nanobiotechnology and nanomedicine. Meticulous synthesis, unique physicochemical properties, manifestation of chemical or biological moieties on the surface of materials make engineered nanostructures suitable for a variety of biomedical applications. Besides, tailored nanomaterials exhibit entirely novel therapeutic applications with better functionality, sensitivity, efficiency and specificity due to their customized unique physicochemical and surface properties. Additionally, such designer made nanomaterials has potential to generate series of interactions with various biological entities including DNA, proteins, membranes, cells and organelles at nano-bio interface. These nano-bio interactions are driven by colloidal forces and predominantly depend on the dynamic physicochemical and surface properties of nanomaterials. Nevertheless, recent development and atomic scale tailoring of various physical, chemical and surface properties of nanomaterials is promising to dictate their interaction in anticipated manner with biological entities for biomedical applications. As a result, rationally designed nanomaterials are in extensive demand for bio-molecular detection and diagnostics, therapeutics, drug and gene delivery, fluorescent labelling, tissue engineering, biochemical sensing and other pharmaceuticals applications. However, toxicity and risk associated with engineered nanomaterials is rather unclear or not well understood; which is gaining considerable attention and the field of nanotoxicology is evolving promptly. Therefore, this review explores current knowledge of articulate engineering of nanomaterials for biomedical applications with special attention on potential toxicological perspectives.
NetiNeti: discovery of scientific names from text using machine learning methods

Directory of Open Access Journals (Sweden)

Akella Lakshmi

2012-08-01

Full Text Available Abstract Background A scientific name for an organism can be associated with almost all biological data. Name identification is an important step in many text mining tasks aiming to extract useful information from biological, biomedical and biodiversity text sources. A scientific name acts as an important metadata element to link biological information. Results We present NetiNeti (Name Extraction from Textual Information-Name Extraction for Taxonomic Indexing, a machine learning based approach for recognition of scientific names including the discovery of new species names from text that will also handle misspellings, OCR errors and other variations in names. The system generates candidate names using rules for scientific names and applies probabilistic machine learning methods to classify names based on structural features of candidate names and features derived from their contexts. NetiNeti can also disambiguate scientific names from other names using the contextual information. We evaluated NetiNeti on legacy biodiversity texts and biomedical literature (MEDLINE. NetiNeti performs better (precision = 98.9% and recall = 70.5% compared to a popular dictionary based approach (precision = 97.5% and recall = 54.3% on a 600-page biodiversity book that was manually marked by an annotator. On a small set of PubMed Central’s full text articles annotated with scientific names, the precision and recall values are 98.5% and 96.2% respectively. NetiNeti found more than 190,000 unique binomial and trinomial names in more than 1,880,000 PubMed records when used on the full MEDLINE database. NetiNeti also successfully identifies almost all of the new species names mentioned within web pages. Conclusions We present NetiNeti, a machine learning based approach for identification and discovery of scientific names. The system implementing the approach can be accessed at http://namefinding.ubio.org.
10 CFR 300.3 - Guidance for defining and naming the reporting entity.

Science.gov (United States)

2010-01-01

... agency or departmental level, but distinct organizational units (such as a Department of the Interior... flexibility in defining themselves at an appropriate level of aggregation, it is essential that the name...
A study of active learning methods for named entity recognition in clinical text.

Science.gov (United States)

Chen, Yukun; Lasko, Thomas A; Mei, Qiaozhu; Denny, Joshua C; Xu, Hua

2015-12-01

Named entity recognition (NER), a sequential labeling task, is one of the fundamental tasks for building clinical natural language processing (NLP) systems. Machine learning (ML) based approaches can achieve good performance, but they often require large amounts of annotated samples, which are expensive to build due to the requirement of domain experts in annotation. Active learning (AL), a sample selection approach integrated with supervised ML, aims to minimize the annotation cost while maximizing the performance of ML-based models. In this study, our goal was to develop and evaluate both existing and new AL methods for a clinical NER task to identify concepts of medical problems, treatments, and lab tests from the clinical notes. Using the annotated NER corpus from the 2010 i2b2/VA NLP challenge that contained 349 clinical documents with 20,423 unique sentences, we simulated AL experiments using a number of existing and novel algorithms in three different categories including uncertainty-based, diversity-based, and baseline sampling strategies. They were compared with the passive learning that uses random sampling. Learning curves that plot performance of the NER model against the estimated annotation cost (based on number of sentences or words in the training set) were generated to evaluate different active learning and the passive learning methods and the area under the learning curve (ALC) score was computed. Based on the learning curves of F-measure vs. number of sentences, uncertainty sampling algorithms outperformed all other methods in ALC. Most diversity-based methods also performed better than random sampling in ALC. To achieve an F-measure of 0.80, the best method based on uncertainty sampling could save 66% annotations in sentences, as compared to random sampling. For the learning curves of F-measure vs. number of words, uncertainty sampling methods again outperformed all other methods in ALC. To achieve 0.80 in F-measure, in comparison to random
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.
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.
Entity associations for search

NARCIS (Netherlands)

Reinanda, R.

2017-01-01

In this thesis, we investigate the broad problem of computing entity associations for search. Specifically, we consider three types of entity association: entity-entity, entity-document, and entity-aspect associations. We touch upon various domains, starting with specific domains such as the
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.
Determination of death: Metaphysical and biomedical discourse

Directory of Open Access Journals (Sweden)

Irayda Jakušovaitė

2016-01-01

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

Science.gov (United States)

Liu, Zengjian; Yang, Ming; Wang, Xiaolong; Chen, Qingcai; Tang, Buzhou; Wang, Zhe; Xu, Hua

2017-07-05

Entity recognition is one of the most primary steps for text analysis and has long attracted considerable attention from researchers. In the clinical domain, various types of entities, such as clinical entities and protected health information (PHI), widely exist in clinical texts. Recognizing these entities has become a hot topic in clinical natural language processing (NLP), and a large number of traditional machine learning methods, such as support vector machine and conditional random field, have been deployed to recognize entities from clinical texts in the past few years. In recent years, recurrent neural network (RNN), one of deep learning methods that has shown great potential on many problems including named entity recognition, also has been gradually used for entity recognition from clinical texts. In this paper, we comprehensively investigate the performance of LSTM (long-short term memory), a representative variant of RNN, on clinical entity recognition and protected health information recognition. The LSTM model consists of three layers: input layer - generates representation of each word of a sentence; LSTM layer - outputs another word representation sequence that captures the context information of each word in this sentence; Inference layer - makes tagging decisions according to the output of LSTM layer, that is, outputting a label sequence. Experiments conducted on corpora of the 2010, 2012 and 2014 i2b2 NLP challenges show that LSTM achieves highest micro-average F1-scores of 85.81% on the 2010 i2b2 medical concept extraction, 92.29% on the 2012 i2b2 clinical event detection, and 94.37% on the 2014 i2b2 de-identification, which is considerably competitive with other state-of-the-art systems. LSTM that requires no hand-crafted feature has great potential on entity recognition from clinical texts. It outperforms traditional machine learning methods that suffer from fussy feature engineering. A possible future direction is how to integrate knowledge
Financial Management of Economic Entity from the Perspective of Alternative Approach

Directory of Open Access Journals (Sweden)

Victor Munteanu

2016-12-01

Full Text Available Throughout the study the financial management presented is divided into three directions, namely financial analysis, financial planning and financial strategy, focusing on increasing the quality of financial management conducted at the economic entity by identifying an easier possible use for a system of alternative decisions in order to increase the profitability. The study also aims to identify new meanings of financial accounting information system in performing the managerial act through alternative decisions, trying to highlight the need to create a management tool generator of variants possible to be adopted with an impact on their application in the economic entity as a whole. Based on qualitative research on the financial management act, it is revealed the importance of the financial management act manifested in the economic entity and also its quality improvement through simulations targeting the management through budget system.
Erratum: Synthesis of Cd-free InP/ZnS Quantum Dots Suitable for Biomedical Applications.

Science.gov (United States)

2016-02-29

A correction was made to: Synthesis of Cd-free InP/ZnS Quantum Dots Suitable for Biomedical Applications. There was an error with an author's given name. The author's name was corrected to: Katye M. Fichter from: Kathryn M. Fichter.
Programming Entity Framework

CERN Document Server

Lerman, Julia

2009-01-01

Programming Entity Framework is a thorough introduction to Microsoft's new core framework for modeling and interacting with data in .NET applications. This highly-acclaimed book not only gives experienced developers a hands-on tour of the Entity Framework and explains its use in a variety of applications, it also provides a deep understanding of its architecture and APIs -- knowledge that will be extremely valuable as you shift to the Entity Framework version in .NET Framework 4.0 and Visual Studio 2010. From the Entity Data Model (EDM) and Object Services to EntityClient and the Metadata Work

EUPHORBIA SINCLAIRIANA, AN OLDER NAME FOR THE WIDESPREAD EUPHORBIA ELATA

Directory of Open Access Journals (Sweden)

BERNAL RODRIGO

2006-12-01

Full Text Available A comparison of collections of Euphorbia elata from accross its range withspecimens of E. sinclairiana from its only known locality, the island of Gorgona,off the Pacific coast of Colombia, shows that the two entities are better treated asconspecific, under the older name E. sinclairiana.
Full text clustering and relationship network analysis of biomedical publications.

Directory of Open Access Journals (Sweden)

Renchu Guan

Full Text Available Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers.
Full text clustering and relationship network analysis of biomedical publications.

Science.gov (United States)

Guan, Renchu; Yang, Chen; Marchese, Maurizio; Liang, Yanchun; Shi, Xiaohu

2014-01-01

Rapid developments in the biomedical sciences have increased the demand for automatic clustering of biomedical publications. In contrast to current approaches to text clustering, which focus exclusively on the contents of abstracts, a novel method is proposed for clustering and analysis of complete biomedical article texts. To reduce dimensionality, Cosine Coefficient is used on a sub-space of only two vectors, instead of computing the Euclidean distance within the space of all vectors. Then a strategy and algorithm is introduced for Semi-supervised Affinity Propagation (SSAP) to improve analysis efficiency, using biomedical journal names as an evaluation background. Experimental results show that by avoiding high-dimensional sparse matrix computations, SSAP outperforms conventional k-means methods and improves upon the standard Affinity Propagation algorithm. In constructing a directed relationship network and distribution matrix for the clustering results, it can be noted that overlaps in scope and interests among BioMed publications can be easily identified, providing a valuable analytical tool for editors, authors and readers.
Determination of death: Metaphysical and biomedical discourse.

Science.gov (United States)

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

2016-01-01

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

Science.gov (United States)

Ward, Kevin; Davenport, Jack

2017-05-01

Creating entity network graphs is a manual, time consuming process for an intelligence analyst. Beyond the traditional big data problems of information overload, individuals are often referred to by multiple names and shifting titles as they advance in their organizations over time which quickly makes simple string or phonetic alignment methods for entities insufficient. Conversely, automated methods for relationship extraction and entity disambiguation typically produce questionable results with no way for users to vet results, correct mistakes or influence the algorithm's future results. We present an entity disambiguation tool, DRADIS, which aims to bridge the gap between human-centric and machinecentric methods. DRADIS automatically extracts entities from multi-source datasets and models them as a complex set of attributes and relationships. Entities are disambiguated across the corpus using a hierarchical model executed in Spark allowing it to scale to operational sized data. Resolution results are presented to the analyst complete with sourcing information for each mention and relationship allowing analysts to quickly vet the correctness of results as well as correct mistakes. Corrected results are used by the system to refine the underlying model allowing analysts to optimize the general model to better deal with their operational data. Providing analysts with the ability to validate and correct the model to produce a system they can trust enables them to better focus their time on producing higher quality analysis products.
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles.

Science.gov (United States)

Cejuela, Juan Miguel; McQuilton, Peter; Ponting, Laura; Marygold, Steven J; Stefancsik, Raymund; Millburn, Gillian H; Rost, Burkhard

2014-01-01

The breadth and depth of biomedical literature are increasing year upon year. To keep abreast of these increases, FlyBase, a database for Drosophila genomic and genetic information, is constantly exploring new ways to mine the published literature to increase the efficiency and accuracy of manual curation and to automate some aspects, such as triaging and entity extraction. Toward this end, we present the 'tagtog' system, a web-based annotation framework that can be used to mark up biological entities (such as genes) and concepts (such as Gene Ontology terms) in full-text articles. tagtog leverages manual user annotation in combination with automatic machine-learned annotation to provide accurate identification of gene symbols and gene names. As part of the BioCreative IV Interactive Annotation Task, FlyBase has used tagtog to identify and extract mentions of Drosophila melanogaster gene symbols and names in full-text biomedical articles from the PLOS stable of journals. We show here the results of three experiments with different sized corpora and assess gene recognition performance and curation speed. We conclude that tagtog-named entity recognition improves with a larger corpus and that tagtog-assisted curation is quicker than manual curation. DATABASE URL: www.tagtog.net, www.flybase.org.
Bibliography of astatine chemistry and biomedical applications

International Nuclear Information System (INIS)

Berei, K.; Vasaros, L.

1992-02-01

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

Directory of Open Access Journals (Sweden)

Deon Scott

2016-03-01

Full Text Available Fair value accounting of biological assets in the public sector was introduced with the adoption of the public-sector-specific accounting standard: Generally Recognised Accounting Practice (GRAP 101. The public sector currently reports on various bases of accounting. Public entities and municipalities report in terms of accrual accounting, and government departments report on the modified cash basis. The lack of a uniform basis of accounting impedes the comparability of financial information. The implementation of GRAP 101 in the public sector is important in facilitating comparability of financial information regarding biological assets. This paper is based on a content analysis of the annual reports of 10 relevant public entities in South Africa and specifically details the challenges that public entities encounter with the application of GRAP 101. These challenges, and how they were addressed by a public entity that adopted and applied GRAP 101, namely the Accelerated and Shared Growth Initiative South Africa – Eastern Cape (AsgiSA-EC, are documented in this research.
Characterizing semantic mappings adaptation via biomedical KOS evolution: a case study investigating SNOMED CT and ICD.

Science.gov (United States)

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

2013-01-01

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

Directory of Open Access Journals (Sweden)

Andreea Mihaela Marin

2016-01-01

Full Text Available Any economic entity operates under probability and risk. In a general acceptation, risk means the validity of the result obtained under pressure of the economic environment; in other words, the risk is the potential damage posed to heritage, interests and affect the entity. In this paper we want to capture, the calculation in terms of the balance sheet analysis of the three risks, which can be measured on the basis of the balance sheet data and indicators, namely: the operational risk, financial risk, and the risk of bankruptcy.
Spatial distribution and influence factors of interprovincial terrestrial physical geographical names in China

Science.gov (United States)

Zhang, S.; Wang, Y.; Ju, H.

2017-12-01

The interprovincial terrestrial physical geographical entities are the key areas of regional integrated management. Based on toponomy dictionaries and different thematic maps, the attributes and the spatial extent of the interprovincial terrestrial physical geographical names (ITPGN, including terrain ITPGN and water ITPGN) were extracted. The coefficient of variation and Moran's I were combined together to measure the spatial variation and spatial association of ITPGN. The influencing factors of the distribution of ITPGN and the implications for the regional management were further discussed. The results showed that 11325 ITPGN were extracted, including 7082 terrain ITPGN and 4243 water ITPGN. Hunan Province had the largest number of ITPGN in China, and Shanghai had the smallest number. The spatial variance of the terrain ITPGN was larger than that of the water ITPGN, and the ITPGN showed a significant agglomeration phenomenon in the southern part of China. Further analysis showed that the number of ITPGN was positively related with the relative elevation and the population where the relative elevation was lower than 2000m and the population was less than 50 million. But the number of ITPGN showed a negative relationship with the two factors when their values became larger, indicating a large number of unnamed entities existed in complex terrain areas and a decreasing number of terrestrial physical geographical entities in densely populated area. Based on these analysis, we suggest the government take the ITPGN as management units to realize a balance development between different parts of the entities and strengthen the geographical names census and the nomination of unnamed interprovincial physical geographical entities. This study also demonstrated that the methods of literature survey, coefficient of variation and Moran's I can be combined to enhance the understanding of the spatial pattern of ITPGN.
Fikční jména, fikční entity a role předstírání: chvála abstinence

Czech Academy of Sciences Publication Activity Database

Koťátko, Petr

2016-01-01

Roč. 26, č. 53 (2016), s. 93-101 ISSN 0862-8440 Institutional support: RVO:67985955 Keywords : fictional names * fictional entities * fictional discourse * abstract entities * pretense Subject RIV: AA - Philosophy ; Religion http://hdl.handle.net/11104/0259936
The Mobile Team of Parasitology-Mycology, a medical entity for educational purposes to serve sick patients.

Science.gov (United States)

Desoubeaux, G; Simon, E G; Perrotin, D; Chandenier, J

2014-06-01

The Mobile Team of Parasitology-Mycology is a movable entity of the Parasitology-Mycology laboratory of Tours University Hospital, France. In contrast to the usual prerogatives of biomedical laboratories, the Mobile Team of Parasitology-Mycology is requested to intervene directly at bedside in various clinical departments, or even outside the hospital facility. Although its actions are of course primarily devoted to specialized diagnostic and therapeutic purposes, the Mobile Team also plays an important educational role in the medical training of undergraduate or graduate students. Copyright © 2013 Elsevier Masson SAS. All rights reserved.
WCP-RNN : a novel RNN-based approach for Bio-NER in Chinese EMRs: Paper ID: FC_17_25

NARCIS (Netherlands)

Li, Jianqiang; Zhao, Shenhe; Yang, Jijiang; Huang, Zhisheng; Liu, Bo; Chen, Shi; Pan, Hui; Wang, Qing

2018-01-01

Deep learning has achieved remarkable success in a wide range of domains. However, it has not been comprehensively evaluated as a solution for the task of Chinese biomedical named entity recognition (Bio-NER). The traditional deep-learning approach for the Bio-NER task is usually based on the
Enhancing of chemical compound and drug name recognition using representative tag scheme and fine-grained tokenization.

Science.gov (United States)

Dai, Hong-Jie; Lai, Po-Ting; Chang, Yung-Chun; Tsai, Richard Tzong-Han

2015-01-01

The functions of chemical compounds and drugs that affect biological processes and their particular effect on the onset and treatment of diseases have attracted increasing interest with the advancement of research in the life sciences. To extract knowledge from the extensive literatures on such compounds and drugs, the organizers of BioCreative IV administered the CHEMical Compound and Drug Named Entity Recognition (CHEMDNER) task to establish a standard dataset for evaluating state-of-the-art chemical entity recognition methods. This study introduces the approach of our CHEMDNER system. Instead of emphasizing the development of novel feature sets for machine learning, this study investigates the effect of various tag schemes on the recognition of the names of chemicals and drugs by using conditional random fields. Experiments were conducted using combinations of different tokenization strategies and tag schemes to investigate the effects of tag set selection and tokenization method on the CHEMDNER task. This study presents the performance of CHEMDNER of three more representative tag schemes-IOBE, IOBES, and IOB12E-when applied to a widely utilized IOB tag set and combined with the coarse-/fine-grained tokenization methods. The experimental results thus reveal that the fine-grained tokenization strategy performance best in terms of precision, recall and F-scores when the IOBES tag set was utilized. The IOBES model with fine-grained tokenization yielded the best-F-scores in the six chemical entity categories other than the "Multiple" entity category. Nonetheless, no significant improvement was observed when a more representative tag schemes was used with the coarse or fine-grained tokenization rules. The best F-scores that were achieved using the developed system on the test dataset of the CHEMDNER task were 0.833 and 0.815 for the chemical documents indexing and the chemical entity mention recognition tasks, respectively. The results herein highlight the importance
Modelling of Argon Cold Atmospheric Plasmas for Biomedical Applications

Science.gov (United States)

Atanasova, M.; Benova, E.; Degrez, G.; van der Mullen, J. A. M.

2018-02-01

Plasmas for biomedical applications are one of the newest fields of plasma utilization. Especially high is the interest toward plasma usage in medicine. Promising results are achieved in blood coagulation, wound healing, treatment of some forms of cancer, diabetic complications, etc. However, the investigations of the biomedical applications from biological and medical viewpoint are much more advanced than the studies on the dynamics of the plasma. In this work we aim to address some specific challenges in the field of plasma modelling, arising from biomedical applications - what are the plasma reactive species’ and electrical fields’ spatial distributions as well as their production mechanisms; what are the fluxes and energies of the various components of the plasma delivers to the treated surfaces; what is the gas flow pattern? The focus is on two devices, namely the capacitive coupled plasma jet and the microwave surface wave sustained discharge. The devices are representatives of the so called cold atmospheric plasmas (CAPs). These are discharges characterized by low gas temperature - less than 40°C at the point of application - and non-equilibrium chemistry.
[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.
Programming Entity Framework

CERN Document Server

Lerman, Julia

2010-01-01

Get a thorough introduction to ADO.NET Entity Framework 4 -- Microsoft's core framework for modeling and interacting with data in .NET applications. The second edition of this acclaimed guide provides a hands-on tour of the framework latest version in Visual Studio 2010 and .NET Framework 4. Not only will you learn how to use EF4 in a variety of applications, you'll also gain a deep understanding of its architecture and APIs. Written by Julia Lerman, the leading independent authority on the framework, Programming Entity Framework covers it all -- from the Entity Data Model and Object Service
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.

Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies.

Science.gov (United States)

Lamy, Jean-Baptiste

2017-07-01

Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Owlready has been successfully
Multifunctional Magnetic-fluorescent Nanocomposites for Biomedical Applications

Directory of Open Access Journals (Sweden)

Rakovich Yury

2008-01-01

Full Text Available AbstractNanotechnology is a fast-growing area, involving the fabrication and use of nano-sized materials and devices. Various nanocomposite materials play a number of important roles in modern science and technology. Magnetic and fluorescent inorganic nanoparticles are of particular importance due to their broad range of potential applications. It is expected that the combination of magnetic and fluorescent properties in one nanocomposite would enable the engineering of unique multifunctional nanoscale devices, which could be manipulated using external magnetic fields. The aim of this review is to present an overview of bimodal “two-in-one” magnetic-fluorescent nanocomposite materials which combine both magnetic and fluorescent properties in one entity, in particular those with potential applications in biotechnology and nanomedicine. There is a great necessity for the development of these multifunctional nanocomposites, but there are some difficulties and challenges to overcome in their fabrication such as quenching of the fluorescent entity by the magnetic core. Fluorescent-magnetic nanocomposites include a variety of materials including silica-based, dye-functionalised magnetic nanoparticles and quantum dots-magnetic nanoparticle composites. The classification and main synthesis strategies, along with approaches for the fabrication of fluorescent-magnetic nanocomposites, are considered. The current and potential biomedical uses, including biological imaging, cell tracking, magnetic bioseparation, nanomedicine and bio- and chemo-sensoring, of magnetic-fluorescent nanocomposites are also discussed.
22 CFR 96.5 - Requirement that accrediting entity be a nonprofit or public entity.

Science.gov (United States)

2010-04-01

... administering standards for entities providing child welfare services; or (b) A public entity (other than a... political subdivision, agency, or instrumentality thereof, that is responsible for licensing adoption agencies in a State and that has expertise in developing and administering standards for entities providing...
Chitosan nanoparticles as drug delivery carriers for biomedical engineering

International Nuclear Information System (INIS)

Shi, L.E.S.; Chen, M.; XINF, L.Y.; Guo, X.F.; Zhao, L.M.

2011-01-01

Chitosan is a rather abundant material, which has been widely used in food industrial and bioengineering aspects, including in encapsulating active food ingredients, in enzyme immobilization, and as a carrier for drug delivery, due to its significant biological and chemical properties such as biodegradable, biocompatible, bioactive and polycationic. This review discussed preparation and applications of chitosan nanoparticles in the biomedical engineering field, namely as a drug delivery carrier for biopharmaceuticals. (author)
Ethical aspects and dilemmas of preparing, writing and publishing of the scientific papers in the biomedical journals.

Science.gov (United States)

Masic, Izet

2012-09-01

In this paper author discussed about preparing and submitting manuscripts - scientific, research, professional papers, reviews and case reports. Author described it from the Editor's perspective, and specially talked about ethical aspects of authorship, conflict of interest, copyright, plagiarism and duplicate publication from the point of view of his experiences as Editor-in-Chief of several biomedical journals and Chief of Task Force of European Federation of Medical Informatics journals and member of Task Force of European Cardiology Society journals. The scientific process relies on trust and credibility. The scientific community demands high ethical standards to conduct biomedical research and to publish scientific contents. During the last decade, disclosure of conflicts of interest (COI ), (also called competing loyalties, competing interests or dual commitments), has been considered as a key element to guarantee the credibility of the scientific process. Biases in design, analysis and interpretation of studies may arise when authors or sponsors have vested interests. Therefore, COI should be made clear to the readers to facilitate their own judgment and interpretation of their relevance and potential implications. Authors are responsible to fully disclose potential COI . In October 2009 the ICMJE proposed an electronic "uniform" format for COI disclosure. Four main areas were addressed: authors´ associations with entities that supported the submitted manuscript (indefinite time frame), associations with commercial entities with potential interest in the general area of the manuscript (time frame 36 months), financial association of their spouse and children and, finally, non-financial associations potentially relevant to the submitted manuscript. Consumers of medical scholarship expect a reliable system of disclosure in which journals and authors make disclosures appropriately and consistently. There is a stigma surrounding the reporting of COI that should
Evaluating Stream Filtering for Entity Profile Updates in TREC 2012, 2013, and 2014 (KBA Track Overview, Notebook Paper)

Science.gov (United States)

2014-11-01

possible future directions that build on the KBA experience. Data Assets In addition to the three hundred run submissions from diverse systems...form name of an entity and assigning a confidence score based on the number of matches of tokens in the name. See code in github [6]. macro-P...131 64 GENDER 4 2 FoundedBy 56 30 NAME 2 2 DateOfDeath 54 12 TOP_MEMBERS_EMPLOYEES 2 1 EmployeeOf 44 19 WON_AWARD 1 1
EPONYMY BASED ON NAMES OF COMPANIES

Directory of Open Access Journals (Sweden)

Éva Kovács

2016-03-01

Full Text Available As is generally defined, eponymy, one of the word-formation processes refers to the derivation of a name of a city, country, era, institution, or other place or thing from that of a person such as sandwich, wellington, mackintosh or cardigan. Eponymy can be classified in several ways, some refer to foods (Pizza Margaritha, diseases (Alzheimer disease, places (Washington, scientific laws (Archimedes’s principle and sport terms (Axel jump, whereas others indicate trademarks, brand names (aspirin, prizes, awards (Nobel Prize, inventions (Rubic’s Cube, ideologies (Darwinism, colleges, universities (Stanford University and companies (Ford. The present paper discusses eponyms which denote companies based on the name of their founder(s (e.g. Porsche, Siemens, Gucci, Campari, Cadbury, McDonald’s and Walt Disney, etc. by revealing what kind of a metonymic relationship is manifested in them. Cognitive linguists, such as Lakoff and Johnson (1980, Radden and Kövecses (1999 and Kövecses (2002 state that metonymy is essentially a conceptual phenomenon, in which one conceptual entity, the vehicle, provides mental access to another conceptual entity, the target, within the same idealized cognitive model. In fact, metonymy is part of our everyday way of thinking, and is grounded in experience. Common metonymies include PRODUCER FOR PRODUCT (Pass me the Shakespeare on the top shelf., PLACE FOR EVENT (Iraq nearly cost Tony Blair the premiership, PLACE FOR INSTITUTION (Downing Street refused comment., PART FOR THE WHOLE (She’s not just a pretty face., WHOLE FOR THE PART (England beat Australia in the 2003 Rugby World Cup final. and EFFECT FOR CAUSE (He has a long face.. Following the cognitive approach to metonyms, I tentatively suggest that the metonymy PRODUCER FOR THE PRODUCT can be observed in the case of car makes, products of famous fashion houses, cosmetics and drinks as is illustrated by examples like He’s bought a Ferrari. I ate a McDonald or
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
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
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
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
Programming Drupal 7 entities

CERN Document Server

Michael, Sammy

2013-01-01

The book follows a standard tutorial-based approach to create, retrieve, update, and delete Drupal 7 entities, their properties and fields.Programming Drupal 7 Entities is perfect for intermediate or advanced developers new to Drupal entity development who are looking to get a good grounding in how to code using the new paradigm. It's assumed that you will have some experience in PHP development already, and being vaguely familiar with Drupal, GIT, and Drush will also help.
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
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.
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.
Surface engineering of graphene-based nanomaterials for biomedical applications.

Science.gov (United States)

Shi, Sixiang; Chen, Feng; Ehlerding, Emily B; Cai, Weibo

2014-09-17

Graphene-based nanomaterials have attracted tremendous interest over the past decade due to their unique electronic, optical, mechanical, and chemical properties. However, the biomedical applications of these intriguing nanomaterials are still limited due to their suboptimal solubility/biocompatibility, potential toxicity, and difficulties in achieving active tumor targeting, just to name a few. In this Topical Review, we will discuss in detail the important role of surface engineering (i.e., bioconjugation) in improving the in vitro/in vivo stability and enriching the functionality of graphene-based nanomaterials, which can enable single/multimodality imaging (e.g., optical imaging, positron emission tomography, magnetic resonance imaging) and therapy (e.g., photothermal therapy, photodynamic therapy, and drug/gene delivery) of cancer. Current challenges and future research directions are also discussed and we believe that graphene-based nanomaterials are attractive nanoplatforms for a broad array of future biomedical applications.
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
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
Implementation and management of a biomedical observation dictionary in a large healthcare information system.

Science.gov (United States)

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

2013-01-01

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

Science.gov (United States)

Cohen, K Bretonnel; Lanfranchi, Arrick; Choi, Miji Joo-Young; Bada, Michael; Baumgartner, William A; Panteleyeva, Natalya; Verspoor, Karin; Palmer, Martha; Hunter, Lawrence E

2017-08-17

Coreference resolution is the task of finding strings in text that have the same referent as other strings. Failures of coreference resolution are a common cause of false negatives in information extraction from the scientific literature. In order to better understand the nature of the phenomenon of coreference in biomedical publications and to increase performance on the task, we annotated the Colorado Richly Annotated Full Text (CRAFT) corpus with coreference relations. The corpus was manually annotated with coreference relations, including identity and appositives for all coreferring base noun phrases. The OntoNotes annotation guidelines, with minor adaptations, were used. Interannotator agreement ranges from 0.480 (entity-based CEAF) to 0.858 (Class-B3), depending on the metric that is used to assess it. The resulting corpus adds nearly 30,000 annotations to the previous release of the CRAFT corpus. Differences from related projects include a much broader definition of markables, connection to extensive annotation of several domain-relevant semantic classes, and connection to complete syntactic annotation. Tool performance was benchmarked on the data. A publicly available out-of-the-box, general-domain coreference resolution system achieved an F-measure of 0.14 (B3), while a simple domain-adapted rule-based system achieved an F-measure of 0.42. An ensemble of the two reached F of 0.46. Following the IDENTITY chains in the data would add 106,263 additional named entities in the full 97-paper corpus, for an increase of 76% percent in the semantic classes of the eight ontologies that have been annotated in earlier versions of the CRAFT corpus. The project produced a large data set for further investigation of coreference and coreference resolution in the scientific literature. The work raised issues in the phenomenon of reference in this domain and genre, and the paper proposes that many mentions that would be considered generic in the general domain are not

Recurrent neural networks with specialized word embeddings for health-domain named-entity recognition.

Science.gov (United States)

Jauregi Unanue, Iñigo; Zare Borzeshi, Ehsan; Piccardi, Massimo

2017-12-01

Previous state-of-the-art systems on Drug Name Recognition (DNR) and Clinical Concept Extraction (CCE) have focused on a combination of text "feature engineering" and conventional machine learning algorithms such as conditional random fields and support vector machines. However, developing good features is inherently heavily time-consuming. Conversely, more modern machine learning approaches such as recurrent neural networks (RNNs) have proved capable of automatically learning effective features from either random assignments or automated word "embeddings". (i) To create a highly accurate DNR and CCE system that avoids conventional, time-consuming feature engineering. (ii) To create richer, more specialized word embeddings by using health domain datasets such as MIMIC-III. (iii) To evaluate our systems over three contemporary datasets. Two deep learning methods, namely the Bidirectional LSTM and the Bidirectional LSTM-CRF, are evaluated. A CRF model is set as the baseline to compare the deep learning systems to a traditional machine learning approach. The same features are used for all the models. We have obtained the best results with the Bidirectional LSTM-CRF model, which has outperformed all previously proposed systems. The specialized embeddings have helped to cover unusual words in DrugBank and MedLine, but not in the i2b2/VA dataset. We present a state-of-the-art system for DNR and CCE. Automated word embeddings has allowed us to avoid costly feature engineering and achieve higher accuracy. Nevertheless, the embeddings need to be retrained over datasets that are adequate for the domain, in order to adequately cover the domain-specific vocabulary. Copyright © 2017 Elsevier Inc. All rights reserved.
Biomedical Research Group, Health Division annual report 1954

Energy Technology Data Exchange (ETDEWEB)

Langham, W.H.; Storer, J.B.

1955-12-31

This report covers the activities of the Biomedical Research Group (H-4) of the Health Division during the period January 1 through December 31, 1954. Organizationally, Group H-4 is divided into five sections, namely, Biochemistry, Radiobiology, Radiopathology, Biophysics, and Organic Chemistry. The activities of the Group are summarized under the headings of the various sections. The general nature of each section`s program, publications, documents and reports originating from its members, and abstracts and summaries of the projects pursued during the year are presented.
Biomedical hypothesis generation by text mining and gene prioritization.

Science.gov (United States)

Petric, Ingrid; Ligeti, Balazs; Gyorffy, Balazs; Pongor, Sandor

2014-01-01

Text mining methods can facilitate the generation of biomedical hypotheses by suggesting novel associations between diseases and genes. Previously, we developed a rare-term model called RaJoLink (Petric et al, J. Biomed. Inform. 42(2): 219-227, 2009) in which hypotheses are formulated on the basis of terms rarely associated with a target domain. Since many current medical hypotheses are formulated in terms of molecular entities and molecular mechanisms, here we extend the methodology to proteins and genes, using a standardized vocabulary as well as a gene/protein network model. The proposed enhanced RaJoLink rare-term model combines text mining and gene prioritization approaches. Its utility is illustrated by finding known as well as potential gene-disease associations in ovarian cancer using MEDLINE abstracts and the STRING database.
[Nonspecific interstitial pneumonitis: a clinicopathologic entity, histologic pattern or unclassified group of heterogeneous interstitial pneumonitis?].

Science.gov (United States)

Morais, António; Moura, M Conceição Souto; Cruz, M Rosa; Gomes, Isabel

2004-01-01

Nonspecific interstitial pneumonitis (NSIP) initially described by Katzenstein and Fiorelli in 1994, seems to be a distinct clinicopathologic entity among idiopathic interstitial pneumonitis (IIP). Besides different histologic features from other IIP, NSIP is characterized by a better long-term outcome, associated with a better steroids responsiveness than idiopathic pulmonar fibrosis (IPF), where usually were included. Thus, differentiating NSIP from other IIP, namely IPF is very significant, since it has important therapeutic and prognostic implications. NSIP encloses different pathologies, namely those with inflammatory predominance (cellular subtype) or fibrous predominance (fibrosing subtype). NSIP is reviewed and discussed by the authors, after two clinical cases description.
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...
GeneView: a comprehensive semantic search engine for PubMed.

Science.gov (United States)

Thomas, Philippe; Starlinger, Johannes; Vowinkel, Alexander; Arzt, Sebastian; Leser, Ulf

2012-07-01

Research results are primarily published in scientific literature and curation efforts cannot keep up with the rapid growth of published literature. The plethora of knowledge remains hidden in large text repositories like MEDLINE. Consequently, life scientists have to spend a great amount of time searching for specific information. The enormous ambiguity among most names of biomedical objects such as genes, chemicals and diseases often produces too large and unspecific search results. We present GeneView, a semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. Annotation is performed by a multitude of state-of-the-art text-mining tools for recognizing mentions from 10 entity classes and for identifying protein-protein interactions. GeneView currently contains annotations for >194 million entities from 10 classes for ∼21 million citations with 271,000 full text bodies. GeneView can be searched at http://bc3.informatik.hu-berlin.de/.
Project Alexander the Great: a study on the world proliferation of bioengineering/biomedical engineering education.

Science.gov (United States)

Abu-Faraj, Ziad O

2008-01-01

Bioengineering/Biomedical Engineering is considered amongst the most reputable fields within the global arena, and will likely be the primer for any future breakthroughs in Medicine and Biology. Bioengineering/biomedical engineering education has evolved since late 1950s and is undergoing advancement in leading academic institutions worldwide. This paper delineates an original study on the world proliferation of bioengineering/biomedical engineering education and bears the name 'Project Alexander the Great'. The initial step of the project was to survey all 10448 universities, recognized by the International Association of Universities, spread among the 193 member states of the United Nations within the six continents. The project aims at identifying, disseminating, and networking, through the world-wide-web, those institutions of higher learning that provide bioengineering/biomedical engineering education. The significance of this project is multifold: i) the inception of a web-based 'world-map' in bioengineering/biomedical engineering education for the potential international student desiring to pursue a career in this field; ii) the global networking of bioengineering/biomedical engineering academic/research programs; iii) the promotion of first-class bioengineering/biomedical engineering education and the catalysis of global proliferation of this field; iv) the erection of bridges among educational institutions, industry, and professional societies or organizations involved in Bioengineering/Biomedical Engineering; and v) the catalysis in the establishment of framework agreements for cooperation among the identified institutions offering curricula in this field. This paper presents the results obtained from Africa and North America. The whole project is due to be completed by 2009.
Testing the Application for Analyzing Structured Entities

OpenAIRE

Ion IVAN; Bogdan VINTILA

2011-01-01

The paper presents the testing process of the application for the analysis of structured text entities. The structured entities are presented. Quality characteristics of structured entities are identified and analyzed. The design and building processes are presented. Rules for building structured entities are described. The steps of building the application for the analysis of structured text entities are presented. The objective of the testing process is defined. Ways of testing the applicat...
Entity ranking using Wikipedia as a pivot

NARCIS (Netherlands)

Kaptein, R.; Serdyukov, P.; de Vries, A.; Kamps, J.; Huang, X.J.; Jones, G.; Koudas, N.; Wu, X.; Collins-Thompson, K.

2010-01-01

In this paper we investigate the task of Entity Ranking on the Web. Searchers looking for entities are arguably better served by presenting a ranked list of entities directly, rather than a list of web pages with relevant but also potentially redundant information about these entities. Since
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
Query containment in entity SQL

OpenAIRE

Rull Fort, Guillem; Bernstein, Philip A.; Garcia dos Santos, Ivo; Katsis, Yannis; Melnik, Sergey; Teniente López, Ernest

2013-01-01

We describe a software architecture we have developed for a constructive containment checker of Entity SQL queries defined over extended ER schemas expressed in Microsoft's Entity Data Model. Our application of interest is compilation of object-to-relational mappings for Microsoft's ADO.NET Entity Framework, which has been shipping since 2007. The supported language includes several features which have been individually addressed in the past but, to the best of our knowledge, they have not be...
Ranking related entities: components and analyses

NARCIS (Netherlands)

Bron, M.; Balog, K.; de Rijke, M.

2010-01-01

Related entity finding is the task of returning a ranked list of homepages of relevant entities of a specified type that need to engage in a given relationship with a given source entity. We propose a framework for addressing this task and perform a detailed analysis of four core components;
Automatically Recognizing Medication and Adverse Event Information From Food and Drug Administration's Adverse Event Reporting System Narratives.

Science.gov (United States)

Polepalli Ramesh, Balaji; Belknap, Steven M; Li, Zuofeng; Frid, Nadya; West, Dennis P; Yu, Hong

2014-06-27

The Food and Drug Administration's (FDA) Adverse Event Reporting System (FAERS) is a repository of spontaneously-reported adverse drug events (ADEs) for FDA-approved prescription drugs. FAERS reports include both structured reports and unstructured narratives. The narratives often include essential information for evaluation of the severity, causality, and description of ADEs that are not present in the structured data. The timely identification of unknown toxicities of prescription drugs is an important, unsolved problem. The objective of this study was to develop an annotated corpus of FAERS narratives and biomedical named entity tagger to automatically identify ADE related information in the FAERS narratives. We developed an annotation guideline and annotate medication information and adverse event related entities on 122 FAERS narratives comprising approximately 23,000 word tokens. A named entity tagger using supervised machine learning approaches was built for detecting medication information and adverse event entities using various categories of features. The annotated corpus had an agreement of over .9 Cohen's kappa for medication and adverse event entities. The best performing tagger achieves an overall performance of 0.73 F1 score for detection of medication, adverse event and other named entities. In this study, we developed an annotated corpus of FAERS narratives and machine learning based models for automatically extracting medication and adverse event information from the FAERS narratives. Our study is an important step towards enriching the FAERS data for postmarketing pharmacovigilance.
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
Enriched vascularity in ameloblastomas, an indeterminate entity: Report of two cases

Directory of Open Access Journals (Sweden)

Usha Hegde

2015-01-01

Full Text Available Vascularity is a highly essential element that is required for the growth, development, and functioning of the body and variations in it can cause pathologies. It is one of the prime features of a proliferating lesion, where it aids in the growth of the lesion through its nutrition supply. Highly increased vascularity in a disease can itself affect the prognosis of the lesion, and in malignancies, it can induce tumor seeding and secondaries. Most of the pathologies including tumors, related to blood vessels, and vascularity are well established. There are some conditions, wherein altered vascularity is one of the prime components along with other diagnostic components of an established disease. In such cases, these lesions are diagnosed with special names, with varying biological behavior and prognosis in comparison to that of established entity. However, there still are few similar conditions whose nature is uncertain due to the rarity of the lesion and the insufficient scientific evidence which eludes the diagnostician. Here is the report of two cases of ameloblastoma, an established entity, with significant vascularity whose nature is indeterminate.
ANTIMICROBIAL REAGENTS AS FUNCTIONAL FINISHING FOR TEXTILES INTENDED FOR BIOMEDICAL APPLICATIONS. I. SYNTHETIC ORGANIC COMPOUNDS

Directory of Open Access Journals (Sweden)

Madalina Zanoaga

2014-06-01

Full Text Available This article offers an overview of some contemporary antimicrobial (biocides and biostatics agents used as functional finishing for textiles intended for biomedical applications. It reviews only synthetic agents, namely quaternary ammonium compounds, halogenated phenols, polybiguanides, N-halamines, and renewable peroxides, as a part of an extensive study currently in progress.
The biomedical disciplines and the structure of biomedical and clinical knowledge.

Science.gov (United States)

Nederbragt, H

2000-11-01

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

International Nuclear Information System (INIS)

Kubala-Kukus, A.; Kuternoga, E.; Braziewicz, J.; Pajek, M.

2004-01-01

In the present paper, which follows our earlier observation that the asymmetric and long-tailed concentration distributions of trace elements in biomedical samples, measured by the X-ray fluorescence techniques, can be modeled by the log-stable distributions, further specific aspects of this observation are discussed. First, we demonstrate that, typically, for a quite substantial fraction (10-20%) of trace elements studied in different kinds of biomedical samples, the measured concentration distributions are described in fact by the 'symmetric' log-stable distributions, i.e. the asymmetric distributions which are described by the symmetric stable distributions. This observation is, in fact, expected for the random multiplicative process, which models the concentration distributions of trace elements in the biomedical samples. The log-stable nature of concentration distribution of trace elements results in several problems of statistical nature, which have to be addressed in XRF data analysis practice. Consequently, in the present paper, the following problems, namely (i) the estimation of parameters for stable distributions and (ii) the testing of the log-stable nature of the concentration distribution by using the Anderson-Darling (A 2 ) test, especially for symmetric stable distributions, are discussed in detail. In particular, the maximum likelihood estimation and Monte Carlo simulation techniques were used, respectively, for estimation of stable distribution parameters and calculation of the critical values for the Anderson-Darling test. The discussed ideas are exemplified by the results of the study of trace element concentration distributions in selected biomedical samples, which were obtained by using the X-ray fluorescence (XRF, TXRF) methods

Drug design and discovery: translational biomedical science varies among countries.

Science.gov (United States)

Weaver, Ian N; Weaver, Donald F

2013-10-01

Drug design and discovery is an innovation process that translates the outcomes of fundamental biomedical research into therapeutics that are ultimately made available to people with medical disorders in many countries throughout the world. To identify which nations succeed, exceed, or fail at the drug design/discovery endeavor--more specifically, which countries, within the context of their national size and wealth, are "pulling their weight" when it comes to developing medications targeting the myriad of diseases that afflict humankind--we compiled and analyzed a comprehensive survey of all new drugs (small molecular entities and biologics) approved annually throughout the world over the 20-year period from 1991 to 2010. Based upon this analysis, we have devised prediction algorithms to ascertain which countries are successful (or not) in contributing to the worldwide need for effective new therapeutics. © 2013 Wiley Periodicals, Inc.
Awareness of Entities, Activities and Contexts in Ambient Systems

DEFF Research Database (Denmark)

Kristensen, Bent Bruun

2013-01-01

Ambient systems are modeled by entities, activities and contexts, where entities exist in contexts and engage in activities. A context supports a dynamic collection of entities by services and offers awareness information about the entities. Activities also exist in contexts and model ongoing...... collaborations between entities. Activities and local contexts also obtain awareness information from the context about the dynamic collection of entities. Similarly activities, local contexts and entities are offered awareness information about activities and local contexts....
New routes to the functionalization patterning and manufacture of graphene-based materials for biomedical applications.

Science.gov (United States)

De Sanctis, A; Russo, S; Craciun, M F; Alexeev, A; Barnes, M D; Nagareddy, V K; Wright, C D

2018-06-06

Graphene-based materials are being widely explored for a range of biomedical applications, from targeted drug delivery to biosensing, bioimaging and use for antibacterial treatments, to name but a few. In many such applications, it is not graphene itself that is used as the active agent, but one of its chemically functionalized forms. The type of chemical species used for functionalization will play a key role in determining the utility of any graphene-based device in any particular biomedical application, because this determines to a large part its physical, chemical, electrical and optical interactions. However, other factors will also be important in determining the eventual uptake of graphene-based biomedical technologies, in particular the ease and cost of manufacture of proposed device and system designs. In this work, we describe three novel routes for the chemical functionalization of graphene using oxygen, iron chloride and fluorine. We also introduce novel in situ methods for controlling and patterning such functionalization on the micro- and nanoscales. Our approaches are readily transferable to large-scale manufacturing, potentially paving the way for the eventual cost-effective production of functionalized graphene-based materials, devices and systems for a range of important biomedical applications.
Testing the Application for Analyzing Structured Entities

Directory of Open Access Journals (Sweden)

Ion IVAN

2011-01-01

Full Text Available The paper presents the testing process of the application for the analysis of structured text entities. The structured entities are presented. Quality characteristics of structured entities are identified and analyzed. The design and building processes are presented. Rules for building structured entities are described. The steps of building the application for the analysis of structured text entities are presented. The objective of the testing process is defined. Ways of testing the application on components and as a whole are established. A testing strategy for different objectives is proposed. The behavior of users during the testing period is analyzed. Statistical analysis regarding the behavior of users in processes of infinite resources access are realized.
Arabic medical entity tagging using distant learning

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Viviana Cotik

2017-04-01

Full Text Available A semantic tagger aiming to detect relevant entities in Arabic medical documents and tagging them with their appropriate semantic class is presented. The system takes profit of a Multilingual Framework covering four languages (Arabic, English, French, and Spanish, in a way that resources available for each language can be used to improve the results of the others, this is specially important for less resourced languages as Arabic. The approach has been evaluated against Wikipedia pages of the four languages belonging to the medical domain. The core of the system is the definition of a base tagset consisting of the three most represented classes in SNOMED-CT taxonomy and the learning of a binary classifier for each semantic category in the tagset and each language, using a distant learning approach over three widely used knowledge resources, namely Wikipedia, Dbpedia, and SNOMED-CT.
Entity Ranking using Wikipedia as a Pivot

NARCIS (Netherlands)

R. Kaptein; P. Serdyukov; A.P. de Vries (Arjen); J. Kamps

2010-01-01

htmlabstractIn this paper we investigate the task of Entity Ranking on the Web. Searchers looking for entities are arguably better served by presenting a ranked list of entities directly, rather than a list of web pages with relevant but also potentially redundant information about
Entity resolution for uncertain data

NARCIS (Netherlands)

Ayat, N.; Akbarinia, R.; Afsarmanesh, H.; Valduriez, P.

2012-01-01

Entity resolution (ER), also known as duplicate detection or record matching, is the problem of identifying the tuples that represent the same real world entity. In this paper, we address the problem of ER for uncertain data, which we call ERUD. We propose two different approaches for the ERUD
31 CFR 595.303 - Entity.

Science.gov (United States)

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Entity. 595.303 Section 595.303 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY TERRORISM SANCTIONS REGULATIONS General Definitions § 595.303 Entity...
26 CFR 301.7701-2 - Business entities; definitions.

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 18 2010-04-01 2010-04-01 false Business entities; definitions. 301.7701-2...) PROCEDURE AND ADMINISTRATION PROCEDURE AND ADMINISTRATION Definitions § 301.7701-2 Business entities; definitions. (a) Business entities. For purposes of this section and § 301.7701-3, a business entity is any...
Recognition of chemical entities: combining dictionary-based and grammar-based approaches

Science.gov (United States)

2015-01-01

Background The past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstructured texts. The BioCreative CHEMDNER challenge invites the development of systems for the automatic recognition of chemicals in text (CEM task) and for ranking the recognized compounds at the document level (CDI task). We investigated an ensemble approach where dictionary-based named entity recognition is used along with grammar-based recognizers to extract compounds from text. We assessed the performance of ten different commercial and publicly available lexical resources using an open source indexing system (Peregrine), in combination with three different chemical compound recognizers and a set of regular expressions to recognize chemical database identifiers. The effect of different stop-word lists, case-sensitivity matching, and use of chunking information was also investigated. We focused on lexical resources that provide chemical structure information. To rank the different compounds found in a text, we used a term confidence score based on the normalized ratio of the term frequencies in chemical and non-chemical journals. Results The use of stop-word lists greatly improved the performance of the dictionary-based recognition, but there was no additional benefit from using chunking information. A combination of ChEBI and HMDB as lexical resources, the LeadMine tool for grammar-based recognition, and the regular expressions, outperformed any of the individual systems. On the test set, the F-scores were 77.8% (recall 71.2%, precision 85.8%) for the CEM task and 77.6% (recall 71.7%, precision 84.6%) for the CDI task. Missed terms were mainly due to tokenization issues, poor recognition of formulas, and term conjunctions. Conclusions We developed an ensemble system that combines dictionary-based and grammar-based approaches for chemical named
Recognition of chemical entities: combining dictionary-based and grammar-based approaches.

Science.gov (United States)

Akhondi, Saber A; Hettne, Kristina M; van der Horst, Eelke; van Mulligen, Erik M; Kors, Jan A

2015-01-01

The past decade has seen an upsurge in the number of publications in chemistry. The ever-swelling volume of available documents makes it increasingly hard to extract relevant new information from such unstructured texts. The BioCreative CHEMDNER challenge invites the development of systems for the automatic recognition of chemicals in text (CEM task) and for ranking the recognized compounds at the document level (CDI task). We investigated an ensemble approach where dictionary-based named entity recognition is used along with grammar-based recognizers to extract compounds from text. We assessed the performance of ten different commercial and publicly available lexical resources using an open source indexing system (Peregrine), in combination with three different chemical compound recognizers and a set of regular expressions to recognize chemical database identifiers. The effect of different stop-word lists, case-sensitivity matching, and use of chunking information was also investigated. We focused on lexical resources that provide chemical structure information. To rank the different compounds found in a text, we used a term confidence score based on the normalized ratio of the term frequencies in chemical and non-chemical journals. The use of stop-word lists greatly improved the performance of the dictionary-based recognition, but there was no additional benefit from using chunking information. A combination of ChEBI and HMDB as lexical resources, the LeadMine tool for grammar-based recognition, and the regular expressions, outperformed any of the individual systems. On the test set, the F-scores were 77.8% (recall 71.2%, precision 85.8%) for the CEM task and 77.6% (recall 71.7%, precision 84.6%) for the CDI task. Missed terms were mainly due to tokenization issues, poor recognition of formulas, and term conjunctions. We developed an ensemble system that combines dictionary-based and grammar-based approaches for chemical named entity recognition, outperforming
7 CFR 1738.16 - Eligible entities.

Science.gov (United States)

2010-01-01

... cooperative, nonprofit, limited dividend or mutual associations, limited liability companies, commercial... or partnerships of individuals are not eligible entities. (2) An entity is not eligible if it serves...
Mountain names in the geographical dictionary of Camagüey Province, environmental studies, and environmental education

Directory of Open Access Journals (Sweden)

Alfonso, L. F.

2014-01-01

Full Text Available The research contributes to the project intended to provide the province of Camagüey with a geographical dictionary, a reference book for economic entities and academic institutions. The article is aimed at standardizing the use of geographical names in education and scientific research in Camagüey. Several methods of geographical research were used, cartographic methods, observing geographic objects in place and field research included. The findings were assessed by means of consulting experts on the topic and computer data processing. The methodology employed follows the guidelines of the national group of advisors for geographical names and the group of advisor of Camagüey province. The most widely used geographical names in the regions were listed in the dictionary.
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.
31 CFR 800.211 - Entity.

Science.gov (United States)

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Entity. 800.211 Section 800.211 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF INVESTMENT... separate legal entity) operated by any one of the foregoing as a business undertaking in a particular...
31 CFR 596.308 - Person; entity.

Science.gov (United States)

2010-07-01

... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY TERRORISM LIST GOVERNMENTS SANCTIONS REGULATIONS General Definitions § 596.308 Person; entity. (a) The term person means an individual or entity. (b) The...
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
Entity resolution in the web of data

CERN Document Server

Christophides, Vassilis; Stefanidis, Kostas

2015-01-01

In recent years, several knowledge bases have been built to enable large-scale knowledge sharing, but also an entity-centric Web search, mixing both structured data and text querying. These knowledge bases offer machine-readable descriptions of real-world entities, e.g., persons, places, published on the Web as Linked Data. However, due to the different information extraction tools and curation policies employed by knowledge bases, multiple, complementary and sometimes conflicting descriptions of the same real-world entities may be provided. Entity resolution aims to identify different descrip
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.
A COMPARISON OF THE CAPITAL STRUCTURES OF THE TOP 40MULTINATIONAL ENTITIES AND THE TOP 40 JSE-LISTED ENTITIES

Directory of Open Access Journals (Sweden)

Lana H. Harmse

2017-01-01

Full Text Available The strategies and policies of multinational entities (MNEscentre onthe focalgoal of any company, which isto maximise profits and shareholder wealth.Management aims for an optimum ownership structure by implementing variousstrategies. One of these strategies is the debt-to-equity ratio (the capital structure.Previous studiesconductedonvariouscountries’locally-listed entities confirmthat the capital structure of an entity has an impact on the value ofthat entity.Thisthen raisesan interesting question as to whetherthecapital structures ofthetop 40Johannesburg Stock Exchange (JSE-listedentitiesare similar to those ofthe top40 global MNEs.Based on market capitalisation on 31December2014, this studysought to compare the capital structures,using the debt-to-equity ratio,ofthe top40JSE-listed entitieswith those ofthe top 40globalMNEs on the Fortune 500list.Independent t-testswere performed on thedebt-to-equity ratios of thetop 40JSE-listed entities and the top 40globalMNEsas a group.Both independent t-tests and the Mann-Whitney testswereperformedonthedebt-to-equity ratiosofapplicable entities of the group divided into threeselectedindustries. The resultsof theindependent t-testindicateastatistical andpractically significant differencebetween the top 40 JSE-listed entities and the top 40 global MNEs’ capitalstructures.The resultsof the Mann-Whitney testsindicatethat if the financialindustry is excluded,there isnostatistical orpractically significant differencebetween the capital structures of the top 40 JSE-listed entities and the top 40MNEs.However, based on the effect size there is a practical visible difference.

In Vitro Models in BiocompatibilityAssessment for Biomedical-Grade Chitosan Derivatives in Wound Management

Directory of Open Access Journals (Sweden)

Lim Chin Keong

2009-03-01

Full Text Available One of the ultimate goals of wound healing research is to find effective healing techniques that utilize the regeneration of similar tissues. This involves the modification of various wound dressing biomaterials for proper wound management. The biopolymer chitosan (b-1,4-D-glucosamine has natural biocompatibility and biodegradability that render it suitable for wound management. By definition, a biocompatible biomaterial does not have toxic or injurious effects on biological systems. Chemical and physical modifications of chitosan influence its biocompatibility and biodegradability to an uncertain degree. Hence, the modified biomedical-grade of chitosan derivatives should be pre-examined in vitro in order to produce high-quality, biocompatible dressings. In vitro toxicity examinations are more favorable than those performed in vivo, as the results are more reproducible and predictive. In this paper, basic in vitro tools were used to evaluate cellular and molecular responses with regard to the biocompatibility of biomedical-grade chitosan. Three paramount experimental parameters of biocompatibility in vitro namely cytocompatibility, genotoxicity and skin pro-inflammatory cytokine expression, were generally reviewed for biomedical-grade chitosan as wound dressing.
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.
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
SOCIAL EFFECTIVENESS OF BUSINESS ENTITIES

Directory of Open Access Journals (Sweden)

Iryna Perevozova

2016-06-01

Full Text Available The article is aimed at investigation of social effectiveness of business entities. Social aspect of business is becoming a necessary component of success, increase of profitability and competitiveness as well as minimization of risks. Social effectiveness is referred to as correspondence between economic activity and main social needs and aims of society, interests of the staff and interests of a certain person. Investigation of social effectiveness of business entities is suggested to analyze with the help of social factors. Social factors are characterized by variability of expectations, relations and interests of society, staff and individuals. We suggest generalized classification of factors which have an impact on social effectiveness of business, we single out external and internal factors. To external factors belong: income of the population, differentiation of population according to income, migration, level of salaries, level of legality of income of population, family status of population, employment rate, age structure of population etc. As for internal factors we single out the following: low level of basic professional training, use of unskilled workers, absence of conditions for creativity, imperfection of system of motivation of professional growth, absence of specialized centers for certification training etc. Quantity and quality analysis of the above mentioned factors will enable to determine the level of social effectiveness of business entities. For analyses of degree of influence of factors on effectiveness we worked out a questionnaire of expert assessment which is represented in the form of assessment scale. We conducted a questionnaire and analyzed expert results and determined degree of influence of factors on social effectiveness of business. Assessment of level of social effectiveness of business entities was carried out by expert method of certain factor and was represented by a formula. The scale of assessment of
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
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
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
78 FR 31822 - Unincorporated Business Entities

Science.gov (United States)

2013-05-28

... framework for Farm Credit System (System) institutions' use of unincorporated business entities (UBEs) organized under State law for certain business activities. A UBE includes limited partnerships (LPs...-AC65 Unincorporated Business Entities AGENCY: Farm Credit Administration. ACTION: Final rule. SUMMARY...
A scalable machine-learning approach to recognize chemical names within large text databases

Directory of Open Access Journals (Sweden)

Wren Jonathan D

2006-09-01

Full Text Available Abstract Motivation The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. Results A first-order Markov Model (MM was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid.
Name agreement in picture naming : An ERP study

NARCIS (Netherlands)

Cheng, Xiaorong; Schafer, Graham; Akyürek, Elkan G.

Name agreement is the extent to which different people agree on a name for a particular picture. Previous studies have found that it takes longer to name low name agreement pictures than high name agreement pictures. To examine the effect of name agreement in the online process of picture naming, we
A family of names : rune-names and ogam-names and their relation to alphabet letter-names

NARCIS (Netherlands)

Griffiths, Alan

2013-01-01

The current consensus is that vernacular names assigned to the runes of the Germanic fuþark and to Irish ogam characters are indigenous creations independent of Mediterranean alphabet traditions. I propose, however, that ogam-names are based on interpretations of Hebrew, Greek or Latin letter-names
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.
High-dimensional data: p >> n in mathematical statistics and bio-medical applications

OpenAIRE

Van De Geer, Sara A.; Van Houwelingen, Hans C.

2004-01-01

The workshop 'High-dimensional data: p >> n in mathematical statistics and bio-medical applications' was held at the Lorentz Center in Leiden from 9 to 20 September 2002. This special issue of Bernoulli contains a selection of papers presented at that workshop. ¶ The introduction of high-throughput micro-array technology to measure gene-expression levels and the publication of the pioneering paper by Golub et al. (1999) has brought to life a whole new branch of data analysis under the name of...
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...
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.
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.
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
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,
Science and technology of biocompatible thin films for implantable biomedical devices.

Energy Technology Data Exchange (ETDEWEB)

Li, W.; Kabius, B.; Auciello, O.; Materials Science Division

2010-01-01

This presentation focuses on reviewing research to develop two critical biocompatible film technologies to enable implantable biomedical devices, namely: (1) development of bioinert/biocompatible coatings for encapsulation of Si chips implantable in the human body (e.g., retinal prosthesis implantable in the human eye) - the coating involves a novel ultrananocrystalline diamond (UNCD) film or hybrid biocompatible oxide/UNCD layered films; and (2) development of biocompatible films with high-dielectric constant and microfabrication process to produce energy storage super-capacitors embedded in the microchip to achieve full miniaturization for implantation into the human body.
46 CFR 403.110 - Accounting entities.

Science.gov (United States)

2010-10-01

... 46 Shipping 8 2010-10-01 2010-10-01 false Accounting entities. 403.110 Section 403.110 Shipping COAST GUARD (GREAT LAKES PILOTAGE), DEPARTMENT OF HOMELAND SECURITY GREAT LAKES PILOTAGE UNIFORM ACCOUNTING SYSTEM General § 403.110 Accounting entities. Each Association shall be a separate accounting...

Code-first development with Entity Framework

CERN Document Server

Barskiy, Sergey

2015-01-01

This book is intended for software developers with some prior experience with the Microsoft .NET framework who want to learn how to use Entity Framework. This book will get you up and running quickly, providing many examples that illustrate all the key concepts of Entity Framework.
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
Society as a crime victim of legal entities

Directory of Open Access Journals (Sweden)

Tanjević Nataša

2011-01-01

Full Text Available Tortious acts of legal entities have unforeseen harmful consequences in all areas. In the greedy desire to gain profit, certain legal entities do not have any regard for the most important resources of individuals and society. Damage resulting from the commission of criminal acts is very high for the whole society, especially when it comes to crimes against the environment. In order to prevent and combat corporate crime in criminal law, an increasingly wider acceptance of criminal liability of legal entities was adopted. This paper discusses the basic characteristics of corporate crime, as well as the reasons for the introduction of the criminal responsibility of legal entities. In this regard, we analyzed the law provisions regarding the liability of legal entities for criminal offenses, and concluded that despite the criminal-political need to react with more serious sanctions to the offenses of legal entities, there are certain obstacles and problems that stand in the way of introducing this responsibility.
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
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.
Discrimination of legal entities: Phenomenological characteristics and legal protection

Directory of Open Access Journals (Sweden)

Petrušić Nevena

2017-01-01

Full Text Available Their social nature encourages people to associate and jointly achieve the goals that they would not be able to achieve individually. Legal entities are created as one of the legal modalities of that association, as separate entities that have their own legal personality independent of the subjectivity of their members. Legal entities are holders of some human rights, depending on the nature of the right, including the right to non-discrimination. All mechanisms envisaged for legal protection against discrimination in the national legislation are available to legal persons. On the other hand, the situation is quite different in terms of access to international forums competent to deal with cases of discrimination. Legal entities do not have access to some international forums, while they may have access to others under the same conditions prescribed for natural persons. Legal entities may be exposed to various forms of direct and indirect discrimination both in the private and in the public sphere of social relations. Phenomenological characteristics of discrimination against legal persons are not substantially different from discrimination against individuals. There are no significant differences regarding the application of discrimination test in cases of discrimination of legal entities as compared to the use of this test in cases involving discrimination of natural persons or groups of persons. Legal entities may be discriminated against on the basis of characteristics of their legal personality, such as those which are objective elements of the legal entity and part of its legal identity. Discrimination of legal entities may be based on personal characteristics of its members (i.e. people who make a personal essence of a legal entity because their characteristics can be 'transferred' to the legal entity and become part of its identity. Legal entities should also be protected from this special form of transferred (associative discrimination.
On the Meaning of Name in Plato’s Cratylus Dialogue and the Epic Tales of Dede Korkut

Directory of Open Access Journals (Sweden)

Vefa Taşdelen

2015-12-01

Full Text Available Being given a name and giving a name are the most basic features of human being. He gives a name to himself as well as other entities in the universe he lives; recognizes them with names and provides introduction; establishes a relationship with them over the names. Everything manifesting itself to human consciousness in the universe and having a relationship with people have a name. From this perspective, giving a name is a problem with language and the origin of language. Asking the origin of names is to ask the origin of language; asking the relationship between names with regard to objects is to ask the relationship between language and reality and increasingly truth. The first work on names hence the philosophy of language was of Plato. Cratylus dialogue among his age of maturity dialogues where he developed his idealistic philosophy was the first work on names and hence the philosophy of language. In this dialogue, two points of view face each other. One of them is conventionalist approach of Hermogenes and the other is naturalist approach of Cratylus. In this frame, the answer will be sought to the following questions: In Tales of Dede Korkut, (1 What is the function of names? (2 How many correct names does a thing/object have? (3 What kind of relationship can be achieved between objects and names? (4 Who gives the names?
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.
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.
A Calculus of Located Entities

Directory of Open Access Journals (Sweden)

Adriana Compagnoni

2014-03-01

Full Text Available We define BioScapeL, a stochastic pi-calculus in 3D-space. A novel aspect of BioScapeL is that entities have programmable locations. The programmer can specify a particular location where to place an entity, or a location relative to the current location of the entity. The motivation for the extension comes from the need to describe the evolution of populations of biochemical species in space, while keeping a sufficiently high level description, so that phenomena like diffusion, collision, and confinement can remain part of the semantics of the calculus. Combined with the random diffusion movement inherited from BioScape, programmable locations allow us to capture the assemblies of configurations of polymers, oligomers, and complexes such as microtubules or actin filaments. Further new aspects of BioScapeL include random translation and scaling. Random translation is instrumental in describing the location of new entities relative to the old ones. For example, when a cell secretes a hydronium ion, the ion should be placed at a given distance from the originating cell, but in a random direction. Additionally, scaling allows us to capture at a high level events such as division and growth; for example, daughter cells after mitosis have half the size of the mother cell.
Entity models for trigger-reaction documents

NARCIS (Netherlands)

Khalid, M.A.; Marx, M.; Makkes, M.X.

2008-01-01

We define the notion of an entity model for a special kind of document popular on the web: an article followed by a list of reactions on that article, usually by many authors, usually inverse chronologically ordered. We call these documents trigger-reactions pairs. The entity model describes which
Understanding semantic mapping evolution by observing changes in biomedical ontologies.

Science.gov (United States)

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

2014-02-01

Knowledge Organization Systems (KOSs) are extensively used in the biomedical domain to support information sharing between software applications. KOSs are proposed covering different, but overlapping subjects, and mappings indicate the semantic relation between concepts from two KOSs. Over time, KOSs change as do the mappings between them. This can result from a new discovery or a revision of existing knowledge which includes corrections of concepts or mappings. Indeed, changes affecting KOS entities may force the underline mappings to be updated in order to ensure their reliability over time. To tackle this open research problem, we study how mappings are affected by KOS evolution. This article presents a detailed descriptive analysis of the impact that changes in KOS have on mappings. As a case study, we use the official mappings established between SNOMED CT and ICD-9-CM from 2009 to 2011. Results highlight factors according to which KOS changes in varying degrees influence the evolution of mappings. Copyright © 2013 Elsevier Inc. All rights reserved.
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.
On the Evaluation of Entity Profiles

DEFF Research Database (Denmark)

de Rijke, Maarten; Balog, Krisztian; Bogers, Toine

be assessed by means of precision and recall values of the descriptive terms produced. However, recent evidence suggests that more sophisticated metrics are needed that go beyond mere lexical matching of system-produced descriptors against a ground truth, allowing for graded relevance and rewarding diversity......Entity profiling is the task of identifying and ranking descriptions of a given entity. The task may be viewed as one where the descriptions being sought are terms that need to be selected from a knowledge source (such as an ontology or thesaurus). In this case, entity profiling systems can...... in the list of descriptors returned. In this note, we motivate and propose such a metric....
Use of systematic review to inform the infection risk for biomedical engineers and technicians servicing biomedical devices

International Nuclear Information System (INIS)

Smith, Anne-Louise

2011-01-01

Full text: Many microorganisms responsible for hospital acquired infections are able to stay viable on surfaces with no visible sign of contamination, in dry conditions and on non-porous surfaces. The infection risk to biomedical staff when servicing biomedical devices is not documented. An indirect approach has been used to examine the different aspects that will affect the risk of infection including a systematic review of microbial contamination and transmission relating to biomedical devices. A systematic review found 58% of biomedical devices have microbial contamination with 13% having at least one pathogenic organism. These microbes can persist for some months. Occupational-infections of biomedical service staff are low compared to other healthcare workers. A biomedical device with contaminated surface or dust was identified as the source of patient outbreaks in 13 papers. The cleaning agent most tested for removal of micro-organisms from devices was alcohol swabs, but sterile water swabs were also effective. However, manufacturers mainly recommend (74%) cleaning devices with water and detergent. Biomedical engineers and technicians have a small risk of being exposed to dangerous micro-organisms on most biomedical devices, but without skin breakage, this exposure is unlikely to cause ill-health. It is recommended that biomedical staff follow good infection control practices, wipe devices with detergent, sterile water or alcohol swabs as recommended by the manufacturer before working on them, and keep alcohol hand rubs accessible at all benches. (author)
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
Entity Framework 4.0 Recipes A Problem-solution Approach

CERN Document Server

Tenny, L

2010-01-01

Entity Framework 4.0 Recipes provides an exhaustive collection of ready-to-use code solutions for Microsoft's Entity Framework, Microsoft's vision for the future of data access. Entity Framework is a model-centric data access platform with an ocean of new concepts and patterns for developers to learn. With this book, you will learn the core concepts of Entity Framework through a broad range of clear and concise solutions to everyday data access tasks. Armed with this experience, you will be ready to dive deep into Entity Framework, experiment with new approaches, and develop ways to solve even
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...
Mastering entity framework

CERN Document Server

Singh, Rahul Rajat

2015-01-01

This book is for .NET developers who are developing data-driven applications using ADO.NET or other data access technologies. This book is going to give you everything you need to effectively develop and manage data-driven applications using Entity Framework.
RUTHERFORD APPLETON: What's in a name?!

International Nuclear Information System (INIS)

Anon.

1995-01-01

Full text: The initials 'RAU are well known in the world of particle physics, but recently the official name of the Laboratory has undergone several transmogrifications. To further complicate matters, the funding body for Particle Physics within the UK has changed too! On 1 April 1994 the Rutherford Appleton Laboratory combined with the Daresbury Laboratory to become a combined laboratory known as the Daresbury and Rutherford Appleton Laboratories (DRAL). At the same time the old Science and Engineering Research Council (SERC) was wound up, and funding was channelled through the newly formed Particle Physics and Astronomy Research Council (PPARC). Also, and just for an interim period, DRAL became part of the new Engineering and Physical Sciences Research Council (EPSRC). One year later a more profound change occurred when DRAL became a Research Council in its own right, and the legal entity created by Royal Charter was named The Council for the Central Laboratory of the Research Councils', abbreviated to CCLRC. On 1 April 1995, DRAL became The Central Laboratory of the Research Councils', and the abbreviation CLRC may be used. In spite of the changes to the official name, the laboratory sited at Chilton, The DAPNIA (Saclay, France) and Argonne transportable polarized target used in 1989- 1990 for a Fermi lab experiment has been used in a new experiment at Dubna. Gilles Durand from DAPNIA (right) and Yuri Usov of Dubna's Joint Institute for Nuclear Research (JINR) were responsible for construction. Oxfordshire, will continue to be known as the Rutherford Appleton Laboratory, or RAL

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.
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.
[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.
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.
17 CFR Appendix A to Part 420 - Separate Reporting Entity

Science.gov (United States)

2010-04-01

... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Separate Reporting Entity A... Part 420—Separate Reporting Entity Subject to the following conditions, one or more aggregating entity(ies) (e.g., parent, subsidiary, or organizational component) in a reporting entity, either separately...
VALUE RELEVANCE OF GROUP FINANCIAL STATEMENTS BASED ON ENTITY VERSUS PARENT COMPANY THEORY: EVIDENCE FROM THE LARGEST THREE EUROPEAN CAPITAL MARKETS

Directory of Open Access Journals (Sweden)

MÃ¼ller Victor-Octavian

2012-07-01

Full Text Available Financial statementsn#8217; main objective is to give information on the financial position, performance and changes in financial position of the reporting entity, which is useful to investors and other users in making economic decisions. In order to be useful, financial information needs to be relevant to the decision-making process of users in general, and investors in particular. Regarding consolidated financial statements, the accounting theory knows four perspectives (theories on which the preparation of those statements is based, namely, the proprietary theory, the parent company theory, the parent company extension theory and the entity theory (Baxter and Spinney, 1975. Of practical importance are especially the parent company extension perspective and the entity perspective. The IASB and FASB decided (within an ED regarding the Improvement of the Conceptual Framework that consolidated financial statements should be presented from the perspective of the group entity, and not from the perspective of the parent-company. However, this support for the entity theory is to our knowledge not backed by empirical findings in the academic literature. Therefore, in our paper we set to contribute with empirical arguments to finding an actual answer to the question about the superior market value relevance of one of the two concurrent perspectives (theories. We set to carry out an empirical association study on the problem of market value relevance of consolidated financial statements based on the entity theory respectively on the parent company (extension theory, searching for an answer to the above question. In this sense, we pursued an analysis of market value relevance of consolidated accounting information (based on the two perspectives of listed entities between 2003-2008 on the largest three European Stock Exchanges (London, Paris and Frankfurt. The obtained results showed that a n#8222;restrainedn#8221; entity perspective, which would combine
WCF multi-layer services development with Entity framework

CERN Document Server

Liu, Mike

2014-01-01

If you are a C#, VB.NET, or C++ developer and want to get started with WCF and Entity Framework, then this book is for you. Competence in Entity Framework will be needed to follow the examples in the book, but experience in creating WCF services using Entity Framework is not necessary. Developers and architects evaluating SOA implementation technologies for their company will find this book useful.
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
INTER–ORGANIZATIONAL COLLABORATIVE CAPACITY OF PUBLIC SECTOR INSTITUTIONS’CONTROL ENTITIES IN EMERGENCY SITUATIONS

Directory of Open Access Journals (Sweden)

Nikola T. STOYANOV

2015-10-01

Full Text Available Environmental challenges and natural disasters demand new tools to support the performance of public institutions in emergency situations. This paper contributes to one of the fundamental objectives – inter–organizational collaboration, namely to the objective to share experience from the implementation of methods and tools and latest research results in support of management in the new security environment. In addition, it focuses on the cognitive and human aspects of collaboration. The goal of the paper is to investigate the impact of different factors and tools for understanding, explaining, and measuring collaborative capacity of public sector institutions’ control organism in emergency situations. The paper will present intermediate results from the research on “Inter–organizational collaborative capacity of public sector institutions’ control entities in emergency situations”. Based on a theoretical model, a draft instrument was developed (i.e., a questionnaire for data collection that can be used to 1 investigate the impact of different factors, 2 localize inefficiencies in public sector institutions’ control organs, and 3 determine measures to achieve better organizational effectiveness of public sector institutions’ control entities in emergency situations.
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)
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.
Nano/micro-scale magnetophoretic devices for biomedical applications

International Nuclear Information System (INIS)

Lim, Byeonghwa; Kim, CheolGi; Vavassori, Paolo; Sooryakumar, R

2017-01-01

In recent years there have been tremendous advances in the versatility of magnetic shuttle technology using nano/micro-scale magnets for digital magnetophoresis. While the technology has been used for a wide variety of single-cell manipulation tasks such as selection, capture, transport, encapsulation, transfection, or lysing of magnetically labeled and unlabeled cells, it has also expanded to include parallel actuation and study of multiple bio-entities. The use of nano/micro-patterned magnetic structures that enable remote control of the applied forces has greatly facilitated integration of the technology with microfluidics, thereby fostering applications in the biomedical arena. The basic design and fabrication of various scaled magnets for remote manipulation of individual and multiple beads/cells, and their associated energies and forces that underlie the broad functionalities of this approach, are presented. One of the most useful features enabled by such advanced integrated engineering is the capacity to remotely tune the magnetic field gradient and energy landscape, permitting such multipurpose shuttles to be implemented within lab-on-chip platforms for a wide range of applications at the intersection of cellular biology and biotechnology. (topical review)
Nano/micro-scale magnetophoretic devices for biomedical applications

Science.gov (United States)

Lim, Byeonghwa; Vavassori, Paolo; Sooryakumar, R.; Kim, CheolGi

2017-01-01

In recent years there have been tremendous advances in the versatility of magnetic shuttle technology using nano/micro-scale magnets for digital magnetophoresis. While the technology has been used for a wide variety of single-cell manipulation tasks such as selection, capture, transport, encapsulation, transfection, or lysing of magnetically labeled and unlabeled cells, it has also expanded to include parallel actuation and study of multiple bio-entities. The use of nano/micro-patterned magnetic structures that enable remote control of the applied forces has greatly facilitated integration of the technology with microfluidics, thereby fostering applications in the biomedical arena. The basic design and fabrication of various scaled magnets for remote manipulation of individual and multiple beads/cells, and their associated energies and forces that underlie the broad functionalities of this approach, are presented. One of the most useful features enabled by such advanced integrated engineering is the capacity to remotely tune the magnetic field gradient and energy landscape, permitting such multipurpose shuttles to be implemented within lab-on-chip platforms for a wide range of applications at the intersection of cellular biology and biotechnology.
Ranking Entities in Networks via Lefschetz Duality

DEFF Research Database (Denmark)

Aabrandt, Andreas; Hansen, Vagn Lundsgaard; Poulsen, Bjarne

2014-01-01

then be ranked according to how essential their positions are in the network by considering the effect of their respective absences. Defining a ranking of a network which takes the individual position of each entity into account has the purpose of assigning different roles to the entities, e.g. agents......, in the network. In this paper it is shown that the topology of a given network induces a ranking of the entities in the network. Further, it is demonstrated how to calculate this ranking and thus how to identify weak sub-networks in any given network....
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
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 ...
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.
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)
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
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.

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).
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
14 CFR Sec. 1-6 - Accounting entities.

Science.gov (United States)

2010-01-01

... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Accounting entities. Sec. 1-6 Section 1-6... REGULATIONS UNIFORM SYSTEM OF ACCOUNTS AND REPORTS FOR LARGE CERTIFICATED AIR CARRIERS General Accounting Provisions Sec. 1-6 Accounting entities. (a) Separate accounting records shall be maintained for each air...
Ranking Very Many Typed Entities on Wikipedia

NARCIS (Netherlands)

Zaragoza, Hugo; Rode, H.; Mika, Peter; Atserias, Jordi; Ciaramita, Massimiliano; Attardi, Guiseppe

2007-01-01

We discuss the problem of ranking very many entities of different types. In particular we deal with a heterogeneous set of types, some being very generic and some very specific. We discuss two approaches for this problem: i) exploiting the entity containment graph and ii) using a Web search engine
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.
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)
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 ...
Concrete Security for Entity Recognition: The Jane Doe Protocol

DEFF Research Database (Denmark)

Lucks, Stefan; Zenner, Erik; Weimerskirch, Andre

2008-01-01

Entity recognition does not ask whether the message is from some entity X, just whether a message is from the same entity as a previous message. This turns turns out to be very useful for low-end devices. The current paper proposes a new protocol – the “Jane Doe Protocol” –, and provides a formal...
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.
Minimizing Co-location Potential of Moving Entities

NARCIS (Netherlands)

Evans, Will; Kirkpatrick, David; Löffler, Maarten; Staals, Frank

2016-01-01

We study the problem of maintaining knowledge of the locations of $n$ entities that are moving, each with some, possibly different, upper bound on their speed. We assume a setting where we can query the current location of any one entity, but this query takes a unit of time, during which we cannot
A waste of time: the problem of common morality in Principles of Biomedical Ethics.

Science.gov (United States)

Karlsen, Jan Reinert; Solbakk, Jan Helge

2011-10-01

From the 5th edition of Beauchamp and Childress' Principles of Biomedical Ethics, the problem of common morality has been given a more prominent role and emphasis. With the publication of the 6th and latest edition, the authors not only attempt to ground their theory in common morality, but there is also an increased tendency to identify the former with the latter. While this stratagem may give the impression of a more robust, and hence stable, foundation for their theoretical construct, we fear that it comes with a cost, namely the need to keep any theory in medical ethics open to, and thereby aware of, the challenges arising from biomedical research and clinical practice, as well as healthcare systems. By too readily identifying the moral life of common morality with rule-following behaviour, Beauchamp and Childress may even be wrong about the nature of common morality as such, thereby founding their, by now, classic theory on quicksand instead of solid rock.
Analysis of citations to biomedical articles affected by scientific misconduct.

Science.gov (United States)

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

2010-06-01

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

Directory of Open Access Journals (Sweden)

Csongor CSŐSZ

2014-06-01

Full Text Available At many entities the net asset value is influenced by the evaluation methods applied for tangible assets, because the value of intangible assets and financial assets is small in most cases. The objective of this paper is to analyze the differences between the procedures / methods of evaluation applied by micro and small entities and medium and large entities for tangible assets in Romania and Hungary. Furthermore, we analyze the differences between the procedures / methods of evaluation applied by micro and small entities in Romania and Hungary, respectively the differences between medium and large entities regarding de evaluation methods for tangible assets in Romania and Hungary. For this empirical study the questionnaire is used – as research technique, and to demonstrate the significant differences between the evaluation methods we used the Kolmogorov – Smirnov Z test.
Enhancement of chemical entity identification in text using semantic similarity validation.

Directory of Open Access Journals (Sweden)

Tiago Grego

Full Text Available With the amount of chemical data being produced and reported in the literature growing at a fast pace, it is increasingly important to efficiently retrieve this information. To tackle this issue text mining tools have been applied, but despite their good performance they still provide many errors that we believe can be filtered by using semantic similarity. Thus, this paper proposes a novel method that receives the results of chemical entity identification systems, such as Whatizit, and exploits the semantic relationships in ChEBI to measure the similarity between the entities found in the text. The method assigns a single validation score to each entity based on its similarities with the other entities also identified in the text. Then, by using a given threshold, the method selects a set of validated entities and a set of outlier entities. We evaluated our method using the results of two state-of-the-art chemical entity identification tools, three semantic similarity measures and two text window sizes. The method was able to increase precision without filtering a significant number of correctly identified entities. This means that the method can effectively discriminate the correctly identified chemical entities, while discarding a significant number of identification errors. For example, selecting a validation set with 75% of all identified entities, we were able to increase the precision by 28% for one of the chemical entity identification tools (Whatizit, maintaining in that subset 97% the correctly identified entities. Our method can be directly used as an add-on by any state-of-the-art entity identification tool that provides mappings to a database, in order to improve their results. The proposed method is included in a freely accessible web tool at www.lasige.di.fc.ul.pt/webtools/ice/.
[Biomedical engineering today : An overview from the viewpoint of the German Biomedical Engineering Society].

Science.gov (United States)

Schlötelburg, C; Becks, T; Stieglitz, T

2010-08-01

Biomedical engineering is characterized by the interdisciplinary co-operation of technology, science, and ways of thinking, probably more than any other technological area. The close interaction of engineering and information sciences with medicine and biology results in innovative products and methods, but also requires high standards for the interdisciplinary transfer of ideas into products for patients' benefits. This article describes the situation of biomedical engineering in Germany. It displays characteristics of the medical device industry and ranks it with respect to the international market. The research landscape is described as well as up-to-date research topics and trends. The national funding situation of research in biomedical engineering is reviewed and existing innovation barriers are discussed.
26 CFR 301.6233-1 - Extension to entities filing partnership returns.

Science.gov (United States)

2010-04-01

... all items of the entity that would be partnership items, as defined in section 6231(a)(3) and the... 26 Internal Revenue 18 2010-04-01 2010-04-01 false Extension to entities filing partnership....6233-1 Extension to entities filing partnership returns. (a) Entities filing a partnership return...
Liponeurocytoma Cerebellar. A new entity; first national case

International Nuclear Information System (INIS)

Cordoba, A.; Tomorrow, G.; Saralegui, P.; Hernandez, P.; Lezue, B.

2004-01-01

The first case of this new entity is presented and accepted within the new SNC (Central nervous system) classification of OMS in 2000. This is about a patient with 52 years old with 9 month of evolution history who presents signs of weight loss and is hospitalized with HEC progressive elements, hydrocephalusand installled coma. The Computerized Axial Tomography reveals expansive process in the posterior fossa hemispheric and cerebellopontine angle 4x5 cms inhomogeneous with bleeding elements and lipid content areas. Is arises the probability of Epidermoid cyst. The surgery is carried out with complete excision of the encapsulated aspiratable lesion. Good postoperative course without gaps. The histopathology revealed typical elements described in the literature: presence of adipose cells and neurocytic proliferation with small elements.This led that the tumor received among others the adult lipomeduloblastoma name but showing a good prognosis in contrast with the classic medulloblastoma. Currently cataloged such as grade II and there are not statistics in the literature because there are only published isolated cases
High-recall protein entity recognition using a dictionary

Science.gov (United States)

Kou, Zhenzhen; Cohen, William W.; Murphy, Robert F.

2010-01-01

Protein name extraction is an important step in mining biological literature. We describe two new methods for this task: semiCRFs and dictionary HMMs. SemiCRFs are a recently-proposed extension to conditional random fields that enables more effective use of dictionary information as features. Dictionary HMMs are a technique in which a dictionary is converted to a large HMM that recognizes phrases from the dictionary, as well as variations of these phrases. Standard training methods for HMMs can be used to learn which variants should be recognized. We compared the performance of our new approaches to that of Maximum Entropy (Max-Ent) and normal CRFs on three datasets, and improvement was obtained for all four methods over the best published results for two of the datasets. CRFs and semiCRFs achieved the highest overall performance according to the widely-used F-measure, while the dictionary HMMs performed the best at finding entities that actually appear in the dictionary—the measure of most interest in our intended application. PMID:15961466
A name is a name is a name: some thoughts and personal opinions about molluscan scientific names

NARCIS (Netherlands)

Dance, S.P.

2009-01-01

Since 1758, with the publication of Systema Naturae by Linnaeus, thousands of scientific names have been proposed for molluscs. The derivation and uses of many of them are here examined from various viewpoints, beginning with names based on appearance, size, vertical distribution, and location.
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 ...

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.
NCBI disease corpus: a resource for disease name recognition and concept normalization.

Science.gov (United States)

Doğan, Rezarta Islamaj; Leaman, Robert; Lu, Zhiyong

2014-02-01

Information encoded in natural language in biomedical literature publications is only useful if efficient and reliable ways of accessing and analyzing that information are available. Natural language processing and text mining tools are therefore essential for extracting valuable information, however, the development of powerful, highly effective tools to automatically detect central biomedical concepts such as diseases is conditional on the availability of annotated corpora. This paper presents the disease name and concept annotations of the NCBI disease corpus, a collection of 793 PubMed abstracts fully annotated at the mention and concept level to serve as a research resource for the biomedical natural language processing community. Each PubMed abstract was manually annotated by two annotators with disease mentions and their corresponding concepts in Medical Subject Headings (MeSH®) or Online Mendelian Inheritance in Man (OMIM®). Manual curation was performed using PubTator, which allowed the use of pre-annotations as a pre-step to manual annotations. Fourteen annotators were randomly paired and differing annotations were discussed for reaching a consensus in two annotation phases. In this setting, a high inter-annotator agreement was observed. Finally, all results were checked against annotations of the rest of the corpus to assure corpus-wide consistency. The public release of the NCBI disease corpus contains 6892 disease mentions, which are mapped to 790 unique disease concepts. Of these, 88% link to a MeSH identifier, while the rest contain an OMIM identifier. We were able to link 91% of the mentions to a single disease concept, while the rest are described as a combination of concepts. In order to help researchers use the corpus to design and test disease identification methods, we have prepared the corpus as training, testing and development sets. To demonstrate its utility, we conducted a benchmarking experiment where we compared three different
Programming Entity Framework Code First

CERN Document Server

Lerman, Julia

2011-01-01

Take advantage of the Code First data modeling approach in ADO.NET Entity Framework, and learn how to build and configure a model based on existing classes in your business domain. With this concise book, you'll work hands-on with examples to learn how Code First can create an in-memory model and database by default, and how you can exert more control over the model through further configuration. Code First provides an alternative to the database first and model first approaches to the Entity Data Model. Learn the benefits of defining your model with code, whether you're working with an exis
PubMed and beyond: a survey of web tools for searching biomedical literature

Science.gov (United States)

Lu, Zhiyong

2011-01-01

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search PMID:21245076
PubMed and beyond: a survey of web tools for searching biomedical literature.

Science.gov (United States)

Lu, Zhiyong

2011-01-01

The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature. This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters. However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth. In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement. Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications. These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed. In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development. Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search. Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field. Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search.
Controlled mutual quantum entity authentication using entanglement swapping

International Nuclear Information System (INIS)

Kang, Min-Sung; Hong, Chang-Ho; Heo, Jino; Lim, Jong-In; Yang, Hyung-Jin

2015-01-01

In this paper, we suggest a controlled mutual quantum entity authentication protocol by which two users mutually certify each other on a quantum network using a sequence of Greenberger–Horne–Zeilinger (GHZ)-like states. Unlike existing unidirectional quantum entity authentication, our protocol enables mutual quantum entity authentication utilizing entanglement swapping; moreover, it allows the managing trusted center (TC) or trusted third party (TTP) to effectively control the certification of two users using the nature of the GHZ-like state. We will also analyze the security of the protocol and quantum channel. (paper)
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. .
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.
Filled carbon nanotubes in biomedical imaging and drug delivery.

Science.gov (United States)

Martincic, Markus; Tobias, Gerard

2015-04-01

Carbon nanotubes have been advocated as promising candidates in the biomedical field in the areas of diagnosis and therapy. In terms of drug delivery, the use of carbon nanotubes can overcome some limitations of 'free' drugs by improving the formulation of poorly water-soluble drugs, allowing targeted delivery and even enabling the co-delivery of two or more drugs for combination therapy. Two different approaches are currently being explored for the delivery of diagnostic and therapeutic agents by carbon nanotubes, namely attachment of the payload to the external sidewalls or encapsulation into the inner cavities. Although less explored, the latter confers additional stability to the chosen diagnostic or therapeutic agents, and leaves the backbone structure of the nanotubes available for its functionalization with dispersing and targeting moieties. Several drug delivery systems and diagnostic agents have been developed in the last years employing the inner tubular cavities of carbon nanotubes. The research discussed in this review focuses on the use of carbon nanotubes that contain in their interior drug molecules and diagnosis-related compounds. The approaches employed for the development of such nanoscale vehicles along with targeting and releasing strategies are discussed. The encapsulation of both biomedical contrast agents and drugs inside carbon nanotubes is further expanding the possibilities to allow an early diagnosis and treatment of diseases.
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.
Biomedical nanomaterials from design to implementation

CERN Document Server

Webster, Thomas

2016-01-01

Biomedical Nanomaterials brings together the engineering applications and challenges of using nanostructured surfaces and nanomaterials in healthcare in a single source. Each chapter covers important and new information in the biomedical applications of nanomaterials.
7 CFR 652.23 - Certification process for private-sector entities.

Science.gov (United States)

2010-01-01

... 7 Agriculture 6 2010-01-01 2010-01-01 false Certification process for private-sector entities. 652... ASSISTANCE Certification § 652.23 Certification process for private-sector entities. (a) A private sector... individual basis as part of the private-sector entity's certification and ensures that the requirements set...
Event-Entity-Relationship Modeling in Data Warehouse Environments

DEFF Research Database (Denmark)

Bækgaard, Lars

We use the event-entity-relationship model (EVER) to illustrate the use of entity-based modeling languages for conceptual schema design in data warehouse environments. EVER is a general-purpose information modeling language that supports the specification of both general schema structures and multi...
For 481 biomedical open access journals, articles are not searchable in the Directory of Open Access Journals nor in conventional biomedical databases.

Science.gov (United States)

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

2015-01-01

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

Directory of Open Access Journals (Sweden)

Mary O'Sullivan

Full Text Available Pictorial stimuli are commonly used by scientists to explore central processes; including memory, attention, and language. Pictures that have been collected and put into sets for these purposes often contain visual ambiguities that lead to name disagreement amongst subjects. In the present work, we propose new norms which reflect these sources of name disagreement, and we apply this method to two sets of pictures: the Snodgrass and Vanderwart (S&V set and the Bank of Standardized Stimuli (BOSS. Naming responses of the presented pictures were classified within response categories based on whether they were correct, incorrect, or equivocal. To characterize the naming strategy where an alternative name was being used, responses were further divided into different sub-categories that reflected various sources of name disagreement. Naming strategies were also compared across the two sets of stimuli. Results showed that the pictures of the S&V set and the BOSS were more likely to elicit alternative specific and equivocal names, respectively. It was also found that the use of incorrect names was not significantly different across stimulus sets but that errors were more likely caused by visual ambiguity in the S&V set and by a misuse of names in the BOSS. Norms for name disagreement presented in this paper are useful for subsequent research for their categorization and elucidation of name disagreement that occurs when choosing visual stimuli from one or both stimulus sets. The sources of disagreement should be examined carefully as they help to provide an explanation of errors and inconsistencies of many concepts during picture naming tasks.
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
How Well can We Learn Interpretable Entity Types from Text?

DEFF Research Database (Denmark)

Hovy, Dirk

2014-01-01

We investigate a largely unsupervised approach to learning interpretable, domain-specific entity types from unlabeled text. It assumes that any common noun in a domain can function as potential entity type, and uses those nouns as hidden variables in a HMM. To constrain training, it extracts co......-occurrence dictionaries of entities and common nouns from the data. We evaluate the learned types by measuring their prediction accuracy for verb arguments in several domains. The results suggest that it is possible to learn domain-specific entity types from unlabeled data. We show significant improvements over...
Pengaruh Struktur Organisasi dan Ukuran Perusahaan Terhadap Penerapan Business Entity Concept

Directory of Open Access Journals (Sweden)

Widya Exsa Marita

2015-10-01

Full Text Available Masalah pengelolaan dana merupakan momok yang sering mengakibatkan kegagalan usaha pada suatu perusahaan terutama UMKM. Pengelolaan dana yang efektif dan efisien dapat tercapai jika suatu perusahaan mampu menerapkan akuntansi yang baik. Penerapan akuntansi yang baik haruslah diawali dengan penerapan konsep akuntansi, salah satunya yaitu business entity concept. Penelitian ini bertujuan untuk mengetahui adanya pengaruh struktur organisasi dan ukuran perusahaan terhadap penerapan business entity concept. Objek penelitian yang diambil adalah UD. Agung Mulia Jaya dengan sampel sebanyak 200 reponden yang diambil dengan menggunakan teknik simple random sampling. Variabel bebas dalam penelitian ini adalah struktur organisasi dan ukuran perusahaan, sedangkan variabel terikatnya adalah penerapan business entity concept. Untuk menguji adanya pengaruh struktur organisasi dan ukuran perusahaan terhadap penerapan business entity concept, maka dilakukan analisis regresi linier berganda. Hasil pengujian secara simultan menunjukkan bahwa kedua variabel bebas yaitu struktur organisasi dan ukuran perusahaan berpengaruh terhadap penerapan business entity concept. Secara parsial, struktur organisasi berpengaruh positif terhadap penerapan business entity concept, namun sebaliknya ukuran perusahaan berpengaruh negatif terhadap penerapan business entity concept. Koefisien determinasi menghasilkan nilai 67,4% yang berarti penerapan business entity concept dapat dijelaskan oleh variabel struktur organisasi dan ukuran perusahaan sebesar 67,4% atau bersifat kuat.
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.
78 FR 45051 - Unincorporated Business Entities; Effective Date

Science.gov (United States)

2013-07-26

... under State law for certain business activities. In accordance with the law, the effective date of the...) institutions' use of unincorporated business entities (UBEs) organized under State law for certain business... business entities, such as unincorporated business trusts, organized under State law. The final rule does...

15 CFR 744.10 - Restrictions on certain entities in Russia.

Science.gov (United States)

2010-01-01

... Russia. 744.10 Section 744.10 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign... REGULATIONS CONTROL POLICY: END-USER AND END-USE BASED § 744.10 Restrictions on certain entities in Russia. (a) General prohibition. Certain entities in Russia are included in Supplement No. 4 to this part 744 (Entity...
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 ...
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.
List of names of persons well informed on new energies; Shin energy yushikisha meibo

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

In order to establish an environment in which local public organizations and local business entities intending introduction of new energies can obtain easily the information about the technologies thereof and introduction examples, a 'list of names of persons well informed on new energies' was prepared. At the same time, a system was set up, with which these well-informed people can be introduced on NEDO home pages. The list of the names has collected data of the well-informed people granted with patents related to the fields defined in the new energy law as their specialty fields. The criterion for extracting the persons calls for persons who have experience of writing theses on new energies, and who have give lectures on the subject. Other new energy related experts acting in local areas, who were not able of having been extracted by using the above method, were extracted through hearings by key persons in each area. Questionnaire surveys were performed on the extracted specialists, whereas 495 effective answers permitting disclosure were obtained, and detailed items of information were collected on these specialists individually. The specialty fields include 23 new energy fields. The names of persons were arranged in the order of bureaus listed in the Ministry of International Trade and Industry. The names in the bureaus were arranged in the Japanese alphabetical order. (NEDO)
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.
The development of biomedical engineering as experienced by one biomedical engineer.

Science.gov (United States)

Newell, Jonathan C

2012-12-12

This personal essay described the development of the field of Biomedical Engineering from its early days, from the perspective of one who lived through that development. It describes the making of a major invention using data that had been rejected by other scientists, the re-discovery of an obscure fact of physiology and its use in developing a major medical instrument, the development of a new medical imaging modality, and the near-death rescue of a research project. The essay concludes with comments about the development and present status of impedance imaging, and recent changes in the evolution of biomedical engineering as a field.
Biomedical Research Institute, Biomedical Research Foundation of Northwest Louisiana, Shreveport, Louisiana

International Nuclear Information System (INIS)

1992-01-01

Department of Energy (DOE) has prepared an Environmental Assessment (EA), DOE/EA-0789, evaluating the environmental impacts of construction and operation of a Biomedical Research Institute (BRI) at the Louisiana State University (LSU) Medical Center, Shreveport, Louisiana. The purpose of the BRI is to accelerate the development of biomedical research in cardiovascular disease, molecular biology, and neurobiology. Based on the analyses in the EA, DOE has determined that the proposed action does not constitute a major Federal action significantly affecting the quality of the human environment within the meaning of the National Environmental Policy Act of 1969 (NEPA). Therefore, the preparation of an Environmental Impact Statement is not required
26 CFR 1.892-5 - Controlled commercial entity.

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 9 2010-04-01 2010-04-01 false Controlled commercial entity. 1.892-5 Section 1.892-5 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Miscellaneous Provisions § 1.892-5 Controlled commercial entity. (a)-(a)(2...
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, ...
Bayesian Modeling of Temporal Coherence in Videos for Entity Discovery and Summarization.

Science.gov (United States)

Mitra, Adway; Biswas, Soma; Bhattacharyya, Chiranjib

2017-03-01

A video is understood by users in terms of entities present in it. Entity Discovery is the task of building appearance model for each entity (e.g., a person), and finding all its occurrences in the video. We represent a video as a sequence of tracklets, each spanning 10-20 frames, and associated with one entity. We pose Entity Discovery as tracklet clustering, and approach it by leveraging Temporal Coherence (TC): the property that temporally neighboring tracklets are likely to be associated with the same entity. Our major contributions are the first Bayesian nonparametric models for TC at tracklet-level. We extend Chinese Restaurant Process (CRP) to TC-CRP, and further to Temporally Coherent Chinese Restaurant Franchise (TC-CRF) to jointly model entities and temporal segments using mixture components and sparse distributions. For discovering persons in TV serial videos without meta-data like scripts, these methods show considerable improvement over state-of-the-art approaches to tracklet clustering in terms of clustering accuracy, cluster purity and entity coverage. The proposed methods can perform online tracklet clustering on streaming videos unlike existing approaches, and can automatically reject false tracklets. Finally we discuss entity-driven video summarization- where temporal segments of the video are selected based on the discovered entities, to create a semantically meaningful summary.
The Compilation of the Shona–English Biomedical Dictionary: Problems and Challenges

Directory of Open Access Journals (Sweden)

Nomalanga Mpofu

2011-10-01

Full Text Available
ABSTRACT: The bilingual Shona–English dictionary of biomedical terms, Duramazwi reUrapi neUtano, was compiled with the aim of improving the efficiency of communication between doctor and patient. The dictionary is composed of terms from both modern and traditional medicinal practices. The article seeks to look at the methods of production of the dictionary, the presentation of entries in the dictionary and the problems and challenges encountered in the compilation proc-ess, namely, developing Shona medical terminology in the cultural context and especially the as-pect of equivalence between English and Shona biomedical terms.
Keywords: BIOMEDICAL, ADOPTIVES, ENTRIES, SYNONYMS, CROSS-REFERENCES, IDIOMS, CIRCUMLOCUTION, STANDARDISATION, HEADWORD, EQUIVALENCE, VARI-ANTS, DEFINITION, CULTURE, EUPHEMISMS, MODERN, TRADITIONAL, MONOLINGUAL, BILINGUAL, CORPUS, BORROWING, SHONA, COMMUNICATION
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OPSOMMING: Die samestelling van die Sjona–Engelse biomediese woorde-boek: Probleme en uitdagings. Die tweetalige Sjona–Engelse woordeboek van biomediese terme, Duramazwi reUrapi neUtano, is saamgestel met die doel om die effektiwiteit van kommunika-sie tussen dokter en pasiënt te verbeter. Die woordeboek bestaan uit terme van sowel moderne as tradisionele geneeskundige praktyke. Die artikel wil die metodes van die totstandkoming van die woordeboek beskou, die aanbieding van die inskrywings in die woordeboek en die probleme en uitdagings wat in die samestellingsproses teëgekom is, naamlik, die ontwikkeling van Sjona- mediese terminolgie binne die kulturele konteks en veral die aspek van ekwivalensie tussen Engel-se en Sjona- biomediese terme.

Sleutelwoorde: BIOMEDIES, LEENWOORDE, INSKRYWINGS, SINONIEME, KRUISVER-WYSINGS, IDIOME, OMSKRYWING, STANDAARDISASIE, TREFWOORD, EKWIVALENSIE, WISSELVORME, DEFINISIE, KULTUUR, EUFEMISMES, MODERN, TRADISIONEEL, EEN-TALIG, TWEETALIG, KORPUS, ONTLENING, KOMMUNIKASIE, SJONA
CONSIDERATION REGARDING CURRENT ASSETS IN THE CONSTRUCTION ENTITIES

Directory of Open Access Journals (Sweden)

Laura Adriana COJOCARU (ALIONESCU

2014-06-01

Full Text Available Accounting for current assets mainly aims to obtain useful information on the management of their best in order to make management decisions. Counting efficiency of these assets, their importance, provides improved performance of the entity. In this paper we want to study the degree of implementation of policies and accounting treatments on the current assets in the specific construction economic entities, the problems of implementation and thus better addressing their theoretical and procedural to improve the information provided by financial statements. Due to the importance of proper conduct of business owned entities, accounting current assets should result in optimal and efficient control of current assets.
Entity-Linking via Graph-Distance Minimization

Directory of Open Access Journals (Sweden)

Roi Blanco

2014-07-01

Full Text Available Entity-linking is a natural-language–processing task that consists in identifying the entities mentioned in a piece of text, linking each to an appropriate item in some knowledge base; when the knowledge base is Wikipedia, the problem comes to be known as wikification (in this case, items are wikipedia articles. One instance of entity-linking can be formalized as an optimization problem on the underlying concept graph, where the quantity to be optimized is the average distance between chosen items. Inspired by this application, we define a new graph problem which is a natural variant of the Maximum Capacity Representative Set. We prove that our problem is NP-hard for general graphs; nonetheless, under some restrictive assumptions, it turns out to be solvable in linear time. For the general case, we propose two heuristics: one tries to enforce the above assumptions and another one is based on the notion of hitting distance; we show experimentally how these approaches perform with respect to some baselines on a real-world dataset.
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
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.
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.
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.
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.
Myalgic Encephalomyelitis, Chronic Fatigue Syndrome, and Systemic Exertion Intolerance Disease: Three Distinct Clinical Entities

Directory of Open Access Journals (Sweden)

Frank N.M. Twisk

2018-04-01

Full Text Available Many researchers consider chronic fatigue syndrome (CFS to be a synonym of Myalgic Encephalomyelitis (ME. However, the case criteria of ME and CFS define two distinct clinical entities. Although some patients will meet both case criteria, other patients can meet the diagnosis of ME and not fulfil the case criteria for CFS, while the diagnosis of CFS is largely insufficient to be qualified as a ME patient. ME is a neuromuscular disease with distinctive muscular symptoms, including prolonged muscle weakness after exertion, and neurological signs implicating cerebral dysfunction, including cognitive impairment and sensory symptoms. The only mandatory symptom of CFS is chronic fatigue. Chronic fatigue must be accompanied by at least four out of eight nonspecific symptoms: substantial impairment in short-term memory or concentration, a sore throat, tender lymph nodes, muscle pain, multijoint pain, a new type of headaches, unrefreshing sleep, and postexertional “malaise” lasting more than 24 h. So, regardless whether the name ME is appropriate or not, ME is not synonymous to CFS. That is not a matter of opinion, but a matter of definition. Due to the definitions of ME and CFS, “ME/CFS” does not exist and cannot be replaced by a new clinical entity (SEID: Systemic Exertion Intolerance Disease, as recently suggested.
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.

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.
Xanthogranulomatous Prostatitis, a Rare Prostatic Entity

Directory of Open Access Journals (Sweden)

Alejandro Noyola

2017-01-01

Full Text Available There are several benign prostatic pathologies that can clinically mimic a prostate adenocarcinoma. Xanthogranulomatous prostatitis is a benign inflammatory condition of the prostate and a rare entity. A 47-year old male, with 3 years of lower urinary tract symptoms, with a palpable hypogastric tumor, digital rectal examination: solid prostate, of approximately 60 g. Initial PSA was 0.90 ng/mL. He underwent surgical excision of the lower abdominal nodule and prostatectomy. Histopathology showed xanthogranulomatous prostatitis, without malignancy. Xanthogranulomatous prostatitis is an extremely rare entity that can simulate prostate adenocarcinoma, therefore having a correct histopathological diagnosis is essential.
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
DOORS to the semantic web and grid with a PORTAL for biomedical computing.

Science.gov (United States)

Taswell, Carl

2008-03-01

The semantic web remains in the early stages of development. It has not yet achieved the goals envisioned by its founders as a pervasive web of distributed knowledge and intelligence. Success will be attained when a dynamic synergism can be created between people and a sufficient number of infrastructure systems and tools for the semantic web in analogy with those for the original web. The domain name system (DNS), web browsers, and the benefits of publishing web pages motivated many people to register domain names and publish web sites on the original web. An analogous resource label system, semantic search applications, and the benefits of collaborative semantic networks will motivate people to register resource labels and publish resource descriptions on the semantic web. The Domain Ontology Oriented Resource System (DOORS) and Problem Oriented Registry of Tags and Labels (PORTAL) are proposed as infrastructure systems for resource metadata within a paradigm that can serve as a bridge between the original web and the semantic web. The Internet Registry Information Service (IRIS) registers [corrected] domain names while DNS publishes domain addresses with mapping of names to addresses for the original web. Analogously, PORTAL registers resource labels and tags while DOORS publishes resource locations and descriptions with mapping of labels to locations for the semantic web. BioPORT is proposed as a prototype PORTAL registry specific for the problem domain of biomedical computing.
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 ...
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
The three names

NARCIS (Netherlands)

Bas Jongenelen

2011-01-01

Two spectators are each asked to think of a girl's name (because your sister in law is pregnant and names are a big issue at the moment in your family.) You explain that you have a boy's name in your head, and you ask the spectators to think what this boy's name might be. You write three names on a
Diabetes Mellitus: Indigenous naming, indigenous diagnosis and self-management in an African setting: the example from Cameroon

Directory of Open Access Journals (Sweden)

Awah Paschal K

2009-02-01

Full Text Available Abstract Background The objective was to examine how the indigenous naming, indigenous self-diagnosis and management of diabetes evolved with awareness in order to develop a socially oriented theoretical model for its care. Methods The data was collected through a one-year extended participant observation in Bafut, a rural health district of Cameroon. The sample consisted of 72 participants in a rural health district of Cameroon (men and women with type 2 diabetes. We used participant observation to collect data through focus group discussions, in depth interviews and fieldwork conversations. The method of analysis entailed a thick description, thematic analysis entailing constant comparison within and across FGD and across individual participants and content analysis. Results The core concepts identified were the evolution of names for diabetes and the indigenous diagnostic and self-management procedures. Participants fell into one of two naming typologies: (a Naming excluding any signs and symptoms of diabetes; (b naming including signs and symptoms of diabetes. Participants fell into two typologies of diagnostic procedures: (a those that use indigenous diagnostic procedures for monitoring and controlling diabetes outcomes and b those that had initially used it only for diagnosis and continued to use them for self management. These typologies varied according to how participants' awareness evolved and the impact on self-diagnosis and management. Conclusion The evolution of names for diabetes was an important factor that influenced the subsequent self-diagnosis and management of diabetes in both traditional and modern biomedical settings.
Balancing exploration and exploitation in transferring research into practice: a comparison of five knowledge translation entity archetypes.

Science.gov (United States)

Oborn, Eivor; Barrett, Michael; Prince, Karl; Racko, Girts

2013-09-05

Translating knowledge from research into clinical practice has emerged as a practice of increasing importance. This has led to the creation of new organizational entities designed to bridge knowledge between research and practice. Within the UK, the Collaborations for Leadership in Applied Health Research and Care (CLAHRC) have been introduced to ensure that emphasis is placed in ensuring research is more effectively translated and implemented in clinical practice. Knowledge translation (KT) can be accomplished in various ways and is affected by the structures, activities, and coordination practices of organizations. We draw on concepts in the innovation literature--namely exploration, exploitation, and ambidexterity--to examine these structures and activities as well as the ensuing tensions between research and implementation. Using a qualitative research approach, the study was based on 106 semi-structured, in-depth interviews with the directors, theme leads and managers, key professionals involved in research and implementation in nine CLAHRCs. Data was also collected from intensive focus group workshops. In this article we develop five archetypes for organizing KT. The results show how the various CLAHRC entities work through partnerships to create explorative research and deliver exploitative implementation. The different archetypes highlight a range of structures that can achieve ambidextrous balance as they organize activity and coordinate practice on a continuum of exploration and exploitation. This work suggests that KT entities aim to reach their goals through a balance between exploration and exploitation in the support of generating new research and ensuring knowledge implementation. We highlight different organizational archetypes that support various ways to maintain ambidexterity, where both exploration and exploitation are supported in an attempt to narrow the knowledge gaps. The KT entity archetypes offer insights on strategies in structuring
Differences in financial statements of business entities in the Czech Republic

Directory of Open Access Journals (Sweden)

Jana Gláserová

2013-01-01

Full Text Available Ministry of Finance in the Czech Republic identifies and defines four types of accounting entities that are engaged in business activities. These are the “normal” business entities, business entities as banks, commercial insurance companies and health insurance companies. For each of these types of entities the Ministry of Finance issued relevant regulations that contain specific accounting policies arising mainly from the specifics of the scope of business activities of these entities. The effects of these specifics are ultimately shown also in the individual parts of the financial statement closing. In contrast the International Financial Reporting Standards (IFRS and also generally accepted accounting principles of the United States (U.S. GAAP are valid for all listed entities regardless of their size and scope of activities. The ongoing globalization of the world, transnational mergers and acquisitions of various companies brings the requirements for unification of accounting policies in order to achieve comparability of financial statements closing of companies from different countries, their transparency and completeness of published information in the individual countries. This paper deals with the definition of significant differences in the items of financial statement closing of different types of business entities in the Czech Republic and with the formulation of proposals for individual types of entities, which would contribute to easier orientation and grater comparability for the needs of different users of accounting information.
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
Intelligent Entity Behavior Within Synthetic Environments. Chapter 3

Science.gov (United States)

Kruk, R. V.; Howells, P. B.; Siksik, D. N.

2007-01-01

This paper describes some elements in the development of realistic performance and behavior in the synthetic entities (players) which support Modeling and Simulation (M&S) applications, particularly military training. Modern human-in-the-loop (virtual) training systems incorporate sophisticated synthetic environments, which provide: 1. The operational environment, including, for example, terrain databases; 2. Physical entity parameters which define performance in engineered systems, such as aircraft aerodynamics; 3. Platform/system characteristics such as acoustic, IR and radar signatures; 4. Behavioral entity parameters which define interactive performance, including knowledge/reasoning about terrain, tactics; and, 5. Doctrine, which combines knowledge and tactics into behavior rule sets. The resolution and fidelity of these model/database elements can vary substantially, but as synthetic environments are designed to be compose able, attributes may easily be added (e.g., adding a new radar to an aircraft) or enhanced (e.g. Amending or replacing missile seeker head/ Electronic Counter Measures (ECM) models to improve the realism of their interaction). To a human in the loop with synthetic entities, their observed veridicality is assessed via engagement responses (e.g. effect of countermeasures upon a closing missile), as seen on systems displays, and visual (image) behavior. The realism of visual models in a simulation (level of detail as well as motion fidelity) remains a challenge in realistic articulation of elements such as vehicle antennae and turrets, or, with human figures; posture, joint articulation, response to uneven ground. Currently the adequacy of visual representation is more dependant upon the quality and resolution of the physical models driving those entities than graphics processing power per Se. Synthetic entities in M&S applications traditionally have represented engineered systems (e.g. aircraft) with human-in-the-loop performance
Towards a Theory of Learning for Naming Rehabilitation: Retrieval Practice, Retrieval Effort, and Spacing Effects

Directory of Open Access Journals (Sweden)

Erica Middleton

2015-04-01

Methods. Four PWA with naming impairment named and gave familiarity ratings to a corpus of 700 pictures of proper noun entities twice over two weeks. For each participant, we selected items the participant knew recognized but could not consistently name for assignment into the conditions, with a minimum of 36 (max=72 items per condition across participants. The design involved a 2-level factor of type of training (retrieval practice versus errorless learning, i.e., repetition and a factor of spacing, which included a massed condition (lag 1 and three spaced conditions (lags 5, 15, and 30. Lag corresponded to the number of training trials for other items that intervened between three presentations of an item for retrieval practice or repetition training. On a repetition trial, the name was presented (seen/heard and the participant repeated the name at picture onset. On a naming trial, only the picture was presented. All trials ended in feedback (i.e., the name was presented. Primary outcome was naming performance on a retention test administered 1-day following training, with a 1-week follow-up test administered to measure persistence of the effects. Results & Conclusions. Mixed regression analyses revealed that the naming condition was associated with superior performance over repetition, observed both at the retention test (p=.001 and follow-up (p=.01; Figure 1, left panel. Also, spaced training conferred superior benefits compared to massed, both at retention test (p<.001 and follow-up (p=.006; Figure 1, right panel. An analysis of the spaced lags in the naming condition revealed that though increasing lag made retrieval practice more effortful (i.e., error-prone during training, increasing lag conferred more powerful learning at retention test. The present study provides definitive evidence of the relevance of retrieval practice, retrieval effort, and spacing for optimizing existing treatments, their explanatory power, and their importance in driving future
Web 2.0-based crowdsourcing for high-quality gold standard development in clinical natural language processing.

Science.gov (United States)

Zhai, Haijun; Lingren, Todd; Deleger, Louise; Li, Qi; Kaiser, Megan; Stoutenborough, Laura; Solti, Imre

2013-04-02

A high-quality gold standard is vital for supervised, machine learning-based, clinical natural language processing (NLP) systems. In clinical NLP projects, expert annotators traditionally create the gold standard. However, traditional annotation is expensive and time-consuming. To reduce the cost of annotation, general NLP projects have turned to crowdsourcing based on Web 2.0 technology, which involves submitting smaller subtasks to a coordinated marketplace of workers on the Internet. Many studies have been conducted in the area of crowdsourcing, but only a few have focused on tasks in the general NLP field and only a handful in the biomedical domain, usually based upon very small pilot sample sizes. In addition, the quality of the crowdsourced biomedical NLP corpora were never exceptional when compared to traditionally-developed gold standards. The previously reported results on medical named entity annotation task showed a 0.68 F-measure based agreement between crowdsourced and traditionally-developed corpora. Building upon previous work from the general crowdsourcing research, this study investigated the usability of crowdsourcing in the clinical NLP domain with special emphasis on achieving high agreement between crowdsourced and traditionally-developed corpora. To build the gold standard for evaluating the crowdsourcing workers' performance, 1042 clinical trial announcements (CTAs) from the ClinicalTrials.gov website were randomly selected and double annotated for medication names, medication types, and linked attributes. For the experiments, we used CrowdFlower, an Amazon Mechanical Turk-based crowdsourcing platform. We calculated sensitivity, precision, and F-measure to evaluate the quality of the crowd's work and tested the statistical significance (Pcrowdsourced and traditionally-developed annotations. The agreement between the crowd's annotations and the traditionally-generated corpora was high for: (1) annotations (0.87, F-measure for medication names
3rd International Conference on Nanotechnologies and Biomedical Engineering

CERN Document Server

Tiginyanu, Ion

2016-01-01

This volume presents the proceedings of the 3rd International Conference on Nanotechnologies and Biomedical Engineering which was held on September 23-26, 2015 in Chisinau, Republic of Moldova. ICNBME-2015 continues the series of International Conferences in the field of nanotechnologies and biomedical engineering. It aims at bringing together scientists and engineers dealing with fundamental and applied research for reporting on the latest theoretical developments and applications involved in the fields. Topics include Nanotechnologies and nanomaterials Plasmonics and metamaterials Bio-micro/nano technologies Biomaterials Biosensors and sensors systems Biomedical instrumentation Biomedical signal processing Biomedical imaging and image processing Molecular, cellular and tissue engineering Clinical engineering, health technology management and assessment; Health informatics, e-health and telemedicine Biomedical engineering education Nuclear and radiation safety and security Innovations and technology transfer...
49 CFR 37.41 - Construction of transportation facilities by public entities.

Science.gov (United States)

2010-10-01

... public entities. 37.41 Section 37.41 Transportation Office of the Secretary of Transportation... transportation facilities by public entities. (a) A public entity shall construct any new facility to be used in providing designated public transportation services so that the facility is readily accessible to and usable...
Compulsive buying: an overlooked entity.

Science.gov (United States)

Basu, Bishnupriya; Basu, Saikat; Basu, Jharna

2011-08-01

Compulsive buying is an under-recognised entity among Indian psychiatrists. A Medline search, hand searching of journals and direct communications with lead investigators in compulsive buying have generated numerous studies. Overseas data indicate a community prevalence between 1% and 8% . The phenomenon can be an independent entity or appears as a comorbidity with another axis I or axis II disorder. A degree of suspicion on part of clinician regarding its possible presence is the key to its detection. A few rating instruments are available to quantify the morbidity and screening for compulsive buying. Management involves pharmacotherapy with SSRIs, psychotherapy, self-help groups and self-help books. Epidemiological and clinical studies on compulsive buying should be undertaken by Indian psychiatrists to provide better services for people suffering from compulsive buying.
Inaccurate Citations in Biomedical Journalism: Effect on the Impact Factor of the American Journal of Roentgenology.

Science.gov (United States)

Karabulut, Nevzat

2017-03-01

The aim of this study is to investigate the frequency of incorrect citations and its effects on the impact factor of a specific biomedical journal: the American Journal of Roentgenology. The Cited Reference Search function of Thomson Reuters' Web of Science database (formerly the Institute for Scientific Information's Web of Knowledge database) was used to identify erroneous citations. This was done by entering the journal name into the Cited Work field and entering "2011-2012" into the Cited Year(s) field. The errors in any part of the inaccurately cited references (e.g., author names, title, year, volume, issue, and page numbers) were recorded, and the types of errors (i.e., absent, deficient, or mistyped) were analyzed. Erroneous citations were corrected using the Suggest a Correction function of the Web of Science database. The effect of inaccurate citations on the impact factor of the AJR was calculated. Overall, 183 of 1055 citable articles published in 2011-2012 were inaccurately cited 423 times (mean [± SD], 2.31 ± 4.67 times; range, 1-44 times). Of these 183 articles, 110 (60.1%) were web-only articles and 44 (24.0%) were print articles. The most commonly identified errors were page number errors (44.8%) and misspelling of an author's name (20.2%). Incorrect citations adversely affected the impact factor of the AJR by 0.065 in 2012 and by 0.123 in 2013. Inaccurate citations are not infrequent in biomedical journals, yet they can be detected and corrected using the Web of Science database. Although the accuracy of references is primarily the responsibility of authors, the journal editorial office should also define a periodic inaccurate citation check task and correct erroneous citations to reclaim unnecessarily lost credit.
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.
Digital fabrication of multi-material biomedical objects

Energy Technology Data Exchange (ETDEWEB)

Cheung, H H; Choi, S H, E-mail: shchoi@hku.h [Department of Industrial and Manufacturing Systems Engineering, University of Hong Kong, Pokfulam Road (Hong Kong)

2009-12-15

This paper describes a multi-material virtual prototyping (MMVP) system for modelling and digital fabrication of discrete and functionally graded multi-material objects for biomedical applications. The MMVP system consists of a DMMVP module, an FGMVP module and a virtual reality (VR) simulation module. The DMMVP module is used to model discrete multi-material (DMM) objects, while the FGMVP module is for functionally graded multi-material (FGM) objects. The VR simulation module integrates these two modules to perform digital fabrication of multi-material objects, which can be subsequently visualized and analysed in a virtual environment to optimize MMLM processes for fabrication of product prototypes. Using the MMVP system, two biomedical objects, including a DMM human spine and an FGM intervertebral disc spacer are modelled and digitally fabricated for visualization and analysis in a VR environment. These studies show that the MMVP system is a practical tool for modelling, visualization, and subsequent fabrication of biomedical objects of discrete and functionally graded multi-materials for biomedical applications. The system may be adapted to control MMLM machines with appropriate hardware for physical fabrication of biomedical objects.

Digital fabrication of multi-material biomedical objects

International Nuclear Information System (INIS)

Cheung, H H; Choi, S H

2009-01-01

This paper describes a multi-material virtual prototyping (MMVP) system for modelling and digital fabrication of discrete and functionally graded multi-material objects for biomedical applications. The MMVP system consists of a DMMVP module, an FGMVP module and a virtual reality (VR) simulation module. The DMMVP module is used to model discrete multi-material (DMM) objects, while the FGMVP module is for functionally graded multi-material (FGM) objects. The VR simulation module integrates these two modules to perform digital fabrication of multi-material objects, which can be subsequently visualized and analysed in a virtual environment to optimize MMLM processes for fabrication of product prototypes. Using the MMVP system, two biomedical objects, including a DMM human spine and an FGM intervertebral disc spacer are modelled and digitally fabricated for visualization and analysis in a VR environment. These studies show that the MMVP system is a practical tool for modelling, visualization, and subsequent fabrication of biomedical objects of discrete and functionally graded multi-materials for biomedical applications. The system may be adapted to control MMLM machines with appropriate hardware for physical fabrication of biomedical objects.
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.
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.
FINANCIAL REPORTING IN PUBLIC INSTITUTIONS AND NON-FINANCIAL ENTITIES. SIMILARITIES AND DIFFERENCES

OpenAIRE

Daniela Vitan

2011-01-01

The present paperwork contains issues regarding financial reporting at the public institutions and non – financial entities. The main aspects are regarding the obligation of all entities to present the financial statements, the content of financial statements in public institutions and non-financial entities. Also, is presented the similarities and the differences aspects between financial reporting of these two patrimonial entities.
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.
Special aspects of the reporting of capital in the budgetary entities

Directory of Open Access Journals (Sweden)

Nadezhda Popova-Yosifova

2018-05-01

Full Text Available The national and international accounting standards state that the equity of an entity is the residual interest in the assets of the entity that remains after deducting all of its liabilities. For that reason in the accounting theory could also be found the terms “net worth” and “net assets” which are used as synonyms. The term “equity” is not used adequately in this wording in respect of the budgetary entities because of some specific characteristics these entities possess. The purpose of this paper is, based on the legislative framework now in force in Bulgaria and the characteristic features of the public sector entities, to present the specific features of the capital reporting in these organizations.
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.
Engineering β-sheet peptide assemblies for biomedical applications.

Science.gov (United States)

Yu, Zhiqiang; Cai, Zheng; Chen, Qiling; Liu, Menghua; Ye, Ling; Ren, Jiaoyan; Liao, Wenzhen; Liu, Shuwen

2016-03-01

Hydrogels have been widely studied in various biomedical applications, such as tissue engineering, cell culture, immunotherapy and vaccines, and drug delivery. Peptide-based nanofibers represent a promising new strategy for current drug delivery approaches and cell carriers for tissue engineering. This review focuses on the recent advances in the use of self-assembling engineered β-sheet peptide assemblies for biomedical applications. The applications of peptide nanofibers in biomedical fields, such as drug delivery, tissue engineering, immunotherapy, and vaccines, are highlighted. The current challenges and future perspectives for self-assembling peptide nanofibers in biomedical applications are discussed.
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.
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.
78 FR 21603 - Proposed Reporting Entity; Request for Comments

Science.gov (United States)

2013-04-11

... FEDERAL ACCOUNTING STANDARDS ADVISORY BOARD Proposed Reporting Entity; Request for Comments AGENCY... seeking input on a proposed Statement of Federal Financial Accounting Standards addressing the Reporting Entity. The Standard is available at http://www.fasab.gov/board-activities/documents-for-comment/exposure...
Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion

Science.gov (United States)

Jonnagaddala, Jitendra; Jue, Toni Rose; Chang, Nai-Wen; Dai, Hong-Jie

2016-01-01

The rapidly increasing biomedical literature calls for the need of an automatic approach in the recognition and normalization of disease mentions in order to increase the precision and effectivity of disease based information retrieval. A variety of methods have been proposed to deal with the problem of disease named entity recognition and normalization. Among all the proposed methods, conditional random fields (CRFs) and dictionary lookup method are widely used for named entity recognition and normalization respectively. We herein developed a CRF-based model to allow automated recognition of disease mentions, and studied the effect of various techniques in improving the normalization results based on the dictionary lookup approach. The dataset from the BioCreative V CDR track was used to report the performance of the developed normalization methods and compare with other existing dictionary lookup based normalization methods. The best configuration achieved an F-measure of 0.77 for the disease normalization, which outperformed the best dictionary lookup based baseline method studied in this work by an F-measure of 0.13. Database URL: https://github.com/TCRNBioinformatics/DiseaseExtract PMID:27504009
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 &
Cuban entities management. Cedrux just around the corner.

Directory of Open Access Journals (Sweden)

Tamara Rodríguez Sánchez

2011-12-01

Full Text Available The direction of the country as part of strengthening entities management and the informatization of Cuban society, presented the need to create a System of Enterprise Resource Planning (ERP, which would be able to computerize management processes of business and budgeted entities on national scale. It is in this way that since July 2008 CEDRUX product was developed composed by 15 subsystems. It will constitute the core on which new solutions will be developed that will extend its functionalities in a constantly way, including new entities management processes and allowing constant updating. In its first operational phase that will be in this very year 2011, Cedrux will only integrate 9 subsystems that will answer the economic needs of any organization.
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...
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.
THE EFFICIENCY OF FOREIGN INVESTMENTS IN THE FINANCING OF AUDITED ENTITIES

Directory of Open Access Journals (Sweden)

Berinde Sorin

2013-07-01

Full Text Available The auditing of the financial statements is a certification service intended to offer the users more credibility regarding the quality of accounting information. This is the reason why the present study selected all the Cluj county entities that, according to the public information, between 2005-2012 were subject to financial audit in order to estimate, at this level, the influence of foreign investments in the financing structure. The information provided by the financial statements of these audited entities (with or without foreign participation in share capital was analyzed for the calculation of the relevant indicators to determine the evolution of the equity financing, the recourse to external financing funds, the ratio of external funds and equity funds used for financing and the assessment of the efficiency of foreign capital invested at the level of these entities. In order to meet this objective, we considered the information from the financial statements of the concerned entities, published between 2008-2011. For the relevance of the study, we eliminated the audited entities that did not have financial statements published in all of the four financial years for various reasons (dissolution, liquidation, merger, or temporary suspension of activity or had negative working capital. The financial statement information was analyzed in view of the calculation for each audited entity of the rate of financial autonomy, the debt ratio, the debt to equity ratio and of the rotation speed of equity. The audited entities were classified into 2 major categories: audited entities with a foreign participation in share capital and audited entities with the whole share capital financed by equity funds. We applied the simple average method at the level of the both audited entities categories for each of the four analyzed indicators. Furthermore, we performed an analysis from the static and dynamic point of view of the results. The conclusions that we
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.
Bridging the gap between clinicians and systems biologists: from network biology to translational biomedical research.

Science.gov (United States)

Jinawath, Natini; Bunbanjerdsuk, Sacarin; Chayanupatkul, Maneerat; Ngamphaiboon, Nuttapong; Asavapanumas, Nithi; Svasti, Jisnuson; Charoensawan, Varodom

2016-11-22

With the wealth of data accumulated from completely sequenced genomes and other high-throughput experiments, global studies of biological systems, by simultaneously investigating multiple biological entities (e.g. genes, transcripts, proteins), has become a routine. Network representation is frequently used to capture the presence of these molecules as well as their relationship. Network biology has been widely used in molecular biology and genetics, where several network properties have been shown to be functionally important. Here, we discuss how such methodology can be useful to translational biomedical research, where scientists traditionally focus on one or a small set of genes, diseases, and drug candidates at any one time. We first give an overview of network representation frequently used in biology: what nodes and edges represent, and review its application in preclinical research to date. Using cancer as an example, we review how network biology can facilitate system-wide approaches to identify targeted small molecule inhibitors. These types of inhibitors have the potential to be more specific, resulting in high efficacy treatments with less side effects, compared to the conventional treatments such as chemotherapy. Global analysis may provide better insight into the overall picture of human diseases, as well as identify previously overlooked problems, leading to rapid advances in medicine. From the clinicians' point of view, it is necessary to bridge the gap between theoretical network biology and practical biomedical research, in order to improve the diagnosis, prevention, and treatment of the world's major diseases.
Public administration social responsibility of business entities

Directory of Open Access Journals (Sweden)

N. H. Shpankovskaya

2016-03-01

Full Text Available Social responsibility of a business entity is seen as an effective tool of public administration. The current stage of development of social responsibility in Ukraine requires state involvement, as its vision by business entities are different, and there is also a need to develop a national model of social responsibility on the basis of international standards, because Ukraine, on the one hand, has the national characteristics of implementation of social initiatives and, on the other, the conditions and resources for their implementation is different from developed market economies. The visions of on social responsibility in the scientific literature are also different. This was the basis for the determination of her essence. We analyzed the interpretations of social responsibility and identified their advantages and disadvantages. Formulation of social responsibility, which is submitted in article, actualizes ecological orientation of the business entity taking into account the need for responsible behavior, and responsibility for actions, which violate the norms of society.

Learning Expressive Linkage Rules for Entity Matching using Genetic Programming

OpenAIRE

Isele, Robert

2013-01-01

A central problem in data integration and data cleansing is to identify pairs of entities in data sets that describe the same real-world object. Many existing methods for matching entities rely on explicit linkage rules, which specify how two entities are compared for equivalence. Unfortunately, writing accurate linkage rules by hand is a non-trivial problem that requires detailed knowledge of the involved data sets. Another important issue is the efficient execution of link...
Parents accidentally substitute similar sounding sibling names more often than dissimilar names.

Directory of Open Access Journals (Sweden)

Zenzi M Griffin

Full Text Available When parents select similar sounding names for their children, do they set themselves up for more speech errors in the future? Questionnaire data from 334 respondents suggest that they do. Respondents whose names shared initial or final sounds with a sibling's reported that their parents accidentally called them by the sibling's name more often than those without such name overlap. Having a sibling of the same gender, similar appearance, or similar age was also associated with more frequent name substitutions. Almost all other name substitutions by parents involved other family members and over 5% of respondents reported a parent substituting the name of a pet, which suggests a strong role for social and situational cues in retrieving personal names for direct address. To the extent that retrieval cues are shared with other people or animals, other names become available and may substitute for the intended name, particularly when names sound similar.
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
49 CFR Appendix C to Part 209 - FRA's Policy Statement Concerning Small Entities

Science.gov (United States)

2010-10-01

... agency personnel respond in a timely and comprehensive fashion to the inquiries of small entities... history of compliance, FRA inspectors consider “such other factors as the immediate circumstances make... eliminating the safety hazard; the entity's culpability; the entity's compliance history; the entity's ability...
Search optimization of named entities from twitter streams

Science.gov (United States)

Fazeel, K. Mohammed; Hassan Mottur, Simama; Norman, Jasmine; Mangayarkarasi, R.

2017-11-01

With Enormous number of tweets, People often face difficulty to get exact information about those tweets. One of the approach followed for getting information about those tweets via Google. There is not any accuracy tool developed for search optimization and as well as getting information about those tweets. So, this system contains the search optimization and functionalities for getting information about those tweets. Another problem faced here are the tweets that contains grammatical errors, misspellings, non-standard abbreviations, and meaningless capitalization. So, these problems can be eliminated by the use of this tool. Lot of time can be saved and as well as by the use of efficient search optimization each information about those particular tweets can be obtained.
An effective XML based name mapping mechanism within StoRM

International Nuclear Information System (INIS)

Corso, E; Forti, A; Ghiselli, A; Magnoni, L; Zappi, R

2008-01-01

In a Grid environment the naming capability allows users to refer to specific data resources in a physical storage system using a high level logical identifier. This logical identifier is typically organized in a file system like structure, a hierarchical tree of names. Storage Resource Manager (SRM) services map the logical identifier to the physical location of data evaluating a set of parameters as the desired quality of services and the VOMS attributes specified in the requests. StoRM is a SRM service developed by INFN and ICTP-EGRID to manage file and space on standard POSIX and high performing parallel and cluster file systems. An upcoming requirement in the Grid data scenario is the orthogonality of the logical name and the physical location of data, in order to refer, with the same identifier, to different copies of data archived in various storage areas with different quality of service. The mapping mechanism proposed in StoRM is based on a XML document that represents the different storage components managed by the service, the storage areas defined by the site administrator, the quality of service they provide and the Virtual Organization that want to use the storage area. An appropriate directory tree is realized in each storage component reflecting the XML schema. In this scenario StoRM is able to identify the physical location of a requested data evaluating the logical identifier and the specified attributes following the XML schema, without querying any database service. This paper presents the namespace schema defined, the different entities represented and the technical details of the StoRM implementation
IMPROVING PERFORMANCES BY USING COST CONTROLLING IN THE MINING INDUSTRY ENTITIES

Directory of Open Access Journals (Sweden)

SORINEL CĂPUŞNEANU

2016-06-01

Full Text Available The aim of this article is to highlight the improving performances of entities from mining industry entities by using cost controlling as an important tool of management accounting, applying the target costing method. The survey is based on questions that led investigation made in the Romanian entities from mining industry and based on data a thorough analysis was done for fulfillment of authors’ purpose. The results obtained by applying the target costing method has allowed a very strict cost control, which ultimately led to increased performances of economic entities from mining industry in Romania. The secondary purpose of this article is to try adjusting the target costing method to the specific of entities in the mining industry. According to studies of specialists this method based on target costing calculation is rather unusual in this sector of mining industry and it relies heavily on the activity-based costing method. The article ends with the authors' conclusions on improving the performances of entities from mining industry based on cost controlling and use of mix information obtained through the applied methods
An information technology emphasis in biomedical informatics education.

Science.gov (United States)

Kane, Michael D; Brewer, Jeffrey L

2007-02-01

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

CERN Document Server

2015-01-01

This book presents the proceedings of the IUPESM World Biomedical Engineering and Medical Physics, a tri-annual high-level policy meeting dedicated exclusively to furthering the role of biomedical engineering and medical physics in medicine. The book offers papers about emerging issues related to the development and sustainability of the role and impact of medical physicists and biomedical engineers in medicine and healthcare. It provides a unique and important forum to secure a coordinated, multileveled global response to the need, demand, and importance of creating and supporting strong academic and clinical teams of biomedical engineers and medical physicists for the benefit of human health.
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.
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
Geographic Names

Data.gov (United States)

Minnesota Department of Natural Resources — The Geographic Names Information System (GNIS), developed by the United States Geological Survey in cooperation with the U.S. Board of Geographic Names, provides...
New frontiers in biomedical science and engineering during 2014-2015.

Science.gov (United States)

Liu, Feng; Lee, Dong-Hoon; Lagoa, Ricardo; Kumar, Sandeep

2015-01-01

The International Conference on Biomedical Engineering and Biotechnology (ICBEB) is an international meeting held once a year. This, the fourth International Conference on Biomedical Engineering and Biotechnology (ICBEB2015), will be held in Shanghai, China, during August 18th-21st, 2015. This annual conference intends to provide an opportunity for researchers and practitioners at home and abroad to present the most recent frontiers and future challenges in the fields of biomedical science, biomedical engineering, biomaterials, bioinformatics and computational biology, biomedical imaging and signal processing, biomechanical engineering and biotechnology, etc. The papers published in this issue are selected from this Conference, which witness the advances in biomedical engineering and biotechnology during 2014-2015.
Quality of the Accounting Information of Brazilian Third Sector Entities

Directory of Open Access Journals (Sweden)

Fernando Maciel Ramos

2015-08-01

Full Text Available In this study, the objective was to analyze the quality of accounting information of Brazilian non-profit organizations. As for the objective the research is characterized as a descriptive one; as for the research strategy it is documental and as for the approach it is quantitative. In order to measure the quality of the accounting information of the analyzed entities, it was prepared a checklist starting from the accounting rules that guide the accounting practice of the third sector entities made up of seven sections and 59 requisites, which enabled the construction of the Quality Index for Accounting Information. The data were analyzed through descriptive statistics (minimum, maximum, mean, standard deviation and the results indicated a low level of the accounting information quality reported by the analyzed entities, especially when compared to for-profit organizations. One comes to the conclusion, based on the findings, that the analyzed entities present a low level of quality as to the accounting information which may jeopardize the information usefulness reported by these entities users.
Diseño de un modelo específico para la predicción de la quiebra de micro-entities // Design of a Specific Model for Predicting Micro-Entities Failure

Directory of Open Access Journals (Sweden)

Antonio J. Blanco Oliver

2016-12-01

Full Text Available La importancia de las micro-entities como generadoras de empleo y propulsoras de la actividad económica conlleva, unida a sus mayores tasas de quiebra y a su dificultad para acceder a las fuentes de financiación, la necesidad de diseñar métodos apropiados que anticipen sus quiebras. Con este fin, en este trabajo se desarrolla un modelo híbrido mediante la combinación de enfoques paramétricos y no paramétricos para la detección de sus quiebras. Para ello, se seleccionan las variables con mayor poder predictivo para detectar la quiebra mediante un modelo híbrido de regresión logística (LR y árboles de regresión y clasificación (CART. Nuestros resultados muestran que este modelo híbrido obtiene una mejor performance que aquellos modelos implementados de forma aislada, además de tener una más fácil interpretación y una convergencia más rápida. Por otra parte, se constata la conveniencia de la introducción de variables no financieras y macroeconómicas que complementen a la información proporcionada por los ratios financieros para la predicción de la quiebra de las micro-entities, lo cual está en línea con las características propias e idiosincrasia de este tamaño empresarial recientemente definido por la Comisión Europea. ------------------------------------ The importance of micro-entities due to their generation of employment and propelling economic activity, together with the fact of their particularities, implies the need to design appropriate methods that anticipate their bankruptcies. For that purpose, a hybrid model by combining parametric and nonparametric approaches is developed in this paper. First, the variables with the highest predictive power to detect bankruptcy are selected using logistic regression (LR. Subsequently, a non-parametric method, namely regression trees and classification (CART, is then applied to companies classified as "bankruptcy" or "non-bankruptcy". Our results show that this model
10 CFR 300.12 - Acceptance of reports and registration of entity emission reductions.

Science.gov (United States)

2010-01-01

... REPORTING PROGRAM: GENERAL GUIDELINES § 300.12 Acceptance of reports and registration of entity emission... provisions of this part. EIA will also review its records to verify that the reporting entity has submitted... credited to the entity as “registered reductions” which can be held by the reporting entity for use...
Entropy and Graph Based Modelling of Document Coherence using Discourse Entities

DEFF Research Database (Denmark)

Petersen, Casper; Lioma, Christina; Simonsen, Jakob Grue

2015-01-01

We present two novel models of document coherence and their application to information retrieval (IR). Both models approximate document coherence using discourse entities, e.g. the subject or object of a sentence. Our first model views text as a Markov process generating sequences of discourse...... entities (entity n-grams); we use the entropy of these entity n-grams to approximate the rate at which new information appears in text, reasoning that as more new words appear, the topic increasingly drifts and text coherence decreases. Our second model extends the work of Guinaudeau & Strube [28......] that represents text as a graph of discourse entities, linked by different relations, such as their distance or adjacency in text. We use several graph topology metrics to approximate different aspects of the discourse flow that can indicate coherence, such as the average clustering or betweenness of discourse...
Generic Entity Resolution in Relational Databases

Science.gov (United States)

Sidló, Csaba István

Entity Resolution (ER) covers the problem of identifying distinct representations of real-world entities in heterogeneous databases. We consider the generic formulation of ER problems (GER) with exact outcome. In practice, input data usually resides in relational databases and can grow to huge volumes. Yet, typical solutions described in the literature employ standalone memory resident algorithms. In this paper we utilize facilities of standard, unmodified relational database management systems (RDBMS) to enhance the efficiency of GER algorithms. We study and revise the problem formulation, and propose practical and efficient algorithms optimized for RDBMS external memory processing. We outline a real-world scenario and demonstrate the advantage of algorithms by performing experiments on insurance customer data.
Service quality measurement for non-executive directors in public entities

OpenAIRE

2012-01-01

D.Comm. In commercial corporations shareholders, at least in theory, evaluate the performance of the boards they have appointed. Such evaluation is mainly based on the financial performance of the entity. Public (state funded) entities have only the state as shareholder and the performance of their boards is not evaluated by the taxpayers who ultimately pay the directors' fees. The term "public entity" refers to 20 corporations with an annual turnover in excess of R 55 billion which are su...
The use of AMS to the biomedical sciences

International Nuclear Information System (INIS)

Vogel, J.S.

1991-04-01

The Center for Accelerator Mass Spectroscopy (AMS) began making AMS measurements in 1989. Biomedical experiments were originally limited by sample preparation techniques, but we expect the number of biomedical samples to increase five-fold. While many of the detailed techniques for making biomedical measurements resemble those used in other fields, biological tracer experiments differ substantially from the observational approaches of earth science investigators. The role of xenobiotius in initiating mutations in cells is of particular interest. One measure of the damage caused to the genetic material is obtained by counting the number of adducts formed by a chemical agent at a given dose. AMS allows direct measurement of the number of adducts through stoichiometric quantification of the 14 C label attached to the DNA after exposure to a labelled carcinogen. Other isotopes of interest include tritium, 36 Cl, 79 SE, 41 Ca, 26 Al and 129 I. Our experiments with low dose environmental carcinogens reflect the protocols which will become a common part of biomedical AMS. In biomedical experiments, the researcher defines the carbon to be analyzed through dissection and/or chemical purification; thus the sample is ''merely'' combusted and graphitized at the AMS facility. However, since biomedical samples can have a 14 C range of five orders of magnitude, preparation of graphite required construction of a special manifold to prevent cross-contamination. Additionally, a strain of 14 C-depleted C57BL/6 mice is being developed to further reduce background in biomedical experiments. AMS has a bright and diverse future in radioisotope tracing. Such work requires a dedicated amalgamation of AMS scientists and biomedical researchers who will redesign experimental protocols to maximize the AMS technique and minimize the danger of catastrophic contamination. 18 refs., 4 figs., 1 tab

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.
43 CFR 426.8 - Nonresident aliens and foreign entities.

Science.gov (United States)

2010-10-01

... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Nonresident aliens and foreign entities..., DEPARTMENT OF THE INTERIOR ACREAGE LIMITATION RULES AND REGULATIONS § 426.8 Nonresident aliens and foreign... reclamation law or these regulations, a nonresident alien or foreign entity that directly holds land in a...
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
Logical Entity Level Sentiment Analysis

DEFF Research Database (Denmark)

Petersen, Niklas Christoffer; Villadsen, Jørgen

2017-01-01

We present a formal logical approach using a combinatory categorial grammar for entity level sentiment analysis that utilizes machine learning techniques for efficient syntactical tagging and performs a deep structural analysis of the syntactical properties of texts in order to yield precise resu...
Big data and biomedical informatics: a challenging opportunity.

Science.gov (United States)

Bellazzi, R

2014-05-22

Big data are receiving an increasing attention in biomedicine and healthcare. It is therefore important to understand the reason why big data are assuming a crucial role for the biomedical informatics community. The capability of handling big data is becoming an enabler to carry out unprecedented research studies and to implement new models of healthcare delivery. Therefore, it is first necessary to deeply understand the four elements that constitute big data, namely Volume, Variety, Velocity, and Veracity, and their meaning in practice. Then, it is mandatory to understand where big data are present, and where they can be beneficially collected. There are research fields, such as translational bioinformatics, which need to rely on big data technologies to withstand the shock wave of data that is generated every day. Other areas, ranging from epidemiology to clinical care, can benefit from the exploitation of the large amounts of data that are nowadays available, from personal monitoring to primary care. However, building big data-enabled systems carries on relevant implications in terms of reproducibility of research studies and management of privacy and data access; proper actions should be taken to deal with these issues. An interesting consequence of the big data scenario is the availability of new software, methods, and tools, such as map-reduce, cloud computing, and concept drift machine learning algorithms, which will not only contribute to big data research, but may be beneficial in many biomedical informatics applications. The way forward with the big data opportunity will require properly applied engineering principles to design studies and applications, to avoid preconceptions or over-enthusiasms, to fully exploit the available technologies, and to improve data processing and data management regulations.
Awareness of the Tuskegee Syphilis Study and the US presidential apology and their influence on minority participation in biomedical research.

Science.gov (United States)

Katz, Ralph V; Kegeles, S Stephen; Kressin, Nancy R; Green, B Lee; James, Sherman A; Wang, Min Qi; Russell, Stefanie L; Claudio, Cristina

2008-06-01

We compared the influence of awareness of the Tuskegee Syphilis Study and the presidential apology for that study on the willingness of Blacks, non-Hispanic Whites, and Hispanics to participate in biomedical research. The Tuskegee Legacy Project Questionnaire was administered to 1133 adults in 4 US cities. This 60-item questionnaire addressed issues related to the recruitment of minorities into biomedical studies. Adjusted multivariate analysis showed that, compared with Whites, Blacks were nearly 4 times as likely to have heard of the Tuskegee Syphilis Study, more than twice as likely to have correctly named Clinton as the president who made the apology, and 2 to 3 times more likely to have been willing to participate in biomedical studies despite having heard about the Tuskegee Syphilis Study (odds ratio [OR]=2.9; 95% confidence interval [CI]=1.4, 6.2) or the presidential apology (OR=2.3; 95% CI=1.4, 3.9). These marked differences likely reflect the cultural reality in the Black community, which has been accustomed to increased risks in many activities. For Whites, this type of information may have been more shocking and at odds with their expectations and, thus, led to a stronger negative impact.
Signal and image analysis for biomedical and life sciences

CERN Document Server

Sun, Changming; Pham, Tuan D; Vallotton, Pascal; Wang, Dadong

2014-01-01

With an emphasis on applications of computational models for solving modern challenging problems in biomedical and life sciences, this book aims to bring collections of articles from biologists, medical/biomedical and health science researchers together with computational scientists to focus on problems at the frontier of biomedical and life sciences. The goals of this book are to build interactions of scientists across several disciplines and to help industrial users apply advanced computational techniques for solving practical biomedical and life science problems. This book is for users in t
Is Alzheimer's disease a homogeneous disease entity?

Science.gov (United States)

Korczyn, Amos D

2013-10-01

The epidemic proportions of dementia in old age are a cause of great concern for the medical profession and the society at large. It is customary to consider Alzheimer's disease (AD) as the most common cause of dementia, and vascular dementia (VaD) as being the second. This dichotomous view of a primary neurodegenerative disease as opposed to a disorder where extrinsic factors cause brain damage led to separate lines of research in these two entities. New biomarkers, particularly the introduction of modern neuroimaging and cerebrospinal fluid changes, have, in recent years, helped to identify anatomical and chemical changes of VaD and of AD. Nevertheless, there is a substantial difference between the two entities. While it is clear that VaD is a heterogeneous entity, AD is supposed to be a single disorder. Nobody attempts to use CADASIL as a template to develops treatment for sporadic VaD. On the other hand, early-onset AD is used to develop therapy for sporadic AD. This paper will discuss the problems relating to this false concept and its consequences.
Review of spectral imaging technology in biomedical engineering: achievements and challenges.

Science.gov (United States)

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

2013-10-01

Spectral imaging is a technology that integrates conventional imaging and spectroscopy to get both spatial and spectral information from an object. Although this technology was originally developed for remote sensing, it has been extended to the biomedical engineering field as a powerful analytical tool for biological and biomedical research. This review introduces the basics of spectral imaging, imaging methods, current equipment, and recent advances in biomedical applications. The performance and analytical capabilities of spectral imaging systems for biological and biomedical imaging are discussed. In particular, the current achievements and limitations of this technology in biomedical engineering are presented. The benefits and development trends of biomedical spectral imaging are highlighted to provide the reader with an insight into the current technological advances and its potential for biomedical research.
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.
[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.
31 CFR 598.303 - Entity.

Science.gov (United States)

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Entity. 598.303 Section 598.303 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS..., organization, network, group, or subgroup, or any form of business collaboration. ...
What's in a Name? Interlocutors Dynamically Update Expectations about Shared Names.

Science.gov (United States)

Gegg-Harrison, Whitney M; Tanenhaus, Michael K

2016-01-01

In order to refer using a name, speakers must believe that their addressee knows about the link between the name and the intended referent. In cases where speakers and addressees learned a subset of names together, speakers are adept at using only the names their partner knows. But speakers do not always share such learning experience with their conversational partners. In these situations, what information guides speakers' choice of referring expression? A speaker who is uncertain about a names' common ground (CG) status often uses a name and description together. This N+D form allows speakers to demonstrate knowledge of a name, and could provide, even in the absence of miscommunication, useful evidence to the addressee regarding the speaker's knowledge. In cases where knowledge of one name is associated with knowledge of other names, this could provide indirect evidence regarding knowledge of other names that could support generalizations used to update beliefs about CG. Using Bayesian approaches to language processing as a guiding framework, we predict that interlocutors can use their partner's choice of referring expression, in particular their use of an N+D form, to generate more accurate beliefs regarding their partner's knowledge of other names. In Experiment 1, we find that domain experts are able to use their partner's referring expression choices to generate more accurate estimates of CG. In Experiment 2, we find that interlocutors are able to infer from a partner's use of an N+D form which other names that partner is likely to know or not know. Our results suggest that interlocutors can use the information conveyed in their partner's choice of referring expression to make generalizations that contribute to more accurate beliefs about what is shared with their partner, and further, that models of CG for reference need to account not just for the status of referents, but the status of means of referring to those referents.
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
Periocular xanthogranuloma: A forgotten entity?

Directory of Open Access Journals (Sweden)

Charalampos Papagoras

2010-03-01

Full Text Available Charalampos Papagoras1, George Kitsos2, Paraskevi V Voulgari1, Anastasia K Zikou3, Maria I Argyropoulou3, Aikaterini Zioga4, Alexandros A Drosos11Rheumatology Clinic, Department of Internal Medicine; 2Department of Ophthalmology; 3Department of Clinical Imaging and Radiology, 4Department of Pathology, Medical School, University of Ioannina, Ioannina, GreeceAbstract: Periocular xanthogranulomatous diseases are a rare group of disorders which are characterized by a predilection to affect the orbit and ocular adnexa and special histopathological features, in particular infiltrates comprising non-Langerhans-derived foamy histiocytes and Touton giant cells. The differential diagnosis is difficult and occasionally definite diagnosis cannot be established even after clinical and histopathological findings are taken together. We describe a case of a middle-aged man who presented with a 10-year history of voluminous eyelid swelling with concomitant late-onset atopic manifestations, namely bronchial asthma and allergic rhinitis with nasal polyps. After thorough clinical and laboratory investigation, including a biopsy of the eyelid, we classified the patient’s disease to a rare entity that has been relatively recently described: periocular xanthogranuloma associated with adult-onset asthma. In a review of the literature, no prospective trials concerning the treatment of this disease were found. The literature mainly contained case reports and case series in which corticosteroids and chemotherapy with alkylating agents have been reported to be beneficial. We treated our patient with a combination of oral corticosteroids and cyclophosphamide pulses and we observed substantial regression of the eyelid masses together with a normalization of systemic immunologic abnormalities.Keywords: periocular xanthogranuloma, adult-onset asthma, non-Langerhans histiocytoses, cyclophosphamide, methylprednisolone
Principles and tools for collaborative entity-based intelligence analysis.

Science.gov (United States)

Bier, Eric A; Card, Stuart K; Bodnar, John W

2010-01-01

Software tools that make it easier for analysts to collaborate as a natural part of their work will lead to better analysis that is informed by more perspectives. We are interested to know if software tools can be designed that support collaboration even as they allow analysts to find documents and organize information (including evidence, schemas, and hypotheses). We have modified the Entity Workspace system, described previously, to test such designs. We have evaluated the resulting design in both a laboratory study and a study where it is situated with an analysis team. In both cases, effects on collaboration appear to be positive. Key aspects of the design include an evidence notebook optimized for organizing entities (rather than text characters), information structures that can be collapsed and expanded, visualization of evidence that emphasizes events and documents (rather than emphasizing the entity graph), and a notification system that finds entities of mutual interest to multiple analysts. Long-term tests suggest that this approach can support both top-down and bottom-up styles of analysis.
PubMed-based quantitative analysis of biomedical publications in the SAARC countries: 1985-2009.

Science.gov (United States)

Azim Majumder, Md Anwarul; Shaban, Sami F; Rahman, Sayeeda; Rahman, Nuzhat; Ahmed, Moslehuddin; Bin Abdulrahman, Khalid A; Islam, Ziauddin

2012-09-01

To conduct a geographical analysis of biomedical publications from the South Asian Association for Regional Cooperation (SAARC) countries over the past 25 years (1985-2009) using the PubMed database. A qualitative study. Web-based search during September 2010. A data extraction program, developed by one of the authors (SFS), was used to extract the raw publication counts from the downloaded PubMed data. A search of PubMed was performed for all journals indexed by selecting the advanced search option and entering the country name in the 'affiliation' field. The publications were normalized by total population, adult illiteracy rate, gross domestic product (GDP), secondary school enrollment ratio and Internet usage rate. The number of PubMed-listed papers published by the SAARC countries over the last 25 years totalled 141,783, which is 1.1% of the total papers indexed by PubMed in the same period. India alone produced 90.5% of total publications generated by SAARC countries. The average number of papers published per year from 1985 to 2009 was 5671 and number of publication increased approximately 242-fold. Normalizing by the population (per million) and GDP (per billion), India (133, 27.6%) and Nepal (323, 37.3%) had the highest publications respectively. There was a marked imbalance among the SAARC countries in terms of biomedical research and publication. Because of huge population and the high disease burden, biomedical research and publication output should receive special attention to formulate health policies, re-orient medical education curricula, and alleviate diseases and poverty.
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
Employee turnover and productivity among small business entities in Nigeria

Directory of Open Access Journals (Sweden)

John N. N. Ugoani

2016-12-01

Full Text Available This study was designed to evaluate the problems of employee turnover on productivity among small business entities in Nigeria, and recommend remedial actions. Employee turnover is the separation of employees from employers and replacement with other employees. Productive manpower is a critical element for the economic survival of any small business entity. The survey research design was used for the study. The sample comprised of 320 respondents. Data generated were analyzed by using descriptive, and Z-test statistical techniques. It was found that employee turnover adversely affects productivity in small business entities.
Categorizing terrorist entities listed by the European Union according to terrorist groups’ underlying motives

Directory of Open Access Journals (Sweden)

Liane Rothenberger

2015-10-01

Full Text Available States and international organizations have compiled lists of a great variety of terrorist groups. The current European Union list includes 44 entities. This study analyzes the underlying motives of the terrorist organizations named in this list. In order to understand the groups’ motivations and consequently be able to advise on methods of countering them with communication strategies, we employ a three-item typology provided by Waldmann (2001. The results show that only five of the 44 groups were religiously motivated to commit terrorism. Most of the groups (n=20 had nationalist-separatist motives, and 19 groups displayed social-revolutionary motives. Based on the respective motives, differing counter-terrorism strategies are proposed, e.g., developing rhetorical counter-narratives that address and reduce the groups’ motivational and identity-generating characteristics.

48 CFR 252.204-7001 - Commercial and Government Entity (CAGE) code reporting.

Science.gov (United States)

2010-10-01

... Entity (CAGE) code reporting. 252.204-7001 Section 252.204-7001 Federal Acquisition Regulations System... Entity (CAGE) Code Reporting (AUG 1999) (a) The offeror is requested to enter its CAGE code on its offer... AND CONTRACT CLAUSES Text of Provisions And Clauses 252.204-7001 Commercial and Government Entity...
Business Entity Selection: Why It Matters to Healthcare Practitioners. Part II--Corporations, Limited Liability Companies, and Professional Entities.

Science.gov (United States)

Nithman, Robert W

2015-01-01

The Bureau of Labor statistics indicates only a 50% four-year survivability rate among businesses classified as "education and health services." Gaining knowledge of IRS business entities can result in cost savings, operational efficiency, reduced liability, and enhanced sustainability. Each entity has unique disadvantages, depending on size, diversity of ownership, desire to expand, and profitability. Business structures should be compatible with organizational mission or vision statements, services and products, and professional codes of ethics. Healthcare reform will require greater business acumen. We have an ethical duty to disseminate and acquire the knowledge to properly establish and manage healthcare practices to ensure sustainable services that protect and serve the community.
What’s in a Name? – Consequences of Naming Non-Human Animals

DEFF Research Database (Denmark)

Borkfelt, Sune

2011-01-01

have consequences for the way we think about animals (human and non-human), peoples, species, places, things etc. Through a blend of history, philosophy and representational theory—and using examples from, among other things, the Bible, Martin Luther, colonialism/imperialism and contemporary ways......The act of naming is among the most basic actions of language. Indeed, it is naming something that enables us to communicate about it in specific terms, whether the object named is human or non-human, animate or inanimate. However, naming is not as uncomplicated as we may usually think and names...... of keeping and regarding non-human animals—this paper attempts to trace the importance of (both specific and generic) naming to our relationships with the non-human. It explores this topic from the naming of the animals in Genesis to the names given and used by scientists, keepers of companion animals, media...
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
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
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.
Biomedical engineering: A platform for research and innovation in ultrasound

Science.gov (United States)

Holland, Christy K.

2004-05-01

An undergraduate or graduate degree in biomedical engineering prepares students to solve problems at the interface between engineering and medicine. Biomedical engineering encompasses evolving areas such as advanced medical imaging for diagnosis and treatment of disease, tissue engineering for designing and manufacturing biological implants for damaged or diseased tissues and organs, and bioinformatics for determining which genes play a major role in health and disease. Biomedical engineering academic programs produce graduates with the ability to pursue successful careers in the biomedical device industry or to obtain advanced degrees leading to careers in biomedical engineering research, medicine, law or business. Biomedical engineering majors take courses in biology, anatomy, physics, chemistry, engineering, mathematics and medical product design and value life-long learning. Students learn to work effectively in interdisciplinary teams comprised of individuals with diverse social, cultural and technical backgrounds. Biomedical engineering is becoming increasingly important in imaging and image-guided research. Some examples of innovative ultrasound technology under development are ultrasound devices to accelerate the dissolution of blood clots, advanced surgical instruments with ultrasound guidance and ultrasound contrast agents for targeted drug delivery. Biomedical engineering is a great career choice for technically minded individuals who endeavor to work on applied problems that are medically relevant.
ECO: A Framework for Entity Co-Occurrence Exploration with Faceted Navigation

Energy Technology Data Exchange (ETDEWEB)

Halliday, K. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2010-08-20

Even as highly structured databases and semantic knowledge bases become more prevalent, a substantial amount of human knowledge is reported as written prose. Typical textual reports, such as news articles, contain information about entities (people, organizations, and locations) and their relationships. Automatically extracting such relationships from large text corpora is a key component of corporate and government knowledge bases. The primary goal of the ECO project is to develop a scalable framework for extracting and presenting these relationships for exploration using an easily navigable faceted user interface. ECO uses entity co-occurrence relationships to identify related entities. The system aggregates and indexes information on each entity pair, allowing the user to rapidly discover and mine relational information.
Blockchain distributed ledger technologies for biomedical and health care applications.

Science.gov (United States)

Kuo, Tsung-Ting; Kim, Hyeon-Eui; Ohno-Machado, Lucila

2017-11-01

To introduce blockchain technologies, including their benefits, pitfalls, and the latest applications, to the biomedical and health care domains. Biomedical and health care informatics researchers who would like to learn about blockchain technologies and their applications in the biomedical/health care domains. The covered topics include: (1) introduction to the famous Bitcoin crypto-currency and the underlying blockchain technology; (2) features of blockchain; (3) review of alternative blockchain technologies; (4) emerging nonfinancial distributed ledger technologies and applications; (5) benefits of blockchain for biomedical/health care applications when compared to traditional distributed databases; (6) overview of the latest biomedical/health care applications of blockchain technologies; and (7) discussion of the potential challenges and proposed solutions of adopting blockchain technologies in biomedical/health care domains. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.
Entity versus incremental theories predict older adults' memory performance.

Science.gov (United States)

Plaks, Jason E; Chasteen, Alison L

2013-12-01

The authors examined whether older adults' implicit theories regarding the modifiability of memory in particular (Studies 1 and 3) and abilities in general (Study 2) would predict memory performance. In Study 1, individual differences in older adults' endorsement of the "entity theory" (a belief that one's ability is fixed) or "incremental theory" (a belief that one's ability is malleable) of memory were measured using a version of the Implicit Theories Measure (Dweck, 1999). Memory performance was assessed with a free-recall task. Results indicated that the higher the endorsement of the incremental theory, the better the free recall. In Study 2, older and younger adults' theories were measured using a more general version of the Implicit Theories Measure that focused on the modifiability of abilities in general. Again, for older adults, the higher the incremental endorsement, the better the free recall. Moreover, as predicted, implicit theories did not predict younger adults' memory performance. In Study 3, participants read mock news articles reporting evidence in favor of either the entity or incremental theory. Those in the incremental condition outperformed those in the entity condition on reading span and free-recall tasks. These effects were mediated by pretask worry such that, for those in the entity condition, higher worry was associated with lower performance. Taken together, these studies suggest that variation in entity versus incremental endorsement represents a key predictor of older adults' memory performance. PsycINFO Database Record (c) 2013 APA, all rights reserved.
Advances in biomedical engineering and biotechnology during 2013-2014.

Science.gov (United States)

Liu, Feng; Wang, Ying; Burkhart, Timothy A; González Penedo, Manuel Francisco; Ma, Shaodong

2014-01-01

The 3rd International Conference on Biomedical Engineering and Biotechnology (iCBEB 2014), held in Beijing from the 25th to the 28th of September 2014, is an annual conference that intends to provide an opportunity for researchers and practitioners around the world to present the most recent advances and future challenges in the fields of biomedical engineering, biomaterials, bioinformatics and computational biology, biomedical imaging and signal processing, biomechanical engineering and biotechnology, amongst others. The papers published in this issue are selected from this conference, which witnesses the advances in biomedical engineering and biotechnology during 2013-2014.
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.
47 CFR 22.229 - Designated entities.

Science.gov (United States)

2010-10-01

... entrepreneur is an entity that, together with its controlling interests and affiliates, has average annual... entrepreneur, as defined in this section, or a consortium of entrepreneurs may use the bidding credit specified...
47 CFR 101.538 - Designated entities.

Science.gov (United States)

2010-10-01

... entrepreneur is an entity that, together with its controlling interests and affiliates, has average gross... entrepreneur, as defined in this section, or a consortium of entrepreneurs may use the bidding credit specified...
What's in a Name? Interlocutors dynamically update expectations about shared names

Directory of Open Access Journals (Sweden)

Whitney Marie Gegg-Harrison

2016-02-01

Full Text Available In order to refer using a name, speakers must know that their addressee knows about the link between the name and the intended referent. In cases where speakers and addressees learned names together, speakers are adept at using names only when their addressee knows them. But speakers do not always share such learning experience with their conversational partners. In these situations, what information guides speakers’ choice of referring expression? A speaker who is uncertain about a names’ common ground (CG status often uses a name and description together. This N+D form allows speakers to demonstrate knowledge of a name, and could provide, even in the absence of miscommunication, useful evidence to the addressee regarding the speaker’s knowledge. In cases where knowledge of one name is associated with knowledge of other names, could provide indirect evidence regarding knowledge of other names that could support generalizations used to update beliefs about CG. Using data explanation approaches to language processing as a guiding framework, we predict that interlocutors can use their partner’s choice of referring expression, in particular their use of an N+D form, to generate more accurate beliefs regarding their partner’s knowledge of other names. In Experiment 1, we find that domain experts are able to use their partner’s referring expression choices to generate more accurate estimates of CG. In Experiment 2, we find that interlocutors are able to infer from a partner’s use of an N+D form which other names that partner is likely to know or not know. Our results suggest that interlocutors can use the information conveyed in their partner’s choice of referring expression to make generalizations that contribute to more accurate beliefs about what is shared with their partner, and further, that models of CG for reference need to account not just for the status of referents, but the status of means of referring to those referents.
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.
31 CFR 594.303 - Entity.

Science.gov (United States)

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Entity. 594.303 Section 594.303 Money and Finance: Treasury Regulations Relating to Money and Finance (Continued) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY GLOBAL TERRORISM SANCTIONS REGULATIONS General Definitions § 594.303...
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

performed better than APG kernel for the BioInfer dataset, in the Area Under Curve (AUC) measure (74% vs 69%). However, for all the other PPI datasets, namely AIMed, HPRD50, IEPA and LLL, ASM is substantially outperformed by the APG kernel in F-score and AUC measures. We demonstrate a high performance Chemical Induced Disease relation extraction, without employing external knowledge sources or task specific heuristics. Our work shows that graph kernels are effective in extracting relations that are expressed in multiple sentences. We also show that the graph kernels, namely the ASM and APG kernels, substantially outperform the tree kernels. Among the graph kernels, we showed the ASM kernel as effective for biomedical relation extraction, with comparable performance to the APG kernel for datasets such as the CID-sentence level relation extraction and BioInfer in PPI. Overall, the APG kernel is shown to be significantly more accurate than the ASM kernel, achieving better performance on most datasets.
Bio-Inspired Extreme Wetting Surfaces for Biomedical Applications

Science.gov (United States)

Shin, Sera; Seo, Jungmok; Han, Heetak; Kang, Subin; Kim, Hyunchul; Lee, Taeyoon

2016-01-01

Biological creatures with unique surface wettability have long served as a source of inspiration for scientists and engineers. More specifically, materials exhibiting extreme wetting properties, such as superhydrophilic and superhydrophobic surfaces, have attracted considerable attention because of their potential use in various applications, such as self-cleaning fabrics, anti-fog windows, anti-corrosive coatings, drag-reduction systems, and efficient water transportation. In particular, the engineering of surface wettability by manipulating chemical properties and structure opens emerging biomedical applications ranging from high-throughput cell culture platforms to biomedical devices. This review describes design and fabrication methods for artificial extreme wetting surfaces. Next, we introduce some of the newer and emerging biomedical applications using extreme wetting surfaces. Current challenges and future prospects of the surfaces for potential biomedical applications are also addressed. PMID:28787916
47 CFR 27.209 - Designated entities; bidding credits; unjust enrichment.

Science.gov (United States)

2010-10-01

... 47 Telecommunication 2 2010-10-01 2010-10-01 false Designated entities; bidding credits; unjust enrichment. 27.209 Section 27.209 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON... 2305-2320 MHz and 2345-2360 MHz Bands § 27.209 Designated entities; bidding credits; unjust enrichment...

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
Event-Entity-Relationship Modeling in Data Warehouse Environments

DEFF Research Database (Denmark)

Bækgaard, Lars

We use the event-entity-relationship model (EVER) to illustrate the use of entity-based modeling languages for conceptual schema design in data warehouse environments. EVER is a general-purpose information modeling language that supports the specification of both general schema structures and multi......-dimensional schemes that are customized to serve specific information needs. EVER is based on an event concept that is very well suited for multi-dimensional modeling because measurement data often represent events in multi-dimensional databases...
Finding Related Entities by Retrieving Relations: UIUC at TREC 2009 Entity Track

Science.gov (United States)

2009-11-01

classes, depending on the categories they belong to. A music album could have any generic name, whereas a laptop model has a more generalizable name. A...names of music albums are simply plain text often capitalized, and so on. Thus, we feel that a better ap- proach would be to first identify the...origin domain of the text to be tagged (e.g., pharmaceutical, music , journal, etc.), and then apply tagging rules that are specific to that domain
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
Names of Southern African grasses: Name changes and additional ...

African Journals Online (AJOL)

The main reasons for changes in botanical names are briefly reviewed, with examples from the lists. At this time, about 1040 grass species and subspecific taxa are recognized in the subcontinent. Keywords: botanical research; botanical research institute; botany; grass; grasses; identification; name change; nomenclature; ...
45 CFR 2550.80 - What are the duties of the State entities?

Science.gov (United States)

2010-10-01

... 45 Public Welfare 4 2010-10-01 2010-10-01 false What are the duties of the State entities? 2550.80... ADMINISTRATIVE ENTITIES § 2550.80 What are the duties of the State entities? Both State commissions and AAEs have..., respite services for adults age 55 or older and caregivers, and transitions for older adults age 55 or...
Biomedical waste management in Ayurveda hospitals - current practices & future prospectives.

Science.gov (United States)

Rajan, Renju; Robin, Delvin T; M, Vandanarani

2018-03-16

Biomedical waste management is an integral part of traditional and contemporary system of health care. The paper focuses on the identification and classification of biomedical wastes in Ayurvedic hospitals, current practices of its management in Ayurveda hospitals and its future prospective. Databases like PubMed (1975-2017 Feb), Scopus (1960-2017), AYUSH Portal, DOAJ, DHARA and Google scholar were searched. We used the medical subject headings 'biomedical waste' and 'health care waste' for identification and classification. The terms 'biomedical waste management', 'health care waste management' alone and combined with 'Ayurveda' or 'Ayurvedic' for current practices and recent advances in the treatment of these wastes were used. We made a humble attempt to categorize the biomedical wastes from Ayurvedic hospitals as the available data about its grouping is very scarce. Proper biomedical waste management is the mainstay of hospital cleanliness, hospital hygiene and maintenance activities. Current disposal techniques adopted for Ayurveda biomedical wastes are - sewage/drains, incineration and land fill. But these methods are having some merits as well as demerits. Our review has identified a number of interesting areas for future research such as the logical application of bioremediation techniques in biomedical waste management and the usage of effective micro-organisms and solar energy in waste disposal. Copyright © 2017 Transdisciplinary University, Bangalore and World Ayurveda Foundation. Published by Elsevier B.V. All rights reserved.
26 CFR 301.7701-2T - Business entities; definitions (temporary).

Science.gov (United States)

2010-04-01

... 26 Internal Revenue 18 2010-04-01 2010-04-01 false Business entities; definitions (temporary). 301... (CONTINUED) PROCEDURE AND ADMINISTRATION PROCEDURE AND ADMINISTRATION Definitions § 301.7701-2T Business entities; definitions (temporary). (a) through (c)(2)(ii) [Reserved] For further guidance, see § 301.7701-2...
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
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
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Science.gov (United States)

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.
Agreeements between entities within the public sector and public procurement rules

Directory of Open Access Journals (Sweden)

Alejandro Huergo Lora

2017-11-01

Full Text Available This paper examines how European and Spanish public procurement rules tackle agreements between entities within the public sector. In Spain these agreemets were initially above those rules, but now they cannot have the same object as a contract. Spanish law is not in line with European law, since under European law agreements are valid even if their object could be attained with a contract, provided that they meet some requirements. On the other hand, attention is paid to these requisites, laid down by Eurepean law, in order to ascertain if agreements are asked to comply with harder rules than «in house providing», and if it has to be so. Public entities are not obliged to «buy» if they can fulfill their needs with their own resources. And «their own resources» include the resources of entities or bodies closely related, or even any entity within the public sector. Otherwise decentralized States, in which there are many autonomous entities whose cooperation involves agreements between independent bodies, would be impaired.
Knowledge environments representing molecular entities for the virtual physiological human.

Science.gov (United States)

Hofmann-Apitius, Martin; Fluck, Juliane; Furlong, Laura; Fornes, Oriol; Kolárik, Corinna; Hanser, Susanne; Boeker, Martin; Schulz, Stefan; Sanz, Ferran; Klinger, Roman; Mevissen, Theo; Gattermayer, Tobias; Oliva, Baldo; Friedrich, Christoph M

2008-09-13

In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.
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 %.
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...
Using Direct Sub-Level Entity Access to Improve Nuclear Stockpile Simulation Modeling

Energy Technology Data Exchange (ETDEWEB)

Parker, Robert Y. [Brigham Young Univ., Provo, UT (United States)

1999-08-01

Direct sub-level entity access is a seldom-used technique in discrete-event simulation modeling that addresses the accessibility of sub-level entity information. The technique has significant advantages over more common, alternative modeling methods--especially where hierarchical entity structures are modeled. As such, direct sub-level entity access is often preferable in modeling nuclear stockpile, life-extension issues, an area to which it has not been previously applied. Current nuclear stockpile, life-extension models were demonstrated to benefit greatly from the advantages of direct sub-level entity access. In specific cases, the application of the technique resulted in models that were up to 10 times faster than functionally equivalent models where alternative techniques were applied. Furthermore, specific implementations of direct sub-level entity access were observed to be more flexible, efficient, functional, and scalable than corresponding implementations using common modeling techniques. Common modeling techniques (''unbatch/batch'' and ''attribute-copying'') proved inefficient and cumbersome in handling many nuclear stockpile modeling complexities, including multiple weapon sites, true defect analysis, and large numbers of weapon and subsystem types. While significant effort was required to enable direct sub-level entity access in the nuclear stockpile simulation models, the enhancements were worth the effort--resulting in more efficient, more capable, and more informative models that effectively addressed the complexities of the nuclear stockpile.
Stimuli-responsive magnetic particles for biomedical applications.

Science.gov (United States)

Medeiros, S F; Santos, A M; Fessi, H; Elaissari, A

2011-01-17

In recent years, magnetic nanoparticles have been studied due to their potential applications as magnetic carriers in biomedical area. These materials have been increasingly exploited as efficient delivery vectors, leading to opportunities of use as magnetic resonance imaging (MRI) agents, mediators of hyperthermia cancer treatment and in targeted therapies. Much attention has been also focused on "smart" polymers, which are able to respond to environmental changes, such as changes in the temperature and pH. In this context, this article reviews the state-of-the art in stimuli-responsive magnetic systems for biomedical applications. The paper describes different types of stimuli-sensitive systems, mainly temperature- and pH sensitive polymers, the combination of this characteristic with magnetic properties and, finally, it gives an account of their preparation methods. The article also discusses the main in vivo biomedical applications of such materials. A survey of the recent literature on various stimuli-responsive magnetic gels in biomedical applications is also included. Copyright © 2010 Elsevier B.V. All rights reserved.
[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
Big Data and Biomedical Informatics: A Challenging Opportunity

Science.gov (United States)

2014-01-01

Summary Big data are receiving an increasing attention in biomedicine and healthcare. It is therefore important to understand the reason why big data are assuming a crucial role for the biomedical informatics community. The capability of handling big data is becoming an enabler to carry out unprecedented research studies and to implement new models of healthcare delivery. Therefore, it is first necessary to deeply understand the four elements that constitute big data, namely Volume, Variety, Velocity, and Veracity, and their meaning in practice. Then, it is mandatory to understand where big data are present, and where they can be beneficially collected. There are research fields, such as translational bioinformatics, which need to rely on big data technologies to withstand the shock wave of data that is generated every day. Other areas, ranging from epidemiology to clinical care, can benefit from the exploitation of the large amounts of data that are nowadays available, from personal monitoring to primary care. However, building big data-enabled systems carries on relevant implications in terms of reproducibility of research studies and management of privacy and data access; proper actions should be taken to deal with these issues. An interesting consequence of the big data scenario is the availability of new software, methods, and tools, such as map-reduce, cloud computing, and concept drift machine learning algorithms, which will not only contribute to big data research, but may be beneficial in many biomedical informatics applications. The way forward with the big data opportunity will require properly applied engineering principles to design studies and applications, to avoid preconceptions or over-enthusiasms, to fully exploit the available technologies, and to improve data processing and data management regulations. PMID:24853034
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.

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.
Object-Relational Management of Multiply Represented Geographic Entities

DEFF Research Database (Denmark)

Friis-Christensen, Anders; Jensen, Christian Søndergaard

2003-01-01

Multiple representation occurs when information about the same geographic entity is represented electronically more than once. This occurs frequently in practice, and it invariably results in the occurrence of inconsistencies among the different representations. We propose to resolve this situation...... by introducing a multiple representation management system (MRMS), the schema of which includes rules that specify how to identify representations of the same entity, rules that specify consistency requirements, and rules used to restore consistency when necessary. In this paper, we demonstrate by means...
Development of Biomedical Polymer-Silicate Nanocomposites: A Materials Science Perspective

Directory of Open Access Journals (Sweden)

Chia-Jung Wu

2010-04-01

Full Text Available Biomedical polymer-silicate nanocomposites have potential to become critically important to the development of biomedical applications, ranging from diagnostic and therapeutic devices, tissue regeneration and drug delivery matrixes to various bio-technologies that are inspired by biology but have only indirect biomedical relation. The fundamental understanding of polymer-nanoparticle interactions is absolutely necessary to control structure-property relationships of materials that need to work within the chemical, physical and biological constraints required by an application. This review summarizes the most recent published strategies to design and develop polymer-silicate nanocomposites (including clay based silicate nanoparticles and bioactive glass nanoparticles for a variety of biomedical applications. Emerging trends in bio-technological and biomedical nanocomposites are highlighted and potential new fields of applications are examined.
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
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
An optimal big data workflow for biomedical image analysis

Directory of Open Access Journals (Sweden)

Aurelle Tchagna Kouanou

Full Text Available Background and objective: In the medical field, data volume is increasingly growing, and traditional methods cannot manage it efficiently. In biomedical computation, the continuous challenges are: management, analysis, and storage of the biomedical data. Nowadays, big data technology plays a significant role in the management, organization, and analysis of data, using machine learning and artificial intelligence techniques. It also allows a quick access to data using the NoSQL database. Thus, big data technologies include new frameworks to process medical data in a manner similar to biomedical images. It becomes very important to develop methods and/or architectures based on big data technologies, for a complete processing of biomedical image data. Method: This paper describes big data analytics for biomedical images, shows examples reported in the literature, briefly discusses new methods used in processing, and offers conclusions. We argue for adapting and extending related work methods in the field of big data software, using Hadoop and Spark frameworks. These provide an optimal and efficient architecture for biomedical image analysis. This paper thus gives a broad overview of big data analytics to automate biomedical image diagnosis. A workflow with optimal methods and algorithm for each step is proposed. Results: Two architectures for image classification are suggested. We use the Hadoop framework to design the first, and the Spark framework for the second. The proposed Spark architecture allows us to develop appropriate and efficient methods to leverage a large number of images for classification, which can be customized with respect to each other. Conclusions: The proposed architectures are more complete, easier, and are adaptable in all of the steps from conception. The obtained Spark architecture is the most complete, because it facilitates the implementation of algorithms with its embedded libraries. Keywords: Biomedical images, Big
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.
IDENTIFYING AND IMPLEMENTATION OF THE FINANCING SOURCES OF TOURIST ENTITIES

Directory of Open Access Journals (Sweden)

Gabriela DAVID

2015-12-01

Full Text Available Located at the intersection of the two spheres (tourism markets and financial ones, the tourism entity in Romania is interested in finding the formula to assure optimum financing by attracting financial resources in the field, on the one hand and on the other hand it is interested in meeting the high demand for profit from tourism and economic sphere. The objective determinant of Romanian tourism entity is to maximize the value by carrying out a profitable activity. The touristic entity must obtain profit to generate sufficient funds to distribute cash dividends to shareholders, while paying creditors at a favorable interest on borrowed funds.
26 CFR 301.7701-5 - Domestic and foreign business entities.

Science.gov (United States)

2010-04-01

... the laws of Country A as a public limited company. It is also an entity that is organized as a limited... or organized as any type of entity (including, but not limited to, a corporation, unincorporated association, general partnership, limited partnership, and limited liability company) in the United States, or...
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.
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
Advances in electronic-nose technologies developed for biomedical applications.

Science.gov (United States)

Wilson, Alphus D; Baietto, Manuela

2011-01-01

The research and development of new electronic-nose applications in the biomedical field has accelerated at a phenomenal rate over the past 25 years. Many innovative e-nose technologies have provided solutions and applications to a wide variety of complex biomedical and healthcare problems. The purposes of this review are to present a comprehensive analysis of past and recent biomedical research findings and developments of electronic-nose sensor technologies, and to identify current and future potential e-nose applications that will continue to advance the effectiveness and efficiency of biomedical treatments and healthcare services for many years. An abundance of electronic-nose applications has been developed for a variety of healthcare sectors including diagnostics, immunology, pathology, patient recovery, pharmacology, physical therapy, physiology, preventative medicine, remote healthcare, and wound and graft healing. Specific biomedical e-nose applications range from uses in biochemical testing, blood-compatibility evaluations, disease diagnoses, and drug delivery to monitoring of metabolic levels, organ dysfunctions, and patient conditions through telemedicine. This paper summarizes the major electronic-nose technologies developed for healthcare and biomedical applications since the late 1980s when electronic aroma detection technologies were first recognized to be potentially useful in providing effective solutions to problems in the healthcare industry.
Advances in Electronic-Nose Technologies Developed for Biomedical Applications

Directory of Open Access Journals (Sweden)

Alphus D. Wilson

2011-01-01

Full Text Available The research and development of new electronic-nose applications in the biomedical field has accelerated at a phenomenal rate over the past 25 years. Many innovative e-nose technologies have provided solutions and applications to a wide variety of complex biomedical and healthcare problems. The purposes of this review are to present a comprehensive analysis of past and recent biomedical research findings and developments of electronic-nose sensor technologies, and to identify current and future potential e-nose applications that will continue to advance the effectiveness and efficiency of biomedical treatments and healthcare services for many years. An abundance of electronic-nose applications has been developed for a variety of healthcare sectors including diagnostics, immunology, pathology, patient recovery, pharmacology, physical therapy, physiology, preventative medicine, remote healthcare, and wound and graft healing. Specific biomedical e-nose applications range from uses in biochemical testing, blood-compatibility evaluations, disease diagnoses, and drug delivery to monitoring of metabolic levels, organ dysfunctions, and patient conditions through telemedicine. This paper summarizes the major electronic-nose technologies developed for healthcare and biomedical applications since the late 1980s when electronic aroma detection technologies were first recognized to be potentially useful in providing effective solutions to problems in the healthcare industry.
Biomedical sensor technologies on the platform of mobile phones

Science.gov (United States)

Liu, Lin; Liu, Jing

2011-06-01

Biomedical sensors have been widely used in various areas of biomedical practices, which play an important role in disease detection, diagnosis, monitoring, treatment, health management, and so on. However, most of them and their related platforms are generally not easily accessible or just too expensive or complicated to be kept at home. As an alternative, new technologies enabled from the mobile phones are gradually changing such situations. As can be freely available to almost everyone, mobile phone offers a unique way to improve the conventional medical care through combining with various biomedical sensors. Moreover, the established systems will be both convenient and low cost. In this paper, we present an overview on the state-of-art biomedical sensors, giving a brief introduction of the fundamental principles and showing several new examples or concepts in the area. The focus was particularly put on interpreting the technical strategies to innovate the biomedical sensor technologies based on the platform of mobile phones. Some challenging issues, including feasibility, usability, security, and effectiveness, were discussed. With the help of electrical and mechanical technologies, it is expected that a full combination between the biomedical sensors and mobile phones will bring a bright future for the coming pervasive medical care.
Distribution of Chinese names

Science.gov (United States)

Huang, Ding-wei

2013-03-01

We present a statistical model for the distribution of Chinese names. Both family names and given names are studied on the same basis. With naive expectation, the distribution of family names can be very different from that of given names. One is affected mostly by genealogy, while the other can be dominated by cultural effects. However, we find that both distributions can be well described by the same model. Various scaling behaviors can be understood as a result of stochastic processes. The exponents of different power-law distributions are controlled by a single parameter. We also comment on the significance of full-name repetition in Chinese population.
Twisted speckle entities inside wave-front reversal mirrors

International Nuclear Information System (INIS)

Okulov, A. Yu

2009-01-01

The previously unknown property of the optical speckle pattern reported. The interference of a speckle with the counterpropagating phase-conjugated (PC) speckle wave produces a randomly distributed ensemble of a twisted entities (ropes) surrounding optical vortex lines. These entities appear in a wide range of a randomly chosen speckle parameters inside the phase-conjugating mirrors regardless to an internal physical mechanism of the wave-front reversal. These numerically generated interference patterns are relevant to the Brillouin PC mirrors and to a four-wave mixing PC mirrors based upon laser trapped ultracold atomic cloud.
Economic performance of Czech business entities in the context of CSRs’ implementation

Directory of Open Access Journals (Sweden)

Marcela Basovníková

2013-01-01

Full Text Available The term responsible entrepreneurship refers to economic success of a business by the inclusion of social and environmental considerations into a company’s operational processes. It satisfies customers’ demands, whilst also managing the expectations of employees, suppliers and the surrounding community. In general, the term Social Corporate Responsibility means a positive contribution to society including management of enterprise’s environmental impacts. The major determinants of the CSR values can be explored such as economic, cultural and leadership factors. Corporate Social Responsibility has been receiving increased attention also from bodies which give certification to companies with CSR in practice. There are different certificates which companies can apply for, if being „responsible“, such as SA 8000, GRI, AA1000, IiP or ISO26000. The aim of this paper is to introduce various certificates, namely SA 8000 and look in details on economic data of 9 companies, chosen from 25 in the Czech Republic, which received this label.Both traditional and modern indicators for assessment of business entities’ economic performance within the entity sample are employed as the inclusion of the economic factors on the CSR. Indices of credibility in order to evaluate the financial status of sample entities are utilised as well. The mentioned economic analysis is managed both in the period before the implementation of the certified CSR system and in the ex-post period. The results of economic analysis in the period before receiving the SA8000 certificate are evaluated using the mathematic-statistical methods to reveal development trend regarding their economic performance and to conduct comparison to respective industrial means.
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.
British Sign Name Customs

Science.gov (United States)

Day, Linda; Sutton-Spence, Rachel

2010-01-01

Research presented here describes the sign names and the customs of name allocation within the British Deaf community. While some aspects of British Sign Language sign names and British Deaf naming customs differ from those in most Western societies, there are many similarities. There are also similarities with other societies outside the more…
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.

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
Preparation of the accounting entity for verification of the final accounts

OpenAIRE

Kučerová, Monika

2009-01-01

Bachelor's thesis deals with preparation of the accounting entity for verification of the final accounts. The work includes the definition of the accounting entity, also includes information about preparation of final accounts and deals with report of auditor.
Xanthogranulomatous endometritis: an unusual pathological entity ...

African Journals Online (AJOL)

Xanthogranulomatous endometritis is an unusual pathological entity mimicking endometrial carcinoma. This shows sheets of foamy histiocytes alongwith other inflammatory cells. We, hereby, report a case of 45 year multigravida female with irregular menstrual history, clinically diagnosed as carcinoma and ...
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)
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.
BiOSS: A system for biomedical ontology selection.

Science.gov (United States)

Martínez-Romero, Marcos; Vázquez-Naya, José M; Pereira, Javier; Pazos, Alejandro

2014-04-01

In biomedical informatics, ontologies are considered a key technology for annotating, retrieving and sharing the huge volume of publicly available data. Due to the increasing amount, complexity and variety of existing biomedical ontologies, choosing the ones to be used in a semantic annotation problem or to design a specific application is a difficult task. As a consequence, the design of approaches and tools addressed to facilitate the selection of biomedical ontologies is becoming a priority. In this paper we present BiOSS, a novel system for the selection of biomedical ontologies. BiOSS evaluates the adequacy of an ontology to a given domain according to three different criteria: (1) the extent to which the ontology covers the domain; (2) the semantic richness of the ontology in the domain; (3) the popularity of the ontology in the biomedical community. BiOSS has been applied to 5 representative problems of ontology selection. It also has been compared to existing methods and tools. Results are promising and show the usefulness of BiOSS to solve real-world ontology selection problems. BiOSS is openly available both as a web tool and a web service. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion.

Science.gov (United States)

Jonnagaddala, Jitendra; Jue, Toni Rose; Chang, Nai-Wen; Dai, Hong-Jie

2016-01-01

The rapidly increasing biomedical literature calls for the need of an automatic approach in the recognition and normalization of disease mentions in order to increase the precision and effectivity of disease based information retrieval. A variety of methods have been proposed to deal with the problem of disease named entity recognition and normalization. Among all the proposed methods, conditional random fields (CRFs) and dictionary lookup method are widely used for named entity recognition and normalization respectively. We herein developed a CRF-based model to allow automated recognition of disease mentions, and studied the effect of various techniques in improving the normalization results based on the dictionary lookup approach. The dataset from the BioCreative V CDR track was used to report the performance of the developed normalization methods and compare with other existing dictionary lookup based normalization methods. The best configuration achieved an F-measure of 0.77 for the disease normalization, which outperformed the best dictionary lookup based baseline method studied in this work by an F-measure of 0.13.Database URL: https://github.com/TCRNBioinformatics/DiseaseExtract. © The Author(s) 2016. Published by Oxford University Press.
What's in a Name

Science.gov (United States)

Bush, Sarah B.; Albanese, Judith; Karp, Karen S.

2016-01-01

Historically, some baby names have been more popular during a specific time span, whereas other names are considered timeless. The Internet article, "How to Tell Someone's Age When All You Know Is Her Name" (Silver and McCann 2014), describes the phenomenon of the rise and fall of name popularity, which served as a catalyst for the…
Biomedical data integration in computational drug design and bioinformatics.

Science.gov (United States)

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

2013-03-01

In recent years, in the post genomic era, more and more data is being generated by biological high throughput technologies, such as proteomics and transcriptomics. This omics data can be very useful, but the real challenge is to analyze all this data, as a whole, after integrating it. Biomedical data integration enables making queries to different, heterogeneous and distributed biomedical data sources. Data integration solutions can be very useful not only in the context of drug design, but also in biomedical information retrieval, clinical diagnosis, system biology, etc. In this review, we analyze the most common approaches to biomedical data integration, such as federated databases, data warehousing, multi-agent systems and semantic technology, as well as the solutions developed using these approaches in the past few years.
UMass at TREC WEB 2014: Entity Query Feature Expansion using Knowledge Base Links

Science.gov (United States)

2014-11-01

task on the category A subset and demonstrate the benefit of entity-centric approaches even for non-entity queries like “dark chocolate health benefits ...category A subset and demonstrate the benefit of entity-centric approaches even for non-entity queries like ???dark chocolate health benefits ???. 15...rogers 289 benefits of yoga Model MAP ERR@20 NDCG@20 SDM 4.18 9.15 12.61 WikiRM1 4.00 9.31 12.80 SDM-RM3 3.53 7.61 11.00 EQFE 4.67 10.00 14.61 (a) Results
Entity information life cycle for big data master data management and information integration

CERN Document Server

Talburt, John R

2015-01-01

Entity Information Life Cycle for Big Data walks you through the ins and outs of managing entity information so you can successfully achieve master data management (MDM) in the era of big data. This book explains big data's impact on MDM and the critical role of entity information management system (EIMS) in successful MDM. Expert authors Dr. John R. Talburt and Dr. Yinle Zhou provide a thorough background in the principles of managing the entity information life cycle and provide practical tips and techniques for implementing an EIMS, strategies for exploiting distributed processing to hand
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.
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.
5th International Conference on Biomedical Engineering in Vietnam

CERN Document Server

Phuong, Tran

2015-01-01

This volume presents the proceedings of the Fifth International Conference on the Development of Biomedical Engineering in Vietnam which was held from June 16-18, 2014 in Ho Chi Minh City. The volume reflects the progress of Biomedical Engineering and discusses problems and solutions. I aims identifying new challenges, and shaping future directions for research in biomedical engineering fields including medical instrumentation, bioinformatics, biomechanics, medical imaging, drug delivery therapy, regenerative medicine and entrepreneurship in medical devices.
Operation of a business entity in the context of globalization

OpenAIRE

PAYONK K.; LYASHENKO V.; KVILINSKYI O.

2015-01-01

The article looks into the problems connected with the operation of a business entity in the context of globalization of economic processes. Interaction of economic systems has been analyzed from the perspective of a business entity on the example of Ukraine. There have been suggested methods of assessment and benchmark definition for choosing strategic directions of a business development.
Supplier Outside of Canada — Tax and Bank Information Form

International Development Research Centre (IDRC) Digital Library (Canada)

Hakan Mustafa

Operating Name of Entity / Individual (if different from legal name). Building # ... Legal Name of Entity/Individual - is your legal name (either as an individual or a corporate entity). ... business operates and the name to which payments are made.
supplier, tax and bank information form

International Development Research Centre (IDRC) Digital Library (Canada)

Hakan Mustafa

Operating Name of Entity / Individual (if different from legal name). Building # ... Legal Name of Entity/Individual - is your legal name (either as an individual or a corporate entity). ... business operates and the name to which payments are made.
A Conceptual Schema Language for the Management of Multiple Representations of Geographic Entities

DEFF Research Database (Denmark)

Friis-Christensen, A.; Jensen, Christian Søndergaard; Nytun, J.P.

2005-01-01

Multiple representation of geographic information occurs when a real-world entity is represented more than once in the same or different databases. This occurs frequently in practice, and it invariably results in the occurrence of inconsistencies among the different representations of the same...... entity. In this paper, we propose an approach to the modeling of multiply represented entities, which is based on the relationships among the entities and their representations. Central to our approach is the Multiple Representation Schema Language that, by intuitive and declarative means, is used...... to specify rules that match objects representing the same entity, maintain consistency among these representations, and restore consistency if necessary. The rules configure a Multiple Representation Management System, the aim of which is to manage multiple representations over a number of autonomous...
The single entity option

International Nuclear Information System (INIS)

Friedlander, M.C.; Roberts, K.M.

1997-01-01

Traditionally, an owner hires an engineer to design a power facility or other project and then circulates the completed plans to several contractors for competitive bidding. Although there are many variations on this theme, there is an alternative method which is growing in popularity--the design-build concept. In this construction method, the same entity designs and constructs the facility. The design builder may be a single firm with both design and construction capacity in-house, or it may be a combination of two or more firms with complementary abilities. If there are multiple firms, they may be structured as a joint venture or with one of the firms prime and the others in a subcontracting role. The critical aspect is that the owner contracts with one entity which has the responsibility for both designing and constructing the facility. According to statistics compiled by the Design-Build Institute of America and F.W. Dodge DATALINE2, a national reporter of construction statistics and information, from April 1995 to April 1996 the number of design-build contracts increased 103 percent over the previous year. Of a total $212 billion construction market, about $37.2 billion--18 percent--was design build. The strongest growth was in the category of industrial--plants, refineries, factories and warehouses--in which the concept use was up more than 300 percent from the previous year
78 FR 3317 - Removal of Persons From the Entity List Based on Removal Request; Implementation of Entity List...

Science.gov (United States)

2013-01-16

... a burden hour estimate of 43.8 minutes for a manual or electronic submission. This rule does not... removing under France, the two French entities: ``Laurence Mattiucci, 8 Rue de la Bruyere, 31120 Pinsaguel...

The AIBS In Yugoslavia: Programs in Biomedical Engineering

Science.gov (United States)

Thompson, Mary-Frances

1978-01-01

Programs in biomedical engineering have been developing worldwide since World War II. This article describes a multidisciplinary program which operates in Yugoslavia through a cooperative effort between that county and the AIBS. A major problem has been the slowness with which hospitals accept the concept of biomedical engineering. (MA)
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
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
Dictionary of Alaska place names

Science.gov (United States)

Orth, Donald J.

1971-01-01

This work is an alphabetical list of the geographic names that are now applied and have been applied to places and features of the Alaska landscape. Principal names, compiled from modem maps and charts and printed in boldface type, generally reflect present-day local usage. They conform to the principles of the U.S. Board on Geographic Names for establishing standard names for use on Government maps and in other Government publications. Each name entry gives the present-day spelling along with variant spellings and names; identifies the feature named; presents the origin and history of the name; and, where possible, gives the meaning of an Eskimo, Aleut, Indian, or foreign name. Variant, obsolete, and doubtful names are alphabetically listed and are cross referenced, where necessary, to the principal entries.
Important skills for biomedical services: The perspectives of Malaysian employers and employees.

Science.gov (United States)

Buntat, Yahya; Saud, Muhammad Sukri; Mokhtar, Mahani; Kamin, Yusri; Feh, Lim Set

2016-10-17

Increase in the occurrence of existing diseases, continual emergence of new or exotic diseases and re-emergence of old diseases have placed increasing demands on biomedical services in Malaysia. Biomedical technicians play an important role in operating biomedical instruments. However, there are no clear specifications about characteristics and traits for these semi-professional employees. Employers in a few studies claimed that biomedical graduates are not ready to enter and face challenges in the job market. Therefore, the purpose of this study is to identify technical and generic skills for a biomedical technician from the perspectives of the biomedical technicians and their employers. A quantitative survey design was employed whereby data were obtained through the administration of an instrument developed by the researchers. The sample consisted of 20 hospital managers and 186 biomedical technicians who are currently working in Malaysian government hospitals. The findings show that there are no difference in the perceptions of hospital managers and biomedical technicians regarding technical and non-technical skills. These findings resulted in a checklist which can be used for institutions to produce future biomedical technician graduates in order to meet job demands. However, future research is needed to validate the findings and explore the variables in depth.
27 CFR 479.70 - Certain government entities.

Science.gov (United States)

2010-04-01

..., any State, or possession of the United States, any political subdivision thereof, or any official police organization of such a government entity engaged in criminal investigations. Any person making a...
[Biomedical health care in Angola and in the Companhia de Diamantes de Angola, circa 1910-1970].

Science.gov (United States)

Varanda, Jorge

2014-01-01

The scope of this paper is to analyze the provision of biomedical care in Angola during the activities of the Companhia de Diamantes de Angola. A comparative analysis of public health policies and practices of various colonial actors, such as the health services of the Company, its state counterpart and other colonial companies, will reveal differences in investment in health, namely in health facilities, personnel and treatment. This survey as well as the living conditions highlight the idiosyncratic and central nature of the health services of the Company in terms of morbidity and mortality in Angola, and the importance of these representations for a caregiving empire.
Micro/Nanostructured Films and Adhesives for Biomedical Applications.

Science.gov (United States)

Lee, Jungkyu K; Kang, Sung Min; Yang, Sung Ho; Cho, Woo Kyung

2015-12-01

The advanced technologies available for micro/nanofabrication have opened new avenues for interdisciplinary approaches to solve the unmet medical needs of regenerative medicine and biomedical devices. This review highlights the recent developments in micro/nanostructured adhesives and films for biomedical applications, including waterproof seals for wounds or surgery sites, drug delivery, sensing human body signals, and optical imaging of human tissues. We describe in detail the fabrication processes required to prepare the adhesives and films, such as tape-based adhesives, nanofilms, and flexible and stretchable film-based electronic devices. We also discuss their biomedical functions, performance in vitro and in vivo, and the future research needed to improve the current systems.
Proceedings of the international society for optical engineering biomedical image processing 2

International Nuclear Information System (INIS)

Bovik, A.G.; Howard, V.

1991-01-01

This book contains the proceedings of biomedical image processing. Topics covered include: Filtering and reconstruction of biomedical images; analysis, classification and recognition of biomedical images; and 3-D microscopy
Introducing the Guard-Stage-Milestone Approach for Specifying Business Entity Lifecycles

Science.gov (United States)

Hull, Richard; Damaggio, Elio; Fournier, Fabiana; Gupta, Manmohan; Heath, Fenno (Terry); Hobson, Stacy; Linehan, Mark; Maradugu, Sridhar; Nigam, Anil; Sukaviriya, Piyawadee; Vaculin, Roman

A promising approach to managing business operations is based on business entities with lifecycles (BEL's) (a.k.a. business artifacts), i.e., key conceptual entities that are central to guiding the operations of a business, and whose content changes as they move through those operations. A BEL type includes both an information model that captures, in either materialized or virtual form, all of the business-relevant data about entities of that type, and a lifecycle model, that specifies the possible ways an entity of that type might progress through the business by responding to events and invoking services, including human activities. Most previous work on BEL's has focused on the use of lifecycle models based on variants of finite state machines. This paper introduces the Guard-Stage-Milestone (GSM) meta-model for lifecycles, which is an evolution of the previous work on BEL's. GSM lifecycles are substantially more declarative than the finite state machine variants, and support hierarchy and parallelism within a single entity instance. The GSM operational semantics are based on a form of Event-Condition-Action (ECA) rules, and provide a basis for formal verification and reasoning. This paper provides an informal, preliminary introduction to the GSM approach, and briefly overviews selected research directions.
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.
Laser surface texturing of polymers for biomedical applications

Science.gov (United States)

Riveiro, Antonio; Maçon, Anthony L. B.; del Val, Jesus; Comesaña, Rafael; Pou, Juan

2018-02-01

Polymers are materials widely used in biomedical science because of their biocompatibility, and good mechanical properties (which, in some cases, are similar to those of human tissues); however, these materials are, in general, chemically and biologically inert. Surface characteristics, such as topography (at the macro-, micro, and nanoscale), surface chemistry, surface energy, charge or wettability are interrelated properties, and they cooperatively influence the biological performance of materials when used for biomedical applications. They regulate the biological response at the implant/tissue interface (e.g., influencing the cell adhesion, cell orientation, cell motility, etc.). Several surface processing techniques have been explored to modulate these properties for biomedical applications. Despite their potentials, these methods have limitations that prevent their applicability. In this regard, laser-based methods, in particular laser surface texturing (LST), can be an interesting alternative. Different works have showed the potentiality of this technique to control the surface properties of biomedical polymers and enhance their biological performance; however, more research is needed to obtain the desired biological response. This work provides a general overview of the basics and applications of LST for the surface modification of polymers currently used in the clinical practice (e.g. PEEK, UHMWPE, PP, etc.). The modification of roughness, wettability, and their impact on the biological response is addressed to offer new insights on the surface modification of biomedical polymers.
Directory of awardee names

Energy Technology Data Exchange (ETDEWEB)

1999-07-01

Standardization of grant and contract awardee names has been an area of concern since the development of the Department`s Procurement and Assistance Data System (PADS). A joint effort was begun in 1983 by the Office of Scientific and Technical Information (OSTI) and the Office of Procurement and Assistance Management/Information Systems and Analysis Division to develop a means for providing uniformity of awardee names. As a result of this effort, a method of assigning vendor identification codes to each unique awardee name, division, city, and state combination was developed and is maintained by OSTI. Changes to vendor identification codes or awardee names contained in PADS can be made only by OSTI. Awardee names in the Directory indicate that the awardee has had a prime contract (excluding purchase orders of $10,000 or less) with, or a financial assistance award from, the Department. Award status--active, inactive, or retired--is not shown. The Directory is in alphabetic sequence based on awardee name and reflects the OSTI-assigned vendor identification code to the right of the name. A vendor identification code is assigned to each unique awardee name, division, city, and state (for place of performance). The same vendor identification code is used for awards throughout the Department.
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.
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
27 CFR 479.104 - Registration of firearms by certain governmental entities.

Science.gov (United States)

2010-04-01

... § 479.104 Registration of firearms by certain governmental entities. Any State, any political subdivision thereof, or any official police organization of such a government entity engaged in criminal.... This section shall not apply to a firearm merely being held for use as evidence in a criminal...
Low-level radioactive biomedical wastes

International Nuclear Information System (INIS)

Casarett, G.W.

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

Science.gov (United States)

Walker, Chris

2014-09-01

Jaspers' nosology is indebted to Immanuel Kant's theory of knowledge. He drew the distinction of form and content from the Transcendental Analytic of Kant's Critique of Pure Reason. The distinction is universal to all knowledge, including psychopathology. Individual experience is constituted by a form or category of the Understanding to give a determinate or knowable object classified into the generic type of a real disease entity. The application of form and content is limited by the boundaries of experience. Beyond this boundary are wholes whose conception requires Ideas of reason drawn from the Transcendental Dialectic. Wholes are regulated by Ideas of reason to give an object or schema of the Idea collected into ideal types of an ideal typical disease entity. Jaspers drew ideal types from Max Weber's social theory. He anticipated that, as knowledge advanced, ideal typical disease entities would become real disease entities. By 1920, this had been the destiny of general paralysis as knowledge of its neuropathology, serology and microbiology emerged. As he presented the final edition of General Psychopathology in 1946, Jaspers was anticipating the transition of schizophrenia from ideal typical to real disease entity. Almost 70 years later, with knowledge of its aetiology still unclear, schizophrenia remains marooned as an ideal typical disease entity - still awaiting that crucial advance! © The Author(s) 2014.
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.
Bootstrapping named entity resources for adaptive question answering systems

OpenAIRE

Pablo Sánchez, César de

2011-01-01

Los Sistemas de Búsqueda de Respuestas (SBR) amplían las capacidades de un buscador de información tradicional con la capacidad de encontrar respuestas precisas a las preguntas del usuario. El objetivo principal es facilitar el acceso a la información y disminuir el tiempo y el esfuerzo que el usuario debe emplear para encontrar una información concreta en una lista de documentos relevantes. En esta investigación se han abordado dos trabajos relacionados con los SBR. La primera parte presenta...

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