Categorizing biomedicine images using novel image features and sparse coding representation

PubMed Central

2013-01-01

Background Images embedded in biomedical publications carry rich information that often concisely summarize key hypotheses adopted, methods employed, or results obtained in a published study. Therefore, they offer valuable clues for understanding main content in a biomedical publication. Prior studies have pointed out the potential of mining images embedded in biomedical publications for automatically understanding and retrieving such images' associated source documents. Within the broad area of biomedical image processing, categorizing biomedical images is a fundamental step for building many advanced image analysis, retrieval, and mining applications. Similar to any automatic categorization effort, discriminative image features can provide the most crucial aid in the process. Method We observe that many images embedded in biomedical publications carry versatile annotation text. Based on the locations of and the spatial relationships between these text elements in an image, we thus propose some novel image features for image categorization purpose, which quantitatively characterize the spatial positions and distributions of text elements inside a biomedical image. We further adopt a sparse coding representation (SCR) based technique to categorize images embedded in biomedical publications by leveraging our newly proposed image features. Results we randomly selected 990 images of the JPG format for use in our experiments where 310 images were used as training samples and the rest were used as the testing cases. We first segmented 310 sample images following the our proposed procedure. This step produced a total of 1035 sub-images. We then manually labeled all these sub-images according to the two-level hierarchical image taxonomy proposed by [1]. Among our annotation results, 316 are microscopy images, 126 are gel electrophoresis images, 135 are line charts, 156 are bar charts, 52 are spot charts, 25 are tables, 70 are flow charts, and the remaining 155 images are of the type "others". A serial of experimental results are obtained. Firstly, each image categorizing results is presented, and next image categorizing performance indexes such as precision, recall, F-score, are all listed. Different features which include conventional image features and our proposed novel features indicate different categorizing performance, and the results are demonstrated. Thirdly, we conduct an accuracy comparison between support vector machine classification method and our proposed sparse representation classification method. At last, our proposed approach is compared with three peer classification method and experimental results verify our impressively improved performance. Conclusions Compared with conventional image features that do not exploit characteristics regarding text positions and distributions inside images embedded in biomedical publications, our proposed image features coupled with the SR based representation model exhibit superior performance for classifying biomedical images as demonstrated in our comparative benchmark study. PMID:24565470

Assessment of the neutron dose field around a biomedical cyclotron: FLUKA simulation and experimental measurements.

PubMed

Infantino, Angelo; Cicoria, Gianfranco; Lucconi, Giulia; Pancaldi, Davide; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano; Marengo, Mario

2016-12-01

In the planning of a new cyclotron facility, an accurate knowledge of the radiation field around the accelerator is fundamental for the design of shielding, the protection of workers, the general public and the environment. Monte Carlo simulations can be very useful in this process, and their use is constantly increasing. However, few data have been published so far as regards the proper validation of Monte Carlo simulation against experimental measurements, particularly in the energy range of biomedical cyclotrons. In this work a detailed model of an existing installation of a GE PETtrace 16.5MeV cyclotron was developed using FLUKA. An extensive measurement campaign of the neutron ambient dose equivalent H ∗ (10) in marked positions around the cyclotron was conducted using a neutron rem-counter probe and CR39 neutron detectors. Data from a previous measurement campaign performed by our group using TLDs were also re-evaluated. The FLUKA model was then validated by comparing the results of high-statistics simulations with experimental data. In 10 out of 12 measurement locations, FLUKA simulations were in agreement within uncertainties with all the three different sets of experimental data; in the remaining 2 positions, the agreement was with 2/3 of the measurements. Our work allows to quantitatively validate our FLUKA simulation setup and confirms that Monte Carlo technique can produce accurate results in the energy range of biomedical cyclotrons. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Factors affecting the effectiveness of biomedical document indexing and retrieval based on terminologies.

PubMed

Dinh, Duy; Tamine, Lynda; Boubekeur, Fatiha

2013-02-01

The aim of this work is to evaluate a set of indexing and retrieval strategies based on the integration of several biomedical terminologies on the available TREC Genomics collections for an ad hoc information retrieval (IR) task. We propose a multi-terminology based concept extraction approach to selecting best concepts from free text by means of voting techniques. We instantiate this general approach on four terminologies (MeSH, SNOMED, ICD-10 and GO). We particularly focus on the effect of integrating terminologies into a biomedical IR process, and the utility of using voting techniques for combining the extracted concepts from each document in order to provide a list of unique concepts. Experimental studies conducted on the TREC Genomics collections show that our multi-terminology IR approach based on voting techniques are statistically significant compared to the baseline. For example, tested on the 2005 TREC Genomics collection, our multi-terminology based IR approach provides an improvement rate of +6.98% in terms of MAP (mean average precision) (p<0.05) compared to the baseline. In addition, our experimental results show that document expansion using preferred terms in combination with query expansion using terms from top ranked expanded documents improve the biomedical IR effectiveness. We have evaluated several voting models for combining concepts issued from multiple terminologies. Through this study, we presented many factors affecting the effectiveness of biomedical IR system including term weighting, query expansion, and document expansion models. The appropriate combination of those factors could be useful to improve the IR performance. Copyright © 2012 Elsevier B.V. All rights reserved.

Placebo studies and ritual theory: a comparative analysis of Navajo, acupuncture and biomedical healing

PubMed Central

Kaptchuk, Ted J.

2011-01-01

Using a comparative analysis of Navajo healing ceremonials, acupuncture and biomedical treatment, this essay examines placebo studies and ritual theory as mutually interpenetrating disciplines. Healing rituals create a receptive person susceptible to the influences of authoritative culturally sanctioned ‘powers’. The healer provides the sufferer with imaginative, emotional, sensory, moral and aesthetic input derived from the palpable symbols and procedures of the ritual process—in the process fusing the sufferer's idiosyncratic narrative unto a universal cultural mythos. Healing rituals involve a drama of evocation, enactment, embodiment and evaluation in a charged atmosphere of hope and uncertainty. Experimental research into placebo effects demonstrates that routine biomedical pharmacological and procedural interventions contain significant ritual dimensions. This research also suggests that ritual healing not only represents changes in affect, self-awareness and self-appraisal of behavioural capacities, but involves modulations of symptoms through neurobiological mechanisms. Recent scientific investigations into placebo acupuncture suggest several ways that observations from ritual studies can be verified experimentally. Placebo effects are often described as ‘non-specific’; the analysis presented here suggests that placebo effects are the ‘specific’ effects of healing rituals. PMID:21576142

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

PubMed

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

2009-01-01

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

Reproducibility2020: Progress and priorities

PubMed Central

Freedman, Leonard P.; Venugopalan, Gautham; Wisman, Rosann

2017-01-01

The preclinical research process is a cycle of idea generation, experimentation, and reporting of results. The biomedical research community relies on the reproducibility of published discoveries to create new lines of research and to translate research findings into therapeutic applications. Since 2012, when scientists from Amgen reported that they were able to reproduce only 6 of 53 “landmark” preclinical studies, the biomedical research community began discussing the scale of the reproducibility problem and developing initiatives to address critical challenges. Global Biological Standards Institute (GBSI) released the “Case for Standards” in 2013, one of the first comprehensive reports to address the rising concern of irreproducible biomedical research. Further attention was drawn to issues that limit scientific self-correction, including reporting and publication bias, underpowered studies, lack of open access to methods and data, and lack of clearly defined standards and guidelines in areas such as reagent validation. To evaluate the progress made towards reproducibility since 2013, GBSI identified and examined initiatives designed to advance quality and reproducibility. Through this process, we identified key roles for funders, journals, researchers and other stakeholders and recommended actions for future progress. This paper describes our findings and conclusions. PMID:28620458

Machine learning, medical diagnosis, and biomedical engineering research - commentary.

PubMed

Foster, Kenneth R; Koprowski, Robert; Skufca, Joseph D

2014-07-05

A large number of papers are appearing in the biomedical engineering literature that describe the use of machine learning techniques to develop classifiers for detection or diagnosis of disease. However, the usefulness of this approach in developing clinically validated diagnostic techniques so far has been limited and the methods are prone to overfitting and other problems which may not be immediately apparent to the investigators. This commentary is intended to help sensitize investigators as well as readers and reviewers of papers to some potential pitfalls in the development of classifiers, and suggests steps that researchers can take to help avoid these problems. Building classifiers should be viewed not simply as an add-on statistical analysis, but as part and parcel of the experimental process. Validation of classifiers for diagnostic applications should be considered as part of a much larger process of establishing the clinical validity of the diagnostic technique.

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

PubMed

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-of-the-art techniques in indexing biomedical images. We propose a novel and automated indexing system based on deep preference learning to characterize biomedical images for developing computer aided diagnosis (CAD) systems in healthcare. Our proposed system shows an outstanding indexing ability and high efficiency for biomedical image retrieval applications and it can be used to collect and annotate the high-resolution images in a biomedical database for further biomedical image research and applications. Copyright © 2018 Elsevier B.V. All rights reserved.

Show and tell: disclosure and data sharing in experimental pathology.

PubMed

Schofield, Paul N; Ward, Jerrold M; Sundberg, John P

2016-06-01

Reproducibility of data from experimental investigations using animal models is increasingly under scrutiny because of the potentially negative impact of poor reproducibility on the translation of basic research. Histopathology is a key tool in biomedical research, in particular for the phenotyping of animal models to provide insights into the pathobiology of diseases. Failure to disclose and share crucial histopathological experimental details compromises the validity of the review process and reliability of the conclusions. We discuss factors that affect the interpretation and validation of histopathology data in publications and the importance of making these data accessible to promote replicability in research. © 2016. Published by The Company of Biologists Ltd.

Ranking support vector machine for multiple kernels output combination in protein-protein interaction extraction from biomedical literature.

PubMed

Yang, Zhihao; Lin, Yuan; Wu, Jiajin; Tang, Nan; Lin, Hongfei; Li, Yanpeng

2011-10-01

Knowledge about protein-protein interactions (PPIs) unveils the molecular mechanisms of biological processes. However, the volume and content of published biomedical literature on protein interactions is expanding rapidly, making it increasingly difficult for interaction database curators to detect and curate protein interaction information manually. We present a multiple kernel learning-based approach for automatic PPI extraction from biomedical literature. The approach combines the following kernels: feature-based, tree, and graph and combines their output with Ranking support vector machine (SVM). Experimental evaluations show that the features in individual kernels are complementary and the kernel combined with Ranking SVM achieves better performance than those of the individual kernels, equal weight combination and optimal weight combination. Our approach can achieve state-of-the-art performance with respect to the comparable evaluations, with 64.88% F-score and 88.02% AUC on the AImed corpus. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Telescience testbed for biomedical experiments in space morphological and physiological experiments of rat musculoskeletal system

NASA Astrophysics Data System (ADS)

Watanabe, Satoru; Tanaka, Masafumi; Wada, Yoshiro; Yanagihara, Dai; Tsujimoto, Naoya; Suzuki, Hideki; Kawai, Noriyo; Yamashita, Masamichi; Nagaoka, Shunji; Shoji, Takatoshi; Higashino, Shinichiro; Sudoh, Hideo

As the second telescience testbed experiment we were examined sophisticated processes of biomedical experiment, such as an implantation of a transmitter into the hmster's abdominal cavity, non-stressful blood sampling, large amountof blood collection, muscle extirpation and biopsy from the hamsters on Feburay 6-8, 1990. To make clear the differences between successful results obtained by an experienced hand and by a non-experienced one, three operators wereselected for three successive experimental days; an engineer who had never experienced any biological experiment, a non-biology student, who experienced on biological experiments, and a veterinary surgeon. Surgical procedures need much experiences on maneuvering and understanding of theory to shorten the elapse time. Especially for a non-experienced hand, graphic instructions were much helpful to understand and to maneuver the procedures. Continuous recordings of ECG from a operator and PIs were of an advantage to grasp an extent of the mental strain, which was compared with their reports requested after end of each experimental day. The mental strain was not related to degrees of scientific achievement, but showed faithfully difficulty of each experimental procedure. Training effects on PIs in successive experimental days were found in their instructions for the operator to let understand the procedures.

A bioinformatics roadmap for the human vaccines project.

PubMed

Scheuermann, Richard H; Sinkovits, Robert S; Schenkelberg, Theodore; Koff, Wayne C

2017-06-01

Biomedical research has become a data intensive science in which high throughput experimentation is producing comprehensive data about biological systems at an ever-increasing pace. The Human Vaccines Project is a new public-private partnership, with the goal of accelerating development of improved vaccines and immunotherapies for global infectious diseases and cancers by decoding the human immune system. To achieve its mission, the Project is developing a Bioinformatics Hub as an open-source, multidisciplinary effort with the overarching goal of providing an enabling infrastructure to support the data processing, analysis and knowledge extraction procedures required to translate high throughput, high complexity human immunology research data into biomedical knowledge, to determine the core principles driving specific and durable protective immune responses.

A theoretical-experimental methodology for assessing the sensitivity of biomedical spectral imaging platforms, assays, and analysis methods.

PubMed

Leavesley, Silas J; Sweat, Brenner; Abbott, Caitlyn; Favreau, Peter; Rich, Thomas C

2018-01-01

Spectral imaging technologies have been used for many years by the remote sensing community. More recently, these approaches have been applied to biomedical problems, where they have shown great promise. However, biomedical spectral imaging has been complicated by the high variance of biological data and the reduced ability to construct test scenarios with fixed ground truths. Hence, it has been difficult to objectively assess and compare biomedical spectral imaging assays and technologies. Here, we present a standardized methodology that allows assessment of the performance of biomedical spectral imaging equipment, assays, and analysis algorithms. This methodology incorporates real experimental data and a theoretical sensitivity analysis, preserving the variability present in biomedical image data. We demonstrate that this approach can be applied in several ways: to compare the effectiveness of spectral analysis algorithms, to compare the response of different imaging platforms, and to assess the level of target signature required to achieve a desired performance. Results indicate that it is possible to compare even very different hardware platforms using this methodology. Future applications could include a range of optimization tasks, such as maximizing detection sensitivity or acquisition speed, providing high utility for investigators ranging from design engineers to biomedical scientists. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Vertex-Group Effects in Entangled Polystyrene-Polyhedral Oligosilsesquioxane (POSS) Copolymers (Preprint)

DTIC Science & Technology

2008-11-17

Storrs, CT 06269 2Current Address: Syracuse Biomaterials Institute and Biomedical and Chemical Engineering Department, Syracuse University...dimension in the range 1-100 nm – in order to realize materials that combine the processibility and property-tuning of polymers with outstanding stiffness...polymers with a variety of vertex-groups: isobutyl (iBu), cyclopentyl (Cp) and cyclohexyl (Cy). EXPERIMENTAL SECTION Materials . In order to

Laser processing of thin-film multilayer structures: comparison between a 3D thermal model and experimental results.

PubMed

Naghshine, Babak B; Kiani, Amirkianoosh

2017-01-01

In this research, a numerical model is introduced for simulation of laser processing of thin film multilayer structures, to predict the temperature and ablated area for a set of laser parameters including average power and repetition rate. Different thin-films on Si substrate were processed by nanosecond Nd:YAG laser pulses and the experimental and numerical results were compared to each other. The results show that applying a thin film on the surface can completely change the temperature field and vary the shape of the heat affected zone. The findings of this paper can have many potential applications including patterning the cell growth for biomedical applications and controlling the grain size in fabrication of polycrystalline silicon (poly-Si) thin-film transistors (TFTs).

A novel photochemical machining process for magnesium aerospace and biomedical microengineering applications

NASA Astrophysics Data System (ADS)

Allen, D. M.; Simpkins, M.; Almond, H.

2010-10-01

Research was carried out to evaluate the feasibility of fabricating perforated (filigree) magnesium microcomponents with metal wire widths of the order of the metal thickness using a photochemical machining (PCM) process. Experimentally, it has been demonstrated for the first time that metal wire widths of 0.15 mm can be achieved within a 2D, 0.25 mm thick magnesium foil to fabricate microcomponents for use as micro air vehicle (MAV) wings or stents through a bespoke PCM process. This etching process differs significantly from the industrial etching process used currently to manufacture magnesium letterpress printing plates and embossing dies.

Telemedicine optoelectronic biomedical data processing system

NASA Astrophysics Data System (ADS)

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.

Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

PubMed

Groza, Tudor; Verspoor, Karin

2015-01-01

Concept recognition (CR) is a foundational task in the biomedical domain. It supports the important process of transforming unstructured resources into structured knowledge. To date, several CR approaches have been proposed, most of which focus on a particular set of biomedical ontologies. Their underlying mechanisms vary from shallow natural language processing and dictionary lookup to specialized machine learning modules. However, no prior approach considers the case sensitivity characteristics and the term distribution of the underlying ontology on the CR process. This article proposes a framework that models the CR process as an information retrieval task in which both case sensitivity and the information gain associated with tokens in lexical representations (e.g., term labels, synonyms) are central components of a strategy for generating term variants. The case sensitivity of a given ontology is assessed based on the distribution of so-called case sensitive tokens in its terms, while information gain is modelled using a combination of divergence from randomness and mutual information. An extensive evaluation has been carried out using the CRAFT corpus. Experimental results show that case sensitivity awareness leads to an increase of up to 0.07 F1 against a non-case sensitive baseline on the Protein Ontology and GO Cellular Component. Similarly, the use of information gain leads to an increase of up to 0.06 F1 against a standard baseline in the case of GO Biological Process and Molecular Function and GO Cellular Component. Overall, subject to the underlying token distribution, these methods lead to valid complementary strategies for augmenting term label sets to improve concept recognition.

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

PubMed

Fu, Jian; Tan, Renbo

2014-01-01

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

[327] Biomedical Research Deferred in the Aftermath of the Apollo Fire: Impact to Progress in Human Spaceflight

NASA Technical Reports Server (NTRS)

Charles, John B.

2017-01-01

Before Apollo fire, early Apollo missions were expected to continue pattern established in Gemini program of accommodating significant scientific and biological experimentation, including human biomedical studies, during flights. Apollo1 and Apollo2, both 2-week engineering test flights, were to carry almost as many biomedical studies as Gemini 7, a 2-week medical test mission.

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

PubMed

Cabello C, Felipe

2013-11-01

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

KaBOB: ontology-based semantic integration of biomedical databases.

PubMed

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 formal reasoning over a wealth of integrated biomedical data.

Porosity Measurements and Analysis for Metal Additive Manufacturing Process Control.

PubMed

Slotwinski, John A; Garboczi, Edward J; Hebenstreit, Keith M

2014-01-01

Additive manufacturing techniques can produce complex, high-value metal parts, with potential applications as critical metal components such as those found in aerospace engines and as customized biomedical implants. Material porosity in these parts is undesirable for aerospace parts - since porosity could lead to premature failure - and desirable for some biomedical implants - since surface-breaking pores allows for better integration with biological tissue. Changes in a part's porosity during an additive manufacturing build may also be an indication of an undesired change in the build process. Here, we present efforts to develop an ultrasonic sensor for monitoring changes in the porosity in metal parts during fabrication on a metal powder bed fusion system. The development of well-characterized reference samples, measurements of the porosity of these samples with multiple techniques, and correlation of ultrasonic measurements with the degree of porosity are presented. A proposed sensor design, measurement strategy, and future experimental plans on a metal powder bed fusion system are also presented.

Porosity Measurements and Analysis for Metal Additive Manufacturing Process Control

PubMed Central

Slotwinski, John A; Garboczi, Edward J; Hebenstreit, Keith M

2014-01-01

Additive manufacturing techniques can produce complex, high-value metal parts, with potential applications as critical metal components such as those found in aerospace engines and as customized biomedical implants. Material porosity in these parts is undesirable for aerospace parts - since porosity could lead to premature failure - and desirable for some biomedical implants - since surface-breaking pores allows for better integration with biological tissue. Changes in a part’s porosity during an additive manufacturing build may also be an indication of an undesired change in the build process. Here, we present efforts to develop an ultrasonic sensor for monitoring changes in the porosity in metal parts during fabrication on a metal powder bed fusion system. The development of well-characterized reference samples, measurements of the porosity of these samples with multiple techniques, and correlation of ultrasonic measurements with the degree of porosity are presented. A proposed sensor design, measurement strategy, and future experimental plans on a metal powder bed fusion system are also presented. PMID:26601041

BioSigPlot: an opensource tool for the visualization of multi-channel biomedical signals with Matlab.

PubMed

Boudet, Samuel; Peyrodie, Laurent; Gallois, Philippe; de l'Aulnoit, Denis Houzé; Cao, Hua; Forzy, Gérard

2013-01-01

This paper presents a Matlab-based software (MathWorks inc.) called BioSigPlot for the visualization of multi-channel biomedical signals, particularly for the EEG. This tool is designed for researchers on both engineering and medicine who have to collaborate to visualize and analyze signals. It aims to provide a highly customizable interface for signal processing experimentation in order to plot several kinds of signals while integrating the common tools for physician. The main advantages compared to other existing programs are the multi-dataset displaying, the synchronization with video and the online processing. On top of that, this program uses object oriented programming, so that the interface can be controlled by both graphic controls and command lines. It can be used as EEGlab plug-in but, since it is not limited to EEG, it would be distributed separately. BioSigPlot is distributed free of charge (http://biosigplot.sourceforge.net), under the terms of GNU Public License for non-commercial use and open source development.

Finite element simulation and Experimental verification of Incremental Sheet metal Forming

NASA Astrophysics Data System (ADS)

Kaushik Yanamundra, Krishna; Karthikeyan, R., Dr.; Naranje, Vishal, Dr

2018-04-01

Incremental sheet metal forming is now a proven manufacturing technique that can be employed to obtain application specific, customized, symmetric or asymmetric shapes that are required by automobile or biomedical industries for specific purposes like car body parts, dental implants or knee implants. Finite element simulation of metal forming process is being performed successfully using explicit dynamics analysis of commercial FE software. The simulation is mainly useful in optimization of the process as well design of the final product. This paper focuses on simulating the incremental sheet metal forming process in ABAQUS, and validating the results using experimental methods. The shapes generated for testing are of trapezoid, dome and elliptical shapes whose G codes are written and fed into the CNC milling machine with an attached forming tool with a hemispherical bottom. The same pre-generated coordinates are used to simulate a similar machining conditions in ABAQUS and the tool forces, stresses and strains in the workpiece while machining are obtained as the output data. The forces experimentally were recorded using a dynamometer. The experimental and simulated results were then compared and thus conclusions were drawn.

Teaching biomedical applications to secondary students.

PubMed

Openshaw, S; Fleisher, A; Ljunggren, C

1999-01-01

Certain aspects of biomedical engineering applications lend themselves well to experimentation that can be done by high school students. This paper describes two experiments done during a six-week summer internship program in which two high school students used electrodes, circuit boards, and computers to mimic a sophisticated heart monitor and also to control a robotic car. Our experience suggests that simple illustrations of complex instrumentation can be effective in introducing adolescents to the biomedical engineering field.

Modeling the Effect of Temperature and Potential on the In Vitro Corrosion Performance of Biomedical Hydroxyapatite Coatings

NASA Astrophysics Data System (ADS)

Coşkun, M. İbrahim; Karahan, İsmail H.; Yücel, Yasin; Golden, Teresa D.

2016-10-01

CoCrMo biomedical alloys were coated with a hydroxyapatite layer to improve biocompatibility and in vitro corrosion performance. A fast electrodeposition process was completed in 5 minutes for the hydroxyapatite coating. Effect of the solution temperature and applied potential on the in vitro corrosion performance of the hydroxyapatite coatings was modeled by response surface methodology (RSM) coupled with central composite design (CCD). A 5-level-2-factor experimental plan designed by CCD was used; the experimental plan contained 13 coating experiments with a temperature range from 283 K to 347 K (10 °C to 74 °C) and potential range from -1.2 to -1.9 V. Corrosion potential ( E corr) of the coatings in a simulated body fluid solution was chosen as response for the model. Predicted and experimental values fitted well with an R 2 value of 0.9481. Response surface plots of the impedance and polarization resistance ( R P) were investigated. Optimized parameters for electrodeposition of hydroxyapatite were determined by RSM as solution temperature of 305.48 K (32.33 °C) and potential of -1.55 V. Hydroxyapatite coatings fabricated at optimized parameters showed excellent crystal formation and high in vitro corrosion resistance.

AggNet: Deep Learning From Crowds for Mitosis Detection in Breast Cancer Histology Images.

PubMed

Albarqouni, Shadi; Baur, Christoph; Achilles, Felix; Belagiannis, Vasileios; Demirci, Stefanie; Navab, Nassir

2016-05-01

The lack of publicly available ground-truth data has been identified as the major challenge for transferring recent developments in deep learning to the biomedical imaging domain. Though crowdsourcing has enabled annotation of large scale databases for real world images, its application for biomedical purposes requires a deeper understanding and hence, more precise definition of the actual annotation task. The fact that expert tasks are being outsourced to non-expert users may lead to noisy annotations introducing disagreement between users. Despite being a valuable resource for learning annotation models from crowdsourcing, conventional machine-learning methods may have difficulties dealing with noisy annotations during training. In this manuscript, we present a new concept for learning from crowds that handle data aggregation directly as part of the learning process of the convolutional neural network (CNN) via additional crowdsourcing layer (AggNet). Besides, we present an experimental study on learning from crowds designed to answer the following questions. 1) Can deep CNN be trained with data collected from crowdsourcing? 2) How to adapt the CNN to train on multiple types of annotation datasets (ground truth and crowd-based)? 3) How does the choice of annotation and aggregation affect the accuracy? Our experimental setup involved Annot8, a self-implemented web-platform based on Crowdflower API realizing image annotation tasks for a publicly available biomedical image database. Our results give valuable insights into the functionality of deep CNN learning from crowd annotations and prove the necessity of data aggregation integration.

Mathematical models used in segmentation and fractal methods of 2-D ultrasound images

NASA Astrophysics Data System (ADS)

Moldovanu, Simona; Moraru, Luminita; Bibicu, Dorin

2012-11-01

Mathematical models are widely used in biomedical computing. The extracted data from images using the mathematical techniques are the "pillar" achieving scientific progress in experimental, clinical, biomedical, and behavioural researches. This article deals with the representation of 2-D images and highlights the mathematical support for the segmentation operation and fractal analysis in ultrasound images. A large number of mathematical techniques are suitable to be applied during the image processing stage. The addressed topics cover the edge-based segmentation, more precisely the gradient-based edge detection and active contour model, and the region-based segmentation namely Otsu method. Another interesting mathematical approach consists of analyzing the images using the Box Counting Method (BCM) to compute the fractal dimension. The results of the paper provide explicit samples performed by various combination of methods.

A resource-saving collective approach to biomedical semantic role labeling

PubMed Central

2014-01-01

Background Biomedical semantic role labeling (BioSRL) is a natural language processing technique that identifies the semantic roles of the words or phrases in sentences describing biological processes and expresses them as predicate-argument structures (PAS’s). Currently, a major problem of BioSRL is that most systems label every node in a full parse tree independently; however, some nodes always exhibit dependency. In general SRL, collective approaches based on the Markov logic network (MLN) model have been successful in dealing with this problem. However, in BioSRL such an approach has not been attempted because it would require more training data to recognize the more specialized and diverse terms found in biomedical literature, increasing training time and computational complexity. Results We first constructed a collective BioSRL system based on MLN. This system, called collective BIOSMILE (CBIOSMILE), is trained on the BioProp corpus. To reduce the resources used in BioSRL training, we employ a tree-pruning filter to remove unlikely nodes from the parse tree and four argument candidate identifiers to retain candidate nodes in the tree. Nodes not recognized by any candidate identifier are discarded. The pruned annotated parse trees are used to train a resource-saving MLN-based system, which is referred to as resource-saving collective BIOSMILE (RCBIOSMILE). Our experimental results show that our proposed CBIOSMILE system outperforms BIOSMILE, which is the top BioSRL system. Furthermore, our proposed RCBIOSMILE maintains the same level of accuracy as CBIOSMILE using 92% less memory and 57% less training time. Conclusions This greatly improved efficiency makes RCBIOSMILE potentially suitable for training on much larger BioSRL corpora over more biomedical domains. Compared to real-world biomedical corpora, BioProp is relatively small, containing only 445 MEDLINE abstracts and 30 event triggers. It is not large enough for practical applications, such as pathway construction. We consider it of primary importance to pursue SRL training on large corpora in the future. PMID:24884358

Experimental Investigation and Thermodynamic Assessment of Phase Equilibria in the PLLA/Dioxane/Water Ternary System for Applications in the Biomedical Field.

PubMed

Ruggiero, Flavia; Netti, Paolo Antonio; Torino, Enza

2015-12-01

Fundamental understanding of thermodynamic of phase separation plays a key role in tuning the desired features of biomedical devices. In particular, phase separation of ternary solution is of remarkable interest in processes to obtain biodegradable and biocompatible architectures applied as artificial devices to repair, replace, or support damaged tissues or organs. In these perspectives, thermally induced phase separation (TIPS) is the most widely used technique to obtained porous morphologies and, in addition, among different ternary systems, polylactic acid (PLLA)/dioxane/water has given promising results and has been largely studied. However, to increase the control of TIPS-based processes and architectures, an investigation of the basic energetic phenomena occurring during phase separation is still required. Here we propose an experimental investigation of the selected ternary system by using isothermal titration calorimetric approach at different solvent/antisolvent ratio and a thermodynamic explanation related to the polymer-solvents interactions in terms of energetic contribution to the phase separation process. Furthermore, relevant information about the phase diagrams and interaction parameters of the studied systems are furnished in terms of liquid-liquid miscibility gap. Indeed, polymer-solvents interactions are responsible for the mechanism of the phase separation process and, therefore, of the final features of the morphologies; the knowledge of such data is fundamental to control processes for the production of membranes, scaffolds and several nanostructures. The behavior of the polymer at different solvent/nonsolvent ratios is discussed in terms of solvation mechanism and a preliminary contribution to the understanding of the role of the hydrogen bonding in the interface phenomena is also reported. It is the first time that thermodynamic data of a ternary system are collected by mean of nano-isothermal titration calorimetry (nano-ITC). Supporting Information is available.

Image cloning beyond diffraction based on coherent population trapping in a hot rubidium vapor.

PubMed

Ding, Dong-Sheng; Zhou, Zhi-Yuan; Shi, Bao-Sen

2014-01-15

Following recent theoretical predictions, we report on an experimental realization of image cloning beyond usual diffraction, through the coherent population trapping (CPT) effect in a hot rubidium vapor. In our experiment, an alphabet letter image was transferred from a coupling field to a probe field, based on the CPT effect. Furthermore, we demonstrate that the cloned probe field carrying the image is transmitted without the usual diffraction. To our best knowledge, this is the first experimental report about image cloning beyond diffraction. We believe this mechanism, based on CPT, has definite and important applications in image metrology, image processing, and biomedical imaging.

CALL FOR PAPERS: Special cluster in Biomedical Optics: honouring Professor Valery Tuchin, Saratov University

NASA Astrophysics Data System (ADS)

Wang, Ruikang K.; Priezzhev, Alexander; Fantini, Sergio

2004-07-01

To honour Professor Valery Tuchin, one of the pioneers in biomedical optics, Journal of Physics D: Applied Physics invites manuscript submissions on topics in biomedical optics, for publication in a Special section in May 2005. Papers may cover a variety of topics related to photon propagation in turbid media, spectroscopy and imaging. This Special cluster will reflect the diversity, breadth and impact of Professor Tuchin's contributions to the field of biomedical optics over the course of his distinguished career. Biomedical optics is a recently emerged discipline providing a broad variety of optical techniques and instruments for diagnostic, therapeutic and basic science applications. Together with contributions from other pioneers in the field, Professor Tuchin's work on fundamental and experimental aspects in tissue optics contributed enormously to the formation of this exciting field. Although general submissions in biomedical optics are invited, the Special cluster Editors especially encourage submissions in areas that are explicitly or implicitly influenced by Professor Tuchin's contributions to the field of biomedical optics. Manuscripts submitted to this Special cluster of Journal of Physics D: Applied Physics will be refereed according to the normal criteria and procedures of the journal, in accordance with the following schedule: Deadline for receipt of contributed papers: 31 November 2004 Deadline for acceptance and completion of refereeing process: 28 February 2005 Publication of special issue: May 2005 Please submit your manuscript electronically to jphysd@iop.org or via the Web site at www.iop.org/Journals. Otherwise, please send a copy of your typescript, a set of original figures and a cover letter to: The Publishing Administrator, Journal of Physics D: Applied Physics, Institute of Physics Publishing, Dirac House, Temple Back, Bristol BS1 6BE, United Kingdom. Further information on how to submit may be obtained upon request by e-mailing the journal at the above address. Alternatively, visit the homepage of the journal on the World Wide Web (http://www.iop.org/journals/jphysd)

Size-controlled magnetic nanoparticles with lecithin for biomedical applications

NASA Astrophysics Data System (ADS)

Park, S. I.; Kim, J. H.; Kim, C. G.; Kim, C. O.

2007-05-01

Lecithin-adsorbed magnetic nanoparticles were prepared by three-step process that the thermal decomposition was combined with ultrasonication. Experimental parameters were three items—molar ratio between Fe(CO) 5 and oleic acid, keeping time at decomposition temperature and lecithin concentration. As the molar ratio between Fe(CO) 5 and oleic acid, and keeping time at decomposition temperature increased, the particle size increased. However, the change of lecithin concentration did not show the remarkable particle size variation.

Commercial opportunities in bioseparations and physiological testing aboard Space Station Freedom

NASA Technical Reports Server (NTRS)

Hymer, W. C.

1992-01-01

The Center for Cell Research (CCR) is a NASA Center for the Commercial Development of Space which has as its main goal encouraging industry-driven biomedical/biotechnology space projects. Space Station Freedom (SSF) will provide long duration, crew-tended microgravity environments which will enhance the opportunities for commercial biomedical/biotechnology projects in bioseparations and physiological testing. The CCR bioseparations program, known as USCEPS (for United States Commercial Electrophoresis Program in Space), is developing access for American industry to continuous-flow electrophoresis aboard SSF. In space, considerable scale-up of continuous free-flow electrophoresis is possible for cells, sub cellular particles, proteins, growth factors, and other biological products. The lack of sedemination and buoyancy-driven convection flow enhances purity of separations and the amount of material processed/time. Through the CCR's physiological testing program, commercial organizations will have access aboard SSF to physiological systems experiments (PSE's); the Penn State Biomodule; and telemicroscopy. Physiological systems experiments involve the use of live animals for pharmaceutical product testing and discovery research. The Penn State Biomodule is a computer-controlled mini lab useful for projects involving live cells or tissues and macro molecular assembly studies, including protein crystallization. Telemicroscopy will enable staff on Earth to manipulate and monitor microscopic specimens on SSF for product development and discovery research or for medical diagnosis of astronaut health problems. Space-based product processing, testing, development, and discovery research using USCEPS and CCR's physiological testing program offer new routes to improved health on Earth. Direct crew involvement-in biomedical/biotechnology projects aboard SSF will enable better experimental outcomes. The current data base shows that there is reason for considerable optimism regarding what the CCDS program and the biomedical/biotechnology industry can expect to gain from a permanent manned presence in space.

Literature Mining for the Discovery of Hidden Connections between Drugs, Genes and Diseases

PubMed Central

Frijters, Raoul; van Vugt, Marianne; Smeets, Ruben; van Schaik, René; de Vlieg, Jacob; Alkema, Wynand

2010-01-01

The scientific literature represents a rich source for retrieval of knowledge on associations between biomedical concepts such as genes, diseases and cellular processes. A commonly used method to establish relationships between biomedical concepts from literature is co-occurrence. Apart from its use in knowledge retrieval, the co-occurrence method is also well-suited to discover new, hidden relationships between biomedical concepts following a simple ABC-principle, in which A and C have no direct relationship, but are connected via shared B-intermediates. In this paper we describe CoPub Discovery, a tool that mines the literature for new relationships between biomedical concepts. Statistical analysis using ROC curves showed that CoPub Discovery performed well over a wide range of settings and keyword thesauri. We subsequently used CoPub Discovery to search for new relationships between genes, drugs, pathways and diseases. Several of the newly found relationships were validated using independent literature sources. In addition, new predicted relationships between compounds and cell proliferation were validated and confirmed experimentally in an in vitro cell proliferation assay. The results show that CoPub Discovery is able to identify novel associations between genes, drugs, pathways and diseases that have a high probability of being biologically valid. This makes CoPub Discovery a useful tool to unravel the mechanisms behind disease, to find novel drug targets, or to find novel applications for existing drugs. PMID:20885778

EASE (Experimental Assembly of Structures in EVA) overview of selected results

NASA Technical Reports Server (NTRS)

Akin, David L.

1987-01-01

Experimental Assembly of Structures in EVA (EASE) objectives, experimental protocol, neutral buoyancy simulation, task time distribution, assembly task performance, metabolic rate/biomedical readouts are summarized. This presentation is shown in charts, figures, and graphs.

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

PubMed

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.

An electro-amalgamation approach to isolate no-carrier-added 177Lu from neutron irradiated Yb for biomedical applications.

PubMed

Chakravarty, Rubel; Das, Tapas; Dash, Ashutosh; Venkatesh, Meera

2010-10-01

A novel two-step separation process for the production of no-carrier-added (NCA) (177)Lu from neutron irradiated Yb target through an electrochemical pathway employing mercury-pool cathode has been developed. A two-cycle electrolysis procedure was adopted for separation of (177)Lu from (177)Lu/Yb mixture in lithium citrate medium. The influence of different experimental parameters on the separation process was investigated and optimized for the quantitative deposition of Yb in presence of (177)Lu. The first electrolysis was performed for 50 min in the (177)Lu/Yb feed solution at pH 6 applying a potential of 8 V using platinum electrode as anode and mercury as the cathode. The second electrolysis was performed under the same conditions using fresh electrodes. The radionuclidic and chemical purity of (177)Lu was determined by using gamma ray spectrometry and atomic absorption spectrometry. The suitability of (177)Lu for biomedical applications was ascertained by labeling 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid D-Phe(1)-Tyr(3)-octreotate(DOTA-TATE) with (177)Lu. This process could provide NCA (177)Lu with >99.99% radionuclidic purity and an overall separation yield of ∼99% was achieved within 3-4 h. The Hg content in the product was determined to be <1 ppm. Radiolabeling yield of >98% was obtained with DOTA-TATE under the optimized reaction conditions. An efficient strategy for the separation of NCA (177)Lu, suitable for biomedical applications, has been developed. Copyright © 2010 Elsevier Inc. All rights reserved.

Determination of effective atomic number of biomedical samples using Gamma ray back-scattering

NASA Astrophysics Data System (ADS)

Singh, Inderjeet; Singh, Bhajan; Sandhu, B. S.; Sabharwal, Arvind D.

2018-05-01

The study of effective atomic number of biomedical sample has been carried out by using a non-destructive multiple back-scattering technique. Also radiation characterization method is used to compare the tissue equivalent material as human tissue. Response function of 3″ × 3″ NaI(Tl) scintillation detector is implemented on recorded pulse-height distribution to boost the counts under the photo-peak and help to reduce the uncertainty in the experimental result. Monte Carlo calculation for multiple back-scattered events supports the reported experimental work.

RysannMD: A biomedical semantic annotator balancing speed and accuracy.

PubMed

Cuzzola, John; Jovanović, Jelena; Bagheri, Ebrahim

2017-07-01

Recently, both researchers and practitioners have explored the possibility of semantically annotating large and continuously evolving collections of biomedical texts such as research papers, medical reports, and physician notes in order to enable their efficient and effective management and use in clinical practice or research laboratories. Such annotations can be automatically generated by biomedical semantic annotators - tools that are specifically designed for detecting and disambiguating biomedical concepts mentioned in text. The biomedical community has already presented several solid automated semantic annotators. However, the existing tools are either strong in their disambiguation capacity, i.e., the ability to identify the correct biomedical concept for a given piece of text among several candidate concepts, or they excel in their processing time, i.e., work very efficiently, but none of the semantic annotation tools reported in the literature has both of these qualities. In this paper, we present RysannMD (Ryerson Semantic Annotator for Medical Domain), a biomedical semantic annotation tool that strikes a balance between processing time and performance while disambiguating biomedical terms. In other words, RysannMD provides reasonable disambiguation performance when choosing the right sense for a biomedical term in a given context, and does that in a reasonable time. To examine how RysannMD stands with respect to the state of the art biomedical semantic annotators, we have conducted a series of experiments using standard benchmarking corpora, including both gold and silver standards, and four modern biomedical semantic annotators, namely cTAKES, MetaMap, NOBLE Coder, and Neji. The annotators were compared with respect to the quality of the produced annotations measured against gold and silver standards using precision, recall, and F 1 measure and speed, i.e., processing time. In the experiments, RysannMD achieved the best median F 1 measure across the benchmarking corpora, independent of the standard used (silver/gold), biomedical subdomain, and document size. In terms of the annotation speed, RysannMD scored the second best median processing time across all the experiments. The obtained results indicate that RysannMD offers the best performance among the examined semantic annotators when both quality of annotation and speed are considered simultaneously. Copyright © 2017 Elsevier Inc. All rights reserved.

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life.

PubMed

Kaput, Jim; van Ommen, Ben; Kremer, Bas; Priami, Corrado; Monteiro, Jacqueline Pontes; Morine, Melissa; Pepping, Fre; Diaz, Zoey; Fenech, Michael; He, Yiwu; Albers, Ruud; Drevon, Christian A; Evelo, Chris T; Hancock, Robert E W; Ijsselmuiden, Carel; Lumey, L H; Minihane, Anne-Marie; Muller, Michael; Murgia, Chiara; Radonjic, Marijana; Sobral, Bruno; West, Keith P

2014-01-01

Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum's one gene-one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of health and disease processes requiring measurements of physiological processes, as well as environmental and social factors, which may alter the expression of genetic information. Analysis of physiological processes with omics technologies to assess systems' responses has only become available over the past decade and remains costly. Studies of environmental and social conditions known to alter health are often not connected to biomedical research. While these facts are widely accepted, developing and conducting comprehensive research programs for health are often beyond financial and human resources of single research groups. We propose a new research program on essential nutrients for optimal underpinning of growth and health (ENOUGH) that will use systems approaches with more comprehensive measurements and biostatistical analysis of the many biological and environmental factors that influence undernutrition. Creating a knowledge base for nutrition and health is a necessary first step toward developing solutions targeted to different populations in diverse social and physical environments for the two billion undernourished people in developed and developing economies.

Plasmonic nanoparticle-generated photothermal bubbles and their biomedical applications

PubMed Central

Lapotko, Dmitri

2009-01-01

This article is focused on the optical generation and detection of photothermal vapor bubbles around plasmonic nanoparticles. We report physical properties of such plasmonic nanobubbles and their biomedical applications as cellular probes. Our experimental studies of gold nanoparticle-generated photothermal bubbles demonstrated the selectivity of photothermal bubble generation, amplification of optical scattering and thermal insulation effect, all realized at the nanoscale. The generation and imaging of photothermal bubbles in living cells (leukemia and carcinoma culture and primary cancerous cells), and tissues (atherosclerotic plaque and solid tumor in animal) demonstrated a noninvasive highly sensitive imaging of target cells by small photothermal bubbles and a selective mechanical, nonthermal damage to the individual target cells by bigger photothermal bubbles due to a rapid disruption of cellular membranes. The analysis of the plasmonic nanobubbles suggests them as theranostic probes, which can be tuned and optically guided at cell level from diagnosis to delivery and therapy during one fast process. PMID:19839816

XCEDE: An Extensible Schema For Biomedical Data

PubMed Central

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

2013-01-01

The XCEDE (XML-based Clinical and Experimental Data Exchange) XML schema, developed by members of the BIRN (Biomedical Informatics Research Network), provides an extensive metadata hierarchy for storing, describing and documenting the data generated by scientific studies. Currently at version 2.0, the XCEDE schema serves as a specification for the exchange of scientific data between databases, analysis tools, and web services. It provides a structured metadata hierarchy, storing information relevant to various aspects of an experiment (project, subject, protocol, etc.). Each hierarchy level also provides for the storage of data provenance information allowing for a traceable record of processing and/or changes to the underlying data. The schema is extensible to support the needs of various data modalities and to express types of data not originally envisioned by the developers. The latest version of the XCEDE schema and manual are available from http://www.xcede.org/ PMID:21479735

Biomedical Simulation Models of Human Auditory Processes

NASA Technical Reports Server (NTRS)

Bicak, Mehmet M. A.

2012-01-01

Detailed acoustic engineering models that explore noise propagation mechanisms associated with noise attenuation and transmission paths created when using hearing protectors such as earplugs and headsets in high noise environments. Biomedical finite element (FE) models are developed based on volume Computed Tomography scan data which provides explicit external ear, ear canal, middle ear ossicular bones and cochlea geometry. Results from these studies have enabled a greater understanding of hearing protector to flesh dynamics as well as prioritizing noise propagation mechanisms. Prioritization of noise mechanisms can form an essential framework for exploration of new design principles and methods in both earplug and earcup applications. These models are currently being used in development of a novel hearing protection evaluation system that can provide experimentally correlated psychoacoustic noise attenuation. Moreover, these FE models can be used to simulate the effects of blast related impulse noise on human auditory mechanisms and brain tissue.

Irreproducibility in Preclinical Biomedical Research: Perceptions, Uncertainties, and Knowledge Gaps.

PubMed

Jarvis, Michael F; Williams, Michael

2016-04-01

Concerns regarding the reliability of biomedical research outcomes were precipitated by two independent reports from the pharmaceutical industry that documented a lack of reproducibility in preclinical research in the areas of oncology, endocrinology, and hematology. Given their potential impact on public health, these concerns have been extensively covered in the media. Assessing the magnitude and scope of irreproducibility is limited by the anecdotal nature of the initial reports and a lack of quantitative data on specific failures to reproduce published research. Nevertheless, remediation activities have focused on needed enhancements in transparency and consistency in the reporting of experimental methodologies and results. While such initiatives can effectively bridge knowledge gaps and facilitate best practices across established and emerging research disciplines and therapeutic areas, concerns remain on how these improve on the historical process of independent replication in validating research findings and their potential to inhibit scientific innovation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Soviet space flight: the human element.

PubMed

Garshnek, V

1988-05-01

Building on past experience and knowledge, the Soviet manned space flight effort has become broad, comprehensive, and forward-looking. Their long-running space station program has provided the capabilities to investigate long-term effects of microgravity on human physiology and behavior and test various countermeasures against microgravity-induced physiological deconditioning. Since the beginning of Soviet manned space flight, the biomedical training and preparation of cosmonauts has evolved from a process that increased human tolerance to space flight factors, to a system of interrelated measures to prepare cosmonauts physically and psychologically to live and work in space. Currently, the Soviet Union is constructing a multimodular space station, the Mir. With the emergence of dedicated laboratory modules, the Soviets have begun the transition from small-scale experimental research to large-scale production activities and specialized scientific work in space. In the future, additional laboratory modules will be added, including one dedicated to biomedical research, called the "Medilab." The longest manned space flight to date (326 days) has been completed by the Soviets. The biomedical effects of previous long-duration flights, and perhaps those of still greater length, may contribute important insight ito the possibility of extended missions beyond Earth, such as a voyage to Mars.

Biologically Relevant Heterogeneity: Metrics and Practical Insights.

PubMed

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

2017-03-01

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

How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries

PubMed Central

Yewdell, Jonathan W.

2009-01-01

Making discoveries is the most important part of being a scientist, and also the most fun. Young scientists need to develop the experimental and mental skill sets that enable them to make discoveries, including how to recognize and exploit serendipity when it strikes. Here, I provide practical advice to young scientists on choosing a research topic, designing, performing and interpreting experiments and, last but not least, on maintaining your sanity in the process. PMID:18401347

Probabilistic reasoning in data analysis.

PubMed

Sirovich, Lawrence

2011-09-20

This Teaching Resource provides lecture notes, slides, and a student assignment for a lecture on probabilistic reasoning in the analysis of biological data. General probabilistic frameworks are introduced, and a number of standard probability distributions are described using simple intuitive ideas. Particular attention is focused on random arrivals that are independent of prior history (Markovian events), with an emphasis on waiting times, Poisson processes, and Poisson probability distributions. The use of these various probability distributions is applied to biomedical problems, including several classic experimental studies.

How to succeed in science: a concise guide for young biomedical scientists. Part II: making discoveries.

PubMed

Yewdell, Jonathan W

2008-06-01

Making discoveries is the most important part of being a scientist, and also the most fun. Young scientists need to develop the experimental and mental skill sets that enable them to make discoveries, including how to recognize and exploit serendipity when it strikes. Here, I provide practical advice to young scientists on choosing a research topic, designing, performing and interpreting experiments and, last but not least, on maintaining your sanity in the process.

Evaluating efforts to diversify the biomedical workforce: the role and function of the Coordination and Evaluation Center of the Diversity Program Consortium.

PubMed

McCreath, Heather E; Norris, Keith C; Calderόn, Nancy E; Purnell, Dawn L; Maccalla, Nicole M G; Seeman, Teresa E

2017-01-01

The National Institutes of Health (NIH)-funded Diversity Program Consortium (DPC) includes a Coordination and Evaluation Center (CEC) to conduct a longitudinal evaluation of the two signature, national NIH initiatives - the Building Infrastructure Leading to Diversity (BUILD) and the National Research Mentoring Network (NRMN) programs - designed to promote diversity in the NIH-funded biomedical, behavioral, clinical, and social sciences research workforce. Evaluation is central to understanding the impact of the consortium activities. This article reviews the role and function of the CEC and the collaborative processes and achievements critical to establishing empirical evidence regarding the efficacy of federally-funded, quasi-experimental interventions across multiple sites. The integrated DPC evaluation is particularly significant because it is a collaboratively developed Consortium Wide Evaluation Plan and the first hypothesis-driven, large-scale systemic national longitudinal evaluation of training programs in the history of NIH/National Institute of General Medical Sciences. To guide the longitudinal evaluation, the CEC-led literature review defined key indicators at critical training and career transition points - or Hallmarks of Success. The multidimensional, comprehensive evaluation of the impact of the DPC framed by these Hallmarks is described. This evaluation uses both established and newly developed common measures across sites, and rigorous quasi-experimental designs within novel multi-methods (qualitative and quantitative). The CEC also promotes shared learning among Consortium partners through working groups and provides technical assistance to support high-quality process and outcome evaluation internally of each program. Finally, the CEC is responsible for developing high-impact dissemination channels for best practices to inform peer institutions, NIH, and other key national and international stakeholders. A strong longitudinal evaluation across programs allows the summative assessment of outcomes, an understanding of factors common to interventions that do and do not lead to success, and elucidates the processes developed for data collection and management. This will provide a framework for the assessment of other training programs and have national implications in transforming biomedical research training.

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

PubMed Central

Schwede, Torsten; Sali, Andrej; Honig, Barry; Levitt, Michael; Berman, Helen M.; Jones, David; Brenner, Steven E.; Burley, Stephen K.; Das, Rhiju; Dokholyan, Nikolay V.; Dunbrack, Roland L.; Fidelis, Krzysztof; Fiser, Andras; Godzik, Adam; Huang, Yuanpeng Janet; Humblet, Christine; Jacobson, Matthew P.; Joachimiak, Andrzej; Krystek, Stanley R.; Kortemme, Tanja; Kryshtafovych, Andriy; Montelione, Gaetano T.; Moult, John; Murray, Diana; Sanchez, Roberto; Sosnick, Tobin R.; Standley, Daron M.; Stouch, Terry; Vajda, Sandor; Vasquez, Max; Westbrook, John D.; Wilson, Ian A.

2009-01-01

Summary We describe the proceedings and conclusions from a “Workshop on Applications of Protein Models in Biomedical Research” that was held at University of California at San Francisco on 11 and 12 July, 2008. At the workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) what the requirements and challenges for different applications are, and (iii) how the interaction between the computational and experimental research communities could be strengthened to advance the field. PMID:19217386

Evaluating the effects of an integrated medical ethics curriculum on first-year students.

PubMed

Chin, Jacqueline J L; Voo, Teck Chuan; Karim, Syahirah Abdul; Chan, Yiong Huak; Campbell, Alastair V

2011-01-01

An integrated biomedical ethics track was implemented as part of the new medical undergraduate curriculum at the National University of Singapore Yong Loo Lin School of Medicine in academic year (AY) 2008/2009. This study analyses the effects of the new curriculum on fi rst-year students' knowledge, confidence and opinions in relation to the subject. In a cohort-based quasi-experimental study, we administered a pre-course and post-course questionnaire to a group of fi rst-year students in AY2008/2009 who underwent the new biomedical ethics curriculum. The same questionnaire was carried out with the fi rst-year cohort of AY2007/2008, who had received only ad hoc teaching in biomedical ethics. The questionnaire focused on the students' opinions on selected taught topics in biomedical ethics and law, and formal ethics education; their confidence in relation to specific clinical ethical competencies; and their knowledge of selected taught topics in the fi rst-year syllabus. The experimental cohort acquired more knowledge and confidence. They rated more positively formal ethics teaching and assessment as a requirement of medical education. Attitudes were found to have been 'professionalised' within the experimental group, with significantly greater receptiveness towards ethical codes of the profession and the regulatory role of the Singapore Medical Council. They were found to be more conservative with respect to legislative changes in healthcare. The pioneer biomedical ethics curriculum had significant effects on the ethical development of fi rst-year medical students. Longitudinal research through further phases of the integrated curriculum is needed to identify learning issues that affect the consolidation of knowledge, confidence and attitudes in medical ethics, law and professionalism.

Expanding the Basic Science Debate: The Role of Physics Knowledge in Interpreting Clinical Findings

ERIC Educational Resources Information Center

Goldszmidt, Mark; Minda, John Paul; Devantier, Sarah L.; Skye, Aimee L.; Woods, Nicole N.

2012-01-01

Current research suggests a role for biomedical knowledge in learning and retaining concepts related to medical diagnosis. However, learning may be influenced by other, non-biomedical knowledge. We explored this idea using an experimental design and examined the effects of causal knowledge on the learning, retention, and interpretation of medical…

Influence on surface characteristics of electron beam melting process (EBM) by varying the process parameters

NASA Astrophysics Data System (ADS)

Dolimont, Adrien; Michotte, Sebastien; Rivière-Lorphèvre, Edouard; Ducobu, François; Vivès, Solange; Godet, Stéphane; Henkes, Tom; Filippi, Enrico

2017-10-01

The use of additive manufacturing processes keeps growing in aerospace and biomedical industry. Among the numerous existing technologies, the Electron Beam Melting process has advantages (good dimensional accuracy, fully dense parts) and disadvantages (powder handling, support structure, high surface roughness). Analyzes of the surface characteristics are interesting to get a better understanding of the EBM operations. But that kind of analyzes is not often found in the literature. The main goal of this study is to determine if it is possible to improve the surface roughness by modifying some parameters of the process (scan speed function, number of contours, order of contours, etc.) on samples with different thicknesses. The experimental work on the surface roughness leads to a statistical analysis of 586 measures of EBM simple geometry parts.

Text Mining in Biomedical Domain with Emphasis on Document Clustering.

PubMed

Renganathan, Vinaitheerthan

2017-07-01

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

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

PubMed Central

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

2011-01-01

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

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

PubMed

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

2011-01-01

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

Eventogram: A Visual Representation of Main Events in Biomedical Signals.

PubMed

Elgendi, Mohamed

2016-09-22

Biomedical signals carry valuable physiological information and many researchers have difficulty interpreting and analyzing long-term, one-dimensional, quasi-periodic biomedical signals. Traditionally, biomedical signals are analyzed and visualized using periodogram, spectrogram, and wavelet methods. However, these methods do not offer an informative visualization of main events within the processed signal. This paper attempts to provide an event-related framework to overcome the drawbacks of the traditional visualization methods and describe the main events within the biomedical signal in terms of duration and morphology. Electrocardiogram and photoplethysmogram signals are used in the analysis to demonstrate the differences between the traditional visualization methods, and their performance is compared against the proposed method, referred to as the " eventogram " in this paper. The proposed method is based on two event-related moving averages that visualizes the main time-domain events in the processed biomedical signals. The traditional visualization methods were unable to find dominant events in processed signals while the eventogram was able to visualize dominant events in signals in terms of duration and morphology. Moreover, eventogram -based detection algorithms succeeded with detecting main events in different biomedical signals with a sensitivity and positive predictivity >95%. The output of the eventogram captured unique patterns and signatures of physiological events, which could be used to visualize and identify abnormal waveforms in any quasi-periodic signal.

The GAAIN Entity Mapper: An Active-Learning System for Medical Data Mapping.

PubMed

Ashish, Naveen; Dewan, Peehoo; Toga, Arthur W

2015-01-01

This work is focused on mapping biomedical datasets to a common representation, as an integral part of data harmonization for integrated biomedical data access and sharing. We present GEM, an intelligent software assistant for automated data mapping across different datasets or from a dataset to a common data model. The GEM system automates data mapping by providing precise suggestions for data element mappings. It leverages the detailed metadata about elements in associated dataset documentation such as data dictionaries that are typically available with biomedical datasets. It employs unsupervised text mining techniques to determine similarity between data elements and also employs machine-learning classifiers to identify element matches. It further provides an active-learning capability where the process of training the GEM system is optimized. Our experimental evaluations show that the GEM system provides highly accurate data mappings (over 90% accuracy) for real datasets of thousands of data elements each, in the Alzheimer's disease research domain. Further, the effort in training the system for new datasets is also optimized. We are currently employing the GEM system to map Alzheimer's disease datasets from around the globe into a common representation, as part of a global Alzheimer's disease integrated data sharing and analysis network called GAAIN. GEM achieves significantly higher data mapping accuracy for biomedical datasets compared to other state-of-the-art tools for database schema matching that have similar functionality. With the use of active-learning capabilities, the user effort in training the system is minimal.

The GAAIN Entity Mapper: An Active-Learning System for Medical Data Mapping

PubMed Central

Ashish, Naveen; Dewan, Peehoo; Toga, Arthur W.

2016-01-01

This work is focused on mapping biomedical datasets to a common representation, as an integral part of data harmonization for integrated biomedical data access and sharing. We present GEM, an intelligent software assistant for automated data mapping across different datasets or from a dataset to a common data model. The GEM system automates data mapping by providing precise suggestions for data element mappings. It leverages the detailed metadata about elements in associated dataset documentation such as data dictionaries that are typically available with biomedical datasets. It employs unsupervised text mining techniques to determine similarity between data elements and also employs machine-learning classifiers to identify element matches. It further provides an active-learning capability where the process of training the GEM system is optimized. Our experimental evaluations show that the GEM system provides highly accurate data mappings (over 90% accuracy) for real datasets of thousands of data elements each, in the Alzheimer's disease research domain. Further, the effort in training the system for new datasets is also optimized. We are currently employing the GEM system to map Alzheimer's disease datasets from around the globe into a common representation, as part of a global Alzheimer's disease integrated data sharing and analysis network called GAAIN1. GEM achieves significantly higher data mapping accuracy for biomedical datasets compared to other state-of-the-art tools for database schema matching that have similar functionality. With the use of active-learning capabilities, the user effort in training the system is minimal. PMID:26793094

The Importance of Context: Risk-based De-identification of Biomedical Data.

PubMed

Prasser, Fabian; Kohlmayer, Florian; Kuhn, Klaus A

2016-08-05

Data sharing is a central aspect of modern biomedical research. It is accompanied by significant privacy concerns and often data needs to be protected from re-identification. With methods of de-identification datasets can be transformed in such a way that it becomes extremely difficult to link their records to identified individuals. The most important challenge in this process is to find an adequate balance between an increase in privacy and a decrease in data quality. Accurately measuring the risk of re-identification in a specific data sharing scenario is an important aspect of data de-identification. Overestimation of risks will significantly deteriorate data quality, while underestimation will leave data prone to attacks on privacy. Several models have been proposed for measuring risks, but there is a lack of generic methods for risk-based data de-identification. The aim of the work described in this article was to bridge this gap and to show how the quality of de-identified datasets can be improved by using risk models to tailor the process of de-identification to a concrete context. We implemented a generic de-identification process and several models for measuring re-identification risks into the ARX de-identification tool for biomedical data. By integrating the methods into an existing framework, we were able to automatically transform datasets in such a way that information loss is minimized while it is ensured that re-identification risks meet a user-defined threshold. We performed an extensive experimental evaluation to analyze the impact of using different risk models and assumptions about the goals and the background knowledge of an attacker on the quality of de-identified data. The results of our experiments show that data quality can be improved significantly by using risk models for data de-identification. On a scale where 100 % represents the original input dataset and 0 % represents a dataset from which all information has been removed, the loss of information content could be reduced by up to 10 % when protecting datasets against strong adversaries and by up to 24 % when protecting datasets against weaker adversaries. The methods studied in this article are well suited for protecting sensitive biomedical data and our implementation is available as open-source software. Our results can be used by data custodians to increase the information content of de-identified data by tailoring the process to a specific data sharing scenario. Improving data quality is important for fostering the adoption of de-identification methods in biomedical research.

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

PubMed

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

2007-11-27

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

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

PubMed Central

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

2007-01-01

Background A huge amount of biomedical textual information has been produced and collected in MEDLINE for decades. In order to easily utilize biomedical information in the free text, document clustering and text summarization together are used as a solution for text information overload problem. In this paper, we introduce a coherent graph-based semantic clustering and summarization approach for biomedical literature. Results Our extensive experimental results show the approach shows 45% cluster quality improvement and 72% clustering reliability improvement, in terms of misclassification index, over Bisecting K-means as a leading document clustering approach. In addition, our approach provides concise but rich text summary in key concepts and sentences. Conclusion Our coherent biomedical literature clustering and summarization approach that takes advantage of ontology-enriched graphical representations significantly improves the quality of document clusters and understandability of documents through summaries. PMID:18047705

Biomedical and Human Factors Requirements for a Manned Earth-Orbiting Station

NASA Technical Reports Server (NTRS)

Reynolds, J. B.

1963-01-01

The study reported here has presented a measurement data pool for the determination of biomedical and behavioral effects of long-term exposure to weightlessness. This includes measures, techniques, equipment, and requirements in terms of weight, power, volume, time, crew activities, subsystem interfaces and experimental programs and designs, and confidence ratings for their effectiveness for determining weightlessness effects.

Text Mining in Biomedical Domain with Emphasis on Document Clustering

PubMed Central

2017-01-01

Objectives With the exponential increase in the number of articles published every year in the biomedical domain, there is a need to build automated systems to extract unknown information from the articles published. Text mining techniques enable the extraction of unknown knowledge from unstructured documents. Methods This paper reviews text mining processes in detail and the software tools available to carry out text mining. It also reviews the roles and applications of text mining in the biomedical domain. Results Text mining processes, such as search and retrieval of documents, pre-processing of documents, natural language processing, methods for text clustering, and methods for text classification are described in detail. Conclusions Text mining techniques can facilitate the mining of vast amounts of knowledge on a given topic from published biomedical research articles and draw meaningful conclusions that are not possible otherwise. PMID:28875048

Predicting Silk Fiber Mechanical Properties through Multiscale Simulation and Protein Design.

PubMed

Rim, Nae-Gyune; Roberts, Erin G; Ebrahimi, Davoud; Dinjaski, Nina; Jacobsen, Matthew M; Martín-Moldes, Zaira; Buehler, Markus J; Kaplan, David L; Wong, Joyce Y

2017-08-14

Silk is a promising material for biomedical applications, and much research is focused on how application-specific, mechanical properties of silk can be designed synthetically through proper amino acid sequences and processing parameters. This protocol describes an iterative process between research disciplines that combines simulation, genetic synthesis, and fiber analysis to better design silk fibers with specific mechanical properties. Computational methods are used to assess the protein polymer structure as it forms an interconnected fiber network through shearing and how this process affects fiber mechanical properties. Model outcomes are validated experimentally with the genetic design of protein polymers that match the simulation structures, fiber fabrication from these polymers, and mechanical testing of these fibers. Through iterative feedback between computation, genetic synthesis, and fiber mechanical testing, this protocol will enable a priori prediction capability of recombinant material mechanical properties via insights from the resulting molecular architecture of the fiber network based entirely on the initial protein monomer composition. This style of protocol may be applied to other fields where a research team seeks to design a biomaterial with biomedical application-specific properties. This protocol highlights when and how the three research groups (simulation, synthesis, and engineering) should be interacting to arrive at the most effective method for predictive design of their material.

A DNA network as an information processing system.

PubMed

Santini, Cristina Costa; Bath, Jonathan; Turberfield, Andrew J; Tyrrell, Andy M

2012-01-01

Biomolecular systems that can process information are sought for computational applications, because of their potential for parallelism and miniaturization and because their biocompatibility also makes them suitable for future biomedical applications. DNA has been used to design machines, motors, finite automata, logic gates, reaction networks and logic programs, amongst many other structures and dynamic behaviours. Here we design and program a synthetic DNA network to implement computational paradigms abstracted from cellular regulatory networks. These show information processing properties that are desirable in artificial, engineered molecular systems, including robustness of the output in relation to different sources of variation. We show the results of numerical simulations of the dynamic behaviour of the network and preliminary experimental analysis of its main components.

RX for science literacy: The what, where, how, and why of health science research (A teacher`s manual about biomedical research)

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

Hoffman, K.S.

1994-12-31

When the North Carolina Association for Biomedical Research (NCABR) surveyed the state`s science teachers in March 1993, 92% of those responding requested information related to biomedical research. Most of the teachers requested lesson plans and activities designed to help them give students an accurate and balanced perspective on research. In response to that need, NCABR has recently completed production of a 300-page teacher`s manual that provides an overview of the biomedical research process and describes the role and care of animals in that process. Rx for Science Literacy incorporates background information, lesson plans, handouts and activities to assist teachers inmore » K-12 classrooms. Developed by a science teacher with assistance from science and education experts, the manual captures the complex biomedical research process in an easy-to-follow, easy-to-use format. In North Carolina, NCABR plans to begin these workshops in fall 1994. The workshops will include a tour of a biomedical research laboratory and on-site presentations by bench scientists. Teacher evaluation of the manual will be structured into the workshop program. The manual is available at cost to all interested individuals and organizations.« less

Biomedical scientists' perception of the social sciences in health research.

PubMed

Albert, Mathieu; Laberge, Suzanne; Hodges, Brian D; Regehr, Glenn; Lingard, Lorelei

2008-06-01

The growing interest in interdisciplinary research within the Canadian health sciences sector has been manifested by initiatives aimed at increasing the involvement of the social sciences in this sector. Drawing on Bourdieu's concept of field and Knorr-Cetina's concept of epistemic culture, this study explores the extent to which it is possible for the social sciences to integrate into, and thrive in, a field in which the experimental paradigm occupies a hegemonic position. Thirty-one semi-structured interviews were conducted to explore biomedical scientists' receptiveness toward the social sciences in general and to qualitative research in particular. We found that these respondents exhibited a predominantly negative posture toward the social sciences; however, we also found considerable variation in their judgments and explanations. Eight biomedical scientists tended to be receptive to the social sciences, 7 ambivalent, and 16 unreceptive. The main rationale expressed by receptive respondents is that the legitimacy of a method depends on its capacity to adequately respond to a research question and not on its conformity to the experimental canon. Unreceptive respondents maintained that the social sciences cannot generate valid and reliable results because they are not conducive to the experimental design as a methodological approach. Ambivalent respondents were characterized by their cautiously accepting posture toward the social sciences and, especially, by their reservations about qualitative methods. Based on the biomedical scientists' limited receptiveness, we can anticipate that the growth of the social sciences will continue to meet obstacles within the health research field in the near future in Canada.

New frontiers in biomedical science and engineering during 2014-2015.

PubMed

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.

Biostatistical analysis of quantitative immunofluorescence microscopy images.

PubMed

Giles, C; Albrecht, M A; Lam, V; Takechi, R; Mamo, J C

2016-12-01

Semiquantitative immunofluorescence microscopy has become a key methodology in biomedical research. Typical statistical workflows are considered in the context of avoiding pseudo-replication and marginalising experimental error. However, immunofluorescence microscopy naturally generates hierarchically structured data that can be leveraged to improve statistical power and enrich biological interpretation. Herein, we describe a robust distribution fitting procedure and compare several statistical tests, outlining their potential advantages/disadvantages in the context of biological interpretation. Further, we describe tractable procedures for power analysis that incorporates the underlying distribution, sample size and number of images captured per sample. The procedures outlined have significant potential for increasing understanding of biological processes and decreasing both ethical and financial burden through experimental optimization. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

A multiple distributed representation method based on neural network for biomedical event extraction.

PubMed

Wang, Anran; Wang, Jian; Lin, Hongfei; Zhang, Jianhai; Yang, Zhihao; Xu, Kan

2017-12-20

Biomedical event extraction is one of the most frontier domains in biomedical research. The two main subtasks of biomedical event extraction are trigger identification and arguments detection which can both be considered as classification problems. However, traditional state-of-the-art methods are based on support vector machine (SVM) with massive manually designed one-hot represented features, which require enormous work but lack semantic relation among words. In this paper, we propose a multiple distributed representation method for biomedical event extraction. The method combines context consisting of dependency-based word embedding, and task-based features represented in a distributed way as the input of deep learning models to train deep learning models. Finally, we used softmax classifier to label the example candidates. The experimental results on Multi-Level Event Extraction (MLEE) corpus show higher F-scores of 77.97% in trigger identification and 58.31% in overall compared to the state-of-the-art SVM method. Our distributed representation method for biomedical event extraction avoids the problems of semantic gap and dimension disaster from traditional one-hot representation methods. The promising results demonstrate that our proposed method is effective for biomedical event extraction.

Biomedical discovery acceleration, with applications to craniofacial development.

PubMed

Leach, Sonia M; Tipney, Hannah; Feng, Weiguo; Baumgartner, William A; Kasliwal, Priyanka; Schuyler, Ronald P; Williams, Trevor; Spritz, Richard A; Hunter, Lawrence

2009-03-01

The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning, and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or using biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. An implementation of this approach, called the Hanalyzer, is demonstrated on a large-scale gene expression array dataset relevant to craniofacial development. The use of the tool was critical in the creation of hypotheses regarding the roles of four genes never previously characterized as involved in craniofacial development; each of these hypotheses was validated by further experimental work.

Schofield memorial lecture. Bull semen and muscle ATP: some evidence of the dawn of medical science in ancient Egypt.

PubMed Central

Schwabe, C W

1986-01-01

The importance of animal experimentation to human and animal health is not well understood by an increasingly articulate segment of the public. This could have very unfortunate consequences for man and his domestic animals. Even veterinarians and physicians are not as conversant as they need be about the great extent to which advances in human health have depended upon animal observations and experiments. Some believe that resort to "animal models" of biomedical phenomena, including diseases--a comparative or analogical approach to medical studies--is a relatively recent event. Even medical historians often treat these subjects as occasionally recurring aberrations which began with the Greeks, thus largely overlooking the historical meaning and continuing importance of "one medicine" irrespective of species. In fact, comparative medicine has probably been basic to medical progress ever since the dawn of a medical science. Recent research indicates that this approach to biomedical mysteries began to evolve in the minds of Egypt's healer-priests long before Aristotle and the later Alexandrian Greeks made the whole process explicit. Here we examine the origins of what were possibly the first two biomedical theories profounded from inferences based upon dissections, confirmed in at least one instance by experiment, and then applied to medical practice. PMID:3530413

Biologically Relevant Heterogeneity: Metrics and Practical Insights

PubMed Central

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

2017-01-01

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

Designing biomedical proteomics experiments: state-of-the-art and future perspectives.

PubMed

Maes, Evelyne; Kelchtermans, Pieter; Bittremieux, Wout; De Grave, Kurt; Degroeve, Sven; Hooyberghs, Jef; Mertens, Inge; Baggerman, Geert; Ramon, Jan; Laukens, Kris; Martens, Lennart; Valkenborg, Dirk

2016-05-01

With the current expanded technical capabilities to perform mass spectrometry-based biomedical proteomics experiments, an improved focus on the design of experiments is crucial. As it is clear that ignoring the importance of a good design leads to an unprecedented rate of false discoveries which would poison our results, more and more tools are developed to help researchers designing proteomic experiments. In this review, we apply statistical thinking to go through the entire proteomics workflow for biomarker discovery and validation and relate the considerations that should be made at the level of hypothesis building, technology selection, experimental design and the optimization of the experimental parameters.

Data management integration for biomedical core facilities

NASA Astrophysics Data System (ADS)

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

2007-03-01

We present the design, development, and pilot-deployment experiences of MIMI, a web-based, Multi-modality Multi-Resource Information Integration environment for biomedical core facilities. This is an easily customizable, web-based software tool that integrates scientific and administrative support for a biomedical core facility involving a common set of entities: researchers; projects; equipments and devices; support staff; services; samples and materials; experimental workflow; large and complex data. With this software, one can: register users; manage projects; schedule resources; bill services; perform site-wide search; archive, back-up, and share data. With its customizable, expandable, and scalable characteristics, MIMI not only provides a cost-effective solution to the overarching data management problem of biomedical core facilities unavailable in the market place, but also lays a foundation for data federation to facilitate and support discovery-driven research.

GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction.

PubMed

Yu, Yao; Tu, Kang; Zheng, Siyuan; Li, Yun; Ding, Guohui; Ping, Jie; Hao, Pei; Li, Yixue

2009-08-25

In the post-genomic era, the development of high-throughput gene expression detection technology provides huge amounts of experimental data, which challenges the traditional pipelines for data processing and analyzing in scientific researches. In our work, we integrated gene expression information from Gene Expression Omnibus (GEO), biomedical ontology from Medical Subject Headings (MeSH) and signaling pathway knowledge from sigPathway entries to develop a context mining tool for gene expression analysis - GEOGLE. GEOGLE offers a rapid and convenient way for searching relevant experimental datasets, pathways and biological terms according to multiple types of queries: including biomedical vocabularies, GDS IDs, gene IDs, pathway names and signature list. Moreover, GEOGLE summarizes the signature genes from a subset of GDSes and estimates the correlation between gene expression and the phenotypic distinction with an integrated p value. This approach performing global searching of expression data may expand the traditional way of collecting heterogeneous gene expression experiment data. GEOGLE is a novel tool that provides researchers a quantitative way to understand the correlation between gene expression and phenotypic distinction through meta-analysis of gene expression datasets from different experiments, as well as the biological meaning behind. The web site and user guide of GEOGLE are available at: http://omics.biosino.org:14000/kweb/workflow.jsp?id=00020.

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

NASA Astrophysics Data System (ADS)

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

1987-09-01

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

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

PubMed Central

2012-01-01

Background 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. Results 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. Conclusions 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. PMID:22901054

UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text.

PubMed

Demner-Fushman, Dina; Mork, James G; Shooshan, Sonya E; Aronson, Alan R

2010-08-01

Identification of medical terms in free text is a first step in such Natural Language Processing (NLP) tasks as automatic indexing of biomedical literature and extraction of patients' problem lists from the text of clinical notes. Many tools developed to perform these tasks use biomedical knowledge encoded in the Unified Medical Language System (UMLS) Metathesaurus. We continue our exploration of automatic approaches to creation of subsets (UMLS content views) which can support NLP processing of either the biomedical literature or clinical text. We found that suppression of highly ambiguous terms in the conservative AutoFilter content view can partially replace manual filtering for literature applications, and suppression of two character mappings in the same content view achieves 89.5% precision at 78.6% recall for clinical applications. Published by Elsevier Inc.

Evaluating the operational risks of biomedical waste using failure mode and effects analysis.

PubMed

Chen, Ying-Chu; Tsai, Pei-Yi

2017-06-01

The potential problems and risks of biomedical waste generation have become increasingly apparent in recent years. This study applied a failure mode and effects analysis to evaluate the operational problems and risks of biomedical waste. The microbiological contamination of biomedical waste seldom receives the attention of researchers. In this study, the biomedical waste lifecycle was divided into seven processes: Production, classification, packaging, sterilisation, weighing, storage, and transportation. Twenty main failure modes were identified in these phases and risks were assessed based on their risk priority numbers. The failure modes in the production phase accounted for the highest proportion of the risk priority number score (27.7%). In the packaging phase, the failure mode 'sharp articles not placed in solid containers' had the highest risk priority number score, mainly owing to its high severity rating. The sterilisation process is the main difference in the treatment of infectious and non-infectious biomedical waste. The failure modes in the sterilisation phase were mainly owing to human factors (mostly related to operators). This study increases the understanding of the potential problems and risks associated with biomedical waste, thereby increasing awareness of how to improve the management of biomedical waste to better protect workers, the public, and the environment.

Mathematical modeling and experimental testing of three bioreactor configurations based on windkessel models

PubMed Central

Ruel, Jean; Lachance, Geneviève

2010-01-01

This paper presents an experimental study of three bioreactor configurations. The bioreactor is intended to be used for the development of tissue-engineered heart valve substitutes. Therefore it must be able to reproduce physiological flow and pressure waveforms accurately. A detailed analysis of three bioreactor arrangements is presented using mathematical models based on the windkessel (WK) approach. First, a review of the many applications of this approach in medical studies enhances its fundamental nature and its usefulness. Then the models are developed with reference to the actual components of the bioreactor. This study emphasizes different conflicting issues arising in the design process of a bioreactor for biomedical purposes, where an optimization process is essential to reach a compromise satisfying all conditions. Two important aspects are the need for a simple system providing ease of use and long-term sterility, opposed to the need for an advanced (thus more complex) architecture capable of a more accurate reproduction of the physiological environment. Three classic WK architectures are analyzed, and experimental results enhance the advantages and limitations of each one. PMID:21977286

Density functional theory calculations of biomolecules adsorption on phosphorene for biomedical applications

NASA Astrophysics Data System (ADS)

Rubio-Pereda, Pamela; H. Cocoletzi, Gregorio

2018-01-01

Recent experimental studies have found that phosphorene, the two-dimensional counterpart of black phosphorus, is more biological-friendly, in comparison with graphene, for the design of bio-integrated electronics based devices for biomedical applications. Following this research line, we theoretically investigate by first principle calculations, accounting for van der Waals effects, the interactions between phosphorene and typical amino acids (nonpolar, aromatic, positively charged and negatively charged). Testing different possible molecular orientations adsorption calculations have been done. Structural analysis, Löwdin electron population analysis and the study of the hydrophobic effect upon adsorption orientation were carried out in order to reveal the nature of the composite system interactions. Results show that amino acid molecules physisorb, mediated by an electron transfer process, on the phosphorene surface with a minimum disruption of their structure. Furthermore, the hydrophilic nature of phosphorene dictates the more energetically preferred adsorbed amino acid orientation. Ultimately, the nature of these interactions manifests the biological-friendly characteristic of phosphorene and its potential to be used as part of bioinorganic interfaces.

High sensitivity pressure transducer based on the phase characteristics of GMI magnetic sensors

NASA Astrophysics Data System (ADS)

Benavides, L. S.; Costa Silva, E.; Costa Monteiro, E.; Hall Barbosa, C. R.

2018-03-01

This paper presents a new configuration for a GMI pressure transducer based on the reading of the phase characteristics of GMI sensor, intended for biomedical applications. The development process of this new class of magnetic field transducers is discussed, beginning with the definition of the ideal conditioning of the GMI sensor elements (dc level and frequency of the excitation current and sample length) and continuing with computational simulations of the full electronic circuit performed using the experimental data obtained from measured GMI curves, and have shown that the improvement in the sensitivity of GMI magnetometers is larger when phase-based transducers are used instead of magnitude-based transducers. Parameters of interest of the developed prototype are thoroughly analyzed, such as: sensitivity, linearity and frequency response. Also, the spectral noise density of the developed pressure transducer is evaluated and its resolution in the passband is estimated. A low-cost GMI pressure transducer was developed, presenting high resolution, high sensitivity and a frequency bandwidth compatible to the desired biomedical applications.

The fluid transport in inkjet-printed liquid rivulets

NASA Astrophysics Data System (ADS)

Singler, Timothy; Liu, Liang; Sun, Xiaoze; Pei, Yunheng; Microfluidic; Interfacial Transport Lab Team

2017-11-01

Inkjet printing holds significant potential for the controlled deposition of solution-processed functional materials spanning applications from microelectronics to biomedical sciences. Although theoretical and experimental investigations addressing the stability criteria of the inkjet-printed liquid rivulets have been discussed in the literature, the associated transport phenomena have received little attention. This study focuses on the experimental investigation of printed rivulets, stable with respect to Rayleigh-Plateau, but exhibiting bulge instability. The morphological evolution and the depth-resolved flow field of the rivulets were assessed via high-speed imaging in conjunction with micro-PIV. We discuss in detail effects of repetitive wave motion induced by periodic drop impact at the leading edge and the associated pulsatile flow, as well as the persistent nonuniform mass distribution in the ridge region of the rivulet. The results provide an experimental foundation for more detailed theoretical modelling of printed rivulet flows.

Astronaut Kenneth Reightler processes biomedical samples in SPACEHAB

NASA Image and Video Library

1994-02-09

STS060-301-003 (3-11 Feb 1994) --- Astronaut Kenneth S. Reightler, STS-60 pilot, processes biomedical samples in a centrifuge aboard the SPACEHAB module. Reightler joined four other NASA astronauts and a Russian cosmonaut for eight days of research aboard the Space Shuttle Discovery.

Photochemical coatings for the prevention of bacterial colonization.

PubMed

Dunkirk, S G; Gregg, S L; Duran, L W; Monfils, J D; Haapala, J E; Marcy, J A; Clapper, D L; Amos, R A; Guire, P E

1991-10-01

Biomaterials are being used with increasing frequency for tissue substitution. Implantable, prosthetic devices are instrumental in the saving of patients' lives and enhancing the quality of life for many others. However, the greatest barrier to expanding the use of biomedical devices is the high probability of bacterial adherence and proliferation, causing very difficult and often untreatable medical-device centered infections. The difficulty in treating such infections results in great danger to the patient, and usually retrieval of the device with considerable pain and suffering. Clearly, development of processes that make biomedical devices resistant to bacterial adherence and colonization would have widespread application in the field of biomedical technology. A photochemical surface modification process is being investigated as a generic means of applying antimicrobial coatings to biomedical devices. The photochemical process results in covalent immobilization of coatings to all classes of medical device polymers. A discussion of the photochemical surface modification process and preliminary results demonstrating the success of photochemical coatings in formulating microbial-resistant surfaces are presented in this paper.

A Machine Learning-based Method for Question Type Classification in Biomedical Question Answering.

PubMed

Sarrouti, Mourad; Ouatik El Alaoui, Said

2017-05-18

Biomedical question type classification is one of the important components of an automatic biomedical question answering system. The performance of the latter depends directly on the performance of its biomedical question type classification system, which consists of assigning a category to each question in order to determine the appropriate answer extraction algorithm. This study aims to automatically classify biomedical questions into one of the four categories: (1) yes/no, (2) factoid, (3) list, and (4) summary. In this paper, we propose a biomedical question type classification method based on machine learning approaches to automatically assign a category to a biomedical question. First, we extract features from biomedical questions using the proposed handcrafted lexico-syntactic patterns. Then, we feed these features for machine-learning algorithms. Finally, the class label is predicted using the trained classifiers. Experimental evaluations performed on large standard annotated datasets of biomedical questions, provided by the BioASQ challenge, demonstrated that our method exhibits significant improved performance when compared to four baseline systems. The proposed method achieves a roughly 10-point increase over the best baseline in terms of accuracy. Moreover, the obtained results show that using handcrafted lexico-syntactic patterns as features' provider of support vector machine (SVM) lead to the highest accuracy of 89.40 %. The proposed method can automatically classify BioASQ questions into one of the four categories: yes/no, factoid, list, and summary. Furthermore, the results demonstrated that our method produced the best classification performance compared to four baseline systems.

In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions

NASA Astrophysics Data System (ADS)

Mwaffo, Violet; Butail, Sachit; Porfiri, Maurizio

2017-01-01

Zebrafish is fast becoming a species of choice in biomedical research for the investigation of functional and dysfunctional processes coupled with their genetic and pharmacological modulation. As with mammals, experimentation with zebrafish constitutes a complicated ethical issue that calls for the exploration of alternative testing methods to reduce the number of subjects, refine experimental designs, and replace live animals. Inspired by the demonstrated advantages of computational studies in other life science domains, we establish an authentic data-driven modelling framework to simulate zebrafish swimming in three dimensions. The model encapsulates burst-and-coast swimming style, speed modulation, and wall interaction, laying the foundations for in-silico experiments of zebrafish behaviour. Through computational studies, we demonstrate the ability of the model to replicate common ethological observables such as speed and spatial preference, and anticipate experimental observations on the correlation between tank dimensions on zebrafish behaviour. Reaching to other experimental paradigms, our framework is expected to contribute to a reduction in animal use and suffering.

In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions

PubMed Central

Mwaffo, Violet; Butail, Sachit; Porfiri, Maurizio

2017-01-01

Zebrafish is fast becoming a species of choice in biomedical research for the investigation of functional and dysfunctional processes coupled with their genetic and pharmacological modulation. As with mammals, experimentation with zebrafish constitutes a complicated ethical issue that calls for the exploration of alternative testing methods to reduce the number of subjects, refine experimental designs, and replace live animals. Inspired by the demonstrated advantages of computational studies in other life science domains, we establish an authentic data-driven modelling framework to simulate zebrafish swimming in three dimensions. The model encapsulates burst-and-coast swimming style, speed modulation, and wall interaction, laying the foundations for in-silico experiments of zebrafish behaviour. Through computational studies, we demonstrate the ability of the model to replicate common ethological observables such as speed and spatial preference, and anticipate experimental observations on the correlation between tank dimensions on zebrafish behaviour. Reaching to other experimental paradigms, our framework is expected to contribute to a reduction in animal use and suffering. PMID:28071731

Figure mining for biomedical research.

PubMed

Rodriguez-Esteban, Raul; Iossifov, Ivan

2009-08-15

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

Histochemistry in biology and medicine: a message from the citing journals.

PubMed

Pellicciari, Carlo

2015-12-23

Especially in recent years, biomedical research has taken advantage of the progress in several disciplines, among which microscopy and histochemistry. To assess the influence of histochemistry in the biomedical field, the articles published during the period 2011-2015 have been selected from different databases and grouped by subject categories: as expected, biological and biomedical studies where histochemistry has been used as a major experimental approach include a wide of basic and applied researches on both humans and other animal or plant organisms. To better understand the impact of histochemical publications onto the different biological and medical disciplines, it was useful to look at the journals where the articles published in a multidisciplinary journal of histochemistry have been cited: it was observed that, in the five-years period considered, 20% only of the citations were in histochemical periodicals, the remaining ones being in journals of Cell & Tissue biology,  general and experimental Medicine, Oncology, Biochemistry & Molecular biology, Neurobiology, Anatomy & Morphology, Pharmacology & Toxicology, Reproductive biology, Veterinary sciences, Physiology, Endocrinology, Tissue engineering & Biomaterials,  as well as in multidisciplinary journals.It is easy to foresee that also in the future the histochemical journals will be an attended forum for basic and applied scientists in the biomedical field. It will be crucial that these journals be open to an audience as varied as possible, publishing articles on the application of refined techniques to very different experimental models: this will stimulate non-histochemist scientists to approach histochemistry whose application horizon could expand to novel and possibly exclusive subjects.

Histochemistry in Biology and Medicine: A Message From the Citing Journals

PubMed Central

2015-01-01

Especially in recent years, biomedical research has taken advantage of the progress in several disciplines, among which microscopy and histochemistry. To assess the influence of histochemistry in the biomedical field, the articles published during the period 2011-2015 have been selected from different databases and grouped by subject categories. As expected, biological and biomedical studies where histochemistry has been used as a major experimental approach include a wide range of basic and applied researches on both humans and other animal or plant organisms. To better understand the impact of histochemical publications onto the different biological and medical disciplines, it was useful to look at the journals where the articles published in a multidisciplinary journal of histochemistry have been cited: it was observed that, in the five-years period considered, 20% only of the citations were in histochemical periodicals, the remaining ones being in journals of Cell & Tissue biology, general and experimental Medicine, Oncology, Biochemistry & Molecular biology, Neurobiology, Anatomy & Morphology, Pharmacology & Toxicology, Reproductive biology, Veterinary sciences, Physiology, Endocrinology, Tissue engineering & Biomaterials, as well as in multidisciplinary journals. It is easy to foresee that also in the future the histochemical journals will be an attended forum for basic and applied scientists in the biomedical field. It will be crucial that these journals be open to an audience as varied as possible, publishing articles on the application of refined techniques to very different experimental models: this will stimulate non-histochemist scientists to approach histochemistry whose application horizon could expand to novel and possibly exclusive subjects. PMID:26708189

A modular framework for biomedical concept recognition

PubMed Central

2013-01-01

Background Concept recognition is an essential task in biomedical information extraction, presenting several complex and unsolved challenges. The development of such solutions is typically performed in an ad-hoc manner or using general information extraction frameworks, which are not optimized for the biomedical domain and normally require the integration of complex external libraries and/or the development of custom tools. Results This article presents Neji, an open source framework optimized for biomedical concept recognition built around four key characteristics: modularity, scalability, speed, and usability. It integrates modules for biomedical natural language processing, such as sentence splitting, tokenization, lemmatization, part-of-speech tagging, chunking and dependency parsing. Concept recognition is provided through dictionary matching and machine learning with normalization methods. Neji also integrates an innovative concept tree implementation, supporting overlapped concept names and respective disambiguation techniques. The most popular input and output formats, namely Pubmed XML, IeXML, CoNLL and A1, are also supported. On top of the built-in functionalities, developers and researchers can implement new processing modules or pipelines, or use the provided command-line interface tool to build their own solutions, applying the most appropriate techniques to identify heterogeneous biomedical concepts. Neji was evaluated against three gold standard corpora with heterogeneous biomedical concepts (CRAFT, AnEM and NCBI disease corpus), achieving high performance results on named entity recognition (F1-measure for overlap matching: species 95%, cell 92%, cellular components 83%, gene and proteins 76%, chemicals 65%, biological processes and molecular functions 63%, disorders 85%, and anatomical entities 82%) and on entity normalization (F1-measure for overlap name matching and correct identifier included in the returned list of identifiers: species 88%, cell 71%, cellular components 72%, gene and proteins 64%, chemicals 53%, and biological processes and molecular functions 40%). Neji provides fast and multi-threaded data processing, annotating up to 1200 sentences/second when using dictionary-based concept identification. Conclusions Considering the provided features and underlying characteristics, we believe that Neji is an important contribution to the biomedical community, streamlining the development of complex concept recognition solutions. Neji is freely available at http://bioinformatics.ua.pt/neji. PMID:24063607

Generation of open biomedical datasets through ontology-driven transformation and integration processes.

PubMed

Carmen Legaz-García, María Del; Miñarro-Giménez, José Antonio; Menárguez-Tortosa, Marcos; Fernández-Breis, Jesualdo Tomás

2016-06-03

Biomedical research usually requires combining large volumes of data from multiple heterogeneous sources, which makes difficult the integrated exploitation of such data. The Semantic Web paradigm offers a natural technological space for data integration and exploitation by generating content readable by machines. Linked Open Data is a Semantic Web initiative that promotes the publication and sharing of data in machine readable semantic formats. We present an approach for the transformation and integration of heterogeneous biomedical data with the objective of generating open biomedical datasets in Semantic Web formats. The transformation of the data is based on the mappings between the entities of the data schema and the ontological infrastructure that provides the meaning to the content. Our approach permits different types of mappings and includes the possibility of defining complex transformation patterns. Once the mappings are defined, they can be automatically applied to datasets to generate logically consistent content and the mappings can be reused in further transformation processes. The results of our research are (1) a common transformation and integration process for heterogeneous biomedical data; (2) the application of Linked Open Data principles to generate interoperable, open, biomedical datasets; (3) a software tool, called SWIT, that implements the approach. In this paper we also describe how we have applied SWIT in different biomedical scenarios and some lessons learned. We have presented an approach that is able to generate open biomedical repositories in Semantic Web formats. SWIT is able to apply the Linked Open Data principles in the generation of the datasets, so allowing for linking their content to external repositories and creating linked open datasets. SWIT datasets may contain data from multiple sources and schemas, thus becoming integrated datasets.

Advances in biomedical engineering and biotechnology during 2013-2014.

PubMed

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.

Technical brief: a comparison of two methods of euthanasia on retinal dopamine levels.

PubMed

Hwang, Christopher K; Iuvone, P Michael

2013-01-01

Mice are commonly used in biomedical research, and euthanasia is an important part of mouse husbandry. Approved, humane methods of euthanasia are designed to minimize the potential for pain or discomfort, but may also influence the measurement of experimental variables. We compared the effects of two approved methods of mouse euthanasia on the levels of retinal dopamine. We examined the level of retinal dopamine, a commonly studied neuromodulator, following euthanasia by carbon dioxide (CO₂)-induced asphyxiation or by cervical dislocation. We found that the level of retinal dopamine in mice euthanized through CO₂ overdose substantially differed from that in mice euthanized through cervical dislocation. The use of CO₂ as a method of euthanasia could result in an experimental artifact that could compromise results when studying labile biologic processes.

Learning to Rank Figures within a Biomedical Article

PubMed Central

Liu, Feifan; Yu, Hong

2014-01-01

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. This ever-increasing sheer volume has made it difficult for scientists to effectively and accurately access figures of their interest, the process of which is crucial for validating research facts and for formulating or testing novel research hypotheses. Current figure search applications can't fully meet this challenge as the “bag of figures” assumption doesn't take into account the relationship among figures. In our previous study, hundreds of biomedical researchers have annotated articles in which they serve as corresponding authors. They ranked each figure in their paper based on a figure's importance at their discretion, referred to as “figure ranking”. Using this collection of annotated data, we investigated computational approaches to automatically rank figures. We exploited and extended the state-of-the-art listwise learning-to-rank algorithms and developed a new supervised-learning model BioFigRank. The cross-validation results show that BioFigRank yielded the best performance compared with other state-of-the-art computational models, and the greedy feature selection can further boost the ranking performance significantly. Furthermore, we carry out the evaluation by comparing BioFigRank with three-level competitive domain-specific human experts: (1) First Author, (2) Non-Author-In-Domain-Expert who is not the author nor co-author of an article but who works in the same field of the corresponding author of the article, and (3) Non-Author-Out-Domain-Expert who is not the author nor co-author of an article and who may or may not work in the same field of the corresponding author of an article. Our results show that BioFigRank outperforms Non-Author-Out-Domain-Expert and performs as well as Non-Author-In-Domain-Expert. Although BioFigRank underperforms First Author, since most biomedical researchers are either in- or out-domain-experts for an article, we conclude that BioFigRank represents an artificial intelligence system that offers expert-level intelligence to help biomedical researchers to navigate increasingly proliferated big data efficiently. PMID:24625719

Learning to rank figures within a biomedical article.

PubMed

Liu, Feifan; Yu, Hong

2014-01-01

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. This ever-increasing sheer volume has made it difficult for scientists to effectively and accurately access figures of their interest, the process of which is crucial for validating research facts and for formulating or testing novel research hypotheses. Current figure search applications can't fully meet this challenge as the "bag of figures" assumption doesn't take into account the relationship among figures. In our previous study, hundreds of biomedical researchers have annotated articles in which they serve as corresponding authors. They ranked each figure in their paper based on a figure's importance at their discretion, referred to as "figure ranking". Using this collection of annotated data, we investigated computational approaches to automatically rank figures. We exploited and extended the state-of-the-art listwise learning-to-rank algorithms and developed a new supervised-learning model BioFigRank. The cross-validation results show that BioFigRank yielded the best performance compared with other state-of-the-art computational models, and the greedy feature selection can further boost the ranking performance significantly. Furthermore, we carry out the evaluation by comparing BioFigRank with three-level competitive domain-specific human experts: (1) First Author, (2) Non-Author-In-Domain-Expert who is not the author nor co-author of an article but who works in the same field of the corresponding author of the article, and (3) Non-Author-Out-Domain-Expert who is not the author nor co-author of an article and who may or may not work in the same field of the corresponding author of an article. Our results show that BioFigRank outperforms Non-Author-Out-Domain-Expert and performs as well as Non-Author-In-Domain-Expert. Although BioFigRank underperforms First Author, since most biomedical researchers are either in- or out-domain-experts for an article, we conclude that BioFigRank represents an artificial intelligence system that offers expert-level intelligence to help biomedical researchers to navigate increasingly proliferated big data efficiently.

DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures

PubMed Central

Yin, Xu-Cheng; Yang, Chun; Pei, Wei-Yi; Man, Haixia; Zhang, Jun; Learned-Miller, Erik; Yu, Hong

2015-01-01

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. Since text is a rich source of information in figures, automatically extracting such text may assist in the task of mining figure information. A high-quality ground truth standard can greatly facilitate the development of an automated system. This article describes DeTEXT: A database for evaluating text extraction from biomedical literature figures. It is the first publicly available, human-annotated, high quality, and large-scale figure-text dataset with 288 full-text articles, 500 biomedical figures, and 9308 text regions. This article describes how figures were selected from open-access full-text biomedical articles and how annotation guidelines and annotation tools were developed. We also discuss the inter-annotator agreement and the reliability of the annotations. We summarize the statistics of the DeTEXT data and make available evaluation protocols for DeTEXT. Finally we lay out challenges we observed in the automated detection and recognition of figure text and discuss research directions in this area. DeTEXT is publicly available for downloading at http://prir.ustb.edu.cn/DeTEXT/. PMID:25951377

Segregation of biomedical waste in an South Indian tertiary care hospital.

PubMed

Sengodan, Vetrivel Chezian

2014-07-01

Hospital wastes pose significant public health hazard if not properly managed. Hence, it is necessary to develop and adopt optimal waste management systems in the hospitals. Biomedical waste generated in Coimbatore Medical College Hospital was color coded (blue, yellow, and red) and the data was analyzed retrospectively on a daily basis for 3 years (January 2010-December 2012). Effective segregation protocols significantly reduced biomedical waste generated from 2011 to 2012. While biomedical waste of red category was significantly higher (>50%), the category yellow was the least. Per unit (per bed per day) total biomedical waste generated was 68.5, 68.8, and 61.3 grams in 2010, 2011, and 2012, respectively. Segregation of biomedical waste at the source of generation is the first and essential step in biomedical waste management. Continuous training, fixing the responsibility on the nursing persons, and constant supervision are the key criteria's in implementing biomedical waste segregation process, which can significantly reduce per unit biomedical waste generated. We highly recommend all hospitals to adopt our protocol and effectively implement them to reduce generation of biomedical waste.

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

PubMed

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

2013-07-01

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

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

PubMed Central

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

2013-01-01

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

Resolving Complex Research Data Management Issues in Biomedical Laboratories: Qualitative Study of an Industry-Academia Collaboration

PubMed Central

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

2016-01-01

This paper describes a distributed collaborative effort between industry and academia to systematize data management in an academic biomedical laboratory. Heterogeneous and voluminous nature of research data created in biomedical laboratories make information management difficult and research unproductive. One such collaborative effort was evaluated over a period of four years using data collection methods including ethnographic observations, semi-structured interviews, web-based surveys, progress reports, conference call summaries, and face-to-face group discussions. Data were analyzed using qualitative methods of data analysis to 1) characterize specific problems faced by biomedical researchers with traditional information management practices, 2) identify intervention areas to introduce a new research information management system called Labmatrix, and finally to 3) evaluate and delineate important general collaboration (intervention) characteristics that can optimize outcomes of an implementation process in biomedical laboratories. Results emphasize the importance of end user perseverance, human-centric interoperability evaluation, and demonstration of return on investment of effort and time of laboratory members and industry personnel for success of implementation process. In addition, there is an intrinsic learning component associated with the implementation process of an information management system. Technology transfer experience in a complex environment such as the biomedical laboratory can be eased with use of information systems that support human and cognitive interoperability. Such informatics features can also contribute to successful collaboration and hopefully to scientific productivity. PMID:26652980

Biomedical and Behavioral Research Scientists: Their Training and Supply. Volume 1: Findings.

ERIC Educational Resources Information Center

National Academy of Sciences - National Research Council, Washington, DC. Office of Scientific and Engineering Personnel.

This is the first of three volumes which presents the Committee on Biomedical and Behavioral Research Personnel's examination of the educational process that leads to doctoral degrees in biomedical and behavioral science (and to postdoctoral study in some cases) and the role of the National Research Service Awards (NRSA) training programs in it.…

Extracting biomedical events from pairs of text entities

PubMed Central

2015-01-01

Background Huge amounts of electronic biomedical documents, such as molecular biology reports or genomic papers are generated daily. Nowadays, these documents are mainly available in the form of unstructured free texts, which require heavy processing for their registration into organized databases. This organization is instrumental for information retrieval, enabling to answer the advanced queries of researchers and practitioners in biology, medicine, and related fields. Hence, the massive data flow calls for efficient automatic methods of text-mining that extract high-level information, such as biomedical events, from biomedical text. The usual computational tools of Natural Language Processing cannot be readily applied to extract these biomedical events, due to the peculiarities of the domain. Indeed, biomedical documents contain highly domain-specific jargon and syntax. These documents also describe distinctive dependencies, making text-mining in molecular biology a specific discipline. Results We address biomedical event extraction as the classification of pairs of text entities into the classes corresponding to event types. The candidate pairs of text entities are recursively provided to a multiclass classifier relying on Support Vector Machines. This recursive process extracts events involving other events as arguments. Compared to joint models based on Markov Random Fields, our model simplifies inference and hence requires shorter training and prediction times along with lower memory capacity. Compared to usual pipeline approaches, our model passes over a complex intermediate problem, while making a more extensive usage of sophisticated joint features between text entities. Our method focuses on the core event extraction of the Genia task of BioNLP challenges yielding the best result reported so far on the 2013 edition. PMID:26201478

ParaBTM: A Parallel Processing Framework for Biomedical Text Mining on Supercomputers.

PubMed

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.

Microgravity sciences application visiting scientist program

NASA Technical Reports Server (NTRS)

1994-01-01

Contract NAS8-38785, Microgravity Experimental and Theoretical Research, is a project involving a large number of individual research programs related to: determination of the structure of human serum albumin and other biomedically important proteins; analysis of thermodynamic properties of various proteins and models of protein nucleation; development of experimental techniques for the growth of protein crystals in space; study of the physics of electrical double layers in the mechanics of liquid interfaces; computational analysis of vapor crystal growth processes in microgravity; analysis of the influence of magnetic fields in damping residual flows in directional solidification processes; crystal growth and characterization of II-VI semiconductor alloys; and production of thin films for nonlinear optics. It is not intended that the programs will be necessarily limited to this set at any one time. The visiting scientists accomplishing these programs shall serve on-site at MSFC to take advantage of existing laboratory facilities and the daily opportunities for technical communications with various senior scientists.

[Application of Fourier transform profilometry in 3D-surface reconstruction].

PubMed

Shi, Bi'er; Lu, Kuan; Wang, Yingting; Li, Zhen'an; Bai, Jing

2011-08-01

With the improvement of system frame and reconstruction methods in fluorescent molecules tomography (FMT), the FMT technology has been widely used as an important experimental tool in biomedical research. It is necessary to get the 3D-surface profile of the experimental object as the boundary constraints of FMT reconstruction algorithms. We proposed a new 3D-surface reconstruction method based on Fourier transform profilometry (FTP) method under the blue-purple light condition. The slice images were reconstructed using proper image processing methods, frequency spectrum analysis and filtering. The results of experiment showed that the method properly reconstructed the 3D-surface of objects and has the mm-level accuracy. Compared to other methods, this one is simple and fast. Besides its well-reconstructed, the proposed method could help monitor the behavior of the object during the experiment to ensure the correspondence of the imaging process. Furthermore, the method chooses blue-purple light section as its light source to avoid the interference towards fluorescence imaging.

Supervised restoration of degraded medical images using multiple-point geostatistics.

PubMed

Pham, Tuan D

2012-06-01

Reducing noise in medical images has been an important issue of research and development for medical diagnosis, patient treatment, and validation of biomedical hypotheses. Noise inherently exists in medical and biological images due to the acquisition and transmission in any imaging devices. Being different from image enhancement, the purpose of image restoration is the process of removing noise from a degraded image in order to recover as much as possible its original version. This paper presents a statistically supervised approach for medical image restoration using the concept of multiple-point geostatistics. Experimental results have shown the effectiveness of the proposed technique which has potential as a new methodology for medical and biological image processing. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Strategies for Derisking Translational Processes for Biomedical Technologies.

PubMed

Abou-El-Enein, Mohamed; Duda, Georg N; Gruskin, Elliott A; Grainger, David W

2017-02-01

Inefficient translational processes for technology-oriented biomedical research have led to some prominent and frequent failures in the development of many leading drug candidates, several designated investigational drugs, and some medical devices, as well as documented patient harm and postmarket product withdrawals. Derisking this process, particularly in the early stages, should increase translational efficiency and streamline resource utilization, especially in an academic setting. In this opinion article, we identify a 12-step guideline for reducing risks typically associated with translating medical technologies as they move toward prototypes, preclinical proof of concept, and possible clinical testing. Integrating the described 12-step process should prove valuable for improving how early-stage academic biomedical concepts are cultivated, culled, and manicured toward intended clinical applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2015-01-01

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

How to locate & hire clinical/biomedical engineers, supervisors, managers & biomedical equipment technicians.

PubMed

Pacela, A F; Brush, L C

1993-01-01

This article has described the process and the resources available for locating and hiring clinical/biomedical engineers, supervisors, managers, and biomedical equipment technicians. First, the employer must determine the qualifications for the position, including job titles, descriptions, pay scales, and certification requirements. Next, the employer must find qualified applicants. The most common way to do this is to use "outside" contacts, such as help-wanted advertising, specialized job placement agencies, schools and colleges, military resources, regional biomedical societies, and nationwide societies. An "inside" search involves limited internal advertising of the position and using personal referrals for candidates. Finally, the employer must screen the applicants. The position description is the obvious first step in this process, but there are other pre-screening techniques, such as employment testing. Interviewing is the most common way to hire for job positions, but the interviewer needs to know about the position and ask the right questions. Post-interview screening is a final step to help determine the best job-person match.

Material Processing and Design of Biodegradable Metal Matrix Composites for Biomedical Applications.

PubMed

Yang, Jingxin; Guo, Jason L; Mikos, Antonios G; He, Chunyan; Cheng, Guang

2018-06-04

In recent years, biodegradable metallic materials have played an important role in biomedical applications. However, as typical for the metal materials, their structure, general properties, preparation technology and biocompatibility are hard to change. Furthermore, biodegradable metals are susceptible to excessive degradation and subsequent disruption of their mechanical integrity; this phenomenon limits the utility of these biomaterials. Therefore, the use of degradable metals, as the base material to prepare metal matrix composite materials, it is an excellent alternative to solve the problems above described. Biodegradable metals can thus be successfully combined with other materials to form biodegradable metallic matrix composites for biomedical applications and functions. The present article describes the processing methods currently available to design biodegradable metal matrix composites for biomedical applications and provides an overview of the current existing biodegradable metal systems. At the end, the manuscript presents and discusses the challenges and future research directions for development of biodegradable metallic matrix composites for biomedical purposes.

Microfluidic impact printer with interchangeable cartridges for versatile non-contact multiplexed micropatterning

PubMed Central

Ding, Yuzhe; Huang, Eric; Lam, Kit S.; Pan, Tingrui

2015-01-01

Biopatterning has been increasingly used for well-defined cellular microenvironment, patterned surface topology, and guided biological cues; however, it meets additional challenges on biocompatibility, temperature and chemical sensitivity and limited reagent volume. In this paper, we target at combining the desired features from the non-contact inkjet printing and the dot-matrix impact printing to establish a versatile multiplexed micropatterning platform, referred to as Microfluidic Impact Printer (MI-Printer), for emerging biomedical applications. Using this platform, we can achieve the distinct features of no cross-contamination, minute volume manipulation with minimal dead volume, high-throughput and biocompatible printing process, multiplexed patterning with automatic alignment, printing availability for complex medium (cell suspension or colloidal solutions), interchangeable/disposable microfluidic cartridge design with out-of-cleanroom microfabrication, simple printing system assembly and configuration, all highly desirable towards biological applications. Specifically, the printing resolution of the MI-printer platform has been experimentally characterized and theoretically analyzed. Printed droplets with 80µm in diameter have been repeatedly obtained. Furthermore, two unique features of MI-printer platform, multiplexed printing and self-alignment printing, have been successfully experimentally demonstrated (less than 10µm misalignment). In addition, combinatorial patterning and biological patterning, which utilizes the multiplexed and self-alignment printing nature of the MI-printer, have been devised to demonstrate the applicability of this robust printing technique for emerging biomedical applications. PMID:23525299

[Reduction of animal experiments in experimental drug testing].

PubMed

Behrensdorf-Nicol, H; Krämer, B

2014-10-01

In order to ensure the quality of biomedical products, an experimental test for every single manufactured batch is required for many products. Especially in vaccine testing, animal experiments are traditionally used for this purpose. For example, efficacy is often determined via challenge experiments in laboratory animals. Safety tests of vaccine batches are also mostly performed using laboratory animals. However, many animal experiments have clear inherent disadvantages (low accuracy, questionable transferability to humans, unclear significance). Furthermore, for ethical reasons and animal welfare aspects animal experiments are also seen very critical by the public. Therefore, there is a strong trend towards replacing animal experiments with methods in which no animals are used ("replacement"). If a replacement is not possible, the required animal experiments should be improved in order to minimize the number of animals necessary ("reduction") and to reduce pain and suffering caused by the experiment to a minimum ("refinement"). This "3R concept" is meanwhile firmly established in legislature. In recent years many mandatory animal experiments have been replaced by alternative in vitro methods or improved according to the 3R principles; numerous alternative methods are currently under development. Nevertheless, the process from the development of a new method to its legal implementation takes a long time. Therefore, supplementary regulatory measures to facilitate validation and acceptance of new alternative methods could contribute to a faster and more consequent implementation of the 3R concept in the testing of biomedical products.

Sensor, signal, and image informatics - state of the art and current topics.

PubMed

Lehmann, T M; Aach, T; Witte, H

2006-01-01

The number of articles published annually in the fields of biomedical signal and image acquisition and processing is increasing. Based on selected examples, this survey aims at comprehensively demonstrating the recent trends and developments. Four articles are selected for biomedical data acquisition covering topics such as dose saving in CT, C-arm X-ray imaging systems for volume imaging, and the replacement of dose-intensive CT-based diagnostic with harmonic ultrasound imaging. Regarding biomedical signal analysis (BSA), the four selected articles discuss the equivalence of different time-frequency approaches for signal analysis, an application to Cochlea implants, where time-frequency analysis is applied for controlling the replacement system, recent trends for fusion of different modalities, and the role of BSA as part of a brain machine interfaces. To cover the broad spectrum of publications in the field of biomedical image processing, six papers are focused. Important topics are content-based image retrieval in medical applications, automatic classification of tongue photographs from traditional Chinese medicine, brain perfusion analysis in single photon emission computed tomography (SPECT), model-based visualization of vascular trees, and virtual surgery, where enhanced visualization and haptic feedback techniques are combined with a sphere-filled model of the organ. The selected papers emphasize the five fields forming the chain of biomedical data processing: (1) data acquisition, (2) data reconstruction and pre-processing, (3) data handling, (4) data analysis, and (5) data visualization. Fields 1 and 2 form the sensor informatics, while fields 2 to 5 form signal or image informatics with respect to the nature of the data considered. Biomedical data acquisition and pre-processing, as well as data handling, analysis and visualization aims at providing reliable tools for decision support that improve the quality of health care. Comprehensive evaluation of the processing methods and their reliable integration in routine applications are future challenges in the field of sensor, signal and image informatics.

Multiple kernel learning in protein-protein interaction extraction from biomedical literature.

PubMed

Yang, Zhihao; Tang, Nan; Zhang, Xiao; Lin, Hongfei; Li, Yanpeng; Yang, Zhiwei

2011-03-01

Knowledge about protein-protein interactions (PPIs) unveils the molecular mechanisms of biological processes. The volume and content of published biomedical literature on protein interactions is expanding rapidly, making it increasingly difficult for interaction database administrators, responsible for content input and maintenance to detect and manually update protein interaction information. The objective of this work is to develop an effective approach to automatic extraction of PPI information from biomedical literature. We present a weighted multiple kernel learning-based approach for automatic PPI extraction from biomedical literature. The approach combines the following kernels: feature-based, tree, graph and part-of-speech (POS) path. In particular, we extend the shortest path-enclosed tree (SPT) and dependency path tree to capture richer contextual information. Our experimental results show that the combination of SPT and dependency path tree extensions contributes to the improvement of performance by almost 0.7 percentage units in F-score and 2 percentage units in area under the receiver operating characteristics curve (AUC). Combining two or more appropriately weighed individual will further improve the performance. Both on the individual corpus and cross-corpus evaluation our combined kernel can achieve state-of-the-art performance with respect to comparable evaluations, with 64.41% F-score and 88.46% AUC on the AImed corpus. As different kernels calculate the similarity between two sentences from different aspects. Our combined kernel can reduce the risk of missing important features. More specifically, we use a weighted linear combination of individual kernels instead of assigning the same weight to each individual kernel, thus allowing the introduction of each kernel to incrementally contribute to the performance improvement. In addition, SPT and dependency path tree extensions can improve the performance by including richer context information. Copyright © 2010 Elsevier B.V. All rights reserved.

Biomedical surface analysis: Evolution and future directions (Review)

PubMed Central

Castner, David G.

2017-01-01

This review describes some of the major advances made in biomedical surface analysis over the past 30–40 years. Starting from a single technique analysis of homogeneous surfaces, it has been developed into a complementary, multitechnique approach for obtaining detailed, comprehensive information about a wide range of surfaces and interfaces of interest to the biomedical community. Significant advances have been made in each surface analysis technique, as well as how the techniques are combined to provide detailed information about biological surfaces and interfaces. The driving force for these advances has been that the surface of a biomaterial is the interface between the biological environment and the biomaterial, and so, the state-of-the-art in instrumentation, experimental protocols, and data analysis methods need to be developed so that the detailed surface structure and composition of biomedical devices can be determined and related to their biological performance. Examples of these advances, as well as areas for future developments, are described for immobilized proteins, complex biomedical surfaces, nanoparticles, and 2D/3D imaging of biological materials. PMID:28438024

Enhancing biomedical text summarization using semantic relation extraction.

PubMed

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

2011-01-01

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

Biomedical informatics: development of a comprehensive data warehouse for clinical and genomic breast cancer research.

PubMed

Hu, Hai; Brzeski, Henry; Hutchins, Joe; Ramaraj, Mohan; Qu, Long; Xiong, Richard; Kalathil, Surendran; Kato, Rand; Tenkillaya, Santhosh; Carney, Jerry; Redd, Rosann; Arkalgudvenkata, Sheshkumar; Shahzad, Kashif; Scott, Richard; Cheng, Hui; Meadow, Stephen; McMichael, John; Sheu, Shwu-Lin; Rosendale, David; Kvecher, Leonid; Ahern, Stephen; Yang, Song; Zhang, Yonghong; Jordan, Rick; Somiari, Stella B; Hooke, Jeffrey; Shriver, Craig D; Somiari, Richard I; Liebman, Michael N

2004-10-01

The Windber Research Institute is an integrated high-throughput research center employing clinical, genomic and proteomic platforms to produce terabyte levels of data. We use biomedical informatics technologies to integrate all of these operations. This report includes information on a multi-year, multi-phase hybrid data warehouse project currently under development in the Institute. The purpose of the warehouse is to host the terabyte-level of internal experimentally generated data as well as data from public sources. We have previously reported on the phase I development, which integrated limited internal data sources and selected public databases. Currently, we are completing phase II development, which integrates our internal automated data sources and develops visualization tools to query across these data types. This paper summarizes our clinical and experimental operations, the data warehouse development, and the challenges we have faced. In phase III we plan to federate additional manual internal and public data sources and then to develop and adapt more data analysis and mining tools. We expect that the final implementation of the data warehouse will greatly facilitate biomedical informatics research.

Children's Naive Concepts of OCD and How They Are Affected by Biomedical Versus Cognitive Behavioural Psychoeducation.

PubMed

Butlin, B; Wilson, C

2018-04-04

How we conceptualize mental health conditions is important as it impacts on a wide range of mediators of treatment outcome. We do not know how children intuitively conceptualize obsessive-compulsive disorder (OCD), nor do we know the relative impact of biomedical or cognitive behavioural conceptual explanations, yet both are being widely used in psychoeducation for children with OCD. This study identified children's naive concepts of OCD, and the comparative impact of biomedical versus cognitive behavioural psychoeducation on perceived prognosis. A within- and between-subjects experimental design was used. After watching a video of a young person describing their OCD, 202 children completed a questionnaire examining their concepts of the condition. They repeated the questionnaire following a second equivalent video, this time preceded by either biomedical or cognitive behavioural psychoeducation. Participants' naive concepts of OCD reflected predominant models of OCD in healthcare. Even at the minimal dose of psychoeducation, participants' conceptualizations of OCD changed. Prior exposure to OCD resulted in a stronger alignment with the biomedical model. Exposure to biomedical psychoeducation resulted in participants predicting a slower recovery with less chance of complete remission. Psychoeducation for childhood OCD is impactful. Despite its wide use by clinicians and mental health services, biomedical psychoeducation appears to have deleterious effects. Children's concepts of OCD merit attention but caution should be applied in how they are targeted.

Uncertainty quantification and validation of 3D lattice scaffolds for computer-aided biomedical applications.

PubMed

Gorguluarslan, Recep M; Choi, Seung-Kyum; Saldana, Christopher J

2017-07-01

A methodology is proposed for uncertainty quantification and validation to accurately predict the mechanical response of lattice structures used in the design of scaffolds. Effective structural properties of the scaffolds are characterized using a developed multi-level stochastic upscaling process that propagates the quantified uncertainties at strut level to the lattice structure level. To obtain realistic simulation models for the stochastic upscaling process and minimize the experimental cost, high-resolution finite element models of individual struts were reconstructed from the micro-CT scan images of lattice structures which are fabricated by selective laser melting. The upscaling method facilitates the process of determining homogenized strut properties to reduce the computational cost of the detailed simulation model for the scaffold. Bayesian Information Criterion is utilized to quantify the uncertainties with parametric distributions based on the statistical data obtained from the reconstructed strut models. A systematic validation approach that can minimize the experimental cost is also developed to assess the predictive capability of the stochastic upscaling method used at the strut level and lattice structure level. In comparison with physical compression test results, the proposed methodology of linking the uncertainty quantification with the multi-level stochastic upscaling method enabled an accurate prediction of the elastic behavior of the lattice structure with minimal experimental cost by accounting for the uncertainties induced by the additive manufacturing process. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

Hengsbach, Stefan; Lantada, Andrés Díaz

2014-08-01

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

Measurement Marker Recognition In A Time Sequence Of Infrared Images For Biomedical Applications

NASA Astrophysics Data System (ADS)

Fiorini, A. R.; Fumero, R.; Marchesi, R.

1986-03-01

In thermographic measurements, quantitative surface temperature evaluation is often uncertain. The main reason is in the lack of available reference points in transient conditions. Reflective markers were used for automatic marker recognition and pixel coordinate computations. An algorithm selects marker icons to match marker references where particular luminance conditions are satisfied. Automatic marker recognition allows luminance compensation and temperature calibration of recorded infrared images. A biomedical application is presented: the dynamic behaviour of the surface temperature distributions is investigated in order to study the performance of two different pumping systems for extracorporeal circulation. Sequences of images are compared and results are discussed. Finally, the algorithm allows to monitor the experimental environment and to alert for the presence of unusual experimental conditions.

Homeopathy: clarifying its relationship to hormesis.

PubMed

Calabrese, Edward J; Jonas, Wayne B

2010-07-01

This paper presents the case that certain types of homeopathic medicine may represent a form of hormesis, that is, either pre- or post-conditioning hormesis. An example of a post-conditioning model by van Wijk and colleagues demonstrated successful enhancement of adaptive responses using below-toxic threshold doses (i.e. hormetic doses) of inducing agents when administered subsequent to a highly toxic chemical exposure, thus satisfying a basic experimental biomedical standard. Of note is that this model uses exposures within a measurable predicted hormetic range, unlike most forms of homeopathy. This experimental framework (along with a pre-conditioning model developed by Bellavite) provides a possible vehicle by which certain aspect(s) of homeopathy may be integrated into mainstream biomedical assessment and clinical practice.

Journal selection decisions: a biomedical library operations research model. I. The framework.

PubMed Central

Kraft, D H; Polacsek, R A; Soergel, L; Burns, K; Klair, A

1976-01-01

The problem of deciding which journal titles to select for acquisition in a biomedical library is modeled. The approach taken is based on cost/benefit ratios. Measures of journal worth, methods of data collection, and journal cost data are considered. The emphasis is on the development of a practical process for selecting journal titles, based on the objectivity and rationality of the model; and on the collection of the approprate data and library statistics in a reasonable manner. The implications of this process towards an overall management information system (MIS) for biomedical serials handling are discussed. PMID:820391

Semantic biomedical resource discovery: a Natural Language Processing framework.

PubMed

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

2015-09-30

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

Animal Experimentation: Issues for the 1980s.

ERIC Educational Resources Information Center

Zola, Judith C.; And Others

1984-01-01

Examines the extent to which issues related to animal experimentation are in conflict and proposes choices that might least comprise them. These issues include animal well-being, human well-being, self-interest of science, scientific validity and responsibility, progress in biomedical and behavioral science, and the future quality of medical care.…

Camera systems in human motion analysis for biomedical applications

NASA Astrophysics Data System (ADS)

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.

Segregation of biomedical waste in an South Indian tertiary care hospital

PubMed Central

Sengodan, Vetrivel Chezian

2014-01-01

Introduction: Hospital wastes pose significant public health hazard if not properly managed. Hence, it is necessary to develop and adopt optimal waste management systems in the hospitals. Material and method: Biomedical waste generated in Coimbatore Medical College Hospital was color coded (blue, yellow, and red) and the data was analyzed retrospectively on a daily basis for 3 years (January 2010-December 2012). Results: Effective segregation protocols significantly reduced biomedical waste generated from 2011 to 2012. While biomedical waste of red category was significantly higher (>50%), the category yellow was the least. Per unit (per bed per day) total biomedical waste generated was 68.5, 68.8, and 61.3 grams in 2010, 2011, and 2012, respectively. Discussion: Segregation of biomedical waste at the source of generation is the first and essential step in biomedical waste management. Continuous training, fixing the responsibility on the nursing persons, and constant supervision are the key criteria's in implementing biomedical waste segregation process, which can significantly reduce per unit biomedical waste generated. Conclusion: We highly recommend all hospitals to adopt our protocol and effectively implement them to reduce generation of biomedical waste. PMID:25097419

Software for biomedical engineering signal processing laboratory experiments.

PubMed

Tompkins, Willis J; Wilson, J

2009-01-01

In the early 1990's we developed a special computer program called UW DigiScope to provide a mechanism for anyone interested in biomedical digital signal processing to study the field without requiring any other instrument except a personal computer. There are many digital filtering and pattern recognition algorithms used in processing biomedical signals. In general, students have very limited opportunity to have hands-on access to the mechanisms of digital signal processing. In a typical course, the filters are designed non-interactively, which does not provide the student with significant understanding of the design constraints of such filters nor their actual performance characteristics. UW DigiScope 3.0 is the first major update since version 2.0 was released in 1994. This paper provides details on how the new version based on MATLAB! works with signals, including the filter design tool that is the programming interface between UW DigiScope and processing algorithms.

An Experimental and numerical Study for squeezing flow

NASA Astrophysics Data System (ADS)

Nathan, Rungun; Lang, Ji; Wu, Qianhong; Vucbmss Team

2017-11-01

We report an experimental and numerical study to examine the transient squeezing flow driven by sudden external impacts. The phenomenon is widely observed in industrial applications, e.g. squeeze dampers, or in biological systems, i.e. joints lubrication. However, there is a lack of investigation that captures the transient flow feature during the process. An experimental setup was developed that contains a piston instrumented with a laser displacement sensor and a pressure transducer. The heavy piston was released from rest, creating a fast compaction on the thin fluid gap underneath. The motion of the piston and the fluid pressure build-up was recorded. For this dynamic process, a CFD simulation was performed which shows excellent agreement with the experimental data. Both the numerical and experimental results show that, the squeezing flow starts with the inviscid limit when the viscous fluid effect has no time to appear, and thereafter becomes a developing flow, in which the inviscid core flow region decreases and the viscous wall region increases until the entire fluid gap is filled with viscous fluid flow. The study presented herein, filling the gap in the literature, will have broad impacts in industrial and biomedical applications. This research was supported by the National Science Foundation under Award 1511096, and supported by the Seed Grant from The Villanova Center for the Advancement of Sustainability in Engineering (VCASE).

Kennedy's Biomedical Laboratory Makes Multi-Tasking Look Easy

NASA Technical Reports Server (NTRS)

Dunn, Carol Anne

2009-01-01

If it is one thing that Florida has in abundance, it is sunshine and with that sunshine heat and humidity. For workers at the Kennedy Space Center that have to work outside in the heat and humidity, heat exhaustion/stroke is a real possibility. It might help people to know that Kennedy's Biomedical Laboratory has been testing some new Koolvests(Trademark) that can be worn underneath SCAPE suits. They have also been working on how to block out high noise levels; in fact, Don Doerr, chief of the Biomedical Lab, says, "The most enjoyable aspect is knowing that the Biomedical Lab and the skills of its employees have been used to support safe space flight, not only for the astronaut flight crew, but just as important for the ground processing personnel as well." The NASA Biomedical Laboratory has existed in the John F. Kennedy's Operations and Checkout Building since the Apollo Program. The primary mission of this laboratory has been the biomedical support to major, manned space programs that have included Apollo, Apollo-Soyuz, Skylab, and Shuttle. In this mission, the laboratory has been responsible in accomplishing much of the technical design, planning, provision, fabrication, and maintenance of flight and ground biomedical monitoring instrumentation. This includes the electronics in the launch flight suit and similar instrumentation systems in the spacecraft. (Note: The Lab checked out the system for STS-128 at Pad A using Firing room 4 and ground support equipment in the lab.) During Apollo, there were six engineers and ten technicians in the facility. This has evolved today to two NASA engineers and two NASA technicians, a Life Science Support contract physiologist and part-time support from an LSSC nurse and physician. Over the years, the lab has enjoyed collaboration with outside agencies and investigators. These have included on-site support to the Ames Research Center bed rest studies (seven years) and the European Space Agency studies in Toulouse, France (two years). The lab has also actively collaborated with the US Army Institute for Surgical Research, the USAF School of Aerospace Medicine, and the USN Naval Experimental Diving Unit. Because the lab often evaluates various forms of commercial-off-the-shelf life support equipment, the laboratory works closely with private companies, both domestic and foreign. The European companies seem to be more proactive and participatory with the advancement of personal protective equipment. Because these companies have viewed the space program's unique need for advanced forms of personal protective equipment, some have responded with new designs based on the prediction that these advances will soon find markets in the commercial sector. Using much of the same skills and equipment, the laboratory also addresses physiological testing of humans by supporting flight experiments and personnel involved with ground processing. While Johnson Space Center is primarily responsible for flight experiments, the Kennedy's Biomedical Lab provides the local support. However, as stated above, there are many challenges facing KSC workers that gain the attention of this lab in the measurement of the problem and the selection and testing of countermeasures. These include respiratory protection, whole body suits, hearing protection and heat stress, among many others.

Judging The Efficacy of Anthrax Fumigations

DTIC Science & Technology

2003-11-20

FUMIGATIONS IN RESPONSE TO 2001 ANTHRAX ATTACKS Most fumigations modeled after biomedical sterilization processes, with established ranges for process...exposure to VHP All BIs recovered aseptically negative for growth of B. stearothermophilus Positive control BIs (5% of BIs) demonstrate growth Negative...of 10 zones was re-fumigated; second fumigation met all requirements HISTORICAL CRITERIA FOR SUCCESSFUL TREATMENT Biomedical sterilizations – FDA

Life sciences payloads analyses and technical program planning studies. [project planning of space missions of space shuttles in aerospace medicine and space biology

NASA Technical Reports Server (NTRS)

1976-01-01

Contractural requirements, project planning, equipment specifications, and technical data for space shuttle biological experiment payloads are presented. Topics discussed are: (1) urine collection and processing on the space shuttle, (2) space processing of biochemical and biomedical materials, (3) mission simulations, and (4) biomedical equipment.

Biomedically relevant chemical and physical properties of coal combustion products.

PubMed Central

Fisher, G L

1983-01-01

The evaluation of the potential public and occupational health hazards of developing and existing combustion processes requires a detailed understanding of the physical and chemical properties of effluents available for human and environmental exposures. These processes produce complex mixtures of gases and aerosols which may interact synergistically or antagonistically with biological systems. Because of the physicochemical complexity of the effluents, the biomedically relevant properties of these materials must be carefully assessed. Subsequent to release from combustion sources, environmental interactions further complicate assessment of the toxicity of combustion products. This report provides an overview of the biomedically relevant physical and chemical properties of coal fly ash. Coal fly ash is presented as a model complex mixture for health and safety evaluation of combustion processes. PMID:6337824

Severe Plastic Deformation of Commercial Pure Titanium (CP-Ti) for Biomedical Applications: A Brief Review

NASA Astrophysics Data System (ADS)

Mahmoodian, Reza; Annuar, N. Syahira M.; Faraji, Ghader; Bahar, Nadia Dayana; Razak, Bushroa Abd; Sparham, Mahdi

2017-11-01

This paper reviews severe plastic deformation (SPD) techniques for producing ultrafine-grained (UFG) and nanostructured commercial pure titanium (CP-Ti) for biomedical applications as the best alternative to titanium alloys. SPD processes, effective parameters, and advantages of nanostructured CP-Ti over coarse-grained (CG) material and Ti alloys are briefly reviewed. It is reported that nanostructured CP-Ti processed via SPD exhibits higher mechanical strength comparable to Ti alloys but better biological response and superior biocompatibility. Also, different surface modification techniques offer different results on UFG and CG CP-Ti, leading to nanoscale surface topography in UFG samples. Overall, it is reported that nanostructured CP-Ti processed by SPD could be considered to be the best candidate for biomedical implants.

Ballistic heat transport in laser generated nano-bubbles

NASA Astrophysics Data System (ADS)

Lombard, Julien; Biben, Thierry; Merabia, Samy

2016-08-01

Nanobubbles generated by laser heated plasmonic nanoparticles are of interest for biomedical and energy harvesting applications. Of utmost importance is the maximal size of these transient bubbles. Here, we report hydrodynamic phase field simulations of the dynamics of laser induced nanobubbles, with the aim to understand which physical processes govern their maximal size. We show that the nanobubble maximal size and lifetime are to a large extent controlled by the ballistic thermal flux which is present inside the bubble. Taking into account this thermal flux, we can reproduce the fluence dependence of the maximal nanobubble radius as reported experimentally. We also discuss the influence of the laser pulse duration on the number of nanobubbles generated and their maximal size. These studies represent a significant step toward the optimization of the nanobubble size, which is of crucial importance for photothermal cancer therapy applications.Nanobubbles generated by laser heated plasmonic nanoparticles are of interest for biomedical and energy harvesting applications. Of utmost importance is the maximal size of these transient bubbles. Here, we report hydrodynamic phase field simulations of the dynamics of laser induced nanobubbles, with the aim to understand which physical processes govern their maximal size. We show that the nanobubble maximal size and lifetime are to a large extent controlled by the ballistic thermal flux which is present inside the bubble. Taking into account this thermal flux, we can reproduce the fluence dependence of the maximal nanobubble radius as reported experimentally. We also discuss the influence of the laser pulse duration on the number of nanobubbles generated and their maximal size. These studies represent a significant step toward the optimization of the nanobubble size, which is of crucial importance for photothermal cancer therapy applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/C6NR02144A

Semantic annotation in biomedicine: the current landscape.

PubMed

Jovanović, Jelena; Bagheri, Ebrahim

2017-09-22

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

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

PubMed

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

2016-04-01

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

Utilization of ontology look-up services in information retrieval for biomedical literature.

PubMed

Vishnyakova, Dina; Pasche, Emilie; Lovis, Christian; Ruch, Patrick

2013-01-01

With the vast amount of biomedical data we face the necessity to improve information retrieval processes in biomedical domain. The use of biomedical ontologies facilitated the combination of various data sources (e.g. scientific literature, clinical data repository) by increasing the quality of information retrieval and reducing the maintenance efforts. In this context, we developed Ontology Look-up services (OLS), based on NEWT and MeSH vocabularies. Our services were involved in some information retrieval tasks such as gene/disease normalization. The implementation of OLS services significantly accelerated the extraction of particular biomedical facts by structuring and enriching the data context. The results of precision in normalization tasks were boosted on about 20%.

Biomedical signal and image processing.

PubMed

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

2011-01-01

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

Reforming the politics of animal research.

PubMed

Levin, Lisa Hara; Reppy, William A

2015-07-01

An unfortunate tension exists between the biomedical research and animal welfare/rights communities. We believe that despite the mistrust between these groups, there are individuals on both sides of the controversy who seek to better understand the other. We recommend an update of institutional policies that will better inform the public about the use of non-human animals in biomedical research and improve a dialogue on such use between concerned individuals who either support or oppose non-human animal-based biomedical research. Such interactions may well determine the longevity of using non-human animals as experimental subjects. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Characterization of Acoustic Droplet Vaporization Using MRI

NASA Astrophysics Data System (ADS)

Li, David; Allen, Steven; Hernandez-Garcia, Luis; Bull, Joseph

2013-11-01

Acoustic droplet vaporization (ADV) is the selective vaporization of liquid droplets to form larger gas bubbles. The ADV process is currently being researched for biomedical applications such as gas embolotherapy, drug delivery, and phase-change contrast agents. In this study an albumin encapsulated dodecafluoropentane (DDFP, CAS: 678-26-2) microdroplet suspension was vaporized using a single element focused (f/2, D = 19 mm) 3.5 MHz transducer (Panametrics A321S, Olympus, Waltham, MA). The resulting DDFP bubble clouds were imaged using both bright field microscopy and MRI (Varian 7T, Agilent Technologies Inc., Santa Clara, CA). Field distortions due to DDFP bubble generation were characterized against the bright field images as a function of acoustic power and bubble cloud size. Experimentally a direct correlation between bubble cloud dimensions generated and field distortions seen in the MRI was observed. Additionally, MR velocimetry was used to measure the flow field resulting from ADV. The field distortions due to the bubbles were further characterized by modeling Maxwell's equations using COMSOL (COMSOL Inc., Burlington, MA). The ability to characterize ADV with alternative imaging modalities may prove useful in further development of ADV based biomedical therapies.

Applications of Semiconductor Fabrication Methods to Nanomedicine: A Review of Recent Inventions and Techniques

PubMed Central

Rajasekhar, Achanta; Gimi, Barjor; Hu, Walter

2013-01-01

We live in a world of convergence where scientific techniques from a variety of seemingly disparate fields are being applied cohesively to the study and solution of biomedical problems. For instance, the semiconductor processing field has been primarily developed to cater to the needs of the ever decreasing transistor size and cost while increasing functionality of electronic circuits. In recent years, pioneers in this field have equipped themselves with a powerful understanding of how the same techniques can be applied in the biomedical field to develop new and efficient systems for the diagnosis, analysis and treatment of various conditions in the human body. In this paper, we review the major inventions and experimental methods which have been developed for nano/micro fluidic channels, nanoparticles fabricated by top-down methods, and in-vivo nanoporous microcages for effective drug delivery. This paper focuses on the information contained in patents as well as the corresponding technical publications. The goal of the paper is to help emerging scientists understand and improvise over these inventions. PMID:24312161

Preparation of electromechanically active silicone composites and some evaluations of their suitability for biomedical applications.

PubMed

Iacob, Mihail; Bele, Adrian; Patras, Xenia; Pasca, Sorin; Butnaru, Maria; Alexandru, Mihaela; Ovezea, Dragos; Cazacu, Maria

2014-10-01

Some films based on electromechanically active polymer composites have been prepared. Polydimethylsiloxane-α,ω-diols (PDMSs) having different molecular masses (Mv=60 700 and Mv=44 200) were used as matrix in which two different active fillers were incorporated: titanium dioxide in situ generated from its titanium isopropoxide precursor and silica particles functionalized with polar aminopropyl groups on surface. A reference sample based on simple crosslinked PDMS was also prepared. The composites processed as films were investigated to evaluate their ability to act as efficient electromechanical actuators for potential biomedical application. Thus, the surface morphology of interest for electrodes compliance was analysed by atomic force microscopy. Mechanical and dielectric characteristics were evaluated by tensile tests and dielectric spectroscopy, respectively. Electromechanical actuation responses were measured by interferometry. The biocompatibility of the obtained materials has been verified through tests in vitro and, for valuable films, in vivo. The experimental, clinical and anatomopathological evaluation of the in vivo tested samples did not reveal significant pathological modifications. Copyright © 2014 Elsevier B.V. All rights reserved.

Semantic similarity measure in biomedical domain leverage web search engine.

PubMed

Chen, Chi-Huang; Hsieh, Sheau-Ling; Weng, Yung-Ching; Chang, Wen-Yung; Lai, Feipei

2010-01-01

Semantic similarity measure plays an essential role in Information Retrieval and Natural Language Processing. In this paper we propose a page-count-based semantic similarity measure and apply it in biomedical domains. Previous researches in semantic web related applications have deployed various semantic similarity measures. Despite the usefulness of the measurements in those applications, measuring semantic similarity between two terms remains a challenge task. The proposed method exploits page counts returned by the Web Search Engine. We define various similarity scores for two given terms P and Q, using the page counts for querying P, Q and P AND Q. Moreover, we propose a novel approach to compute semantic similarity using lexico-syntactic patterns with page counts. These different similarity scores are integrated adapting support vector machines, to leverage the robustness of semantic similarity measures. Experimental results on two datasets achieve correlation coefficients of 0.798 on the dataset provided by A. Hliaoutakis, 0.705 on the dataset provide by T. Pedersen with physician scores and 0.496 on the dataset provided by T. Pedersen et al. with expert scores.

A gene catalogue of the Sprague-Dawley rat gut metagenome.

PubMed

Pan, Hudan; Guo, Ruijin; Zhu, Jie; Wang, Qi; Ju, Yanmei; Xie, Ying; Zheng, Yanfang; Wang, Zhifeng; Li, Ting; Liu, Zhongqiu; Lu, Linlin; Li, Fei; Tong, Bin; Xiao, Liang; Xu, Xun; Li, Runze; Yuan, Zhongwen; Yang, Huanming; Wang, Jian; Kristiansen, Karsten; Jia, Huijue; Liu, Liang

2018-05-01

Laboratory rats such as the Sprague-Dawley (SD) rats are an important model for biomedical studies in relation to human physiological or pathogenic processes. Here we report the first catalog of microbial genes in fecal samples from Sprague-Dawley rats. The catalog was established using 98 fecal samples from 49 SD rats, divided in 7 experimental groups, and collected at different time points 30 days apart. The established gene catalog comprises 5,130,167 non-redundant genes with an average length of 750 bp, among which 64.6% and 26.7% were annotated to phylum and genus levels, respectively. Functionally, 53.1%, 21.8%,and 31% of the genes could be annotated to KEGG orthologous groups, modules, and pathways, respectively. A comparison of rat gut metagenome catalogue with human or mouse revealed a higher pairwise overlap between rats and humans (2.47%) than between mice and humans (1.19%) at the gene level. Ninety-seven percent of the functional pathways in the human catalog were present in the rat catalogue, underscoring the potential use of rats for biomedical research.

Navigating the Path to a Biomedical Science Career

NASA Astrophysics Data System (ADS)

Zimmerman, Andrea McNeely

The number of biomedical PhD scientists being trained and graduated far exceeds the number of academic faculty positions and academic research jobs. If this trend is compelling biomedical PhD scientists to increasingly seek career paths outside of academia, then more should be known about their intentions, desires, training experiences, and career path navigation. Therefore, the purpose of this study was to understand the process through which biomedical PhD scientists are trained and supported for navigating future career paths. In addition, the study sought to determine whether career development support efforts and opportunities should be redesigned to account for the proportion of PhD scientists following non-academic career pathways. Guided by the social cognitive career theory (SCCT) framework this study sought to answer the following central research question: How does a southeastern tier 1 research university train and support its biomedical PhD scientists for navigating their career paths? Key findings are: Many factors influence PhD scientists' career sector preference and job search process, but the most influential were relationships with faculty, particularly the mentor advisor; Planned activities are a significant aspect of the training process and provide skills for career success; and Planned activities provided skills necessary for a career, but influential factors directed the career path navigated. Implications for practice and future research are discussed.

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

PubMed

Sarrouti, Mourad; Ouatik El Alaoui, Said

2017-04-01

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

MODELING MICROBUBBLE DYNAMICS IN BIOMEDICAL APPLICATIONS*

PubMed Central

CHAHINE, Georges L.; HSIAO, Chao-Tsung

2012-01-01

Controlling microbubble dynamics to produce desirable biomedical outcomes when and where necessary and avoid deleterious effects requires advanced knowledge, which can be achieved only through a combination of experimental and numerical/analytical techniques. The present communication presents a multi-physics approach to study the dynamics combining viscous- in-viscid effects, liquid and structure dynamics, and multi bubble interaction. While complex numerical tools are developed and used, the study aims at identifying the key parameters influencing the dynamics, which need to be included in simpler models. PMID:22833696

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

PubMed

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

2016-10-01

In the era of digitalization, information retrieval (IR), which retrieves and ranks documents from large collections according to users' search queries, has been popularly applied in the biomedical domain. Building patient cohorts using electronic health records (EHRs) and searching literature for topics of interest are some IR use cases. Meanwhile, natural language processing (NLP), such as tokenization or Part-Of-Speech (POS) tagging, has been developed for processing clinical documents or biomedical literature. We hypothesize that NLP can be incorporated into IR to strengthen the conventional IR models. In this study, we propose two NLP-empowered IR models, POS-BoW and POS-MRF, which incorporate automatic POS-based term weighting schemes into bag-of-word (BoW) and Markov Random Field (MRF) IR models, respectively. In the proposed models, the POS-based term weights are iteratively calculated by utilizing a cyclic coordinate method where golden section line search algorithm is applied along each coordinate to optimize the objective function defined by mean average precision (MAP). In the empirical experiments, we used the data sets from the Medical Records track in Text REtrieval Conference (TREC) 2011 and 2012 and the Genomics track in TREC 2004. The evaluation on TREC 2011 and 2012 Medical Records tracks shows that, for the POS-BoW models, the mean improvement rates for IR evaluation metrics, MAP, bpref, and P@10, are 10.88%, 4.54%, and 3.82%, compared to the BoW models; and for the POS-MRF models, these rates are 13.59%, 8.20%, and 8.78%, compared to the MRF models. Additionally, we experimentally verify that the proposed weighting approach is superior to the simple heuristic and frequency based weighting approaches, and validate our POS category selection. Using the optimal weights calculated in this experiment, we tested the proposed models on the TREC 2004 Genomics track and obtained average of 8.63% and 10.04% improvement rates for POS-BoW and POS-MRF, respectively. These significant improvements verify the effectiveness of leveraging POS tagging for biomedical IR tasks. Copyright © 2016 Elsevier Inc. All rights reserved.

Biomedical informatics and translational medicine.

PubMed

Sarkar, Indra Neil

2010-02-26

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

Data publication with the structural biology data grid supports live analysis

DOE PAGES

Meyer, Peter A.; Socias, Stephanie; Key, Jason; ...

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis

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

Meyer, Peter A.; Socias, Stephanie; Key, Jason

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis.

PubMed

Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Fromme, J Christopher; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

Data publication with the structural biology data grid supports live analysis

PubMed Central

Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M. J. J.; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Christopher Fromme, J.; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R. N C.; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis. PMID:26947396

The Academy for Future Science Faculty: randomized controlled trial of theory-driven coaching to shape development and diversity of early-career scientists.

PubMed

Thakore, Bhoomi K; Naffziger-Hirsch, Michelle E; Richardson, Jennifer L; Williams, Simon N; McGee, Richard

2014-08-02

Approaches to training biomedical scientists have created a talented research community. However, they have failed to create a professional workforce that includes many racial and ethnic minorities and women in proportion to their representation in the population or in PhD training. This is particularly true at the faculty level. Explanations for the absence of diversity in faculty ranks can be found in social science theories that reveal processes by which individuals develop identities, experiences, and skills required to be seen as legitimate within the profession. Using the social science theories of Communities of Practice, Social Cognitive Career Theory, identity formation, and cultural capital, we have developed and are testing a novel coaching-based model to address some of the limitations of previous diversity approaches. This coaching intervention (The Academy for Future Science Faculty) includes annual in-person meetings of students and trained faculty Career Coaches, along with ongoing virtual coaching, group meetings and communication. The model is being tested as a randomized controlled trial with two cohorts of biomedical PhD students from across the U.S., one recruited at the start of their PhDs and one nearing completion. Stratification into the experimental and control groups, and to coaching groups within the experimental arms, achieved equal numbers of students by race, ethnicity and gender to the extent possible. A fundamental design element of the Academy is to teach and make visible the social science principles which highly influence scientific advancement, as well as acknowledging the extra challenges faced by underrepresented groups working to be seen as legitimate within the scientific communities. The strategy being tested is based upon a novel application of the well-established principles of deploying highly skilled coaches, selected and trained for their ability to develop talents of others. This coaching model is intended to be a complement, rather than a substitute, for traditional mentoring in biomedical research training, and is being tested as such.

Integrating a Hypernymic Proposition Interpreter into a Semantic Processor for Biomedical Texts

PubMed Central

Fiszman, Marcelo; Rindflesch, Thomas C.; Kilicoglu, Halil

2003-01-01

Semantic processing provides the potential for producing high quality results in natural language processing (NLP) applications in the biomedical domain. In this paper, we address a specific semantic phenomenon, the hypernymic proposition, and concentrate on integrating the interpretation of such predications into a more general semantic processor in order to improve overall accuracy. A preliminary evaluation assesses the contribution of hypernymic propositions in providing more specific semantic predications and thus improving effectiveness in retrieving treatment propositions in MEDLINE abstracts. Finally, we discuss the generalization of this methodology to additional semantic propositions as well as other types of biomedical texts. PMID:14728170

Laboratory animal science: a resource to improve the quality of science.

PubMed

Forni, M

2007-08-01

The contribution of animal experimentation to biomedical research is of undoubted value, nevertheless the real usefulness of animal models is still being hotly debated. Laboratory Animal Science is a multidisciplinary approach to humane animal experimentation that allows the choice of the correct animal model and the collection of unbiased data. Refinement, Reduction and Replacement, the "3Rs rule", are now widely accepted and have a major influence on animal experimentation procedures. Refinement, namely any decrease in the incidence or severity of inhumane procedures applied to animals, has been today extended to the entire lives of the experimental animals. Reduction of the number of animals used to obtain statistically significant data may be achieved by improving experimental design and statistical analysis of data. Replacement refers to the development of validated alternative methods. A Laboratory Animal Science training program in biomedical degrees can promote the 3Rs and improve the welfare of laboratory animals as well as the quality of science with ethical, scientific and economic advantages complying with the European requirement that "persons who carry out, take part in, or supervise procedures on animals, or take care of animals used in procedures, shall have had appropriate education and training".

From Nuremberg to bioethics: an educational project for students of dentistry and dental prosthesis

PubMed Central

Marinozzi, Silvia; Corbellini, Gilberto; Ottolenghi, Livia; Ripari, Francesca; Pizzuti, Antonio; Pezzetti, Marcello; Gaj, Fabio

2013-01-01

Summary In the lessons of medical-scientific methodologies of the medical faculty at the Sapienza University of Rome, basic notions on the ethical and deontologic aspects characterizing the history of the medical profession are provided, including the formulation and application of bioethical principles to clinics and biomedical research. Within such framework, an educational project has been initiated on the historical origin of the current normative and juridic dispositions in the regulation of experimental biomedical research and the relationship between health operators and patients, with particular attention to the procedure, the meaning the value either professional or deontologic, of ethics and the legality of the informed consensus. Emphasis is put on medical and experimental abuses that occurred in Germany during the nazi regime. PMID:23741533

Peace propaganda and biomedical experimentation: influential uses of radioisotopes in endocrinology and molecular genetics in Spain (1947-1971).

PubMed

Santesmases, María Jesús

2006-01-01

A political discourse of peace marked the distribution and use of radioisotopes in biomedical research and in medical diagnosis and therapy in the post-World War II period. This occurred during the era of expansion and strengthening of the United States' influence on the promotion of sciences and technologies in Europe as a collaborative effort, initially encouraged by the policies and budgetary distribution of the Marshall Plan. This article follows the importation of radioisotopes by two Spanish research groups, one in experimental endocrinology and one in molecular biology. For both groups foreign funds were instrumental in the early establishment of their laboratories. The combination of funding and access to previously scarce radioisotopes helped position these groups at the forefront of research in Spain.

Empirical data on corpus design and usage in biomedical natural language processing.

PubMed

Cohen, K Bretonnel; Fox, Lynne; Ogren, Philip V; Hunter, Lawrence

2005-01-01

This paper describes the design of six publicly available biomedical corpora. We then present usage data for the six corpora. We show that corpora that are carefully annotated with respect to structural and linguistic characteristics and that are distributed in standard formats are more widely used than corpora that are not. These findings have implications for the design of the next generation of biomedical corpora.

Writing intelligible English prose for biomedical journals.

PubMed

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.

A neural joint model for entity and relation extraction from biomedical text.

PubMed

Li, Fei; Zhang, Meishan; Fu, Guohong; Ji, Donghong

2017-03-31

Extracting biomedical entities and their relations from text has important applications on biomedical research. Previous work primarily utilized feature-based pipeline models to process this task. Many efforts need to be made on feature engineering when feature-based models are employed. Moreover, pipeline models may suffer error propagation and are not able to utilize the interactions between subtasks. Therefore, we propose a neural joint model to extract biomedical entities as well as their relations simultaneously, and it can alleviate the problems above. Our model was evaluated on two tasks, i.e., the task of extracting adverse drug events between drug and disease entities, and the task of extracting resident relations between bacteria and location entities. Compared with the state-of-the-art systems in these tasks, our model improved the F1 scores of the first task by 5.1% in entity recognition and 8.0% in relation extraction, and that of the second task by 9.2% in relation extraction. The proposed model achieves competitive performances with less work on feature engineering. We demonstrate that the model based on neural networks is effective for biomedical entity and relation extraction. In addition, parameter sharing is an alternative method for neural models to jointly process this task. Our work can facilitate the research on biomedical text mining.

An efficient sampling algorithm for uncertain abnormal data detection in biomedical image processing and disease prediction.

PubMed

Liu, Fei; Zhang, Xi; Jia, Yan

2015-01-01

In this paper, we propose a computer information processing algorithm that can be used for biomedical image processing and disease prediction. A biomedical image is considered a data object in a multi-dimensional space. Each dimension is a feature that can be used for disease diagnosis. We introduce a new concept of the top (k1,k2) outlier. It can be used to detect abnormal data objects in the multi-dimensional space. This technique focuses on uncertain space, where each data object has several possible instances with distinct probabilities. We design an efficient sampling algorithm for the top (k1,k2) outlier in uncertain space. Some improvement techniques are used for acceleration. Experiments show our methods' high accuracy and high efficiency.

Natural Language Processing Methods and Systems for Biomedical Ontology Learning

PubMed Central

Liu, Kaihong; Hogan, William R.; Crowley, Rebecca S.

2010-01-01

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they must achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships as well as difficulty in updating the ontology as knowledge changes. Methodologies developed in the fields of natural language processing, information extraction, information retrieval and machine learning provide techniques for automating the enrichment of an ontology from free-text documents. In this article, we review existing methodologies and developed systems, and discuss how existing methods can benefit the development of biomedical ontologies. PMID:20647054

A Diagram Editor for Efficient Biomedical Knowledge Capture and Integration

PubMed Central

Yu, Bohua; Jakupovic, Elvis; Wilson, Justin; Dai, Manhong; Xuan, Weijian; Mirel, Barbara; Athey, Brian; Watson, Stanley; Meng, Fan

2008-01-01

Understanding the molecular mechanisms underlying complex disorders requires the integration of data and knowledge from different sources including free text literature and various biomedical databases. To facilitate this process, we created the Biomedical Concept Diagram Editor (BCDE) to help researchers distill knowledge from data and literature and aid the process of hypothesis development. A key feature of BCDE is the ability to capture information with a simple drag-and-drop. This is a vast improvement over manual methods of knowledge and data recording and greatly increases the efficiency of the biomedical researcher. BCDE also provides a unique concept matching function to enforce consistent terminology, which enables conceptual relationships deposited by different researchers in the BCDE database to be mined and integrated for intelligible and useful results. We hope BCDE will promote the sharing and integration of knowledge from different researchers for effective hypothesis development. PMID:21347131

A New, Dynamic Era for Somatic Cell Nuclear Transfer?

PubMed

Loi, Pasqualino; Iuso, Domenico; Czernik, Marta; Ogura, Atsuo

2016-10-01

Cloning animals by somatic cell nuclear transfer (SCNT) has remained an uncontrollable process for many years. High rates of embryonic losses, stillbirths, and postnatal mortality have been typical outcomes. These developmental problems arise from abnormal genomic reprogramming: the capacity of the oocyte to reset the differentiated memory of a somatic cell. However, effective reprogramming strategies are now available. These target the whole genome or single domains such as the Xist gene, and their effectiveness has been validated with the ability of experimental animals to develop to term. Thus, SCNT has become a controllable process that can be used to 'rescue' endangered species, and for biomedical research such as therapeutic cloning and the isolation of induced pluripotent stem cells (iPSCs). Copyright © 2016 Elsevier Ltd. All rights reserved.

Experimental analysis on semi-finishing machining of Ti6Al4V additively manufactured by direct melting laser sintering

NASA Astrophysics Data System (ADS)

Imbrogno, Stano; Bordin, Alberto; Bruschi, Stefania; Umbrello, Domenico

2016-10-01

The Additive Manufacturing (AM) techniques are particularly appealing especially for titanium aerospace and biomedical components because they permit to achieve a strong reduction of the buy-to-fly ratio. However, finishing machining operations are often necessary to reduce the uneven surface roughness and geometrics because of local missing accuracy. This work shows the influence of the cutting parameters, cutting speed and feed rate, on the cutting forces as well as on the thermal field observed in the cutting zone, during a turning operation carried out on bars made of Ti6Al4V obtained by the AM process called Direct Metal Laser Sintering (DMLS). Moreover, the sub-surface microstructure alterations due to the process are also showed and commented.

Biomedical image analysis and processing in clouds

NASA Astrophysics Data System (ADS)

Bednarz, Tomasz; Szul, Piotr; Arzhaeva, Yulia; Wang, Dadong; Burdett, Neil; Khassapov, Alex; Chen, Shiping; Vallotton, Pascal; Lagerstrom, Ryan; Gureyev, Tim; Taylor, John

2013-10-01

Cloud-based Image Analysis and Processing Toolbox project runs on the Australian National eResearch Collaboration Tools and Resources (NeCTAR) cloud infrastructure and allows access to biomedical image processing and analysis services to researchers via remotely accessible user interfaces. By providing user-friendly access to cloud computing resources and new workflow-based interfaces, our solution enables researchers to carry out various challenging image analysis and reconstruction tasks. Several case studies will be presented during the conference.

The present and future role of microfluidics in biomedical research.

PubMed

Sackmann, Eric K; Fulton, Anna L; Beebe, David J

2014-03-13

Microfluidics, a technology characterized by the engineered manipulation of fluids at the submillimetre scale, has shown considerable promise for improving diagnostics and biology research. Certain properties of microfluidic technologies, such as rapid sample processing and the precise control of fluids in an assay, have made them attractive candidates to replace traditional experimental approaches. Here we analyse the progress made by lab-on-a-chip microtechnologies in recent years, and discuss the clinical and research areas in which they have made the greatest impact. We also suggest directions that biologists, engineers and clinicians can take to help this technology live up to its potential.

Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning.

PubMed

Hoehndorf, Robert; Dumontier, Michel; Oellrich, Anika; Rebholz-Schuhmann, Dietrich; Schofield, Paul N; Gkoutos, Georgios V

2011-01-01

Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data- and knowledge bases. Formal ontologies make the semantics of terms and relations explicit such that automated reasoning can be used to verify the consistency of knowledge. However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge discovery. We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions. We describe the semi-automated repair of contradictions and demonstrate expressive queries over interoperable ontologies. Our work forms an important cornerstone for data integration, automatic inference and knowledge discovery based on formal representations of knowledge. Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies.

Tiny giants of gene regulation: experimental strategies for microRNA functional studies

PubMed Central

Steinkraus, Bruno R.; Toegel, Markus

2016-01-01

The discovery over two decades ago of short regulatory microRNAs (miRNAs) has led to the inception of a vast biomedical research field dedicated to understanding these powerful orchestrators of gene expression. Here we aim to provide a comprehensive overview of the methods and techniques underpinning the experimental pipeline employed for exploratory miRNA studies in animals. Some of the greatest challenges in this field have been uncovering the identity of miRNA–target interactions and deciphering their significance with regard to particular physiological or pathological processes. These endeavors relied almost exclusively on the development of powerful research tools encompassing novel bioinformatics pipelines, high‐throughput target identification platforms, and functional target validation methodologies. Thus, in an unparalleled manner, the biomedical technology revolution unceasingly enhanced and refined our ability to dissect miRNA regulatory networks and understand their roles in vivo in the context of cells and organisms. Recurring motifs of target recognition have led to the creation of a large number of multifactorial bioinformatics analysis platforms, which have proved instrumental in guiding experimental miRNA studies. Subsequently, the need for discovery of miRNA–target binding events in vivo drove the emergence of a slew of high‐throughput multiplex strategies, which now provide a viable prospect for elucidating genome‐wide miRNA–target binding maps in a variety of cell types and tissues. Finally, deciphering the functional relevance of miRNA post‐transcriptional gene silencing under physiological conditions, prompted the evolution of a host of technologies enabling systemic manipulation of miRNA homeostasis as well as high‐precision interference with their direct, endogenous targets. WIREs Dev Biol 2016, 5:311–362. doi: 10.1002/wdev.223 For further resources related to this article, please visit the WIREs website. PMID:26950183

Improve Biomedical Information Retrieval using Modified Learning to Rank Methods.

PubMed

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

2016-06-14

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

Enhancing Biomedical Text Summarization Using Semantic Relation Extraction

PubMed Central

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

2011-01-01

Automatic text summarization for a biomedical concept can help researchers to get the key points of a certain topic from large amount of biomedical literature efficiently. In this paper, we present a method for generating text summary for a given biomedical concept, e.g., H1N1 disease, from multiple documents based on semantic relation extraction. Our approach includes three stages: 1) We extract semantic relations in each sentence using the semantic knowledge representation tool SemRep. 2) We develop a relation-level retrieval method to select the relations most relevant to each query concept and visualize them in a graphic representation. 3) For relations in the relevant set, we extract informative sentences that can interpret them from the document collection to generate text summary using an information retrieval based method. Our major focus in this work is to investigate the contribution of semantic relation extraction to the task of biomedical text summarization. The experimental results on summarization for a set of diseases show that the introduction of semantic knowledge improves the performance and our results are better than the MEAD system, a well-known tool for text summarization. PMID:21887336

Alternative methods for the use of non-human primates in biomedical research.

PubMed

Burm, Saskia M; Prins, Jan-Bas; Langermans, Jan; Bajramovic, Jeffrey J

2014-01-01

The experimental use of non-human primates (NHP) in Europe is tightly regulated and is only permitted when there are no alternatives available. As a result, NHP are most often used in late, pre-clinical phases of biomedical research. Although the impetus for scientists, politicians and the general public to replace, reduce and refine NHP in biomedical research is strong, the development of 3Rs technology for NHP poses specific challenges. In February 2014 a workshop on "Alternative methods for the use of NHP in biomedical research" was organized within the international exchange program of EUPRIM-Net II, a European infrastructure initiative that links biomedical primate research centers. The workshop included lectures by key scientists in the field of alternatives as well as by experts from governmental and non-governmental organizations. Furthermore, parallel sessions were organized to stimulate discussion on the challenges of advancing the use of alternative methods for NHP. Subgroups voted on four statements and together composed a list with opportunities and priorities. This report summarizes the presentations that were held, the content of the discussion sessions and concludes with recommendations on 3Rs development for NHP specifically. These include technical, conceptual as well as political topics.

Hand-in-hand advances in biomedical engineering and sensorimotor restoration.

PubMed

Pisotta, Iolanda; Perruchoud, David; Ionta, Silvio

2015-05-15

Living in a multisensory world entails the continuous sensory processing of environmental information in order to enact appropriate motor routines. The interaction between our body and our brain is the crucial factor for achieving such sensorimotor integration ability. Several clinical conditions dramatically affect the constant body-brain exchange, but the latest developments in biomedical engineering provide promising solutions for overcoming this communication breakdown. The ultimate technological developments succeeded in transforming neuronal electrical activity into computational input for robotic devices, giving birth to the era of the so-called brain-machine interfaces. Combining rehabilitation robotics and experimental neuroscience the rise of brain-machine interfaces into clinical protocols provided the technological solution for bypassing the neural disconnection and restore sensorimotor function. Based on these advances, the recovery of sensorimotor functionality is progressively becoming a concrete reality. However, despite the success of several recent techniques, some open issues still need to be addressed. Typical interventions for sensorimotor deficits include pharmaceutical treatments and manual/robotic assistance in passive movements. These procedures achieve symptoms relief but their applicability to more severe disconnection pathologies is limited (e.g. spinal cord injury or amputation). Here we review how state-of-the-art solutions in biomedical engineering are continuously increasing expectances in sensorimotor rehabilitation, as well as the current challenges especially with regards to the translation of the signals from brain-machine interfaces into sensory feedback and the incorporation of brain-machine interfaces into daily activities. Copyright © 2015 Elsevier B.V. All rights reserved.

Normalizing biomedical terms by minimizing ambiguity and variability

PubMed Central

Tsuruoka, Yoshimasa; McNaught, John; Ananiadou, Sophia

2008-01-01

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. PMID:18426547

Minimum Information about a Genotyping Experiment (MIGEN)

PubMed Central

Huang, Jie; Mirel, Daniel; Pugh, Elizabeth; Xing, Chao; Robinson, Peter N.; Pertsemlidis, Alexander; Ding, LiangHao; Kozlitina, Julia; Maher, Joseph; Rios, Jonathan; Story, Michael; Marthandan, Nishanth; Scheuermann, Richard H.

2011-01-01

Genotyping experiments are widely used in clinical and basic research laboratories to identify associations between genetic variations and normal/abnormal phenotypes. Genotyping assay techniques vary from single genomic regions that are interrogated using PCR reactions to high throughput assays examining genome-wide sequence and structural variation. The resulting genotype data may include millions of markers of thousands of individuals, requiring various statistical, modeling or other data analysis methodologies to interpret the results. To date, there are no standards for reporting genotyping experiments. Here we present the Minimum Information about a Genotyping Experiment (MIGen) standard, defining the minimum information required for reporting genotyping experiments. MIGen standard covers experimental design, subject description, genotyping procedure, quality control and data analysis. MIGen is a registered project under MIBBI (Minimum Information for Biological and Biomedical Investigations) and is being developed by an interdisciplinary group of experts in basic biomedical science, clinical science, biostatistics and bioinformatics. To accommodate the wide variety of techniques and methodologies applied in current and future genotyping experiment, MIGen leverages foundational concepts from the Ontology for Biomedical Investigations (OBI) for the description of the various types of planned processes and implements a hierarchical document structure. The adoption of MIGen by the research community will facilitate consistent genotyping data interpretation and independent data validation. MIGen can also serve as a framework for the development of data models for capturing and storing genotyping results and experiment metadata in a structured way, to facilitate the exchange of metadata. PMID:22180825

BER balanced program plan: oil shale technology. [23 suggested biomedical and environmental research projects

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

Schulte, H.F.; Stoker, A.K.; Campbell, E.E.

1976-06-01

Oil shale technology has been divided into two sub-technologies: surface processing and in-situ processing. Definition of the research programs is essentially an amplification of the five King-Muir categories: (A) pollutants: characterization, measurement, and monitoring; (B) physical and chemical processes and effects; (C) health effects; (D) ecological processes and effects; and (E) integrated assessment. Twenty-three biomedical and environmental research projects are described as to program title, scope, milestones, technolgy time frame, program unit priority, and estimated program unit cost.

New Windows based Color Morphological Operators for Biomedical Image Processing

NASA Astrophysics Data System (ADS)

Pastore, Juan; Bouchet, Agustina; Brun, Marcel; Ballarin, Virginia

2016-04-01

Morphological image processing is well known as an efficient methodology for image processing and computer vision. With the wide use of color in many areas, the interest on the color perception and processing has been growing rapidly. Many models have been proposed to extend morphological operators to the field of color images, dealing with some new problems not present previously in the binary and gray level contexts. These solutions usually deal with the lattice structure of the color space, or provide it with total orders, to be able to define basic operators with required properties. In this work we propose a new locally defined ordering, in the context of window based morphological operators, for the definition of erosions-like and dilation-like operators, which provides the same desired properties expected from color morphology, avoiding some of the drawbacks of the prior approaches. Experimental results show that the proposed color operators can be efficiently used for color image processing.

[The processes of manuscript evaluation and publication in Medicina Clínica. The editorial committee of Medicina Clínica].

PubMed

Ribera, Josep M; Cardellach, Francesc; Selva, Albert

2005-12-01

The decision-making process includes a series of activities undertaken in biomedical journals from the moment a manuscript is received until it is accepted or rejected. Firstly, the manuscript is evaluated by the members of the Editorial Board, who analyze both its suitability for the journal and its scientific quality. After this initial evaluation, the article is evaluated by peer reviewers, an essential process to guarantee its scientific validity. Both the Editorial Board and the peer reviewers usually use checklists which are of enormous help in this task. Once the biomedical article has been accepted, the publication process is started, which in turn includes a series of steps, beginning with technical and medical review of the article's contents and ending with the article's publication in the journal. The present article provides a detailed description of the main technical and ethical issues involved in the processes of decision-making and publication of biomedical articles.

Logical Experimental Design and Execution in the Biomedical Sciences.

PubMed

Holder, Daniel J; Marino, Michael J

2017-03-17

Lack of reproducibility has been highlighted as a significant problem in biomedical research. The present unit is devoted to describing ways to help ensure that research findings can be replicated by others, with a focus on the design and execution of laboratory experiments. Essential components for this include clearly defining the question being asked, using available information or information from pilot studies to aid in the design the experiment, and choosing manipulations under a logical framework based on Mill's "methods of knowing" to build confidence in putative causal links. Final experimental design requires systematic attention to detail, including the choice of controls, sample selection, blinding to avoid bias, and the use of power analysis to determine the sample size. Execution of the experiment is done with care to ensure that the independent variables are controlled and the measurements of the dependent variables are accurate. While there are always differences among laboratories with respect to technical expertise, equipment, and suppliers, execution of the steps itemized in this unit will ensure well-designed and well-executed experiments to answer any question in biomedical research. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Fabrication of chitosan-silver nanoparticle hybrid 3D porous structure as a SERS substrate for biomedical applications

NASA Astrophysics Data System (ADS)

Jung, Gyeong-Bok; Kim, Ji-Hye; Burm, Jin Sik; Park, Hun-Kuk

2013-05-01

We propose a simple, low-cost, large-area, and functional surface enhanced Raman scattering (SERS) substrate for biomedical applications. The SERS substrate with chitosan-silver nanoparticles (chitosan-Ag NPs) hybrid 3D porous structure was fabricated simply by a one-step method. The chitosan was used as a template for the Ag NPs deposition. SERS enhancement by the chitosan-Ag NPs substrate was experimentally verified using rhodamine B as an analyte. Thiolated single stranded DNA was also measured for atopic dermatitis genetic markers (chemokines CCL17) at a low concentration of 5 pM. We successfully designed a novel SERS substrate with silver nanoparticle hybridized 3D porous chitosan that has the potential to become a highly sensitive and selective tool for biomedical applications.

Exploiting Novel Calcium-Mediated Apoptotic Processes for the Treatment of Human Breast Cancers with Elevated Nqo1 Levels

DTIC Science & Technology

2008-03-01

in β-Lapachone-induced programmed necrosis. Biomedical Graduate Student Symposium, Case Western Reserve University, Cleveland, OH April 2002-06.  o...of β- lapachone-induced cell death” October, 2005  o The Vance Lemmon Poster Award, Biomedical Graduate Student Symposium, Case Western Reserve...cell death” April, 2005  o The Marcus Singer Poster Award, Biomedical Graduate Student Symposium, Case Western Reserve University, Cleveland, OH for

Balanced program plan: analysis for biomedical and environmental research. Volume 5. Oil shale technology

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

Not Available

1976-06-01

Oil shale technology has been divided into two sub-technologies: surfaceprocessing and in-situ processing. Definition of the research programs is essentially an amplification of the five King-Muir categories: (A) pollutants: characterization, measurement, and monitoring; (B) physical and chemical processes and effects; (C) health effects; (D) ecological processes and effects; and (E) integrated assessment. Twenty-three biomedical and environmental research projects are described as to program title, scope, milestones, technology time frame, program unit priority, and estimated program unit cost.

Specificity of Good Manufacturing Practice (GMP) for Biomedical Cell Products.

PubMed

Tulina, M A; Pyatigorskaya, N V

2018-03-01

The article describes special aspects of Good Manufacturing Practice (GMP) for biomedical cell products (BMCP) that imply high standards of aseptics throughout the entire productio process, strict requirements to donors and to the procedure of biomaterial isolation, guaranty of tracing BMCP products, defining processing procedures which allow to identify BMCP as minimally manipulated; continuous quality control and automation of the control process at all stages of manufacturing, which will ensure product release simultaneously with completion of technological operations.

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

PubMed

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

2003-09-01

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

[Triple-type theory of statistics and its application in the scientific research of biomedicine].

PubMed

Hu, Liang-ping; Liu, Hui-gang

2005-07-20

To point out the crux of why so many people failed to grasp statistics and to bring forth a "triple-type theory of statistics" to solve the problem in a creative way. Based on the experience in long-time teaching and research in statistics, the "three-type theory" was raised and clarified. Examples were provided to demonstrate that the 3 types, i.e., expressive type, prototype and the standardized type are the essentials for people to apply statistics rationally both in theory and practice, and moreover, it is demonstrated by some instances that the "three types" are correlated with each other. It can help people to see the essence by interpreting and analyzing the problems of experimental designs and statistical analyses in medical research work. Investigations reveal that for some questions, the three types are mutually identical; for some questions, the prototype is their standardized type; however, for some others, the three types are distinct from each other. It has been shown that in some multifactor experimental researches, it leads to the nonexistence of the standardized type corresponding to the prototype at all, because some researchers have committed the mistake of "incomplete control" in setting experimental groups. This is a problem which should be solved by the concept and method of "division". Once the "triple-type" for each question is clarified, a proper experimental design and statistical method can be carried out easily. "Triple-type theory of statistics" can help people to avoid committing statistical mistakes or at least to decrease the misuse rate dramatically and improve the quality, level and speed of biomedical research during the process of applying statistics. It can also help people to improve the quality of statistical textbooks and the teaching effect of statistics and it has demonstrated how to advance biomedical statistics.

Fabrication of three-dimensional collagen scaffold using an inverse mould-leaching process.

PubMed

Ahn, SeungHyun; Lee, SuYeon; Cho, Youngseok; Chun, Wook; Kim, GeunHyung

2011-09-01

Natural biopolymers, such as collagen or chitosan, are considered ideal for biomedical scaffolds. However, low processability of the materials has hindered the fabrication of designed pore structures controlled by various solid freeform-fabrication methods. A new technique to fabricate a biomedical three-dimensional collagen scaffold, supplemented with a sacrificial poly(ethylene oxide) mould is proposed. The fabricated collagen scaffold shows a highly porous surface and a three-dimensional structure with high porosity as well as mechanically stable structure. To show its feasibility for biomedical applications, fibroblasts/keratinocytes were co-cultured on the scaffold, and the cell proliferation and cell migration of the scaffold was more favorable than that obtained with a spongy-type collagen scaffold.

Lipid Biomembrane in Ionic Liquids

NASA Astrophysics Data System (ADS)

Yoo, Brian; Jing, Benxin; Shah, Jindal; Maginn, Ed; Zhu, Y. Elaine; Department of Chemical and Biomolecular Engineering Team

2014-03-01

Ionic liquids (ILs) have been recently explored as new ``green'' chemicals in several chemical and biomedical processes. In our pursuit of understanding their toxicities towards aquatic and terrestrial organisms, we have examined the IL interaction with lipid bilayers as model cell membranes. Experimentally by fluorescence microscopy, we have directly observed the disruption of lipid bilayer by added ILs. Depending on the concentration, alkyl chain length, and anion hydrophobicity of ILs, the interaction of ILs with lipid bilayers leads to the formation of micelles, fibrils, and multi-lamellar vesicles for IL-lipid complexes. By MD computer simulations, we have confirmed the insertion of ILs into lipid bilayers to modify the spatial organization of lipids in the membrane. The combined experimental and simulation results correlate well with the bioassay results of IL-induced suppression in bacteria growth, thereby suggesting a possible mechanism behind the IL toxicity. National Science Foundation, Center for Research Computing at Notre Dame.

Detection of Practice Pattern Trends through Natural Language Processing of Clinical Narratives and Biomedical Literature

PubMed Central

Chen, Elizabeth S.; Stetson, Peter D.; Lussier, Yves A.; Markatou, Marianthi; Hripcsak, George; Friedman, Carol

2007-01-01

Clinical knowledge, best evidence, and practice patterns evolve over time. The ability to track these changes and study practice trends may be valuable for performance measurement and quality improvement efforts. The goal of this study was to assess the feasibility and validity of methods to generate and compare trends in biomedical literature and clinical narrative. We focused on the challenge of detecting trends in medication usage over time for two diseases: HIV/AIDS and asthma. Information about disease-specific medications in published randomized control trials and discharge summaries at New York-Presbyterian Hospital over a ten-year period were extracted using Natural Language Processing. This paper reports on the ability of our semi-automated process to discover disease-drug practice pattern trends and interpretation of findings across the biomedical and clinical text sources. PMID:18693810

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

PubMed

Ganapathiraju, Madhavi K; Orii, Naoki

2013-08-30

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

A knowledge-driven approach to biomedical document conceptualization.

PubMed

Zheng, Hai-Tao; Borchert, Charles; Jiang, Yong

2010-06-01

Biomedical document conceptualization is the process of clustering biomedical documents based on ontology-represented domain knowledge. The result of this process is the representation of the biomedical documents by a set of key concepts and their relationships. Most of clustering methods cluster documents based on invariant domain knowledge. The objective of this work is to develop an effective method to cluster biomedical documents based on various user-specified ontologies, so that users can exploit the concept structures of documents more effectively. We develop a flexible framework to allow users to specify the knowledge bases, in the form of ontologies. Based on the user-specified ontologies, we develop a key concept induction algorithm, which uses latent semantic analysis to identify key concepts and cluster documents. A corpus-related ontology generation algorithm is developed to generate the concept structures of documents. Based on two biomedical datasets, we evaluate the proposed method and five other clustering algorithms. The clustering results of the proposed method outperform the five other algorithms, in terms of key concept identification. With respect to the first biomedical dataset, our method has the F-measure values 0.7294 and 0.5294 based on the MeSH ontology and gene ontology (GO), respectively. With respect to the second biomedical dataset, our method has the F-measure values 0.6751 and 0.6746 based on the MeSH ontology and GO, respectively. Both results outperforms the five other algorithms in terms of F-measure. Based on the MeSH ontology and GO, the generated corpus-related ontologies show informative conceptual structures. The proposed method enables users to specify the domain knowledge to exploit the conceptual structures of biomedical document collections. In addition, the proposed method is able to extract the key concepts and cluster the documents with a relatively high precision. Copyright 2010 Elsevier B.V. All rights reserved.

Bacterial cellulose-kaolin nanocomposites for application as biomedical wound healing materials

NASA Astrophysics Data System (ADS)

Wanna, Dwi; Alam, Catharina; Toivola, Diana M.; Alam, Parvez

2013-12-01

This short communication provides preliminary experimental details on the structure-property relationships of novel biomedical kaolin-bacterial cellulose nanocomposites. Bacterial cellulose is an effective binding agent for kaolin particles forming reticulated structures at kaolin-cellulose interfaces and entanglements when the cellulose fraction is sufficiently high. The mechanical performance of these materials hence improves with an increased fraction of bacterial cellulose, though this also causes the rate of blood clotting to decrease. These composites have combined potential as both short-term (kaolin) and long-term (bacterial cellulose) wound healing materials.

Cryogenics free production of hyperpolarized 129Xe and 83Kr for biomedical MRI applications

NASA Astrophysics Data System (ADS)

Hughes-Riley, Theodore; Six, Joseph S.; Lilburn, David M. L.; Stupic, Karl F.; Dorkes, Alan C.; Shaw, Dominick E.; Pavlovskaya, Galina E.; Meersmann, Thomas

2013-12-01

As an alternative to cryogenic gas handling, hyperpolarized (hp) gas mixtures were extracted directly from the spin exchange optical pumping (SEOP) process through expansion followed by compression to ambient pressure for biomedical MRI applications. The omission of cryogenic gas separation generally requires the usage of high xenon or krypton concentrations at low SEOP gas pressures to generate hp 129Xe or hp 83Kr with sufficient MR signal intensity for imaging applications. Two different extraction schemes for the hp gasses were explored with focus on the preservation of the nuclear spin polarization. It was found that an extraction scheme based on an inflatable, pressure controlled balloon is sufficient for hp 129Xe handling, while 83Kr can efficiently be extracted through a single cycle piston pump. The extraction methods were tested for ex vivo MRI applications with excised rat lungs. Precise mixing of the hp gases with oxygen, which may be of interest for potential in vivo applications, was accomplished during the extraction process using a piston pump. The 83Kr bulk gas phase T1 relaxation in the mixtures containing more than approximately 1% O2 was found to be slower than that of 129Xe in corresponding mixtures. The experimental setup also facilitated 129Xe T1 relaxation measurements as a function of O2 concentration within excised lungs.

Cryogenics free production of hyperpolarized 129Xe and 83Kr for biomedical MRI applications☆

PubMed Central

Hughes-Riley, Theodore; Six, Joseph S.; Lilburn, David M.L.; Stupic, Karl F.; Dorkes, Alan C.; Shaw, Dominick E.; Pavlovskaya, Galina E.; Meersmann, Thomas

2013-01-01

As an alternative to cryogenic gas handling, hyperpolarized (hp) gas mixtures were extracted directly from the spin exchange optical pumping (SEOP) process through expansion followed by compression to ambient pressure for biomedical MRI applications. The omission of cryogenic gas separation generally requires the usage of high xenon or krypton concentrations at low SEOP gas pressures to generate hp 129Xe or hp 83Kr with sufficient MR signal intensity for imaging applications. Two different extraction schemes for the hp gasses were explored with focus on the preservation of the nuclear spin polarization. It was found that an extraction scheme based on an inflatable, pressure controlled balloon is sufficient for hp 129Xe handling, while 83Kr can efficiently be extracted through a single cycle piston pump. The extraction methods were tested for ex vivo MRI applications with excised rat lungs. Precise mixing of the hp gases with oxygen, which may be of interest for potential in vivo applications, was accomplished during the extraction process using a piston pump. The 83Kr bulk gas phase T1 relaxation in the mixtures containing more than approximately 1% O2 was found to be slower than that of 129Xe in corresponding mixtures. The experimental setup also facilitated 129Xe T1 relaxation measurements as a function of O2 concentration within excised lungs. PMID:24135800

Cryogenics free production of hyperpolarized 129Xe and 83Kr for biomedical MRI applications.

PubMed

Hughes-Riley, Theodore; Six, Joseph S; Lilburn, David M L; Stupic, Karl F; Dorkes, Alan C; Shaw, Dominick E; Pavlovskaya, Galina E; Meersmann, Thomas

2013-12-01

As an alternative to cryogenic gas handling, hyperpolarized (hp) gas mixtures were extracted directly from the spin exchange optical pumping (SEOP) process through expansion followed by compression to ambient pressure for biomedical MRI applications. The omission of cryogenic gas separation generally requires the usage of high xenon or krypton concentrations at low SEOP gas pressures to generate hp (129)Xe or hp (83)Kr with sufficient MR signal intensity for imaging applications. Two different extraction schemes for the hp gasses were explored with focus on the preservation of the nuclear spin polarization. It was found that an extraction scheme based on an inflatable, pressure controlled balloon is sufficient for hp (129)Xe handling, while (83)Kr can efficiently be extracted through a single cycle piston pump. The extraction methods were tested for ex vivo MRI applications with excised rat lungs. Precise mixing of the hp gases with oxygen, which may be of interest for potential in vivo applications, was accomplished during the extraction process using a piston pump. The (83)Kr bulk gas phase T1 relaxation in the mixtures containing more than approximately 1% O2 was found to be slower than that of (129)Xe in corresponding mixtures. The experimental setup also facilitated (129)Xe T1 relaxation measurements as a function of O2 concentration within excised lungs. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Electrochemical Behavior of Biomedical Titanium Alloys Coated with Diamond Carbon in Hanks' Solution

NASA Astrophysics Data System (ADS)

Gnanavel, S.; Ponnusamy, S.; Mohan, L.; Radhika, R.; Muthamizhchelvan, C.; Ramasubramanian, K.

2018-03-01

Biomedical implants in the knee and hip are frequent failures because of corrosion and stress on the joints. To solve this important problem, metal implants can be coated with diamond carbon, and this coating plays a critical role in providing an increased resistance to implants toward corrosion. In this study, we have employed diamond carbon coating over Ti-6Al-4V and Ti-13Nb-13Zr alloys using hot filament chemical vapor deposition method which is well-established coating process that significantly improves the resistance toward corrosion, wears and hardness. The diamond carbon-coated Ti-13Nb-13Zr alloy showed an increased microhardness in the range of 850 HV. Electrochemical impedance spectroscopy and polarization studies in SBF solution (simulated body fluid solution) were carried out to understand the in vitro behavior of uncoated as well as coated titanium alloys. The experimental results showed that the corrosion resistance of Ti-13Nb-13Zr alloy is relatively higher when compared with diamond carbon-coated Ti-6Al-4V alloys due to the presence of β phase in the Ti-13Nb-13Zr alloy. Electrochemical impedance results showed that the diamond carbon-coated alloys behave as an ideal capacitor in the body fluid solution. Moreover, the stability in mechanical properties during the corrosion process was maintained for diamond carbon-coated titanium alloys.

A survey of quality assurance practices in biomedical open source software projects.

PubMed

Koru, Günes; El Emam, Khaled; Neisa, Angelica; Umarji, Medha

2007-05-07

Open source (OS) software is continuously gaining recognition and use in the biomedical domain, for example, in health informatics and bioinformatics. Given the mission critical nature of applications in this domain and their potential impact on patient safety, it is important to understand to what degree and how effectively biomedical OS developers perform standard quality assurance (QA) activities such as peer reviews and testing. This would allow the users of biomedical OS software to better understand the quality risks, if any, and the developers to identify process improvement opportunities to produce higher quality software. A survey of developers working on biomedical OS projects was conducted to examine the QA activities that are performed. We took a descriptive approach to summarize the implementation of QA activities and then examined some of the factors that may be related to the implementation of such practices. Our descriptive results show that 63% (95% CI, 54-72) of projects did not include peer reviews in their development process, while 82% (95% CI, 75-89) did include testing. Approximately 74% (95% CI, 67-81) of developers did not have a background in computing, 80% (95% CI, 74-87) were paid for their contributions to the project, and 52% (95% CI, 43-60) had PhDs. A multivariate logistic regression model to predict the implementation of peer reviews was not significant (likelihood ratio test = 16.86, 9 df, P = .051) and neither was a model to predict the implementation of testing (likelihood ratio test = 3.34, 9 df, P = .95). Less attention is paid to peer review than testing. However, the former is a complementary, and necessary, QA practice rather than an alternative. Therefore, one can argue that there are quality risks, at least at this point in time, in transitioning biomedical OS software into any critical settings that may have operational, financial, or safety implications. Developers of biomedical OS applications should invest more effort in implementing systemic peer review practices throughout the development and maintenance processes.

New Software Developments for Quality Mesh Generation and Optimization from Biomedical Imaging Data

PubMed Central

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

2013-01-01

In this paper we present a new software toolkit for generating and optimizing surface and volumetric meshes from three-dimensional (3D) biomedical imaging data, targeted at image-based finite element analysis of some biomedical activities in a single material domain. Our toolkit includes a series of geometric processing algorithms including surface re-meshing and quality-guaranteed tetrahedral mesh generation and optimization. All methods described have been encapsulated into a user-friendly graphical interface for easy manipulation and informative visualization of biomedical images and mesh models. Numerous examples are presented to demonstrate the effectiveness and efficiency of the described methods and toolkit. PMID:24252469

Micro/Nanostructured Films and Adhesives for Biomedical Applications.

PubMed

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.

NASA Biomedical Informatics Capabilities and Needs

NASA Technical Reports Server (NTRS)

Johnson-Throop, Kathy A.

2009-01-01

To improve on-orbit clinical capabilities by developing and providing operational support for intelligent, robust, reliable, and secure, enterprise-wide and comprehensive health care and biomedical informatics systems with increasing levels of autonomy, for use on Earth, low Earth orbit & exploration class missions. Biomedical Informatics is an emerging discipline that has been defined as the study, invention, and implementation of structures and algorithms to improve communication, understanding and management of medical information. The end objective of biomedical informatics is the coalescing of data, knowledge, and the tools necessary to apply that data and knowledge in the decision-making process, at the time and place that a decision needs to be made.

What Do I Want to Be with My PhD? The Roles of Personal Values and Structural Dynamics in Shaping the Career Interests of Recent Biomedical Science PhD Graduates

ERIC Educational Resources Information Center

Gibbs, Kenneth D., Jr.; Griffin, Kimberly A.

2013-01-01

Interest in faculty careers decreases as graduate training progresses; however, the process underlying career-interest formation remains poorly defined. To better understand this process and whether/how it differs across social identity (i.e., race/ethnicity, gender), we conducted focus groups with 38 biomedical scientists who received PhDs…

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

PubMed

Couto, Francisco M; Pinto, H Sofia

2013-10-01

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

Outlook for Development of High-throughput Cryopreservation for Small-bodied Biomedical Model Fishes★

PubMed Central

Tiersch, Terrence R.; Yang, Huiping; Hu, E.

2011-01-01

With the development of genomic research technologies, comparative genome studies among vertebrate species are becoming commonplace for human biomedical research. Fish offer unlimited versatility for biomedical research. Extensive studies are done using these fish models, yielding tens of thousands of specific strains and lines, and the number is increasing every day. Thus, high-throughput sperm cryopreservation is urgently needed to preserve these genetic resources. Although high-throughput processing has been widely applied for sperm cryopreservation in livestock for decades, application in biomedical model fishes is still in the concept-development stage because of the limited sample volumes and the biological characteristics of fish sperm. High-throughput processing in livestock was developed based on advances made in the laboratory and was scaled up for increased processing speed, capability for mass production, and uniformity and quality assurance. Cryopreserved germplasm combined with high-throughput processing constitutes an independent industry encompassing animal breeding, preservation of genetic diversity, and medical research. Currently, there is no specifically engineered system available for high-throughput of cryopreserved germplasm for aquatic species. This review is to discuss the concepts and needs for high-throughput technology for model fishes, propose approaches for technical development, and overview future directions of this approach. PMID:21440666

Annual tendency of research papers used ICR mice as experimental animals in biomedical research fields.

PubMed

Kim, Ji Eun; Nam, Jung Hoon; Cho, Joon Young; Kim, Kil Soo; Hwang, Dae Youn

2017-06-01

Institute of Cancer Research (ICR) mice have been widely used in various research fields including toxicology, oncology, pharmacology, and pharmaceutical product safety testing for decades. However, annual tendency of research papers involving ICR mice in various biomedical fields has not been previously analyzed. In this study, we examined the numbers of papers that used ICR mice as experimental animals in the social science, natural science, engineering, medicine-pharmacy, marine agriculture-fishery, and art-kinesiology fields by analyzing big data. Numbers of ICR mouse-used papers gradually increased from 1961 to 2014, but small decreases were observed in 2015 and 2016. The largest number of ICR-used papers were published in the medicine-pharmacy field, followed by natural science and art-kinesiology fields. There were no ICR mouse-used papers in other fields. Furthermore, ICR mice have been widely employed in cell biology studies within the natural science field as well as in biochemistry and pathology in the medicine-pharmacy field. Few ICR mouse-used papers were published in exercise biochemistry and exercise nutrition in the art-kinesiology field. Regardless in most fields, the total numbers of published papers involving ICR mice were higher in 2014 than in other years, although the numbers in some fields including dentistry, veterinary science, and dermatology were high in 2016. Taken together, the present study shows that various ICR stocks, including Korl:ICR mice, are widely employed as experimental animals in various biomedical research fields.

Annual tendency of research papers used ICR mice as experimental animals in biomedical research fields

PubMed Central

Kim, Ji Eun; Nam, Jung Hoon; Cho, Joon Young; Kim, Kil Soo

2017-01-01

Institute of Cancer Research (ICR) mice have been widely used in various research fields including toxicology, oncology, pharmacology, and pharmaceutical product safety testing for decades. However, annual tendency of research papers involving ICR mice in various biomedical fields has not been previously analyzed. In this study, we examined the numbers of papers that used ICR mice as experimental animals in the social science, natural science, engineering, medicine-pharmacy, marine agriculture-fishery, and art-kinesiology fields by analyzing big data. Numbers of ICR mouse-used papers gradually increased from 1961 to 2014, but small decreases were observed in 2015 and 2016. The largest number of ICR-used papers were published in the medicine-pharmacy field, followed by natural science and art-kinesiology fields. There were no ICR mouse-used papers in other fields. Furthermore, ICR mice have been widely employed in cell biology studies within the natural science field as well as in biochemistry and pathology in the medicine-pharmacy field. Few ICR mouse-used papers were published in exercise biochemistry and exercise nutrition in the art-kinesiology field. Regardless in most fields, the total numbers of published papers involving ICR mice were higher in 2014 than in other years, although the numbers in some fields including dentistry, veterinary science, and dermatology were high in 2016. Taken together, the present study shows that various ICR stocks, including Korl:ICR mice, are widely employed as experimental animals in various biomedical research fields. PMID:28747984

An Ontology-Enabled Natural Language Processing Pipeline for Provenance Metadata Extraction from Biomedical Text (Short Paper).

PubMed

Valdez, Joshua; Rueschman, Michael; Kim, Matthew; Redline, Susan; Sahoo, Satya S

2016-10-01

Extraction of structured information from biomedical literature is a complex and challenging problem due to the complexity of biomedical domain and lack of appropriate natural language processing (NLP) techniques. High quality domain ontologies model both data and metadata information at a fine level of granularity, which can be effectively used to accurately extract structured information from biomedical text. Extraction of provenance metadata, which describes the history or source of information, from published articles is an important task to support scientific reproducibility. Reproducibility of results reported by previous research studies is a foundational component of scientific advancement. This is highlighted by the recent initiative by the US National Institutes of Health called "Principles of Rigor and Reproducibility". In this paper, we describe an effective approach to extract provenance metadata from published biomedical research literature using an ontology-enabled NLP platform as part of the Provenance for Clinical and Healthcare Research (ProvCaRe). The ProvCaRe-NLP tool extends the clinical Text Analysis and Knowledge Extraction System (cTAKES) platform using both provenance and biomedical domain ontologies. We demonstrate the effectiveness of ProvCaRe-NLP tool using a corpus of 20 peer-reviewed publications. The results of our evaluation demonstrate that the ProvCaRe-NLP tool has significantly higher recall in extracting provenance metadata as compared to existing NLP pipelines such as MetaMap.

From Bench to Bedside: A communal utility value intervention to enhance students' biomedical science motivation.

PubMed

Brown, Elizabeth R; Smith, Jessi L; Thoman, Dustin B; Allen, Jill M; Muragishi, Gregg

2015-11-01

Motivating students to pursue science careers is a top priority among many science educators. We add to the growing literature by examining the impact of a utility value intervention to enhance student's perceptions that biomedical science affords important utility work values. Using an expectancy-value perspective we identify and test two types of utility value: communal (other-oriented) and agentic (self-oriented). The culture of science is replete with examples emphasizing high levels of agentic value, but communal values are often (stereotyped as) absent from science. However, people in general want an occupation that has communal utility. We predicted and found that an intervention emphasizing the communal utility value of biomedical research increased students' motivation for biomedical science (Studies 1-3). We refined whether different types of communal utility value (working with, helping, and forming relationships with others) might be more or less important, demonstrating that helping others was an especially important predictor of student motivation (Study 2). Adding agentic utility value to biomedical research did not further increase student motivation (Study 3). Furthermore, the communal value intervention indirectly impacted students' motivation because students believed that biomedical research was communal and thus subsequently more important (Studies 1-3). This is key, because enhancing student communal value beliefs about biomedical research (Studies 1-3) and science (Study 4) was associated both with momentary increases in motivation in experimental settings (Studies 1-3) and increased motivation over time among students highly identified with biomedicine (Study 4). We discuss recommendations for science educators, practitioners, and faculty mentors who want to broaden participation in science.

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

PubMed

Schulz, Stefan; López-García, Pablo

2015-08-01

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

Animal experimentation--a personal view.

PubMed

Gershoff, Stanley N

2009-02-01

Disagreement about the use of animals in biomedical research has resulted in absurd positions by both sides. Increasingly, some zealots against animal experimentation have resorted to violence or other illegal acts to support their points of view. The value of animal research in providing better health for man and animals is incontrovertible. This is illustrated by references to animal research in the field of nutrition.

A System for Information Management in BioMedical Studies—SIMBioMS

PubMed Central

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

2009-01-01

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

Biomedical signal acquisition, processing and transmission using smartphone

NASA Astrophysics Data System (ADS)

Roncagliolo, Pablo; Arredondo, Luis; González, Agustín

2007-11-01

This article describes technical aspects involved in the programming of a system of acquisition, processing and transmission of biomedical signals by using mobile devices. This task is aligned with the permanent development of new technologies for the diagnosis and sickness treatment, based on the feasibility of measuring continuously different variables as electrocardiographic signals, blood pressure, oxygen concentration, pulse or simply temperature. The contribution of this technology is settled on its portability and low cost, which allows its massive use. Specifically this work analyzes the feasibility of acquisition and the processing of signals from a standard smartphone. Work results allow to state that nowadays these equipments have enough processing capacity to execute signals acquisition systems. These systems along with external servers make it possible to imagine a near future where the possibility of making continuous measures of biomedical variables will not be restricted only to hospitals but will also begin to be more frequently used in the daily life and at home.

SOA-based digital library services and composition in biomedical applications.

PubMed

Zhao, Xia; Liu, Enjie; Clapworthy, Gordon J; Viceconti, Marco; Testi, Debora

2012-06-01

Carefully collected, high-quality data are crucial in biomedical visualization, and it is important that the user community has ready access to both this data and the high-performance computing resources needed by the complex, computational algorithms that will process it. Biological researchers generally require data, tools and algorithms from multiple providers to achieve their goals. This paper illustrates our response to the problems that result from this. The Living Human Digital Library (LHDL) project presented in this paper has taken advantage of Web Services to build a biomedical digital library infrastructure that allows clinicians and researchers not only to preserve, trace and share data resources, but also to collaborate at the data-processing level. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

eHealth and IMIA's Strategic Planning Process - IMIA conference introductory address.

PubMed

Murray, Peter; Haux, Reinhold; Lorenzi, Nancy

2008-01-01

The International Medical Informatics Association (IMIA) is the only organization in health and biomedical informatics which is fully international in scope, bridging the academic, health practice, education, and health industry worlds through conferences, working groups, special interest groups and publications. Authored by the IMIA Interim Vice President for Strategic Planning Implementation and co-authored by the current IMIA President and the IMIA Past-President, the intention of this paper is to introduce IMIA's current strategic planning process and to set this process in relation to 'eHealth: Combining Health Telematics, Telemedicine, Biomedical Engineering and Bioinformatics to the Edge', the theme of this conference. From the viewpoint of an international organization such as IMIA, an eHealth strategy needs to be considered in a comprehensive way, including broadly stimulating high-quality health and biomedical informatics research and education, as well as providing support to bridging outcomes towards a new practice of health care in a changing world.

Cloud Based Metalearning System for Predictive Modeling of Biomedical Data

PubMed Central

Vukićević, Milan

2014-01-01

Rapid growth and storage of biomedical data enabled many opportunities for predictive modeling and improvement of healthcare processes. On the other side analysis of such large amounts of data is a difficult and computationally intensive task for most existing data mining algorithms. This problem is addressed by proposing a cloud based system that integrates metalearning framework for ranking and selection of best predictive algorithms for data at hand and open source big data technologies for analysis of biomedical data. PMID:24892101

Design study of beam transport lines for BioLEIR facility at CERN

NASA Astrophysics Data System (ADS)

Ghithan, S.; Roy, G.; Schuh, S.

2017-09-01

The biomedical community has asked CERN to investigate the possibility to transform the Low Energy Ion Ring (LEIR) accelerator into a multidisciplinary, biomedical research facility (BioLEIR) that could provide ample, high-quality beams of a range of light ions suitable for clinically oriented, fundamental research on cell cultures and for radiation instrumentation development. The present LEIR machine uses fast beam extraction to the next accelerator in the chain, eventually leading to the Large Hadron Collider (LHC) . To provide beam for a biomedical research facility, a new slow extraction system must be installed. Two horizontal and one vertical experimental beamlines were designed for transporting the extracted beam to three experimental end-stations. The vertical beamline (pencil beam) was designed for a maximum energy of 75 MeV/u for low-energy radiobiological research, while the two horizontal beamlines could deliver up to 440 MeV/u. One horizontal beamline shall be used preferentially for biomedical experiments and shall provide pencil beam and a homogeneous broad beam, covering an area of 5 × 5 cm2 with a beam homogeneity of ±5%. The second horizontal beamline will have pencil beam only and is intended for hardware developments in the fields of (micro-)dosimetry and detector development. The minimum full aperture of the beamlines is approximately 100 mm at all magnetic elements, to accommodate the expected beam envelopes. Seven dipoles and twenty quadrupoles are needed for a total of 65 m of beamlines to provide the specified beams. In this paper we present the optical design for the three beamlines.

An enhanced approach for biomedical image restoration using image fusion techniques

NASA Astrophysics Data System (ADS)

Karam, Ghada Sabah; Abbas, Fatma Ismail; Abood, Ziad M.; Kadhim, Kadhim K.; Karam, Nada S.

2018-05-01

Biomedical image is generally noisy and little blur due to the physical mechanisms of the acquisition process, so one of the common degradations in biomedical image is their noise and poor contrast. The idea of biomedical image enhancement is to improve the quality of the image for early diagnosis. In this paper we are using Wavelet Transformation to remove the Gaussian noise from biomedical images: Positron Emission Tomography (PET) image and Radiography (Radio) image, in different color spaces (RGB, HSV, YCbCr), and we perform the fusion of the denoised images resulting from the above denoising techniques using add image method. Then some quantive performance metrics such as signal -to -noise ratio (SNR), peak signal-to-noise ratio (PSNR), and Mean Square Error (MSE), etc. are computed. Since this statistical measurement helps in the assessment of fidelity and image quality. The results showed that our approach can be applied of Image types of color spaces for biomedical images.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Preparing chimpanzees for laboratory research.

PubMed

Bloomsmith, Mollie A; Schapiro, Steven J; Strobert, Elizabeth A

2006-01-01

The chimpanzee is the only representative of the Great Apes that is extensively involved in biomedical research in primate laboratories. These apes are used as animal models in a variety of studies, including research on infectious disease, parasitic disease, pharmacokinetic studies, neuroscience, cognition, and behavior. Chimpanzees used in biomedical research in the United States reside largely in six specialized research and holding facilities, and most of the research with them is conducted at these sites. Given the relatively small population of chimpanzees and its importance to biomedical research, it is imperative that we carefully manage the care, production, and use of these animals in biomedical research studies. Selection criteria and preparation techniques are reviewed in this article in an effort to begin a discussion on best practices for choosing and handling chimpanzees participating in biomedical research. The use of routine health assessment information is described for subject selection, as are behavioral issues to be considered. Due to the relatively small number of chimpanzees available, issues related to experimental design and multiple uses of chimpanzees are discussed. Practices related to the transportation and acclimation of chimpanzees are described. Finally, behavioral conditioning procedures are discussed, including habituation, desensitization, and positive reinforcement training that have been applied to reduce animal distress and improve the quality of the science being conducted with chimpanzee subjects.

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

PubMed

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.

Home telecare system using cable television plants--an experimental field trial.

PubMed

Lee, R G; Chen, H S; Lin, C C; Chang, K C; Chen, J H

2000-03-01

To solve the inconvenience of routine transportation of chronically ill and handicapped patients, this paper proposes a platform based on a hybrid fiber coaxial (HFC) network in Taiwan designed to make a home telecare system feasible. The aim of this home telecare system is to combine biomedical data, including three-channel electrocardiogram (ECG) and blood pressure (BP), video, and audio into a National Television Standard Committee (NTSC) channel for communication between the patient and healthcare provider. Digitized biomedical data and output from medical devices can be further modulated to a second audio program (SAP) subchannel which can be used for second-language audio in NTSC television signals. For long-distance transmission, we translate the digital biomedical data into the frequency domain using frequency shift key (FSK) technology and insert this signal into an SAP band. The whole system has been implemented and tested. The results obtained using this system clearly demonstrated that real-time video, audio, and biomedical data transmission are very clear with a carrier-to-noise ratio up to 43 dB.

Bridging medicine and biomedical technology: enhance translation of fundamental research to patient care

PubMed Central

Raff, Adam B.; Seiler, Theo G.; Apiou-Sbirlea, Gabriela

2017-01-01

The ‘Bridging medicine and biomedical technology’ special all-congress session took place for the first time at the OSA Biophotonics Congress: Optics in Life Sciences in 2017 (http://www.osa.org/enus/meetings/osa_meetings/optics_in_the_life_sciences/bridging_medicine_and_biomedical_technology_specia/). The purpose was to identify key challenges the biomedical scientists in academia have to overcome to translate their discoveries into clinical practice through robust collaborations with industry and discuss best practices to facilitate and accelerate the process. Our paper is intended to complement the session by providing a deeper insight into the concept behind the structure and the content we developed. PMID:29296473

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

PubMed

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

2014-01-01

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

A comparison of basic and state-of-the-arts skills sets of biomedical science technical staff in Lagos public universities.

PubMed

John, T A

2011-12-01

Biomedical science has advanced drastically in developed countries in the last two decades with many health and economic benefits. In Nigeria, biomedical science has not thrived and the contribution from Nigerian universities, indeed African universities, to publications in global high impact journals is low. The present work was based on the hypothesis that there is a lack of state-of-the-arts experimentation in Nigerian biomedical science experiments. An investigation was carried out on the professional skills of biomedical science technical staff of the two (federal and state) public universities in Lagos, Nigeria using a closed-ended questionnaire survey. The 17 respondents were asked about their training, the frequency of utilization of 99 skills, and their expertise. The respondents were "untrained" more in state-of-the-arts skills (34% for electrophoresis, 28% for genomics, 22% for immunochemistry, and 34% for proteomics skills) than in general professional skills (5%), basic technical equipment skills (16%), or general biomedical science knowledge and skills (16%). Frequencies of responses were higher for general skills than for state-of-the-arts skills in the responses "utilizing frequently" (9.96%-31-61% versus 0.36%-4.2%), and "I'm expert" (9.55%-19.88% versus 5.88%-8.48%). It was projected that with continued investment in modern equipment and infrastructure, there will be increased drive for training and usage of modern bioscience research skills and multidisciplinary approaches and production of high-tech scientific publications.

Multichannel biomedical time series clustering via hierarchical probabilistic latent semantic analysis.

PubMed

Wang, Jin; Sun, Xiangping; Nahavandi, Saeid; Kouzani, Abbas; Wu, Yuchuan; She, Mary

2014-11-01

Biomedical time series clustering that automatically groups a collection of time series according to their internal similarity is of importance for medical record management and inspection such as bio-signals archiving and retrieval. In this paper, a novel framework that automatically groups a set of unlabelled multichannel biomedical time series according to their internal structural similarity is proposed. Specifically, we treat a multichannel biomedical time series as a document and extract local segments from the time series as words. We extend a topic model, i.e., the Hierarchical probabilistic Latent Semantic Analysis (H-pLSA), which was originally developed for visual motion analysis to cluster a set of unlabelled multichannel time series. The H-pLSA models each channel of the multichannel time series using a local pLSA in the first layer. The topics learned in the local pLSA are then fed to a global pLSA in the second layer to discover the categories of multichannel time series. Experiments on a dataset extracted from multichannel Electrocardiography (ECG) signals demonstrate that the proposed method performs better than previous state-of-the-art approaches and is relatively robust to the variations of parameters including length of local segments and dictionary size. Although the experimental evaluation used the multichannel ECG signals in a biometric scenario, the proposed algorithm is a universal framework for multichannel biomedical time series clustering according to their structural similarity, which has many applications in biomedical time series management. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

PubMed Central

Bodenreider, O.

2008-01-01

Summary Objectives To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support. Methods Biomedical ontologies selected for their practical impact are examined from a functional perspective. Examples of applications are taken from operational systems and the biomedical literature, with a bias towards recent journal articles. Results The ontologies under investigation in this survey include SNOMED CT, the Logical Observation Identifiers, Names, and Codes (LOINC), the Foundational Model of Anatomy, the Gene Ontology, RxNorm, the National Cancer Institute Thesaurus, the International Classification of Diseases, the Medical Subject Headings (MeSH) and the Unified Medical Language System (UMLS). The roles played by biomedical ontologies are classified into three major categories: knowledge management (indexing and retrieval of data and information, access to information, mapping among ontologies); data integration, exchange and semantic interoperability; and decision support and reasoning (data selection and aggregation, decision support, natural language processing applications, knowledge discovery). Conclusions Ontologies play an important role in biomedical research through a variety of applications. While ontologies are used primarily as a source of vocabulary for standardization and integration purposes, many applications also use them as a source of computable knowledge. Barriers to the use of ontologies in biomedical applications are discussed. PMID:18660879

The Implicitome: A Resource for Rationalizing Gene-Disease Associations

PubMed Central

van der Horst, Eelke; Kaliyaperumal, Rajaram; Mina, Eleni; Tatum, Zuotian; Laros, Jeroen F. J.; van Mulligen, Erik M.; Schuemie, Martijn; Aten, Emmelien; Li, Tong Shu; Bruskiewich, Richard; Good, Benjamin M.; Su, Andrew I.; Kors, Jan A.; den Dunnen, Johan; van Ommen, Gert-Jan B.; Roos, Marco; ‘t Hoen, Peter A.C.; Mons, Barend; Schultes, Erik A.

2016-01-01

High-throughput experimental methods such as medical sequencing and genome-wide association studies (GWAS) identify increasingly large numbers of potential relations between genetic variants and diseases. Both biological complexity (millions of potential gene-disease associations) and the accelerating rate of data production necessitate computational approaches to prioritize and rationalize potential gene-disease relations. Here, we use concept profile technology to expose from the biomedical literature both explicitly stated gene-disease relations (the explicitome) and a much larger set of implied gene-disease associations (the implicitome). Implicit relations are largely unknown to, or are even unintended by the original authors, but they vastly extend the reach of existing biomedical knowledge for identification and interpretation of gene-disease associations. The implicitome can be used in conjunction with experimental data resources to rationalize both known and novel associations. We demonstrate the usefulness of the implicitome by rationalizing known and novel gene-disease associations, including those from GWAS. To facilitate the re-use of implicit gene-disease associations, we publish our data in compliance with FAIR Data Publishing recommendations [https://www.force11.org/group/fairgroup] using nanopublications. An online tool (http://knowledge.bio) is available to explore established and potential gene-disease associations in the context of other biomedical relations. PMID:26919047

Cross-correlation between EMG and center of gravity during quiet stance: theory and simulations.

PubMed

Kohn, André Fabio

2005-11-01

Several signal processing tools have been employed in the experimental study of the postural control system in humans. Among them, the cross-correlation function has been used to analyze the time relationship between signals such as the electromyogram and the horizontal projection of the center of gravity. The common finding is that the electromyogram precedes the biomechanical signal, a result that has been interpreted in different ways, for example, the existence of feedforward control or the preponderance of a velocity feedback. It is shown here, analytically and by simulation, that the cross-correlation function is dependent in a complicated way on system parameters and on noise spectra. Results similar to those found experimentally, e.g., electromyogram preceding the biomechanical signal may be obtained in a postural control model without any feedforward control and without any velocity feedback. Therefore, correct interpretations of experimentally obtained cross-correlation functions may require additional information about the system. The results extend to other biomedical applications where two signals from a closed loop system are cross-correlated.

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

PubMed Central

2012-01-01

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

[Application of the life sciences platform based on oracle to biomedical informations].

PubMed

Zhao, Zhi-Yun; Li, Tai-Huan; Yang, Hong-Qiao

2008-03-01

The life sciences platform based on Oracle database technology is introduced in this paper. By providing a powerful data access, integrating a variety of data types, and managing vast quantities of data, the software presents a flexible, safe and scalable management platform for biomedical data processing.

Biomedical engineers and participation in judicial executions: capital punishment as a technical problem.

PubMed

Doyle, John

2007-01-01

This paper discusses the topic of judicial execution from the perspective of the intersection of the technological issues and the professional ethics issues. Although physicians are generally ethically forbidden from any involvement in the judicial execution process, this does not appear to be the case for engineering professionals. This creates an interesting but controversial opportunity for the engineering community (especially biomedical engineers) to improve the humaneness and reliability of the judicial execution process.

From Bench to Bedside: A communal utility value intervention to enhance students’ biomedical science motivation

PubMed Central

Brown, Elizabeth R.; Smith, Jessi L.; Thoman, Dustin B.; Allen, Jill M.; Muragishi, Gregg

2015-01-01

Motivating students to pursue science careers is a top priority among many science educators. We add to the growing literature by examining the impact of a utility value intervention to enhance student’s perceptions that biomedical science affords important utility work values. Using an expectancy-value perspective we identify and test two types of utility value: communal (other-oriented) and agentic (self-oriented). The culture of science is replete with examples emphasizing high levels of agentic value, but communal values are often (stereotyped as) absent from science. However, people in general want an occupation that has communal utility. We predicted and found that an intervention emphasizing the communal utility value of biomedical research increased students’ motivation for biomedical science (Studies 1–3). We refined whether different types of communal utility value (working with, helping, and forming relationships with others) might be more or less important, demonstrating that helping others was an especially important predictor of student motivation (Study 2). Adding agentic utility value to biomedical research did not further increase student motivation (Study 3). Furthermore, the communal value intervention indirectly impacted students’ motivation because students believed that biomedical research was communal and thus subsequently more important (Studies 1–3). This is key, because enhancing student communal value beliefs about biomedical research (Studies 1–3) and science (Study 4) was associated both with momentary increases in motivation in experimental settings (Studies 1–3) and increased motivation over time among students highly identified with biomedicine (Study 4). We discuss recommendations for science educators, practitioners, and faculty mentors who want to broaden participation in science. PMID:26617417

Sol-gel processing of bioactive glass nanoparticles: A review.

PubMed

Zheng, Kai; Boccaccini, Aldo R

2017-11-01

Silicate-based bioactive glass nanoparticles (BGN) are gaining increasing attention in various biomedical applications due to their unique properties. Controlled synthesis of BGN is critical to their effective use in biomedical applications since BGN characteristics, such as morphology and composition, determining the properties of BGN, are highly related to the synthesis process. In the last decade, numerous investigations focusing on BGN synthesis have been reported. BGN can mainly be produced through the conventional melt-quench approach or by sol-gel methods. The latter approaches are drawing widespread attention, considering the convenience and versatility they offer to tune the properties of BGN. In this paper, we review the strategies of sol-gel processing of BGN, including those adopting different catalysts for initiating the hydrolysis and condensation of silicate precursors as well as those combining sol-gel chemistry with other techniques. The processes and mechanism of different synthesis approaches are introduced and discussed in detail. Considering the importance of the BGN morphology and composition to their biomedical applications, strategies put forward to control the size, shape, pore structure and composition of BGN are discussed. BGN are particularly interesting biomaterials for bone-related applications, however, they also have potential for other biomedical applications, e.g. in soft tissue regeneration/repair. Therefore, in the last part of this review, recently reported applications of BGN in soft tissue repair and wound healing are presented. Copyright © 2017 Elsevier B.V. All rights reserved.

Geometry-constraint-scan imaging for in-line phase contrast micro-CT.

PubMed

Fu, Jian; Yu, Guangyuan; Fan, Dekai

2014-01-01

X-ray phase contrast computed tomography (CT) uses the phase shift that x-rays undergo when passing through matter, rather than their attenuation, as the imaging signal and may provide better image quality in soft-tissue and biomedical materials with low atomic number. Here a geometry-constraint-scan imaging technique for in-line phase contrast micro-CT is reported. It consists of two circular-trajectory scans with x-ray detector at different positions, the phase projection extraction method with the Fresnel free-propagation theory and the filter back-projection reconstruction algorithm. This method removes the contact-detector scan and the pure phase object assumption in classical in-line phase contrast Micro-CT. Consequently it relaxes the experimental conditions and improves the image contrast. This work comprises a numerical study of this technique and its experimental verification using a biomedical composite dataset measured at an x-ray tube source Micro-CT setup. The numerical and experimental results demonstrate the validity of the presented method. It will be of interest for a wide range of in-line phase contrast Micro-CT applications in biology and medicine.

ProNormz--an integrated approach for human proteins and protein kinases normalization.

PubMed

Subramani, Suresh; Raja, Kalpana; Natarajan, Jeyakumar

2014-02-01

The task of recognizing and normalizing protein name mentions in biomedical literature is a challenging task and important for text mining applications such as protein-protein interactions, pathway reconstruction and many more. In this paper, we present ProNormz, an integrated approach for human proteins (HPs) tagging and normalization. In Homo sapiens, a greater number of biological processes are regulated by a large human gene family called protein kinases by post translational phosphorylation. Recognition and normalization of human protein kinases (HPKs) is considered to be important for the extraction of the underlying information on its regulatory mechanism from biomedical literature. ProNormz distinguishes HPKs from other HPs besides tagging and normalization. To our knowledge, ProNormz is the first normalization system available to distinguish HPKs from other HPs in addition to gene normalization task. ProNormz incorporates a specialized synonyms dictionary for human proteins and protein kinases, a set of 15 string matching rules and a disambiguation module to achieve the normalization. Experimental results on benchmark BioCreative II training and test datasets show that our integrated approach achieve a fairly good performance and outperforms more sophisticated semantic similarity and disambiguation systems presented in BioCreative II GN task. As a freely available web tool, ProNormz is useful to developers as extensible gene normalization implementation, to researchers as a standard for comparing their innovative techniques, and to biologists for normalization and categorization of HPs and HPKs mentions in biomedical literature. URL: http://www.biominingbu.org/pronormz. Copyright © 2013 Elsevier Inc. All rights reserved.

A low-cost biomedical signal transceiver based on a Bluetooth wireless system.

PubMed

Fazel-Rezai, Reza; Pauls, Mark; Slawinski, David

2007-01-01

Most current wireless biomedical signal transceivers use range-limiting communication. This work presents a low-cost biomedical signal transceiver that uses Bluetooth wireless technology. The design is implemented in a modular form to be adaptable to different types of biomedical signals. The signal front end obtains and processes incoming signals, which are then transmitted via a microcontroller and wireless module. Near real-time receive software in LabVIEW was developed to demonstrate the system capability. The completed transmitter prototype successfully transmits ECG signals, and is able to simultaneously send multiple signals. The sampling rate of the transmitter is fast enough to send up to thirteen ECG signals simultaneously, with an error rate below 0.1% for transmission exceeding 65 meters. A low-cost wireless biomedical transceiver has many applications, such as real-time monitoring of patients with a known condition in non-clinical settings.

BioStar models of clinical and genomic data for biomedical data warehouse design

PubMed Central

Wang, Liangjiang; Ramanathan, Murali

2008-01-01

Biomedical research is now generating large amounts of data, ranging from clinical test results to microarray gene expression profiles. The scale and complexity of these datasets give rise to substantial challenges in data management and analysis. It is highly desirable that data warehousing and online analytical processing technologies can be applied to biomedical data integration and mining. The major difficulty probably lies in the task of capturing and modelling diverse biological objects and their complex relationships. This paper describes multidimensional data modelling for biomedical data warehouse design. Since the conventional models such as star schema appear to be insufficient for modelling clinical and genomic data, we develop a new model called BioStar schema. The new model can capture the rich semantics of biomedical data and provide greater extensibility for the fast evolution of biological research methodologies. PMID:18048122

Concept recognition for extracting protein interaction relations from biomedical text

PubMed Central

Baumgartner, William A; Lu, Zhiyong; Johnson, Helen L; Caporaso, J Gregory; Paquette, Jesse; Lindemann, Anna; White, Elizabeth K; Medvedeva, Olga; Cohen, K Bretonnel; Hunter, Lawrence

2008-01-01

Background: Reliable information extraction applications have been a long sought goal of the biomedical text mining community, a goal that if reached would provide valuable tools to benchside biologists in their increasingly difficult task of assimilating the knowledge contained in the biomedical literature. We present an integrated approach to concept recognition in biomedical text. Concept recognition provides key information that has been largely missing from previous biomedical information extraction efforts, namely direct links to well defined knowledge resources that explicitly cement the concept's semantics. The BioCreative II tasks discussed in this special issue have provided a unique opportunity to demonstrate the effectiveness of concept recognition in the field of biomedical language processing. Results: Through the modular construction of a protein interaction relation extraction system, we present several use cases of concept recognition in biomedical text, and relate these use cases to potential uses by the benchside biologist. Conclusion: Current information extraction technologies are approaching performance standards at which concept recognition can begin to deliver high quality data to the benchside biologist. Our system is available as part of the BioCreative Meta-Server project and on the internet . PMID:18834500

A Theoretical and Experimental Study for a Developing Flow in a Thin Fluid Gap

NASA Astrophysics Data System (ADS)

Wu, Qianhong; Lang, Ji; Jen, Kei-Peng; Nathan, Rungun; Vucbmss Team

2016-11-01

In this paper, we report a novel theoretical and experimental approach to examine a fast developing flow in a thin fluid gap. Although the phenomena are widely observed in industrial applications and biological systems, there is a lack of analytical approach that captures the instantaneous fluid response to a sudden impact. An experimental setup was developed that contains a piston instrumented with a laser displacement sensor and a pressure transducer. A sudden impact was imposed on the piston, creating a fast compaction on the thin fluid gap underneath. The motion of the piston was captured by the laser displacement sensor, and the fluid pressure build-up and relaxation was recorded by the pressure transducer. For this dynamic process, a novel analytical approach was developed. It starts with the inviscid limit when the viscous fluid effect has no time to appear. This short process is followed by a developing flow, in which the inviscid core flow region decreases and the viscous wall region increases until the entire fluid gap is filled with viscous fluid flow. A boundary layer integral method is used during the process. Lastly, the flow is completely viscous dominant featured by a typical squeeze flow in a thin gap. Excellent agreement between the theory and the experiment was achieved. The study presented herein, filling the gap in the literature, will have broad impact in industrial and biomedical applications. This research was supported by the National Science Foundation under Award #1511096.

SERS microscopy: plasmonic nanoparticle probes and biomedical applications

NASA Astrophysics Data System (ADS)

Gellner, M.; Schütz, M.; Salehi, M.; Packeisen, J.; Ströbel, P.; Marx, A.; Schmuck, C.; Schlücker, S.

2010-08-01

Nanoparticle probes for use in targeted detection schemes and readout by surface-enhanced Raman scattering (SERS) comprise a metal core, Raman reporter molecules and a protective shell. One design of SERS labels specifically optimized for biomedical applications in conjunction with red laser excitation is based on tunable gold/silver nanoshells, which are completely covered by a self-assembled monolayer (SAM) of Raman reporters. A shell around the SAM-coated metal core stabilizes the colloid and prevents particle aggregation. The optical properties and SERS efficiencies of these plasmonic nanostructures are characterized both experimentally and theoretically. Subsequent bioconjugation of SERS probes to ligands such as antibodies is a prerequisite for the selective detection of the corresponding target molecule via the characteristic Raman signature of the label. Biomedical imaging applications of SERS-labeled antibodies for tumor diagnostics by SERS microscopy are presented, using the localization of the tumor suppressor p63 in prostate tissue sections as an example.

Reflections on biomedical informatics: from cybernetics to genomic medicine and nanomedicine.

PubMed

Maojo, Victor; Kulikowski, Casimir A

2006-01-01

Expanding on our previous analysis of Biomedical Informatics (BMI), the present perspective ranges from cybernetics to nanomedicine, based on its scientific, historical, philosophical, theoretical, experimental, and technological aspects as they affect systems developments, simulation and modelling, education, and the impact on healthcare. We then suggest that BMI is still searching for strong basic scientific principles around which it can crystallize. As -omic biological knowledge increasingly impacts the future of medicine, ubiquitous computing and informatics become even more essential, not only for the technological infrastructure, but as a part of the scientific enterprise itself. The Virtual Physiological Human and investigations into nanomedicine will surely produce yet more unpredictable opportunities, leading to significant changes in biomedical research and practice. As a discipline involved in making such advances possible, BMI is likely to need to re-define itself and extend its research horizons to meet the new challenges.

Biomedical programs operations plans

NASA Technical Reports Server (NTRS)

Walbrecher, H. F.

1974-01-01

Operational guidelines for the space shuttle life sciences payloads are presented. An operational assessment of the medical experimental altitude test for Skylab, and Skylab life sciences documentation are discussed along with the operations posture and collection of space shuttle operational planning data.

Exploiting semantic patterns over biomedical knowledge graphs for predicting treatment and causative relations.

PubMed

Bakal, Gokhan; Talari, Preetham; Kakani, Elijah V; Kavuluru, Ramakanth

2018-06-01

Identifying new potential treatment options for medical conditions that cause human disease burden is a central task of biomedical research. Since all candidate drugs cannot be tested with animal and clinical trials, in vitro approaches are first attempted to identify promising candidates. Likewise, identifying different causal relations between biomedical entities is also critical to understand biomedical processes. Generally, natural language processing (NLP) and machine learning are used to predict specific relations between any given pair of entities using the distant supervision approach. To build high accuracy supervised predictive models to predict previously unknown treatment and causative relations between biomedical entities based only on semantic graph pattern features extracted from biomedical knowledge graphs. We used 7000 treats and 2918 causes hand-curated relations from the UMLS Metathesaurus to train and test our models. Our graph pattern features are extracted from simple paths connecting biomedical entities in the SemMedDB graph (based on the well-known SemMedDB database made available by the U.S. National Library of Medicine). Using these graph patterns connecting biomedical entities as features of logistic regression and decision tree models, we computed mean performance measures (precision, recall, F-score) over 100 distinct 80-20% train-test splits of the datasets. For all experiments, we used a positive:negative class imbalance of 1:10 in the test set to model relatively more realistic scenarios. Our models predict treats and causes relations with high F-scores of 99% and 90% respectively. Logistic regression model coefficients also help us identify highly discriminative patterns that have an intuitive interpretation. We are also able to predict some new plausible relations based on false positives that our models scored highly based on our collaborations with two physician co-authors. Finally, our decision tree models are able to retrieve over 50% of treatment relations from a recently created external dataset. We employed semantic graph patterns connecting pairs of candidate biomedical entities in a knowledge graph as features to predict treatment/causative relations between them. We provide what we believe is the first evidence in direct prediction of biomedical relations based on graph features. Our work complements lexical pattern based approaches in that the graph patterns can be used as additional features for weakly supervised relation prediction. Copyright © 2018 Elsevier Inc. All rights reserved.

Drawing lithography for microneedles: a review of fundamentals and biomedical applications.

PubMed

Lee, Kwang; Jung, Hyungil

2012-10-01

A microneedle is a three-dimensional (3D) micromechanical structure and has been in the spotlight recently as a drug delivery system (DDS). Because a microneedle delivers the target drug after penetrating the skin barrier, the therapeutic effects of microneedles proceed from its 3D structural geometry. Various types of microneedles have been fabricated using subtractive micromanufacturing methods which are based on the inherently planar two-dimensional (2D) geometries. However, traditional subtractive processes are limited for flexible structural microneedles and makes functional biomedical applications for efficient drug delivery difficult. The authors of the present study propose drawing lithography as a unique additive process for the fabrication of a microneedle directly from 2D planar substrates, thus overcoming a subtractive process shortcoming. The present article provides the first overview of the principal drawing lithography technology: fundamentals and biomedical applications. The continuous drawing technique for an ultrahigh-aspect ratio (UHAR) hollow microneedle, stepwise controlled drawing technique for a dissolving microneedle, and drawing technique with antidromic isolation for a hybrid electro-microneedle (HEM) are reviewed, and efficient biomedical applications by drawing lithography-mediated microneedles as an innovative drug and gene delivery system are described. Drawing lithography herein can provide a great breakthrough in the development of materials science and biotechnology. Copyright © 2012 Elsevier Ltd. All rights reserved.

"On-screen" writing and composing: two years experience with Manuscript Manager, Apple II and IBM-PC versions.

PubMed

Offerhaus, L

1989-06-01

The problems of the direct composition of a biomedical manuscript on a personal computer are discussed. Most word processing software is unsuitable because literature references, once stored, cannot be rearranged if major changes are necessary. These obstacles have been overcome in Manuscript Manager, a combination of word processing and database software. As it follows Council of Biology Editors and Vancouver rules, the printouts should be technically acceptable to most leading biomedical journals.

Knowledge acquisition for medical diagnosis using collective intelligence.

PubMed

Hernández-Chan, G; Rodríguez-González, A; Alor-Hernández, G; Gómez-Berbís, J M; Mayer-Pujadas, M A; Posada-Gómez, R

2012-11-01

The wisdom of the crowds (WOC) is the process of taking into account the collective opinion of a group of individuals rather than a single expert to answer a question. Based on this assumption, the use of processes based on WOC techniques to collect new biomedical knowledge represents a challenging and cutting-edge trend on biomedical knowledge acquisition. The work presented in this paper shows a new schema to collect diagnosis information in Diagnosis Decision Support Systems (DDSS) based on collective intelligence and consensus methods.

The Academy for Future Science Faculty: randomized controlled trial of theory-driven coaching to shape development and diversity of early-career scientists

PubMed Central

2014-01-01

Background Approaches to training biomedical scientists have created a talented research community. However, they have failed to create a professional workforce that includes many racial and ethnic minorities and women in proportion to their representation in the population or in PhD training. This is particularly true at the faculty level. Explanations for the absence of diversity in faculty ranks can be found in social science theories that reveal processes by which individuals develop identities, experiences, and skills required to be seen as legitimate within the profession. Methods/Design Using the social science theories of Communities of Practice, Social Cognitive Career Theory, identity formation, and cultural capital, we have developed and are testing a novel coaching-based model to address some of the limitations of previous diversity approaches. This coaching intervention (The Academy for Future Science Faculty) includes annual in-person meetings of students and trained faculty Career Coaches, along with ongoing virtual coaching, group meetings and communication. The model is being tested as a randomized controlled trial with two cohorts of biomedical PhD students from across the U.S., one recruited at the start of their PhDs and one nearing completion. Stratification into the experimental and control groups, and to coaching groups within the experimental arms, achieved equal numbers of students by race, ethnicity and gender to the extent possible. A fundamental design element of the Academy is to teach and make visible the social science principles which highly influence scientific advancement, as well as acknowledging the extra challenges faced by underrepresented groups working to be seen as legitimate within the scientific communities. Discussion The strategy being tested is based upon a novel application of the well-established principles of deploying highly skilled coaches, selected and trained for their ability to develop talents of others. This coaching model is intended to be a complement, rather than a substitute, for traditional mentoring in biomedical research training, and is being tested as such. PMID:25084625

Toward modular biological models: defining analog modules based on referent physiological mechanisms

PubMed Central

2014-01-01

Background Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project’s requirements. In particular, modularity facilitates component reuse and model integration for models with different use cases, including the ability to exchange modules during or between simulations. The heterogeneous nature of biology and vast range of wet-lab experimental platforms call for modular models designed to satisfy a variety of use cases. We argue that software analogs of biological mechanisms are reasonable candidates for modularization. Biomimetic software mechanisms comprised of physiomimetic mechanism modules offer benefits that are unique or especially important to multi-scale, biomedical modeling and simulation. Results We present a general, scientific method of modularizing mechanisms into reusable software components that we call physiomimetic mechanism modules (PMMs). PMMs utilize parametric containers that partition and expose state information into physiologically meaningful groupings. To demonstrate, we modularize four pharmacodynamic response mechanisms adapted from an in silico liver (ISL). We verified the modularization process by showing that drug clearance results from in silico experiments are identical before and after modularization. The modularized ISL achieves validation targets drawn from propranolol outflow profile data. In addition, an in silico hepatocyte culture (ISHC) is created. The ISHC uses the same PMMs and required no refactoring. The ISHC achieves validation targets drawn from propranolol intrinsic clearance data exhibiting considerable between-lab variability. The data used as validation targets for PMMs originate from both in vitro to in vivo experiments exhibiting large fold differences in time scale. Conclusions This report demonstrates the feasibility of PMMs and their usefulness across multiple model use cases. The pharmacodynamic response module developed here is robust to changes in model context and flexible in its ability to achieve validation targets in the face of considerable experimental uncertainty. Adopting the modularization methods presented here is expected to facilitate model reuse and integration, thereby accelerating the pace of biomedical research. PMID:25123169

Toward modular biological models: defining analog modules based on referent physiological mechanisms.

PubMed

Petersen, Brenden K; Ropella, Glen E P; Hunt, C Anthony

2014-08-16

Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think more deeply about the role of the model and to more completely address a modeling project's requirements. In particular, modularity facilitates component reuse and model integration for models with different use cases, including the ability to exchange modules during or between simulations. The heterogeneous nature of biology and vast range of wet-lab experimental platforms call for modular models designed to satisfy a variety of use cases. We argue that software analogs of biological mechanisms are reasonable candidates for modularization. Biomimetic software mechanisms comprised of physiomimetic mechanism modules offer benefits that are unique or especially important to multi-scale, biomedical modeling and simulation. We present a general, scientific method of modularizing mechanisms into reusable software components that we call physiomimetic mechanism modules (PMMs). PMMs utilize parametric containers that partition and expose state information into physiologically meaningful groupings. To demonstrate, we modularize four pharmacodynamic response mechanisms adapted from an in silico liver (ISL). We verified the modularization process by showing that drug clearance results from in silico experiments are identical before and after modularization. The modularized ISL achieves validation targets drawn from propranolol outflow profile data. In addition, an in silico hepatocyte culture (ISHC) is created. The ISHC uses the same PMMs and required no refactoring. The ISHC achieves validation targets drawn from propranolol intrinsic clearance data exhibiting considerable between-lab variability. The data used as validation targets for PMMs originate from both in vitro to in vivo experiments exhibiting large fold differences in time scale. This report demonstrates the feasibility of PMMs and their usefulness across multiple model use cases. The pharmacodynamic response module developed here is robust to changes in model context and flexible in its ability to achieve validation targets in the face of considerable experimental uncertainty. Adopting the modularization methods presented here is expected to facilitate model reuse and integration, thereby accelerating the pace of biomedical research.

[Application of the mixed programming with Labview and Matlab in biomedical signal analysis].

PubMed

Yu, Lu; Zhang, Yongde; Sha, Xianzheng

2011-01-01

This paper introduces the method of mixed programming with Labview and Matlab, and applies this method in a pulse wave pre-processing and feature detecting system. The method has been proved suitable, efficient and accurate, which has provided a new kind of approach for biomedical signal analysis.

TERMA Framework for Biomedical Signal Analysis: An Economic-Inspired Approach.

PubMed

Elgendi, Mohamed

2016-11-02

Biomedical signals contain features that represent physiological events, and each of these events has peaks. The analysis of biomedical signals for monitoring or diagnosing diseases requires the detection of these peaks, making event detection a crucial step in biomedical signal processing. Many researchers have difficulty detecting these peaks to investigate, interpret and analyze their corresponding events. To date, there is no generic framework that captures these events in a robust, efficient and consistent manner. A new method referred to for the first time as two event-related moving averages ("TERMA") involves event-related moving averages and detects events in biomedical signals. The TERMA framework is flexible and universal and consists of six independent LEGO building bricks to achieve high accuracy detection of biomedical events. Results recommend that the window sizes for the two moving averages ( W 1 and W 2 ) have to follow the inequality ( 8 × W 1 ) ≥ W 2 ≥ ( 2 × W 1 ) . Moreover, TERMA is a simple yet efficient event detector that is suitable for wearable devices, point-of-care devices, fitness trackers and smart watches, compared to more complex machine learning solutions.

Digital fabrication of multi-material biomedical objects.

PubMed

Cheung, H H; Choi, S H

2009-12-01

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.

CAVEman: Standardized anatomical context for biomedical data mapping.

PubMed

Turinsky, Andrei L; Fanea, Elena; Trinh, Quang; Wat, Stephen; Hallgrímsson, Benedikt; Dong, Xiaoli; Shu, Xueling; Stromer, Julie N; Hill, Jonathan W; Edwards, Carol; Grosenick, Brenda; Yajima, Masumi; Sensen, Christoph W

2008-01-01

The authors have created a software system called the CAVEman, for the visual integration and exploration of heterogeneous anatomical and biomedical data. The CAVEman can be applied for both education and research tasks. The main component of the system is a three-dimensional digital atlas of the adult male human anatomy, structured according to the nomenclature of Terminologia Anatomica. The underlying data-indexing mechanism uses standard ontologies to map a range of biomedical data types onto the atlas. The CAVEman system is now used to visualize genetic processes in the context of the human anatomy and to facilitate visual exploration of the data. Through the use of Javatrade mark software, the atlas-based system is portable to virtually any computer environment, including personal computers and workstations. Existing Java tools for biomedical data analysis have been incorporated into the system. The affordability of virtual-reality installations has increased dramatically over the last several years. This creates new opportunities for educational scenarios that model important processes in a patient's body, including gene expression patterns, metabolic activity, the effects of interventions such as drug treatments, and eventually surgical simulations.

IEEE International Symposium on Biomedical Imaging.

PubMed

2017-01-01

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

Suppression of Metastasis by Primary Tumor and Acceleration of Metastasis Following Primary Tumor Resection: A Natural Law?

PubMed

Hanin, Leonid; Rose, Jason

2018-03-01

We study metastatic cancer progression through an extremely general individual-patient mathematical model that is rooted in the contemporary understanding of the underlying biomedical processes yet is essentially free of specific biological assumptions of mechanistic nature. The model accounts for primary tumor growth and resection, shedding of metastases off the primary tumor and their selection, dormancy and growth in a given secondary site. However, functional parameters descriptive of these processes are assumed to be essentially arbitrary. In spite of such generality, the model allows for computing the distribution of site-specific sizes of detectable metastases in closed form. Under the assumption of exponential growth of metastases before and after primary tumor resection, we showed that, regardless of other model parameters and for every set of site-specific volumes of detected metastases, the model-based likelihood-maximizing scenario is always the same: complete suppression of metastatic growth before primary tumor resection followed by an abrupt growth acceleration after surgery. This scenario is commonly observed in clinical practice and is supported by a wealth of experimental and clinical studies conducted over the last 110 years. Furthermore, several biological mechanisms have been identified that could bring about suppression of metastasis by the primary tumor and accelerated vascularization and growth of metastases after primary tumor resection. To the best of our knowledge, the methodology for uncovering general biomedical principles developed in this work is new.

Damping and impact properties of laminated scaffolds and glass columns evaluated through the use of computational methods

NASA Astrophysics Data System (ADS)

Nieves, Ian

Dynamic finite element analysis (FEA) was used to verify the ability of a novel percussion instrument to characterize the composition and structure of laminated materials and glass columns and to elucidate key facets of this process. Initial simulations modeling the percussion process with varying probe geometries were performed to access which configuration most accurately represented in situ diagnostic activity. Percussion testing of monoliths and laminated duplex scaffolds consisting of PTFE and 6061 Al was simulated to assess the ability of the numeric methodology to model intrinsic damping in laminated scaffolds and determine the potential contributions of size effects, gripping configurations, and probe friction to the loading response of the material being tested. Percussion testing of laminated scaffolds and monoliths composed of either PMMA or PLGA was modeled to investigate the effects of defects on the impact response and to evaluate promising strategies for enhancing damping that promotes tissue regeneration in biomedical materials. Percussion testing of virgin and cracked glass columns was modeled and the resulting probe acceleration predictions compared to corresponding experimental findings to evaluate the overall accuracy of the methodology and to discern its capacity for elucidating facets of defect detection in rigid materials. Overall, the modeling the results validated the effectiveness of the numeric methodology for modeling and elucidating the mechanics of percussion testing and suggested strategies whereby this procedure can facilitate the development of innovative biomedical materials designed to promote tissue regeneration.

Wavelet transform: fundamentals, applications, and implementation using acousto-optic correlators

NASA Astrophysics Data System (ADS)

DeCusatis, Casimer M.; Koay, J.; Litynski, Daniel M.; Das, Pankaj K.

1995-10-01

In recent years there has been a great deal of interest in the use of wavelets to supplement or replace conventional Fourier transform signal processing. This paper provides a review of wavelet transforms for signal processing applications, and discusses several emerging applications which benefit from the advantages of wavelets. The wavelet transform can be implemented as an acousto-optic correlator; perfect reconstruction of digital signals may also be achieved using acousto-optic finite impulse response filter banks. Acousto-optic image correlators are discussed as a potential implementation of the wavelet transform, since a 1D wavelet filter bank may be encoded as a 2D image. We discuss applications of the wavelet transform including nondestructive testing of materials, biomedical applications in the analysis of EEG signals, and interference excision in spread spectrum communication systems. Computer simulations and experimental results for these applications are also provided.

Materials processing in space

NASA Technical Reports Server (NTRS)

1975-01-01

The feasibility and possible advantages of processing materials in a nongravitational field are considered. Areas of investigation include biomedical applications, the processing of inorganic materials, and flight programs and funding.

Nikolai Fedorovich Gamaliya (1932-2016).

PubMed

2016-06-01

Professor Nikolai Fedorovich Gamaliya, well-known scientist in the field of laser biomedical research, biophysicist, authority in experimental oncology, Laureate of the State Prize in Science and Techno-logy of Ukraine, Head of the Department of Biological Effects of Ionizing and Non-Ionizing Radiation of R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology of the National Academy of Sciences (NAS) of Ukraine died on June 14, 2016 at the age of 83.

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

PubMed

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

2013-03-01

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

Noise-assisted data processing with empirical mode decomposition in biomedical signals.

PubMed

Karagiannis, Alexandros; Constantinou, Philip

2011-01-01

In this paper, a methodology is described in order to investigate the performance of empirical mode decomposition (EMD) in biomedical signals, and especially in the case of electrocardiogram (ECG). Synthetic ECG signals corrupted with white Gaussian noise are employed and time series of various lengths are processed with EMD in order to extract the intrinsic mode functions (IMFs). A statistical significance test is implemented for the identification of IMFs with high-level noise components and their exclusion from denoising procedures. Simulation campaign results reveal that a decrease of processing time is accomplished with the introduction of preprocessing stage, prior to the application of EMD in biomedical time series. Furthermore, the variation in the number of IMFs according to the type of the preprocessing stage is studied as a function of SNR and time-series length. The application of the methodology in MIT-BIH ECG records is also presented in order to verify the findings in real ECG signals.

Which experimental systems should we use for human microbiome science?

PubMed

Douglas, Angela E

2018-03-01

Microbiome science is revealing that the phenotype and health of animals, including humans, depend on the sustained function of their resident microorganisms. In this essay, I argue for thoughtful choice of model systems for human microbiome science. A greater variety of experimental systems, including wider use of invertebrate models, would benefit biomedical research, while systems ill-suited to experimental and genetic manipulation can be used to address very limited sets of scientific questions. Microbiome science benefits from the coordinated use of multiple systems, which is facilitated by networks of researchers with expertise in different experimental systems.

Accounting for reciprocal host-microbiome interactions in experimental science.

PubMed

Stappenbeck, Thaddeus S; Virgin, Herbert W

2016-06-09

Mammals are defined by their metagenome, a combination of host and microbiome genes. This knowledge presents opportunities to further basic biology with translation to human diseases. However, the now-documented influence of the metagenome on experimental results and the reproducibility of in vivo mammalian models present new challenges. Here we provide the scientific basis for calling on all investigators, editors and funding agencies to embrace changes that will enhance reproducible and interpretable experiments by accounting for metagenomic effects. Implementation of new reporting and experimental design principles will improve experimental work, speed discovery and translation, and properly use substantial investments in biomedical research.

A computational model of in vitro angiogenesis based on extracellular matrix fibre orientation.

PubMed

Edgar, Lowell T; Sibole, Scott C; Underwood, Clayton J; Guilkey, James E; Weiss, Jeffrey A

2013-01-01

Recent interest in the process of vascularisation within the biomedical community has motivated numerous new research efforts focusing on the process of angiogenesis. Although the role of chemical factors during angiogenesis has been well documented, the role of mechanical factors, such as the interaction between angiogenic vessels and the extracellular matrix, remains poorly understood. In vitro methods for studying angiogenesis exist; however, measurements available using such techniques often suffer from limited spatial and temporal resolutions. For this reason, computational models have been extensively employed to investigate various aspects of angiogenesis. This paper outlines the formulation and validation of a simple and robust computational model developed to accurately simulate angiogenesis based on length, branching and orientation morphometrics collected from vascularised tissue constructs. Microvessels were represented as a series of connected line segments. The morphology of the vessels was determined by a linear combination of the collagen fibre orientation, the vessel density gradient and a random walk component. Excellent agreement was observed between computational and experimental morphometric data over time. Computational predictions of microvessel orientation within an anisotropic matrix correlated well with experimental data. The accuracy of this modelling approach makes it a valuable platform for investigating the role of mechanical interactions during angiogenesis.

Characterizing microstructural features of biomedical samples by statistical analysis of Mueller matrix images

NASA Astrophysics Data System (ADS)

He, Honghui; Dong, Yang; Zhou, Jialing; Ma, Hui

2017-03-01

As one of the salient features of light, polarization contains abundant structural and optical information of media. Recently, as a comprehensive description of polarization property, the Mueller matrix polarimetry has been applied to various biomedical studies such as cancerous tissues detections. In previous works, it has been found that the structural information encoded in the 2D Mueller matrix images can be presented by other transformed parameters with more explicit relationship to certain microstructural features. In this paper, we present a statistical analyzing method to transform the 2D Mueller matrix images into frequency distribution histograms (FDHs) and their central moments to reveal the dominant structural features of samples quantitatively. The experimental results of porcine heart, intestine, stomach, and liver tissues demonstrate that the transformation parameters and central moments based on the statistical analysis of Mueller matrix elements have simple relationships to the dominant microstructural properties of biomedical samples, including the density and orientation of fibrous structures, the depolarization power, diattenuation and absorption abilities. It is shown in this paper that the statistical analysis of 2D images of Mueller matrix elements may provide quantitative or semi-quantitative criteria for biomedical diagnosis.

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

PubMed

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

1989-01-01

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

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

PubMed

Martin-Sanchez, F; Maojo, V

2009-01-01

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

Skin optical clearing potential of disaccharides

NASA Astrophysics Data System (ADS)

Feng, Wei; Shi, Rui; Ma, Ning; Tuchina, Daria K.; Tuchin, Valery V.; Zhu, Dan

2016-08-01

Skin optical clearing can significantly enhance the ability of biomedical optical imaging. Some alcohols and sugars have been selected to be optical clearing agents (OCAs). In this work, we paid attention to the optical clearing potential of disaccharides. Sucrose and maltose were chosen as typical disaccharides to compare with fructose, an excellent monosaccharide-OCA, by using molecular dynamics simulation and an ex vivo experiment. The experimental results indicated that the optical clearing efficacy of skin increases linearly with the concentration for each OCA. Both the theoretical predication and experimental results revealed that the two disaccharides exerted a better optical clearing potential than fructose at the same concentration, and sucrose is optimal. Since maltose has an extremely low saturation concentration, the other two OCAs with saturation concentrations were treated topically on rat skin in vivo, and optical coherence tomography imaging was applied to monitor the optical clearing process. The results demonstrated that sucrose could cause a more significant increase in imaging depth and signal intensity than fructose.

Fabrication of Titanium-Niobium-Zirconium-Tantalium Alloy (TNZT) Bioimplant Components with Controllable Porosity by Spark Plasma Sintering

PubMed Central

Rechtin, Jack; Torresani, Elisa; Ivanov, Eugene; Olevsky, Eugene

2018-01-01

Spark Plasma Sintering (SPS) is used to fabricate Titanium-Niobium-Zirconium-Tantalum alloy (TNZT) powder—based bioimplant components with controllable porosity. The developed densification maps show the effects of final SPS temperature, pressure, holding time, and initial particle size on final sample relative density. Correlations between the final sample density and mechanical properties of the fabricated TNZT components are also investigated and microstructural analysis of the processed material is conducted. A densification model is proposed and used to calculate the TNZT alloy creep activation energy. The obtained experimental data can be utilized for the optimized fabrication of TNZT components with specific microstructural and mechanical properties suitable for biomedical applications. PMID:29364165

Identification of Tool Wear when Machining of Austenitic Steels and Titatium by Miniature Machining

NASA Astrophysics Data System (ADS)

Pilc, Jozef; Kameník, Roman; Varga, Daniel; Martinček, Juraj; Sadilek, Marek

2016-12-01

Application of miniature machining is currently rapidly increasing mainly in biomedical industry and machining of hard-to-machine materials. Machinability of materials with increased level of toughness depends on factors that are important in the final state of surface integrity. Because of this, it is necessary to achieve high precision (varying in microns) in miniature machining. If we want to guarantee machining high precision, it is necessary to analyse tool wear intensity in direct interaction with given machined materials. During long-term cutting process, different cutting wedge deformations occur, leading in most cases to a rapid wear and destruction of the cutting wedge. This article deal with experimental monitoring of tool wear intensity during miniature machining.

Chemically induced phospholipid translocation across biological membranes.

PubMed

Gurtovenko, Andrey A; Onike, Olajide I; Anwar, Jamshed

2008-09-02

Chemical means of manipulating the distribution of lipids across biological membranes is of considerable interest for many biomedical applications as a characteristic lipid distribution is vital for numerous cellular functions. Here we employ atomic-scale molecular simulations to shed light on the ability of certain amphiphilic compounds to promote lipid translocation (flip-flops) across membranes. We show that chemically induced lipid flip-flops are most likely pore-mediated: the actual flip-flop event is a very fast process (time scales of tens of nanoseconds) once a transient water defect has been induced by the amphiphilic chemical (dimethylsulfoxide in this instance). Our findings are consistent with available experimental observations and further emphasize the importance of transient membrane defects for chemical control of lipid distribution across cell membranes.

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

Yin, Lan; Harburg, Daniel V.; Rogers, John A., E-mail: jrogers@illinois.edu

Tungsten interconnects in silicon integrated circuits built at the 90 nm node with releasable configurations on silicon on insulator wafers serve as the basis for advanced forms of water-soluble electronics. These physically transient systems have potential uses in applications that range from temporary biomedical implants to zero-waste environmental sensors. Systematic experimental studies and modeling efforts reveal essential aspects of electrical performance in field effect transistors and complementary ring oscillators with as many as 499 stages. Accelerated tests reveal timescales for dissolution of the various constituent materials, including tungsten, silicon, and silicon dioxide. The results demonstrate that silicon complementary metal-oxide-semiconductor circuits formedmore » with tungsten interconnects in foundry-compatible fabrication processes can serve as a path to high performance, mass-produced transient electronic systems.« less

In vitro and in vivo biological performance of porous Ti alloys prepared by powder metallurgy.

PubMed

do Prado, Renata Falchete; Esteves, Gabriela Campos; Santos, Evelyn Luzia De Souza; Bueno, Daiane Acácia Griti; Cairo, Carlos Alberto Alves; Vasconcellos, Luis Gustavo Oliveira De; Sagnori, Renata Silveira; Tessarin, Fernanda Bastos Pereira; Oliveira, Felipe Eduardo; Oliveira, Luciane Dias De; Villaça-Carvalho, Maria Fernanda Lima; Henriques, Vinicius André Rodrigues; Carvalho, Yasmin Rodarte; De Vasconcellos, Luana Marotta Reis

2018-01-01

Titanium (Ti) and Ti-6 Aluminium-4 Vanadium alloys are the most common materials in implants composition but β type alloys are promising biomaterials because they present better mechanical properties. Besides the composition of biomaterial, many factors influence the performance of the biomaterial. For example, porous surface may modify the functional cellular response and accelerate osseointegration. This paper presents in vitro and in vivo evaluations of powder metallurgy-processed porous samples composed by different titanium alloys and pure Ti, aiming to show their potential for biomedical applications. The porous surfaces samples were produced with different designs to in vitro and in vivo tests. Samples were characterized with scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and elastic modulus analyses. Osteogenic cells from newborn rat calvaria were plated on discs of different materials: G1-commercially pure Ti group (CpTi); G2-Ti-6Al-4V alloy; G3-Ti-13 Niobium-13 Zirconium alloy; G4-Ti-35 Niobium alloy; G5-Ti-35 Niobium-7 Zirconium-5 Tantalum alloy. Cell adhesion and viability, total protein content, alkaline phosphatase activity, mineralization nodules and gene expression (alkaline phosphatase, Runx-2, osteocalcin and osteopontin) were assessed. After 2 and 4 weeks of implantation in rabbit tibia, bone ingrowth was analyzed using micro-computed tomography (μCT). EDS analysis confirmed the material production of each group. Metallographic and SEM analysis revealed interconnected pores, with mean pore size of 99,5μm and mean porosity of 42%, without significant difference among the groups (p>0.05). The elastic modulus values did not exhibit difference among the groups (p>0.05). Experimental alloys demonstrated better results than CpTi and Ti-6Al-4V, in gene expression and cytokines analysis, especially in early experimental periods. In conclusion, our data suggests that the experimental alloys can be used for biomedical application since they contributed to excellent cellular behavior and osseointegration besides presenting lower elastic modulus.

Guidelines for Developing and Reporting Machine Learning Predictive Models in Biomedical Research: A Multidisciplinary View

PubMed Central

2016-01-01

Background As more and more researchers are turning to big data for new opportunities of biomedical discoveries, machine learning models, as the backbone of big data analysis, are mentioned more often in biomedical journals. However, owing to the inherent complexity of machine learning methods, they are prone to misuse. Because of the flexibility in specifying machine learning models, the results are often insufficiently reported in research articles, hindering reliable assessment of model validity and consistent interpretation of model outputs. Objective To attain a set of guidelines on the use of machine learning predictive models within clinical settings to make sure the models are correctly applied and sufficiently reported so that true discoveries can be distinguished from random coincidence. Methods A multidisciplinary panel of machine learning experts, clinicians, and traditional statisticians were interviewed, using an iterative process in accordance with the Delphi method. Results The process produced a set of guidelines that consists of (1) a list of reporting items to be included in a research article and (2) a set of practical sequential steps for developing predictive models. Conclusions A set of guidelines was generated to enable correct application of machine learning models and consistent reporting of model specifications and results in biomedical research. We believe that such guidelines will accelerate the adoption of big data analysis, particularly with machine learning methods, in the biomedical research community. PMID:27986644

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

PubMed

An, Gary

2009-01-01

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

Measurement of OH, NO, O and N atoms in helium plasma jet for ROS/RNS controlled biomedical processes

NASA Astrophysics Data System (ADS)

Yonemori, Seiya; Kamakura, Taku; Ono, Ryo

2014-10-01

Atmospheric-pressure plasmas are of emerging interest for new plasma applications such as cancer treatment, cell activation and sterilization. In those biomedical processes, reactive oxygen/nitrogen species (ROS/RNS) are said that they play significant role. It is though that active species give oxidative stress and induce biomedical reactions. In this study, we measured OH, NO, O and N atoms using laser induced fluorescence (LIF) measurement and found that voltage polarity affect particular ROS. When negative high voltage was applied to the plasma jet, O atom density was tripled compared to the case of positive applied voltage. In that case, O atom density was around 3 × 1015 [cm-3] at maximum. In contrast, OH and NO density did not change their density depending on the polarity of applied voltage, measured as in order of 1013 and 1014 [cm-3] at maximum, respectively. From ICCD imaging measurement, it could be seen that negative high voltage enhanced secondary emission in plasma bullet propagation and it can affect the effective production of particular ROS. Since ROS/RNS dose can be a quantitative criterion to control plasma biomedical application, those measurement results is able to be applied for in vivo and in vitro plasma biomedical experiments. This study is supported by the Grant-in-Aid for Science Research by the Ministry of Education, Culture, Sport, Science and Technology.

Ensemble Deep Learning for Biomedical Time Series Classification

PubMed Central

2016-01-01

Ensemble learning has been proved to improve the generalization ability effectively in both theory and practice. In this paper, we briefly outline the current status of research on it first. Then, a new deep neural network-based ensemble method that integrates filtering views, local views, distorted views, explicit training, implicit training, subview prediction, and Simple Average is proposed for biomedical time series classification. Finally, we validate its effectiveness on the Chinese Cardiovascular Disease Database containing a large number of electrocardiogram recordings. The experimental results show that the proposed method has certain advantages compared to some well-known ensemble methods, such as Bagging and AdaBoost. PMID:27725828

Discovery and validation of gene classifiers for endocrine-disrupting chemicals in zebrafish (Danio rerio)

EPA Science Inventory

Development and application of transcriptomics-based gene classifiers for ecotoxicological applications lag far behind those of human biomedical science. Many such classifiers discovered thus far lack vigorous statistical and experimental validations, with their stability and rel...

Eukaryotic acquisition of a bacterial operon

USDA-ARS?s Scientific Manuscript database

The yeast Saccharomyces cerevisiae is one of the champions of basic biomedical research due to its compact eukaryotic genome and ease of experimental manipulation. Despite these immense strengths, its impact on understanding the genetic basis of natural phenotypic variation has been limited by strai...

Foreword: Additive Manufacturing: Interrelationships of Fabrication, Constitutive Relationships Targeting Performance, and Feedback to Process Control

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

Carpenter, John S.; Beese, Allison M.; Bourell, David L.

Additive manufacturing (AM) offers distinct advantages over conventional manufacturing processes including the capability to both build and repair complex part shapes; to integrate and consolidate parts and thus overcome joining concerns; and to locally tailor material compositions as well as properties. Moreover, a variety of fields such as aerospace, military, automotive, and biomedical are employing this manufacturing technique as a way to decrease costs, increase manufacturing agility, and explore novel geometry/functionalities. In order to increase acceptance of AM as a viable processing method, pathways for qualifying both the material and the process need to be developed and, perhaps, standardized. Thismore » symposium was designed to serve as a venue for the international AM community—including government, academia, and industry—to define the fundamental interrelationships between feedstock, processing, microstructure, shape, mechanical behavior/materials properties, and function/performance. Eventually, insight into the connections between processing, microstructure, property, and performance will be achieved through experimental observations, theoretical advances, and computational modeling of physical processes. Finally, once this insight matures, AM will be able to move from the realm of making parts to making qualified materials that are certified for use with minimal need for post-fabrication characterization.« less

Foreword: Additive Manufacturing: Interrelationships of Fabrication, Constitutive Relationships Targeting Performance, and Feedback to Process Control

DOE PAGES

Carpenter, John S.; Beese, Allison M.; Bourell, David L.; ...

2015-06-26

Additive manufacturing (AM) offers distinct advantages over conventional manufacturing processes including the capability to both build and repair complex part shapes; to integrate and consolidate parts and thus overcome joining concerns; and to locally tailor material compositions as well as properties. Moreover, a variety of fields such as aerospace, military, automotive, and biomedical are employing this manufacturing technique as a way to decrease costs, increase manufacturing agility, and explore novel geometry/functionalities. In order to increase acceptance of AM as a viable processing method, pathways for qualifying both the material and the process need to be developed and, perhaps, standardized. Thismore » symposium was designed to serve as a venue for the international AM community—including government, academia, and industry—to define the fundamental interrelationships between feedstock, processing, microstructure, shape, mechanical behavior/materials properties, and function/performance. Eventually, insight into the connections between processing, microstructure, property, and performance will be achieved through experimental observations, theoretical advances, and computational modeling of physical processes. Finally, once this insight matures, AM will be able to move from the realm of making parts to making qualified materials that are certified for use with minimal need for post-fabrication characterization.« less

Maximizing the return on taxpayers' investments in fundamental biomedical research.

PubMed

Lorsch, Jon R

2015-05-01

The National Institute of General Medical Sciences (NIGMS) at the U.S. National Institutes of Health has an annual budget of more than $2.3 billion. The institute uses these funds to support fundamental biomedical research and training at universities, medical schools, and other institutions across the country. My job as director of NIGMS is to work to maximize the scientific returns on the taxpayers' investments. I describe how we are optimizing our investment strategies and funding mechanisms, and how, in the process, we hope to create a more efficient and sustainable biomedical research enterprise.

Pacific Northwest Laboratory annual report for 1983 to the DOE Office of Energy Research. Part 1. Biomedical sciences

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

Drucker, H.

1983-02-01

Biomedical and health effects research conducted at PNL in 1982 on the evaluation of risk to man from existing and/or developing energy-related technologies are described. Most of the studies described in this report relate to activities for three major energy technologies: nuclear fuel cycle; fossil fuel cycle (oil, gas, and coal process technologies, mining, and utilization; synfuel development), and fudion (biomagnetic effects). The report is organized under these technologies. In addition, research reports are included on the application of nuclear energy to biomedical problems. Individual projects are indexed separately.

Maximizing the return on taxpayers' investments in fundamental biomedical research

PubMed Central

Lorsch, Jon R.

2015-01-01

The National Institute of General Medical Sciences (NIGMS) at the U.S. National Institutes of Health has an annual budget of more than $2.3 billion. The institute uses these funds to support fundamental biomedical research and training at universities, medical schools, and other institutions across the country. My job as director of NIGMS is to work to maximize the scientific returns on the taxpayers' investments. I describe how we are optimizing our investment strategies and funding mechanisms, and how, in the process, we hope to create a more efficient and sustainable biomedical research enterprise. PMID:25926703

Introducing meta-services for biomedical information extraction

PubMed Central

Leitner, Florian; Krallinger, Martin; Rodriguez-Penagos, Carlos; Hakenberg, Jörg; Plake, Conrad; Kuo, Cheng-Ju; Hsu, Chun-Nan; Tsai, Richard Tzong-Han; Hung, Hsi-Chuan; Lau, William W; Johnson, Calvin A; Sætre, Rune; Yoshida, Kazuhiro; Chen, Yan Hua; Kim, Sun; Shin, Soo-Yong; Zhang, Byoung-Tak; Baumgartner, William A; Hunter, Lawrence; Haddow, Barry; Matthews, Michael; Wang, Xinglong; Ruch, Patrick; Ehrler, Frédéric; Özgür, Arzucan; Erkan, Güneş; Radev, Dragomir R; Krauthammer, Michael; Luong, ThaiBinh; Hoffmann, Robert; Sander, Chris; Valencia, Alfonso

2008-01-01

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; ). This prototype platform is a joint effort of 13 research groups and provides automatically generated annotations for PubMed/Medline abstracts. Annotation types cover gene names, gene IDs, species, and protein-protein interactions. The annotations are distributed by the meta-server in both human and machine readable formats (HTML/XML). This service is intended to be used by biomedical researchers and database annotators, and in biomedical language processing. The platform allows direct comparison, unified access, and result aggregation of the annotations. PMID:18834497

Parameters of Microcirculation in the Broad Ligament of the Uterus in Wistar Rats after Injection of Autologous Biomedical Cell Product.

PubMed

Dergacheva, T I; Lykov, A P; Shurlygina, A V; Starkova, E V; Poveshchenko, O V; Bondarenko, N A; Kim, I I; Tenditnik, M V; Borodin, Yu I; Konenkov, V I

2015-10-01

We studied the effects of autologous biomedical cell product (bone marrow multipotent mesenchymal stromal cells and their conditioned media) on the parameters of the microcirculatory bed in the broad ligament of the uterus of normal Wistar rats were studied. The parameters of microcirculation and lymph drainage in the broad ligament changed in opposite directions in response to injection of autologous biomedical cell product via different routes. This fact should be taken into consideration when prescribing cell therapy for inflammatory degenerative processes in the pelvic organs.

Biomedical Informatics for Computer-Aided Decision Support Systems: A Survey

PubMed Central

Belle, Ashwin; Kon, Mark A.; Najarian, Kayvan

2013-01-01

The volumes of current patient data as well as their complexity make clinical decision making more challenging than ever for physicians and other care givers. This situation calls for the use of biomedical informatics methods to process data and form recommendations and/or predictions to assist such decision makers. The design, implementation, and use of biomedical informatics systems in the form of computer-aided decision support have become essential and widely used over the last two decades. This paper provides a brief review of such systems, their application protocols and methodologies, and the future challenges and directions they suggest. PMID:23431259

Large-scale online semantic indexing of biomedical articles via an ensemble of multi-label classification models.

PubMed

Papanikolaou, Yannis; Tsoumakas, Grigorios; Laliotis, Manos; Markantonatos, Nikos; Vlahavas, Ioannis

2017-09-22

In this paper we present the approach that we employed to deal with large scale multi-label semantic indexing of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge (2013-2017), a challenge concerned with biomedical semantic indexing and question answering. Our main contribution is a MUlti-Label Ensemble method (MULE) that incorporates a McNemar statistical significance test in order to validate the combination of the constituent machine learning algorithms. Some secondary contributions include a study on the temporal aspects of the BioASQ corpus (observations apply also to the BioASQ's super-set, the PubMed articles collection) and the proper parametrization of the algorithms used to deal with this challenging classification task. The ensemble method that we developed is compared to other approaches in experimental scenarios with subsets of the BioASQ corpus giving positive results. In our participation in the BioASQ challenge we obtained the first place in 2013 and the second place in the four following years, steadily outperforming MTI, the indexing system of the National Library of Medicine (NLM). The results of our experimental comparisons, suggest that employing a statistical significance test to validate the ensemble method's choices, is the optimal approach for ensembling multi-label classifiers, especially in contexts with many rare labels.

A fast discrete S-transform for biomedical signal processing.

PubMed

Brown, Robert A; Frayne, Richard

2008-01-01

Determining the frequency content of a signal is a basic operation in signal and image processing. The S-transform provides both the true frequency and globally referenced phase measurements characteristic of the Fourier transform and also generates local spectra, as does the wavelet transform. Due to this combination, the S-transform has been successfully demonstrated in a variety of biomedical signal and image processing tasks. However, the computational demands of the S-transform have limited its application in medicine to this point in time. This abstract introduces the fast S-transform, a more efficient discrete implementation of the classic S-transform with dramatically reduced computational requirements.

Expanding the basic science debate: the role of physics knowledge in interpreting clinical findings.

PubMed

Goldszmidt, Mark; Minda, John Paul; Devantier, Sarah L; Skye, Aimee L; Woods, Nicole N

2012-10-01

Current research suggests a role for biomedical knowledge in learning and retaining concepts related to medical diagnosis. However, learning may be influenced by other, non-biomedical knowledge. We explored this idea using an experimental design and examined the effects of causal knowledge on the learning, retention, and interpretation of medical information. Participants studied a handout about several respiratory disorders and how to interpret respiratory exam findings. The control group received the information in standard "textbook" format and the experimental group was presented with the same information as well as a causal explanation about how sound travels through lungs in both the normal and disease states. Comprehension and memory of the information was evaluated with a multiple-choice exam. Several questions that were not related to the causal knowledge served as control items. Questions related to the interpretation of physical exam findings served as the critical test items. The experimental group outperformed the control group on the critical test items, and our study shows that a causal explanation can improve a student's memory for interpreting clinical details. We suggest an expansion of which basic sciences are considered fundamental to medical education.

Blastocyst microinjection automation.

PubMed

Mattos, Leonardo S; Grant, Edward; Thresher, Randy; Kluckman, Kimberly

2009-09-01

Blastocyst microinjections are routinely involved in the process of creating genetically modified mice for biomedical research, but their efficiency is highly dependent on the skills of the operators. As a consequence, much time and resources are required for training microinjection personnel. This situation has been aggravated by the rapid growth of genetic research, which has increased the demand for mutant animals. Therefore, increased productivity and efficiency in this area are highly desired. Here, we pursue these goals through the automation of a previously developed teleoperated blastocyst microinjection system. This included the design of a new system setup to facilitate automation, the definition of rules for automatic microinjections, the implementation of video processing algorithms to extract feedback information from microscope images, and the creation of control algorithms for process automation. Experimentation conducted with this new system and operator assistance during the cells delivery phase demonstrated a 75% microinjection success rate. In addition, implantation of the successfully injected blastocysts resulted in a 53% birth rate and a 20% yield of chimeras. These results proved that the developed system was capable of automatic blastocyst penetration and retraction, demonstrating the success of major steps toward full process automation.

The biomedical model of mental disorder: a critical analysis of its validity, utility, and effects on psychotherapy research.

PubMed

Deacon, Brett J

2013-11-01

The biomedical model posits that mental disorders are brain diseases and emphasizes pharmacological treatment to target presumed biological abnormalities. A biologically-focused approach to science, policy, and practice has dominated the American healthcare system for more than three decades. During this time, the use of psychiatric medications has sharply increased and mental disorders have become commonly regarded as brain diseases caused by chemical imbalances that are corrected with disease-specific drugs. However, despite widespread faith in the potential of neuroscience to revolutionize mental health practice, the biomedical model era has been characterized by a broad lack of clinical innovation and poor mental health outcomes. In addition, the biomedical paradigm has profoundly affected clinical psychology via the adoption of drug trial methodology in psychotherapy research. Although this approach has spurred the development of empirically supported psychological treatments for numerous mental disorders, it has neglected treatment process, inhibited treatment innovation and dissemination, and divided the field along scientist and practitioner lines. The neglected biopsychosocial model represents an appealing alternative to the biomedical approach, and an honest and public dialog about the validity and utility of the biomedical paradigm is urgently needed. Copyright © 2013 Elsevier Ltd. All rights reserved.

TERMA Framework for Biomedical Signal Analysis: An Economic-Inspired Approach

PubMed Central

Elgendi, Mohamed

2016-01-01

Biomedical signals contain features that represent physiological events, and each of these events has peaks. The analysis of biomedical signals for monitoring or diagnosing diseases requires the detection of these peaks, making event detection a crucial step in biomedical signal processing. Many researchers have difficulty detecting these peaks to investigate, interpret and analyze their corresponding events. To date, there is no generic framework that captures these events in a robust, efficient and consistent manner. A new method referred to for the first time as two event-related moving averages (“TERMA”) involves event-related moving averages and detects events in biomedical signals. The TERMA framework is flexible and universal and consists of six independent LEGO building bricks to achieve high accuracy detection of biomedical events. Results recommend that the window sizes for the two moving averages (W1 and W2) have to follow the inequality (8×W1)≥W2≥(2×W1). Moreover, TERMA is a simple yet efficient event detector that is suitable for wearable devices, point-of-care devices, fitness trackers and smart watches, compared to more complex machine learning solutions. PMID:27827852

Disambiguating ambiguous biomedical terms in biomedical narrative text: an unsupervised method.

PubMed

Liu, H; Lussier, Y A; Friedman, C

2001-08-01

With the growing use of Natural Language Processing (NLP) techniques for information extraction and concept indexing in the biomedical domain, a method that quickly and efficiently assigns the correct sense of an ambiguous biomedical term in a given context is needed concurrently. The current status of word sense disambiguation (WSD) in the biomedical domain is that handcrafted rules are used based on contextual material. The disadvantages of this approach are (i) generating WSD rules manually is a time-consuming and tedious task, (ii) maintenance of rule sets becomes increasingly difficult over time, and (iii) handcrafted rules are often incomplete and perform poorly in new domains comprised of specialized vocabularies and different genres of text. This paper presents a two-phase unsupervised method to build a WSD classifier for an ambiguous biomedical term W. The first phase automatically creates a sense-tagged corpus for W, and the second phase derives a classifier for W using the derived sense-tagged corpus as a training set. A formative experiment was performed, which demonstrated that classifiers trained on the derived sense-tagged corpora achieved an overall accuracy of about 97%, with greater than 90% accuracy for each individual ambiguous term.

A heuristic method for simulating open-data of arbitrary complexity that can be used to compare and evaluate machine learning methods.

PubMed

Moore, Jason H; Shestov, Maksim; Schmitt, Peter; Olson, Randal S

2018-01-01

A central challenge of developing and evaluating artificial intelligence and machine learning methods for regression and classification is access to data that illuminates the strengths and weaknesses of different methods. Open data plays an important role in this process by making it easy for computational researchers to easily access real data for this purpose. Genomics has in some examples taken a leading role in the open data effort starting with DNA microarrays. While real data from experimental and observational studies is necessary for developing computational methods it is not sufficient. This is because it is not possible to know what the ground truth is in real data. This must be accompanied by simulated data where that balance between signal and noise is known and can be directly evaluated. Unfortunately, there is a lack of methods and software for simulating data with the kind of complexity found in real biological and biomedical systems. We present here the Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (HIBACHI) method and prototype software for simulating complex biological and biomedical data. Further, we introduce new methods for developing simulation models that generate data that specifically allows discrimination between different machine learning methods.

Biomedical instruments versus toys:a preliminary comparison of force platforms and the nintendo wii balance board - biomed 2011.

PubMed

Pagnacco, Guido; Oggero, Elena; Wright, Cameron H G

2011-01-01

Biomedical sciences rely heavily on devices to acquire and analyze the physiological data needed to understand and model the biological processes of humans and animals. Therefore, the results of the investigations, clinical or academic, depend heavily on the instrumentation used. Unfortunately, all too often the users do not understand their instruments and end up compromising the results of their investigations by choosing an inadequate instrument or by not using it appropriately. One field where this is particularly apparent is posturography: the misconceptions about instruments are so widespread and deep that just recently there have been articles published in scientific journals suggesting the use of a “toy”, the Nintendo Wii Balance Board, instead of instrument grade force platform to acquire posturographic data. Characterizing the tools used for research becomes the first and probably the most important step in producing sound research and clinical results, and in the case of posturographic force platforms and the Nintendo Wii Balance Board a simple experimental setup can be used to find their characteristics. Furthermore, based on the preliminary results of this investigation, a mathematical formula can be used to predict the behavior of a posturographic tool, once its noise characteristics and “dead weight” response are known.

Mid-infrared (MIR) photonics: MIR passive and active fiberoptics chemical and biomedical, sensing and imaging

NASA Astrophysics Data System (ADS)

Seddon, Angela B.

2016-10-01

The case for new, portable, real-time mid-infrared (MIR) molecular sensing and imaging is discussed. We set a record in demonstrating extreme broad-band supercontinuum (SC) generated light 1.4-13.3 μm in a specially engineered, step-index MIR optical fiber of high numerical aperture. This was the first experimental demonstration truly to reveal the potential of MIR fibers to emit across the MIR molecular "fingerprint spectral region" and a key first step towards bright, portable, broadband MIR sources for chemical and biomedical, molecular sensing and imaging in real-time. Potential applications are in the healthcare, security, energy, environmental monitoring, chemical-processing, manufacturing and the agriculture sectors. MIR narrow-line fiber lasers are now required to pump the fiber MIR-SC for a compact all-fiber solution. Rare-earth-ion (RE-) doped MIR fiber lasers are not yet demonstrated >=4 μm wavelength. We have fabricated small-core RE-fiber with photoluminescence across 3.5-6 μm, and long excited-state lifetimes. MIR-RE-fiber lasers are also applicable as discrete MIR fiber sensors in their own right, for applications including: ship-to-ship free-space communications, aircraft counter-measures, coherent MIR imaging, MIR-optical coherent tomography, laser-cutting/ patterning of soft materials and new wavelengths for fiber laser medical surgery.

A Biocompatible and Biodegradable Protein Hydrogel with Green and Red Autofluorescence: Preparation, Characterization and In Vivo Biodegradation Tracking and Modeling

PubMed Central

Ma, Xiaoyu; Sun, Xiangcheng; Hargrove, Derek; Chen, Jun; Song, Donghui; Dong, Qiuchen; Lu, Xiuling; Fan, Tai-Hsi; Fu, Youjun; Lei, Yu

2016-01-01

Because of its good biocompatibility and biodegradability, albumins such as bovine serum albumin (BSA) and human serum albumin (HSA) have found a wide range of biomedical applications. Herein, we report that glutaraldehyde cross-linked BSA (or HSA) forms a novel fluorescent biological hydrogel, exhibiting new green and red autofluorescence in vitro and in vivo without the use of any additional fluorescent labels. UV-vis spectra studies, in conjunction with the fluorescence spectra studies including emission, excitation and synchronous scans, indicated that three classes of fluorescent compounds are presumably formed during the gelation process. SEM, FTIR and mechanical tests were further employed to investigate the morphology, the specific chemical structures and the mechanical strength of the as-prepared autofluorescent hydrogel, respectively. Its biocompatibility and biodegradability were also demonstrated through extensive in vitro and in vivo studies. More interestingly, the strong red autofluorescence of the as-prepared hydrogel allows for conveniently and non-invasively tracking and modeling its in vivo degradation based on the time-dependent fluorescent images of mice. A mathematical model was proposed and was in good agreement with the experimental results. The developed facile strategy to prepare novel biocompatible and biodegradable autofluorescent protein hydrogels could significantly expand the scope of protein hydrogels in biomedical applications. PMID:26813916

A simple method for the production of large volume 3D macroporous hydrogels for advanced biotechnological, medical and environmental applications

NASA Astrophysics Data System (ADS)

Savina, Irina N.; Ingavle, Ganesh C.; Cundy, Andrew B.; Mikhalovsky, Sergey V.

2016-02-01

The development of bulk, three-dimensional (3D), macroporous polymers with high permeability, large surface area and large volume is highly desirable for a range of applications in the biomedical, biotechnological and environmental areas. The experimental techniques currently used are limited to the production of small size and volume cryogel material. In this work we propose a novel, versatile, simple and reproducible method for the synthesis of large volume porous polymer hydrogels by cryogelation. By controlling the freezing process of the reagent/polymer solution, large-scale 3D macroporous gels with wide interconnected pores (up to 200 μm in diameter) and large accessible surface area have been synthesized. For the first time, macroporous gels (of up to 400 ml bulk volume) with controlled porous structure were manufactured, with potential for scale up to much larger gel dimensions. This method can be used for production of novel 3D multi-component macroporous composite materials with a uniform distribution of embedded particles. The proposed method provides better control of freezing conditions and thus overcomes existing drawbacks limiting production of large gel-based devices and matrices. The proposed method could serve as a new design concept for functional 3D macroporous gels and composites preparation for biomedical, biotechnological and environmental applications.

Health Benefits of Animal Research: The Rat in Biomedical Research.

ERIC Educational Resources Information Center

Gill, Thomas J.

1985-01-01

Discusses major uses of rats as experimental animals for studying health concerns, pointing out that their size, gestation, and histocompatibility make them useful in various studies. Topic areas addressed include aging, autoimmune disease, genetics, cancer, diabetes, hypertension, infection, reproduction, and behavior. (DH)

The center for expanded data annotation and retrieval

PubMed Central

Bean, Carol A; Cheung, Kei-Hoi; Dumontier, Michel; Durante, Kim A; Gevaert, Olivier; Gonzalez-Beltran, Alejandra; Khatri, Purvesh; Kleinstein, Steven H; O’Connor, Martin J; Pouliot, Yannick; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Wiser, Jeffrey A

2015-01-01

The Center for Expanded Data Annotation and Retrieval is studying the creation of comprehensive and expressive metadata for biomedical datasets to facilitate data discovery, data interpretation, and data reuse. We take advantage of emerging community-based standard templates for describing different kinds of biomedical datasets, and we investigate the use of computational techniques to help investigators to assemble templates and to fill in their values. We are creating a repository of metadata from which we plan to identify metadata patterns that will drive predictive data entry when filling in metadata templates. The metadata repository not only will capture annotations specified when experimental datasets are initially created, but also will incorporate links to the published literature, including secondary analyses and possible refinements or retractions of experimental interpretations. By working initially with the Human Immunology Project Consortium and the developers of the ImmPort data repository, we are developing and evaluating an end-to-end solution to the problems of metadata authoring and management that will generalize to other data-management environments. PMID:26112029

Experiment for validation of fluid-structure interaction models and algorithms.

PubMed

Hessenthaler, A; Gaddum, N R; Holub, O; Sinkus, R; Röhrle, O; Nordsletten, D

2017-09-01

In this paper a fluid-structure interaction (FSI) experiment is presented. The aim of this experiment is to provide a challenging yet easy-to-setup FSI test case that addresses the need for rigorous testing of FSI algorithms and modeling frameworks. Steady-state and periodic steady-state test cases with constant and periodic inflow were established. Focus of the experiment is on biomedical engineering applications with flow being in the laminar regime with Reynolds numbers 1283 and 651. Flow and solid domains were defined using computer-aided design (CAD) tools. The experimental design aimed at providing a straightforward boundary condition definition. Material parameters and mechanical response of a moderately viscous Newtonian fluid and a nonlinear incompressible solid were experimentally determined. A comprehensive data set was acquired by using magnetic resonance imaging to record the interaction between the fluid and the solid, quantifying flow and solid motion. Copyright © 2016 The Authors. International Journal for Numerical Methods in Biomedical Engineering published by John Wiley & Sons Ltd.

Preparing for motherhood: authoritative knowledge and the undercurrents of shared experience in two childbirth education courses in Cagliari, Italy.

PubMed

Ketler, S K

2000-06-01

This article compares the social settings and teaching organization of two differently structured childbirth education courses in Cagliari, Italy, in order to understand how social processes and contexts work to negotiate authoritative knowledge. Although the explicit goal of both courses was to transmit biomedical knowledge, knowledge based in women's experience nonetheless dominated some course sessions. Thus, I examine the social processes and interactions that enabled women's experiential knowledge to dominate discussions and subsequently share in the authority of biomedical knowledge in some situations. Because few existing studies do so, this article also addresses a gap in our current understanding by exploring not only how experiential knowledge comes to share authority with biomedical knowledge, but also, why it is important that it does. Focusing on the efficacy of differently structured courses, this article informs the planning of future childbirth education courses in similar settings.

Modeling a description logic vocabulary for cancer research.

PubMed

Hartel, Frank W; de Coronado, Sherri; Dionne, Robert; Fragoso, Gilberto; Golbeck, Jennifer

2005-04-01

The National Cancer Institute has developed the NCI Thesaurus, a biomedical vocabulary for cancer research, covering terminology across a wide range of cancer research domains. A major design goal of the NCI Thesaurus is to facilitate translational research. We describe: the features of Ontylog, a description logic used to build NCI Thesaurus; our methodology for enhancing the terminology through collaboration between ontologists and domain experts, and for addressing certain real world challenges arising in modeling the Thesaurus; and finally, we describe the conversion of NCI Thesaurus from Ontylog into Web Ontology Language Lite. Ontylog has proven well suited for constructing big biomedical vocabularies. We have capitalized on the Ontylog constructs Kind and Role in the collaboration process described in this paper to facilitate communication between ontologists and domain experts. The artifacts and processes developed by NCI for collaboration may be useful in other biomedical terminology development efforts.

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

PubMed

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

2014-01-01

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

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

PubMed

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

2017-11-30

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

Incorporating domain knowledge in chemical and biomedical named entity recognition with word representations.

PubMed

Munkhdalai, Tsendsuren; Li, Meijing; Batsuren, Khuyagbaatar; Park, Hyeon Ah; Choi, Nak Hyeon; Ryu, Keun Ho

2015-01-01

Chemical and biomedical Named Entity Recognition (NER) is an essential prerequisite task before effective text mining can begin for biochemical-text data. Exploiting unlabeled text data to leverage system performance has been an active and challenging research topic in text mining due to the recent growth in the amount of biomedical literature. We present a semi-supervised learning method that efficiently exploits unlabeled data in order to incorporate domain knowledge into a named entity recognition model and to leverage system performance. The proposed method includes Natural Language Processing (NLP) tasks for text preprocessing, learning word representation features from a large amount of text data for feature extraction, and conditional random fields for token classification. Other than the free text in the domain, the proposed method does not rely on any lexicon nor any dictionary in order to keep the system applicable to other NER tasks in bio-text data. We extended BANNER, a biomedical NER system, with the proposed method. This yields an integrated system that can be applied to chemical and drug NER or biomedical NER. We call our branch of the BANNER system BANNER-CHEMDNER, which is scalable over millions of documents, processing about 530 documents per minute, is configurable via XML, and can be plugged into other systems by using the BANNER Unstructured Information Management Architecture (UIMA) interface. BANNER-CHEMDNER achieved an 85.68% and an 86.47% F-measure on the testing sets of CHEMDNER Chemical Entity Mention (CEM) and Chemical Document Indexing (CDI) subtasks, respectively, and achieved an 87.04% F-measure on the official testing set of the BioCreative II gene mention task, showing remarkable performance in both chemical and biomedical NER. BANNER-CHEMDNER system is available at: https://bitbucket.org/tsendeemts/banner-chemdner.

A Cross-Lingual Similarity Measure for Detecting Biomedical Term Translations

PubMed Central

Bollegala, Danushka; Kontonatsios, Georgios; Ananiadou, Sophia

2015-01-01

Bilingual dictionaries for technical terms such as biomedical terms are an important resource for machine translation systems as well as for humans who would like to understand a concept described in a foreign language. Often a biomedical term is first proposed in English and later it is manually translated to other languages. Despite the fact that there are large monolingual lexicons of biomedical terms, only a fraction of those term lexicons are translated to other languages. Manually compiling large-scale bilingual dictionaries for technical domains is a challenging task because it is difficult to find a sufficiently large number of bilingual experts. We propose a cross-lingual similarity measure for detecting most similar translation candidates for a biomedical term specified in one language (source) from another language (target). Specifically, a biomedical term in a language is represented using two types of features: (a) intrinsic features that consist of character n-grams extracted from the term under consideration, and (b) extrinsic features that consist of unigrams and bigrams extracted from the contextual windows surrounding the term under consideration. We propose a cross-lingual similarity measure using each of those feature types. First, to reduce the dimensionality of the feature space in each language, we propose prototype vector projection (PVP)—a non-negative lower-dimensional vector projection method. Second, we propose a method to learn a mapping between the feature spaces in the source and target language using partial least squares regression (PLSR). The proposed method requires only a small number of training instances to learn a cross-lingual similarity measure. The proposed PVP method outperforms popular dimensionality reduction methods such as the singular value decomposition (SVD) and non-negative matrix factorization (NMF) in a nearest neighbor prediction task. Moreover, our experimental results covering several language pairs such as English–French, English–Spanish, English–Greek, and English–Japanese show that the proposed method outperforms several other feature projection methods in biomedical term translation prediction tasks. PMID:26030738

Processing composite materials

NASA Technical Reports Server (NTRS)

Baucom, R. M.

1982-01-01

The fabrication of several composite structural articles including DC-10 upper aft rudders, L-1011 vertical fins and composite biomedical appliances are discussed. Innovative composite processing methods are included.

Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping.

PubMed

Soh, Jung; Turinsky, Andrei L; Trinh, Quang M; Chang, Jasmine; Sabhaney, Ajay; Dong, Xiaoli; Gordon, Paul Mk; Janzen, Ryan Pw; Hau, David; Xia, Jianguo; Wishart, David S; Sensen, Christoph W

2009-01-01

We have developed a computational framework for spatiotemporal integration of molecular and anatomical datasets in a virtual reality environment. Using two case studies involving gene expression data and pharmacokinetic data, respectively, we demonstrate how existing knowledge bases for molecular data can be semantically mapped onto a standardized anatomical context of human body. Our data mapping methodology uses ontological representations of heterogeneous biomedical datasets and an ontology reasoner to create complex semantic descriptions of biomedical processes. This framework provides a means to systematically combine an increasing amount of biomedical imaging and numerical data into spatiotemporally coherent graphical representations. Our work enables medical researchers with different expertise to simulate complex phenomena visually and to develop insights through the use of shared data, thus paving the way for pathological inference, developmental pattern discovery and biomedical hypothesis testing.

Creating a Controlled Vocabulary for the Ethics of Human Research: Towards a Biomedical Ethics Ontology

PubMed Central

Koepsell, David; Arp, Robert; Fostel, Jennifer; Smith, Barry

2009-01-01

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology (BMEO) would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. PMID:19374479

Finding and accessing diagrams in biomedical publications.

PubMed

Kuhn, Tobias; Luong, ThaiBinh; Krauthammer, Michael

2012-01-01

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

Discovery informatics in biological and biomedical sciences: research challenges and opportunities.

PubMed

Honavar, Vasant

2015-01-01

New discoveries in biological, biomedical and health sciences are increasingly being driven by our ability to acquire, share, integrate and analyze, and construct and simulate predictive models of biological systems. While much attention has focused on automating routine aspects of management and analysis of "big data", realizing the full potential of "big data" to accelerate discovery calls for automating many other aspects of the scientific process that have so far largely resisted automation: identifying gaps in the current state of knowledge; generating and prioritizing questions; designing studies; designing, prioritizing, planning, and executing experiments; interpreting results; forming hypotheses; drawing conclusions; replicating studies; validating claims; documenting studies; communicating results; reviewing results; and integrating results into the larger body of knowledge in a discipline. Against this background, the PSB workshop on Discovery Informatics in Biological and Biomedical Sciences explores the opportunities and challenges of automating discovery or assisting humans in discovery through advances (i) Understanding, formalization, and information processing accounts of, the entire scientific process; (ii) Design, development, and evaluation of the computational artifacts (representations, processes) that embody such understanding; and (iii) Application of the resulting artifacts and systems to advance science (by augmenting individual or collective human efforts, or by fully automating science).

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education.

PubMed

Burley, Stephen K; Berman, Helen M; Christie, Cole; Duarte, Jose M; Feng, Zukang; Westbrook, John; Young, Jasmine; Zardecki, Christine

2018-01-01

The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open-access, digital-data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

PubMed Central

Berman, Helen M.; Christie, Cole; Duarte, Jose M.; Feng, Zukang; Westbrook, John; Young, Jasmine; Zardecki, Christine

2017-01-01

Abstract The Protein Data Bank (PDB) is one of two archival resources for experimental data central to biomedical research and education worldwide (the other key Primary Data Archive in biology being the International Nucleotide Sequence Database Collaboration). The PDB currently houses >134,000 atomic level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. It was established in 1971 as the first open‐access, digital‐data resource in biology, and is managed by the Worldwide Protein Data Bank partnership (wwPDB; wwpdb.org). US PDB operations are conducted by the RCSB Protein Data Bank (RCSB PDB; RCSB.org; Rutgers University and UC San Diego) and funded by NSF, NIH, and DoE. The RCSB PDB serves as the global Archive Keeper for the wwPDB. During calendar 2016, >591 million structure data files were downloaded from the PDB by Data Consumers working in every sovereign nation recognized by the United Nations. During this same period, the RCSB PDB processed >5300 new atomic level biomolecular structures plus experimental data and metadata coming into the archive from Data Depositors working in the Americas and Oceania. In addition, RCSB PDB served >1 million RCSB.org users worldwide with PDB data integrated with ∼40 external data resources providing rich structural views of fundamental biology, biomedicine, and energy sciences, and >600,000 PDB101.rcsb.org educational website users around the globe. RCSB PDB resources are described in detail together with metrics documenting the impact of access to PDB data on basic and applied research, clinical medicine, education, and the economy. PMID:29067736

Building a biomedical tokenizer using the token lattice design pattern and the adapted Viterbi algorithm

PubMed Central

2011-01-01

Background Tokenization is an important component of language processing yet there is no widely accepted tokenization method for English texts, including biomedical texts. Other than rule based techniques, tokenization in the biomedical domain has been regarded as a classification task. Biomedical classifier-based tokenizers either split or join textual objects through classification to form tokens. The idiosyncratic nature of each biomedical tokenizer’s output complicates adoption and reuse. Furthermore, biomedical tokenizers generally lack guidance on how to apply an existing tokenizer to a new domain (subdomain). We identify and complete a novel tokenizer design pattern and suggest a systematic approach to tokenizer creation. We implement a tokenizer based on our design pattern that combines regular expressions and machine learning. Our machine learning approach differs from the previous split-join classification approaches. We evaluate our approach against three other tokenizers on the task of tokenizing biomedical text. Results Medpost and our adapted Viterbi tokenizer performed best with a 92.9% and 92.4% accuracy respectively. Conclusions Our evaluation of our design pattern and guidelines supports our claim that the design pattern and guidelines are a viable approach to tokenizer construction (producing tokenizers matching leading custom-built tokenizers in a particular domain). Our evaluation also demonstrates that ambiguous tokenizations can be disambiguated through POS tagging. In doing so, POS tag sequences and training data have a significant impact on proper text tokenization. PMID:21658288

Magnetic hydroxyapatite: a promising multifunctional platform for nanomedicine application

PubMed Central

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

2017-01-01

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

The genetic composition of populations of cynomolgus macaques (Macaca fascicularis) used in biomedical research.

PubMed

Kanthaswamy, S; Ng, J; Satkoski Trask, J; George, D A; Kou, A J; Hoffman, L N; Doherty, T B; Houghton, P; Smith, D G

2013-06-01

The genetic composition of cynomolgus macaques used in biomedical research is not as well-characterized as that of rhesus macaques. Populations of cynomolgus macaques from Sumatra, Corregidor, Mauritius, Singapore, Cambodia, and Zamboanga were analyzed using 24 STRs. The Sumatran and Cambodian populations exhibited the highest allelic diversity, while the Mauritian population exhibited the lowest. Sumatran cynomolgus macaques were the most genetically similar to all others, consistent with an Indonesian origin of the species. The high diversity among Cambodian animals may result from interbreeding with rhesus macaques. The Philippine and Mauritian samples were the most divergent from other populations, the former due to separation from the Sunda Shelf by deepwater and the latter due to anthropogenic translocation and extreme founder effects. Investigators should verify their research subjects' origin, ancestry, and pedigree to minimize risks to biomedical experimentation from genetic variance stemming from close kinship and mixed ancestry as these can obscure treatment effects. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Quantitative phase microscopy via optimized inversion of the phase optical transfer function.

PubMed

Jenkins, Micah H; Gaylord, Thomas K

2015-10-01

Although the field of quantitative phase imaging (QPI) has wide-ranging biomedical applicability, many QPI methods are not well-suited for such applications due to their reliance on coherent illumination and specialized hardware. By contrast, methods utilizing partially coherent illumination have the potential to promote the widespread adoption of QPI due to their compatibility with microscopy, which is ubiquitous in the biomedical community. Described herein is a new defocus-based reconstruction method that utilizes a small number of efficiently sampled micrographs to optimally invert the partially coherent phase optical transfer function under assumptions of weak absorption and slowly varying phase. Simulation results are provided that compare the performance of this method with similar algorithms and demonstrate compatibility with large phase objects. The accuracy of the method is validated experimentally using a microlens array as a test phase object. Lastly, time-lapse images of live adherent cells are obtained with an off-the-shelf microscope, thus demonstrating the new method's potential for extending QPI capability widely in the biomedical community.

UCSC genome browser: deep support for molecular biomedical research.

PubMed

Mangan, Mary E; Williams, Jennifer M; Lathe, Scott M; Karolchik, Donna; Lathe, Warren C

2008-01-01

The volume and complexity of genomic sequence data, and the additional experimental data required for annotation of the genomic context, pose a major challenge for display and access for biomedical researchers. Genome browsers organize this data and make it available in various ways to extract useful information to advance research projects. The UCSC Genome Browser is one of these resources. The official sequence data for a given species forms the framework to display many other types of data such as expression, variation, cross-species comparisons, and more. Visual representations of the data are available for exploration. Data can be queried with sequences. Complex database queries are also easily achieved with the Table Browser interface. Associated tools permit additional query types or access to additional data sources such as images of in situ localizations. Support for solving researcher's issues is provided with active discussion mailing lists and by providing updated training materials. The UCSC Genome Browser provides a source of deep support for a wide range of biomedical molecular research (http://genome.ucsc.edu).

Unsupervised Transfer Learning via Multi-Scale Convolutional Sparse Coding for Biomedical Applications

PubMed Central

Chang, Hang; Han, Ju; Zhong, Cheng; Snijders, Antoine M.; Mao, Jian-Hua

2017-01-01

The capabilities of (I) learning transferable knowledge across domains; and (II) fine-tuning the pre-learned base knowledge towards tasks with considerably smaller data scale are extremely important. Many of the existing transfer learning techniques are supervised approaches, among which deep learning has the demonstrated power of learning domain transferrable knowledge with large scale network trained on massive amounts of labeled data. However, in many biomedical tasks, both the data and the corresponding label can be very limited, where the unsupervised transfer learning capability is urgently needed. In this paper, we proposed a novel multi-scale convolutional sparse coding (MSCSC) method, that (I) automatically learns filter banks at different scales in a joint fashion with enforced scale-specificity of learned patterns; and (II) provides an unsupervised solution for learning transferable base knowledge and fine-tuning it towards target tasks. Extensive experimental evaluation of MSCSC demonstrates the effectiveness of the proposed MSCSC in both regular and transfer learning tasks in various biomedical domains. PMID:28129148

[Letters to the editor published in Peruvian biomedical journals indexed in SciELO-Peru 2006-2013].

PubMed

Montenegro-Idrogo, Juan José; Mejía-Dolores, Jhon William; Chalco-Huamán, Joel L

2015-01-01

This bibliometric study describes the characteristics of letters to the editor published between 2006-2013 in biomedical journals indexed in SciELO-Peru.253 letters (10.3% of total publications) were collected. Most letters (139) were in the Peruvian Journal of Experimental Medicine and Public Health, with marked increase throughout those years. 25% of letters submitted included medical student participation. 14% of authors presented with international affiliations and 27% with endogenous affiliation - common in university journals (Anales de la Facultad de Medicina, Revista Médica Herediana).The usual criteria justifying the publication of letters were: opinion of medical fact or public domain (35.6%) and discussion of results, methodological flaws or interpretation (22.9%). In biomedical journals indexed in SciELO Peru the letters to the editor comprise a percentage of publications that has increased in recent years, with low publication of letters of findings or primary data, compared with opinion or criticism.

Technical editing of research reports in biomedical journals.

PubMed

Wager, Elizabeth; Middleton, Philippa

2008-10-08

Most journals try to improve their articles by technical editing processes such as proof-reading, editing to conform to 'house styles', grammatical conventions and checking accuracy of cited references. Despite the considerable resources devoted to technical editing, we do not know whether it improves the accessibility of biomedical research findings or the utility of articles. This is an update of a Cochrane methodology review first published in 2003. To assess the effects of technical editing on research reports in peer-reviewed biomedical journals, and to assess the level of accuracy of references to these reports. We searched The Cochrane Library Issue 2, 2007; MEDLINE (last searched July 2006); EMBASE (last searched June 2007) and checked relevant articles for further references. We also searched the Internet and contacted researchers and experts in the field. Prospective or retrospective comparative studies of technical editing processes applied to original research articles in biomedical journals, as well as studies of reference accuracy. Two review authors independently assessed each study against the selection criteria and assessed the methodological quality of each study. One review author extracted the data, and the second review author repeated this. We located 32 studies addressing technical editing and 66 surveys of reference accuracy. Only three of the studies were randomised controlled trials. A 'package' of largely unspecified editorial processes applied between acceptance and publication was associated with improved readability in two studies and improved reporting quality in another two studies, while another study showed mixed results after stricter editorial policies were introduced. More intensive editorial processes were associated with fewer errors in abstracts and references. Providing instructions to authors was associated with improved reporting of ethics requirements in one study and fewer errors in references in two studies, but no difference was seen in the quality of abstracts in one randomised controlled trial. Structuring generally improved the quality of abstracts, but increased their length. The reference accuracy studies showed a median citation error rate of 38% and a median quotation error rate of 20%. Surprisingly few studies have evaluated the effects of technical editing rigorously. However there is some evidence that the 'package' of technical editing used by biomedical journals does improve papers. A substantial number of references in biomedical articles are cited or quoted inaccurately.

A laboratory animal science pioneer.

PubMed

Kostomitsopoulos, Nikolaos

2014-11-01

Nikolaos Kostomitsopoulos, DVM, PhD, is Head of Laboratory Animal Facilities and Designated Veterinarian, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece. Dr. Kostomitsopoulos discusses his successes in implementing laboratory animal science legislation and fostering collaboration among scientists in Greece.

Secure management of biomedical data with cryptographic hardware.

PubMed

Canim, Mustafa; Kantarcioglu, Murat; Malin, Bradley

2012-01-01

The biomedical community is increasingly migrating toward research endeavors that are dependent on large quantities of genomic and clinical data. At the same time, various regulations require that such data be shared beyond the initial collecting organization (e.g., an academic medical center). It is of critical importance to ensure that when such data are shared, as well as managed, it is done so in a manner that upholds the privacy of the corresponding individuals and the overall security of the system. In general, organizations have attempted to achieve these goals through deidentification methods that remove explicitly, and potentially, identifying features (e.g., names, dates, and geocodes). However, a growing number of studies demonstrate that deidentified data can be reidentified to named individuals using simple automated methods. As an alternative, it was shown that biomedical data could be shared, managed, and analyzed through practical cryptographic protocols without revealing the contents of any particular record. Yet, such protocols required the inclusion of multiple third parties, which may not always be feasible in the context of trust or bandwidth constraints. Thus, in this paper, we introduce a framework that removes the need for multiple third parties by collocating services to store and to process sensitive biomedical data through the integration of cryptographic hardware. Within this framework, we define a secure protocol to process genomic data and perform a series of experiments to demonstrate that such an approach can be run in an efficient manner for typical biomedical investigations.

Secure Management of Biomedical Data With Cryptographic Hardware

PubMed Central

Canim, Mustafa; Kantarcioglu, Murat; Malin, Bradley

2014-01-01

The biomedical community is increasingly migrating toward research endeavors that are dependent on large quantities of genomic and clinical data. At the same time, various regulations require that such data be shared beyond the initial collecting organization (e.g., an academic medical center). It is of critical importance to ensure that when such data are shared, as well as managed, it is done so in a manner that upholds the privacy of the corresponding individuals and the overall security of the system. In general, organizations have attempted to achieve these goals through deidentification methods that remove explicitly, and potentially, identifying features (e.g., names, dates, and geocodes). However, a growing number of studies demonstrate that deidentified data can be reidentified to named individuals using simple automated methods. As an alternative, it was shown that biomedical data could be shared, managed, and analyzed through practical cryptographic protocols without revealing the contents of any particular record. Yet, such protocols required the inclusion of multiple third parties, which may not always be feasible in the context of trust or bandwidth constraints. Thus, in this paper, we introduce a framework that removes the need for multiple third parties by collocating services to store and to process sensitive biomedical data through the integration of cryptographic hardware. Within this framework, we define a secure protocol to process genomic data and perform a series of experiments to demonstrate that such an approach can be run in an efficient manner for typical biomedical investigations. PMID:22010157

Using semantics for representing experimental protocols.

PubMed

Giraldo, Olga; García, Alexander; López, Federico; Corcho, Oscar

2017-11-13

An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols. In this paper we present "SMART Protocols ontology", an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample. Improving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/ .

Bio-media Citizenship and Chronic Kidney Disease of Unknown Etiology in Sri Lanka.

PubMed

de Silva, M W Amarasiri

2018-04-01

In this article, I examine the crucial role of the biomedical industry, epidemiological and biomedical research, and the media in forming attitudes to and the understanding of chronic kidney disease of unknown etiology (CKDu) in Sri Lanka. Local conceptions of CKDu have been shaped by the circulation in the media of epidemiological research findings pertaining to the disease, biomedical interventions in the management of the disease in hospitals and clinics, community programs involving mass blood surveys and the testing of well water, and local food and health education programs carried out through village health committees. This process of circulation I identify as bio-media citizenship.

Instructions to Prospective Authors by Indian Biomedical Journals: An Opportunity to Promote Responsible Conduct of Research.

PubMed

Bhat, Anup; Shah, Akash; Sherighar, Swathi G

2017-04-01

Journals provide instructions to prospective authors to facilitate the process of manuscript publication. The information provided under such instructions could be a potential opportunity to promote responsible conduct of research (RCR). We analyzed 74 Indian biomedical journals for the type of information provided in the "instructions to authors" section and adherence to the International Committee of Medical Journal Editors (ICMJE) recommendations. Among the 71 journals that had an "instructions to authors" section, 53 journals adhered to ICMJE recommendations. We discuss sections of the ICMJE recommendations detailed by Indian biomedical journals under the "instructions to authors" section and emphasize components that require greater exposure.

Translations on USSR Science and Technology, Biomedical and Behavioral Sciences, Number 45, Effects of Nonionizing Electromagnetic Radiation.

DTIC Science & Technology

1978-09-22

klinicheskoy fizioterapii" (Pressing problems in experimental and clinical physiotherapy ), Moscow, 1976, pp 56-58. 23. Schwan, H. P., "Interaction of...Union conference on experimental health resort treatment and physiotherapy ), Moscow, 1970, pp 217-220. 53. Henderson, H. M. , Hergenroeder, K., and...187-190 [Article by Prof I. S. Cherkasov and students V. A. Nedzvetskiy and A. V. Gilenko, Department of Eye Diseases, Odessa Medical Institute

Animal models in biological and biomedical research - experimental and ethical concerns.

PubMed

Andersen, Monica L; Winter, Lucile M F

2017-09-04

Animal models have been used in experimental research to increase human knowledge and contribute to finding solutions to biological and biomedical questions. However, increased concern for the welfare of the animals used, and a growing awareness of the concept of animal rights, has brought a greater focus on the related ethical issues. In this review, we intend to give examples on how animals are used in the health research related to some major health problems in Brazil, as well as to stimulate discussion about the application of ethics in the use of animals in research and education, highlighting the role of National Council for the Control of Animal Experimentation (Conselho Nacional de Controle de Experimentação Animal - CONCEA) in these areas. In 2008, Brazil emerged into a new era of animal research regulation, with the promulgation of Law 11794, previously known as the Arouca Law, resulting in an increased focus, and rapid learning experience, on questions related to all aspects of animal experimentation. The law reinforces the idea that animal experiments must be based on ethical considerations and integrity-based assumptions, and provides a regulatory framework to achieve this. This review describes the health research involving animals and the current Brazilian framework for regulating laboratory animal science, and hopes to help to improve the awareness of the scientific community of these ethical and legal rules.

Experimental study on titanium wire drawing with ultrasonic vibration.

PubMed

Liu, Shen; Shan, Xiaobiao; Guo, Kai; Yang, Yuancai; Xie, Tao

2018-02-01

Titanium and its alloys have been widely used in aerospace and biomedical industries, however, they are classified as difficult-to-machine materials. In this paper, ultrasonic vibration is imposed on the die to overcome the difficulties during conventional titanium wire drawing processes at the room temperature. Numerical simulations were performed to investigate the variation of axial stress within the contacting region and study the change of the drawing stress with several factors in terms of the longitudinal amplitude and frequency of the applied ultrasonic vibration, the diameter reduction ratio, and the drawing force. An experimental testing equipment was established to measure the drawing torque and rotational velocity of the coiler drum during the wire drawing process. The result indicates the drawing force increases with the growth of the drawing velocity and the reduction ratio, whether with or without vibrations. Application of either form of ultrasonic vibrations contributes to the further decrease of the drawing force, especially the longitudinal vibration with larger amplitude. SEM was employed to detect the surface morphology of the processed wires drawn under the three circumstances. The surface quality of the drawn wires with ultrasonic vibrations was apparently improved compared with those using conventional method. In addition, the longitudinal and torsional composite vibration was more effective for surface quality improvement than pure longitudinal vibration, however, at the cost of weakened drawing force reduction effect. Copyright © 2017 Elsevier B.V. All rights reserved.

Biomedical image segmentation using geometric deformable models and metaheuristics.

PubMed

Mesejo, Pablo; Valsecchi, Andrea; Marrakchi-Kacem, Linda; Cagnoni, Stefano; Damas, Sergio

2015-07-01

This paper describes a hybrid level set approach for medical image segmentation. This new geometric deformable model combines region- and edge-based information with the prior shape knowledge introduced using deformable registration. Our proposal consists of two phases: training and test. The former implies the learning of the level set parameters by means of a Genetic Algorithm, while the latter is the proper segmentation, where another metaheuristic, in this case Scatter Search, derives the shape prior. In an experimental comparison, this approach has shown a better performance than a number of state-of-the-art methods when segmenting anatomical structures from different biomedical image modalities. Copyright © 2013 Elsevier Ltd. All rights reserved.

Indicators for the use of robotic labs in basic biomedical research: a literature analysis

PubMed Central

2017-01-01

Robotic labs, in which experiments are carried out entirely by robots, have the potential to provide a reproducible and transparent foundation for performing basic biomedical laboratory experiments. In this article, we investigate whether these labs could be applicable in current experimental practice. We do this by text mining 1,628 papers for occurrences of methods that are supported by commercial robotic labs. Using two different concept recognition tools, we find that 86%–89% of the papers have at least one of these methods. This and our other results provide indications that robotic labs can serve as the foundation for performing many lab-based experiments. PMID:29134146

Tubular nanostructured materials for bioapplications

NASA Astrophysics Data System (ADS)

Xie, Jining; Chen, Linfeng; Srivatsan, Malathi; Varadan, Vijay K.

2009-03-01

Tubular nanomaterials possess hollow structures as well as high aspect ratios. In addition to their unique physical and chemical properties induced by their nanoscale dimensions, their inner voids and outer surfaces make them ideal candidates for a number of biomedical applications. In this work, three types of tubular nanomaterials including carbon nanotubes, hematite nanotubes, and maghemite nanotubes, were synthesized by different chemical techniques. Their structural and crystalline properties were characterized. For potential bioapplications of tubular nanomaterials, experimental investigations were carried out to demonstrate the feasibility of using carbon nanotubes, hematite nanotubes, and maghemite nanotubes in glucose sensing, neuronal growth, and drug delivery, respectively. Preliminary results show the promise of tubular nanomaterials in future biomedical applications.

Wireless power transmission for biomedical implants: The role of near-zero threshold CMOS rectifiers.

PubMed

Mohammadi, Ali; Redoute, Jean-Michel; Yuce, Mehmet R

2015-01-01

Biomedical implants require an electronic power conditioning circuitry to provide a stable electrical power supply. The efficiency of wireless power transmission is strongly dependent on the power conditioning circuitry specifically the rectifier. A cross-connected CMOS bridge rectifier is implemented to demonstrate the impact of thresholds of rectifiers on wireless power transfer. The performance of the proposed rectifier is experimentally compared with a conventional Schottky diode full wave rectifier over 9 cm distance of air and tissue medium between the transmitter and receiver. The output voltage generated by the CMOS rectifier across a 1 KΩ resistive load is around twice as much as the Schottky rectifier.

Reviewing Manuscripts for Biomedical Journals

PubMed Central

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

Getting to zero the biomedical way in Africa: outcomes of deliberation at the 2013 Biomedical HIV Prevention Forum in Abuja, Nigeria

PubMed Central

2014-01-01

Background Over the last few decades, biomedical HIV prevention research had engaged multiple African stakeholders. There have however been few platforms to enable regional stakeholders to engage with one another. In partnership with the World AIDS Campaign International, the Institute of Public Health of Obafemi Awolowo University, and the National Agency for the Control of AIDS in Nigeria, the New HIV Vaccine and Microbicide Advocacy Society hosted a forum on biomedical HIV prevention research in Africa. Stakeholders’ present explored evidences related to biomedical HIV prevention research and development in Africa, and made recommendations to inform policy, guidelines and future research agenda. Discussion The BHPF hosted 342 participants. Topics discussed included the use of antiretrovirals for HIV prevention, considerations for biomedical HIV prevention among key populations; HIV vaccine development; HIV cure; community and civil society engagement; and ethical considerations in implementation of biomedical HIV prevention research. Participants identified challenges for implementation of proven efficacious interventions and discovery of other new prevention options for Africa. Concerns raised included limited funding by African governments, lack of cohesive advocacy and policy agenda for biomedical HIV prevention research and development by Africa, varied ethical practices, and limited support to communities’ capacity to actively engaged with clinical trial conducts. Participants recommended that the African Government implement the Abuja +12 declaration; the civil society build stronger partnerships with diverse stakeholders, and develop a coherent advocacy agenda that also enhances community research literacy; and researchers and sponsors of trials on the African continent establish a process for determining appropriate standards for trial conduct on the continent. Conclusion By highlighting key considerations for biomedical HIV prevention research and development in Africa, the forum has helped identify key advocacy issues that Civil Society can expend efforts on so as to strengthen support for future biomedical HIV prevention research on the continent. PMID:26636825

Getting to zero the biomedical way in Africa: outcomes of deliberation at the 2013 Biomedical HIV Prevention Forum in Abuja, Nigeria.

PubMed

Folayan, Morenike Oluwatoyin; Gottemoeller, Megan; Mburu, Rosemary; Brown, Brandon

2014-01-01

Over the last few decades, biomedical HIV prevention research had engaged multiple African stakeholders. There have however been few platforms to enable regional stakeholders to engage with one another. In partnership with the World AIDS Campaign International, the Institute of Public Health of Obafemi Awolowo University, and the National Agency for the Control of AIDS in Nigeria, the New HIV Vaccine and Microbicide Advocacy Society hosted a forum on biomedical HIV prevention research in Africa. Stakeholders' present explored evidences related to biomedical HIV prevention research and development in Africa, and made recommendations to inform policy, guidelines and future research agenda. The BHPF hosted 342 participants. Topics discussed included the use of antiretrovirals for HIV prevention, considerations for biomedical HIV prevention among key populations; HIV vaccine development; HIV cure; community and civil society engagement; and ethical considerations in implementation of biomedical HIV prevention research. Participants identified challenges for implementation of proven efficacious interventions and discovery of other new prevention options for Africa. Concerns raised included limited funding by African governments, lack of cohesive advocacy and policy agenda for biomedical HIV prevention research and development by Africa, varied ethical practices, and limited support to communities' capacity to actively engaged with clinical trial conducts. Participants recommended that the African Government implement the Abuja +12 declaration; the civil society build stronger partnerships with diverse stakeholders, and develop a coherent advocacy agenda that also enhances community research literacy; and researchers and sponsors of trials on the African continent establish a process for determining appropriate standards for trial conduct on the continent. By highlighting key considerations for biomedical HIV prevention research and development in Africa, the forum has helped identify key advocacy issues that Civil Society can expend efforts on so as to strengthen support for future biomedical HIV prevention research on the continent.

Community outreach at biomedical research facilities.

PubMed

Goldman, M; Hedetniemi, J N; Herbert, E R; Sassaman, J S; Walker, B C

2000-12-01

For biomedical researchers to fulfill their responsibility for protecting the environment, they must do more than meet the scientific challenge of reducing the number and volume of hazardous materials used in their laboratories and the engineering challenge of reducing pollution and shifting to cleaner energy sources. They must also meet the public relations challenge of informing and involving their neighbors in these efforts. The experience of the Office of Community Liaison of the National Institutes of Health (NIH) in meeting the latter challenge offers a model and several valuable lessons for other biomedical research facilities to follow. This paper is based on presentations by an expert panel during the Leadership Conference on Biomedical Research and the Environment held 1--2 November 1999 at NIH, Bethesda, Maryland. The risks perceived by community members are often quite different from those identified by officials at the biomedical research facility. The best antidote for misconceptions is more and better information. If community organizations are to be informed participants in the decision-making process, they need a simple but robust mechanism for identifying and evaluating the environmental hazards in their community. Local government can and should be an active and fully informed partner in planning and emergency preparedness. In some cases this can reduce the regulatory burden on the biomedical research facility. In other cases it might simplify and expedite the permitting process or help the facility disseminate reliable information to the community. When a particular risk, real or perceived, is of special concern to the community, community members should be involved in the design, implementation, and evaluation of targeted risk assessment activities. Only by doing so will the community have confidence in the results of those activities. NIH has involved community members in joint efforts to deal with topics as varied as recycling and soil testing. These ad hoc efforts are more likely to succeed if community members and groups have also been included in larger and longer term advisory committees. These committees institutionalize the outreach process. This can provide the facility with vocal and influential allies who create an independent line of communication with the larger community.

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

PubMed

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.

Utilization of flax fibers for biomedical applications.

PubMed

Michel, Sophie A A X; Vogels, Ruben R M; Bouvy, Nicole D; Knetsch, Menno L W; van den Akker, Nynke M S; Gijbels, Marion J J; van der Marel, Cees; Vermeersch, Jan; Molin, Daniel G M; Koole, Leo H

2014-04-01

Over the past decades, a large number of animal-derived materials have been introduced for several biomedical applications. Surprisingly, the use of plant-based materials has lagged behind. To study the feasibility of plant-derived biomedical materials, we chose flax (Linum usitatissimum). Flax fibers possess excellent physical-mechanical properties, are nonbiodegradable, and there is extensive know-how on weaving/knitting of them. One area where they could be useful is as implantable mesh structures in surgery, in particular for the repair of incisional hernias of the abdominal wall. Starting with a bleached flax thread, a prototype mesh was specifically knitted for this study, and its cytocompatibility was studied in vitro and in vivo. The experimental data revealed that application of flax in surgery first requires a robust method to remove endotoxins and purify the flax fiber. Such a method was developed, and purified meshes did not cause loss of cell viability in vitro. In addition, endotoxins determined using limulus amebocyte lysate test were at acceptable levels. In vivo, the flax meshes showed only mild inflammation, comparable to commercial polypropylene meshes. This study revealed that plant-derived biomaterials can provide a new class of implantable materials that could be used as surgical meshes or for other biomedical applications. Copyright © 2013 Wiley Periodicals, Inc.

Envisioning the future of 'big data' biomedicine.

PubMed

Bui, Alex A T; Van Horn, John Darrell

2017-05-01

Through the increasing availability of more efficient data collection procedures, biomedical scientists are now confronting ever larger sets of data, often finding themselves struggling to process and interpret what they have gathered. This, while still more data continues to accumulate. This torrent of biomedical information necessitates creative thinking about how the data are being generated, how they might be best managed, analyzed, and eventually how they can be transformed into further scientific understanding for improving patient care. Recognizing this as a major challenge, the National Institutes of Health (NIH) has spearheaded the "Big Data to Knowledge" (BD2K) program - the agency's most ambitious biomedical informatics effort ever undertaken to date. In this commentary, we describe how the NIH has taken on "big data" science head-on, how a consortium of leading research centers are developing the means for handling large-scale data, and how such activities are being marshalled for the training of a new generation of biomedical data scientists. All in all, the NIH BD2K program seeks to position data science at the heart of 21 st Century biomedical research. Copyright © 2017 Elsevier Inc. All rights reserved.

Materials and fabrication sequences for water soluble silicon integrated circuits at the 90 nm node

NASA Astrophysics Data System (ADS)

Yin, Lan; Bozler, Carl; Harburg, Daniel V.; Omenetto, Fiorenzo; Rogers, John A.

2015-01-01

Tungsten interconnects in silicon integrated circuits built at the 90 nm node with releasable configurations on silicon on insulator wafers serve as the basis for advanced forms of water-soluble electronics. These physically transient systems have potential uses in applications that range from temporary biomedical implants to zero-waste environmental sensors. Systematic experimental studies and modeling efforts reveal essential aspects of electrical performance in field effect transistors and complementary ring oscillators with as many as 499 stages. Accelerated tests reveal timescales for dissolution of the various constituent materials, including tungsten, silicon, and silicon dioxide. The results demonstrate that silicon complementary metal-oxide-semiconductor circuits formed with tungsten interconnects in foundry-compatible fabrication processes can serve as a path to high performance, mass-produced transient electronic systems.

Modeling microcirculatory blood flow: current state and future perspectives.

PubMed

Gompper, Gerhard; Fedosov, Dmitry A

2016-01-01

Microvascular blood flow determines a number of important physiological processes of an organism in health and disease. Therefore, a detailed understanding of microvascular blood flow would significantly advance biophysical and biomedical research and its applications. Current developments in modeling of microcirculatory blood flow already allow to go beyond available experimental measurements and have a large potential to elucidate blood flow behavior in normal and diseased microvascular networks. There exist detailed models of blood flow on a single cell level as well as simplified models of the flow through microcirculatory networks, which are reviewed and discussed here. The combination of these models provides promising prospects for better understanding of blood flow behavior and transport properties locally as well as globally within large microvascular networks. © 2015 Wiley Periodicals, Inc.

A recent advance in the automatic indexing of the biomedical literature.

PubMed

Névéol, Aurélie; Shooshan, Sonya E; Humphrey, Susanne M; Mork, James G; Aronson, Alan R

2009-10-01

The volume of biomedical literature has experienced explosive growth in recent years. This is reflected in the corresponding increase in the size of MEDLINE, the largest bibliographic database of biomedical citations. Indexers at the US National Library of Medicine (NLM) need efficient tools to help them accommodate the ensuing workload. After reviewing issues in the automatic assignment of Medical Subject Headings (MeSH terms) to biomedical text, we focus more specifically on the new subheading attachment feature for NLM's Medical Text Indexer (MTI). Natural Language Processing, statistical, and machine learning methods of producing automatic MeSH main heading/subheading pair recommendations were assessed independently and combined. The best combination achieves 48% precision and 30% recall. After validation by NLM indexers, a suitable combination of the methods presented in this paper was integrated into MTI as a subheading attachment feature producing MeSH indexing recommendations compliant with current state-of-the-art indexing practice.

Finding and Accessing Diagrams in Biomedical Publications

PubMed Central

Kuhn, Tobias; Luong, ThaiBinh; Krauthammer, Michael

2012-01-01

Complex relationships in biomedical publications are often communicated by diagrams such as bar and line charts, which are a very effective way of summarizing and communicating multi-faceted data sets. Given the ever-increasing amount of published data, we argue that the precise retrieval of such diagrams is of great value for answering specific and otherwise hard-to-meet information needs. To this end, we demonstrate the use of advanced image processing and classification for identifying bar and line charts by the shape and relative location of the different image elements that make up the charts. With recall and precisions of close to 90% for the detection of relevant figures, we discuss the use of this technology in an existing biomedical image search engine, and outline how it enables new forms of literature queries over biomedical relationships that are represented in these charts. PMID:23304318

Scientific Programs and Funding Opportunities at the National Institute of Biomedical Imaging and Bioengineering

NASA Astrophysics Data System (ADS)

Baird, Richard

2006-03-01

The mission of the National Institute of Biomedical Imaging and Bioengineering (NIBIB) is to improve human health by promoting the development and translation of emerging technologies in biomedical imaging and bioengineering. To this end, NIBIB supports a coordinated agenda of research programs in advanced imaging technologies and engineering methods that enable fundamental biomedical discoveries across a broad spectrum of biological processes, disorders, and diseases and have significant potential for direct medical application. These research programs dramatically advance the Nation's healthcare by improving the detection, management and, ultimately, the prevention of disease. The research promoted and supported by NIBIB also is strongly synergistic with other NIH Institutes and Centers as well as across government agencies. This presentation will provide an overview of the scientific programs and funding opportunities supported by NIBIB, highlighting those that are of particular important to the field of medical physics.

Science, Medicine, and Animals: Teacher's Guide

ERIC Educational Resources Information Center

Moran, Lisa C.

2005-01-01

"Science, Medicine, and Animals" explains the role that animals play in biomedical research and the ways in which scientists, governments, and citizens have tried to balance the experimental use of animals with a concern for all living creatures. An accompanying "Teacher's Guide" is available to help teachers of middle and high…

Nanofinishing of freeform/sculptured surfaces: state-of-the-art

NASA Astrophysics Data System (ADS)

Nagdeve, Leeladhar; Jain, V. K.; Ramkumar, J.

2018-06-01

Freeform surfaces are being used in a multiplicity of applications in different kinds of industries related to Bio-medical (Bio-implants), micro channels in micro fluidics, automotives, turbine blades, impellers of artificial heart pumps, automobiles etc. Different parts in these industries need nano-level surface finish as their functional inevitability. It is very difficult and challenging to achieve high level of surface finish, especially on the components having freeform (or sculptured) surfaces, complex shapes, and 3-D features. Surface finish is a significant factor, which affects life and functionality of a product. Many traditional and advanced finishing processes have been developed for finishing of freeform/sculptured surfaces but still it has not been possible to achieve uniform nano level surface finish specially in case of freeform surfaces. To overcome the limitations of the existing nanofinishing processes, researchers are developing new processes for uniform nanofinishing of freeform surfaces. In this article, an attempt has been made to review different nanofinishing processes employed for freeform surfaces useful in different types of applications. In addition, experimental work, theoretical analysis and existing challenges of the finishing processes have been identified to fill the research gap.

Spinning disc atomisation process: Modelling and computations

NASA Astrophysics Data System (ADS)

Li, Yuan; Sisoev, Grigory; Shikhmurzaev, Yulii

2016-11-01

The atomisation of liquids using a spinning disc (SDA), where the centrifugal force is used to generate a continuous flow, with the liquid eventually disintegrating into drops which, on solidification, become particles, is a key element in many technologies. Examples of such technologies range from powder manufacturing in metallurgy to various biomedical applications. In order to be able to control the SDA process, it is necessary to understand it as a whole, from the feeding of the liquid and the wave pattern developing on the disc to the disintegration of the liquid film into filaments and these into drops. The SDA process has been the subject of a number of experimental studies and some elements of it, notably the film on a spinning disc and the dynamics of the jets streaming out from it, have been investigated theoretically. However, to date there have been no studies of the process as a whole, including, most importantly, the transition zone where the film that has already developed a certain wave pattern disintegrates into jets that spiral out. The present work reports some results of an ongoing project aimed at producing a definitive map of regimes occurring in the SDA process and their outcome.

Self-regulated learning processes of medical students during an academic learning task.

PubMed

Gandomkar, Roghayeh; Mirzazadeh, Azim; Jalili, Mohammad; Yazdani, Kamran; Fata, Ladan; Sandars, John

2016-10-01

This study was designed to identify the self-regulated learning (SRL) processes of medical students during a biomedical science learning task and to examine the associations of the SRL processes with previous performance in biomedical science examinations and subsequent performance on a learning task. A sample of 76 Year 1 medical students were recruited based on their performance in biomedical science examinations and stratified into previous high and low performers. Participants were asked to complete a biomedical science learning task. Participants' SRL processes were assessed before (self-efficacy, goal setting and strategic planning), during (metacognitive monitoring) and after (causal attributions and adaptive inferences) their completion of the task using an SRL microanalytic interview. Descriptive statistics were used to analyse the means and frequencies of SRL processes. Univariate and multiple logistic regression analyses were conducted to examine the associations of SRL processes with previous examination performance and the learning task performance. Most participants (from 88.2% to 43.4%) reported task-specific processes for SRL measures. Students who exhibited higher self-efficacy (odds ratio [OR] 1.44, 95% confidence interval [CI] 1.09-1.90) and reported task-specific processes for metacognitive monitoring (OR 6.61, 95% CI 1.68-25.93) and causal attributions (OR 6.75, 95% CI 2.05-22.25) measures were more likely to be high previous performers. Multiple analysis revealed that similar SRL measures were associated with previous performance. The use of task-specific processes for causal attributions (OR 23.00, 95% CI 4.57-115.76) and adaptive inferences (OR 27.00, 95% CI 3.39-214.95) measures were associated with being a high learning task performer. In multiple analysis, only the causal attributions measure was associated with high learning task performance. Self-efficacy, metacognitive monitoring and causal attributions measures were associated positively with previous performance. Causal attributions and adaptive inferences measures were associated positively with learning task performance. These findings may inform remediation interventions in the early years of medical school training. © 2016 John Wiley & Sons Ltd and The Association for the Study of Medical Education.

Induction of engineered residual stresses fields and enhancement of fatigue life of high reliability metallic components by laser shock processing

NASA Astrophysics Data System (ADS)

Ocaña, J. L.; Porro, J. A.; Díaz, M.; Ruiz de Lara, L.; Correa, C.; Gil-Santos, A.; Peral, D.

2013-02-01

Laser shock processing (LSP) is being increasingly applied as an effective technology for the improvement of metallic materials mechanical and surface properties in different types of components as a means of enhancement of their corrosion and fatigue life behavior. As reported in previous contributions by the authors, a main effect resulting from the application of the LSP technique consists on the generation of relatively deep compression residual stresses field into metallic alloy pieces allowing an improved mechanical behaviour, explicitly the life improvement of the treated specimens against wear, crack growth and stress corrosion cracking. Additional results accomplished by the authors in the line of practical development of the LSP technique at an experimental level (aiming its integral assessment from an interrelated theoretical and experimental point of view) are presented in this paper. Concretely, follow-on experimental results on the residual stress profiles and associated surface properties modification successfully reached in typical materials (especially Al and Ti alloys characteristic of high reliability components in the aerospace, nuclear and biomedical sectors) under different LSP irradiation conditions are presented along with a practical correlated analysis on the protective character of the residual stress profiles obtained under different irradiation strategies. Additional remarks on the improved character of the LSP technique over the traditional "shot peening" technique in what concerns depth of induced compressive residual stresses fields are also made through the paper.

Cognitive and learning sciences in biomedical and health instructional design: A review with lessons for biomedical informatics education.

PubMed

Patel, Vimla L; Yoskowitz, Nicole A; Arocha, Jose F; Shortliffe, Edward H

2009-02-01

Theoretical and methodological advances in the cognitive and learning sciences can greatly inform curriculum and instruction in biomedicine and also educational programs in biomedical informatics. It does so by addressing issues such as the processes related to comprehension of medical information, clinical problem-solving and decision-making, and the role of technology. This paper reviews these theories and methods from the cognitive and learning sciences and their role in addressing current and future needs in designing curricula, largely using illustrative examples drawn from medical education. The lessons of this past work are also applicable, however, to biomedical and health professional curricula in general, and to biomedical informatics training, in particular. We summarize empirical studies conducted over two decades on the role of memory, knowledge organization and reasoning as well as studies of problem-solving and decision-making in medical areas that inform curricular design. The results of this research contribute to the design of more informed curricula based on empirical findings about how people learn and think, and more specifically, how expertise is developed. Similarly, the study of practice can also help to shape theories of human performance, technology-based learning, and scientific and professional collaboration that extend beyond the domain of medicine. Just as biomedical science has revolutionized health care practice, research in the cognitive and learning sciences provides a scientific foundation for education in biomedicine, the health professions, and biomedical informatics.

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

PubMed

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

2007-02-01

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

Adolescent Self-Consent for Biomedical Human Immunodeficiency Virus Prevention Research.

PubMed

Gilbert, Amy Lewis; Knopf, Amelia S; Fortenberry, J Dennis; Hosek, Sybil G; Kapogiannis, Bill G; Zimet, Gregory D

2015-07-01

The Adolescent Medicine Trials Network Protocol 113 (ATN113) is an open-label, multisite demonstration project and Phase II safety study of human immunodeficiency virus (HIV) preexposure prophylaxis with 15- to 17-year-old young men who have sex with men that requires adolescent consent for participation. The purpose of this study was to examine factors related to the process by which Institutional Review Boards (IRBs) and researchers made decisions regarding whether to approve and implement ATN113 so as to inform future biomedical HIV prevention research with high-risk adolescent populations. Participants included 17 researchers at 13 sites in 12 states considering ATN113 implementation. Qualitative descriptive methods were used. Data sources included interviews and documents generated during the initiation process. A common process for initiating ATN113 emerged, and informants described how they identified and addressed practical, ethical, and legal challenges that arose. Informants described the process as responding to the protocol, preparing for IRB submission, abstaining from or proceeding with submission, responding to IRB concerns, and reacting to the outcomes. A complex array of factors impacting approval and implementation were identified, and ATN113 was ultimately implemented in seven of 13 sites. Informants also reflected on lessons learned that may help inform future biomedical HIV prevention research with high-risk adolescent populations. The results illustrate factors for consideration in determining whether to implement such trials, demonstrate that such protocols have the potential to be approved, and highlight a need for clearer standards regarding biomedical HIV prevention research with high-risk adolescent populations. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Beamlines of the Biomedical Imaging and Therapy Facility at the Canadian Light Source - Part 2

NASA Astrophysics Data System (ADS)

Wysokinski, T. W.; Chapman, D.; Adams, G.; Renier, M.; Suortti, P.; Thomlinson, W.

2013-03-01

The BioMedical Imaging and Therapy (BMIT) facility provides a world class facility with unique synchrotron-specific imaging and therapy capabilities. This paper describes Insertion Device (ID) beamline 05ID-2 with the beam terminated in the first experimental hutch: POE-2. The experimental methods available in POE-2 include: Microbeam Radiation Therapy (MRT), Synchrotron Stereotactic Radiation Therapy (SSRT) and absorption imaging (projection and Computed Tomography (CT)). The source for the ID beamline is a multi-pole superconductive 4.3 T wiggler, which can generate ~30 kW of radiative power and deliver dose as high as 3000 Gy/s required for MRT program. The optics in POE-1 hutch prepares either monochromatic or filtered white beam that is used in POE-2. The Double Crystal (DC), bent Laue monochromator will prepare a beam over 10 cm wide at sample point, while spanning an energy range appropriate for imaging studies of animals (20-100+ keV). The experimental hutch will have a flexible positioning system that can handle subjects up to 120 kg. Several different cameras will be available with resolutions ranging from 4 μm to 150 μm. The latest update on the status of 05B1-1 bending magnet (BM) beamline, described in Part 1 [1], is also included.

The role of real-time in biomedical science: a meta-analysis on computational complexity, delay and speedup.

PubMed

Faust, Oliver; Yu, Wenwei; Rajendra Acharya, U

2015-03-01

The concept of real-time is very important, as it deals with the realizability of computer based health care systems. In this paper we review biomedical real-time systems with a meta-analysis on computational complexity (CC), delay (Δ) and speedup (Sp). During the review we found that, in the majority of papers, the term real-time is part of the thesis indicating that a proposed system or algorithm is practical. However, these papers were not considered for detailed scrutiny. Our detailed analysis focused on papers which support their claim of achieving real-time, with a discussion on CC or Sp. These papers were analyzed in terms of processing system used, application area (AA), CC, Δ, Sp, implementation/algorithm (I/A) and competition. The results show that the ideas of parallel processing and algorithm delay were only recently introduced and journal papers focus more on Algorithm (A) development than on implementation (I). Most authors compete on big O notation (O) and processing time (PT). Based on these results, we adopt the position that the concept of real-time will continue to play an important role in biomedical systems design. We predict that parallel processing considerations, such as Sp and algorithm scaling, will become more important. Copyright © 2015 Elsevier Ltd. All rights reserved.

DataMed - an open source discovery index for finding biomedical datasets.

PubMed

Chen, Xiaoling; Gururaj, Anupama E; Ozyurt, Burak; Liu, Ruiling; Soysal, Ergin; Cohen, Trevor; Tiryaki, Firat; Li, Yueling; Zong, Nansu; Jiang, Min; Rogith, Deevakar; Salimi, Mandana; Kim, Hyeon-Eui; Rocca-Serra, Philippe; Gonzalez-Beltran, Alejandra; Farcas, Claudiu; Johnson, Todd; Margolis, Ron; Alter, George; Sansone, Susanna-Assunta; Fore, Ian M; Ohno-Machado, Lucila; Grethe, Jeffrey S; Xu, Hua

2018-01-13

Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain. DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium. It consists of 2 main components: (1) a data ingestion pipeline that collects and transforms original metadata information to a unified metadata model, called DatA Tag Suite (DATS), and (2) a search engine that finds relevant datasets based on user-entered queries. In addition to describing its architecture and techniques, we evaluated individual components within DataMed, including the accuracy of the ingestion pipeline, the prevalence of the DATS model across repositories, and the overall performance of the dataset retrieval engine. Our manual review shows that the ingestion pipeline could achieve an accuracy of 90% and core elements of DATS had varied frequency across repositories. On a manually curated benchmark dataset, the DataMed search engine achieved an inferred average precision of 0.2033 and a precision at 10 (P@10, the number of relevant results in the top 10 search results) of 0.6022, by implementing advanced natural language processing and terminology services. Currently, we have made the DataMed system publically available as an open source package for the biomedical community. © The Author 2018. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Biomedical patents and ethics: a Canadian solution.

PubMed

Gold, E R

2000-05-01

World Trade Organization member states are preparing for the upcoming renegotiation of the Agreement on Trade-Related Aspects of Intellectual Property Rights. One of the important elements of that renegotiation is the ethical considerations regarding the patenting of higher life forms and their component parts (e.g. DNA and cell-lines). The interface between the genetic revolution, patentability, and ethical considerations is the subject of this article. The author identifies, explores, and critiques four possible positions Canada may adopt in respect of patentability of biomedical material. First, Canada could do nothing. This approach would mean keeping biomedical materials outside the patent system and outside the stream of commerce. Canada would simply wait for an international consensus to develop before adopting a position of its own. Second, Canada could go it alone. It could implement a policy that balances the incentive effects of patents with the need to incorporate ethical and social values into the decision-making process regarding the use of biomedical materials. In respect of this option, the author proposes a model whereby non-profit bodies would hold the exclusive rights to research, use, and exploit biomedical materials. Third, Canada could follow the United States, Europe, and Japan by providing for almost unrestricted patenting of biomedical materials. This would be the most industry-friendly alternative. The fourth and final option is to use the medicare system to promote discussion of ethical considerations involved in the use of biomedical materials. The power of provincial health agencies may be used as a lever to ensure the discussion of ethical considerations concerning the use of biomedical materials. The author concludes that the fourth and final option is the best alternative for Canada while waiting for an international consensus to emerge.

BIOSSES: a semantic sentence similarity estimation system for the biomedical domain.

PubMed

Sogancioglu, Gizem; Öztürk, Hakime; Özgür, Arzucan

2017-07-15

The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English. However, our experiments showed that such approaches do not effectively cover biomedical knowledge and produce poor results for biomedical text. We propose several approaches for sentence-level semantic similarity computation in the biomedical domain, including string similarity measures and measures based on the distributed vector representations of sentences learned in an unsupervised manner from a large biomedical corpus. In addition, ontology-based approaches are presented that utilize general and domain-specific ontologies. Finally, a supervised regression based model is developed that effectively combines the different similarity computation metrics. A benchmark data set consisting of 100 sentence pairs from the biomedical literature is manually annotated by five human experts and used for evaluating the proposed methods. The experiments showed that the supervised semantic sentence similarity computation approach obtained the best performance (0.836 correlation with gold standard human annotations) and improved over the state-of-the-art domain-independent systems up to 42.6% in terms of the Pearson correlation metric. A web-based system for biomedical semantic sentence similarity computation, the source code, and the annotated benchmark data set are available at: http://tabilab.cmpe.boun.edu.tr/BIOSSES/ . gizemsogancioglu@gmail.com or arzucan.ozgur@boun.edu.tr. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

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

PubMed Central

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

2017-01-01

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

Decision-making and motivation to participate in biomedical research in southwest Nigeria.

PubMed

Osamor, Pauline E; Kass, Nancy

2012-08-01

Motivations and decision-making styles that influence participation in biomedical research vary across study types, cultures, and countries. While there is a small amount of literature on informed consent in non-western cultures, few studies have examined how participants make the decision to join research. This study was designed to identify the factors motivating people to participate in biomedical research in a traditional Nigerian community, assess the degree to which participants involve others in the decision-making process, and examine issues of autonomy in decision-making for research. A descriptive cross-sectional study was conducted with 100 adults (50 men, 50 women) in an urban Nigerian community who had participated in a biomedical research study. Subjects were interviewed using a survey instrument. Two-thirds of the respondents reported participating in the biomedical study to learn more about their illness, while 30% hoped to get some medical care. Over three-quarters (78%) of participants discussed the enrollment decision with someone else and 39% reported obtaining permission from a spouse or family member to participate in the study. Women were more than twice as likely as men to report obtaining permission from someone else before participating. More specifically, half of the female participants reported seeking permission from a spouse before enrolling. The findings suggest that informed consent in this community is understood and practised as a relational activity that involves others in the decision making process. Further studies are needed in non-Western countries concerning autonomy, decision-making, and motivation to participate in research studies. © 2012 Blackwell Publishing Ltd.

Guidelines for Developing and Reporting Machine Learning Predictive Models in Biomedical Research: A Multidisciplinary View.

PubMed

Luo, Wei; Phung, Dinh; Tran, Truyen; Gupta, Sunil; Rana, Santu; Karmakar, Chandan; Shilton, Alistair; Yearwood, John; Dimitrova, Nevenka; Ho, Tu Bao; Venkatesh, Svetha; Berk, Michael

2016-12-16

As more and more researchers are turning to big data for new opportunities of biomedical discoveries, machine learning models, as the backbone of big data analysis, are mentioned more often in biomedical journals. However, owing to the inherent complexity of machine learning methods, they are prone to misuse. Because of the flexibility in specifying machine learning models, the results are often insufficiently reported in research articles, hindering reliable assessment of model validity and consistent interpretation of model outputs. To attain a set of guidelines on the use of machine learning predictive models within clinical settings to make sure the models are correctly applied and sufficiently reported so that true discoveries can be distinguished from random coincidence. A multidisciplinary panel of machine learning experts, clinicians, and traditional statisticians were interviewed, using an iterative process in accordance with the Delphi method. The process produced a set of guidelines that consists of (1) a list of reporting items to be included in a research article and (2) a set of practical sequential steps for developing predictive models. A set of guidelines was generated to enable correct application of machine learning models and consistent reporting of model specifications and results in biomedical research. We believe that such guidelines will accelerate the adoption of big data analysis, particularly with machine learning methods, in the biomedical research community. ©Wei Luo, Dinh Phung, Truyen Tran, Sunil Gupta, Santu Rana, Chandan Karmakar, Alistair Shilton, John Yearwood, Nevenka Dimitrova, Tu Bao Ho, Svetha Venkatesh, Michael Berk. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 16.12.2016.

Photoacoustic sensor for medical diagnostics

NASA Astrophysics Data System (ADS)

Wolff, Marcus; Groninga, Hinrich G.; Harde, Hermann

2004-03-01

The development of new optical sensor technologies has a major impact on the progress of diagnostic methods. Of the permanently increasing number of non-invasive breath tests, the 13C-Urea Breath Test (UBT) for the detection of Helicobacter pylori is the most prominent. However, many recent developments, like the detection of cancer by breath test, go beyond gastroenterological applications. We present a new detection scheme for breath analysis that employs an especially compact and simple set-up. Photoacoustic Spectroscopy (PAS) represents an offset-free technique that allows for short absorption paths and small sample cells. Using a single-frequency diode laser and taking advantage of acoustical resonances of the sample cell, we performed extremely sensitive and selective measurements. The smart data processing method contributes to the extraordinary sensitivity and selectivity as well. Also, the reasonable acquisition cost and low operational cost make this detection scheme attractive for many biomedical applications. The experimental set-up and data processing method, together with exemplary isotope-selective measurements on carbon dioxide, are presented.

Priming nanoparticle-guided diagnostics and therapeutics towards human organs-on-chips microphysiological system

NASA Astrophysics Data System (ADS)

Choi, Jin-Ha; Lee, Jaewon; Shin, Woojung; Choi, Jeong-Woo; Kim, Hyun Jung

2016-10-01

Nanotechnology and bioengineering have converged over the past decades, by which the application of multi-functional nanoparticles (NPs) has been emerged in clinical and biomedical fields. The NPs primed to detect disease-specific biomarkers or to deliver biopharmaceutical compounds have beena validated in conventional in vitro culture models including two dimensional (2D) cell cultures or 3D organoid models. However, a lack of experimental models that have strong human physiological relevance has hampered accurate validation of the safety and functionality of NPs. Alternatively, biomimetic human "Organs-on-Chips" microphysiological systems have recapitulated the mechanically dynamic 3D tissue interface of human organ microenvironment, in which the transport, cytotoxicity, biocompatibility, and therapeutic efficacy of NPs and their conjugates may be more accurately validated. Finally, integration of NP-guided diagnostic detection and targeted nanotherapeutics in conjunction with human organs-on-chips can provide a novel avenue to accelerate the NP-based drug development process as well as the rapid detection of cellular secretomes associated with pathophysiological processes.

Cell-oriented modeling of angiogenesis.

PubMed

Guidolin, Diego; Rebuffat, Piera; Albertin, Giovanna

2011-01-01

Due to its significant involvement in various physiological and pathological conditions, angiogenesis (the development of new blood vessels from an existing vasculature) represents an important area of the actual biological research and a field in which mathematical modeling proved particularly useful in supporting the experimental work. In this paper, we focus on a specific modeling strategy, known as "cell-centered" approach. This type of mathematical models work at a "mesoscopic scale," assuming the cell as the natural level of abstraction for computational modeling of development. They treat cells phenomenologically, considering their essential behaviors to study how tissue structure and organization emerge from the collective dynamics of multiple cells. The main contributions of the cell-oriented approach to the study of the angiogenic process will be described. From one side, they have generated "basic science understanding" about the process of capillary assembly during development, growth, and pathology. On the other side, models were also developed supporting "applied biomedical research" for the purpose of identifying new therapeutic targets and clinically relevant approaches for either inhibiting or stimulating angiogenesis.

Numerical investigation of homogeneous cavitation nucleation in a microchannel

NASA Astrophysics Data System (ADS)

Lyu, Xiuxiu; Pan, Shucheng; Hu, Xiangyu; Adams, Nikolaus A.

2018-06-01

The physics of nucleation in water is an important issue for many areas, ranging from biomedical to engineering applications. Within the present study, we investigate numerically homogeneous nucleation in a microchannel induced by shock reflection to gain a better understanding of the mechanism of homogeneous nucleation. The liquid expands due to the reflected shock and homogeneous cavitation nuclei are generated. An Eulerian-Lagrangian approach is employed for modeling this process in a microchanel. Two-dimensional axisymmetric Euler equations are solved for obtaining the time evolution of shock, gas bubble, and the ambient fluid. The dynamics of dispersed vapor bubbles is coupled with the surrounding fluid in a Lagrangian framework, describing bubble location and bubble size variation. Our results reproduce nuclei distributions at different stages of homogeneous nucleation and are in good agreement with experimental results. We obtain numerical data for the negative pressure that water can sustain under the process of homogeneous nucleation. An energy transformation description for the homogeneous nucleation inside a microchannel flow is derived and analyzed in detail.

Simplified generation of biomedical 3D surface model data for embedding into 3D portable document format (PDF) files for publication and education.

PubMed

Newe, Axel; Ganslandt, Thomas

2013-01-01

The usefulness of the 3D Portable Document Format (PDF) for clinical, educational, and research purposes has recently been shown. However, the lack of a simple tool for converting biomedical data into the model data in the necessary Universal 3D (U3D) file format is a drawback for the broad acceptance of this new technology. A new module for the image processing and rapid prototyping framework MeVisLab does not only provide a platform-independent possibility to create surface meshes out of biomedical/DICOM and other data and to export them into U3D--it also lets the user add meta data to these meshes to predefine colors and names that can be processed by a PDF authoring software while generating 3D PDF files. Furthermore, the source code of the respective module is available and well documented so that it can easily be modified for own purposes.

A unified architecture for biomedical search engines based on semantic web technologies.

PubMed

Jalali, Vahid; Matash Borujerdi, Mohammad Reza

2011-04-01

There is a huge growth in the volume of published biomedical research in recent years. Many medical search engines are designed and developed to address the over growing information needs of biomedical experts and curators. Significant progress has been made in utilizing the knowledge embedded in medical ontologies and controlled vocabularies to assist these engines. However, the lack of common architecture for utilized ontologies and overall retrieval process, hampers evaluating different search engines and interoperability between them under unified conditions. In this paper, a unified architecture for medical search engines is introduced. Proposed model contains standard schemas declared in semantic web languages for ontologies and documents used by search engines. Unified models for annotation and retrieval processes are other parts of introduced architecture. A sample search engine is also designed and implemented based on the proposed architecture in this paper. The search engine is evaluated using two test collections and results are reported in terms of precision vs. recall and mean average precision for different approaches used by this search engine.

Adaptive Biomedical Innovation: Evolving Our Global System to Sustainably and Safely Bring New Medicines to Patients in Need

PubMed Central

Trusheim, M; Cobbs, E; Bala, M; Garner, S; Hartman, D; Isaacs, K; Lumpkin, M; Lim, R; Oye, K; Pezalla, E; Saltonstall, P; Selker, H

2016-01-01

The current system of biomedical innovation is unable to keep pace with scientific advancements. We propose to address this gap by reengineering innovation processes to accelerate reliable delivery of products that address unmet medical needs. Adaptive biomedical innovation (ABI) provides an integrative, strategic approach for process innovation. Although the term “ABI” is new, it encompasses fragmented “tools” that have been developed across the global pharmaceutical industry, and could accelerate the evolution of the system through more coordinated application. ABI involves bringing stakeholders together to set shared objectives, foster trust, structure decision‐making, and manage expectations through rapid‐cycle feedback loops that maximize product knowledge and reduce uncertainty in a continuous, adaptive, and sustainable learning healthcare system. Adaptive decision‐making, a core element of ABI, provides a framework for structuring decision‐making designed to manage two types of uncertainty – the maturity of scientific and clinical knowledge, and the behaviors of other critical stakeholders. PMID:27626610

Impact of interventions to improve the quality of peer review of biomedical journals: a systematic review and meta-analysis.

PubMed

Bruce, Rachel; Chauvin, Anthony; Trinquart, Ludovic; Ravaud, Philippe; Boutron, Isabelle

2016-06-10

The peer review process is a cornerstone of biomedical research. We aimed to evaluate the impact of interventions to improve the quality of peer review for biomedical publications. We performed a systematic review and meta-analysis. We searched CENTRAL, MEDLINE (PubMed), Embase, Cochrane Database of Systematic Reviews, and WHO ICTRP databases, for all randomized controlled trials (RCTs) evaluating the impact of interventions to improve the quality of peer review for biomedical publications. We selected 22 reports of randomized controlled trials, for 25 comparisons evaluating training interventions (n = 5), the addition of a statistical peer reviewer (n = 2), use of a checklist (n = 2), open peer review (i.e., peer reviewers informed that their identity would be revealed; n = 7), blinded peer review (i.e., peer reviewers blinded to author names and affiliation; n = 6) and other interventions to increase the speed of the peer review process (n = 3). Results from only seven RCTs were published since 2004. As compared with the standard peer review process, training did not improve the quality of the peer review report and use of a checklist did not improve the quality of the final manuscript. Adding a statistical peer review improved the quality of the final manuscript (standardized mean difference (SMD), 0.58; 95 % CI, 0.19 to 0.98). Open peer review improved the quality of the peer review report (SMD, 0.14; 95 % CI, 0.05 to 0.24), did not affect the time peer reviewers spent on the peer review (mean difference, 0.18; 95 % CI, -0.06 to 0.43), and decreased the rate of rejection (odds ratio, 0.56; 95 % CI, 0.33 to 0.94). Blinded peer review did not affect the quality of the peer review report or rejection rate. Interventions to increase the speed of the peer review process were too heterogeneous to allow for pooling the results. Despite the essential role of peer review, only a few interventions have been assessed in randomized controlled trials. Evidence-based peer review needs to be developed in biomedical journals.

Multimodal computational microscopy based on transport of intensity equation

NASA Astrophysics Data System (ADS)

Li, Jiaji; Chen, Qian; Sun, Jiasong; Zhang, Jialin; Zuo, Chao

2016-12-01

Transport of intensity equation (TIE) is a powerful tool for phase retrieval and quantitative phase imaging, which requires intensity measurements only at axially closely spaced planes without a separate reference beam. It does not require coherent illumination and works well on conventional bright-field microscopes. The quantitative phase reconstructed by TIE gives valuable information that has been encoded in the complex wave field by passage through a sample of interest. Such information may provide tremendous flexibility to emulate various microscopy modalities computationally without requiring specialized hardware components. We develop a requisite theory to describe such a hybrid computational multimodal imaging system, which yields quantitative phase, Zernike phase contrast, differential interference contrast, and light field moment imaging, simultaneously. It makes the various observations for biomedical samples easy. Then we give the experimental demonstration of these ideas by time-lapse imaging of live HeLa cell mitosis. Experimental results verify that a tunable lens-based TIE system, combined with the appropriate postprocessing algorithm, can achieve a variety of promising imaging modalities in parallel with the quantitative phase images for the dynamic study of cellular processes.

Autophagy in Dictyostelium: Mechanisms, regulation and disease in a simple biomedical model.

PubMed

Mesquita, Ana; Cardenal-Muñoz, Elena; Dominguez, Eunice; Muñoz-Braceras, Sandra; Nuñez-Corcuera, Beatriz; Phillips, Ben A; Tábara, Luis C; Xiong, Qiuhong; Coria, Roberto; Eichinger, Ludwig; Golstein, Pierre; King, Jason S; Soldati, Thierry; Vincent, Olivier; Escalante, Ricardo

2017-01-02

Autophagy is a fast-moving field with an enormous impact on human health and disease. Understanding the complexity of the mechanism and regulation of this process often benefits from the use of simple experimental models such as the social amoeba Dictyostelium discoideum. Since the publication of the first review describing the potential of D. discoideum in autophagy, significant advances have been made that demonstrate both the experimental advantages and interest in using this model. Since our previous review, research in D. discoideum has shed light on the mechanisms that regulate autophagosome formation and contributed significantly to the study of autophagy-related pathologies. Here, we review these advances, as well as the current techniques to monitor autophagy in D. discoideum. The comprehensive bioinformatics search of autophagic proteins that was a substantial part of the previous review has not been revisited here except for those aspects that challenged previous predictions such as the composition of the Atg1 complex. In recent years our understanding of, and ability to investigate, autophagy in D. discoideum has evolved significantly and will surely enable and accelerate future research using this model.

Effects of Interfacial Translation-rotation Coupling for Confined Ferrofluids

NASA Astrophysics Data System (ADS)

Fang, Angbo

2011-03-01

Ferrofluids have wide applications ranging from semiconductor fabrications to biomedical processes. The hydrodynamic spin diffusion theory for ferrofluids has been successful in explaining many experimental data, but it suffers from some fatal flaws. For example, it fails to predict the incorrect flow direction for a ferrofluid confined in a concentric cylinder channel in the presence of a rotating magnetic field. In this work we develop a method to establish the general hydrodynamic boundary conditions (BCs) for micro-polar fluids such as ferrofluids. Through a dynamic generalization of the mesoscopic diffuse interface model, we are able to obtain the surface dissipation functional, in which the interfacial translation-rotation coupling plays a significant role. The generalized hydrodynamic BCs can be obtained straightforwardly by using Onsager's variational approach. The resulted velocity profile and other quantities compares well with the experimental data, strikingly different from traditional theories. The methodology can be applied to study the hydrodynamic behavior of other structured fluids in confined channels or multi-phase flows. The work is supported by a research award made by the King Abdullah University of Science and Technology.

Surface enhanced Raman spectroscopic studies on aspirin : An experimental and theoretical approach

NASA Astrophysics Data System (ADS)

Premkumar, R.; Premkumar, S.; Rekha, T. N.; Parameswari, A.; Mathavan, T.; Benial, A. Milton Franklin

2016-05-01

Surface enhanced Raman scattering (SERS) studies on aspirin molecule adsorbed on silver nanoparticles (AgNPs) were investigated by experimental and density functional theory approach. The AgNPs were synthesized by the solution-combustion method and characterized by the X-ray diffraction and high resolution-transmission electron microscopy techniques. The averaged particle size of synthesized AgNPs was calculated as ˜55 nm. The normal Raman spectrum (nRs) and SERS spectrum of the aspirin were recorded. The molecular structure of the aspirin and aspirin adsorbed on silver cluster were optimized by the DFT/ B3PW91 method with LanL2DZ basis set. The vibrational frequencies were calculated and assigned on the basis of potential energy distribution calculation. The calculated nRs and SERS frequencies were correlated well with the observed frequencies. The flat-on orientation was predicted from the nRs and SERS spectra, when the aspirin adsorbed on the AgNPs. Hence, the present studies lead to the understanding of adsorption process of aspirin on the AgNPs, which paves the way for biomedical applications.

Surface enhanced Raman spectroscopic studies on aspirin : An experimental and theoretical approach

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

Premkumar, R.; Premkumar, S.; Parameswari, A.

Surface enhanced Raman scattering (SERS) studies on aspirin molecule adsorbed on silver nanoparticles (AgNPs) were investigated by experimental and density functional theory approach. The AgNPs were synthesized by the solution-combustion method and characterized by the X-ray diffraction and high resolution-transmission electron microscopy techniques. The averaged particle size of synthesized AgNPs was calculated as ∼55 nm. The normal Raman spectrum (nRs) and SERS spectrum of the aspirin were recorded. The molecular structure of the aspirin and aspirin adsorbed on silver cluster were optimized by the DFT/ B3PW91 method with LanL2DZ basis set. The vibrational frequencies were calculated and assigned on the basismore » of potential energy distribution calculation. The calculated nRs and SERS frequencies were correlated well with the observed frequencies. The flat-on orientation was predicted from the nRs and SERS spectra, when the aspirin adsorbed on the AgNPs. Hence, the present studies lead to the understanding of adsorption process of aspirin on the AgNPs, which paves the way for biomedical applications.« less

The cost of quality: Implementing generalization and suppression for anonymizing biomedical data with minimal information loss.

PubMed

Kohlmayer, Florian; Prasser, Fabian; Kuhn, Klaus A

2015-12-01

With the ARX data anonymization tool structured biomedical data can be de-identified using syntactic privacy models, such as k-anonymity. Data is transformed with two methods: (a) generalization of attribute values, followed by (b) suppression of data records. The former method results in data that is well suited for analyses by epidemiologists, while the latter method significantly reduces loss of information. Our tool uses an optimal anonymization algorithm that maximizes output utility according to a given measure. To achieve scalability, existing optimal anonymization algorithms exclude parts of the search space by predicting the outcome of data transformations regarding privacy and utility without explicitly applying them to the input dataset. These optimizations cannot be used if data is transformed with generalization and suppression. As optimal data utility and scalability are important for anonymizing biomedical data, we had to develop a novel method. In this article, we first confirm experimentally that combining generalization with suppression significantly increases data utility. Next, we proof that, within this coding model, the outcome of data transformations regarding privacy and utility cannot be predicted. As a consequence, existing algorithms fail to deliver optimal data utility. We confirm this finding experimentally. The limitation of previous work can be overcome at the cost of increased computational complexity. However, scalability is important for anonymizing data with user feedback. Consequently, we identify properties of datasets that may be predicted in our context and propose a novel and efficient algorithm. Finally, we evaluate our solution with multiple datasets and privacy models. This work presents the first thorough investigation of which properties of datasets can be predicted when data is anonymized with generalization and suppression. Our novel approach adopts existing optimization strategies to our context and combines different search methods. The experiments show that our method is able to efficiently solve a broad spectrum of anonymization problems. Our work shows that implementing syntactic privacy models is challenging and that existing algorithms are not well suited for anonymizing data with transformation models which are more complex than generalization alone. As such models have been recommended for use in the biomedical domain, our results are of general relevance for de-identifying structured biomedical data. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

An Insufferable Business: Ethics, Nonhuman Animals and Biomedical Experiments

PubMed Central

Peggs, Kay

2015-01-01

Simple Summary This paper explores the ways in which biomedical research that uses nonhuman animal subjects generates financial profits and gains for humans who are associated with the industry. Research establishments, scientists, regulators and persons that inspect laboratories for compliance, those associated with granting licences, companies that sell nonhuman animal subjects and that supply equipment for the research, and corporations that market the resulting products are among those that benefit financially. These profits are rarely discussed—they seem to be camouflaged by the focus of the moral convention that assumes that human health-related needs prevail over those of the nonhuman animals who are so used. The paper concludes by calling for an end to the denigration of nonhuman animals as experimental subjects who can be used as commodities for profit-maximisation and as tools in experiments for human health benefits. Abstract Each year millions of nonhuman animals suffer in biomedical experiments for human health benefits. Clinical ethics demand that nonhuman animals are used in the development of pharmaceuticals and vaccines. Nonhuman animals are also used for fundamental biomedical research. Biomedical research that uses nonhuman animals is big business but the financial gains are generally occluded. This paper explores how such research generates profits and gains for those associated with the industry. Research establishments, scientists, laboratories, companies that sell nonhuman animal subjects, that supply equipment for the research, and corporations that market the resulting products are among those that benefit financially. Given the complex articulation of ethical codes, enormous corporate profits that are secured and personal returns that are made, the accepted moral legitimacy of such experiments is compromised. In order to address this, within the confines of the moral orthodoxy, more could to be done to ensure transparency and to extricate the vested financial interests from the human health benefits. But such a determination would not address the fundamental issues that should be at the heart of human actions in respect of the nonhuman animals who are used in experiments. The paper concludes with such an address by calling for an end to the denigration of nonhuman animals as experimental subjects who can be used as commodities for profit-maximisation and as tools in experiments for human health benefits, and the implementation of a more inclusive ethic that is informed by universal concern about the suffering of and compassion for all oppressed beings. PMID:26479378

Choosing experiments to accelerate collective discovery

DOE PAGES

Rzhetsky, Andrey; Foster, Jacob G.; Foster, Ian T.; ...

2015-11-24

Scientists perform a tiny subset of all possible experiments. What characterizes the experiments they choose? What are the consequences of those choices for the pace of scientific discovery? We model scientific knowledge as a network and science as a sequence of experiments designed to gradually uncover it. By analyzing millions of biomedical articles published over 30 y, we find that biomedical scientists pursue conservative research strategies exploring the local neighborhood of central, important molecules. Although such strategies probably serve scientific careers, we show that they slow scientific advance, especially in mature fields, where more risk and less redundant experimentation wouldmore » accelerate discovery of the network. Lastly, we also consider institutional arrangements that could help science pursue these more efficient strategies.« less

On the promotion of human flourishing

PubMed Central

VanderWeele, Tyler J.

2017-01-01

Many empirical studies throughout the social and biomedical sciences focus only on very narrow outcomes such as income, or a single specific disease state, or a measure of positive affect. Human well-being or flourishing, however, consists in a much broader range of states and outcomes, certainly including mental and physical health, but also encompassing happiness and life satisfaction, meaning and purpose, character and virtue, and close social relationships. The empirical literature from longitudinal, experimental, and quasiexperimental studies is reviewed in attempt to identify major determinants of human flourishing, broadly conceived. Measures of human flourishing are proposed. Discussion is given to the implications of a broader conception of human flourishing, and of the research reviewed, for policy, and for future research in the biomedical and social sciences. PMID:28705870

Of mice and rats: key species variations in the sexual differentiation of brain and behavior.

PubMed

Bonthuis, P J; Cox, K H; Searcy, B T; Kumar, P; Tobet, S; Rissman, E F

2010-07-01

Mice and rats are important mammalian models in biomedical research. In contrast to other biomedical fields, work on sexual differentiation of brain and behavior has traditionally utilized comparative animal models. As mice are gaining in popularity, it is essential to acknowledge the differences between these two rodents. Here we review neural and behavioral sexual dimorphisms in rats and mice, which highlight species differences and experimental gaps in the literature, that are needed for direct species comparisons. Moving forward, investigators must answer fundamental questions about their chosen organism, and attend to both species and strain differences as they select the optimal animal models for their research questions. Copyright 2010 Elsevier Inc. All rights reserved.

Animals in biomedical space research

NASA Astrophysics Data System (ADS)

Phillips, Robert W.

The use of experimental animals has been a major component of biomedical research progress. Using animals in space presents special problems, but also provides special opportunities. Rat and squirrel monkeys experiments have been planned in concert with human experiments to help answer fundamental questions concerning the effect of weightlessness on mammalian function. For the most part, these experiments focus on identified changes noted in humans during space flight. Utilizing space laboratory facilities, manipulative experiments can be completed while animals are still in orbit. Other experiments are designed to study changes in gravity receptor structure and function and the effect of weightlessness on early vertebrate development. Following these preliminary animals experiments on Spacelab Shuttle flights, longer term programs of animal investigation will be conducted on Space Station.

Tuning the interaction between propagating and localized surface plasmons for surface enhanced Raman scattering in water for biomedical and environmental applications

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

Shioi, Masahiko, E-mail: shioi.masahiko@jp.panasonic.com; Department of Electric and Electronic Engineering, Graduate School of Engineering, Kobe University, Rokkodai, Nada, Kobe 657-8501; Jans, Hilde

With a view to biomedical and environmental applications, we investigate the plasmonic properties of a rectangular gold nanodisk array in water to boost surface enhanced Raman scattering (SERS) effects. To control the resonance wavelengths of the surface plasmon polariton and the localized surface plasmon, their dependence on the array period and diameter in water is studied in detail using a finite difference time domain method. A good agreement is obtained between calculated resonant wavelengths and those of gold nanodisk arrays fabricated using electron beam lithography. For the optimized structure, a SERS enhancement factor of 7.8 × 10{sup 7} is achieved in watermore » experimentally.« less

From the Law of European Delegation to the Legislative Decree on experiments with animals: consequences for biomedical research.

PubMed

Petrini, C

2014-01-01

The provisions contained in the Legislative Decree no.26 signed by Italy's President on 4th March 2014 will have a considerable impact on the future of experiments with animals. The article briefly describes the stages of the decree's complicated passage through Parliament and the resulting text, which includes bans on: the use of animals for xenotransplants or research on drugs of abuse; the breeding of dogs, cats and non-human primates for experimental use; research without anaesthetic or analgesics that causes pain to the animal, except when anaesthetics or analgesics are being investigated. There is widespread feeling in the scientific community that these provisions will hinder the advancement of biomedical research in Italy.

Chromosomal Mapping and Candidate Gene Discovery of Chicken Developmental Mutants and Genome-wide Variation Analysis of MHC-congenics

USDA-ARS?s Scientific Manuscript database

The chicken has been widely used in experimental research given its importance to agriculture and its utility as a model for vertebrate biology and biomedical pursuits for over 100 years. Herein we used recently developed advanced technologies to investigate the genomic characteristics of specialize...

Synthesis and characterization of L-lactide and polylactic acid (PLA) from L-lactic acid for biomedical applications

NASA Astrophysics Data System (ADS)

Rahmayetty, Sukirno, Prasetya, Bambang; Gozan, Misri

2017-02-01

Lactide is the monomer for the polymer polylactic acid (PLA) from lactic acid through polycondensation and depolymerization process. The properties of PLA strongly depend on the quality of the lactide monomer from which it is synthesized. Optical purity of lactide produced in depolymerization process confirmed to be L-lactide. The highest yield of crude lactide was 38.5% at temperature 210 °C with average molecular weight (Mn) of oligomer was 2389. Ring opening polymerization of lactide using Candida rugosa lipase as biocatalyst to PLLA synthesis has been achieved to generate useful biomedical materials free from heavy metal.

Rotation covariant image processing for biomedical applications.

PubMed

Skibbe, Henrik; Reisert, Marco

2013-01-01

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

Electrophoretic deposition of biomaterials

PubMed Central

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

2010-01-01

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

Spectroscopic studies of non-thermal plasma jet at atmospheric pressure formed in low-current nonsteady-state plasmatron for biomedical applications

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

Demkin, V. P.; Melnichuk, S. V.; Demkin, O. V.

The optical and electrophysical characteristics of the nonequilibrium low-temperature plasma formed by a low-current nonsteady-state plasmatron are experimentally investigated in the present work. It is demonstrated that experimental data on the optical diagnostics of the plasma jet can provide a basis for the construction of a self-consistent physical and mathematical plasma model and for the creation of plasma sources with controllable electrophysical parameters intended for the generation of the required concentration of active particles. Results of spectroscopic diagnostics of plasma of the low-current nonsteady-state plasmatron confirm that the given source is efficient for the generation of charged particles and short-wavelengthmore » radiation—important plasma components for biomedical problems of an increase in the efficiency of treatment of biological tissues by charged particles. Measurement of the spatial distribution of the plasma jet potential by the probe method has demonstrated that a negative space charge is formed in the plasma jet possibly due to the formation of electronegative oxygen ions.« less

Fluid displacement during droplet formation at microfluidic flow-focusing junctions.

PubMed

Huang, Haishui; He, Xiaoming

2015-11-07

Microdroplets and microcapsules have been widely produced using microfluidic flow-focusing junctions for biomedical and chemical applications. However, the multiphase microfluidic flow at the flow-focusing junction has not been well investigated. In this study, the displacement of two (core and shell) aqueous fluids that disperse into droplets altogether in a carrier oil emulsion was investigated both numerically and experimentally. It was found that extensive displacement of the two aqueous fluids within the droplet during its formation could occur as a result of the shear effect of the carrier fluid and the capillary effect of interfacial tension. We further identified that the two mechanisms of fluid displacement can be evaluated by two dimensionless parameters. The quantitative relationship between the degree of fluid displacement and these two dimensionless parameters was determined experimentally. Finally, we demonstrated that the degree of fluid displacement could be controlled to generate hydrogel microparticles of different morphologies using planar or nonplanar flow-focusing junctions. These findings should provide useful guidance to the microfluidic production of microscale droplets or capsules for various biomedical and chemical applications.

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

PubMed Central

Gaheen, Sharon; Lijowski, Michal; Heiskanen, Mervi; Klemm, Juli

2015-01-01

Summary The cancer Nanotechnology Laboratory (caNanoLab) data portal is an online nanomaterial database that allows users to submit and retrieve information on well-characterized nanomaterials, including composition, in vitro and in vivo experimental characterizations, experimental protocols, and related publications. Initiated in 2006, caNanoLab serves as an established resource with an infrastructure supporting the structured collection of nanotechnology data to address the needs of the cancer biomedical and nanotechnology communities. The portal contains over 1,000 curated nanomaterial data records that are publicly accessible for review, comparison, and re-use, with the ultimate goal of accelerating the translation of nanotechnology-based cancer therapeutics, diagnostics, and imaging agents to the clinic. In this paper, we will discuss challenges associated with developing a nanomaterial database and recognized needs for nanotechnology data curation and sharing in the biomedical research community. We will also describe the latest version of caNanoLab, caNanoLab 2.0, which includes enhancements and new features to improve usability such as personalized views of data and enhanced search and navigation. PMID:26425409

Study of low-modulus biomedical β Ti-Nb-Zr alloys based on single-crystal elastic constants modeling.

PubMed

Wang, Xing; Zhang, Ligang; Guo, Ziyi; Jiang, Yun; Tao, Xiaoma; Liu, Libin

2016-09-01

CALPHAD-type modeling was used to describe the single-crystal elastic constants of the bcc solution phase in the ternary Ti-Nb-Zr system. The parameters in the model were evaluated based on the available experimental data and first-principle calculations. The composition-elastic properties of the full compositions were predicted and the results were in good agreement with the experimental data. It is found that the β phase can be divided into two regions which are separated by a critical dynamical stability composition line. The corresponding valence electron number per atom and the polycrystalline Young׳s modulus of the critical compositions are 4.04-4.17 and 30-40GPa respectively. Orientation dependencies of single-crystal Young׳s modulus show strong elastic anisotropy on the Ti-rich side. Alloys compositions with a Young׳s modulus along the <100> direction matching that of bone were found. The current results present an effective strategy for designing low modulus biomedical alloys using computational modeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Practical methods for generating alternating magnetic fields for biomedical research

NASA Astrophysics Data System (ADS)

Christiansen, Michael G.; Howe, Christina M.; Bono, David C.; Perreault, David J.; Anikeeva, Polina

2017-08-01

Alternating magnetic fields (AMFs) cause magnetic nanoparticles (MNPs) to dissipate heat while leaving surrounding tissue unharmed, a mechanism that serves as the basis for a variety of emerging biomedical technologies. Unfortunately, the challenges and costs of developing experimental setups commonly used to produce AMFs with suitable field amplitudes and frequencies present a barrier to researchers. This paper first presents a simple, cost-effective, and robust alternative for small AMF working volumes that uses soft ferromagnetic cores to focus the flux into a gap. As the experimental length scale increases to accommodate animal models (working volumes of 100s of cm3 or greater), poor thermal conductivity and volumetrically scaled core losses render that strategy ineffective. Comparatively feasible strategies for these larger volumes instead use low loss resonant tank circuits to generate circulating currents of 1 kA or greater in order to produce the comparable field amplitudes. These principles can be extended to the problem of identifying practical routes for scaling AMF setups to humans, an infrequently acknowledged challenge that influences the extent to which many applications of MNPs may ever become clinically relevant.

Statistics and bioinformatics in nutritional sciences: analysis of complex data in the era of systems biology⋆

PubMed Central

Fu, Wenjiang J.; Stromberg, Arnold J.; Viele, Kert; Carroll, Raymond J.; Wu, Guoyao

2009-01-01

Over the past two decades, there have been revolutionary developments in life science technologies characterized by high throughput, high efficiency, and rapid computation. Nutritionists now have the advanced methodologies for the analysis of DNA, RNA, protein, low-molecular-weight metabolites, as well as access to bioinformatics databases. Statistics, which can be defined as the process of making scientific inferences from data that contain variability, has historically played an integral role in advancing nutritional sciences. Currently, in the era of systems biology, statistics has become an increasingly important tool to quantitatively analyze information about biological macromolecules. This article describes general terms used in statistical analysis of large, complex experimental data. These terms include experimental design, power analysis, sample size calculation, and experimental errors (type I and II errors) for nutritional studies at population, tissue, cellular, and molecular levels. In addition, we highlighted various sources of experimental variations in studies involving microarray gene expression, real-time polymerase chain reaction, proteomics, and other bioinformatics technologies. Moreover, we provided guidelines for nutritionists and other biomedical scientists to plan and conduct studies and to analyze the complex data. Appropriate statistical analyses are expected to make an important contribution to solving major nutrition-associated problems in humans and animals (including obesity, diabetes, cardiovascular disease, cancer, ageing, and intrauterine fetal retardation). PMID:20233650

Improving Validity of Informed Consent for Biomedical Research in Zambia Using a Laboratory Exposure Intervention

PubMed Central

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

2014-01-01

Background Complex biomedical research can lead to disquiet in communities with limited exposure to scientific discussions, leading to rumours or to high drop-out rates. We set out to test an intervention designed to address apprehensions commonly encountered in a community where literacy is uncommon, and where complex biomedical research has been conducted for over a decade. We aimed to determine if it could improve the validity of consent. Methods Data were collected using focus group discussions, key informant interviews and observations. We designed an intervention that exposed participants to a detailed demonstration of laboratory processes. Each group was interviewed twice in a day, before and after exposure to the intervention in order to assess changes in their views. Results Factors that motivated people to participate in invasive biomedical research included a desire to stay healthy because of the screening during the recruitment process, regular advice from doctors, free medical services, and trust in the researchers. Inhibiting factors were limited knowledge about samples taken from their bodies during endoscopic procedures, the impact of endoscopy on the function of internal organs, and concerns about the use of biomedical samples. The belief that blood can be used for Satanic practices also created insecurities about drawing of blood samples. Further inhibiting factors included a fear of being labelled as HIV positive if known to consult heath workers repeatedly, and gender inequality. Concerns about the use and storage of blood and tissue samples were overcome by a laboratory exposure intervention. Conclusion Selecting a group of members from target community and engaging them in a laboratory exposure intervention could be a useful tool for enhancing specific aspects of consent for biomedical research. Further work is needed to determine the extent to which improved understanding permeates beyond the immediate group participating in the intervention. PMID:25254378

Ethics and fraud in science: a review of scientific misconduct and applications to craniofacial research.

PubMed

Eliades, Theodore; Athanasiou, Athanasios E; Papadopulos, Jannis S

2005-01-01

The purpose of this article is to review and discuss the occurrence of fraud in biomedical research and analyze the definition, origin, and various forms of scientific misconduct. Fraud in research most often involves reporting data for which no records of experiment or population are present; manipulating research materials, equipment, or procedures to arrive at the desirable result; adding, changing, or omitting results, which positively or negatively relate to the hypothesis that the research intends to test; and incorporating ideas, statements, procedures of others' work without permission and appropriate credit to the source. The etiologic factors contributing to this deviant behavior, and measures taken by relevant bodies to eliminate this phenomenon are discussed. Ethical and integrity aspects of craniofacial research are explored and a set of criteria to facilitate rigorous assessment of the integrity of clinical and basic research protocols is proposed. These include (1) an integrity-focused training of researchers to adhere to specific laboratory procedure and tactics which discourage fraud; (2) appointment of external reviewers to detect unusual and suspicious experimental process or data patterns; and (3) encouragement of multicenter trials. Although it is widely recognized that the sole determinant of scientific misconduct is the individual investigator's integrity, a number of precautions may effectively reduce the prevalence of this event, which may affect the status and trends of biomedical research in general.

MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format.

PubMed

Ahmed, Zeeshan; Dandekar, Thomas

2015-01-01

Published scientific literature contains millions of figures, including information about the results obtained from different scientific experiments e.g. PCR-ELISA data, microarray analysis, gel electrophoresis, mass spectrometry data, DNA/RNA sequencing, diagnostic imaging (CT/MRI and ultrasound scans), and medicinal imaging like electroencephalography (EEG), magnetoencephalography (MEG), echocardiography  (ECG), positron-emission tomography (PET) images. The importance of biomedical figures has been widely recognized in scientific and medicine communities, as they play a vital role in providing major original data, experimental and computational results in concise form. One major challenge for implementing a system for scientific literature analysis is extracting and analyzing text and figures from published PDF files by physical and logical document analysis. Here we present a product line architecture based bioinformatics tool 'Mining Scientific Literature (MSL)', which supports the extraction of text and images by interpreting all kinds of published PDF files using advanced data mining and image processing techniques. It provides modules for the marginalization of extracted text based on different coordinates and keywords, visualization of extracted figures and extraction of embedded text from all kinds of biological and biomedical figures using applied Optimal Character Recognition (OCR). Moreover, for further analysis and usage, it generates the system's output in different formats including text, PDF, XML and images files. Hence, MSL is an easy to install and use analysis tool to interpret published scientific literature in PDF format.

Translational physiology: from molecules to public health.

PubMed

Seals, Douglas R

2013-07-15

The term 'translational research' was coined 20 years ago and has become a guiding influence in biomedical research. It refers to a process by which the findings of basic research are extended to the clinical research setting (bench to bedside) and then to clinical practice and eventually health policy (bedside to community). It is a dynamic, multidisciplinary research approach. The concept of translational physiology applies the translational research model to the physiological sciences. It differs from the traditional areas of integrative and clinical physiology by its broad investigative scope of basic research to community health. Translational physiology offers exciting opportunities, but presently is under-developed and -utilized. A key challenge will be to expand physiological research by extending investigations to communities of patients and healthy (or at risk) individuals. This will allow bidirectional physiological investigation throughout the translational continuum: basic research observations can be studied up to the population level, and mechanisms can be assessed by 'reverse translation' in clinical research settings and preclinical models based on initial observations made in populations. Examples of translational physiology questions, experimental approaches, roadblocks and strategies for promotion are discussed. Translational physiology provides a novel framework for physiology programs and an investigational platform for physiologists to study function from molecular events to public health. It holds promise for enhancing the completeness and societal impact of our work, while further solidifying the critical role of physiology in the biomedical research enterprise.

Translational physiology: from molecules to public health

PubMed Central

Seals, Douglas R

2013-01-01

The term ‘translational research’ was coined 20 years ago and has become a guiding influence in biomedical research. It refers to a process by which the findings of basic research are extended to the clinical research setting (bench to bedside) and then to clinical practice and eventually health policy (bedside to community). It is a dynamic, multidisciplinary research approach. The concept of translational physiology applies the translational research model to the physiological sciences. It differs from the traditional areas of integrative and clinical physiology by its broad investigative scope of basic research to community health. Translational physiology offers exciting opportunities, but presently is under-developed and -utilized. A key challenge will be to expand physiological research by extending investigations to communities of patients and healthy (or at risk) individuals. This will allow bidirectional physiological investigation throughout the translational continuum: basic research observations can be studied up to the population level, and mechanisms can be assessed by ‘reverse translation’ in clinical research settings and preclinical models based on initial observations made in populations. Examples of translational physiology questions, experimental approaches, roadblocks and strategies for promotion are discussed. Translational physiology provides a novel framework for physiology programs and an investigational platform for physiologists to study function from molecular events to public health. It holds promise for enhancing the completeness and societal impact of our work, while further solidifying the critical role of physiology in the biomedical research enterprise. PMID:23732641

Size-controlled synthesis of superparamagnetic iron oxide nanoparticles and their surface coating by gold for biomedical applications

NASA Astrophysics Data System (ADS)

Maleki, H.; Simchi, A.; Imani, M.; Costa, B. F. O.

2012-11-01

The size mono-dispersity, saturation magnetization, and surface chemistry of magnetic nanoparticles (NPs) are recognized as critical factors for efficient biomedical applications. Here, we performed modified water-in-oil inverse nano-emulsion procedure for preparation of stable colloidal superparamagnetic iron oxide NPs (SPIONs) with high saturation magnetization. To achieve mono-dispersed SPIONs, optimization process was probed on several important factors including molar ratio of iron salts [Fe3+ and Fe2+], the concentration of ammonium hydroxide as reducing agent, and molar ratio of water to surfactant. The biocompatibility of the obtained NPs, at various concentrations, was evaluated via MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay and the results showed that the NPs were non-toxic at concentrations <0.1 mg/mL. Surface functionalization was performed by conformal coating of the NPs with a thin shell of gold (˜4 nm) through chemical reduction of attached gold salts at the surface of the SPIONs. The Fe3O4 core/Au shell particles demonstrate strong plasmon resonance absorption and can be separated from solution using an external magnetic field. Experimental data from both physical and chemical determinations of the changes in particle size, surface plasmon resonance optical band, phase components, core-shell surface composition, and magnetic properties have confirmed the formation of the mono-dispersed core-shell nanostructure.

A simple method for the production of large volume 3D macroporous hydrogels for advanced biotechnological, medical and environmental applications

PubMed Central

Savina, Irina N.; Ingavle, Ganesh C.; Cundy, Andrew B.; Mikhalovsky, Sergey V.

2016-01-01

The development of bulk, three-dimensional (3D), macroporous polymers with high permeability, large surface area and large volume is highly desirable for a range of applications in the biomedical, biotechnological and environmental areas. The experimental techniques currently used are limited to the production of small size and volume cryogel material. In this work we propose a novel, versatile, simple and reproducible method for the synthesis of large volume porous polymer hydrogels by cryogelation. By controlling the freezing process of the reagent/polymer solution, large-scale 3D macroporous gels with wide interconnected pores (up to 200 μm in diameter) and large accessible surface area have been synthesized. For the first time, macroporous gels (of up to 400 ml bulk volume) with controlled porous structure were manufactured, with potential for scale up to much larger gel dimensions. This method can be used for production of novel 3D multi-component macroporous composite materials with a uniform distribution of embedded particles. The proposed method provides better control of freezing conditions and thus overcomes existing drawbacks limiting production of large gel-based devices and matrices. The proposed method could serve as a new design concept for functional 3D macroporous gels and composites preparation for biomedical, biotechnological and environmental applications. PMID:26883390

Translating standards into practice - one Semantic Web API for Gene Expression.

PubMed

Deus, Helena F; Prud'hommeaux, Eric; Miller, Michael; Zhao, Jun; Malone, James; Adamusiak, Tomasz; McCusker, Jim; Das, Sudeshna; Rocca Serra, Philippe; Fox, Ronan; Marshall, M Scott

2012-08-01

Sharing and describing experimental results unambiguously with sufficient detail to enable replication of results is a fundamental tenet of scientific research. In today's cluttered world of "-omics" sciences, data standards and standardized use of terminologies and ontologies for biomedical informatics play an important role in reporting high-throughput experiment results in formats that can be interpreted by both researchers and analytical tools. Increasing adoption of Semantic Web and Linked Data technologies for the integration of heterogeneous and distributed health care and life sciences (HCLSs) datasets has made the reuse of standards even more pressing; dynamic semantic query federation can be used for integrative bioinformatics when ontologies and identifiers are reused across data instances. We present here a methodology to integrate the results and experimental context of three different representations of microarray-based transcriptomic experiments: the Gene Expression Atlas, the W3C BioRDF task force approach to reporting Provenance of Microarray Experiments, and the HSCI blood genomics project. Our approach does not attempt to improve the expressivity of existing standards for genomics but, instead, to enable integration of existing datasets published from microarray-based transcriptomic experiments. SPARQL Construct is used to create a posteriori mappings of concepts and properties and linking rules that match entities based on query constraints. We discuss how our integrative approach can encourage reuse of the Experimental Factor Ontology (EFO) and the Ontology for Biomedical Investigations (OBIs) for the reporting of experimental context and results of gene expression studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Development and Experimental Study of Education Through the Synergetic Training for the Engineering Enhanced Medicine “ESTEEM” in Tohoku University

NASA Astrophysics Data System (ADS)

Yamano, Masahiro; Matsuki, Noriaki; Numayama, Keiko; Takeda, Motohiro; Hayasaka, Tomoaki; Ishikawa, Takuji; Yamaguchi, Takami

We developed new bio-medical engineering curriculum for industrial engineers, and we confirmed that the engineer's needs and the educative effects by holding a trail program. This study in Tohoku University was supported by the Ministry of Economy, Trade and Industry (METI) . We named the curriculum as “ESTEEM” which is acronym of project title “Education through the Synergetic Training for the Engineering Enhanced Medicine” . In Tohoku University, the “REDEEM” curriculum which is an entry level course of bio-medical engineering for engineers has been already held. The positioning of “ESTEEM” program is an advanced course to enhance knowledge and experience in clinical point of view. The program is consisted of the problem based learning (PBL) style lectures, practical training, and observation learning in hospital. It is a unique opportunity to have instruction by doctors, from diagnosis to surgical operation, from traditional technique to front-line medical equipment. In this paper, we report and discuss on the progress of the new bio-medical engineering curriculum.

GOClonto: an ontological clustering approach for conceptualizing PubMed abstracts.

PubMed

Zheng, Hai-Tao; Borchert, Charles; Kim, Hong-Gee

2010-02-01

Concurrent with progress in biomedical sciences, an overwhelming of textual knowledge is accumulating in the biomedical literature. PubMed is the most comprehensive database collecting and managing biomedical literature. To help researchers easily understand collections of PubMed abstracts, numerous clustering methods have been proposed to group similar abstracts based on their shared features. However, most of these methods do not explore the semantic relationships among groupings of documents, which could help better illuminate the groupings of PubMed abstracts. To address this issue, we proposed an ontological clustering method called GOClonto for conceptualizing PubMed abstracts. GOClonto uses latent semantic analysis (LSA) and gene ontology (GO) to identify key gene-related concepts and their relationships as well as allocate PubMed abstracts based on these key gene-related concepts. Based on two PubMed abstract collections, the experimental results show that GOClonto is able to identify key gene-related concepts and outperforms the STC (suffix tree clustering) algorithm, the Lingo algorithm, the Fuzzy Ants algorithm, and the clustering based TRS (tolerance rough set) algorithm. Moreover, the two ontologies generated by GOClonto show significant informative conceptual structures.

Laser surface texturing of polymers for biomedical applications

NASA Astrophysics Data System (ADS)

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.

Discovering and visualizing indirect associations between biomedical concepts

PubMed Central

Tsuruoka, Yoshimasa; Miwa, Makoto; Hamamoto, Kaisei; Tsujii, Jun'ichi; Ananiadou, Sophia

2011-01-01

Motivation: Discovering useful associations between biomedical concepts has been one of the main goals in biomedical text-mining, and understanding their biomedical contexts is crucial in the discovery process. Hence, we need a text-mining system that helps users explore various types of (possibly hidden) associations in an easy and comprehensible manner. Results: This article describes FACTA+, a real-time text-mining system for finding and visualizing indirect associations between biomedical concepts from MEDLINE abstracts. The system can be used as a text search engine like PubMed with additional features to help users discover and visualize indirect associations between important biomedical concepts such as genes, diseases and chemical compounds. FACTA+ inherits all functionality from its predecessor, FACTA, and extends it by incorporating three new features: (i) detecting biomolecular events in text using a machine learning model, (ii) discovering hidden associations using co-occurrence statistics between concepts, and (iii) visualizing associations to improve the interpretability of the output. To the best of our knowledge, FACTA+ is the first real-time web application that offers the functionality of finding concepts involving biomolecular events and visualizing indirect associations of concepts with both their categories and importance. Availability: FACTA+ is available as a web application at http://refine1-nactem.mc.man.ac.uk/facta/, and its visualizer is available at http://refine1-nactem.mc.man.ac.uk/facta-visualizer/. Contact: tsuruoka@jaist.ac.jp PMID:21685059

An analysis of reported motivational orientation in students undertaking doctoral studies in the biomedical sciences

PubMed Central

2014-01-01

Background As the source of a sizeable percentage of research output and the future arbiters of science policy, practice and direction, doctoral (Ph.D.) students represent a key demographic in the biomedical research community. Despite this, doctoral learning in the biomedical sciences has, to date, received little research attention. Methods In the present study we aimed to qualitatively describe the motivational orientations present in semi-structured interview transcripts from a cohort of seventeen biomedical Ph.D. students drawn from two research intensive Australian Group of Eight universities. Results Applying elements of self-determination theory, external and introjected control loci (both strongly associated with alienation, disengagement and poor learning outcomes) were identified as common motivational determinants in this cohort. Conclusions The importance of these findings to doctoral learning is discussed in light of previous research undertaken in higher education settings in the United States and the European Union. With motivation accepted as a malleable, context-sensitive factor, these data provide for both a better understanding of doctoral learning and highlight a potential avenue for future research aimed at improving outcomes and promoting meaningful learning processes in the biomedical doctorate. PMID:24571918

Desiderata for ontologies to be used in semantic annotation of biomedical documents.

PubMed

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.

Experimental investigation and oral bioavailability enhancement of nano-sized curcumin by using supercritical anti-solvent process.

PubMed

Anwar, Mohammed; Ahmad, Iqbal; Warsi, Musarrat H; Mohapatra, Sharmistha; Ahmad, Niyaz; Akhter, Sohail; Ali, Asgar; Ahmad, Farhan J

2015-10-01

The biomedical applications of curcumin (CUR) are limited due to its poor oral bioavailability. In this work, CUR nanoparticles were successfully prepared by combining the supercritical anti-solvent (SAS) process with Tween 80 as a solubilizing agent and permeation enhancer. Different processing parameters that can govern the mean particle size and size distribution of nanoparticles were well investigated by manipulating the types of solvents, mixing vessel pressure, mixing vessel temperature, CO2 flow rate, solution flow rate and solution concentration. Solid state characterization was done by Fourier Transform infrared spectroscopy, differential scanning calorimetry, dynamic light scattering, scanning electron microscopy, and powder X-ray diffraction study. Solubility and dissolution profile of SAS-processed CUR were found to be significantly increased in comparison with native CUR. Further, a validated ultra-performance liquid chromatographic method with quadrupole-time of flight-mass spectrometry was developed to investigate the pharmacokinetic parameters after a single oral dose (100mg/kg) administration of CUR (before/after SAS-processed) in male Wistar rats. From the plasma concentration vs. time profile graph, oral bioavailability of SAS-processed CUR was found to be increased approximately 11.6-fold (p<0.001) as compared to native CUR. Copyright © 2015 Elsevier B.V. All rights reserved.

Degree of deacetylation chitosan from pen shell (Atrina pectinata) with multistage deacetylation process

NASA Astrophysics Data System (ADS)

Pursetyo, Kustiawan Tri; Purbowati, Pinta; Sulmartiwi, Laksmi

2017-02-01

The utilization of pen shell (Atrina pectinata) generally in some areas only as edible portion adductor muscle (meat) so the shells become fishery waste. Shells are raw materials that contain chitin and chitosan. Benefits of chitin and chitosan in various fields of modern industry are quite a lot, including in the pharmaceutical industry, biochemistry, biotechnology, biomedical, food, nutrition, paper, textile, agriculture, cosmetics, and healthcare membrane. Quality of chitosan is influenced by deacetylation degree which is one of the most important chemical characteristics. Deacetylation degree gives affect in application of chitosan, due to the value of amina chain and used to differentiate between chitin and chitosan. Deacetylation degrees of chitosan are determined by several factors such as NaOH concentration, temperature and time process. In addition, treatment of deacetylation process of chitin can give effect to deacetylation degree value of chitosan. The method that was used in this research was an experimental method with a statistical analysis of the data. The results showed that stage deacetylation process of chitin have the effect to increase deacetylation degree of chitosan. Multistage deacetylation process of chitin with 3 stage process was capable to make the deacetylation degree on average 75% with 82.91% of solubility. The increase result of deacetylation degree of chitosan is directly proportional with the increase in solubility

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

PubMed

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

2013-11-01

General guidelines for teaching clinical reasoning have received much attention, despite a paucity of instructional approaches with demonstrated effectiveness. As suggested in a recent experimental study, self-explanation while solving clinical cases may be an effective strategy to foster reasoning in clinical clerks dealing with less familiar cases. However, the mechanisms that mediate this benefit have not been specifically investigated. The aim of this study was to explore the types of knowledge used by students when solving familiar and less familiar clinical cases with self-explanation. In a previous study, 36 third-year medical students diagnosed familiar and less familiar clinical cases either by engaging in self-explanation or not. Based on an analysis of previously collected data, the present study compared the content of self-explanation protocols generated by seven randomly selected students while solving four familiar and four less familiar cases. In total, 56 verbal protocols (28 familiar and 28 less familiar) were segmented and coded using the following categories: paraphrases, biomedical inferences, clinical inferences, monitoring statements and errors. Students provided more self-explanation segments from less familiar cases (M = 275.29) than from familiar cases (M = 248.71, p = 0.046). They provided significantly more paraphrases (p = 0.001) and made more errors (p = 0.008). A significant interaction was found between familiarity and the type of inferences (biomedical versus clinical, p = 0.016). When self-explaining less familiar cases, students provided significantly more biomedical inferences than familiar cases. Lack of familiarity with a case seems to stimulate medical students to engage in more extensive thinking during self-explanation. Less familiar cases seem to activate students' biomedical knowledge, which in turn helps them to create new links between biomedical and clinical knowledge, and eventually construct a more coherent mental representation of diseases. This may clarify the previously found positive effect that self-explanation has on the diagnosis of unfamiliar cases. © 2013 John Wiley & Sons Ltd.

Comparing methods for analysis of biomedical hyperspectral image data

NASA Astrophysics Data System (ADS)

Leavesley, Silas J.; Sweat, Brenner; Abbott, Caitlyn; Favreau, Peter F.; Annamdevula, Naga S.; Rich, Thomas C.

2017-02-01

Over the past 2 decades, hyperspectral imaging technologies have been adapted to address the need for molecule-specific identification in the biomedical imaging field. Applications have ranged from single-cell microscopy to whole-animal in vivo imaging and from basic research to clinical systems. Enabling this growth has been the availability of faster, more effective hyperspectral filtering technologies and more sensitive detectors. Hence, the potential for growth of biomedical hyperspectral imaging is high, and many hyperspectral imaging options are already commercially available. However, despite the growth in hyperspectral technologies for biomedical imaging, little work has been done to aid users of hyperspectral imaging instruments in selecting appropriate analysis algorithms. Here, we present an approach for comparing the effectiveness of spectral analysis algorithms by combining experimental image data with a theoretical "what if" scenario. This approach allows us to quantify several key outcomes that characterize a hyperspectral imaging study: linearity of sensitivity, positive detection cut-off slope, dynamic range, and false positive events. We present results of using this approach for comparing the effectiveness of several common spectral analysis algorithms for detecting weak fluorescent protein emission in the midst of strong tissue autofluorescence. Results indicate that this approach should be applicable to a very wide range of applications, allowing a quantitative assessment of the effectiveness of the combined biology, hardware, and computational analysis for detecting a specific molecular signature.

A possible biomedical facility at the European Organization for Nuclear Research (CERN).

PubMed

Dosanjh, M; Jones, B; Myers, S

2013-05-01

A well-attended meeting, called "Brainstorming discussion for a possible biomedical facility at CERN", was held by the European Organization for Nuclear Research (CERN) at the European Laboratory for Particle Physics on 25 June 2012. This was concerned with adapting an existing, but little used, 78-m circumference CERN synchrotron to deliver a wide range of ion species, preferably from protons to at least neon ions, with beam specifications that match existing clinical facilities. The potential extensive research portfolio discussed included beam ballistics in humanoid phantoms, advanced dosimetry, remote imaging techniques and technical developments in beam delivery, including gantry design. In addition, a modern laboratory for biomedical characterisation of these beams would allow important radiobiological studies, such as relative biological effectiveness, in a dedicated facility with standardisation of experimental conditions and biological end points. A control photon and electron beam would be required nearby for relative biological effectiveness comparisons. Research beam time availability would far exceed that at other facilities throughout the world. This would allow more rapid progress in several biomedical areas, such as in charged hadron therapy of cancer, radioisotope production and radioprotection. The ethos of CERN, in terms of open access, peer-reviewed projects and governance has been so successful for High Energy Physics that application of the same to biomedicine would attract high-quality research, with possible contributions from Europe and beyond, along with potential new funding streams.

A possible biomedical facility at the European Organization for Nuclear Research (CERN)

PubMed Central

Dosanjh, M; Myers, S

2013-01-01

A well-attended meeting, called “Brainstorming discussion for a possible biomedical facility at CERN”, was held by the European Organization for Nuclear Research (CERN) at the European Laboratory for Particle Physics on 25 June 2012. This was concerned with adapting an existing, but little used, 78-m circumference CERN synchrotron to deliver a wide range of ion species, preferably from protons to at least neon ions, with beam specifications that match existing clinical facilities. The potential extensive research portfolio discussed included beam ballistics in humanoid phantoms, advanced dosimetry, remote imaging techniques and technical developments in beam delivery, including gantry design. In addition, a modern laboratory for biomedical characterisation of these beams would allow important radiobiological studies, such as relative biological effectiveness, in a dedicated facility with standardisation of experimental conditions and biological end points. A control photon and electron beam would be required nearby for relative biological effectiveness comparisons. Research beam time availability would far exceed that at other facilities throughout the world. This would allow more rapid progress in several biomedical areas, such as in charged hadron therapy of cancer, radioisotope production and radioprotection. The ethos of CERN, in terms of open access, peer-reviewed projects and governance has been so successful for High Energy Physics that application of the same to biomedicine would attract high-quality research, with possible contributions from Europe and beyond, along with potential new funding streams. PMID:23549990

Applicability Analysis of Validation Evidence for Biomedical Computational Models

DOE PAGES

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

2017-09-07

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

Applicability Analysis of Validation Evidence for Biomedical Computational Models

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

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

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

Livestock in biomedical research: history, current status and future prospective.

PubMed

Polejaeva, Irina A; Rutigliano, Heloisa M; Wells, Kevin D

2016-01-01

Livestock models have contributed significantly to biomedical and surgical advances. Their contribution is particularly prominent in the areas of physiology and assisted reproductive technologies, including understanding developmental processes and disorders, from ancient to modern times. Over the past 25 years, biomedical research that traditionally embraced a diverse species approach shifted to a small number of model species (e.g. mice and rats). The initial reasons for focusing the main efforts on the mouse were the availability of murine embryonic stem cells (ESCs) and genome sequence data. This powerful combination allowed for precise manipulation of the mouse genome (knockouts, knockins, transcriptional switches etc.) leading to ground-breaking discoveries on gene functions and regulation, and their role in health and disease. Despite the enormous contribution to biomedical research, mouse models have some major limitations. Their substantial differences compared with humans in body and organ size, lifespan and inbreeding result in pronounced metabolic, physiological and behavioural differences. Comparative studies of strategically chosen domestic species can complement mouse research and yield more rigorous findings. Because genome sequence and gene manipulation tools are now available for farm animals (cattle, pigs, sheep and goats), a larger number of livestock genetically engineered (GE) models will be accessible for biomedical research. This paper discusses the use of cattle, goats, sheep and pigs in biomedical research, provides an overview of transgenic technology in farm animals and highlights some of the beneficial characteristics of large animal models of human disease compared with the mouse. In addition, status and origin of current regulation of GE biomedical models is also reviewed.

Emerging applications of nanoparticles: Biomedical and environmental

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Peer Review Practices for Evaluating Biomedical Research Grants: A Scientific Statement From the American Heart Association.

PubMed

Liaw, Lucy; Freedman, Jane E; Becker, Lance B; Mehta, Nehal N; Liscum, Laura

2017-08-04

The biomedical research enterprise depends on the fair and objective peer review of research grants, leading to the distribution of resources through efficient and robust competitive methods. In the United States, federal funding agencies and foundations collectively distribute billions of dollars annually to support biomedical research. For the American Heart Association, a Peer Review Subcommittee is charged with establishing the highest standards for peer review. This scientific statement reviews the current literature on peer review practices, describes the current American Heart Association peer review process and those of other agencies, analyzes the strengths and weaknesses of American Heart Association peer review practices, and recommends best practices for the future. © 2017 American Heart Association, Inc.

Wireless plataforms for the monitoring of biomedical variables

NASA Astrophysics Data System (ADS)

Bianco, Román; Laprovitta, Agustín; Misa, Alberto; Toselli, Eduardo; Castagnola, Juan Luis

2007-11-01

The present paper aims to analyze and to compare two wireless platforms for the monitoring of biomedical variables. They must obtain the vital signals of the patients, transmit them through a radio frequency bond and centralize them for their process, storage and monitoring in real time. The implementation of this system permit us to obtain two important benefits; The patient will enjoy greater comfort during the internment, and the doctors will be able to know the state of the biomedical variables of each patient, in simultaneous form. In order to achieve the objective of this work, two communication systems for wireless transmissions data were developed and implemented. The CC1000 transceiver was used in the first system and the Bluetooth module was used in the other system.

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

PubMed

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

2015-01-01

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

Biomedical data mining in clinical routine: expanding the impact of hospital information systems.

PubMed

Müller, Marcel; Markó, Kornel; Daumke, Philipp; Paetzold, Jan; Roesner, Arnold; Klar, Rüdiger

2007-01-01

In this paper we want to describe how the promising technology of biomedical data mining can improve the use of hospital information systems: a large set of unstructured, narrative clinical data from a dermatological university hospital like discharge letters or other dermatological reports were processed through a morpho-semantic text retrieval engine ("MorphoSaurus") and integrated with other clinical data using a web-based interface and brought into daily clinical routine. The user evaluation showed a very high user acceptance - this system seems to meet the clinicians' requirements for a vertical data mining in the electronic patient records. What emerges is the need for integration of biomedical data mining into hospital information systems for clinical, scientific, educational and economic reasons.

In vitro and in vivo biological performance of porous Ti alloys prepared by powder metallurgy

PubMed Central

Vasconcellos, Luis Gustavo Oliveira De; Oliveira, Felipe Eduardo; Oliveira, Luciane Dias De; Henriques, Vinicius André Rodrigues; Carvalho, Yasmin Rodarte; De Vasconcellos, Luana Marotta Reis

2018-01-01

Titanium (Ti) and Ti-6 Aluminium-4 Vanadium alloys are the most common materials in implants composition but β type alloys are promising biomaterials because they present better mechanical properties. Besides the composition of biomaterial, many factors influence the performance of the biomaterial. For example, porous surface may modify the functional cellular response and accelerate osseointegration. This paper presents in vitro and in vivo evaluations of powder metallurgy-processed porous samples composed by different titanium alloys and pure Ti, aiming to show their potential for biomedical applications. The porous surfaces samples were produced with different designs to in vitro and in vivo tests. Samples were characterized with scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and elastic modulus analyses. Osteogenic cells from newborn rat calvaria were plated on discs of different materials: G1—commercially pure Ti group (CpTi); G2—Ti-6Al-4V alloy; G3—Ti-13 Niobium-13 Zirconium alloy; G4—Ti-35 Niobium alloy; G5—Ti-35 Niobium-7 Zirconium-5 Tantalum alloy. Cell adhesion and viability, total protein content, alkaline phosphatase activity, mineralization nodules and gene expression (alkaline phosphatase, Runx-2, osteocalcin and osteopontin) were assessed. After 2 and 4 weeks of implantation in rabbit tibia, bone ingrowth was analyzed using micro-computed tomography (μCT). EDS analysis confirmed the material production of each group. Metallographic and SEM analysis revealed interconnected pores, with mean pore size of 99,5μm and mean porosity of 42%, without significant difference among the groups (p>0.05). The elastic modulus values did not exhibit difference among the groups (p>0.05). Experimental alloys demonstrated better results than CpTi and Ti-6Al-4V, in gene expression and cytokines analysis, especially in early experimental periods. In conclusion, our data suggests that the experimental alloys can be used for biomedical application since they contributed to excellent cellular behavior and osseointegration besides presenting lower elastic modulus. PMID:29771925

Character-level neural network for biomedical named entity recognition.

PubMed

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 Recent Advance in the Automatic Indexing of the Biomedical Literature

PubMed Central

Névéol, Aurélie; Shooshan, Sonya E.; Humphrey, Susanne M.; Mork, James G.; Aronson, Alan R.

2009-01-01

The volume of biomedical literature has experienced explosive growth in recent years. This is reflected in the corresponding increase in the size of MEDLINE®, the largest bibliographic database of biomedical citations. Indexers at the U.S. National Library of Medicine (NLM) need efficient tools to help them accommodate the ensuing workload. After reviewing issues in the automatic assignment of Medical Subject Headings (MeSH® terms) to biomedical text, we focus more specifically on the new subheading attachment feature for NLM’s Medical Text Indexer (MTI). Natural Language Processing, statistical, and machine learning methods of producing automatic MeSH main heading/subheading pair recommendations were assessed independently and combined. The best combination achieves 48% precision and 30% recall. After validation by NLM indexers, a suitable combination of the methods presented in this paper was integrated into MTI as a subheading attachment feature producing MeSH indexing recommendations compliant with current state-of-the-art indexing practice. PMID:19166973

Commercialising genetically engineered animal biomedical products.

PubMed

Sullivan, Eddie J; Pommer, Jerry; Robl, James M

2008-01-01

Research over the past two decades has increased the quality and quantity of tools available to produce genetically engineered animals. The number of potentially viable biomedical products from genetically engineered animals is increasing. However, moving from cutting-edge research to development and commercialisation of a biomedical product that is useful and wanted by the public has significant challenges. Even early stage development of genetically engineered animal applications requires consideration of many steps, including quality assurance and quality control, risk management, gap analysis, founder animal establishment, cell banking, sourcing of animals and animal-derived material, animal facilities, product collection facilities and processing facilities. These steps are complicated and expensive. Biomedical applications of genetically engineered animals have had some recent successes and many applications are well into development. As researchers consider applications for their findings, having a realistic understanding of the steps involved in the development and commercialisation of a product, produced in genetically engineered animals, is useful in determining the risk of genetic modification to the animal nu. the potential public benefit of the application.

Collective intelligence for translational medicine: Crowdsourcing insights and innovation from an interdisciplinary biomedical research community.

PubMed

Budge, Eleanor Jane; Tsoti, Sandra Maria; Howgate, Daniel James; Sivakumar, Shivan; Jalali, Morteza

2015-01-01

Translational medicine bridges the gap between discoveries in biomedical science and their safe and effective clinical application. Despite the gross opportunity afforded by modern research for unparalleled advances in this field, the process of translation remains protracted. Efforts to expedite science translation have included the facilitation of interdisciplinary collaboration within both academic and clinical environments in order to generate integrated working platforms fuelling the sharing of knowledge, expertise, and tools to align biomedical research with clinical need. However, barriers to scientific translation remain, and further progress is urgently required. Collective intelligence and crowdsourcing applications offer the potential for global online networks, allowing connection and collaboration between a wide variety of fields. This would drive the alignment of biomedical science with biotechnology, clinical need, and patient experience, in order to deliver evidence-based innovation which can revolutionize medical care worldwide. Here we discuss the critical steps towards implementing collective intelligence in translational medicine using the experience of those in other fields of science and public health.

Application of fluorescence resonance energy transfer in protein studies

PubMed Central

Ma, Linlin; Yang, Fan; Zheng, Jie

2014-01-01

Since the physical process of fluorescence resonance energy transfer (FRET) was elucidated more than six decades ago, this peculiar fluorescence phenomenon has turned into a powerful tool for biomedical research due to its compatibility in scale with biological molecules as well as rapid developments in novel fluorophores and optical detection techniques. A wide variety of FRET approaches have been devised, each with its own advantages and drawbacks. Especially in the last decade or so, we are witnessing a flourish of FRET applications in biological investigations, many of which exemplify clever experimental design and rigorous analysis. Here we review the current stage of FRET methods development with the main focus on its applications in protein studies in biological systems, by summarizing the basic components of FRET techniques, most established quantification methods, as well as potential pitfalls, illustrated by example applications. PMID:25368432

Phenomenological model of photoluminescence degradation and photoinduced defect formation in silicon nanocrystal ensembles under singlet oxygen generation

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

Gongalsky, Maxim B., E-mail: mgongalsky@gmail.com; Timoshenko, Victor Yu.

2014-12-28

We propose a phenomenological model to explain photoluminescence degradation of silicon nanocrystals under singlet oxygen generation in gaseous and liquid systems. The model considers coupled rate equations, which take into account the exciton radiative recombination in silicon nanocrystals, photosensitization of singlet oxygen generation, defect formation on the surface of silicon nanocrystals as well as quenching processes for both excitons and singlet oxygen molecules. The model describes well the experimentally observed power law dependences of the photoluminescence intensity, singlet oxygen concentration, and lifetime versus photoexcitation time. The defect concentration in silicon nanocrystals increases by power law with a fractional exponent, whichmore » depends on the singlet oxygen concentration and ambient conditions. The obtained results are discussed in a view of optimization of the photosensitized singlet oxygen generation for biomedical applications.« less

Laser Desorption Mass Spectrometry for DNA Sequencing and Analysis

NASA Astrophysics Data System (ADS)

Chen, C. H. Winston; Taranenko, N. I.; Golovlev, V. V.; Isola, N. R.; Allman, S. L.

1998-03-01

Rapid DNA sequencing and/or analysis is critically important for biomedical research. In the past, gel electrophoresis has been the primary tool to achieve DNA analysis and sequencing. However, gel electrophoresis is a time-consuming and labor-extensive process. Recently, we have developed and used laser desorption mass spectrometry (LDMS) to achieve sequencing of ss-DNA longer than 100 nucleotides. With LDMS, we succeeded in sequencing DNA in seconds instead of hours or days required by gel electrophoresis. In addition to sequencing, we also applied LDMS for the detection of DNA probes for hybridization LDMS was also used to detect short tandem repeats for forensic applications. Clinical applications for disease diagnosis such as cystic fibrosis caused by base deletion and point mutation have also been demonstrated. Experimental details will be presented in the meeting. abstract.

Combining rules, background knowledge and change patterns to maintain semantic annotations.

PubMed

Cardoso, Silvio Domingos; Chantal, Reynaud-Delaître; Da Silveira, Marcos; Pruski, Cédric

2017-01-01

Knowledge Organization Systems (KOS) play a key role in enriching biomedical information in order to make it machine-understandable and shareable. This is done by annotating medical documents, or more specifically, associating concept labels from KOS with pieces of digital information, e.g., images or texts. However, the dynamic nature of KOS may impact the annotations, thus creating a mismatch between the evolved concept and the associated information. To solve this problem, methods to maintain the quality of the annotations are required. In this paper, we define a framework based on rules, background knowledge and change patterns to drive the annotation adaption process. We evaluate experimentally the proposed approach in realistic cases-studies and demonstrate the overall performance of our approach in different KOS considering the precision, recall, F1-score and AUC value of the system.

Combining rules, background knowledge and change patterns to maintain semantic annotations

PubMed Central

Cardoso, Silvio Domingos; Chantal, Reynaud-Delaître; Da Silveira, Marcos; Pruski, Cédric

2017-01-01

Knowledge Organization Systems (KOS) play a key role in enriching biomedical information in order to make it machine-understandable and shareable. This is done by annotating medical documents, or more specifically, associating concept labels from KOS with pieces of digital information, e.g., images or texts. However, the dynamic nature of KOS may impact the annotations, thus creating a mismatch between the evolved concept and the associated information. To solve this problem, methods to maintain the quality of the annotations are required. In this paper, we define a framework based on rules, background knowledge and change patterns to drive the annotation adaption process. We evaluate experimentally the proposed approach in realistic cases-studies and demonstrate the overall performance of our approach in different KOS considering the precision, recall, F1-score and AUC value of the system. PMID:29854115

Towards self-learning based hypotheses generation in biomedical text domain.

PubMed

Gopalakrishnan, Vishrawas; Jha, Kishlay; Xun, Guangxu; Ngo, Hung Q; Zhang, Aidong

2018-06-15

The overwhelming amount of research articles in the domain of bio-medicine might cause important connections to remain unnoticed. Literature Based Discovery is a sub-field within biomedical text mining that peruses these articles to formulate high confident hypotheses on possible connections between medical concepts. Although many alternate methodologies have been proposed over the last decade, they still suffer from scalability issues. The primary reason, apart from the dense inter-connections between biological concepts, is the absence of information on the factors that lead to the edge-formation. In this work, we formulate this problem as a collaborative filtering task and leverage a relatively new concept of word-vectors to learn and mimic the implicit edge-formation process. Along with single-class classifier, we prune the search-space of redundant and irrelevant hypotheses to increase the efficiency of the system and at the same time maintaining and in some cases even boosting the overall accuracy. We show that our proposed framework is able to prune up to 90% of the hypotheses while still retaining high recall in top-K results. This level of efficiency enables the discovery algorithm to look for higher-order hypotheses, something that was infeasible until now. Furthermore, the generic formulation allows our approach to be agile to perform both open and closed discovery. We also experimentally validate that the core data-structures upon which the system bases its decision has a high concordance with the opinion of the experts.This coupled with the ability to understand the edge formation process provides us with interpretable results without any manual intervention. The relevant JAVA codes are available at: https://github.com/vishrawas/Medline-Code_v2. Supplementary data are available at Bioinformatics online.

Investigation of antibacterial and wettability behaviours of plasma-modified PMMA films for application in ophthalmology

NASA Astrophysics Data System (ADS)

Rezaei, Fatemeh; Abbasi-Firouzjah, Marzieh; Shokri, Babak

2014-02-01

The main objective of this research is the experimental investigation of the surface properties of polymethyl methacrylate (PMMA) such as wettability and the roughness effect on Escherichia coli (gram negative) cell adhesion. Radio frequency (RF; 13.56 MHz) oxygen plasma was used to enhance the antibacterial and wettability properties of this polymer for biomedical applications, especially ophthalmology. The surface was activated by O2 plasma to produce hydrophilic functional groups. Samples were treated with various RF powers from 10 to 80 W and different gas flow rates from 20 to 120 sccm. Optical emission spectroscopy was used to monitor the plasma process. The modified surface hydrophilicity, morphology and transparency characteristics were studied by water contact angle measurements, atomic force microscopy and UV-vis spectroscopy, respectively. Based on the contact angle measurements of three liquids, surface free energy variations were investigated. Moreover, the antibacterial properties were evaluated utilizing the method of plate counting of Escherichia coli. Also, in order to investigate stability of the plasma treatment, an ageing study was carried out by water contact angle measurements repeated in the days after the treatment. For biomedical applications, especially eye lenses, highly efficient antibacterial surfaces with appropriate hydrophilicity and transparency are of great importance. In this study, it is shown that the plasma process is a reliable and convenient method to achieve these purposes. A significant alteration in the hydrophilicity of a pristine PMMA surface was observed after treatment. Also, our results indicated that the plasma-modified PMMAs exhibit appropriate antibacterial performance. Moreover, surface hydrophilicity and surface charge have more influence on bacterial adhesion rate than surface roughness. UV-vis analysis results do not show a considerable difference for transparency of samples after plasma treatment.

An automatic experimental apparatus to study arm reaching in New World monkeys.

PubMed

Yin, Allen; An, Jehi; Lehew, Gary; Lebedev, Mikhail A; Nicolelis, Miguel A L

2016-05-01

Several species of the New World monkeys have been used as experimental models in biomedical and neurophysiological research. However, a method for controlled arm reaching tasks has not been developed for these species. We have developed a fully automated, pneumatically driven, portable, and reconfigurable experimental apparatus for arm-reaching tasks suitable for these small primates. We have utilized the apparatus to train two owl monkeys in a visually-cued arm-reaching task. Analysis of neural recordings demonstrates directional tuning of the M1 neurons. Our apparatus allows automated control, freeing the experimenter from manual experiments. The presented apparatus provides a valuable tool for conducting neurophysiological research on New World monkeys. Copyright © 2016. Published by Elsevier B.V.

Reconstruction of Mammary Gland Structure Using Three-Dimensional Computer-Based Microscopy

DTIC Science & Technology

2004-08-01

for image analysis in cytology" Ortiz de Solorzano C., R . Malladi , Lockett S. In: Geometric methods in bio-medical image processing. Ravikanth Malladi ...Deschamps T., Idica A.K., Malladi R ., Ortiz de Solorzano C. Journal of Biomedical Optics 9(3):445-453, 2004.. Manuscripts (in preparation): "* "Three...Deschamps T., Idica A.K., 16 Malladi R ., Ortiz de Solorzano C., Proceedings of Photonics West 2003, Vol. 4964, 2003 "* "Automatic and segmentation

Nanodiamonds of Laser Synthesis for Biomedical Applications.

PubMed

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

2015-02-01

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

CheNER: a tool for the identification of chemical entities and their classes in biomedical literature.

PubMed

Usié, Anabel; Cruz, Joaquim; Comas, Jorge; Solsona, Francesc; Alves, Rui

2015-01-01

Small chemical molecules regulate biological processes at the molecular level. Those molecules are often involved in causing or treating pathological states. Automatically identifying such molecules in biomedical text is difficult due to both, the diverse morphology of chemical names and the alternative types of nomenclature that are simultaneously used to describe them. To address these issues, the last BioCreAtIvE challenge proposed a CHEMDNER task, which is a Named Entity Recognition (NER) challenge that aims at labelling different types of chemical names in biomedical text. To address this challenge we tested various approaches to recognizing chemical entities in biomedical documents. These approaches range from linear Conditional Random Fields (CRFs) to a combination of CRFs with regular expression and dictionary matching, followed by a post-processing step to tag those chemical names in a corpus of Medline abstracts. We named our best performing systems CheNER. We evaluate the performance of the various approaches using the F-score statistics. Higher F-scores indicate better performance. The highest F-score we obtain in identifying unique chemical entities is 72.88%. The highest F-score we obtain in identifying all chemical entities is 73.07%. We also evaluate the F-Score of combining our system with ChemSpot, and find an increase from 72.88% to 73.83%. CheNER presents a valid alternative for automated annotation of chemical entities in biomedical documents. In addition, CheNER may be used to derive new features to train newer methods for tagging chemical entities. CheNER can be downloaded from http://metres.udl.cat and included in text annotation pipelines.

Sortal anaphora resolution to enhance relation extraction from biomedical literature.

PubMed

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.

BioLemmatizer: a lemmatization tool for morphological processing of biomedical text

PubMed Central

2012-01-01

Background The wide variety of morphological variants of domain-specific technical terms contributes to the complexity of performing natural language processing of the scientific literature related to molecular biology. For morphological analysis of these texts, lemmatization has been actively applied in the recent biomedical research. Results In this work, we developed a domain-specific lemmatization tool, BioLemmatizer, for the morphological analysis of biomedical literature. The tool focuses on the inflectional morphology of English and is based on the general English lemmatization tool MorphAdorner. The BioLemmatizer is further tailored to the biological domain through incorporation of several published lexical resources. It retrieves lemmas based on the use of a word lexicon, and defines a set of rules that transform a word to a lemma if it is not encountered in the lexicon. An innovative aspect of the BioLemmatizer is the use of a hierarchical strategy for searching the lexicon, which enables the discovery of the correct lemma even if the input Part-of-Speech information is inaccurate. The BioLemmatizer achieves an accuracy of 97.5% in lemmatizing an evaluation set prepared from the CRAFT corpus, a collection of full-text biomedical articles, and an accuracy of 97.6% on the LLL05 corpus. The contribution of the BioLemmatizer to accuracy improvement of a practical information extraction task is further demonstrated when it is used as a component in a biomedical text mining system. Conclusions The BioLemmatizer outperforms other tools when compared with eight existing lemmatizers. The BioLemmatizer is released as an open source software and can be downloaded from http://biolemmatizer.sourceforge.net. PMID:22464129

Featured Article: Genotation: Actionable knowledge for the scientific reader.

PubMed

Nagahawatte, Panduka; Willis, Ethan; Sakauye, Mark; Jose, Rony; Chen, Hao; Davis, Robert L

2016-06-01

We present an article viewer application that allows a scientific reader to easily discover and share knowledge by linking genomics-related concepts to knowledge of disparate biomedical databases. High-throughput data streams generated by technical advancements have contributed to scientific knowledge discovery at an unprecedented rate. Biomedical Informaticists have created a diverse set of databases to store and retrieve the discovered knowledge. The diversity and abundance of such resources present biomedical researchers a challenge with knowledge discovery. These challenges highlight a need for a better informatics solution. We use a text mining algorithm, Genomine, to identify gene symbols from the text of a journal article. The identified symbols are supplemented with information from the GenoDB knowledgebase. Self-updating GenoDB contains information from NCBI Gene, Clinvar, Medgen, dbSNP, KEGG, PharmGKB, Uniprot, and Hugo Gene databases. The journal viewer is a web application accessible via a web browser. The features described herein are accessible on www.genotation.org The Genomine algorithm identifies gene symbols with an accuracy shown by .65 F-Score. GenoDB currently contains information regarding 59,905 gene symbols, 5633 drug-gene relationships, 5981 gene-disease relationships, and 713 pathways. This application provides scientific readers with actionable knowledge related to concepts of a manuscript. The reader will be able to save and share supplements to be visualized in a graphical manner. This provides convenient access to details of complex biological phenomena, enabling biomedical researchers to generate novel hypothesis to further our knowledge in human health. This manuscript presents a novel application that integrates genomic, proteomic, and pharmacogenomic information to supplement content of a biomedical manuscript and enable readers to automatically discover actionable knowledge. © 2016 by the Society for Experimental Biology and Medicine.

Development of a Biomedical Micro/Nano Robot for Drug Delivery.

PubMed

Zhang, Zhenhai; Li, Zhifei; Yu, Wei; Li, Kejie; Xie, Zhihong

2015-04-01

Flagellated bacteria have been utilized as potential swimming micro-robotic bodies for propulsion of spherical liposome by attaching several bacteria on their surface. Liposome as a drug delivery vehicle can contain biologically active compounds. In this work, the antibody binding technique is developed to attach bacteria to liposome's surface. Consequently, the stochastic effect of bacterial propulsion of liposome is investigated analytically and experimentally. It is shown that the mobility of liposome with bacteria was higher than that of liposome without bacteria. Experimental data matches well with statistical calculation.

Translating orthopaedic basic science into clinical relevance.

PubMed

Madry, Henning

2014-12-01

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

Snore related signals processing in a private cloud computing system.

PubMed

Qian, Kun; Guo, Jian; Xu, Huijie; Zhu, Zhaomeng; Zhang, Gongxuan

2014-09-01

Snore related signals (SRS) have been demonstrated to carry important information about the obstruction site and degree in the upper airway of Obstructive Sleep Apnea-Hypopnea Syndrome (OSAHS) patients in recent years. To make this acoustic signal analysis method more accurate and robust, big SRS data processing is inevitable. As an emerging concept and technology, cloud computing has motivated numerous researchers and engineers to exploit applications both in academic and industry field, which could have an ability to implement a huge blue print in biomedical engineering. Considering the security and transferring requirement of biomedical data, we designed a system based on private cloud computing to process SRS. Then we set the comparable experiments of processing a 5-hour audio recording of an OSAHS patient by a personal computer, a server and a private cloud computing system to demonstrate the efficiency of the infrastructure we proposed.

Liquid crystal thermography and true-colour digital image processing

NASA Astrophysics Data System (ADS)

Stasiek, J.; Stasiek, A.; Jewartowski, M.; Collins, M. W.

2006-06-01

In the last decade thermochromic liquid crystals (TLC) and true-colour digital image processing have been successfully used in non-intrusive technical, industrial and biomedical studies and applications. Thin coatings of TLCs at surfaces are utilized to obtain detailed temperature distributions and heat transfer rates for steady or transient processes. Liquid crystals also can be used to make visible the temperature and velocity fields in liquids by the simple expedient of directly mixing the liquid crystal material into the liquid (water, glycerol, glycol, and silicone oils) in very small quantities to use as thermal and hydrodynamic tracers. In biomedical situations e.g., skin diseases, breast cancer, blood circulation and other medical application, TLC and image processing are successfully used as an additional non-invasive diagnostic method especially useful for screening large groups of potential patients. The history of this technique is reviewed, principal methods and tools are described and some examples are also presented.

The Applicability of Lean and Six Sigma Techniques to Clinical and Translational Research

PubMed Central

Schweikhart, Sharon A.; Dembe, Allard E

2010-01-01

Background Lean and Six Sigma are business management strategies commonly used in production industries to improve process efficiency and quality. During the past decade, these process improvement techniques increasingly have been applied outside of the manufacturing sector, for example, in health care and in software development. This article concerns the potential use of Lean and Six Sigma to improve the processes involved in clinical and translational research. Improving quality, avoiding delays and errors, and speeding up the time to implementation of biomedical discoveries are prime objectives of the NIH Roadmap for Biomedical Research and the NIH Clinical and Translational Science Award (CTSA) program. Methods This article presents a description of the main principles, practices, and methodologies used in Lean and Six Sigma. Available literature involving applications of Lean and Six Sigma to health care, laboratory science, and clinical and translational research is reviewed. Specific issues concerning the use of these techniques in different phases of translational research are identified. Results Examples are provided of Lean and Six Sigma applications that are being planned at a current CTSA site, which could potentially be replicated elsewhere. We describe how different process improvement approaches are best adapted for particularly translational research phases. Conclusions Lean and Six Sigma process improvement methodologies are well suited to help achieve NIH’s goal of making clinical and translational research more efficient and cost-effective, enhancing the quality of the research, and facilitating the successful adoption of biomedical research findings into practice. PMID:19730130

An entrepreneurial training model to enhance undergraduate training in biomedical research.

PubMed

Kamangar, Farin; Silver, Gillian; Hohmann, Christine; Hughes-Darden, Cleo; Turner-Musa, Jocelyn; Haines, Robert Trent; Jackson, Avis; Aguila, Nelson; Sheikhattari, Payam

2017-01-01

Undergraduate students who are interested in biomedical research typically work on a faculty member's research project, conduct one distinct task (e.g., running gels), and, step by step, enhance their skills. This "apprenticeship" model has been helpful in training many distinguished scientists over the years, but it has several potential drawbacks. For example, the students have limited autonomy, and may not understand the big picture, which may result in students giving up on their goals for a research career. Also, the model is costly and may greatly depend on a single mentor. The NIH Building Infrastructure Leading to Diversity (BUILD) Initiative has been established to fund innovative undergraduate research training programs and support institutional and faculty development of the recipient university. The training model at Morgan State University (MSU), namely " A S tudent- C entered En trepreneurship D evelopment training model" (ASCEND), is one of the 10 NIH BUILD-funded programs, and offers a novel, experimental "entrepreneurial" training approach. In the ASCEND training model, the students take the lead. They own the research, understand the big picture, and experience the entire scope of the research process, which we hypothesize will lead to a greater sense of self-efficacy and research competency, as well as an enhanced sense of science identity. They are also immersed in environments with substantial peer support, where they can exchange research ideas and share experiences. This is important for underrepresented minority students who might have fewer role models and less peer support in conducting research. In this article, we describe the MSU ASCEND entrepreneurial training model's components, rationale, and history, and how it may enhance undergraduate training in biomedical research that may be of benefit to other institutions. We also discuss evaluation methods, possible sustainability solutions, and programmatic challenges that can affect all types of science training interventions.

Theory and experiment in biomedical science

NASA Astrophysics Data System (ADS)

Allen, Roland

2012-10-01

A physicist might regard a person as a collection of electrons and quarks, and a biologist might regard her as an assemblage of biochemical molecules. But according to some speakers at a recent Welch conference [1] biology is a branch of physics. Then biomedical research is a branch of applied physics. Even if one adopts a more modest perspective, it is still true that physics can contribute strongly to biomedical research. An example on the experimental side is the recent studies of G protein-coupled receptors (targeted by more than 50 percent of therapeutic drugs) using synchrotron radiation and nuclear magnetic resonance. On the theory side, one might classify models as microscopic (e.g., simulations of molecules, ions, or electrons), mesoscopic (e.g., simulations of pathways within a cell), or macroscopic (e.g., calculations of processes involving the whole body). We have recently introduced a new macroscopic method for estimating the biochemical response to pharmaceuticals, surgeries, or other medical interventions, and applied it in a simple model of the response to bariatric surgeries [2]. An amazing effect is that the most widely used bariatric surgery (Roux-en-Y-gastric bypass) usually leads to remission of type 2 diabetes in days, long before there is any significant weight loss (with further beneficial effects in the subsequent months and years). Our results confirm that this effect can be largely explained by the enhanced post-meal excretion of glucagon-like peptide 1 (GLP-1), an incretin that increases insulin secretion from the pancreas, but also suggest that other mechanisms are likely to be involved, possibly including an additional insulin-independent pathway for glucose transport into cells. [4pt] [1] Physical Biology, from Atoms to Medicine, edited by Ahmed H. Zewail (Imperial College Press, London, 2008).[0pt] [2] Roland E. Allen, Tyler D. Hughes, Jia Lerd Ng, Roberto D. Ortiz, Michel Abou Ghantous, Othmane Bouhali, Abdelilah Arredouani, ``Biochemical response and the effects of bariatric surgeries on type 2 diabetes'' (submitted).

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

PubMed

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 wheelbarrows in 33.7% (N = 29). Biomedical waste was disposed of in old incinerators or in artisanal ovens with a great deal of smoke emanating from these. Working conditions were deemed poor by 81.3% (N = 61) of employees interviewed and personal protection equipment was available in 45.3% (N = 39) of services. Knowledge about biomedical waste management was deemed satisfactory by 62.6% (N = 47) of interviewees and 80% (N = 60) were aware of the health risks related to biomedical waste. The poor management of biomedical waste is a reality in hospital facilities in Dakar. This can be addressed by increasing the awareness of managers for an effective application of the legislation, implementing realistic management programmes and providing the appropriate on-the-job training to staff members.

An active visual search interface for Medline.

PubMed

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

2007-01-01

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

A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data.

PubMed

Delussu, Giovanni; Lianas, Luca; Frexia, Francesca; Zanetti, Gianluigi

2016-01-01

This work presents a scalable data access layer, called PyEHR, designed to support the implementation of data management systems for secondary use of structured heterogeneous biomedical and clinical data. PyEHR adopts the openEHR's formalisms to guarantee the decoupling of data descriptions from implementation details and exploits structure indexing to accelerate searches. Data persistence is guaranteed by a driver layer with a common driver interface. Interfaces for two NoSQL Database Management Systems are already implemented: MongoDB and Elasticsearch. We evaluated the scalability of PyEHR experimentally through two types of tests, called "Constant Load" and "Constant Number of Records", with queries of increasing complexity on synthetic datasets of ten million records each, containing very complex openEHR archetype structures, distributed on up to ten computing nodes.

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases.

PubMed

Berger, Seth I; Posner, Jeremy M; Ma'ayan, Avi

2007-10-04

In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP), generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes. Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes.

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

PubMed

Walter, Lutz

2004-01-01

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

Problems of quality and equity in pain management: exploring the role of biomedical culture.

PubMed

Crowley-Matoka, Megan; Saha, Somnath; Dobscha, Steven K; Burgess, Diana J

2009-10-01

To explore how social scientific analyses of the culture of biomedicine may contribute to advancing our understanding of ongoing issues of quality and equity in pain management. Drawing upon the rich body of social scientific literature on the culture of biomedicine, we identify key features of biomedical culture with particular salience for pain management. We then examine how these cultural features of biomedicine may shape key phases of the pain management process in ways that have implications not just for quality, but for equity in pain management as well. We bring together a range of literatures in developing our analysis, including literatures on the culture of biomedicine, pain management and health care disparities. We surveyed the relevant literatures to identify and inter-relate key features of biomedical culture, key phases of the pain management process, and key dimensions of identified problems with suboptimal and inequitable treatment of pain. We identified three key features of biomedical culture with critical implications for pain management: 1) mind-body dualism; 2) a focus on disease vs illness; and 3) a bias toward cure vs care. Each of these cultural features play a role in the key phases of pain management, specifically pain-related communication, assessment and treatment decision-making, in ways that may hinder successful treatment of pain in general -- and of pain patients from disadvantaged groups in particular. Deepening our understanding of the role of biomedical culture in pain management has implications for education, policy and research as part of ongoing efforts to ameliorate problems in both quality and equity in managing pain. In particular, we suggest that building upon the existing the cultural competence movement in medicine to include fostering a deeper understanding of biomedical culture and its impact on physicians may be useful. From a policy perspective, we identify pain management as an area where the need for a shift to a more biopsychosocial model of health care is particularly pressing, and suggest prioritization of inter-disciplinary, multimodal approaches to pain as one key strategy in realizing this shift. Finally, in terms of research, we identify the need for empirical research to assess aspects of biomedical culture that may influence physician's attitudes and behaviors related to pain management, as well as to explore how these cultural values and their effects may vary across different settings within the practice of medicine.

Recent advances in bulk metallic glasses for biomedical applications.

PubMed

Li, H F; Zheng, Y F

2016-05-01

With a continuously increasing aging population and the improvement of living standards, large demands of biomaterials are expected for a long time to come. Further development of novel biomaterials, that are much safer and of much higher quality, in terms of both biomedical and mechanical properties, are therefore of great interest for both the research scientists and clinical surgeons. Compared with the conventional crystalline metallic counterparts, bulk metallic glasses have unique amorphous structures, and thus exhibit higher strength, lower Young's modulus, improved wear resistance, good fatigue endurance, and excellent corrosion resistance. For this purpose, bulk metallic glasses (BMGs) have recently attracted much attention for biomedical applications. This review discusses and summarizes the recent developments and advances of bulk metallic glasses, including Ti-based, Zr-based, Fe-based, Mg-based, Zn-based, Ca-based and Sr-based alloying systems for biomedical applications. Future research directions will move towards overcoming the brittleness, increasing the glass forming ability (GFA) thus obtaining corresponding bulk metallic glasses with larger sizes, removing/reducing toxic elements, and surface modifications. Bulk metallic glasses (BMGs), also known as amorphous alloys or liquid metals, are relative newcomers in the field of biomaterials. They have gained increasing attention during the past decades, as they exhibit an excellent combination of properties and processing capabilities desired for versatile biomedical implant applications. The present work reviewed the recent developments and advances of biomedical BMGs, including Ti-based, Zr-based, Fe-based, Mg-based, Zn-based, Ca-based and Sr-based BMG alloying systems. Besides, the critical analysis and in-depth discussion on the current status, challenge and future development of biomedical BMGs are included. The possible solution to the BMG size limitation, the brittleness of BMGs has been proposed. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Biomedical image classification based on a cascade of an SVM with a reject option and subspace analysis.

PubMed

Lin, Dongyun; Sun, Lei; Toh, Kar-Ann; Zhang, Jing Bo; Lin, Zhiping

2018-05-01

Automated biomedical image classification could confront the challenges of high level noise, image blur, illumination variation and complicated geometric correspondence among various categorical biomedical patterns in practice. To handle these challenges, we propose a cascade method consisting of two stages for biomedical image classification. At stage 1, we propose a confidence score based classification rule with a reject option for a preliminary decision using the support vector machine (SVM). The testing images going through stage 1 are separated into two groups based on their confidence scores. Those testing images with sufficiently high confidence scores are classified at stage 1 while the others with low confidence scores are rejected and fed to stage 2. At stage 2, the rejected images from stage 1 are first processed by a subspace analysis technique called eigenfeature regularization and extraction (ERE), and then classified by another SVM trained in the transformed subspace learned by ERE. At both stages, images are represented based on two types of local features, i.e., SIFT and SURF, respectively. They are encoded using various bag-of-words (BoW) models to handle biomedical patterns with and without geometric correspondence, respectively. Extensive experiments are implemented to evaluate the proposed method on three benchmark real-world biomedical image datasets. The proposed method significantly outperforms several competing state-of-the-art methods in terms of classification accuracy. Copyright © 2018 Elsevier Ltd. All rights reserved.

An overview on characterization, utilization and leachate analysis of biomedical waste incinerator ash.

PubMed

Rajor, Anita; Xaxa, Monika; Mehta, Ratika; Kunal

2012-10-15

Solid waste management is one of the major global environmental issues, as there is continuous increase in industrial globalization and generation of waste. Solid wastes encompass the heterogeneous mass of throwaways from the urban community as well as the homogeneous accumulations of agricultural, industrial and mineral wastes. Biomedical waste pose a significant impact on health and environment. A proper waste management system should be required to dispose hazardous biomedical waste and incineration should be the best available technology to reduce the volume of this hazardous waste. The incineration process destroys pathogens and reduces the waste volume and weight but leaves a solid material called biomedical waste ash as residue which increases the levels of heavy metals, inorganic salts and organic compounds in the environment. Disposal of biomedical waste ash in landfill may cause contamination of groundwater as metals are not destroyed during incineration. The limited space and the high cost for land disposal led to the development of recycling technologies and the reuse of ash in different systems. In order to minimize leaching of its hazardous components into the environment several studies confirmed the successful utilization of biomedical waste ash in agriculture and construction sector. This paper presents the overview on the beneficial use of ash in agriculture and construction materials and its leachate characteristics. This review also stressed on the need to further evaluate the leachate studies of the ashes and slag for their proper disposal and utilization. Copyright © 2012 Elsevier Ltd. All rights reserved.

Data Analysis and Data Mining: Current Issues in Biomedical Informatics

PubMed Central

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

2011-01-01

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

Unsupervised discovery of information structure in biomedical documents.

PubMed

Kiela, Douwe; Guo, Yufan; Stenius, Ulla; Korhonen, Anna

2015-04-01

Information structure (IS) analysis is a text mining technique, which classifies text in biomedical articles into categories that capture different types of information, such as objectives, methods, results and conclusions of research. It is a highly useful technique that can support a range of Biomedical Text Mining tasks and can help readers of biomedical literature find information of interest faster, accelerating the highly time-consuming process of literature review. Several approaches to IS analysis have been presented in the past, with promising results in real-world biomedical tasks. However, all existing approaches, even weakly supervised ones, require several hundreds of hand-annotated training sentences specific to the domain in question. Because biomedicine is subject to considerable domain variation, such annotations are expensive to obtain. This makes the application of IS analysis across biomedical domains difficult. In this article, we investigate an unsupervised approach to IS analysis and evaluate the performance of several unsupervised methods on a large corpus of biomedical abstracts collected from PubMed. Our best unsupervised algorithm (multilevel-weighted graph clustering algorithm) performs very well on the task, obtaining over 0.70 F scores for most IS categories when applied to well-known IS schemes. This level of performance is close to that of lightly supervised IS methods and has proven sufficient to aid a range of practical tasks. Thus, using an unsupervised approach, IS could be applied to support a wide range of tasks across sub-domains of biomedicine. We also demonstrate that unsupervised learning brings novel insights into IS of biomedical literature and discovers information categories that are not present in any of the existing IS schemes. The annotated corpus and software are available at http://www.cl.cam.ac.uk/∼dk427/bio14info.html. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Luminescent nanodiamonds for biomedical applications.

PubMed

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

2011-12-01

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

Joint inflight biomedical experiments performed during the ASTP spaceflight. [bacteriological experiments

NASA Technical Reports Server (NTRS)

Taylor, G. R.; Rogers, T. D.; Brower, M. E.; Kropp, K.

1976-01-01

Two joint inflight biomedical experiments were conducted during the unique Apollo-Soyuz Test Project (ASTP) spaceflight. One experiment evaluated rhythmicity of spore production of Streptomyces levoris. The other evaluated components of the infectious disease process by measuring alteration in: (1) the composition of the microbial population inhabiting USA and USSR crewmembers and spacecraft; (2) the ability of each crewmember's defense mechanism to resist infection; and (3) the ability of certain microorganisms to originate infections. These two experiments are described and the major results discussed.

The Connectivity Map: a new tool for biomedical research.

PubMed

Lamb, Justin

2007-01-01

The ultimate objective of biomedical research is to connect human diseases with the genes that underlie them and drugs that treat them. But this remains a daunting task, and even the most inspired researchers still have to resort to laborious screens of genetic or chemical libraries. What if at least some parts of this screening process could be systematized and centralized? And hits found and hypotheses generated with something resembling an internet search engine? These are the questions the Connectivity Map project set out to answer.

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator.

PubMed

Tchechmedjiev, Andon; Abdaoui, Amine; Emonet, Vincent; Melzi, Soumia; Jonnagaddala, Jitendra; Jonquet, Clement

2018-06-01

Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical data, but not very suitable for clinical text annotation. In order to add new functionalities to the NCBO Annotator without hosting or modifying the original Web service, we have designed a proxy architecture that enables seamless extensions by pre-processing of the input text and parameters, and post processing of the annotations. We have then implemented enhanced functionalities for annotating and indexing free text such as: scoring, detection of context (negation, experiencer, temporality), new output formats and coarse-grained concept recognition (with UMLS Semantic Groups). In this paper, we present the NCBO Annotator+, a Web service which incorporates these new functionalities as well as a small set of evaluation results for concept recognition and clinical context detection on two standard evaluation tasks (Clef eHealth 2017, SemEval 2014). The Annotator+ has been successfully integrated into the SIFR BioPortal platform-an implementation of NCBO BioPortal for French biomedical terminologies and ontologies-to annotate English text. A Web user interface is available for testing and ontology selection (http://bioportal.lirmm.fr/ncbo_annotatorplus); however the Annotator+ is meant to be used through the Web service application programming interface (http://services.bioportal.lirmm.fr/ncbo_annotatorplus). The code is openly available, and we also provide a Docker packaging to enable easy local deployment to process sensitive (e.g. clinical) data in-house (https://github.com/sifrproject). andon.tchechmedjiev@lirmm.fr. Supplementary data are available at Bioinformatics online.

Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora.

PubMed

Islamaj Doğan, Rezarta; Comeau, Donald C; Yeganova, Lana; Wilbur, W John

2014-01-01

BioC is a recently created XML format to share text data and annotations, and an accompanying input/output library to promote interoperability of data and tools for natural language processing of biomedical text. This article reports the use of BioC to address a common challenge in processing biomedical text information-that of frequent entity name abbreviation. We selected three different abbreviation definition identification modules, and used the publicly available BioC code to convert these independent modules into BioC-compatible components that interact seamlessly with BioC-formatted data, and other BioC-compatible modules. In addition, we consider four manually annotated corpora of abbreviations in biomedical text: the Ab3P corpus of 1250 PubMed abstracts, the BIOADI corpus of 1201 PubMed abstracts, the old MEDSTRACT corpus of 199 PubMed(®) citations and the Schwartz and Hearst corpus of 1000 PubMed abstracts. Annotations in these corpora have been re-evaluated by four annotators and their consistency and quality levels have been improved. We converted them to BioC-format and described the representation of the annotations. These corpora are used to measure the three abbreviation-finding algorithms and the results are given. The BioC-compatible modules, when compared with their original form, have no difference in their efficiency, running time or any other comparable aspects. They can be conveniently used as a common pre-processing step for larger multi-layered text-mining endeavors. Database URL: Code and data are available for download at the BioC site: http://bioc.sourceforge.net. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

Rotation Covariant Image Processing for Biomedical Applications

PubMed Central

Reisert, Marco

2013-01-01

With the advent of novel biomedical 3D image acquisition techniques, the efficient and reliable analysis of volumetric images has become more and more important. The amount of data is enormous and demands an automated processing. The applications are manifold, ranging from image enhancement, image reconstruction, and image description to object/feature detection and high-level contextual feature extraction. In most scenarios, it is expected that geometric transformations alter the output in a mathematically well-defined manner. In this paper we emphasis on 3D translations and rotations. Many algorithms rely on intensity or low-order tensorial-like descriptions to fulfill this demand. This paper proposes a general mathematical framework based on mathematical concepts and theories transferred from mathematical physics and harmonic analysis into the domain of image analysis and pattern recognition. Based on two basic operations, spherical tensor differentiation and spherical tensor multiplication, we show how to design a variety of 3D image processing methods in an efficient way. The framework has already been applied to several biomedical applications ranging from feature and object detection tasks to image enhancement and image restoration techniques. In this paper, the proposed methods are applied on a variety of different 3D data modalities stemming from medical and biological sciences. PMID:23710255

Leading change: curriculum reform in graduate education in the biomedical sciences.

PubMed

Dasgupta, Shoumita; Symes, Karen; Hyman, Linda

2015-01-01

The Division of Graduate Medical Sciences at the Boston University School of Medicine houses numerous dynamic graduate programs. Doctoral students began their studies with laboratory rotations and classroom training in a variety of fundamental disciplines. Importantly, with 15 unique pathways of admission to these doctoral programs, there were also 15 unique curricula. Departments and programs offered courses independently, and students participated in curricula that were overlapping combinations of these courses. This system created curricula that were not coordinated and that had redundant course content as well as content gaps. A partnership of key stakeholders began a curriculum reform process to completely restructure doctoral education at the Boston University School of Medicine. The key pedagogical goals, objectives, and elements designed into the new curriculum through this reform process created a curriculum designed to foster the interdisciplinary thinking that students are ultimately asked to utilize in their research endeavors. We implemented comprehensive student and peer evaluation of the new Foundations in Biomedical Sciences integrated curriculum to assess the new curriculum. Furthermore, we detail how this process served as a gateway toward creating a more fully integrated graduate experience, under the umbrella of the Program in Biomedical Sciences. © 2015 The International Union of Biochemistry and Molecular Biology.

Biomedical Terminology Mapper for UML projects.

PubMed

Thibault, Julien C; Frey, Lewis

2013-01-01

As the biomedical community collects and generates more and more data, the need to describe these datasets for exchange and interoperability becomes crucial. This paper presents a mapping algorithm that can help developers expose local implementations described with UML through standard terminologies. The input UML class or attribute name is first normalized and tokenized, then lookups in a UMLS-based dictionary are performed. For the evaluation of the algorithm 142 UML projects were extracted from caGrid and automatically mapped to National Cancer Institute (NCI) terminology concepts. Resulting mappings at the UML class and attribute levels were compared to the manually curated annotations provided in caGrid. Results are promising and show that this type of algorithm could speed-up the tedious process of mapping local implementations to standard biomedical terminologies.

Biomedical Terminology Mapper for UML projects

PubMed Central

Thibault, Julien C.; Frey, Lewis

As the biomedical community collects and generates more and more data, the need to describe these datasets for exchange and interoperability becomes crucial. This paper presents a mapping algorithm that can help developers expose local implementations described with UML through standard terminologies. The input UML class or attribute name is first normalized and tokenized, then lookups in a UMLS-based dictionary are performed. For the evaluation of the algorithm 142 UML projects were extracted from caGrid and automatically mapped to National Cancer Institute (NCI) terminology concepts. Resulting mappings at the UML class and attribute levels were compared to the manually curated annotations provided in caGrid. Results are promising and show that this type of algorithm could speed-up the tedious process of mapping local implementations to standard biomedical terminologies. PMID:24303278

Functional Electrospun Nanofibrous Scaffolds for Biomedical Applications

PubMed Central

Liang, Dehai; Hsiao, Benjamin S.; Chu, Benjamin

2009-01-01

Functional nanofibrous scaffolds produced by electrospinning have great potential in many biomedical applications, such as tissue engineering, wound dressing, enzyme immobilization and drug (gene) delivery. For a specific successful application, the chemical, physical and biological properties of electrospun scaffolds should be adjusted to match the environment by using a combination of multi-component compositions and fabrication techniques where electrospinning has often become a pivotal tool. The property of the nanofibrous scaffold can be further improved with innovative development in electrospinning processes, such as two-component electrospinning and in-situ mixing electrospinning. Post modifications of electrospun membranes also provide effective means to render the electrospun scaffolds with controlled anisotropy and porosity. In this review, we review the materials, techniques and post modification methods to functionalize electrospun nanofibrous scaffolds suitable for biomedical applications. PMID:17884240

Interpretation of the Lempel-Ziv complexity measure in the context of biomedical signal analysis.

PubMed

Aboy, Mateo; Hornero, Roberto; Abásolo, Daniel; Alvarez, Daniel

2006-11-01

Lempel-Ziv complexity (LZ) and derived LZ algorithms have been extensively used to solve information theoretic problems such as coding and lossless data compression. In recent years, LZ has been widely used in biomedical applications to estimate the complexity of discrete-time signals. Despite its popularity as a complexity measure for biosignal analysis, the question of LZ interpretability and its relationship to other signal parameters and to other metrics has not been previously addressed. We have carried out an investigation aimed at gaining a better understanding of the LZ complexity itself, especially regarding its interpretability as a biomedical signal analysis technique. Our results indicate that LZ is particularly useful as a scalar metric to estimate the bandwidth of random processes and the harmonic variability in quasi-periodic signals.

Biomedical applications of a real-time terahertz color scanner

PubMed Central

Schirmer, Markus; Fujio, Makoto; Minami, Masaaki; Miura, Jiro; Araki, Tsutomu; Yasui, Takeshi

2010-01-01

A real-time THz color scanner has the potential to further expand the application scope of THz spectral imaging based on its rapid image acquisition rate. We demonstrated three possible applications of a THz color scanner in the biomedical field: imaging of pharmaceutical tablets, human teeth, and human hair. The first application showed the scanner’s potential in total inspection for rapid quality control of pharmaceutical tablets moving on a conveyor belt. The second application demonstrated that the scanner can be used to identify a potential indicator for crystallinity of dental tissue. In the third application, the scanner was successfully used to visualize the drying process of wet hairs. These demonstrations indicated the high potential of the THz color scanner for practical applications in the biomedical field. PMID:21258472