Systems-Level Analysis of Innate Immunity

PubMed Central

Zak, Daniel E.; Tam, Vincent C.; Aderem, Alan

2014-01-01

Systems-level analysis of biological processes strives to comprehensively and quantitatively evaluate the interactions between the relevant molecular components over time, thereby enabling development of models that can be employed to ultimately predict behavior. Rapid development in measurement technologies (omics), when combined with the accessible nature of the cellular constituents themselves, is allowing the field of innate immunity to take significant strides toward this lofty goal. In this review, we survey exciting results derived from systems biology analyses of the immune system, ranging from gene regulatory networks to influenza pathogenesis and systems vaccinology. PMID:24655298

Human Connectome Project Informatics: quality control, database services, and data visualization

PubMed Central

Marcus, Daniel S.; Harms, Michael P.; Snyder, Abraham Z.; Jenkinson, Mark; Wilson, J Anthony; Glasser, Matthew F.; Barch, Deanna M.; Archie, Kevin A.; Burgess, Gregory C.; Ramaratnam, Mohana; Hodge, Michael; Horton, William; Herrick, Rick; Olsen, Timothy; McKay, Michael; House, Matthew; Hileman, Michael; Reid, Erin; Harwell, John; Coalson, Timothy; Schindler, Jon; Elam, Jennifer S.; Curtiss, Sandra W.; Van Essen, David C.

2013-01-01

The Human Connectome Project (HCP) has developed protocols, standard operating and quality control procedures, and a suite of informatics tools to enable high throughput data collection, data sharing, automated data processing and analysis, and data mining and visualization. Quality control procedures include methods to maintain data collection consistency over time, to measure head motion, and to establish quantitative modality-specific overall quality assessments. Database services developed as customizations of the XNAT imaging informatics platform support both internal daily operations and open access data sharing. The Connectome Workbench visualization environment enables user interaction with HCP data and is increasingly integrated with the HCP's database services. Here we describe the current state of these procedures and tools and their application in the ongoing HCP study. PMID:23707591

Accurate radiation temperature and chemical potential from quantitative photoluminescence analysis of hot carrier populations.

PubMed

Gibelli, François; Lombez, Laurent; Guillemoles, Jean-François

2017-02-15

In order to characterize hot carrier populations in semiconductors, photoluminescence measurement is a convenient tool, enabling us to probe the carrier thermodynamical properties in a contactless way. However, the analysis of the photoluminescence spectra is based on some assumptions which will be discussed in this work. We especially emphasize the importance of the variation of the material absorptivity that should be considered to access accurate thermodynamical properties of the carriers, especially by varying the excitation power. The proposed method enables us to obtain more accurate results of thermodynamical properties by taking into account a rigorous physical description and finds direct application in investigating hot carrier solar cells, which are an adequate concept for achieving high conversion efficiencies with a relatively simple device architecture.

Completeness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources

PubMed Central

Wu, Tai-luan; Tseng, Ling-li

2017-01-01

This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic), two aggregate institutional repositories (OAIster and OpenDOAR), and two physics-related open sources (arXiv.org and Astrophysics Data System). The 2001–2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations. Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems. The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system. PMID:29267327

Toward Accurate and Quantitative Comparative Metagenomics

PubMed Central

Nayfach, Stephen; Pollard, Katherine S.

2016-01-01

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

Multi-Intelligence Analytics for Next Generation Analysts (MIAGA)

NASA Astrophysics Data System (ADS)

Blasch, Erik; Waltz, Ed

2016-05-01

Current analysts are inundated with large volumes of data from which extraction, exploitation, and indexing are required. A future need for next-generation analysts is an appropriate balance between machine analytics from raw data and the ability of the user to interact with information through automation. Many quantitative intelligence tools and techniques have been developed which are examined towards matching analyst opportunities with recent technical trends such as big data, access to information, and visualization. The concepts and techniques summarized are derived from discussions with real analysts, documented trends of technical developments, and methods to engage future analysts with multiintelligence services. For example, qualitative techniques should be matched against physical, cognitive, and contextual quantitative analytics for intelligence reporting. Future trends include enabling knowledge search, collaborative situational sharing, and agile support for empirical decision-making and analytical reasoning.

Toward Accurate and Quantitative Comparative Metagenomics.

PubMed

Nayfach, Stephen; Pollard, Katherine S

2016-08-25

Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

Mapping the Binding Interface of VEGF and a Monoclonal Antibody Fab-1 Fragment with Fast Photochemical Oxidation of Proteins (FPOP) and Mass Spectrometry

NASA Astrophysics Data System (ADS)

Zhang, Ying; Wecksler, Aaron T.; Molina, Patricia; Deperalta, Galahad; Gross, Michael L.

2017-05-01

We previously analyzed the Fab-1:VEGF (vascular endothelial growth factor) system described in this work, with both native top-down mass spectrometry and bottom-up mass spectrometry (carboxyl-group or GEE footprinting) techniques. This work continues bottom-up mass spectrometry analysis using a fast photochemical oxidation of proteins (FPOP) platform to map the solution binding interface of VEGF and a fragment antigen binding region of an antibody (Fab-1). In this study, we use FPOP to compare the changes in solvent accessibility by quantitating the extent of oxidative modification in the unbound versus bound states. Determining the changes in solvent accessibility enables the inference of the protein binding sites (epitope and paratopes) and a comparison to the previously published Fab-1:VEGF crystal structure, adding to the top-down and bottom-up data. Using this method, we investigated peptide-level and residue-level changes in solvent accessibility between the unbound proteins and bound complex. Mapping these data onto the Fab-1:VEGF crystal structure enabled successful characterization of both the binding region and regions of remote conformation changes. These data, coupled with our previous higher order structure (HOS) studies, demonstrate the value of a comprehensive toolbox of methods for identifying the putative epitopes and paratopes for biotherapeutic antibodies.

Learning from “Knocks in Life”: Food Insecurity among Low-Income Lone Senior Women

PubMed Central

Green-LaPierre, Rebecca J.; Williams, Patricia L.; Glanville, N. Theresa; Norris, Deborah; Hunter, Heather C.; Watt, Cynthia G.

2012-01-01

Building on earlier quantitative work where we showed that lone senior households reliant on public pensions in Nova Scotia (NS), Canada lacked the necessary funds for a basic nutritious diet, here we present findings from a qualitative study involving in-depth interviews with eight low-income lone senior women living in an urban area of NS. Using a phenomenological inquiry approach, in-depth interviews were used to explore lone senior women's experiences accessing food with limited financial resources. Drawing upon Bronfenbrenner's Ecological Systems Theory, we explored their perceived ability to access a nutritionally adequate and personally acceptable diet, and the barriers and enablers to do so; as well in light of our previous quantitative research, we explored their perceptions related to adequacy of income, essential expenses, and their strategies to manage personal finances. Seven key themes emerged: world view, income adequacy, transportation, health/health problems, community program use, availability of family and friends, and personal food management strategies. World view exerted the largest influence on seniors' personal perception of food security status. The implications of the findings and policy recommendations to reduce the nutritional health inequities among this vulnerable subset of the senior population are considered. PMID:22997580

Learning from "Knocks in Life": Food Insecurity among Low-Income Lone Senior Women.

PubMed

Green-Lapierre, Rebecca J; Williams, Patricia L; Glanville, N Theresa; Norris, Deborah; Hunter, Heather C; Watt, Cynthia G

2012-01-01

Building on earlier quantitative work where we showed that lone senior households reliant on public pensions in Nova Scotia (NS), Canada lacked the necessary funds for a basic nutritious diet, here we present findings from a qualitative study involving in-depth interviews with eight low-income lone senior women living in an urban area of NS. Using a phenomenological inquiry approach, in-depth interviews were used to explore lone senior women's experiences accessing food with limited financial resources. Drawing upon Bronfenbrenner's Ecological Systems Theory, we explored their perceived ability to access a nutritionally adequate and personally acceptable diet, and the barriers and enablers to do so; as well in light of our previous quantitative research, we explored their perceptions related to adequacy of income, essential expenses, and their strategies to manage personal finances. Seven key themes emerged: world view, income adequacy, transportation, health/health problems, community program use, availability of family and friends, and personal food management strategies. World view exerted the largest influence on seniors' personal perception of food security status. The implications of the findings and policy recommendations to reduce the nutritional health inequities among this vulnerable subset of the senior population are considered.

A layered microchip conductance detector with through-layer access to detection fields and high sensitivity to dielectric constant.

PubMed

Suganuma, Y; Dhirani, A-A

2011-04-01

The present study explores a novel apertured microchip conductance detector (AMCD) that is sensitive to dielectric constant. Fashioned on silicon oxide/silicon using optical microlithography, the detector has novel parallel-plate geometry with a top mesh electrode, a middle apertured insulator, and a bottom conducting electrode. This monolithic apertured architecture is planar and may be provided with a thin insulator layer enabling large capacitances, while the top mesh electrode and middle apertured-insulator enable access to regions of the capacitor where electric fields are strong. Hence, the detector is sensitive yet mechanically robust. To test its response, the AMCD was immersed in various solvents, namely water, methanol, acetonitrile, and hexanes. Its response was found to vary in proportion to the solvents' respective dielectric constants. The AMCD was also able to distinguish quantitatively the presence of various molecules in solution, including molecules with chromophores [such as acetylsalicylic acid (ASA)] in methanol and those without chrompohores [such as polyethylene glycol 200 Daltons (PEG200)] in methanol or water. The universal nature of dielectric constant and the microchip detector's sensitivity point to a wide range of potential applications. © 2011 American Institute of Physics

Internet-based system for simulation-based medical planning for cardiovascular disease.

PubMed

Steele, Brooke N; Draney, Mary T; Ku, Joy P; Taylor, Charles A

2003-06-01

Current practice in vascular surgery utilizes only diagnostic and empirical data to plan treatments, which does not enable quantitative a priori prediction of the outcomes of interventions. We have previously described simulation-based medical planning methods to model blood flow in arteries and plan medical treatments based on physiologic models. An important consideration for the design of these patient-specific modeling systems is the accessibility to physicians with modest computational resources. We describe a simulation-based medical planning environment developed for the World Wide Web (WWW) using the Virtual Reality Modeling Language (VRML) and the Java programming language.

Critical behavior of subcellular density organization during neutrophil activation and migration.

PubMed

Baker-Groberg, Sandra M; Phillips, Kevin G; Healy, Laura D; Itakura, Asako; Porter, Juliana E; Newton, Paul K; Nan, Xiaolin; McCarty, Owen J T

2015-12-01

Physical theories of active matter continue to provide a quantitative understanding of dynamic cellular phenomena, including cell locomotion. Although various investigations of the rheology of cells have identified important viscoelastic and traction force parameters for use in these theoretical approaches, a key variable has remained elusive both in theoretical and experimental approaches: the spatiotemporal behavior of the subcellular density. The evolution of the subcellular density has been qualitatively observed for decades as it provides the source of image contrast in label-free imaging modalities (e.g., differential interference contrast, phase contrast) used to investigate cellular specimens. While these modalities directly visualize cell structure, they do not provide quantitative access to the structures being visualized. We present an established quantitative imaging approach, non-interferometric quantitative phase microscopy, to elucidate the subcellular density dynamics in neutrophils undergoing chemokinesis following uniform bacterial peptide stimulation. Through this approach, we identify a power law dependence of the neutrophil mean density on time with a critical point, suggesting a critical density is required for motility on 2D substrates. Next we elucidate a continuum law relating mean cell density, area, and total mass that is conserved during neutrophil polarization and migration. Together, our approach and quantitative findings will enable investigators to define the physics coupling cytoskeletal dynamics with subcellular density dynamics during cell migration.

Critical behavior of subcellular density organization during neutrophil activation and migration

PubMed Central

Baker-Groberg, Sandra M.; Phillips, Kevin G.; Healy, Laura D.; Itakura, Asako; Porter, Juliana E.; Newton, Paul K.; Nan, Xiaolin; McCarty, Owen J.T.

2015-01-01

Physical theories of active matter continue to provide a quantitative understanding of dynamic cellular phenomena, including cell locomotion. Although various investigations of the rheology of cells have identified important viscoelastic and traction force parameters for use in these theoretical approaches, a key variable has remained elusive both in theoretical and experimental approaches: the spatiotemporal behavior of the subcellular density. The evolution of the subcellular density has been qualitatively observed for decades as it provides the source of image contrast in label-free imaging modalities (e.g., differential interference contrast, phase contrast) used to investigate cellular specimens. While these modalities directly visualize cell structure, they do not provide quantitative access to the structures being visualized. We present an established quantitative imaging approach, non-interferometric quantitative phase microscopy, to elucidate the subcellular density dynamics in neutrophils undergoing chemokinesis following uniform bacterial peptide stimulation. Through this approach, we identify a power law dependence of the neutrophil mean density on time with a critical point, suggesting a critical density is required for motility on 2D substrates. Next we elucidate a continuum law relating mean cell density, area, and total mass that is conserved during neutrophil polarization and migration. Together, our approach and quantitative findings will enable investigators to define the physics coupling cytoskeletal dynamics with subcellular density dynamics during cell migration. PMID:26640599

Deterministic phase slips in mesoscopic superconducting rings

PubMed Central

Petković, I.; Lollo, A.; Glazman, L. I.; Harris, J. G. E.

2016-01-01

The properties of one-dimensional superconductors are strongly influenced by topological fluctuations of the order parameter, known as phase slips, which cause the decay of persistent current in superconducting rings and the appearance of resistance in superconducting wires. Despite extensive work, quantitative studies of phase slips have been limited by uncertainty regarding the order parameter's free-energy landscape. Here we show detailed agreement between measurements of the persistent current in isolated flux-biased rings and Ginzburg–Landau theory over a wide range of temperature, magnetic field and ring size; this agreement provides a quantitative picture of the free-energy landscape. We also demonstrate that phase slips occur deterministically as the barrier separating two competing order parameter configurations vanishes. These results will enable studies of quantum and thermal phase slips in a well-characterized system and will provide access to outstanding questions regarding the nature of one-dimensional superconductivity. PMID:27882924

Deterministic phase slips in mesoscopic superconducting rings.

PubMed

Petković, I; Lollo, A; Glazman, L I; Harris, J G E

2016-11-24

The properties of one-dimensional superconductors are strongly influenced by topological fluctuations of the order parameter, known as phase slips, which cause the decay of persistent current in superconducting rings and the appearance of resistance in superconducting wires. Despite extensive work, quantitative studies of phase slips have been limited by uncertainty regarding the order parameter's free-energy landscape. Here we show detailed agreement between measurements of the persistent current in isolated flux-biased rings and Ginzburg-Landau theory over a wide range of temperature, magnetic field and ring size; this agreement provides a quantitative picture of the free-energy landscape. We also demonstrate that phase slips occur deterministically as the barrier separating two competing order parameter configurations vanishes. These results will enable studies of quantum and thermal phase slips in a well-characterized system and will provide access to outstanding questions regarding the nature of one-dimensional superconductivity.

General solution for quantitative dark-field contrast imaging with grating interferometers

NASA Astrophysics Data System (ADS)

Strobl, M.

2014-11-01

Grating interferometer based imaging with X-rays and neutrons has proven to hold huge potential for applications in key research fields conveying biology and medicine as well as engineering and magnetism, respectively. The thereby amenable dark-field imaging modality implied the promise to access structural information beyond reach of direct spatial resolution. However, only here a yet missing approach is reported that finally allows exploiting this outstanding potential for non-destructive materials characterizations. It enables to obtain quantitative structural small angle scattering information combined with up to 3-dimensional spatial image resolution even at lab based x-ray or at neutron sources. The implied two orders of magnitude efficiency gain as compared to currently available techniques in this regime paves the way for unprecedented structural investigations of complex sample systems of interest for material science in a vast range of fields.

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

Petković, Ivana; Lollo, A.; Glazman, L. I.

The properties of one-dimensional superconductors are strongly influenced by topological fluctuations of the order parameter, known as phase slips, which cause the decay of persistent current in superconducting rings and the appearance of resistance in superconducting wires. Despite extensive work, quantitative studies of phase slips have been limited by uncertainty regarding the order parameter’s free-energy landscape. Here we show detailed agreement between measurements of the persistent current in isolated flux-biased rings and Ginzburg–Landau theory over a wide range of temperature, magnetic field and ring size; this agreement provides a quantitative picture of the free-energy landscape. Furthermore, we also demonstrate thatmore » phase slips occur deterministically as the barrier separating two competing order parameter configurations vanishes. These results will enable studies of quantum and thermal phase slips in a well-characterized system and will provide access to outstanding questions regarding the nature of one-dimensional superconductivity.« less

Enabling Interactive Measurements from Large Coverage Microscopy

PubMed Central

Bajcsy, Peter; Vandecreme, Antoine; Amelot, Julien; Chalfoun, Joe; Majurski, Michael; Brady, Mary

2017-01-01

Microscopy could be an important tool for characterizing stem cell products if quantitative measurements could be collected over multiple spatial and temporal scales. With the cells changing states over time and being several orders of magnitude smaller than cell products, modern microscopes are already capable of imaging large spatial areas, repeat imaging over time, and acquiring images over several spectra. However, characterizing stem cell products from such large image collections is challenging because of data size, required computations, and lack of interactive quantitative measurements needed to determine release criteria. We present a measurement web system consisting of available algorithms, extensions to a client-server framework using Deep Zoom, and the configuration know-how to provide the information needed for inspecting the quality of a cell product. The cell and other data sets are accessible via the prototype web-based system at http://isg.nist.gov/deepzoomweb. PMID:28663600

Deterministic phase slips in mesoscopic superconducting rings

DOE PAGES

Petković, Ivana; Lollo, A.; Glazman, L. I.; ...

2016-11-24

The properties of one-dimensional superconductors are strongly influenced by topological fluctuations of the order parameter, known as phase slips, which cause the decay of persistent current in superconducting rings and the appearance of resistance in superconducting wires. Despite extensive work, quantitative studies of phase slips have been limited by uncertainty regarding the order parameter’s free-energy landscape. Here we show detailed agreement between measurements of the persistent current in isolated flux-biased rings and Ginzburg–Landau theory over a wide range of temperature, magnetic field and ring size; this agreement provides a quantitative picture of the free-energy landscape. Furthermore, we also demonstrate thatmore » phase slips occur deterministically as the barrier separating two competing order parameter configurations vanishes. These results will enable studies of quantum and thermal phase slips in a well-characterized system and will provide access to outstanding questions regarding the nature of one-dimensional superconductivity.« less

Factors influencing physical activity and rehabilitation in survivors of critical illness: a systematic review of quantitative and qualitative studies.

PubMed

Parry, Selina M; Knight, Laura D; Connolly, Bronwen; Baldwin, Claire; Puthucheary, Zudin; Morris, Peter; Mortimore, Jessica; Hart, Nicholas; Denehy, Linda; Granger, Catherine L

2017-04-01

To identify, evaluate and synthesise studies examining the barriers and enablers for survivors of critical illness to participate in physical activity in the ICU and post-ICU settings from the perspective of patients, caregivers and healthcare providers. Systematic review of articles using five electronic databases: MEDLINE, CINAHL, EMBASE, Cochrane Library, Scopus. Quantitative and qualitative studies that were published in English in a peer-reviewed journal and assessed barriers or enablers for survivors of critical illness to perform physical activity were included. Prospero ID: CRD42016035454. Eighty-nine papers were included. Five major themes and 28 sub-themes were identified, encompassing: (1) patient physical and psychological capability to perform physical activity, including delirium, sedation, illness severity, comorbidities, weakness, anxiety, confidence and motivation; (2) safety influences, including physiological stability and concern for lines, e.g. risk of dislodgement; (3) culture and team influences, including leadership, interprofessional communication, administrative buy-in, clinician expertise and knowledge; (4) motivation and beliefs regarding the benefits/risks; and (5) environmental influences, including funding, access to rehabilitation programs, staffing and equipment. The main barriers identified were patient physical and psychological capability to perform physical activity, safety concerns, lack of leadership and ICU culture of mobility, lack of interprofessional communication, expertise and knowledge, and lack of staffing/equipment and funding to provide rehabilitation programs. Barriers and enablers are multidimensional and span diverse factors. The majority of these barriers are modifiable and can be targeted in future clinical practice.

P-MartCancer-Interactive Online Software to Enable Analysis of Shotgun Cancer Proteomic Datasets.

PubMed

Webb-Robertson, Bobbie-Jo M; Bramer, Lisa M; Jensen, Jeffrey L; Kobold, Markus A; Stratton, Kelly G; White, Amanda M; Rodland, Karin D

2017-11-01

P-MartCancer is an interactive web-based software environment that enables statistical analyses of peptide or protein data, quantitated from mass spectrometry-based global proteomics experiments, without requiring in-depth knowledge of statistical programming. P-MartCancer offers a series of statistical modules associated with quality assessment, peptide and protein statistics, protein quantification, and exploratory data analyses driven by the user via customized workflows and interactive visualization. Currently, P-MartCancer offers access and the capability to analyze multiple cancer proteomic datasets generated through the Clinical Proteomics Tumor Analysis Consortium at the peptide, gene, and protein levels. P-MartCancer is deployed as a web service (https://pmart.labworks.org/cptac.html), alternatively available via Docker Hub (https://hub.docker.com/r/pnnl/pmart-web/). Cancer Res; 77(21); e47-50. ©2017 AACR . ©2017 American Association for Cancer Research.

CPTAC Assay Portal: a repository of targeted proteomic assays

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

Whiteaker, Jeffrey R.; Halusa, Goran; Hoofnagle, Andrew N.

2014-06-27

To address these issues, the Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute (NCI) has launched an Assay Portal (http://assays.cancer.gov) to serve as a public repository of well-characterized quantitative, MS-based, targeted proteomic assays. The purpose of the CPTAC Assay Portal is to facilitate widespread adoption of targeted MS assays by disseminating SOPs, reagents, and assay characterization data for highly characterized assays. A primary aim of the NCI-supported portal is to bring together clinicians or biologists and analytical chemists to answer hypothesis-driven questions using targeted, MS-based assays. Assay content is easily accessed through queries and filters, enabling investigatorsmore » to find assays to proteins relevant to their areas of interest. Detailed characterization data are available for each assay, enabling researchers to evaluate assay performance prior to launching the assay in their own laboratory.« less

The Rényi divergence enables accurate and precise cluster analysis for localisation microscopy.

PubMed

Staszowska, Adela D; Fox-Roberts, Patrick; Hirvonen, Liisa M; Peddie, Christopher J; Collinson, Lucy M; Jones, Gareth E; Cox, Susan

2018-06-01

Clustering analysis is a key technique for quantitatively characterising structures in localisation microscopy images. To build up accurate information about biological structures, it is critical that the quantification is both accurate (close to the ground truth) and precise (has small scatter and is reproducible). Here we describe how the Rényi divergence can be used for cluster radius measurements in localisation microscopy data. We demonstrate that the Rényi divergence can operate with high levels of background and provides results which are more accurate than Ripley's functions, Voronoi tesselation or DBSCAN. Data supporting this research will be made accessible via a web link. Software codes developed for this work can be accessed via http://coxphysics.com/Renyi_divergence_software.zip. Implemented in C ++. Correspondence and requests for materials can be also addressed to the corresponding author. adela.staszowska@gmail.com or susan.cox@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

Quantitative Imaging with a Mobile Phone Microscope

PubMed Central

Skandarajah, Arunan; Reber, Clay D.; Switz, Neil A.; Fletcher, Daniel A.

2014-01-01

Use of optical imaging for medical and scientific applications requires accurate quantification of features such as object size, color, and brightness. High pixel density cameras available on modern mobile phones have made photography simple and convenient for consumer applications; however, the camera hardware and software that enables this simplicity can present a barrier to accurate quantification of image data. This issue is exacerbated by automated settings, proprietary image processing algorithms, rapid phone evolution, and the diversity of manufacturers. If mobile phone cameras are to live up to their potential to increase access to healthcare in low-resource settings, limitations of mobile phone–based imaging must be fully understood and addressed with procedures that minimize their effects on image quantification. Here we focus on microscopic optical imaging using a custom mobile phone microscope that is compatible with phones from multiple manufacturers. We demonstrate that quantitative microscopy with micron-scale spatial resolution can be carried out with multiple phones and that image linearity, distortion, and color can be corrected as needed. Using all versions of the iPhone and a selection of Android phones released between 2007 and 2012, we show that phones with greater than 5 MP are capable of nearly diffraction-limited resolution over a broad range of magnifications, including those relevant for single cell imaging. We find that automatic focus, exposure, and color gain standard on mobile phones can degrade image resolution and reduce accuracy of color capture if uncorrected, and we devise procedures to avoid these barriers to quantitative imaging. By accommodating the differences between mobile phone cameras and the scientific cameras, mobile phone microscopes can be reliably used to increase access to quantitative imaging for a variety of medical and scientific applications. PMID:24824072

Polymer on Top: Current Limits and Future Perspectives of Quantitatively Evaluating Surface Grafting.

PubMed

Michalek, Lukas; Barner, Leonie; Barner-Kowollik, Christopher

2018-03-07

Well-defined polymer strands covalently tethered onto solid substrates determine the properties of the resulting functional interface. Herein, the current approaches to determine quantitative grafting densities are assessed. Based on a brief introduction into the key theories describing polymer brush regimes, a user's guide is provided to estimating maximum chain coverage and-importantly-examine the most frequently employed approaches for determining grafting densities, i.e., dry thickness measurements, gravimetric assessment, and swelling experiments. An estimation of the reliability of these determination methods is provided via carefully evaluating their assumptions and assessing the stability of the underpinning equations. A practical access guide for comparatively and quantitatively evaluating the reliability of a given approach is thus provided, enabling the field to critically judge experimentally determined grafting densities and to avoid the reporting of grafting densities that fall outside the physically realistic parameter space. The assessment is concluded with a perspective on the development of advanced approaches for determination of grafting density, in particular, on single-chain methodologies. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Developing methods for systematic reviewing in health services delivery and organization: an example from a review of access to health care for people with learning disabilities. Part 2. Evaluation of the literature--a practical guide.

PubMed

Alborz, Alison; McNally, Rosalind

2004-12-01

To develop methods to facilitate the 'systematic' review of evidence from a range of methodologies on diffuse or 'soft' topics, as exemplified by 'access to health care'. Twenty-eight bibliographic databases, research registers, organizational websites or library catalogues. Reference lists from identified studies. Contact with experts and service users. Current awareness and contents alerting services in the area of learning disabilities. Inclusion criteria were English language literature from 1980 onwards, relating to people with learning disabilities of any age and all study designs. The main criteria for assessment was relevance to Guillifords' model of access to health care which was adapted to the circumstances of people with learning disabilities. Selected studies were evaluated for scientific rigour then data was extracted and the results synthesized. Quality assessment was by an initial set of 'generic' quality indicators. This enabled further evidence selection before evaluation of findings according to specific criteria for qualitative, quantitative or mixed-method studies. Eighty-two studies were fully evaluated. Five studies were rated 'highly rigorous', 22 'rigorous', 46 'less rigorous' and nine 'poor' papers were retained as the sole evidence covering aspects of the guiding model. The majority of studies were quantitative but used only descriptive statistics. Most evidence lacked methodological detail, which often lowered final quality ratings. The application of a consistent structure to quality evaluation can facilitate data appraisal, extraction and synthesis across a range of methodologies in diffuse or 'soft' topics. Synthesis can be facilitated further by using software, such as the microsoft 'access' database, for managing information.

Glucosinolate pattern in Isatis tinctoria and I. indigotica seeds.

PubMed

Mohn, Tobias; Hamburger, Matthias

2008-06-01

The glucosinolate patterns in seeds of five ISATIS TINCTORIA and two ISATIS INDIGOTICA accessions were assessed with a recently developed and validated LC-MS assay for direct analysis of glucosinolates without prior desulfatation. Glucosinolate peaks were identified with in-source fragmentation and detection of the sulfate anion ( M/Z = 97), and by MS/MS experiments. The glucosinolate patterns of the seeds showed characteristic differences compared to leaves. Glucoisatisin and epiglucoisatisin were diagnostic of seed samples. Qualitative and quantitative differences in glucosinolate patterns between both ISATIS species were found for seed samples, enabling a differentiation of the two medicinal plants at the level of seed material.

LudusScope: Accessible Interactive Smartphone Microscopy for Life-Science Education.

PubMed

Kim, Honesty; Gerber, Lukas Cyrill; Chiu, Daniel; Lee, Seung Ah; Cira, Nate J; Xia, Sherwin Yuyang; Riedel-Kruse, Ingmar H

2016-01-01

For centuries, observational microscopy has greatly facilitated biology education, but we still cannot easily and playfully interact with the microscopic world we see. We therefore developed the LudusScope, an accessible, interactive do-it-yourself smartphone microscopy platform that promotes exploratory stimulation and observation of microscopic organisms, in a design that combines the educational modalities of build, play, and inquire. The LudusScope's touchscreen and joystick allow the selection and stimulation of phototactic microorganisms such as Euglena gracilis with light. Organismal behavior is tracked and displayed in real time, enabling open and structured game play as well as scientific inquiry via quantitative experimentation. Furthermore, we used the Scratch programming language to incorporate biophysical modeling. This platform is designed as an accessible, low-cost educational kit for easy construction and expansion. User testing with both teachers and students demonstrates the educational potential of the LudusScope, and we anticipate additional synergy with the maker movement. Transforming observational microscopy into an interactive experience will make microbiology more tangible to society, and effectively support the interdisciplinary learning required by the Next Generation Science Standards.

LudusScope: Accessible Interactive Smartphone Microscopy for Life-Science Education

PubMed Central

Kim, Honesty; Gerber, Lukas Cyrill; Chiu, Daniel; Lee, Seung Ah; Cira, Nate J.; Xia, Sherwin Yuyang; Riedel-Kruse, Ingmar H.

2016-01-01

For centuries, observational microscopy has greatly facilitated biology education, but we still cannot easily and playfully interact with the microscopic world we see. We therefore developed the LudusScope, an accessible, interactive do-it-yourself smartphone microscopy platform that promotes exploratory stimulation and observation of microscopic organisms, in a design that combines the educational modalities of build, play, and inquire. The LudusScope’s touchscreen and joystick allow the selection and stimulation of phototactic microorganisms such as Euglena gracilis with light. Organismal behavior is tracked and displayed in real time, enabling open and structured game play as well as scientific inquiry via quantitative experimentation. Furthermore, we used the Scratch programming language to incorporate biophysical modeling. This platform is designed as an accessible, low-cost educational kit for easy construction and expansion. User testing with both teachers and students demonstrates the educational potential of the LudusScope, and we anticipate additional synergy with the maker movement. Transforming observational microscopy into an interactive experience will make microbiology more tangible to society, and effectively support the interdisciplinary learning required by the Next Generation Science Standards. PMID:27706189

Intramolecular carbon and nitrogen isotope analysis by quantitative dry fragmentation of the phenylurea herbicide isoproturon in a combined injector/capillary reactor prior to GC separation.

PubMed

Penning, Holger; Elsner, Martin

2007-11-01

Potentially, compound-specific isotope analysis may provide unique information on source and fate of pesticides in natural systems. Yet for isotope analysis, LC-based methods that are based on the use of organic solvents often cannot be used and GC-based analysis is frequently not possible due to thermolability of the analyte. A typical example of a compound with such properties is isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea), belonging to the worldwide extensively used phenylurea herbicides. To make isoproturon accessible to carbon and nitrogen isotope analysis, we developed a GC-based method during which isoproturon was quantitatively fragmented to dimethylamine and 4-isopropylphenylisocyanate. Fragmentation occurred only partially in the injector but was mainly achieved on a heated capillary column. The fragments were then chromatographically separated and individually measured by isotope ratio mass spectrometry. The reliability of the method was tested in hydrolysis experiments with three isotopically different batches of isoproturon. For all three products, the same isotope fractionation factors were observed during conversion and the difference in isotope composition between the batches was preserved. This study demonstrates that fragmentation of phenylurea herbicides does not only make them accessible to isotope analysis but even enables determination of intramolecular isotope fractionation.

Macrostrat and GeoDeepDive: A Platform for Geological Data Integration and Deep-Time Research

NASA Astrophysics Data System (ADS)

Husson, J. M.; Peters, S. E.; Ross, I.; Czaplewski, J. J.

2016-12-01

Characterizing the quantity, lithology, age, and properties of rocks and sediments in the upper crust is central to many questions in Earth science. Although a large number of geological maps, regional syntheses, and sample-based measurements have been published in a variety of formats, there is no system for integrating and accessing rock record-derived data or for facilitating the large-scale quantitative interrogation of the physical, chemical, and biological properties of Earth's crust. Here we describe two data resources that aim to overcome some of these limitations: 1) Macrostrat, a geospatial database and supporting cyberinfrastructure that is designed to enable quantitative analyses of the entire assemblage of surface and subsurface sedimentary, igneous and metamorphic rocks, and 2) GeoDeepDive, a digital library and high throughput computing system designed to facilitate the location and extraction of information and data from the published literature. Macrostrat currently contains general summaries of the age and lithology of rocks and sediments in the upper crust at 1,474 regions in North and Central America, the Caribbean, New Zealand, and the deep sea. Distributed among these geographic regions are nearly 34,000 lithologically and chronologically-defined geological units, many of which are linked to a bedrock geologic map database with more than 1.7 million globally distributed units. Sample-derived data, including fossil occurrences in the Paleobiology Database and more than 180,000 geochemical and outcrop-derived measurements are linked to Macrostrat units and/or lithologies within those units. The rock names, lithological terms, and geological time intervals that are applied to Macrostrat units define a hierarchical, spatially and temporally indexed vocabulary that is leveraged by GeoDeepDive in order to provide researchers access to data within the scientific literature as it is published and ingested into the infrastructure. All data in Macrostrat are accessible via an Application Programming Interface, which enables the development of mobile and analytical applications. The GeoDeepDive infrastructure also supports the development and execution of applications that are tailored to the specific, literature-based data location and extraction needs of geoscientists.

Classification of cassava genotypes based on qualitative and quantitative data.

PubMed

Oliveira, E J; Oliveira Filho, O S; Santos, V S

2015-02-02

We evaluated the genetic variation of cassava accessions based on qualitative (binomial and multicategorical) and quantitative traits (continuous). We characterized 95 accessions obtained from the Cassava Germplasm Bank of Embrapa Mandioca e Fruticultura; we evaluated these accessions for 13 continuous, 10 binary, and 25 multicategorical traits. First, we analyzed the accessions based only on quantitative traits; next, we conducted joint analysis (qualitative and quantitative traits) based on the Ward-MLM method, which performs clustering in two stages. According to the pseudo-F, pseudo-t2, and maximum likelihood criteria, we identified five and four groups based on quantitative trait and joint analysis, respectively. The smaller number of groups identified based on joint analysis may be related to the nature of the data. On the other hand, quantitative data are more subject to environmental effects in the phenotype expression; this results in the absence of genetic differences, thereby contributing to greater differentiation among accessions. For most of the accessions, the maximum probability of classification was >0.90, independent of the trait analyzed, indicating a good fit of the clustering method. Differences in clustering according to the type of data implied that analysis of quantitative and qualitative traits in cassava germplasm might explore different genomic regions. On the other hand, when joint analysis was used, the means and ranges of genetic distances were high, indicating that the Ward-MLM method is very useful for clustering genotypes when there are several phenotypic traits, such as in the case of genetic resources and breeding programs.

Portable, one-step, and rapid GMR biosensor platform with smartphone interface.

PubMed

Choi, Joohong; Gani, Adi Wijaya; Bechstein, Daniel J B; Lee, Jung-Rok; Utz, Paul J; Wang, Shan X

2016-11-15

Quantitative immunoassay tests in clinical laboratories require trained technicians, take hours to complete with multiple steps, and the instruments used are generally immobile-patient samples have to be sent in to the labs for analysis. This prevents quantitative immunoassay tests to be performed outside laboratory settings. A portable, quantitative immunoassay device will be valuable in rural and resource-limited areas, where access to healthcare is scarce or far away. We have invented Eigen Diagnosis Platform (EDP), a portable quantitative immunoassay platform based on Giant Magnetoresistance (GMR) biosensor technology. The platform does not require a trained technician to operate, and only requires one-step user involvement. It displays quantitative results in less than 15min after sample insertion, and each test costs less than US$4. The GMR biosensor employed in EDP is capable of detecting multiple biomarkers in one test, enabling a wide array of immune diagnostics to be performed simultaneously. In this paper, we describe the design of EDP, and demonstrate its capability. Multiplexed assay of human immunoglobulin G and M (IgG and IgM) antibodies with EDP achieves sensitivities down to 0.07 and 0.33 nanomolar, respectively. The platform will allow lab testing to be performed in remote areas, and open up applications of immunoassay testing in other non-clinical settings, such as home, school, and office. Copyright © 2016 Elsevier B.V. All rights reserved.

An exploration of the enablers and barriers in access to the Dutch healthcare system among Ghanaians in Amsterdam

PubMed Central

2012-01-01

Background Sub-Saharan African populations are growing in many European countries. Data on the health of these populations are rare. Additionally, many sub-Saharan African migrants are confronted with issues of low socio-economic status, acculturation and language difficulties, which may hamper their access to health care. Despite the identification of some of those barriers, little is known about the enabling factors. Knowledge about the enablers and barriers in access to healthcare experienced is important in addressing their health needs and promoting healthcare access. This study aimed to investigate the enabling factors as well as barriers in access to the Dutch healthcare system among the largest sub-Saharan African migrant group (Ghanaians) living in Amsterdam, the Netherlands. Methods Six focus groups were conducted from November 2009 to February 2010. A semi-structured interview guideline was used. Discussions were conducted in English or Twi (Ghanaian dialect), recorded and transcribed verbatim. Analysis was based on the Andersen model of healthcare utilisation using MAXQDA software. Results Knowledge and perceived quality of the health system, awareness of diseases, family and community support, community initiatives and availability of social support were the main enablers to the healthcare system. Difficulties with the Dutch language and mistrust in health care providers were major barriers in access to healthcare. Conclusions Access to healthcare is facilitated mainly by knowledge of and the perceived efficiency and quality of the Dutch healthcare system. However, poor Dutch language proficiency and mistrust in health care providers appear to be important barriers in accessing healthcare. The enablers and barriers identified by this study provide useful information for promoting healthcare access among this and similar Sub-Saharan African communities. PMID:22443162

An exploration of the enablers and barriers in access to the Dutch healthcare system among Ghanaians in Amsterdam.

PubMed

Boateng, Linda; Nicolaou, Mary; Dijkshoorn, Henriëtte; Stronks, Karien; Agyemang, Charles

2012-03-24

Sub-Saharan African populations are growing in many European countries. Data on the health of these populations are rare. Additionally, many sub-Saharan African migrants are confronted with issues of low socio-economic status, acculturation and language difficulties, which may hamper their access to health care. Despite the identification of some of those barriers, little is known about the enabling factors. Knowledge about the enablers and barriers in access to healthcare experienced is important in addressing their health needs and promoting healthcare access. This study aimed to investigate the enabling factors as well as barriers in access to the Dutch healthcare system among the largest sub-Saharan African migrant group (Ghanaians) living in Amsterdam, the Netherlands. Six focus groups were conducted from November 2009 to February 2010. A semi-structured interview guideline was used. Discussions were conducted in English or Twi (Ghanaian dialect), recorded and transcribed verbatim. Analysis was based on the Andersen model of healthcare utilisation using MAXQDA software. Knowledge and perceived quality of the health system, awareness of diseases, family and community support, community initiatives and availability of social support were the main enablers to the healthcare system. Difficulties with the Dutch language and mistrust in health care providers were major barriers in access to healthcare. Access to healthcare is facilitated mainly by knowledge of and the perceived efficiency and quality of the Dutch healthcare system. However, poor Dutch language proficiency and mistrust in health care providers appear to be important barriers in accessing healthcare. The enablers and barriers identified by this study provide useful information for promoting healthcare access among this and similar Sub-Saharan African communities.

A Systematic Review of Individual and Contextual Factors Affecting ART Initiation, Adherence, and Retention for HIV-Infected Pregnant and Postpartum Women

PubMed Central

Hodgson, Ian; Plummer, Mary L.; Konopka, Sarah N.; Colvin, Christopher J.; Jonas, Edna; Albertini, Jennifer; Amzel, Anouk; Fogg, Karen P.

2014-01-01

Background Despite progress reducing maternal mortality, HIV-related maternal deaths remain high, accounting, for example, for up to 24 percent of all pregnancy-related deaths in sub-Saharan Africa. Antiretroviral therapy (ART) is effective in improving outcomes among HIV-infected pregnant and postpartum women, yet rates of initiation, adherence, and retention remain low. This systematic literature review synthesized evidence about individual and contextual factors affecting ART use among HIV-infected pregnant and postpartum women. Methods Searches were conducted for studies addressing the population (HIV-infected pregnant and postpartum women), intervention (ART), and outcomes of interest (initiation, adherence, and retention). Quantitative and qualitative studies published in English since January 2008 were included. Individual and contextual enablers and barriers to ART use were extracted and organized thematically within a framework of individual, interpersonal, community, and structural categories. Results Thirty-four studies were included in the review. Individual-level factors included both those within and outside a woman’s awareness and control (e.g., commitment to child’s health or age). Individual-level barriers included poor understanding of HIV, ART, and prevention of mother-to-child transmission, and difficulty managing practical demands of ART. At an interpersonal level, disclosure to a spouse and spousal involvement in treatment were associated with improved initiation, adherence, and retention. Fear of negative consequences was a barrier to disclosure. At a community level, stigma was a major barrier. Key structural barriers and enablers were related to health system use and engagement, including access to services and health worker attitudes. Conclusions To be successful, programs seeking to expand access to and continued use of ART by integrating maternal health and HIV services must identify and address the relevant barriers and enablers in their own context that are described in this review. Further research on this population, including those who drop out of or never access health services, is needed to inform effective implementation. PMID:25372479

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University

PubMed Central

Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

2010-01-01

We developed, TNAURice: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx. PMID:21364829

TNAURice: Database on rice varieties released from Tamil Nadu Agricultural University.

PubMed

Ramalingam, Jegadeesan; Arul, Loganathan; Sathishkumar, Natarajan; Vignesh, Dhandapani; Thiyagarajan, Katiannan; Samiyappan, Ramasamy

2010-11-27

WE DEVELOPED, TNAURICE: a database comprising of the rice varieties released from a public institution, Tamil Nadu Agricultural University (TNAU), Coimbatore, India. Backed by MS-SQL, and ASP-Net at the front end, this database provide information on both quantitative and qualitative descriptors of the rice varities inclusive of their parental details. Enabled by an user friendly search utility, the database can be effectively searched by the varietal descriptors, and the entire contents are navigable as well. The database comes handy to the plant breeders involved in the varietal improvement programs to decide on the choice of parental lines. TNAURice is available for public access at http://www.btistnau.org/germdefault.aspx.

Isotopic 13C NMR spectrometry to assess counterfeiting of active pharmaceutical ingredients: site-specific 13C content of aspirin and paracetamol.

PubMed

Silvestre, Virginie; Mboula, Vanessa Maroga; Jouitteau, Catherine; Akoka, Serge; Robins, Richard J; Remaud, Gérald S

2009-10-15

Isotope profiling is a well-established technique to obtain information about the chemical history of a given compound. However, the current methodology using IRMS can only determine the global (13)C content, leading to the loss of much valuable data. The development of quantitative isotopic (13)C NMR spectrometry at natural abundance enables the measurement of the (13)C content of each carbon within a molecule, thus giving simultaneous access to a number of isotopic parameters. When it is applied to active pharmaceutical ingredients, each manufactured batch can be characterized better than by IRMS. Here, quantitative isotopic (13)C NMR is shown to be a very promising and effective tool for assessing the counterfeiting of medicines, as exemplified by an analysis of aspirin (acetylsalicylic acid) and paracetamol (acetaminophen) samples collected from pharmacies in different countries. It is proposed as an essential complement to (2)H NMR and IRMS.

Remote Access to Wireless Communications Systems Laboratory--New Technology Approach

ERIC Educational Resources Information Center

Kafadarova, Nadezhda; Sotirov, Sotir; Milev, Mihail

2012-01-01

Technology nowadays enables the remote access to laboratory equipment and instruments via Internet. This is especially useful in engineering education, where students can conduct laboratory experiment remotely. Such remote laboratory access can enable students to use expensive laboratory equipment, which is not usually available to students. In…

Light sheet theta microscopy for rapid high-resolution imaging of large biological samples.

PubMed

Migliori, Bianca; Datta, Malika S; Dupre, Christophe; Apak, Mehmet C; Asano, Shoh; Gao, Ruixuan; Boyden, Edward S; Hermanson, Ola; Yuste, Rafael; Tomer, Raju

2018-05-29

Advances in tissue clearing and molecular labeling methods are enabling unprecedented optical access to large intact biological systems. These developments fuel the need for high-speed microscopy approaches to image large samples quantitatively and at high resolution. While light sheet microscopy (LSM), with its high planar imaging speed and low photo-bleaching, can be effective, scaling up to larger imaging volumes has been hindered by the use of orthogonal light sheet illumination. To address this fundamental limitation, we have developed light sheet theta microscopy (LSTM), which uniformly illuminates samples from the same side as the detection objective, thereby eliminating limits on lateral dimensions without sacrificing the imaging resolution, depth, and speed. We present a detailed characterization of LSTM, and demonstrate its complementary advantages over LSM for rapid high-resolution quantitative imaging of large intact samples with high uniform quality. The reported LSTM approach is a significant step for the rapid high-resolution quantitative mapping of the structure and function of very large biological systems, such as a clarified thick coronal slab of human brain and uniformly expanded tissues, and also for rapid volumetric calcium imaging of highly motile animals, such as Hydra, undergoing non-isomorphic body shape changes.

Test-bed for the remote health monitoring system for bridge structures using FBG sensors

NASA Astrophysics Data System (ADS)

Lee, Chin-Hyung; Park, Ki-Tae; Joo, Bong-Chul; Hwang, Yoon-Koog

2009-05-01

This paper reports on test-bed for the long-term health monitoring system for bridge structures employing fiber Bragg grating (FBG) sensors, which is remotely accessible via the web, to provide real-time quantitative information on a bridge's response to live loading and environmental changes, and fast prediction of the structure's integrity. The sensors are attached on several locations of the structure and connected to a data acquisition system permanently installed onsite. The system can be accessed through remote communication using an optical cable network, through which the evaluation of the bridge behavior under live loading can be allowed at place far away from the field. Live structural data are transmitted continuously to the server computer at the central office. The server computer is connected securely to the internet, where data can be retrieved, processed and stored for the remote web-based health monitoring. Test-bed revealed that the remote health monitoring technology will enable practical, cost-effective, and reliable condition assessment and maintenance of bridge structures.

WormQTL—public archive and analysis web portal for natural variation data in Caenorhabditis spp

PubMed Central

Snoek, L. Basten; Van der Velde, K. Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O.; Poulin, Gino B.; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C.; Kammenga, Jan E.; Swertz, Morris A.

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers. PMID:23180786

WormQTL--public archive and analysis web portal for natural variation data in Caenorhabditis spp.

PubMed

Snoek, L Basten; Van der Velde, K Joeri; Arends, Danny; Li, Yang; Beyer, Antje; Elvin, Mark; Fisher, Jasmin; Hajnal, Alex; Hengartner, Michael O; Poulin, Gino B; Rodriguez, Miriam; Schmid, Tobias; Schrimpf, Sabine; Xue, Feng; Jansen, Ritsert C; Kammenga, Jan E; Swertz, Morris A

2013-01-01

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.

The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility.

PubMed

Lamontanara, Allan Joaquim; Georgeon, Sandrine; Tria, Giancarlo; Svergun, Dmitri I; Hantschel, Oliver

2014-11-17

The activity of protein kinases is regulated by multiple molecular mechanisms, and their disruption is a common driver of oncogenesis. A central and almost universal control element of protein kinase activity is the activation loop that utilizes both conformation and phosphorylation status to determine substrate access. In this study, we use recombinant Abl tyrosine kinases and conformation-specific kinase inhibitors to quantitatively analyse structural changes that occur after Abl activation. Allosteric SH2-kinase domain interactions were previously shown to be essential for the leukemogenesis caused by the Bcr-Abl oncoprotein. We find that these allosteric interactions switch the Abl activation loop from a closed to a fully open conformation. This enables the trans-autophosphorylation of the activation loop and requires prior phosphorylation of the SH2-kinase linker. Disruption of the SH2-kinase interaction abolishes activation loop phosphorylation. Our analysis provides a molecular mechanism for the SH2 domain-dependent activation of Abl that may also regulate other tyrosine kinases.

The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility

NASA Astrophysics Data System (ADS)

Lamontanara, Allan Joaquim; Georgeon, Sandrine; Tria, Giancarlo; Svergun, Dmitri I.; Hantschel, Oliver

2014-11-01

The activity of protein kinases is regulated by multiple molecular mechanisms, and their disruption is a common driver of oncogenesis. A central and almost universal control element of protein kinase activity is the activation loop that utilizes both conformation and phosphorylation status to determine substrate access. In this study, we use recombinant Abl tyrosine kinases and conformation-specific kinase inhibitors to quantitatively analyse structural changes that occur after Abl activation. Allosteric SH2-kinase domain interactions were previously shown to be essential for the leukemogenesis caused by the Bcr-Abl oncoprotein. We find that these allosteric interactions switch the Abl activation loop from a closed to a fully open conformation. This enables the trans-autophosphorylation of the activation loop and requires prior phosphorylation of the SH2-kinase linker. Disruption of the SH2-kinase interaction abolishes activation loop phosphorylation. Our analysis provides a molecular mechanism for the SH2 domain-dependent activation of Abl that may also regulate other tyrosine kinases.

HIV Viral RNA Extraction in Wax Immiscible Filtration Assisted by Surface Tension (IFAST) Devices

PubMed Central

Berry, Scott M.; LaVanway, Alex J.; Pezzi, Hannah M.; Guckenberger, David J.; Anderson, Meghan A.; Loeb, Jennifer M.; Beebe, David J.

2015-01-01

The monitoring of viral load is critical for proper management of antiretroviral therapy for HIV-positive patients. Unfortunately, in the developing world, significant economic and geographical barriers exist, limiting access to this test. The complexity of current viral load assays makes them expensive and their access limited to advanced facilities. We attempted to address these limitations by replacing conventional RNA extraction, one of the essential processes in viral load quantitation, with a simplified technique known as immiscible filtration assisted by surface tension (IFAST). Furthermore, these devices were produced via the embossing of wax, enabling local populations to produce and dispose of their own devices with minimal training or infrastructure, potentially reducing the total assay cost. In addition, IFAST can be used to reduce cold chain dependence during transportation. Viral RNA extracted from raw samples stored at 37°C for 1 week exhibited nearly complete degradation. However, IFAST-purified RNA could be stored at 37°C for 1 week without significant loss. These data suggest that RNA isolated at the point of care (eg, in a rural clinic) via IFAST could be shipped to a central laboratory for quantitative RT-PCR without a cold chain. Using this technology, we have demonstrated accurate and repeatable measurements of viral load on samples with as low as 50 copies per milliliter of sample. PMID:24613822

Developing Guidelines for Evaluating the Adaptation of Accessible Web-Based Learning Materials

ERIC Educational Resources Information Center

Radovan, Marko; Perdih, Mojca

2016-01-01

E-learning is a rapidly developing form of education. One of the key characteristics of e-learning is flexibility, which enables easier access to knowledge for everyone. Information and communications technology (ICT), which is e-learning's main component, enables alternative means of accessing the web-based learning materials that comprise the…

Remote Access Laboratories in Australia and Europe

ERIC Educational Resources Information Center

Ku, H.; Ahfock, T.; Yusaf, T.

2011-01-01

Remote access laboratories (RALs) were first developed in 1994 in Australia and Switzerland. The main purposes of developing them are to enable students to do their experiments at their own pace, time and locations and to enable students and teaching staff to get access to facilities beyond their institutions. Currently, most of the experiments…

Integrated radiologist's workstation enabling the radiologist as an effective clinical consultant

NASA Astrophysics Data System (ADS)

McEnery, Kevin W.; Suitor, Charles T.; Hildebrand, Stan; Downs, Rebecca; Thompson, Stephen K.; Shepard, S. Jeff

2002-05-01

Since February 2000, radiologists at the M. D. Anderson Cancer Center have accessed clinical information through an internally developed radiologist's clinical interpretation workstation called RadStation. This project provides a fully integrated digital dictation workstation with clinical data review. RadStation enables the radiologist as an effective clinical consultant with access to pertinent sources of clinical information at the time of dictation. Data sources not only include prior radiology reports from the radiology information system (RIS) but access to pathology data, laboratory data, history and physicals, clinic notes, and operative reports. With integrated clinical information access, a radiologists's interpretation not only comments on morphologic findings but also can enable evaluation of study findings in the context of pertinent clinical presentation and history. Image access is enabled through the integration of an enterprise image archive (Stentor, San Francisco). Database integration is achieved by a combination of real time HL7 messaging and queries to SQL-based legacy databases. A three-tier system architecture accommodates expanding access to additional databases including real-time patient schedule as well as patient medications and allergies.

Workforce characteristics of privately practicing nurse practitioners in Australia: Results from a national survey.

PubMed

Currie, Jane; Chiarella, Mary; Buckley, Thomas

2016-10-01

Australian private practice nurse practitioner (PPNP) services have grown since legislative changes in 2010 enabled eligible nurse practitioners (NPs) to access reimbursement for care delivered through the Medicare Benefits Schedule (MBS) and Pharmaceutical Benefits Scheme (PBS). This article provides data from a national survey on the workforce characteristics of PPNPs in Australia. PPNPs in Australia were invited to complete an electronic survey. Quantitative data were analyzed using descriptive statistics and qualitative data using thematic analysis. There were 73 completed surveys. One of the intentions of expanding access to MBS and PBS for patients treated by NPs was to increase patients' access to health care through greater flexibility in the healthcare workforce. The results of this survey confirm that the workforce characteristics of PPNPs provide a potentially untapped resource to meet current primary healthcare demand. The findings of this study allow us to understand the characteristics of PPNP services, which are significant for workforce planning. The focus of PPNP practice is toward primary health care with PPNPs working predominantly in general practice settings. The largest age group of PPNPs is over 50 years and means a proportion will be retiring in the next 15 years. ©2016 American Association of Nurse Practitioners.

Comparability analysis of protein therapeutics by bottom-up LC-MS with stable isotope-tagged reference standards

PubMed Central

Manuilov, Anton V; Radziejewski, Czeslaw H

2011-01-01

Comparability studies lie at the heart of assessments that evaluate differences amongst manufacturing processes and stability studies of protein therapeutics. Low resolution chromatographic and electrophoretic methods facilitate quantitation, but do not always yield detailed insight into the effect of the manufacturing change or environmental stress. Conversely, mass spectrometry (MS) can provide high resolution information on the molecule, but conventional methods are not very quantitative. This gap can be reconciled by use of a stable isotope-tagged reference standard (SITRS), a version of the analyte protein that is uniformly labeled with 13C6-arginine and 13C6-lysine. The SITRS serves as an internal control that is trypsin-digested and analyzed by liquid chromatography (LC)-MS with the analyte sample. The ratio of the ion intensities of each unlabeled and labeled peptide pair is then compared to that of other sample(s). A comparison of these ratios provides a readily accessible way to spot even minute differences among samples. In a study of a monoclonal antibody (mAb) spiked with varying amounts of the same antibody bearing point mutations, peptides containing the mutations were readily identified and quantified at concentrations as low as 2% relative to unmodified peptides. The method was robust, reproducible and produced a linear response for every peptide that was monitored. The method was also successfully used to distinguish between two batches of a mAb that were produced in two different cell lines while two batches produced from the same cell line were found to be highly comparable. Finally, the use of the SITRS method in the comparison of two stressed mAb samples enabled the identification of sites susceptible to deamidation and oxidation, as well as their quantitation. The experimental results indicate that use of a SITRS in a peptide mapping experiment with MS detection enables sensitive and quantitative comparability studies of proteins at high resolution. PMID:21654206

Comparability analysis of protein therapeutics by bottom-up LC-MS with stable isotope-tagged reference standards.

PubMed

Manuilov, Anton V; Radziejewski, Czeslaw H; Lee, David H

2011-01-01

Comparability studies lie at the heart of assessments that evaluate differences amongst manufacturing processes and stability studies of protein therapeutics. Low resolution chromatographic and electrophoretic methods facilitate quantitation, but do not always yield detailed insight into the effect of the manufacturing change or environmental stress. Conversely, mass spectrometry (MS) can provide high resolution information on the molecule, but conventional methods are not very quantitative. This gap can be reconciled by use of a stable isotope-tagged reference standard (SITRS), a version of the analyte protein that is uniformly labeled (13)C6-arginine and (13)C6-lysine. The SITRS serves as an internal control that is trypsin-digested and analyzed by liquid chromatography (LC)-MS with the analyte sample. The ratio of the ion intensities of each unlabeled and labeled peptide pair is then compared to that of other sample(s). A comparison of these ratios provides a readily accessible way to spot even minute differences among samples. In a study of a monoclonal antibody (mAb) spiked with varying amounts of the same antibody bearing point mutations, peptides containing the mutations were readily identified and quantified at concentrations as low as 2% relative to unmodified peptides. The method is robust, reproducible and produced a linear response for every peptide that was monitored. The method was also successfully used to distinguish between two batches of a mAb that were produced in two different cell lines while two batches produced from the same cell line were found to be highly comparable. Finally, the use of the SITRS method in the comparison of two stressed mAb samples enabled the identification of sites susceptible to deamidation and oxidation, as well as their quantitation. The experimental results indicate that use of a SITRS in a peptide mapping experiment with MS detection enables sensitive and quantitative comparability studies of proteins at high resolution.

Field-deployable, quantitative, rapid identification of active Ebola virus infection in unprocessed blood† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc03281a

PubMed Central

Shah, Kavit; Bentley, Emma; Tyler, Adam; Richards, Kevin S. R.; Wright, Edward; Easterbrook, Linda; Lee, Diane; Cleaver, Claire; Usher, Louise; Burton, Jane E.; Pitman, James K.; Bruce, Christine B.; Edge, David; Lee, Martin; Nazareth, Nelson; Norwood, David A.

2017-01-01

The West African Ebola virus outbreak underlined the importance of delivering mass diagnostic capability outside the clinical or primary care setting in effectively containing public health emergencies caused by infectious disease. Yet, to date, there is no solution for reliably deploying at the point of need the gold standard diagnostic method, real time quantitative reverse transcription polymerase chain reaction (RT-qPCR), in a laboratory infrastructure-free manner. In this proof of principle work, we demonstrate direct performance of RT-qPCR on fresh blood using far-red fluorophores to resolve fluorogenic signal inhibition and controlled, rapid freeze/thawing to achieve viral genome extraction in a single reaction chamber assay. The resulting process is entirely free of manual or automated sample pre-processing, requires no microfluidics or magnetic/mechanical sample handling and thus utilizes low cost consumables. This enables a fast, laboratory infrastructure-free, minimal risk and simple standard operating procedure suited to frontline, field use. Developing this novel approach on recombinant bacteriophage and recombinant human immunodeficiency virus (HIV; Lentivirus), we demonstrate clinical utility in symptomatic EBOV patient screening using live, infectious Filoviruses and surrogate patient samples. Moreover, we evidence assay co-linearity independent of viral particle structure that may enable viral load quantification through pre-calibration, with no loss of specificity across an 8 log-linear maximum dynamic range. The resulting quantitative rapid identification (QuRapID) molecular diagnostic platform, openly accessible for assay development, meets the requirements of resource-limited countries and provides a fast response solution for mass public health screening against emerging biosecurity threats. PMID:29163915

Failure to Integrate Quantitative Measurement Methods of Ocular Inflammation Hampers Clinical Practice and Trials on New Therapies for Posterior Uveitis.

PubMed

Herbort, Carl P; Tugal-Tutkun, Ilknur; Neri, Piergiorgio; Pavésio, Carlos; Onal, Sumru; LeHoang, Phuc

2017-05-01

Uveitis is one of the fields in ophthalmology where a tremendous evolution took place in the past 25 years. Not only did we gain access to more efficient, more targeted, and better tolerated therapies, but also in parallel precise and quantitative measurement methods developed allowing the clinician to evaluate these therapies and adjust therapeutic intervention with a high degree of precision. Objective and quantitative measurement of the global level of intraocular inflammation became possible for most inflammatory diseases with direct or spill-over anterior chamber inflammation, thanks to laser flare photometry. The amount of retinal inflammation could be quantified by using fluorescein angiography to score retinal angiographic signs. Indocyanine green angiography gave imaging insight into the hitherto inaccessible choroidal compartment, rendering possible the quantification of choroiditis by scoring indocyanine green angiographic signs. Optical coherence tomography has enabled measurement and objective monitoring of retinal and choroidal thickness. This multimodal quantitative appraisal of intraocular inflammation represents an exquisite security in monitoring uveitis. What is enigmatic, however, is the slow pace with which these improvements are integrated in some areas. What is even more difficult to understand is the fact that clinical trials to assess new therapeutic agents still mostly rely on subjective parameters such as clinical evaluation of vitreous haze as a main endpoint; whereas a whole array of precise, quantitative, and objective modalities are available for the design of clinical studies. The scope of this work was to review the quantitative investigations that improved the management of uveitis in the past 2-3 decades.

Computer Security Systems Enable Access.

ERIC Educational Resources Information Center

Riggen, Gary

1989-01-01

A good security system enables access and protects information from damage or tampering, but the most important aspects of a security system aren't technical. A security procedures manual addresses the human element of computer security. (MLW)

Open Access Enabling Courses: Risking Academic Standards or Meeting Equity Aspirations

ERIC Educational Resources Information Center

Shah, Mahsood; Whannell, Robert

2017-01-01

Open access enabling courses have experienced growth in Australia. The growth is evidenced in student enrolments and the number of public and private institutions offering such courses. Traditionally these courses have provided a second chance to many students from various equity groups who have been unable to access tertiary education due to poor…

Using Learning Analytics to Assess Student Engagement and Academic Outcomes in Open Access Enabling Programmes

ERIC Educational Resources Information Center

Atherton, Mirella; Shah, Mahsood; Vazquez, Jenny; Griffiths, Zoe; Jackson, Brian; Burgess, Catherine

2017-01-01

Curriculum design, teaching methods, assessments and range of academic support need to be inclusive in Open Access Enabling courses. The findings of this study confirm a correlation between student access to online learning materials and a positive impact on grades in science courses. More specifically, students who frequently use the online…

What's Next for NASA? Life After the Shuttle Program

NASA Technical Reports Server (NTRS)

MacLaughlin, Mary; Petro, Janet E.

2012-01-01

KSC is the world's preeminent launch complex for government and commercial space access, enabling the world to explore and work in space. KSC safely manages, develops, integrates, and sustains space systems through partnerships that enable innovative, diverse access to space and inspires the Nation's future explorers capabilities to make accessing space less costly and more routine.

Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.

PubMed

Hempel, Kristina; Herbst, Florian-Alexander; Moche, Martin; Hecker, Michael; Becher, Dörte

2011-04-01

Staphylococcus aureus is capable of colonizing and infecting humans by its arsenal of surface-exposed and secreted proteins. Iron-limited conditions in mammalian body fluids serve as a major environmental signal to bacteria to express virulence determinants. Here we present a comprehensive, gel-free, and GeLC-MS/MS-based quantitative proteome profiling of S. aureus under this infection-relevant situation. (14)N(15)N metabolic labeling and three complementing approaches were combined for relative quantitative analyses of surface-associated proteins. The surface-exposed and secreted proteome profiling approaches comprise trypsin shaving, biotinylation, and precipitation of the supernatant. By analysis of the outer subproteomic and cytoplasmic protein fraction, 1210 proteins could be identified including 221 surface-associated proteins. Thus, access was enabled to 70% of the predicted cell wall-associated proteins, 80% of the predicted sortase substrates, two/thirds of lipoproteins and more than 50% of secreted and cytoplasmic proteins. For iron-deficiency, 158 surface-associated proteins were quantified. Twenty-nine proteins were found in altered amounts showing particularly surface-exposed proteins strongly induced, such as the iron-regulated surface determinant proteins IsdA, IsdB, IsdC and IsdD as well as lipid-anchored iron compound-binding proteins. The work presents a crucial subject for understanding S. aureus pathophysiology by the use of methods that allow quantitative surface proteome profiling.

Improving the efficacy of healthcare services for Aboriginal Australians.

PubMed

Gwynne, Kylie; Jeffries, Thomas; Lincoln, Michelle

2018-01-16

Objective The aim of the present systematic review was to examine the enablers for effective health service delivery for Aboriginal Australians. Methods This systematic review was undertaken in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. Papers were included if they had data related to health services for Australian Aboriginal people and were published between 2000 and 2015. The 21 papers that met the inclusion criteria were assessed using the Effective Public Health Practice Project Quality Assessment Tool for Quantitative Studies. Seven papers were subsequently excluded due to weak methodological approaches. Results There were two findings in the present study: (1) that Aboriginal people fare worse than non-Aboriginal people when accessing usual healthcare services; and (2) there are five enablers for effective health care services for Australian Aboriginal people: cultural competence, participation rates, organisational, clinical governance and compliance, and availability of services. Conclusions Health services for Australian Aboriginal people must be tailored and implementation of the five enablers is likely to affect the effectiveness of health services for Aboriginal people. The findings of the present study have significant implications in directing the future design, funding, delivery and evaluation of health care services for Aboriginal Australians. What is known about the topic? There is significant evidence about poor health outcomes and the 10-year gap in life expectancy between Aboriginal and non-Aboriginal people, and limited evidence about improving health service efficacy. What does this paper add? This systematic review found that with usual health care delivery, Aboriginal people experience worse health outcomes. This paper identifies five strategies in the literature that improve the effectiveness of health care services intended for Aboriginal people. What are the implications for practitioners? Aboriginal people fare worse in both experience and outcomes when they access usual care services. Health services intended for Aboriginal people should be tailored using the five enablers to provide timely, culturally safe and high-quality care.

An intelligent data model for the storage of structured grids

NASA Astrophysics Data System (ADS)

Clyne, John; Norton, Alan

2013-04-01

With support from the U.S. National Science Foundation we have developed, and currently maintain, VAPOR: a geosciences-focused, open source visual data analysis package. VAPOR enables highly interactive exploration, as well as qualitative and quantitative analysis of high-resolution simulation outputs using only a commodity, desktop computer. The enabling technology behind VAPOR's ability to interact with a data set, whose size would overwhelm all but the largest analysis computing resources, is a progressive data access file format, called the VAPOR Data Collection (VDC). The VDC is based on the discrete wavelet transform and their information compaction properties. Prior to analysis, raw data undergo a wavelet transform, concentrating the information content into a fraction of the coefficients. The coefficients are then sorted by their information content (magnitude) into a small number of bins. Data are reconstructed by applying an inverse wavelet transform. If all of the coefficient bins are used during reconstruction the process is lossless (up to floating point round-off). If only a subset of the bins are used, an approximation of the original data is produced. A crucial point here is that the principal benefit to reconstruction from a subset of wavelet coefficients is a reduction in I/O. Further, if smaller coefficients are simply discarded, or perhaps stored on more capacious tertiary storage, secondary storage requirements (e.g. disk) can be reduced as well. In practice, these reductions in I/O or storage can be on the order of tens or even hundreds. This talk will briefly describe the VAPOR Data Collection, and will present real world success stories from the geosciences that illustrate how progressive data access enables highly interactive exploration of Big Data.

Informatics methods to enable sharing of quantitative imaging research data.

PubMed

Levy, Mia A; Freymann, John B; Kirby, Justin S; Fedorov, Andriy; Fennessy, Fiona M; Eschrich, Steven A; Berglund, Anders E; Fenstermacher, David A; Tan, Yongqiang; Guo, Xiaotao; Casavant, Thomas L; Brown, Bartley J; Braun, Terry A; Dekker, Andre; Roelofs, Erik; Mountz, James M; Boada, Fernando; Laymon, Charles; Oborski, Matt; Rubin, Daniel L

2012-11-01

The National Cancer Institute Quantitative Research Network (QIN) is a collaborative research network whose goal is to share data, algorithms and research tools to accelerate quantitative imaging research. A challenge is the variability in tools and analysis platforms used in quantitative imaging. Our goal was to understand the extent of this variation and to develop an approach to enable sharing data and to promote reuse of quantitative imaging data in the community. We performed a survey of the current tools in use by the QIN member sites for representation and storage of their QIN research data including images, image meta-data and clinical data. We identified existing systems and standards for data sharing and their gaps for the QIN use case. We then proposed a system architecture to enable data sharing and collaborative experimentation within the QIN. There are a variety of tools currently used by each QIN institution. We developed a general information system architecture to support the QIN goals. We also describe the remaining architecture gaps we are developing to enable members to share research images and image meta-data across the network. As a research network, the QIN will stimulate quantitative imaging research by pooling data, algorithms and research tools. However, there are gaps in current functional requirements that will need to be met by future informatics development. Special attention must be given to the technical requirements needed to translate these methods into the clinical research workflow to enable validation and qualification of these novel imaging biomarkers. Copyright © 2012 Elsevier Inc. All rights reserved.

Synthesizing qualitative and quantitative evidence on non-financial access barriers: implications for assessment at the district level.

PubMed

O'Connell, Thomas S; Bedford, K Juliet A; Thiede, Michael; McIntyre, Di

2015-06-09

A key element of the global drive to universal health coverage is ensuring access to needed health services for everyone, and to pursue this goal in an equitable way. This requires concerted efforts to reduce disparities in access through understanding and acting on barriers facing communities with the lowest utilisation levels. Financial barriers dominate the empirical literature on health service access. Unless the full range of access barriers are investigated, efforts to promote equitable access to health care are unlikely to succeed. This paper therefore focuses on exploring the nature and extent of non-financial access barriers. We draw upon two structured literature reviews on barriers to access and utilization of maternal, newborn and child health services in Ghana, Bangladesh, Vietnam and Rwanda. One review analyses access barriers identified in published literature using qualitative research methods; the other in published literature using quantitative analysis of household survey data. We then synthesised the key qualitative and quantitative findings through a conjoint iterative analysis. Five dominant themes on non-financial access barriers were identified: ethnicity; religion; physical accessibility; decision-making, gender and autonomy; and knowledge, information and education. The analysis highlighted that non-financial factors pose considerable barriers to access, many of which relate to the acceptability dimension of access and are challenging to address. Another key finding is that quantitative research methods, while yielding important findings, are inadequate for understanding non-financial access barriers in sufficient detail to develop effective responses. Qualitative research is critical in filling this gap. The analysis also indicates that the nature of non-financial access barriers vary considerably, not only between countries but also between different communities within individual countries. To adequately understand access barriers as a basis for developing effective strategies to address them, mixed-methods approaches are required. From an equity perspective, communities with the lowest utilisation levels should be prioritised and the access barriers specific to that community identified. It is, therefore, critical to develop approaches that can be used at the district level to diagnose and act upon access barriers if we are to pursue an equitable path to universal health coverage.

Quantitative nephelometry

MedlinePlus

... this page: //medlineplus.gov/ency/article/003545.htm Quantitative nephelometry test To use the sharing features on this page, please enable JavaScript. Quantitative nephelometry is a lab test to quickly and ...

Breakthrough Science Enabled by Regular Access to Orbits Beyond Earth

NASA Astrophysics Data System (ADS)

Gorjian, V.

2018-02-01

Regular launches to the Deep Space Gateway (DSG) will enable smallsats to access orbits not currently easily available to low cost missions. These orbits will allow great new science, especially when using the DSG as an optical hub for downlink.

A soft, wearable microfluidic device for the capture, storage, and colorimetric sensing of sweat.

PubMed

Koh, Ahyeon; Kang, Daeshik; Xue, Yeguang; Lee, Seungmin; Pielak, Rafal M; Kim, Jeonghyun; Hwang, Taehwan; Min, Seunghwan; Banks, Anthony; Bastien, Philippe; Manco, Megan C; Wang, Liang; Ammann, Kaitlyn R; Jang, Kyung-In; Won, Phillip; Han, Seungyong; Ghaffari, Roozbeh; Paik, Ungyu; Slepian, Marvin J; Balooch, Guive; Huang, Yonggang; Rogers, John A

2016-11-23

Capabilities in health monitoring enabled by capture and quantitative chemical analysis of sweat could complement, or potentially obviate the need for, approaches based on sporadic assessment of blood samples. Established sweat monitoring technologies use simple fabric swatches and are limited to basic analysis in controlled laboratory or hospital settings. We present a collection of materials and device designs for soft, flexible, and stretchable microfluidic systems, including embodiments that integrate wireless communication electronics, which can intimately and robustly bond to the surface of the skin without chemical and mechanical irritation. This integration defines access points for a small set of sweat glands such that perspiration spontaneously initiates routing of sweat through a microfluidic network and set of reservoirs. Embedded chemical analyses respond in colorimetric fashion to markers such as chloride and hydronium ions, glucose, and lactate. Wireless interfaces to digital image capture hardware serve as a means for quantitation. Human studies demonstrated the functionality of this microfluidic device during fitness cycling in a controlled environment and during long-distance bicycle racing in arid, outdoor conditions. The results include quantitative values for sweat rate, total sweat loss, pH, and concentration of chloride and lactate. Copyright © 2016, American Association for the Advancement of Science.

Elucidation of Peptide-Directed Palladium Surface Structure for Biologically Tunable Nanocatalysts

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

Bedford, Nicholas M.; Ramezani-Dakhel, Hadi; Slocik, Joseph M.

Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, whichmore » was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then eluddated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences« less

Computer vision and machine learning for robust phenotyping in genome-wide studies

PubMed Central

Zhang, Jiaoping; Naik, Hsiang Sing; Assefa, Teshale; Sarkar, Soumik; Reddy, R. V. Chowda; Singh, Arti; Ganapathysubramanian, Baskar; Singh, Asheesh K.

2017-01-01

Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems. PMID:28272456

Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts.

PubMed

Bedford, Nicholas M; Ramezani-Dakhel, Hadi; Slocik, Joseph M; Briggs, Beverly D; Ren, Yang; Frenkel, Anatoly I; Petkov, Valeri; Heinz, Hendrik; Naik, Rajesh R; Knecht, Marc R

2015-05-26

Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then elucidated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences.

Green light for quantitative live-cell imaging in plants.

PubMed

Grossmann, Guido; Krebs, Melanie; Maizel, Alexis; Stahl, Yvonne; Vermeer, Joop E M; Ott, Thomas

2018-01-29

Plants exhibit an intriguing morphological and physiological plasticity that enables them to thrive in a wide range of environments. To understand the cell biological basis of this unparalleled competence, a number of methodologies have been adapted or developed over the last decades that allow minimal or non-invasive live-cell imaging in the context of tissues. Combined with the ease to generate transgenic reporter lines in specific genetic backgrounds or accessions, we are witnessing a blooming in plant cell biology. However, the imaging of plant cells entails a number of specific challenges, such as high levels of autofluorescence, light scattering that is caused by cell walls and their sensitivity to environmental conditions. Quantitative live-cell imaging in plants therefore requires adapting or developing imaging techniques, as well as mounting and incubation systems, such as micro-fluidics. Here, we discuss some of these obstacles, and review a number of selected state-of-the-art techniques, such as two-photon imaging, light sheet microscopy and variable angle epifluorescence microscopy that allow high performance and minimal invasive live-cell imaging in plants. © 2018. Published by The Company of Biologists Ltd.

Direct molecular dynamics simulation of Ge deposition on amorphous SiO 2 at experimentally relevant conditions

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

Chuang, Claire Y.; Zepeda-Ruiz, Luis A.; Han, Sang M.

2015-06-01

Molecular dynamics simulations were used to study Ge island nucleation and growth on amorphous SiO 2 substrates. This process is relevant in selective epitaxial growth of Ge on Si, for which SiO 2 is often used as a template mask. The islanding process was studied over a wide range of temperatures and fluxes, using a recently proposed empirical potential model for the Si–SiO 2–Ge system. The simulations provide an excellent quantitative picture of the Ge islanding and compare well with detailed experimental measurements. These quantitative comparisons were enabled by an analytical rate model as a bridge between simulations and experimentsmore » despite the fact that deposition fluxes accessible in simulations and experiments are necessarily different by many orders of magnitude. In particular, the simulations led to accurate predictions of the critical island size and the scaling of island density as a function of temperature. Lastly, the overall approach used here should be useful not just for future studies in this particular system, but also for molecular simulations of deposition in other materials.« less

The jmzQuantML programming interface and validator for the mzQuantML data standard.

PubMed

Qi, Da; Krishna, Ritesh; Jones, Andrew R

2014-03-01

The mzQuantML standard from the HUPO Proteomics Standards Initiative has recently been released, capturing quantitative data about peptides and proteins, following analysis of MS data. We present a Java application programming interface (API) for mzQuantML called jmzQuantML. The API provides robust bridges between Java classes and elements in mzQuantML files and allows random access to any part of the file. The API provides read and write capabilities, and is designed to be embedded in other software packages, enabling mzQuantML support to be added to proteomics software tools (http://code.google.com/p/jmzquantml/). The mzQuantML standard is designed around a multilevel validation system to ensure that files are structurally and semantically correct for different proteomics quantitative techniques. In this article, we also describe a Java software tool (http://code.google.com/p/mzquantml-validator/) for validating mzQuantML files, which is a formal part of the data standard. © 2014 The Authors. Proteomics published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

2D IR Spectroscopy using Four-Wave Mixing, Pulse Shaping, and IR Upconversion: A Quantitative Comparison

PubMed Central

Rock, William; Li, Yun-Liang; Pagano, Philip; Cheatum, Christopher M.

2013-01-01

Recent technological advances have led to major changes in the apparatuses used to collect 2D IR spectra. Pulse shaping offers several advantages including rapid data collection, inherent phase stability, and phase cycling capabilities. Visible array detection via upconversion allows the use of visible detectors that are cheaper, faster, more sensitive, and less noisy than IR detectors. However, despite these advantages, many researchers are reluctant to implement these technologies. Here we present a quantitative study of the S/N of 2D IR spectra collected with a traditional four-wave mixing (FWM) apparatus, with a pulse shaping apparatus, and with visible detection via upconversion to address the question of whether or not weak chromophores at low concentrations are still accessible with such an apparatus. We find that the enhanced averaging capability of the pulse shaping apparatus enables the detection of small signals that would be challenging to measure even with the traditional FWM apparatus, and we demonstrate this ability on a sample of cyanylated dihydrofolate reductase (DHFR). PMID:23687988

Keep Up or Fall Behind

ERIC Educational Resources Information Center

Ramaswami, Rama

2007-01-01

In the race to enable information access and collaboration, institutions are taking advantage of new tools to drive content management innovation. New content management systems (CMS) features and functions are driving true innovation in content management, and enabling information access, sharing, collaboration, and tracking on a scale heretofore…

The Architecture of Access: A Grounded Theory on the Nature of Access to Early Childhood Services within a Children's Centre, Derived from Nine Parent Voices

ERIC Educational Resources Information Center

Hayward, Kate; Fletcher, Colin; Whalley, Margy; McKinnon, Eddie; Gallagher, Tracy; Prodger, Angela; Donoyou, Heather; Potts, Judy; Young, Elaine

2013-01-01

This was a collaborative action research study by lead staff, researchers and parents at the Pen Green Centre for Children and their Families in England. The study focuses on the factors enabling access to children's services by nine parents from challenging family contexts. The critical questions were: What enabled some parents to overcome…

An eHealth Intervention for Patients in Rural Areas: Preliminary Findings From a Pilot Feasibility Study

PubMed Central

Schrader, Geoffrey; Harris, Melanie; Newman, Lareen; Lynn, Sarah; Peterson, Leigh; Battersby, Malcolm

2014-01-01

Background eHealth facilitation of chronic disease management has potential to increase engagement and effectiveness and extend access to care in rural areas. Objective The objective of this study was to demonstrate the feasibility and acceptability of an eHealth system for the management of chronic conditions in a rural setting. Methods We developed an online management program which incorporated content from the Flinders Chronic Condition Management Program (Flinders Program) and used an existing software platform (goACT), which is accessible by patients and health care workers using either Web-enabled mobile phone or Internet, enabling communication between patients and clinicians. We analyzed the impact of this eHealth system using qualitative and simple quantitative methods. Results The eHealth system was piloted with 8 recently hospitalized patients from rural areas, average age 63 (SD 9) years, each with an average of 5 chronic conditions and high level of psychological distress with an average K10 score of 32.20 (SD 5.81). Study participants interacted with the eHealth system. The average number of logins to the eHealth system by the study participants was 26.4 (SD 23.5) over 29 weeks. The login activity was higher early in the week. Conclusions The pilot demonstrated the feasibility of implementing and delivering a chronic disease management program using a Web-based patient-clinician application. A qualitative analysis revealed burden of illness and low levels of information technology literacy as barriers to patient engagement. PMID:24927511

An eHealth Intervention for Patients in Rural Areas: Preliminary Findings From a Pilot Feasibility Study.

PubMed

Schrader, Geoffrey; Bidargaddi, Niranjan; Harris, Melanie; Newman, Lareen; Lynn, Sarah; Peterson, Leigh; Battersby, Malcolm

2014-06-12

eHealth facilitation of chronic disease management has potential to increase engagement and effectiveness and extend access to care in rural areas. The objective of this study was to demonstrate the feasibility and acceptability of an eHealth system for the management of chronic conditions in a rural setting. We developed an online management program which incorporated content from the Flinders Chronic Condition Management Program (Flinders Program) and used an existing software platform (goACT), which is accessible by patients and health care workers using either Web-enabled mobile phone or Internet, enabling communication between patients and clinicians. We analyzed the impact of this eHealth system using qualitative and simple quantitative methods. The eHealth system was piloted with 8 recently hospitalized patients from rural areas, average age 63 (SD 9) years, each with an average of 5 chronic conditions and high level of psychological distress with an average K10 score of 32.20 (SD 5.81). Study participants interacted with the eHealth system. The average number of logins to the eHealth system by the study participants was 26.4 (SD 23.5) over 29 weeks. The login activity was higher early in the week. The pilot demonstrated the feasibility of implementing and delivering a chronic disease management program using a Web-based patient-clinician application. A qualitative analysis revealed burden of illness and low levels of information technology literacy as barriers to patient engagement.

Students' perceptions of clinical teaching and learning strategies: a Pakistani perspective.

PubMed

Khan, Basnama Ayaz; Ali, Fauziya; Vazir, Nilofar; Barolia, Rubina; Rehan, Seema

2012-01-01

The complexity of the health care environment is increasing with the explosion of technology, coupled with the issues of patients' access, equity, time efficiency, and cost containment. Nursing education must focus on means that enable students to develop the processes of active learning, problem-solving, and critical thinking, in order to enable them to deal with the complexities. This study aims at identifying the nursing students' perceptions about the effectiveness of utilized teaching and learning strategies of clinical education, in improving students' knowledge, skills, and attitudes. A descriptive cross sectional study design was utilized using both qualitative and quantitative approaches. Data were collected from 74 students, using a questionnaire that was developed for the purpose of the study and analyzed using descriptive and non-parametric statistics. The findings revealed that demonstration was the most effective strategy for improving students' skills; reflection, for improving attitudes; and problem based learning and concept map for improving their knowledge. Students' responses to open-ended questions confirmed the effectiveness of these strategies in improving their learning outcomes. Recommendations have been provided based on the findings. Copyright © 2011 Elsevier Ltd. All rights reserved.

Quantitative and Qualitative Differences in Morphological Traits Revealed between Diploid Fragaria Species

PubMed Central

SARGENT, DANIEL J.; GEIBEL, M.; HAWKINS, J. A.; WILKINSON, M. J.; BATTEY, N. H.; SIMPSON, D. W.

2004-01-01

• Background and Aims The aims of this investigation were to highlight the qualitative and quantitative diversity apparent between nine diploid Fragaria species and produce interspecific populations segregating for a large number of morphological characters suitable for quantitative trait loci analysis. • Methods A qualitative comparison of eight described diploid Fragaria species was performed and measurements were taken of 23 morphological traits from 19 accessions including eight described species and one previously undescribed species. A principal components analysis was performed on 14 mathematically unrelated traits from these accessions, which partitioned the species accessions into distinct morphological groups. Interspecific crosses were performed with accessions of species that displayed significant quantitative divergence and, from these, populations that should segregate for a range of quantitative traits were raised. • Key Results Significant differences between species were observed for all 23 morphological traits quantified and three distinct groups of species accessions were observed after the principal components analysis. Interspecific crosses were performed between these groups, and F2 and backcross populations were raised that should segregate for a range of morphological characters. In addition, the study highlighted a number of distinctive morphological characters in many of the species studied. • Conclusions Diploid Fragaria species are morphologically diverse, yet remain highly interfertile, making the group an ideal model for the study of the genetic basis of phenotypic differences between species through map-based investigation using quantitative trait loci. The segregating interspecific populations raised will be ideal for such investigations and could also provide insights into the nature and extent of genome evolution within this group. PMID:15469944

Risk Assessment and Integration Team (RAIT) Portfolio Risk Analysis Strategy

NASA Technical Reports Server (NTRS)

Edwards, Michelle

2010-01-01

Impact at management level: Qualitative assessment of risk criticality in conjunction with risk consequence, likelihood, and severity enable development of an "investment policy" towards managing a portfolio of risks. Impact at research level: Quantitative risk assessments enable researchers to develop risk mitigation strategies with meaningful risk reduction results. Quantitative assessment approach provides useful risk mitigation information.

Quantitative Glycomics Strategies*

PubMed Central

Mechref, Yehia; Hu, Yunli; Desantos-Garcia, Janie L.; Hussein, Ahmed; Tang, Haixu

2013-01-01

The correlations between protein glycosylation and many biological processes and diseases are increasing the demand for quantitative glycomics strategies enabling sensitive monitoring of changes in the abundance and structure of glycans. This is currently attained through multiple strategies employing several analytical techniques such as capillary electrophoresis, liquid chromatography, and mass spectrometry. The detection and quantification of glycans often involve labeling with ionic and/or hydrophobic reagents. This step is needed in order to enhance detection in spectroscopic and mass spectrometric measurements. Recently, labeling with stable isotopic reagents has also been presented as a very viable strategy enabling relative quantitation. The different strategies available for reliable and sensitive quantitative glycomics are herein described and discussed. PMID:23325767

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences.

PubMed

Shieh, Fwu-Shan; Jongeneel, Patrick; Steffen, Jamin D; Lin, Selena; Jain, Surbhi; Song, Wei; Su, Ying-Hsiu

2017-01-01

Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq's pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community.

ChimericSeq: An open-source, user-friendly interface for analyzing NGS data to identify and characterize viral-host chimeric sequences

PubMed Central

Shieh, Fwu-Shan; Jongeneel, Patrick; Steffen, Jamin D.; Lin, Selena; Jain, Surbhi; Song, Wei

2017-01-01

Identification of viral integration sites has been important in understanding the pathogenesis and progression of diseases associated with particular viral infections. The advent of next-generation sequencing (NGS) has enabled researchers to understand the impact that viral integration has on the host, such as tumorigenesis. Current computational methods to analyze NGS data of virus-host junction sites have been limited in terms of their accessibility to a broad user base. In this study, we developed a software application (named ChimericSeq), that is the first program of its kind to offer a graphical user interface, compatibility with both Windows and Mac operating systems, and optimized for effectively identifying and annotating virus-host chimeric reads within NGS data. In addition, ChimericSeq’s pipeline implements custom filtering to remove artifacts and detect reads with quantitative analytical reporting to provide functional significance to discovered integration sites. The improved accessibility of ChimericSeq through a GUI interface in both Windows and Mac has potential to expand NGS analytical support to a broader spectrum of the scientific community. PMID:28829778

Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues

PubMed Central

Steiner, Carine; Ducret, Axel; Tille, Jean-Christophe; Thomas, Marlene; McKee, Thomas A; Rubbia-Brandt, Laura A; Scherl, Alexander; Lescuyer, Pierre; Cutler, Paul

2014-01-01

Proteomic analysis of tissues has advanced in recent years as instruments and methodologies have evolved. The ability to retrieve peptides from formalin-fixed paraffin-embedded tissues followed by shotgun or targeted proteomic analysis is offering new opportunities in biomedical research. In particular, access to large collections of clinically annotated samples should enable the detailed analysis of pathologically relevant tissues in a manner previously considered unfeasible. In this paper, we review the current status of proteomic analysis of formalin-fixed paraffin-embedded tissues with a particular focus on targeted approaches and the potential for this technique to be used in clinical research and clinical diagnosis. We also discuss the limitations and perspectives of the technique, particularly with regard to application in clinical diagnosis and drug discovery. PMID:24339433

OIPAV: an integrated software system for ophthalmic image processing, analysis and visualization

NASA Astrophysics Data System (ADS)

Zhang, Lichun; Xiang, Dehui; Jin, Chao; Shi, Fei; Yu, Kai; Chen, Xinjian

2018-03-01

OIPAV (Ophthalmic Images Processing, Analysis and Visualization) is a cross-platform software which is specially oriented to ophthalmic images. It provides a wide range of functionalities including data I/O, image processing, interaction, ophthalmic diseases detection, data analysis and visualization to help researchers and clinicians deal with various ophthalmic images such as optical coherence tomography (OCT) images and color photo of fundus, etc. It enables users to easily access to different ophthalmic image data manufactured from different imaging devices, facilitate workflows of processing ophthalmic images and improve quantitative evaluations. In this paper, we will present the system design and functional modules of the platform and demonstrate various applications. With a satisfying function scalability and expandability, we believe that the software can be widely applied in ophthalmology field.

SE-FIT

NASA Technical Reports Server (NTRS)

Chen, Yongkang; Weislogel, Mark; Schaeffer, Ben; Semerjian, Ben; Yang, Lihong; Zimmerli, Gregory

2012-01-01

The mathematical theory of capillary surfaces has developed steadily over the centuries, but it was not until the last few decades that new technologies have put a more urgent demand on a substantially more qualitative and quantitative understanding of phenomena relating to capillarity in general. So far, the new theory development successfully predicts the behavior of capillary surfaces for special cases. However, an efficient quantitative mathematical prediction of capillary phenomena related to the shape and stability of geometrically complex equilibrium capillary surfaces remains a significant challenge. As one of many numerical tools, the open-source Surface Evolver (SE) algorithm has played an important role over the last two decades. The current effort was undertaken to provide a front-end to enhance the accessibility of SE for the purposes of design and analysis. Like SE, the new code is open-source and will remain under development for the foreseeable future. The ultimate goal of the current Surface Evolver Fluid Interface Tool (SEFIT) development is to build a fully integrated front-end with a set of graphical user interface (GUI) elements. Such a front-end enables the access to functionalities that are developed along with the GUIs to deal with pre-processing, convergence computation operation, and post-processing. In other words, SE-FIT is not just a GUI front-end, but an integrated environment that can perform sophisticated computational tasks, e.g. importing industry standard file formats and employing parameter sweep functions, which are both lacking in SE, and require minimal interaction by the user. These functions are created using a mixture of Visual Basic and the SE script language. These form the foundation for a high-performance front-end that substantially simplifies use without sacrificing the proven capabilities of SE. The real power of SE-FIT lies in its automated pre-processing, pre-defined geometries, convergence computation operation, computational diagnostic tools, and crash-handling capabilities to sustain extensive computations. SE-FIT performance is enabled by its so-called file-layer mechanism. During the early stages of SE-FIT development, it became necessary to modify the original SE code to enable capabilities required for an enhanced and synchronized communication. To this end, a file-layer was created that serves as a command buffer to ensure a continuous and sequential execution of commands sent from the front-end to SE. It also establishes a proper means for handling crashes. The file layer logs input commands and SE output; it also supports user interruption requests, back and forward operation (i.e. undo and redo), and others. It especially enables the batch mode computation of a series of equilibrium surfaces and the searching of critical parameter values in studying the stability of capillary surfaces. In this way, the modified SE significantly extends the capabilities of the original SE.

Expanding access to off-grid rural electrification in Africa: An analysis of community-based micro-grids in Kenya

NASA Astrophysics Data System (ADS)

Kirubi, Charles Gathu

Community micro-grids have played a central role in increasing access to off-grid rural electrification (RE) in many regions of the developing world, notably South Asia. However, the promise of community micro-grids in sub-Sahara Africa remains largely unexplored. My study explores the potential and limits of community micro-grids as options for increasing access to off-grid RE in sub-Sahara Africa. Contextualized in five community micro-grids in rural Kenya, my study is framed through theories of collective action and combines qualitative and quantitative methods, including household surveys, electronic data logging and regression analysis. The main contribution of my research is demonstrating the circumstances under which community micro-grids can contribute to rural development and the conditions under which individuals are likely to initiate and participate in such projects collectively. With regard to rural development, I demonstrate that access to electricity enables the use of electric equipment and tools by small and micro-enterprises, resulting in significant improvement in productivity per worker (100--200% depending on the task at hand) and a corresponding growth in income levels in the order of 20--70%, depending on the product made. Access to electricity simultaneously enables and improves delivery of social and business services from a wide range of village-level infrastructure (e.g. schools, markets, water pumps) while improving the productivity of agricultural activities. Moreover, when local electricity users have an ability to charge and enforce cost-reflective tariffs and electricity consumption is closely linked to productive uses that generate incomes, cost recovery is feasible. By their nature---a new technology delivering highly valued services by the elites and other members, limited local experience and expertise, high capital costs---community micro-grids are good candidates for elite-domination. Even so, elite control does not necessarily lead to elite capture. Experiences from different micro-grid settings illustrate the manner in which a coincidence of interest between the elites and the rest of members and access to external support can create incentives and mechanisms to enable community-wide access to scarce services, hence mitigating elite capture. Moreover, access to external support was found to increase the likelihood of participation for the relatively poor households. The policy-relevant message from this research is two-fold. In rural areas with suitable sites for micro-hydro power, the potential for community micro-grids appear considerable to the extent that this option would seem to represent "the road not taken" as far as policies and initiatives aimed at expanding RE are concerned in Kenya and other African countries with comparable settings. However, local participatory initiatives not complimented by external technical assistance run a considerable risk of locking rural households into relatively more costly and poor-quality services. By taking advantage of existing and/or building a dense network of local organizations, including micro-finance agencies, the government and development partners can make available to local communities the necessary support---financial, technical or regulatory---essential for efficient design of micro-grids in addition to facilitating equitable distribution of electricity benefits.

NCBI2RDF: enabling full RDF-based access to NCBI databases.

PubMed

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.

Purdue ionomics information management system. An integrated functional genomics platform.

PubMed

Baxter, Ivan; Ouzzani, Mourad; Orcun, Seza; Kennedy, Brad; Jandhyala, Shrinivas S; Salt, David E

2007-02-01

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.

Avoiding the Peril of Publishing Qualitative Scholarship in Predatory Journals

ERIC Educational Resources Information Center

Beall, Jeffrey

2013-01-01

Scholarly communication is caught between the traditions of the past and the possibilities of the future. Specifically, scholarly open-access publishing is enabling greater access to research but, at the same time, is enabling an abundance of low quality publishers and an apparent increase in author misconduct. In this article I examine six…

Service composition towards increasing end-user accessibility.

PubMed

Kaklanis, Nikolaos; Votis, Konstantinos; Tzovaras, Dimitrios

2015-01-01

This paper presents the Cloud4all Service Synthesizer Tool, a framework that enables efficient orchestration of accessibility services, as well as their combination into complex forms, providing more advanced functionalities towards increasing the accessibility of end-users with various types of functional limitations. The supported services are described formally within an ontology, enabling, thus, semantic service composition. The proposed service composition approach is based on semantic matching between services specifications on the one hand and user needs/preferences and current context of use on the other hand. The use of automatic composition of accessibility services can significantly enhance end-users' accessibility, especially in cases where assistive solutions are not available in their device.

Improving access and continuity of care for homeless people: how could general practitioners effectively contribute? Results from a mixed study

PubMed Central

Grassineau, Dominique; Balique, Hubert; Loundou, Anderson; Sambuc, Roland; Daguzan, Alexandre; Gentile, Gaetan; Gentile, Stéphanie

2016-01-01

Objectives To analyse the views of general practitioners (GPs) about how they can provide care to homeless people (HP) and to explore which measures could influence their views. Design Mixed-methods design (qualitative –> quantitative (cross-sectional observational) → qualitative). Qualitative data were collected through semistructured interviews and through questionnaires with closed questions. Quantitative data were analysed with descriptive statistical analyses on SPPS; a content analysis was applied on qualitative data. Setting Primary care; views of urban GPs working in a deprived area in Marseille were explored by questionnaires and/or semistructured interview. Participants 19 GPs involved in HP's healthcare were recruited for phase 1 (qualitative); for phase 2 (quantitative), 150 GPs who provide routine healthcare (‘standard’ GPs) were randomised, 144 met the inclusion criteria and 105 responded to the questionnaire; for phase 3 (qualitative), data were explored on 14 ‘standard’ GPs. Results In the quantitative phase, 79% of the 105 GPs already treated HP. Most of the difficulties they encountered while treating HP concerned social matters (mean level of perceived difficulties=3.95/5, IC 95 (3.74 to 4.17)), lack of medical information (mn=3.78/5, IC 95 (3.55 to 4.01)) patient's compliance (mn=3.67/5, IC 95 (3.45 to 3.89)), loneliness in practice (mn=3.45/5, IC 95 (3.18 to 3.72)) and time required for the doctor (mn=3.25, IC 95 (3 to 3.5)). From qualitative analysis we understood that maintaining a stable follow-up was a major condition for GPs to contribute effectively to the care of HP. Acting on health system organisation, developing a medical and psychosocial approach with closer relation with social workers and enhancing the collaboration between tailored and non-tailored programmes were also other key answers. Conclusions If we adapt the conditions of GPs practice, they could contribute to the improvement of HP's health. These results will enable the construction of a new model of primary care organisation aiming to improve access to healthcare for HP. PMID:27903566

CILogon: An Integrated Identity and Access Management Platform for Science

NASA Astrophysics Data System (ADS)

Basney, J.

2016-12-01

When scientists work together, they use web sites and other software to share their ideas and data. To ensure the integrity of their work, these systems require the scientists to log in and verify that they are part of the team working on a particular science problem. Too often, the identity and access verification process is a stumbling block for the scientists. Scientific research projects are forced to invest time and effort into developing and supporting Identity and Access Management (IAM) services, distracting them from the core goals of their research collaboration. CILogon provides an IAM platform that enables scientists to work together to meet their IAM needs more effectively so they can allocate more time and effort to their core mission of scientific research. The CILogon platform enables federated identity management and collaborative organization management. Federated identity management enables researchers to use their home organization identities to access cyberinfrastructure, rather than requiring yet another username and password to log on. Collaborative organization management enables research projects to define user groups for authorization to collaboration platforms (e.g., wikis, mailing lists, and domain applications). CILogon's IAM platform serves the unique needs of research collaborations, namely the need to dynamically form collaboration groups across organizations and countries, sharing access to data, instruments, compute clusters, and other resources to enable scientific discovery. CILogon provides a software-as-a-service platform to ease integration with cyberinfrastructure, while making all software components publicly available under open source licenses to enable re-use. Figure 1 illustrates the components and interfaces of this platform. CILogon has been operational since 2010 and has been used by over 7,000 researchers from more than 170 identity providers to access cyberinfrastructure including Globus, LIGO, Open Science Grid, SeedMe, and XSEDE. The "CILogon 2.0" platform, launched in 2016, adds support for virtual organization (VO) membership management, identity linking, international collaborations, and standard integration protocols, through integration with the Internet2 COmanage collaboration software.

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments. PMID:23984425

Enabling access to new WHO essential medicines: the case for nicotine replacement therapies

PubMed Central

2010-01-01

Nicotine replacement therapies (NRT) are powerful tools for the successful treatment of nicotine addiction and tobacco use. The medicines are clinically effective, supported by the Framework Convention on Tobacco Control, and are now World Health Organization-approved essential medicines. Enabling global access to NRT remains a challenge given ongoing confusion and misperceptions about their efficacy, cost-effectiveness, and availability with respect to other tobacco control and public health opportunities. In this commentary, we review existing evidence and guidelines to make the case for global access to NRT highlighting the smoker's right to access treatment to sensibly address nicotine addiction. PMID:21092092

Educational Access in India. Country Policy Brief

ERIC Educational Resources Information Center

Online Submission, 2009

2009-01-01

This Policy Brief describes and explains patterns of access to schools in India. It outlines policy and legislation on access to education and provides an analysis of access, vulnerability and exclusion. The quantitative data is supported by a review of research which explains the patterns of access and exclusion. It is based on findings from the…

Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions.

PubMed

Zakrzewski, Martha; Proietti, Carla; Ellis, Jonathan J; Hasan, Shihab; Brion, Marie-Jo; Berger, Bernard; Krause, Lutz

2017-03-01

Calypso is an easy-to-use online software suite that allows non-expert users to mine, interpret and compare taxonomic information from metagenomic or 16S rDNA datasets. Calypso has a focus on multivariate statistical approaches that can identify complex environment-microbiome associations. The software enables quantitative visualizations, statistical testing, multivariate analysis, supervised learning, factor analysis, multivariable regression, network analysis and diversity estimates. Comprehensive help pages, tutorials and videos are provided via a wiki page. The web-interface is accessible via http://cgenome.net/calypso/ . The software is programmed in Java, PERL and R and the source code is available from Zenodo ( https://zenodo.org/record/50931 ). The software is freely available for non-commercial users. l.krause@uq.edu.au. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Asymmetric counteranion-directed Lewis acid organocatalysis for the scalable cyanosilylation of aldehydes

NASA Astrophysics Data System (ADS)

Zhang, Zhipeng; Bae, Han Yong; Guin, Joyram; Rabalakos, Constantinos; van Gemmeren, Manuel; Leutzsch, Markus; Klussmann, Martin; List, Benjamin

2016-08-01

Due to the high versatility of chiral cyanohydrins, the catalytic asymmetric cyanation reaction of carbonyl compounds has attracted widespread interest. However, efficient protocols that function at a preparative scale with low catalyst loading are still rare. Here, asymmetric counteranion-directed Lewis acid organocatalysis proves to be remarkably successful in addressing this problem and enabled a molar-scale cyanosilylation in quantitative yield and with excellent enantioselectivity. Also, the catalyst loading could be lowered to a part-per-million level (50 ppm: 0.005 mol%). A readily accessible chiral disulfonimide was used, which in combination with trimethylsilyl cyanide, turned into the active silylium Lewis acid organocatalyst. The nature of a peculiar phenomenon referred to as a ``dormant period'', which is mainly induced by water, was systematically investigated by means of in situ Fourier transform infrared analysis.

Measuring the effectiveness and impact of an open innovation platform.

PubMed

Carroll, Glenn P; Srivastava, Sanjay; Volini, Adam S; Piñeiro-Núñez, Marta M; Vetman, Tatiana

2017-05-01

Today, most pharmaceutical companies complement their traditional R&D models with some variation on the Open Innovation (OI) approach in an effort to better access global scientific talent, ideas and hypotheses. Traditional performance indicators that measure economic returns from R&D through commercialization are often not applicable to the practical assessment of these OI approaches, particularly within the context of early drug discovery. This leaves OI programs focused on early R&D without a standard assessment framework from which to evaluate overall performance. This paper proposes a practical dashboard for such assessment, encompassing quantitative and qualitative elements, to enable decision-making and improvement of future performance. The use of this dashboard is illustrated using real-time data from the Lilly Open Innovation Drug Discovery (OIDD) program. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Quantitation of Cellular Dynamics in Growing Arabidopsis Roots with Light Sheet Microscopy

PubMed Central

Birnbaum, Kenneth D.; Leibler, Stanislas

2011-01-01

To understand dynamic developmental processes, living tissues have to be imaged frequently and for extended periods of time. Root development is extensively studied at cellular resolution to understand basic mechanisms underlying pattern formation and maintenance in plants. Unfortunately, ensuring continuous specimen access, while preserving physiological conditions and preventing photo-damage, poses major barriers to measurements of cellular dynamics in growing organs such as plant roots. We present a system that integrates optical sectioning through light sheet fluorescence microscopy with hydroponic culture that enables us to image, at cellular resolution, a vertically growing Arabidopsis root every few minutes and for several consecutive days. We describe novel automated routines to track the root tip as it grows, to track cellular nuclei and to identify cell divisions. We demonstrate the system's capabilities by collecting data on divisions and nuclear dynamics. PMID:21731697

Focal spot size reduction using asymmetric collimation to enable reduced anode angles with a conventional angiographic x-ray tube for use with high resolution detectors.

PubMed

Russ, M; Shankar, A; Setlur Nagesh, S V; Ionita, C N; Bednarek, D R; Rudin, S

2017-02-11

The high-resolution requirements for neuro-endovascular image-guided interventions (EIGIs) necessitate the use of a small focal-spot size; however, the maximum tube output limits for such small focal-spot sizes may not enable sufficient x-ray fluence after attenuation through the human head to support the desired image quality. This may necessitate the use of a larger focal spot, thus contributing to the overall reduction in resolution. A method for creating a higher-output small effective focal spot based on the line-focus principle has been demonstrated and characterized. By tilting the C-arm gantry, the anode-side of the x-ray field-of-view is accessible using a detector placed off-axis. This tilted central axis diminishes the resultant focal spot size in the anode-cathode direction by the tangent of the effective anode angle, allowing a medium focal spot to be used in place of a small focal spot with minimal losses in resolution but with increased tube output. Images were acquired of two different objects at the central axis, and with the C-arm tilted away from the central axis at 1° increments from 0°-7°. With standard collimation settings, only 6° was accessible, but using asymmetric extended collimation a maximum of 7° was accessed for enhanced comparisons. All objects were positioned perpendicular to the anode-cathode direction and images were compared qualitatively. The increasing advantage of the off-axis focal spots was quantitatively evidenced at each subsequent angle using the Generalized Measured-Relative Object Detectability metric (GM-ROD). This anode-tilt method is a simple and robust way of increasing tube output for a small field-of-view detector without diminishing the overall apparent resolution for neuro-EIGIs.

Focal spot size reduction using asymmetric collimation to enable reduced anode angles with a conventional angiographic x-ray tube for use with high resolution detectors

NASA Astrophysics Data System (ADS)

Russ, M.; Shankar, A.; Setlur Nagesh, S. V.; Ionita, C. N.; Bednarek, D. R.; Rudin, S.

2017-03-01

The high-resolution requirements for neuro-endovascular image-guided interventions (EIGIs) necessitate the use of a small focal-spot size; however, the maximum tube output limits for such small focal-spot sizes may not enable sufficient x-ray fluence after attenuation through the human head to support the desired image quality. This may necessitate the use of a larger focal spot, thus contributing to the overall reduction in resolution. A method for creating a higher-output small effective focal spot based on the line-focus principle has been demonstrated and characterized. By tilting the C-arm gantry, the anode-side of the x-ray field-of-view is accessible using a detector placed off-axis. This tilted central axis diminishes the resultant focal spot size in the anode-cathode direction by the tangent of the effective anode angle, allowing a medium focal spot to be used in place of a small focal spot with minimal losses in resolution but with increased tube output. Images were acquired of two different objects at the central axis, and with the C-arm tilted away from the central axis at 1° increments from 0°-7°. With standard collimation settings, only 6° was accessible, but using asymmetric extended collimation a maximum of 7° was accessed for enhanced comparisons. All objects were positioned perpendicular to the anode-cathode direction and images were compared qualitatively. The increasing advantage of the off-axis focal spots was quantitatively evidenced at each subsequent angle using the Generalized Measured-Relative Object Detectability metric (GM-ROD). This anode-tilt method is a simple and robust way of increasing tube output for a small field-of-view detector without diminishing the overall apparent resolution for neuro-EIGIs.

Enabling Scientists: Serving Sci-Tech Library Users with Disabilities.

ERIC Educational Resources Information Center

Coonin, Bryna

2001-01-01

Discusses how librarians in scientific and technical libraries can contribute to an accessible electronic library environment for users with disabilities to ensure independent access to information. Topics include relevant assistive technologies; creating accessible Web pages; monitoring accessibility of electronic databases; preparing accessible…

Assessing local capacity to expand rural breast cancer screening and patient navigation: An iterative mixed-method tool.

PubMed

Inrig, Stephen J; Higashi, Robin T; Tiro, Jasmin A; Argenbright, Keith E; Lee, Simon J Craddock

2017-04-01

Despite federal funding for breast cancer screening, fragmented infrastructure and limited organizational capacity hinder access to the full continuum of breast cancer screening and clinical follow-up procedures among rural-residing women. We proposed a regional hub-and-spoke model, partnering with local providers to expand access across North Texas. We describe development and application of an iterative, mixed-method tool to assess county capacity to conduct community outreach and/or patient navigation in a partnership model. Our tool combined publicly-available quantitative data with qualitative assessments during site visits and semi-structured interviews. Application of our tool resulted in shifts in capacity designation in 10 of 17 county partners: 8 implemented local outreach with hub navigation; 9 relied on the hub for both outreach and navigation. Key factors influencing capacity: (1) formal linkages between partner organizations; (2) inter-organizational relationships; (3) existing clinical service protocols; (4) underserved populations. Qualitative data elucidate how our tool captured these capacity changes. Our capacity assessment tool enabled the hub to establish partnerships with county organizations by tailoring support to local capacity and needs. Absent a vertically integrated provider network for preventive services in these rural counties, our tool facilitated a virtually integrated regional network to extend access to breast cancer screening to underserved women. Copyright © 2016 Elsevier Ltd. All rights reserved.

Retrieval of complex χ(2) parts for quantitative analysis of sum-frequency generation intensity spectra

PubMed Central

Hofmann, Matthias J.; Koelsch, Patrick

2015-01-01

Vibrational sum-frequency generation (SFG) spectroscopy has become an established technique for in situ surface analysis. While spectral recording procedures and hardware have been optimized, unique data analysis routines have yet to be established. The SFG intensity is related to probing geometries and properties of the system under investigation such as the absolute square of the second-order susceptibility χ(2)2. A conventional SFG intensity measurement does not grant access to the complex parts of χ(2) unless further assumptions have been made. It is therefore difficult, sometimes impossible, to establish a unique fitting solution for SFG intensity spectra. Recently, interferometric phase-sensitive SFG or heterodyne detection methods have been introduced to measure real and imaginary parts of χ(2) experimentally. Here, we demonstrate that iterative phase-matching between complex spectra retrieved from maximum entropy method analysis and fitting of intensity SFG spectra (iMEMfit) leads to a unique solution for the complex parts of χ(2) and enables quantitative analysis of SFG intensity spectra. A comparison between complex parts retrieved by iMEMfit applied to intensity spectra and phase sensitive experimental data shows excellent agreement between the two methods. PMID:26450297

Quantified Trust Levels for Authentication

NASA Astrophysics Data System (ADS)

Thomas, Ivonne; Menzel, Michael; Meinel, Christoph

Service-oriented Architectures (SOAs) facilitate applications to integrate seamlessly services from collaborating business partners regardless of organizational borders. In order to secure access to these services, mechanisms for authentication and authorisation must be deployed that control the access based on identity-related information. To enable a business partners’ users to access the provided services, an identity federation is often established that enables the brokering of identity information across organisational borders. The establishment of such a federation requires complex agreements and contracts that define common policies, obligations and procedures. Generally, this includes obligations on the authentication process as well.

Quantitative proteomics in cardiovascular research: global and targeted strategies

PubMed Central

Shen, Xiaomeng; Young, Rebeccah; Canty, John M.; Qu, Jun

2014-01-01

Extensive technical advances in the past decade have substantially expanded quantitative proteomics in cardiovascular research. This has great promise for elucidating the mechanisms of cardiovascular diseases (CVD) and the discovery of cardiac biomarkers used for diagnosis and treatment evaluation. Global and targeted proteomics are the two major avenues of quantitative proteomics. While global approaches enable unbiased discovery of altered proteins via relative quantification at the proteome level, targeted techniques provide higher sensitivity and accuracy, and are capable of multiplexed absolute quantification in numerous clinical/biological samples. While promising, technical challenges need to be overcome to enable full utilization of these techniques in cardiovascular medicine. Here we discuss recent advances in quantitative proteomics and summarize applications in cardiovascular research with an emphasis on biomarker discovery and elucidating molecular mechanisms of disease. We propose the integration of global and targeted strategies as a high-throughput pipeline for cardiovascular proteomics. Targeted approaches enable rapid, extensive validation of biomarker candidates discovered by global proteomics. These approaches provide a promising alternative to immunoassays and other low-throughput means currently used for limited validation. PMID:24920501

75 FR 373 - Agency Information Collection Activities; Submission for Office of Management and Budget Review...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-05

... Request; Experimental Study: Presentation of Quantitative Effectiveness Information to Consumers in Direct... clearance. Experimental Study: Presentation of Quantitative Effectiveness Information to Consumers in Direct... research has proposed that providing quantitative information about product efficacy enables consumers to...

Homeless people's access to primary care physiotherapy services: an exploratory, mixed-method investigation using a follow-up qualitative extension to core quantitative research.

PubMed

Dawes, Jo; Deaton, Stuart; Greenwood, Nan

2017-06-30

The purpose of this study was to appraise referrals of homeless patients to physiotherapy services and explore perceptions of barriers to access. This exploratory mixed-method study used a follow-up qualitative extension to core quantitative research design. Over 9 months, quantitative data were gathered from the healthcare records of homeless patients referred to physiotherapy by a general practitioner (GP) practice, including the number of referrals and demographic data of all homeless patients referred. Corresponding physiotherapy records of those people referred to physiotherapy were searched for the outcome of their care. Qualitative semi-structured telephone interviews, based on the quantitative findings, were carried out with staff involved with patient care from the referring GP practice and were used to expand insight into the quantitative findings. Two primary care sites provided data for this study: a GP practice dedicated exclusively to homeless people and the physiotherapy department receiving their referrals. Quantitative data from the healthcare records of 34 homeless patient referrals to physiotherapy were collected and analysed. In addition, five staff involved in patient care were interviewed. 34 referrals of homeless people were made to physiotherapy in a 9-month period. It was possible to match 25 of these to records from the physiotherapy department. Nine (36%) patients did not attend their first appointment; seven (28%) attended an initial appointment, but did not attend a subsequent appointment and were discharged from the service; five (20%) completed treatment and four patients (16%) had ongoing treatment. Semi-structured interviews revealed potential barriers preventing homeless people from accessing physiotherapy services, the complex factors being faced by those making referrals and possible ways to improve physiotherapy access. Homeless people with musculoskeletal problems may fail to access physiotherapy treatment, but opportunities exist to make access to physiotherapy easier. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Natural variation in stomatal abundance of Arabidopsis thaliana includes cryptic diversity for different developmental processes

PubMed Central

Delgado, Dolores; Alonso-Blanco, Carlos; Fenoll, Carmen; Mena, Montaña

2011-01-01

Background and Aims Current understanding of stomatal development in Arabidopsis thaliana is based on mutations producing aberrant, often lethal phenotypes. The aim was to discover if naturally occurring viable phenotypes would be useful for studying stomatal development in a species that enables further molecular analysis. Methods Natural variation in stomatal abundance of A. thaliana was explored in two collections comprising 62 wild accessions by surveying adaxial epidermal cell-type proportion (stomatal index) and density (stomatal and pavement cell density) traits in cotyledons and first leaves. Organ size variation was studied in a subset of accessions. For all traits, maternal effects derived from different laboratory environments were evaluated. In four selected accessions, distinct stomatal initiation processes were quantitatively analysed. Key Results and Conclusions Substantial genetic variation was found for all six stomatal abundance-related traits, which were weakly or not affected by laboratory maternal environments. Correlation analyses revealed overall relationships among all traits. Within each organ, stomatal density highly correlated with the other traits, suggesting common genetic bases. Each trait correlated between organs, supporting supra-organ control of stomatal abundance. Clustering analyses identified accessions with uncommon phenotypic patterns, suggesting differences among genetic programmes controlling the various traits. Variation was also found in organ size, which negatively correlated with cell densities in both organs and with stomatal index in the cotyledon. Relative proportions of primary and satellite lineages varied among the accessions analysed, indicating that distinct developmental components contribute to natural diversity in stomatal abundance. Accessions with similar stomatal indices showed different lineage class ratios, revealing hidden developmental phenotypes and showing that genetic determinants of primary and satellite lineage initiation combine in several ways. This first systematic, comprehensive natural variation survey for stomatal abundance in A. thaliana reveals cryptic developmental genetic variation, and provides relevant relationships amongst stomatal traits and extreme or uncommon accessions as resources for the genetic dissection of stomatal development. PMID:21447490

Typology of person-environment fit constellations: a platform addressing accessibility problems in the built environment for people with functional limitations.

PubMed

Slaug, Björn; Schilling, Oliver; Iwarsson, Susanne; Carlsson, Gunilla

2015-09-02

Making the built environment accessible for all regardless of functional capacity is an important goal for public health efforts. Considerable impediments to achieving this goal suggest the need for valid measurements of acccessibility and for greater attention to the complexity of person-environment fit issues. To address these needs, this study aimed to provide a methodological platform, useful for further research and instrument development within accessibility research. This was accomplished by the construction of a typology of problematic person-environment fit constellations, utilizing an existing methodology developed to assess and analyze accessibility problems in the built environment. By means of qualitative review and statistical methods we classified the person-environment fit components covered by an existing application which targets housing accessibility: the Housing Enabler (HE) instrument. The International Classification of Functioning, Disability and Health (ICF) was used as a conceptual framework. Qualitative classification principles were based on conceptual similarities and for quantitative analysis of similarities, Principal Component Analysis was carried out. We present a typology of problematic person-environment fit constellations classified along three dimensions: 1) accessibility problem range and severity 2) aspects of functioning 3) environmental context. As a result of the classification of the HE components, 48 typical person-environment fit constellations were recognised. The main contribution of this study is the proposed typology of person-environment fit constellations. The typology provides a methodological platform for the identification and quantification of problematic person-environment fit constellations. Its link to the globally accepted ICF classification system facilitates communication within the scientific and health care practice communities. The typology also highlights how relations between aspects of functioning and physical environmental barriers generate typical accessibility problems, and thereby furnishes a reference point for research oriented to how the built environment may be designed to be supportive for activity, participation and health.

Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages.

PubMed

Taminau, Jonatan; Meganck, Stijn; Lazar, Cosmin; Steenhoff, David; Coletta, Alain; Molter, Colin; Duque, Robin; de Schaetzen, Virginie; Weiss Solís, David Y; Bersini, Hugues; Nowé, Ann

2012-12-24

With an abundant amount of microarray gene expression data sets available through public repositories, new possibilities lie in combining multiple existing data sets. In this new context, analysis itself is no longer the problem, but retrieving and consistently integrating all this data before delivering it to the wide variety of existing analysis tools becomes the new bottleneck. We present the newly released inSilicoMerging R/Bioconductor package which, together with the earlier released inSilicoDb R/Bioconductor package, allows consistent retrieval, integration and analysis of publicly available microarray gene expression data sets. Inside the inSilicoMerging package a set of five visual and six quantitative validation measures are available as well. By providing (i) access to uniformly curated and preprocessed data, (ii) a collection of techniques to remove the batch effects between data sets from different sources, and (iii) several validation tools enabling the inspection of the integration process, these packages enable researchers to fully explore the potential of combining gene expression data for downstream analysis. The power of using both packages is demonstrated by programmatically retrieving and integrating gene expression studies from the InSilico DB repository [https://insilicodb.org/app/].

Neuroscience imaging enabled by new highly tunable and high peak power femtosecond lasers

NASA Astrophysics Data System (ADS)

Hakulinen, T.; Klein, J.

2017-02-01

Neuroscience applications benefit from recent developments in industrial femtosecond laser technology. New laser sources provide several megawatts of peak power at wavelength of 1040 nm, which enables simultaneous optogenetics photoactivation of tens or even hundreds of neurons using red shifted opsins. Another recent imaging trend is to move towards longer wavelengths, which would enable access to deeper layers of tissue due to lower scattering and lower absorption in the tissue. Femtosecond lasers pumping a non-collinear optical parametric amplifier (NOPA) enable the access to longer wavelengths with high peak powers. High peak powers of >10 MW at 1300 nm and 1700 nm allow effective 3-photon excitation of green and red shifted calcium indicators respectively and access to deeper, sub-cortex layers of the brain. Early results include in vivo detection of spontaneous activity in hippocampus within an intact mouse brain, where neurons express GCaMP6 activated in a 3-photon process at 1320 nm.

Molecular and agronomic analysis of intraspecific variability in Capsicum baccatum var. pendulum accessions.

PubMed

Leite, P S S; Rodrigues, R; Silva, R N O; Pimenta, S; Medeiros, A M; Bento, C S; Gonçalves, L S A

2016-10-05

Capsicum baccatum is one of the most important chili peppers in South America, since this region is considered to be the center of origin and diversity of this species. In Brazil, C. baccatum has been widely explored by family farmers and there are different local names for each fruit phenotype, such as cambuci and dedo-de-moça (lady's finger). Although very popular among farmers and consumers, C. baccatum has been less extensively studied than other Capsicum species. This study describes the phenotypic and genotypic variability in C. baccatum var. pendulum accessions. Twenty-nine accessions from the Universidade Estadual do Norte Fluminense Darcy Ribeiro gene bank, and one commercial genotype ('BRS-Mari') were evaluated for 53 morphoagronomic descriptors (31 qualitative and 22 quantitative traits). In addition, accessions were genotyped using 30 microsatellite primers. Three accessions from the C. annuum complex were included in the molecular characterization. Nine of 31 qualitative descriptors were monomorphic, while all quantitative descriptors were highly significant different between accessions (P < 0.01). Using the unweighted pair group method using arithmetic averages, four groups were obtained based on multicategoric variables and five groups were obtained based on quantitative variables. In the genotyping analysis, 12 polymorphic simple sequence repeat primers amplified in C. baccatum with dissimilarity between accessions ranging from 0.13 to 0.91, permitting the formation of two distinct groups for Bayesian analysis. These results indicate wide variability among the accessions comparing phenotypic and genotypic data and revealed distinct patterns of dissimilarity between matrices, indicating that both steps are valuable for the characterization of C. baccatum var. pendulum accessions.

Geoscience data visualization and analysis using GeoMapApp

NASA Astrophysics Data System (ADS)

Ferrini, Vicki; Carbotte, Suzanne; Ryan, William; Chan, Samantha

2013-04-01

Increased availability of geoscience data resources has resulted in new opportunities for developing visualization and analysis tools that not only promote data integration and synthesis, but also facilitate quantitative cross-disciplinary access to data. Interdisciplinary investigations, in particular, frequently require visualizations and quantitative access to specialized data resources across disciplines, which has historically required specialist knowledge of data formats and software tools. GeoMapApp (www.geomapapp.org) is a free online data visualization and analysis tool that provides direct quantitative access to a wide variety of geoscience data for a broad international interdisciplinary user community. While GeoMapApp provides access to online data resources, it can also be packaged to work offline through the deployment of a small portable hard drive. This mode of operation can be particularly useful during field programs to provide functionality and direct access to data when a network connection is not possible. Hundreds of data sets from a variety of repositories are directly accessible in GeoMapApp, without the need for the user to understand the specifics of file formats or data reduction procedures. Available data include global and regional gridded data, images, as well as tabular and vector datasets. In addition to basic visualization and data discovery functionality, users are provided with simple tools for creating customized maps and visualizations and to quantitatively interrogate data. Specialized data portals with advanced functionality are also provided for power users to further analyze data resources and access underlying component datasets. Users may import and analyze their own geospatial datasets by loading local versions of geospatial data and can access content made available through Web Feature Services (WFS) and Web Map Services (WMS). Once data are loaded in GeoMapApp, a variety options are provided to export data and/or 2D/3D visualizations into common formats including grids, images, text files, spreadsheets, etc. Examples of interdisciplinary investigations that make use of GeoMapApp visualization and analysis functionality will be provided.

Help seeking in older Asian people with dementia in Melbourne: using the Cultural Exchange Model to explore barriers and enablers.

PubMed

Haralambous, Betty; Dow, Briony; Tinney, Jean; Lin, Xiaoping; Blackberry, Irene; Rayner, Victoria; Lee, Sook-Meng; Vrantsidis, Freda; Lautenschlager, Nicola; Logiudice, Dina

2014-03-01

The prevalence of dementia is increasing in Australia. Limited research is available on access to Cognitive Dementia and Memory Services (CDAMS) for people with dementia from Culturally and Linguistically Diverse (CALD) communities. This study aimed to determine the barriers and enablers to accessing CDAMS for people with dementia and their families of Chinese and Vietnamese backgrounds. Consultations with community members, community workers and health professionals were conducted using the "Cultural Exchange Model" framework. For carers, barriers to accessing services included the complexity of the health system, lack of time, travel required to get to services, language barriers, interpreters and lack of knowledge of services. Similarly, community workers and health professionals identified language, interpreters, and community perceptions as key barriers to service access. Strategies to increase knowledge included providing information via radio, printed material and education in community group settings. The "Cultural Exchange Model" enabled engagement with and modification of the approaches to meet the needs of the targeted CALD communities.

47 CFR 54.601 - Eligibility.

Code of Federal Regulations, 2011 CFR

2011-10-01

...). (2) Internet access and limited toll-free access to internet. (i) For purposes of this subpart, eligible Internet access is an information service that enables rural health care providers to post their...) Internet access shall be eligible for universal service support under § 54.621(a). (iii) Limited toll-free...

7 CFR 1739.3 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... terrestrial technology having the capacity to provide transmission facilities that enable subscribers of the...) Computer Access Points and wireless access, that is used for the purposes of providing free access to and..., and after normal working hours and on Saturdays or Sunday. Computer Access Point means a new computer...

TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network

PubMed Central

Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L.; Costanzo, Michael; Andrews, Brenda; Boone, Charles

2017-01-01

Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae. In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. PMID:28325812

TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network.

PubMed

Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L; Costanzo, Michael; Andrews, Brenda; Boone, Charles

2017-05-05

Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. Copyright © 2017 Usaj et al.

An optimized framework for quantitative magnetization transfer imaging of the cervical spinal cord in vivo

PubMed Central

Grussu, Francesco; Ianus, Andrada; Schneider, Torben; Prados, Ferran; Fairney, James; Ourselin, Sebastien; Alexander, Daniel C.; Cercignani, Mara; Gandini Wheeler‐Kingshott, Claudia A.M.; Samson, Rebecca S.

2017-01-01

Purpose To develop a framework to fully characterize quantitative magnetization transfer indices in the human cervical cord in vivo within a clinically feasible time. Methods A dedicated spinal cord imaging protocol for quantitative magnetization transfer was developed using a reduced field‐of‐view approach with echo planar imaging (EPI) readout. Sequence parameters were optimized based in the Cramer‐Rao‐lower bound. Quantitative model parameters (i.e., bound pool fraction, free and bound pool transverse relaxation times [ T2F, T2B], and forward exchange rate [k FB]) were estimated implementing a numerical model capable of dealing with the novelties of the sequence adopted. The framework was tested on five healthy subjects. Results Cramer‐Rao‐lower bound minimization produces optimal sampling schemes without requiring the establishment of a steady‐state MT effect. The proposed framework allows quantitative voxel‐wise estimation of model parameters at the resolution typically used for spinal cord imaging (i.e. 0.75 × 0.75 × 5 mm3), with a protocol duration of ∼35 min. Quantitative magnetization transfer parametric maps agree with literature values. Whole‐cord mean values are: bound pool fraction = 0.11(±0.01), T2F = 46.5(±1.6) ms, T2B = 11.0(±0.2) µs, and k FB = 1.95(±0.06) Hz. Protocol optimization has a beneficial effect on reproducibility, especially for T2B and k FB. Conclusion The framework developed enables robust characterization of spinal cord microstructure in vivo using qMT. Magn Reson Med 79:2576–2588, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:28921614

Young Children's Everyday Concepts of the Internet: A Platform for Cyber-Safety Education in the Early Years

ERIC Educational Resources Information Center

Edwards, Susan; Nolan, Andrea; Henderson, Michael; Mantilla, Ana; Plowman, Lydia; Skouteris, Helen

2018-01-01

Young children from around the world are accessing the internet in ever increasing numbers. The rapid increase in internet activity by children aged 4-5 years in particular is due to the ease access enabled them by touchscreen internet-enabled tablet technologies. With young children now online, often independently of adult supervision, the need…

Attitude and confidence of undergraduate medical programme educators to practice and teach evidence-based healthcare: a cross-sectional survey.

PubMed

Young, Taryn; Esterhuizen, Tonya M; Volmink, Jimmy; Clarke, Mike

2016-06-01

Medical student educators play critical roles in evidence-based healthcare (EBHC) teaching and learning and as role models practicing EBHC. This study assessed their confidence to practice and teach EBHC, their attitude to EBHC and barriers to practicing and teaching EBHC. We conducted a cross-sectional online survey of educators of undergraduate medical students at a South African academic institution. STATA 12 was used for quantitative data analysis. Responses to open-ended questions were coded, and further interpretation done using thematic content analysis. Forty two (19%) educators from various departments responded to the invitation sent to everyone formally involved in teaching undergraduate medical students. They had high levels of knowledge and understanding of EBHC. Many had received training in teaching and learning approaches, although EBHC training received was mainly on enabling competencies. Limitations to practicing EBHC included lack of time, clinical workload, limited access to Internet and resources, knowledge and skills. One quarter of the respondents indicated that they teach EBHC. Perceived barriers to teaching EBHC reported related to students (e.g. lack of interest), context (e.g. access to databases) and educators (e.g. competing priorities). Respondents' suggestions for support included reliable Internet access, easy point-of-care access to databases and resources, increasing awareness of EBHC, building capacity to practice and facilitate learning of EBHC and a supportive community of practice. Educators play a critical role in facilitating EBHC learning not just in the classroom, but also in practice. Without adequate support, training and development, they are ill equipped to be the role models future healthcare professionals need.

Health information needs of professional nurses required at the point of care.

PubMed

Ricks, Esmeralda; ten Ham, Wilma

2015-06-11

Professional nurses work in dynamic environments and need to keep up to date with relevant information for practice in nursing to render quality patient care. Keeping up to date with current information is often challenging because of heavy workload, diverse information needs and the accessibility of the required information at the point of care. The aim of the study was to explore and describe the information needs of professional nurses at the point of care in order to make recommendations to stakeholders to develop a mobile library accessible by means of smart phones when needed. The researcher utilised a quantitative, descriptive survey design to conduct this study. The target population comprised 757 professional nurses employed at a state hospital. Simple random sampling was used to select a sample of the wards, units and departments for inclusion in the study. A convenience sample of 250 participants was selected. Two hundred and fifty structured self-administered questionnaires were distributed amongst the participants. Descriptive statistics were used to analyse the data. A total of 136 completed questionnaires were returned. The findings highlighted the types and accessible sources of information. Information needs of professional nurses were identified such as: extremely drug-resistant tuberculosis, multi-drug-resistant tuberculosis, HIV, antiretrovirals and all chronic lifestyle diseases. This study has enabled the researcher to identify the information needs required by professional nurses at the point of care to enhance the delivery of patient care. The research results were used to develop a mobile library that could be accessed by professional nurses.

Purdue Ionomics Information Management System. An Integrated Functional Genomics Platform1[C][W][OA

PubMed Central

Baxter, Ivan; Ouzzani, Mourad; Orcun, Seza; Kennedy, Brad; Jandhyala, Shrinivas S.; Salt, David E.

2007-01-01

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics. PMID:17189337

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

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

Rubel, Oliver; Greiner, Annette; Cholia, Shreyas

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data accessmore » (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.« less

Utilizing Fission Technology to Enable Rapid and Affordable Access to any Point in the Solar System

NASA Technical Reports Server (NTRS)

Houts, Mike; Bonometti, Joe; Morton, Jeff; Hrbud, Ivana; Bitteker, Leo; VanDyke, Melissa; Godfroy, T.; Pedersen, K.; Dobson, C.; Patton, B.;

Open Access Theses in Institutional Repositories: An Exploratory Study of the Perceptions of Doctoral Students

ERIC Educational Resources Information Center

Stanton, Kate Valentine; Liew, Chern Li

2011-01-01

Introduction: We examine doctoral students' awareness of and attitudes to open access forms of publication. Levels of awareness of open access and the concept of institutional repositories, publishing behaviour and perceptions of benefits and risks of open access publishing were explored. Method: Qualitative and quantitative data were collected…

Addressing legal and policy barriers to male circumcision for adolescent boys in South Africa.

PubMed

Strode, A E; Toohey, J D; Slack, C M

2016-12-01

With millions of adolescents becoming infected with HIV globally, it is essential that barriers to much-needed interventions are reduced for at-risk adolescents. In this article we review the legal and policy framework in South Africa for adolescent access to male circumcision. We are of the view that the framework does confer protection for adolescent boys while enabling access to male circumcision; however, we identify ambiguities and tensions that exist between the Children's Act, regulations and national guidelines. We recommend reform to further enable access by this vulnerable group to this prevention modality.

AFSC Standardization Conference, 1553, 1589, 1750, 1760, Ada, November 18-20, 1980, Dayton Convention Center, Dayton, Ohio, Volume II. Proceedings Standards,

DTIC Science & Technology

1980-11-01

4006 DMAE Direct Memory Access Enable: ’Ibis command enables direct memory access (DMA). 4007 I)MAi) Direct Memory Access Disable: This command...72 DLI 72 DLR 72 DM 111 DMAD 30 DMAE 30 DMR 111 ONEG 103 DR 117 DS 104 OSAR 53 141 373 ’., M1L-STD-1750A (USAF) 2 July 1980 OSBI 29 OSCR 54 OSIC 48...in 4.7.7, the connectors shall show no defects detrimental to the operation of the connectors and shall A-7 461 -meet the subsequent test requirements

Building a Generic Virtual Research Environment Framework for Multiple Earth and Space Science Domains and a Diversity of Users.

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Fraser, R.; Evans, B. J. K.; Friedrich, C.; Klump, J. F.; Lescinsky, D. T.

2017-12-01

Virtual Research Environments (VREs) are now part of academic infrastructures. Online research workflows can be orchestrated whereby data can be accessed from multiple external repositories with processing taking place on public or private clouds, and centralised supercomputers using a mixture of user codes, and well-used community software and libraries. VREs enable distributed members of research teams to actively work together to share data, models, tools, software, workflows, best practices, infrastructures, etc. These environments and their components are increasingly able to support the needs of undergraduate teaching. External to the research sector, they can also be reused by citizen scientists, and be repurposed for industry users to help accelerate the diffusion and hence enable the translation of research innovations. The Virtual Geophysics Laboratory (VGL) in Australia was started in 2012, built using a collaboration between CSIRO, the National Computational Infrastructure (NCI) and Geoscience Australia, with support funding from the Australian Government Department of Education. VGL comprises three main modules that provide an interface to enable users to first select their required data; to choose a tool to process that data; and then access compute infrastructure for execution. VGL was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools. Over the years it has evolved into a multi-purpose Earth science platform with access to an increased variety of data (e.g., Natural Hazards, Geochemistry), a broader range of software packages, and an increasing diversity of compute infrastructures. This expansion has been possible because of the approach to loosely couple data, tools and compute resources via interfaces that are built on international standards and accessed as network-enabled services wherever possible. Built originally for researchers that were not fussy about general usability, increasing emphasis on User Interfaces (UIs) and stability will lead to increased uptake in the education and industry sectors. Simultaneously, improvements are being added to facilitate access to data and tools by experienced researchers who want direct access to both data and flexible workflows.

The impact of mobility assistive technology devices on participation for individuals with disabilities.

PubMed

Carver, Jordan; Ganus, Ashley; Ivey, Jon Mark; Plummer, Teresa; Eubank, Ann

2016-08-01

This study aims to address the gap in research and contribute to the body of knowledge on the perspectives assistive technology device users have toward their devices. Mixed methods were used to better understand the impact of mobility assistive technology devices (MATDs) on participation for individuals with disabilities. The Functional Mobility Assessment was administered in conjunction with two qualitative questions developed by the research team allowing participants to expound on the impact of their MATD experience. Participants were recruited online via the National Spinal Cord Injury Association website and in-person at Abilities Expo in Atlanta, Georgia, and the International Seating Symposium in Nashville, Tennessee. Results are consistent with findings from prior research regarding accessibility for individuals with disabilities. Corresponding findings were found in both the quantitative and qualitative data and are categorized into several major themes: environment (indoor and outdoor), surface heights, transportation, dependence, independence, quality of life and participation. Quantitative data from this study indicate that users of MATD are satisfied with the way in which their devices enable maneuvering indoors, while qualitative data suggest otherwise. Implications for healthcare practitioners are described and future recommendations are provided. Implications for Rehabilitation Healthcare professionals should advocate for proper mobility assistive technology devices (MATDs) for their patients in order to enable increased independence, safety and efficiency. Healthcare professionals must be cognizant of the impact of the environment and/or environmental barriers when prescribing MATD. Additional areas of interest for future research may include investigating the impact of MATD in association with date of onset of disability, according to diagnoses, or specific to length of time since acquiring the device.

Exchange Coupling Interactions from the Density Matrix Renormalization Group and N-Electron Valence Perturbation Theory: Application to a Biomimetic Mixed-Valence Manganese Complex.

PubMed

Roemelt, Michael; Krewald, Vera; Pantazis, Dimitrios A

2018-01-09

The accurate description of magnetic level energetics in oligonuclear exchange-coupled transition-metal complexes remains a formidable challenge for quantum chemistry. The density matrix renormalization group (DMRG) brings such systems for the first time easily within reach of multireference wave function methods by enabling the use of unprecedentedly large active spaces. But does this guarantee systematic improvement in predictive ability and, if so, under which conditions? We identify operational parameters in the use of DMRG using as a test system an experimentally characterized mixed-valence bis-μ-oxo/μ-acetato Mn(III,IV) dimer, a model for the oxygen-evolving complex of photosystem II. A complete active space of all metal 3d and bridge 2p orbitals proved to be the smallest meaningful starting point; this is readily accessible with DMRG and greatly improves on the unrealistic metal-only configuration interaction or complete active space self-consistent field (CASSCF) values. Orbital optimization is critical for stabilizing the antiferromagnetic state, while a state-averaged approach over all spin states involved is required to avoid artificial deviations from isotropic behavior that are associated with state-specific calculations. Selective inclusion of localized orbital subspaces enables probing the relative contributions of different ligands and distinct superexchange pathways. Overall, however, full-valence DMRG-CASSCF calculations fall short of providing a quantitative description of the exchange coupling owing to insufficient recovery of dynamic correlation. Quantitatively accurate results can be achieved through a DMRG implementation of second order N-electron valence perturbation theory (NEVPT2) in conjunction with a full-valence metal and ligand active space. Perspectives for future applications of DMRG-CASSCF/NEVPT2 to exchange coupling in oligonuclear clusters are discussed.

Hyperspectral imaging with near-infrared-enabled mobile phones for tissue oximetry

NASA Astrophysics Data System (ADS)

Lin, Jonathan L.; Ghassemi, Pejhman; Chen, Yu; Pfefer, Joshua

2018-02-01

Hyperspectral reflectance imaging (HRI) is an emerging clinical tool for characterizing spatial and temporal variations in blood perfusion and oxygenation for applications such as burn assessment, wound healing, retinal exams and intraoperative tissue viability assessment. Since clinical HRI-based oximeters often use near-infrared (NIR) light, NIR-enabled mobile phones may provide a useful platform for future point-of-care devices. Furthermore, quantitative NIR imaging on mobile phones may dramatically increase the availability and accessibility of medical diagnostics for low-resource settings. We have evaluated the potential for phone-based NIR oximetry imaging and elucidated factors affecting performance using devices from two different manufacturers, as well as a scientific CCD. A broadband light source and liquid crystal tunable filter were used for imaging at 10 nm bands from 650 to 1000 nm. Spectral sensitivity measurements indicated that mobile phones with standard NIR blocking filters had minimal response beyond 700 nm, whereas one modified phone showed sensitivity to 800 nm and another to 1000 nm. Red pixel channels showed the greatest sensitivity up to 800 nm, whereas all channels provided essentially equivalent sensitivity at longer wavelengths. Referencing of blood oxygenation levels was performed with a CO-oximeter. HRI measurements were performed using cuvettes filled with hemoglobin solutions of different oxygen saturation levels. Good agreement between absorbance spectra measured with mobile phone and a CCD cameras were seen for wavelengths below 900 nm. Saturation estimates showed root-mean-squared-errors of 5.2% and 4.5% for the CCD and phone, respectively. Overall, this work provides strong evidence of the potential for mobile phones to provide quantitative spectral imaging in the NIR for applications such as oximetry, and generates practical insights into factors that impact performance as well as test methods for performance assessment.

Quantitative PLIF Imaging in High-Pressure Combustion

NASA Technical Reports Server (NTRS)

Hanson, R. K.

1997-01-01

This is the final report for a research project aimed at developing planar laser-induced fluorescence (PLIF) techniques for quantitative 2-D species imaging in fuel-lean, high-pressure combustion gases, relevant to modem aircraft gas turbine combustors. The program involved both theory and experiment. The theoretical activity led to spectroscopic models that allow calculation of the laser-induced fluorescence produced in OH, NO and 02 for arbitrary excitation wavelength, pressure, temperature, gas mixture and laser linewidth. These spectroscopic models incorporate new information on line- broadening, energy transfer and electronic quench rates. Extensive calculations have been made with these models in order to identify optimum excitation strategies, particularly for detecting low levels (ppm) of NO in the presence of large 02 mole fractions (10% is typical for the fuel-lean combustion of interest). A promising new measurement concept has emerged from these calculations, namely that excitation at specific wavelengths, together with detection of fluorescence in multiple spectral bands, promises to enable simultaneous detection of both NO (at ppm levels) and 02 or possibly NO, 02 and temperature. Calculations have been made to evaluate the expected performance of such a diagnostic for a variety of conditions and choices of excitation and detection wavelengths. The experimental effort began with assembly of a new high-pressure combustor to provide controlled high-temperature and high-pressure combustion products. The non-premixed burner enables access to postflame gases at high temperatures (to 2000 K) and high pressures (to 13 atm), and a range of fuel-air equivalence ratios. The chamber also allowed use of a sampling probe, for chemiluminescent detection of NO/NO2, and thermocouples for measurement of gas temperature. Experiments were conducted to confirm the spectroscopic models for OH, NO and 02.

3D Printed Fluidic Hardware for DNA Assembly

DTIC Science & Technology

2015-04-10

A3909 stepper motor driver, were soldered onto the milled circuit board (Supplementary Figure 8). Custom Arduino - based firmware was written to take...initiatives such as the FabLab Foundation10. Access to digital fabrication tools and open electronics, such as Arduino and Raspberry Pi, enables access to...hardware for assembly of DNA- based genetic circuits. Solid-phase DNA synthesis has declined in price, enabling researchers to routinely design and

Tunable, Quantitative Fenton-RAFT Polymerization via Metered Reagent Addition.

PubMed

Nothling, Mitchell D; McKenzie, Thomas G; Reyhani, Amin; Qiao, Greg G

2018-05-10

A continuous supply of radical species is a key requirement for activating chain growth and accessing quantitative monomer conversions in reversible addition-fragmentation chain transfer (RAFT) polymerization. In Fenton-RAFT, activation is provided by hydroxyl radicals, whose indiscriminate reactivity and short-lived nature poses a challenge to accessing extended polymerization times and quantitative monomer conversions. Here, an alternative Fenton-RAFT procedure is presented, whereby radical generation can be finely controlled via metered dosing of a component of the Fenton redox reaction (H 2 O 2 ) using an external pumping system. By limiting the instantaneous flux of radicals and ensuring sustained radical generation over tunable time periods, metered reagent addition reduces unwanted radical "wasting" reactions and provides access to consistent quantitative monomer conversions with high chain-end fidelity. Fine tuning of radical concentration during polymerization is achieved simply via adjustment of reagent dose rate, offering significant potential for automation. This modular strategy holds promise for extending traditional RAFT initiation toward more tightly regulated radical concentration profiles and affords excellent prospects for the automation of Fenton-RAFT polymerization. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ontology-based geospatial data query and integration

USGS Publications Warehouse

Zhao, T.; Zhang, C.; Wei, M.; Peng, Z.-R.

2008-01-01

Geospatial data sharing is an increasingly important subject as large amount of data is produced by a variety of sources, stored in incompatible formats, and accessible through different GIS applications. Past efforts to enable sharing have produced standardized data format such as GML and data access protocols such as Web Feature Service (WFS). While these standards help enabling client applications to gain access to heterogeneous data stored in different formats from diverse sources, the usability of the access is limited due to the lack of data semantics encoded in the WFS feature types. Past research has used ontology languages to describe the semantics of geospatial data but ontology-based queries cannot be applied directly to legacy data stored in databases or shapefiles, or to feature data in WFS services. This paper presents a method to enable ontology query on spatial data available from WFS services and on data stored in databases. We do not create ontology instances explicitly and thus avoid the problems of data replication. Instead, user queries are rewritten to WFS getFeature requests and SQL queries to database. The method also has the benefits of being able to utilize existing tools of databases, WFS, and GML while enabling query based on ontology semantics. ?? 2008 Springer-Verlag Berlin Heidelberg.

Breach Risk Magnitude: A Quantitative Measure of Database Security.

PubMed

Yasnoff, William A

2016-01-01

A quantitative methodology is described that provides objective evaluation of the potential for health record system breaches. It assumes that breach risk increases with the number of potential records that could be exposed, while it decreases when more authentication steps are required for access. The breach risk magnitude (BRM) is the maximum value for any system user of the common logarithm of the number of accessible database records divided by the number of authentication steps needed to achieve such access. For a one million record relational database, the BRM varies from 5.52 to 6 depending on authentication protocols. For an alternative data architecture designed specifically to increase security by separately storing and encrypting each patient record, the BRM ranges from 1.3 to 2.6. While the BRM only provides a limited quantitative assessment of breach risk, it may be useful to objectively evaluate the security implications of alternative database organization approaches.

A continuum model of transcriptional bursting

PubMed Central

Corrigan, Adam M; Tunnacliffe, Edward; Cannon, Danielle; Chubb, Jonathan R

2016-01-01

Transcription occurs in stochastic bursts. Early models based upon RNA hybridisation studies suggest bursting dynamics arise from alternating inactive and permissive states. Here we investigate bursting mechanism in live cells by quantitative imaging of actin gene transcription, combined with molecular genetics, stochastic simulation and probabilistic modelling. In contrast to early models, our data indicate a continuum of transcriptional states, with a slowly fluctuating initiation rate converting the gene between different levels of activity, interspersed with extended periods of inactivity. We place an upper limit of 40 s on the lifetime of fluctuations in elongation rate, with initiation rate variations persisting an order of magnitude longer. TATA mutations reduce the accessibility of high activity states, leaving the lifetime of on- and off-states unchanged. A continuum or spectrum of gene states potentially enables a wide dynamic range for cell responses to stimuli. DOI: http://dx.doi.org/10.7554/eLife.13051.001 PMID:26896676

Tomography of a Probe Potential Using Atomic Sensors on Graphene.

PubMed

Wyrick, Jonathan; Natterer, Fabian D; Zhao, Yue; Watanabe, Kenji; Taniguchi, Takashi; Cullen, William G; Zhitenev, Nikolai B; Stroscio, Joseph A

2016-12-27

Our ability to access and explore the quantum world has been greatly advanced by the power of atomic manipulation and local spectroscopy with scanning tunneling and atomic force microscopes, where the key technique is the use of atomically sharp probe tips to interact with an underlying substrate. Here we employ atomic manipulation to modify and quantify the interaction between the probe and the system under study that can strongly affect any measurement in low charge density systems, such as graphene. We transfer Co atoms from a graphene surface onto a probe tip to change and control the probe's physical structure, enabling us to modify the induced potential at a graphene surface. We utilize single Co atoms on a graphene field-effect device as atomic scale sensors to quantitatively map the modified potential exerted by the scanning probe over the whole relevant spatial and energy range.

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

NASA Astrophysics Data System (ADS)

Thubagere, Anupama J.; Thachuk, Chris; Berleant, Joseph; Johnson, Robert F.; Ardelean, Diana A.; Cherry, Kevin M.; Qian, Lulu

2017-02-01

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

NASA Astrophysics Data System (ADS)

Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

2016-04-01

Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue.

Smart Sensing Based on DNA-Metal Interaction Enables a Label-Free and Resettable Security Model of Electrochemical Molecular Keypad Lock.

PubMed

Du, Yan; Han, Xu; Wang, Chenxu; Li, Yunhui; Li, Bingling; Duan, Hongwei

2018-01-26

Recently, molecular keypad locks have received increasing attention. As a new subgroup of smart biosensors, they show great potential for protecting information as a molecular security data processor, rather than merely molecular recognition and quantitation. Herein, label-free electrochemically transduced Ag + and cysteine (Cys) sensors were developed. A molecular keypad lock model with reset function was successfully realized based on the balanced interaction of metal ion with its nucleic acid and chemical ligands. The correct input of "1-2-3" (i.e., "Ag + -Cys-cDNA") is the only password of such molecular keypad lock. Moreover, the resetting process of either correct or wrong input order could be easily made by Cys, buffer, and DI water treatment. Therefore, our system provides an even smarter system of molecular keypad lock, which could inhibit illegal access of unauthorized users, holding great promise in information protection at the molecular level.

Very Low Abundance Single-Cell Transcript Quantification with 5-Plex ddPCRTM Assays.

PubMed

Karlin-Neumann, George; Zhang, Bin; Litterst, Claudia

2018-01-01

Gene expression studies have provided one of the most accessible windows for understanding the molecular basis of cell and tissue phenotypes and how these change in response to stimuli. Current PCR-based and next generation sequencing methods offer great versatility in allowing the focused study of the roles of small numbers of genes or comprehensive profiling of the entire transcriptome of a sample at one time. Marrying of these approaches to various cell sorting technologies has recently enabled the profiling of expression in single cells, thereby increasing the resolution and sensitivity and strengthening the inferences from observed expression levels and changes. This chapter presents a quick and efficient 1-day workflow for sorting single cells with a small laboratory cell-sorter followed by an ultrahigh sensitivity, multiplexed digital PCR method for quantitative tracking of changes in 5-10 genes per single cell.

Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

PubMed Central

Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

2016-01-01

Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue. PMID:27063397

Enabling three-dimensional densitometric measurements using laboratory source X-ray micro-computed tomography

NASA Astrophysics Data System (ADS)

Pankhurst, M. J.; Fowler, R.; Courtois, L.; Nonni, S.; Zuddas, F.; Atwood, R. C.; Davis, G. R.; Lee, P. D.

2018-01-01

We present new software allowing significantly improved quantitative mapping of the three-dimensional density distribution of objects using laboratory source polychromatic X-rays via a beam characterisation approach (c.f. filtering or comparison to phantoms). One key advantage is that a precise representation of the specimen material is not required. The method exploits well-established, widely available, non-destructive and increasingly accessible laboratory-source X-ray tomography. Beam characterisation is performed in two stages: (1) projection data are collected through a range of known materials utilising a novel hardware design integrated into the rotation stage; and (2) a Python code optimises a spectral response model of the system. We provide hardware designs for use with a rotation stage able to be tilted, yet the concept is easily adaptable to virtually any laboratory system and sample, and implicitly corrects the image artefact known as beam hardening.

Using a virtual population to authentically teach epidemiology and biostatistics

NASA Astrophysics Data System (ADS)

Dunn, Peter K.; Donnison, Sharn; Cole, Rachel; Bulmer, Michael

2017-02-01

Epidemiology is the study of the distribution of disease in human populations. This means that authentically teaching primary data collection in epidemiology is difficult as students cannot easily access suitable human populations. Using an action research methodology, this paper studied the use of a virtual human population (called The Island) to enable students to experience many features of authentic primary data collection in epidemiological research. The Island was used in a course introducing epidemiology and biostatistics for students in non-quantitative disciplines. This paper discusses how The Island was introduced into the course, and then evaluates the change. Students were highly engaged, and students and teaching staff responded favourably to the use of The Island, with 70% of students agreeing or strongly agreeing that The Island was easy to use, and 64% agreeing or strongly agreeing that the use of a virtual population was beneficial to their understanding of epidemiology.

Design of a Virtual Reality System for Affect Analysis in Facial Expressions (VR-SAAFE); Application to Schizophrenia.

PubMed

Bekele, E; Bian, D; Peterman, J; Park, S; Sarkar, N

2017-06-01

Schizophrenia is a life-long, debilitating psychotic disorder with poor outcome that affects about 1% of the population. Although pharmacotherapy can alleviate some of the acute psychotic symptoms, residual social impairments present a significant barrier that prevents successful rehabilitation. With limited resources and access to social skills training opportunities, innovative technology has emerged as a potentially powerful tool for intervention. In this paper, we present a novel virtual reality (VR)-based system for understanding facial emotion processing impairments that may lead to poor social outcome in schizophrenia. We henceforth call it a VR System for Affect Analysis in Facial Expressions (VR-SAAFE). This system integrates a VR-based task presentation platform that can minutely control facial expressions of an avatar with or without accompanying verbal interaction, with an eye-tracker to quantitatively measure a participants real-time gaze and a set of physiological sensors to infer his/her affective states to allow in-depth understanding of the emotion recognition mechanism of patients with schizophrenia based on quantitative metrics. A usability study with 12 patients with schizophrenia and 12 healthy controls was conducted to examine processing of the emotional faces. Preliminary results indicated that there were significant differences in the way patients with schizophrenia processed and responded towards the emotional faces presented in the VR environment compared with healthy control participants. The preliminary results underscore the utility of such a VR-based system that enables precise and quantitative assessment of social skill deficits in patients with schizophrenia.

Developing methods for systematic reviewing in health services delivery and organisation

PubMed Central

Alborz, Alison; McNally, Rosalind

2007-01-01

Objectives To develop methods to facilitate the ‘systematic’ review of evidence from a range of methodologies on diffuse or ‘soft’ topics, as exemplified by ‘access to healthcare’. Data sources 28 bibliographic databases, research registers, organisational web sites or library catalogues. Reference lists from identified studies. Contact with experts and service users. Current awareness and contents alerting services in the area of learning disabilities. Review methods Inclusion criteria were English language literature from 1980 onwards, relating to people with learning disabilities of any age and all study designs. The main criteria for assessment was relevance to Guillifords’ model of access to health care which was adapted to the circumstances of people with learning disabilities. Selected studies were evaluated for scientific rigour then data was extracted and the results synthesised. Quality assessment was by an initial set of ‘generic’ quality indicators. This enabled further evidence selection before evaluation of findings according to specific criteria for qualitative, quantitative or mixed-method studies. Results 82 studies were fully evaluated. Five studies were rated ‘highly rigorous’, 22 ‘rigorous’, 46 ‘less rigorous’ and 9 ‘poor’ papers were retained as the sole evidence covering aspects of the guiding model. The majority of studies were quantitative but used only descriptive statistics. Most evidence lacked methodological detail, which often lowered final quality ratings. Conclusions The application of a consistent structure to quality evaluation can facilitate data appraisal, extraction and synthesis across a range of methodologies in diffuse or ‘soft’ topics. Synthesis can be facilitated further by using software, such as the Microsoft ‘Access’ database, for managing information. PMID:15606880

Multiplexed homogeneous assays of proteolytic activity using a smartphone and quantum dots.

PubMed

Petryayeva, Eleonora; Algar, W Russ

2014-03-18

Semiconductor quantum dot (QD) bioconjugates, with their unique and highly advantageous physicochemical and optical properties, have been extensively utilized as probes for bioanalysis and continue to generate widespread interest for these applications. An important consideration for expanding the utility of QDs and making their use routine is to make assays with QDs more accessible for laboratories that do not specialize in nanomaterials. Here, we show that digital color imaging of QD photoluminescence (PL) with a smartphone camera is a viable, easily accessible readout platform for quantitative, multiplexed, and real-time bioanalyses. Red-, green-, and blue-emitting CdSeS/ZnS QDs were conjugated with peptides that were labeled with a deep-red fluorescent dye, Alexa Fluor 647, and the dark quenchers, QSY9 and QSY35, respectively, to generate Förster resonance energy transfer (FRET) pairs sensitive to proteolytic activity. Changes in QD PL caused by the activity of picomolar to nanomolar concentrations of protease were detected as changes in the red-green-blue (RGB) channel intensities in digital color images. Importantly, measurements of replicate samples made with smartphone imaging and a sophisticated fluorescence plate reader yielded the same quantitative results, including initial proteolytic rates and specificity constants. Homogeneous two-plex and three-plex assays for the activity of trypsin, chymotrypsin, and enterokinase were demonstrated with RGB imaging. Given the ubiquity of smartphones, this work largely removes any instrumental impediments to the adoption of QDs as routine tools for bioanalysis in research laboratories and is a critical step toward the use of QDs for point-of-care diagnostics. This work also adds to the growing utility of smartphones in analytical methods by enabling multiplexed fluorimetric assays within a single sample volume and across multiple samples in parallel.

The feasibility of community level interventions for pre-eclampsia in South Asia and Sub-Saharan Africa: a mixed-methods design.

PubMed

Khowaja, Asif Raza; Qureshi, Rahat Najam; Sawchuck, Diane; Oladapo, Olufemi T; Adetoro, Olalekan O; Orenuga, Elizabeth A; Bellad, Mrutyunjaya; Mallapur, Ashalata; Charantimath, Umesh; Sevene, Esperança; Munguambe, Khátia; Boene, Helena Edith; Vidler, Marianne; Bhutta, Zulfiqar A; von Dadelszen, Peter

2016-06-08

Globally, pre-eclampsia and eclampsia are major contributors to maternal and perinatal mortality; of which the vast majority of deaths occur in less developed countries. In addition, a disproportionate number of morbidities and mortalities occur due to delayed access to health services. The Community Level Interventions for Pre-eclampsia (CLIP) Trial aims to task-shift to community health workers the identification and emergency management of pre-eclampsia and eclampsia to improve access and timely care. Literature revealed paucity of published feasibility assessments prior to initiating large-scale community-based interventions. Arguably, well-conducted feasibility studies can provide valuable information about the potential success of clinical trials prior to implementation. Failure to fully understand the study context risks the effective implementation of the intervention and limits the likelihood of post-trial scale-up. Therefore, it was imperative to conduct community-level feasibility assessments for a trial of this magnitude. A mixed methods design guided by normalization process theory was used for this study in Nigeria, Mozambique, Pakistan, and India to explore enabling and impeding factors for the CLIP Trial implementation. Qualitative data were collected through participant observation, document review, focus group discussion and in-depth interviews with diverse groups of community members, key informants at community level, healthcare providers, and policy makers. Quantitative data were collected through health facility assessments, self-administered community health worker surveys, and household demographic and health surveillance. Refer to CLIP Trial feasibility publications in the current and/or forthcoming supplement. Feasibility assessments for community level interventions, particularly those involving task-shifting across diverse regions, require an appropriate theoretical framework and careful selection of research methods. The use of qualitative and quantitative methods increased the data richness to better understand the community contexts. NCT01911494.

The Development of Mathematical Knowledge for Teaching for Quantitative Reasoning Using Video-Based Instruction

ERIC Educational Resources Information Center

Walters, Charles David

2017-01-01

Quantitative reasoning (P. W. Thompson, 1990, 1994) is a powerful mathematical tool that enables students to engage in rich problem solving across the curriculum. One way to support students' quantitative reasoning is to develop prospective secondary teachers' (PSTs) mathematical knowledge for teaching (MKT; Ball, Thames, & Phelps, 2008)…

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos.

PubMed

Trivedi, Vikas; Choi, Harry M T; Fraser, Scott E; Pierce, Niles A

2018-01-08

For decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the anatomy, relying on embryo microdissection, dissociation, cell sorting and/or homogenization. Here, we eliminate the trade-off between quantitation and anatomical context, using quantitative in situ hybridization chain reaction (qHCR) to perform accurate and precise relative quantitation of mRNA expression with subcellular resolution within whole-mount vertebrate embryos. Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional expression space to anatomical space reveals those anatomical locations in which selected gene co-expression relationships occur. As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular anatomical context, they enable bi-directional queries that open a new era for in situ hybridization. © 2018. Published by The Company of Biologists Ltd.

Community-level antibiotic access and use (ABACUS) in low- and middle-income countries: Finding targets for social interventions to improve appropriate antimicrobial use – an observational multi-centre study

PubMed Central

Wertheim, Heiman F.L.; Chuc, Nguyen Thi Kim; Punpuing, Sureeporn; Khan, Wasif Ali; Gyapong, Margaret; Asante, Kwaku Poku; Munguambe, Khatia; Gómez-Olivé, F. Xavier; Ariana, Proochista; John-Langba, Johannes; Sigauque, Betuel; Toan, Tran Khanh; Tollman, Stephen; Cremers, Amelieke J.H.; Do, Nga T.T.; Nadjm, Behzad; van Doorn, H. Rogier; Kinsman, John; Sankoh, Osman

2017-01-01

In many low- and middle-income countries (LMICs), a poor link between antibiotic policies and practices exists. Numerous contextual factors may influence the degree of antibiotic access, appropriateness of antibiotic provision, and actual use in communities. Therefore, improving appropriateness of antibiotic use in different communities in LMICs probably requires interventions tailored to the setting of interest, accounting for cultural context. Here we present the ABACUS study (AntiBiotic ACcess and USe), which employs a unique approach and infrastructure, enabling quantitative validation, contextualization of determinants, and cross-continent comparisons of antibiotic access and use. The community infrastructure for this study is the INDEPTH-Network (International Network for the Demographic Evaluation of Populations and Their Health in Developing Countries), which facilitates health and population research through an established health and demographic surveillance system. After an initial round of formative qualitative research with community members and antibiotic suppliers in three African and three Asian countries, household surveys will assess the appropriateness of antibiotic access, provision and use. Results from this sample will be validated against a systematically conducted inventory of suppliers. All potential antibiotic suppliers will be mapped and characterized. Subsequently, their supply of antibiotics to the community will be measured through customer exit interviews, which tend to be more reliable than bulk purchase or sales data. Discrepancies identified between reported and observed antibiotic practices will be investigated in further qualitative interviews. Amartya Sen’s Capability Approach will be employed to identify the conversion factors that determine whether or not, and the extent to which appropriate provision of antibiotics may lead to appropriate access and use of antibiotics. Currently, the study is ongoing and expected to conclude by 2019. ABACUS will provide important new insights into antibiotic practices in LMICs to inform social interventions aimed at promoting optimal antibiotic use, thereby preserving antibiotic effectiveness. PMID:29707652

Rapid Induction of Cerebral Organoids From Human Induced Pluripotent Stem Cells Using a Chemically Defined Hydrogel and Defined Cell Culture Medium.

PubMed

Lindborg, Beth A; Brekke, John H; Vegoe, Amanda L; Ulrich, Connor B; Haider, Kerri T; Subramaniam, Sandhya; Venhuizen, Scott L; Eide, Cindy R; Orchard, Paul J; Chen, Weili; Wang, Qi; Pelaez, Francisco; Scott, Carolyn M; Kokkoli, Efrosini; Keirstead, Susan A; Dutton, James R; Tolar, Jakub; O'Brien, Timothy D

2016-07-01

Tissue organoids are a promising technology that may accelerate development of the societal and NIH mandate for precision medicine. Here we describe a robust and simple method for generating cerebral organoids (cOrgs) from human pluripotent stem cells by using a chemically defined hydrogel material and chemically defined culture medium. By using no additional neural induction components, cOrgs appeared on the hydrogel surface within 10-14 days, and under static culture conditions, they attained sizes up to 3 mm in greatest dimension by day 28. Histologically, the organoids showed neural rosette and neural tube-like structures and evidence of early corticogenesis. Immunostaining and quantitative reverse-transcription polymerase chain reaction demonstrated protein and gene expression representative of forebrain, midbrain, and hindbrain development. Physiologic studies showed responses to glutamate and depolarization in many cells, consistent with neural behavior. The method of cerebral organoid generation described here facilitates access to this technology, enables scalable applications, and provides a potential pathway to translational applications where defined components are desirable. Tissue organoids are a promising technology with many potential applications, such as pharmaceutical screens and development of in vitro disease models, particularly for human polygenic conditions where animal models are insufficient. This work describes a robust and simple method for generating cerebral organoids from human induced pluripotent stem cells by using a chemically defined hydrogel material and chemically defined culture medium. This method, by virtue of its simplicity and use of defined materials, greatly facilitates access to cerebral organoid technology, enables scalable applications, and provides a potential pathway to translational applications where defined components are desirable. ©AlphaMed Press.

Perceived Barriers to Health Care Access Among Rural Older Adults: A Qualitative Study

ERIC Educational Resources Information Center

Goins, R. Turner; Williams, Kimberly A.; Carter, Mary W.; Spencer, S. Melinda; Solovieva, Tatiana

2005-01-01

Context: Many rural elders experience limited access to health care. The majority of what we know about this issue has been based upon quantitative studies, yet qualitative studies might offer additional insight into individual perceptions of health care access. Purpose: To examine what barriers rural elders report when accessing needed health…

Perceived Barriers to Health Care Access among Rural Older Adults: A Qualitative Study

ERIC Educational Resources Information Center

Goins, R. Turner; Williams, Kimberly A.; Carter, Mary W.; Spencer, S. Melinda; Solovieva, Tatiana

2005-01-01

Context: Many rural elders experience limited access to health care. The majority of what we know about this issue has been based upon quantitative studies, yet qualitative studies might offer additional insight into individual perceptions of health care access. Purpose: To examine what barriers rural elders report when accessing needed health…

New spectral imaging techniques for blood oximetry in the retina

NASA Astrophysics Data System (ADS)

Alabboud, Ied; Muyo, Gonzalo; Gorman, Alistair; Mordant, David; McNaught, Andrew; Petres, Clement; Petillot, Yvan R.; Harvey, Andrew R.

2007-07-01

Hyperspectral imaging of the retina presents a unique opportunity for direct and quantitative mapping of retinal biochemistry - particularly of the vasculature where blood oximetry is enabled by the strong variation of absorption spectra with oxygenation. This is particularly pertinent both to research and to clinical investigation and diagnosis of retinal diseases such as diabetes, glaucoma and age-related macular degeneration. The optimal exploitation of hyperspectral imaging however, presents a set of challenging problems, including; the poorly characterised and controlled optical environment of structures within the retina to be imaged; the erratic motion of the eye ball; and the compounding effects of the optical sensitivity of the retina and the low numerical aperture of the eye. We have developed two spectral imaging techniques to address these issues. We describe first a system in which a liquid crystal tuneable filter is integrated into the illumination system of a conventional fundus camera to enable time-sequential, random access recording of narrow-band spectral images. Image processing techniques are described to eradicate the artefacts that may be introduced by time-sequential imaging. In addition we describe a unique snapshot spectral imaging technique dubbed IRIS that employs polarising interferometry and Wollaston prism beam splitters to simultaneously replicate and spectrally filter images of the retina into multiple spectral bands onto a single detector array. Results of early clinical trials acquired with these two techniques together with a physical model which enables oximetry map are reported.

Portable (handheld) clinical device for quantitative spectroscopy of skin, utilizing spatial frequency domain reflectance techniques

NASA Astrophysics Data System (ADS)

Saager, Rolf B.; Dang, An N.; Huang, Samantha S.; Kelly, Kristen M.; Durkin, Anthony J.

2017-09-01

Spatial Frequency Domain Spectroscopy (SFDS) is a technique for quantifying in-vivo tissue optical properties. SFDS employs structured light patterns that are projected onto tissues using a spatial light modulator, such as a digital micromirror device. In combination with appropriate models of light propagation, this technique can be used to quantify tissue optical properties (absorption, μa, and scattering, μs', coefficients) and chromophore concentrations. Here we present a handheld implementation of an SFDS device that employs line (one dimensional) imaging. This instrument can measure 1088 spatial locations that span a 3 cm line as opposed to our original benchtop SFDS system that only collects a single 1 mm diameter spot. This imager, however, retains the spectral resolution (˜1 nm) and range (450-1000 nm) of our original benchtop SFDS device. In the context of homogeneous turbid media, we demonstrate that this new system matches the spectral response of our original system to within 1% across a typical range of spatial frequencies (0-0.35 mm-1). With the new form factor, the device has tremendously improved mobility and portability, allowing for greater ease of use in a clinical setting. A smaller size also enables access to different tissue locations, which increases the flexibility of the device. The design of this portable system not only enables SFDS to be used in clinical settings but also enables visualization of properties of layered tissues such as skin.

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

PubMed

Caetano, Fabiana A; Dirk, Brennan S; Tam, Joshua H K; Cavanagh, P Craig; Goiko, Maria; Ferguson, Stephen S G; Pasternak, Stephen H; Dikeakos, Jimmy D; de Bruyn, John R; Heit, Bryan

2015-12-01

Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

Enabling Virtual Access to Latin-American Southern Observatories

NASA Astrophysics Data System (ADS)

Filippi, G.

2010-12-01

EVALSO (Enabling Virtual Access to Latin-American Southern Observatories) is an international consortium of nine astronomical organisations and research network operators, part-funded under the European Commission FP7, to create and exploit high-speed bandwidth connections to South American observatories. A brief description of the project is presented. The EVALSO Consortium inaugurated a fibre link between the Paranal Observatory and international networks on 4 November 2010 capable of 10 Gigabit per second.

Tool independence for the Web Accessibility Quantitative Metric.

PubMed

Vigo, Markel; Brajnik, Giorgio; Arrue, Myriam; Abascal, Julio

2009-07-01

The Web Accessibility Quantitative Metric (WAQM) aims at accurately measuring the accessibility of web pages. One of the main features of WAQM among others is that it is evaluation tool independent for ranking and accessibility monitoring scenarios. This article proposes a method to attain evaluation tool independence for all foreseeable scenarios. After demonstrating that homepages have a more similar error profile than any other web page in a given web site, 15 homepages were measured with 10,000 different values of WAQM parameters using EvalAccess and LIFT, two automatic evaluation tools for accessibility. A similar procedure was followed with random pages and with several test files obtaining several tuples that minimise the difference between both tools. One thousand four hundred forty-nine web pages from 15 web sites were measured with these tuples and those values that minimised the difference between the tools were selected. Once the WAQM was tuned, the accessibility of 15 web sites was measured with two metrics for web sites, concluding that even if similar values can be produced, obtaining the same scores is undesirable since evaluation tools behave in a different way.

Access to Education with Online Learning and Open Educational Resources: Can They Close the Gap?

ERIC Educational Resources Information Center

Geith, Christine; Vignare, Karen

2008-01-01

One of the key concepts in the right to education is access: access to the means to fully develop as human beings as well as access to the means to gain skills, knowledge and credentials. This is an important perspective through which to examine the solutions to access enabled by Open Educational Resources (OER) and online learning. The authors…

Autonomy and Housing Accessibility Among Powered Mobility Device Users

PubMed Central

Brandt, Åse; Lexell, Eva Månsson; Iwarsson, Susanne

2015-01-01

OBJECTIVE. To describe environmental barriers, accessibility problems, and powered mobility device (PMD) users’ autonomy indoors and outdoors; to determine the home environmental barriers that generated the most housing accessibility problems indoors, at entrances, and in the close exterior surroundings; and to examine personal factors and environmental components and their association with indoor and outdoor autonomy. METHOD. This cross-sectional study was based on data collected from a sample of 48 PMD users with a spinal cord injury (SCI) using the Impact of Participation and Autonomy and the Housing Enabler instruments. Descriptive statistics and logistic regression were used. RESULTS. More years living with SCI predicted less restriction in autonomy indoors, whereas more functional limitations and accessibility problems related to entrance doors predicted more restriction in autonomy outdoors. CONCLUSION. To enable optimized PMD use, practitioners must pay attention to the relationship between client autonomy and housing accessibility problems. PMID:26356666

Globalising Accessibility: Drawing on the Experiences of Developed Countries to Enable the Participation of Disabled People in Zambia

ERIC Educational Resources Information Center

Banda-Chalwe, Martha; Nitz, Jennifer C.; de Jonge, Desleigh

2012-01-01

This paper explores the accessibility situation in a developing country such as Zambia. The global view of accessibility for disabled people is provided to examine the accessibility situation in developed and developing countries, highlighting the role of the environment in achieving rights for disabled people. Recognition of disability rights…

Enabling Remote Access to Fieldwork: Gaining Insight into the Pedagogic Effectiveness of "Direct" and "Remote" Field Activities

ERIC Educational Resources Information Center

Stokes, Alison; Collins, Trevor; Maskall, John; Lea, John; Lunt, Paul; Davies, Sarah

2012-01-01

This study considers the pedagogical effectiveness of remote access to fieldwork locations. Forty-one students from across the GEES disciplines (geography, earth and environmental sciences) undertook a fieldwork exercise, supported by two lecturers. Twenty students accessed the field site directly and the remainder accessed the site remotely using…

Building transparent data access for ocean observatories: Coordination of U.S. IOOS DMAC with NSF's OOI Cyberinfrastructure

USGS Publications Warehouse

Arrott, M.; Alexander, Corrine; Graybeal, J.; Mueller, C.; Signell, R.; de La Beaujardière, J.; Taylor, A.; Wilkin, J.; Powell, B.; Orcutt, J.

2011-01-01

The NOAA-led U.S. Integrated Ocean Observing System (IOOS) and the National Science Foundation's Ocean Observatories Initiative (OOI) have been collaborating since 2007 on advanced tools and technologies that ensure open access to ocean observations and models. Initial collaboration focused on serving ocean data via cloud computing-a key component of the OOI cyberinfrastructure (CI) architecture. As the OOI transitioned from planning to execution in the Fall of 2009, an OOI/IOOS team developed a customer-based "use case" to align more closely with the emerging objectives of OOI-CI team's first software release scheduled for Summer 2011 and provide a quantitative capacity for stress-testing these tools and protocols. A requirements process was initiated with coastal modelers, focusing on improved workflows to deliver ocean observation data. Accomplishments to date include the documentation and assessment of scientific workflows for two "early adopter" modeling teams from IOOS Regional partners (Rutgers-the State University of New Jersey and University of Hawaii's School of Ocean and Earth Science and Technology) to enable full understanding of data sources and needs; generation of all-inclusive lists of the data sets required and those obtainable through IOOS; a more complete understanding of areas where IOOS can expand data access capabilities to better serve the needs of the modeling community; and development of "data set agents" (software) to facilitate data acquisition from numerous data providers and conversions of the data format to the OOI-CI canonical form. ?? 2011 MTS.

Assessing Barriers to Neurosurgical Care in Sub-Saharan Africa: The Role of Resources and Infrastructure.

PubMed

Sader, Elie; Yee, Philip; Hodaie, Mojgan

2017-02-01

Quantitative estimates of surgical capacity and infrastructure and perceived care limitations in low-resource countries are essential baseline measures that can provide strategies for improving access to surgical care. Information about these barriers in Africa is scarce, particularly with respect to neurosurgery. We conducted a survey to better understand the unmet surgical need and resources available for the care of neurosurgery patients in Sub-Saharan Africa. Using SurveyMonkey, we administered a neurosurgery-specific survey to neurosurgery attending surgeons and residents in Sub-Saharan African countries. Key outcome measures included workforce, access to imaging modalities and instruments, volume and breakdown of neurosurgical cases, and perceived limitations of care. We obtained a 41% survey response (129/314 sent). In addition to the expected large gap in workforce between low- and high-income countries, we found a dramatic paucity of neurosurgical resources in Central Africa, whereas specific pockets in West and South Africa have better neurosurgical care. Access to neuroimaging was not a major limitation in Sub-Saharan African countries. The most commonly perceived limitations of care included infrastructure, anesthesia/nursing availability, wait times, and strength of training. This large survey defines important self-perceived limitations to care within neurosurgery and highlights the importance of infrastructure and allied professions in this role. A clear understanding of areas of focus will enable a more efficient and sustainable response to the limitations in surgical care in low-resource areas. Copyright © 2016 Elsevier Inc. All rights reserved.

Using QR codes to enable quick access to information in acute cancer care.

PubMed

Upton, Joanne; Olsson-Brown, Anna; Marshall, Ernie; Sacco, Joseph

2017-05-25

Quick access to toxicity management information ensures timely access to steroids/immunosuppressive treatment for cancer patients experiencing immune-related adverse events, thus reducing length of hospital stays or avoiding hospital admission entirely. This article discusses a project to add a QR (quick response) code to a patient-held immunotherapy alert card. As QR code generation is free and the immunotherapy clinical management algorithms were already publicly available through the trust's clinical network website, the costs of integrating a QR code into the alert card, after printing, were low, while the potential benefits are numerous. Patient-held alert cards are widely used for patients receiving anti-cancer treatment, and this established standard of care has been modified to enable rapid access of information through the incorporation of a QR code.

A Case-Series Test of the Interactive Two-Step Model of Lexical Access: Predicting Word Repetition from Picture Naming

ERIC Educational Resources Information Center

Dell, Gary S.; Martin, Nadine; Schwartz, Myrna F.

2007-01-01

Lexical access in language production, and particularly pathologies of lexical access, are often investigated by examining errors in picture naming and word repetition. In this article, we test a computational approach to lexical access, the two-step interactive model, by examining whether the model can quantitatively predict the repetition-error…

High Tech and Library Access for People with Disabilities.

ERIC Educational Resources Information Center

Roatch, Mary A.

1992-01-01

Describes tools that enable people with disabilities to access print information, including optical character recognition, synthetic voice output, other input devices, Braille access devices, large print displays, television and video, TDD (Telecommunications Devices for the Deaf), and Telebraille. Use of technology by libraries to meet mandates…

GLIDE: a grid-based light-weight infrastructure for data-intensive environments

NASA Technical Reports Server (NTRS)

Mattmann, Chris A.; Malek, Sam; Beckman, Nels; Mikic-Rakic, Marija; Medvidovic, Nenad; Chrichton, Daniel J.

2005-01-01

The promise of the grid is that it will enable public access and sharing of immense amounts of computational and data resources among dynamic coalitions of individuals and institutions. However, the current grid solutions make several limiting assumptions that curtail their widespread adoption. To address these limitations, we present GLIDE, a prototype light-weight, data-intensive middleware infrastructure that enables access to the robust data and computational power of the grid on DREAM platforms.

Transformation of personal computers and mobile phones into genetic diagnostic systems.

PubMed

Walker, Faye M; Ahmad, Kareem M; Eisenstein, Michael; Soh, H Tom

2014-09-16

Molecular diagnostics based on the polymerase chain reaction (PCR) offer rapid and sensitive means for detecting infectious disease, but prohibitive costs have impeded their use in resource-limited settings where such diseases are endemic. In this work, we report an innovative method for transforming a desktop computer and a mobile camera phone--devices that have become readily accessible in developing countries--into a highly sensitive DNA detection system. This transformation was achieved by converting a desktop computer into a de facto thermal cycler with software that controls the temperature of the central processing unit (CPU), allowing for highly efficient PCR. Next, we reconfigured the mobile phone into a fluorescence imager by adding a low-cost filter, which enabled us to quantitatively measure the resulting PCR amplicons. Our system is highly sensitive, achieving quantitative detection of as little as 9.6 attograms of target DNA, and we show that its performance is comparable to advanced laboratory instruments at approximately 1/500th of the cost. Finally, in order to demonstrate clinical utility, we have used our platform for the successful detection of genomic DNA from the parasite that causes Chagas disease, Trypanosoma cruzi, directly in whole, unprocessed human blood at concentrations 4-fold below the clinical titer of the parasite.

Transformation of Personal Computers and Mobile Phones into Genetic Diagnostic Systems

PubMed Central

2014-01-01

Molecular diagnostics based on the polymerase chain reaction (PCR) offer rapid and sensitive means for detecting infectious disease, but prohibitive costs have impeded their use in resource-limited settings where such diseases are endemic. In this work, we report an innovative method for transforming a desktop computer and a mobile camera phone—devices that have become readily accessible in developing countries—into a highly sensitive DNA detection system. This transformation was achieved by converting a desktop computer into a de facto thermal cycler with software that controls the temperature of the central processing unit (CPU), allowing for highly efficient PCR. Next, we reconfigured the mobile phone into a fluorescence imager by adding a low-cost filter, which enabled us to quantitatively measure the resulting PCR amplicons. Our system is highly sensitive, achieving quantitative detection of as little as 9.6 attograms of target DNA, and we show that its performance is comparable to advanced laboratory instruments at approximately 1/500th of the cost. Finally, in order to demonstrate clinical utility, we have used our platform for the successful detection of genomic DNA from the parasite that causes Chagas disease, Trypanosoma cruzi, directly in whole, unprocessed human blood at concentrations 4-fold below the clinical titer of the parasite. PMID:25223929

A Study of Students' Learning Styles, Discipline Attitudes and Knowledge Acquisition in Technology-Enhanced Probability and Statistics Education.

PubMed

Christou, Nicolas; Dinov, Ivo D

2010-09-01

Many modern technological advances have direct impact on the format, style and efficacy of delivery and consumption of educational content. For example, various novel communication and information technology tools and resources enable efficient, timely, interactive and graphical demonstrations of diverse scientific concepts. In this manuscript, we report on a meta-study of 3 controlled experiments of using the Statistics Online Computational Resources in probability and statistics courses. Web-accessible SOCR applets, demonstrations, simulations and virtual experiments were used in different courses as treatment and compared to matched control classes utilizing traditional pedagogical approaches. Qualitative and quantitative data we collected for all courses included Felder-Silverman-Soloman index of learning styles, background assessment, pre and post surveys of attitude towards the subject, end-point satisfaction survey, and varieties of quiz, laboratory and test scores. Our findings indicate that students' learning styles and attitudes towards a discipline may be important confounds of their final quantitative performance. The observed positive effects of integrating information technology with established pedagogical techniques may be valid across disciplines within the broader spectrum courses in the science education curriculum. The two critical components of improving science education via blended instruction include instructor training, and development of appropriate activities, simulations and interactive resources.

Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length scales

PubMed Central

Hogstrom, L. J.; Guo, S. M.; Murugadoss, K.; Bathe, M.

2016-01-01

Brain function emerges from hierarchical neuronal structure that spans orders of magnitude in length scale, from the nanometre-scale organization of synaptic proteins to the macroscopic wiring of neuronal circuits. Because the synaptic electrochemical signal transmission that drives brain function ultimately relies on the organization of neuronal circuits, understanding brain function requires an understanding of the principles that determine hierarchical neuronal structure in living or intact organisms. Recent advances in fluorescence imaging now enable quantitative characterization of neuronal structure across length scales, ranging from single-molecule localization using super-resolution imaging to whole-brain imaging using light-sheet microscopy on cleared samples. These tools, together with correlative electron microscopy and magnetic resonance imaging at the nanoscopic and macroscopic scales, respectively, now facilitate our ability to probe brain structure across its full range of length scales with cellular and molecular specificity. As these imaging datasets become increasingly accessible to researchers, novel statistical and computational frameworks will play an increasing role in efforts to relate hierarchical brain structure to its function. In this perspective, we discuss several prominent experimental advances that are ushering in a new era of quantitative fluorescence-based imaging in neuroscience along with novel computational and statistical strategies that are helping to distil our understanding of complex brain structure. PMID:26855758

A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity.

PubMed

Isom, Daniel G; Marguet, Philippe R; Oas, Terrence G; Hellinga, Homme W

2011-04-01

Protein thermodynamic stability is a fundamental physical characteristic that determines biological function. Furthermore, alteration of thermodynamic stability by macromolecular interactions or biochemical modifications is a powerful tool for assessing the relationship between protein structure, stability, and biological function. High-throughput approaches for quantifying protein stability are beginning to emerge that enable thermodynamic measurements on small amounts of material, in short periods of time, and using readily accessible instrumentation. Here we present such a method, fast quantitative cysteine reactivity, which exploits the linkage between protein stability, sidechain protection by protein structure, and structural dynamics to characterize the thermodynamic and kinetic properties of proteins. In this approach, the reaction of a protected cysteine and thiol-reactive fluorogenic indicator is monitored over a gradient of temperatures after a short incubation time. These labeling data can be used to determine the midpoint of thermal unfolding, measure the temperature dependence of protein stability, quantify ligand-binding affinity, and, under certain conditions, estimate folding rate constants. Here, we demonstrate the fQCR method by characterizing these thermodynamic and kinetic properties for variants of Staphylococcal nuclease and E. coli ribose-binding protein engineered to contain single, protected cysteines. These straightforward, information-rich experiments are likely to find applications in protein engineering and functional genomics. Copyright © 2010 Wiley-Liss, Inc.

A Study of Students' Learning Styles, Discipline Attitudes and Knowledge Acquisition in Technology-Enhanced Probability and Statistics Education

PubMed Central

Christou, Nicolas; Dinov, Ivo D.

2011-01-01

Many modern technological advances have direct impact on the format, style and efficacy of delivery and consumption of educational content. For example, various novel communication and information technology tools and resources enable efficient, timely, interactive and graphical demonstrations of diverse scientific concepts. In this manuscript, we report on a meta-study of 3 controlled experiments of using the Statistics Online Computational Resources in probability and statistics courses. Web-accessible SOCR applets, demonstrations, simulations and virtual experiments were used in different courses as treatment and compared to matched control classes utilizing traditional pedagogical approaches. Qualitative and quantitative data we collected for all courses included Felder-Silverman-Soloman index of learning styles, background assessment, pre and post surveys of attitude towards the subject, end-point satisfaction survey, and varieties of quiz, laboratory and test scores. Our findings indicate that students' learning styles and attitudes towards a discipline may be important confounds of their final quantitative performance. The observed positive effects of integrating information technology with established pedagogical techniques may be valid across disciplines within the broader spectrum courses in the science education curriculum. The two critical components of improving science education via blended instruction include instructor training, and development of appropriate activities, simulations and interactive resources. PMID:21603097

Discovering the Quantity of Quality: Scoring "Regional Identity" for Quantitative Research

ERIC Educational Resources Information Center

Miller, Daniel A.

2008-01-01

The variationist paradigm in sociolinguistics is at a disadvantage when dealing with variables that are traditionally treated qualitatively, e.g., "identity". This study essays to level the accuracy and descriptive value of qualitative research in a quantitative setting by rendering such a variable quantitatively accessible. To this end,…

Attitude and confidence of undergraduate medical programme educators to practice and teach evidence-based healthcare: a cross-sectional survey

PubMed Central

Young, Taryn; Esterhuizen, Tonya M.; Volmink, Jimmy; Clarke, Mike

2016-01-01

ABSTRACT Aim: Medical student educators play critical roles in evidence-based healthcare (EBHC) teaching and learning and as role models practicing EBHC. This study assessed their confidence to practice and teach EBHC, their attitude to EBHC and barriers to practicing and teaching EBHC. Methods: We conducted a cross-sectional online survey of educators of undergraduate medical students at a South African academic institution. STATA 12 was used for quantitative data analysis. Responses to open-ended questions were coded, and further interpretation done using thematic content analysis. Results: Forty two (19%) educators from various departments responded to the invitation sent to everyone formally involved in teaching undergraduate medical students. They had high levels of knowledge and understanding of EBHC. Many had received training in teaching and learning approaches, although EBHC training received was mainly on enabling competencies. Limitations to practicing EBHC included lack of time, clinical workload, limited access to Internet and resources, knowledge and skills. One quarter of the respondents indicated that they teach EBHC. Perceived barriers to teaching EBHC reported related to students (e.g. lack of interest), context (e.g. access to databases) and educators (e.g. competing priorities). Respondents’ suggestions for support included reliable Internet access, easy point-of-care access to databases and resources, increasing awareness of EBHC, building capacity to practice and facilitate learning of EBHC and a supportive community of practice. Conclusion: Educators play a critical role in facilitating EBHC learning not just in the classroom, but also in practice. Without adequate support, training and development, they are ill equipped to be the role models future healthcare professionals need. PMID:26626283

Health System Barriers to Access and Use of Magnesium Sulfate for Women with Severe Pre-Eclampsia and Eclampsia in Pakistan: Evidence for Policy and Practice

PubMed Central

Bigdeli, Maryam; Zafar, Shamsa; Assad, Hafeez; Ghaffar, Adbul

2013-01-01

Severe pre-eclampsia and eclampsia are rare but serious complications of pregnancy that threaten the lives of mothers during childbirth. Evidence supports the use of magnesium sulfate (MgSO4) as the first line treatment option for severe pre-eclampsia and eclampsia. Eclampsia is the third major cause of maternal mortality in Pakistan. As in many other Low- and Middle-Income Countries (LMIC), it is suspected that MgSO4 is critically under-utilized in the country. There is however a lack of information on context-specific health system barriers that prevent optimal use of this life-saving medicine in Pakistan. Combining quantitative and qualitative methods, namely policy document review, key informant interviews, focus group discussions and direct observation at health facility, we explored context-specific health system barriers and enablers that affect access and use of MgSO4 for severe pre-eclampsia and eclampsia in Pakistan. Our study finds that while international recommendations on MgSO4 have been adequately translated in national policies in Pakistan, the gap remains in implementation of national policies into practice. Barriers to access to and effective use of MgSO4 occur at health facility level where the medicine was not available and health staff was reluctant to use it. Low price of the medicine and the small market related to its narrow indications acted as disincentives for effective marketing. Results of our survey were further discussed in a multi-stakeholder round-table meeting and an action plan for increasing access to this life-saving medicine was identified. PMID:23555626

Attitudes toward information and communication technology (ICT) in residential aged care in Western Australia.

PubMed

Loh, Poh-Kooi; Flicker, Leon; Horner, Barbara

2009-07-01

Determine why introduction of health consulting services via Telehealth video conference consultations failed in residential aged care facilities (RACF). Semistructured interview groups and quantitative survey. Two participating not-for-profit RACF. Managers, employed carers, physiotherapist, occupational therapist, registered nurses, and residents from RACF. A survey initially followed by focus groups that centered on 4 questions. How can computers help improve care? What kind of electronic services and products could help improve care? Who should have access to the technology and why was the technology not used? The survey revealed there was awareness of information and communication technology (ICT) in RACF. However, respondents were uncertain of potential benefits provided to their clients. Only 43% of respondents thought a minority of clients would receive the benefits of ICT use. The focus groups revealed several themes regarding the attitudes toward ICT in RACF. Positive attitudes to ICT included themes of saving time, easier doctor access, cost saving, and improved communications. Negative attitudes included themes of loss of human contact, inadequate training, security barriers, not user friendly, limited ability to comply with suggestions, privacy issues, and capital cost. Residents were also concerned about confidentiality and loss of human interaction with the use of Telehealth in residential aged facilities. More training for staff is required to enable them to use ICT efficiently. ICT hardware and software at the user interface must be designed to maintain confidentiality with ease of access. Access to Telehealth services should not impede the routine delivery of personal care and human contact for residents. Studies are required as to where human input to residents is unable to be replaced by Telehealth services.

Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios.

PubMed

Tumino, Giorgio; Voorrips, Roeland E; Rizza, Fulvia; Badeck, Franz W; Morcia, Caterina; Ghizzoni, Roberta; Germeier, Christoph U; Paulo, Maria-João; Terzi, Valeria; Smulders, Marinus J M

2016-09-01

Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option. Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward's clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits.

[A comparison of convenience sampling and purposive sampling].

PubMed

Suen, Lee-Jen Wu; Huang, Hui-Man; Lee, Hao-Hsien

2014-06-01

Convenience sampling and purposive sampling are two different sampling methods. This article first explains sampling terms such as target population, accessible population, simple random sampling, intended sample, actual sample, and statistical power analysis. These terms are then used to explain the difference between "convenience sampling" and purposive sampling." Convenience sampling is a non-probabilistic sampling technique applicable to qualitative or quantitative studies, although it is most frequently used in quantitative studies. In convenience samples, subjects more readily accessible to the researcher are more likely to be included. Thus, in quantitative studies, opportunity to participate is not equal for all qualified individuals in the target population and study results are not necessarily generalizable to this population. As in all quantitative studies, increasing the sample size increases the statistical power of the convenience sample. In contrast, purposive sampling is typically used in qualitative studies. Researchers who use this technique carefully select subjects based on study purpose with the expectation that each participant will provide unique and rich information of value to the study. As a result, members of the accessible population are not interchangeable and sample size is determined by data saturation not by statistical power analysis.

Barriers and enablers to healthcare access and use among Arabic-speaking and Caucasian English-speaking patients with type 2 diabetes mellitus: a qualitative comparative study

PubMed Central

Alzubaidi, H; Mc Namara, K; Browning, Colette; Marriott, J

2015-01-01

Objective The objective of this study was to explore the decision-making processes and associated barriers and enablers that determine access and use of healthcare services in Arabic-speaking and English-speaking Caucasian patients with diabetes in Australia. Study setting and design Face-to-face semistructured individual interviews and group interviews were conducted at various healthcare settings—diabetes outpatient clinics in 2 tertiary referral hospitals, 6 primary care practices and 10 community centres in Melbourne, Australia. Participants A total of 100 participants with type 2 diabetes mellitus were recruited into 2 groups: 60 Arabic-speaking and 40 English-speaking Caucasian. Data collection Interviews were audio-taped, translated into English when necessary, transcribed and coded thematically. Sociodemographic and clinical information was gathered using a self-completed questionnaire and medical records. Principal findings Only Arabic-speaking migrants intentionally delayed access to healthcare services when obvious signs of diabetes were experienced, missing opportunities to detect diabetes at an early stage. Four major barriers and enablers to healthcare access and use were identified: influence of significant other(s), unique sociocultural and religious beliefs, experiences with healthcare providers and lack of knowledge about healthcare services. Compared with Arabic-speaking migrants, English-speaking participants had no reluctance to access and use medical services when signs of ill-health appeared; their treatment-seeking behaviours were straightforward. Conclusions Arabic-speaking migrants appear to intentionally delay access to medical services even when symptomatic. Four barriers to health services access have been identified. Tailored interventions must be developed for Arabic-speaking migrants to improve access to available health services, facilitate timely diagnosis of diabetes and ultimately to improve glycaemic control. PMID:26576809

Improving Access to Data While Protecting Confidentiality: Prospects for the Future.

ERIC Educational Resources Information Center

Duncan, George T.; Pearson, Robert W.

Providing researchers, especially those in the social sciences, with access to publicly collected microdata furthers research while advancing public policy goals in a democratic society. However, while technological improvements have eased remote access to these databases and enabled computer using researchers to perform sophisticated statistical…

5 CFR 1320.14 - Public access.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Public access. 1320.14 Section 1320.14 Administrative Personnel OFFICE OF MANAGEMENT AND BUDGET OMB DIRECTIVES CONTROLLING PAPERWORK BURDENS ON THE PUBLIC § 1320.14 Public access. (a) In order to enable the public to participate in and provide comments...

Enabling Discoveries in Earth Sciences Through the Geosciences Network (GEON)

NASA Astrophysics Data System (ADS)

Seber, D.; Baru, C.; Memon, A.; Lin, K.; Youn, C.

2005-12-01

Taking advantage of the state-of-the-art information technology resources GEON researchers are building a cyberinfrastructure designed to enable data sharing, semantic data integration, high-end computations and 4D visualization in easy-to-use web-based environments. The GEON Network currently allows users to search and register Earth science resources such as data sets (GIS layers, GMT files, geoTIFF images, ASCII files, relational databases etc), software applications or ontologies. Portal based access mechanisms enable developers to built dynamic user interfaces to conduct advanced processing and modeling efforts across distributed computers and supercomputers. Researchers and educators can access the networked resources through the GEON portal and its portlets that were developed to conduct better and more comprehensive science and educational studies. For example, the SYNSEIS portlet in GEON enables users to access in near-real time seismic waveforms from the IRIS Data Management Center, easily build a 3D geologic model within the area of the seismic station(s) and the epicenter and perform a 3D synthetic seismogram analysis to understand the lithospheric structure and earthquake source parameters for any given earthquake in the US. Similarly, GEON's workbench area enables users to create their own work environment and copy, visualize and analyze any data sets within the network, and create subsets of the data sets for their own purposes. Since all these resources are built as part of a Service-oriented Architecture (SOA), they are also used in other development platforms. One such platform is Kepler Workflow system which can access web service based resources and provides users with graphical programming interfaces to build a model to conduct computations and/or visualization efforts using the networked resources. Developments in the area of semantic integration of the networked datasets continue to advance and prototype studies can be accessed via the GEON portal at www.geongrid.org

Quantitative Determination of Aluminum in Deodorant Brands: A Guided Inquiry Learning Experience in Quantitative Analysis Laboratory

ERIC Educational Resources Information Center

Sedwick, Victoria; Leal, Anne; Turner, Dea; Kanu, A. Bakarr

2018-01-01

The monitoring of metals in commercial products is essential for protecting public health against the hazards of metal toxicity. This article presents a guided inquiry (GI) experimental lab approach in a quantitative analysis lab class that enabled students' to determine the levels of aluminum in deodorant brands. The utility of a GI experimental…

Label-free quantitative cell division monitoring of endothelial cells by digital holographic microscopy

NASA Astrophysics Data System (ADS)

Kemper, Björn; Bauwens, Andreas; Vollmer, Angelika; Ketelhut, Steffi; Langehanenberg, Patrik; Müthing, Johannes; Karch, Helge; von Bally, Gert

2010-05-01

Digital holographic microscopy (DHM) enables quantitative multifocus phase contrast imaging for nondestructive technical inspection and live cell analysis. Time-lapse investigations on human brain microvascular endothelial cells demonstrate the use of DHM for label-free dynamic quantitative monitoring of cell division of mother cells into daughter cells. Cytokinetic DHM analysis provides future applications in toxicology and cancer research.

Integrative review of cervical cancer screening in Western Asian and Middle Eastern Arab countries.

PubMed

Ali, Suhailah; Skirton, Heather; Clark, Maria T; Donaldson, Craig

2017-12-01

Population-based screening programs have resulted in minimizing mortality and morbidity from cervical cancer. The aim of this integrative review was to explore the factors influencing access of women from Western Asian and Middle Eastern Arab countries to cervical cancer screening. A systematic search for studies conducted in Arab countries in those regions, and published in English between January 2002 and January 2017, was undertaken. Thirteen papers were selected and subjected to quality appraisal. A three step analysis was used, which involved a summary of the evidence, analysis of both quantitative and qualitative data, and integration of the results in narrative form. Few population-based cervical cancer screening programs had been implemented in the relevant countries, with low knowledge of, and perceptions about, cervical screening among Arab women, the majority of whom are Muslim. Factors affecting the uptake of cervical cancer screening practices were the absence of organized, systematic programs, low screening knowledge among women, healthcare professionals' attitudes toward screening, pain and embarrassment, stigma, and sociocultural beliefs. Policy changes are urgently needed to promote population-based screening programs. Future research should address the promotion of culturally-sensitive strategies to enable better access of Arab Muslim women to cervical cancer screening. © 2017 John Wiley & Sons Australia, Ltd.

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

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

Woods, Daniel P.; Bednarek, Ryland; Bouché, Frédéric

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time.more » A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.« less

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

DOE PAGES

Woods, Daniel P.; Bednarek, Ryland; Bouché, Frédéric; ...

2016-10-14

The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time.more » A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.« less

Prediction of Intrinsic Cesium Desorption from Na-Smectite in Mixed Cation Solutions.

PubMed

Fukushi, Keisuke; Fukiage, Tomo

2015-09-01

Quantitative understanding of the stability of sorbed radionuclides in smectite is necessary to assess the performance of engineering barriers used for nuclear waste disposal. Our previous study demonstrated that the spatial organization of the smectite platelets triggered by the divalent cations led to the apparent fixation of intrinsic Cs in smectite, because some Cs is retained inside the formed tactoids. Natural water is usually a mixture of Na(+) and divalent cations (Ca(2+) and Mg(2+)). This study therefore investigated the desorption behavior of intrinsic Cs in Na-smecite in mixed Na(+)-divalent cation solutions under widely various cation concentrations using batch experiments, grain size measurements, and cation exchange modeling (CEM). Results show that increased Na(+) concentrations facilitate Cs desorption because Na(+) serves as the dispersion agent. A linear relation was obtained between the logarithm of the Na(+) fraction and the accessible Cs fraction in smectite. That relation enables the prediction of accessible Cs fraction as a function of solution cationic compositions. The corrected CEM considering the effects of the spatial organization suggests that the stability of intrinsic Cs in the smectite is governed by the Na(+) concentration, and suggests that it is almost independent of the concentrations of divalent cations in natural water.

Two-Photon Flow Cytometry

NASA Technical Reports Server (NTRS)

Zhog, Cheng Frank; Ye, Jing Yong; Norris, Theodore B.; Myc, Andrzej; Cao, Zhengyl; Bielinska, Anna; Thomas, Thommey; Baker, James R., Jr.

2004-01-01

Flow cytometry is a powerful technique for obtaining quantitative information from fluorescence in cells. Quantitation is achieved by assuring a high degree of uniformity in the optical excitation and detection, generally by using a highly controlled flow such as is obtained via hydrodynamic focusing. In this work, we demonstrate a two-beam, two- channel detection and two-photon excitation flow cytometry (T(sup 3)FC) system that enables multi-dye analysis to be performed very simply, with greatly relaxed requirements on the fluid flow. Two-photon excitation using a femtosecond near-infrared (NIR) laser has the advantages that it enables simultaneous excitation of multiple dyes and achieves very high signal-to-noise ratio through simplified filtering and fluorescence background reduction. By matching the excitation volume to the size of a cell, single-cell detection is ensured. Labeling of cells by targeted nanoparticles with multiple fluorophores enables normalization of the fluorescence signal and thus ratiometric measurements under nonuniform excitation. Quantitative size measurements can also be done even under conditions of nonuniform flow via a two-beam layout. This innovative detection scheme not only considerably simplifies the fluid flow system and the excitation and collection optics, it opens the way to quantitative cytometry in simple and compact microfluidics systems, or in vivo. Real-time detection of fluorescent microbeads in the vasculature of mouse ear demonstrates the ability to do flow cytometry in vivo. The conditions required to perform quantitative in vivo cytometry on labeled cells will be presented.

Strategies for Success: Open Access Policies at North American Educational Institutions

ERIC Educational Resources Information Center

Fruin, Christine; Sutton, Shan

2016-01-01

Recognizing the paucity of quantitative and qualitative data from North American educational institutions that have pursued open access policies, the authors devised a survey to collect information on the characteristics of these institutions, as well as the elements of the open access policies, the methods of promoting these policies, faculty…

Accessible Adult Learning in the Health Professions: Interactive Uses of Distance Technology.

ERIC Educational Resources Information Center

Townsend, Elizabeth; Curran-Smith, Janet

This paper describes a study of students' perceptions of the impact of accessibility and interactivity on successful distance education in the Health Professions. The study utilized both quantitative and qualitative data to determine how students perceived issues of accessibility and interactivity affecting their success in distance courses. The…

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

PubMed

Corces, M Ryan; Trevino, Alexandro E; Hamilton, Emily G; Greenside, Peyton G; Sinnott-Armstrong, Nicholas A; Vesuna, Sam; Satpathy, Ansuman T; Rubin, Adam J; Montine, Kathleen S; Wu, Beijing; Kathiria, Arwa; Cho, Seung Woo; Mumbach, Maxwell R; Carter, Ava C; Kasowski, Maya; Orloff, Lisa A; Risca, Viviana I; Kundaje, Anshul; Khavari, Paul A; Montine, Thomas J; Greenleaf, William J; Chang, Howard Y

2017-10-01

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

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Consumers’ experiences of back pain in rural Western Australia: access to information and services, and self-management behaviours

PubMed Central

2012-01-01

Background Coordinated, interdisciplinary services, supported by self-management underpin effective management for chronic low back pain (CLBP). However, a combination of system, provider and consumer-based barriers exist which limit the implementation of such models into practice, particularly in rural areas where unique access issues exist. In order to improve health service delivery for consumers with CLBP, policymakers and service providers require a more in depth understanding of these issues. The objective of this qualitative study was to explore barriers experienced by consumers in rural settings in Western Australia (WA) to accessing information and services and implementing effective self-management behaviours for CLBP. Methods Fourteen consumers with a history of CLBP from three rural sites in WA participated. Maximum variation sampling was employed to ensure a range of experiences were captured. An interviewer, blinded to quantitative pain history data, conducted semi-structured telephone interviews using a standardised schedule to explore individuals’ access to information and services for CLBP, and self-management behaviours. Interviews were digitally recorded and transcribed verbatim. Inductive analysis techniques were used to derive and refine key themes. Results Five key themes were identified that affected individuals’ experiences of managing CLBP in a rural setting, including: 1) poor access to information and services in rural settings; 2) inadequate knowledge and skills among local practitioners; 3) feelings of isolation and frustration; 4) psychological burden associated with CLBP; and 5) competing lifestyle demands hindering effective self-management for CLBP. Conclusions Consumers in rural WA experienced difficulties in knowing where to access relevant information for CLBP and expressed frustration with the lack of service delivery options to access interdisciplinary and specialist services for CLBP. Competing lifestyle demands such as work and family commitments were cited as key barriers to adopting regular self-management practices. Consumer expectations for improved health service coordination and a workforce skilled in pain management are relevant to future service planning, particularly in the contexts of workforce capacity, community health services, and enablers to effective service delivery in primary care. PMID:23057669

Spatial access priority mapping (SAPM) with fishers: a quantitative GIS method for participatory planning.

PubMed

Yates, Katherine L; Schoeman, David S

2013-01-01

Spatial management tools, such as marine spatial planning and marine protected areas, are playing an increasingly important role in attempts to improve marine management and accommodate conflicting needs. Robust data are needed to inform decisions among different planning options, and early inclusion of stakeholder involvement is widely regarded as vital for success. One of the biggest stakeholder groups, and the most likely to be adversely impacted by spatial restrictions, is the fishing community. In order to take their priorities into account, planners need to understand spatial variation in their perceived value of the sea. Here a readily accessible, novel method for quantitatively mapping fishers' spatial access priorities is presented. Spatial access priority mapping, or SAPM, uses only basic functions of standard spreadsheet and GIS software. Unlike the use of remote-sensing data, SAPM actively engages fishers in participatory mapping, documenting rather than inferring their priorities. By so doing, SAPM also facilitates the gathering of other useful data, such as local ecological knowledge. The method was tested and validated in Northern Ireland, where over 100 fishers participated in a semi-structured questionnaire and mapping exercise. The response rate was excellent, 97%, demonstrating fishers' willingness to be involved. The resultant maps are easily accessible and instantly informative, providing a very clear visual indication of which areas are most important for the fishers. The maps also provide quantitative data, which can be used to analyse the relative impact of different management options on the fishing industry and can be incorporated into planning software, such as MARXAN, to ensure that conservation goals can be met at minimum negative impact to the industry. This research shows how spatial access priority mapping can facilitate the early engagement of fishers and the ready incorporation of their priorities into the decision-making process in a transparent, quantitative way.

Combining data from multiple sources using the CUAHSI Hydrologic Information System

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Ames, D. P.; Horsburgh, J. S.; Goodall, J. L.

2012-12-01

The Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) has developed a Hydrologic Information System (HIS) to provide better access to data by enabling the publication, cataloging, discovery, retrieval, and analysis of hydrologic data using web services. The CUAHSI HIS is an Internet based system comprised of hydrologic databases and servers connected through web services as well as software for data publication, discovery and access. The HIS metadata catalog lists close to 100 web services registered to provide data through this system, ranging from large federal agency data sets to experimental watersheds managed by University investigators. The system's flexibility in storing and enabling public access to similarly formatted data and metadata has created a community data resource from governmental and academic data that might otherwise remain private or analyzed only in isolation. Comprehensive understanding of hydrology requires integration of this information from multiple sources. HydroDesktop is the client application developed as part of HIS to support data discovery and access through this system. HydroDesktop is founded on an open source GIS client and has a plug-in architecture that has enabled the integration of modeling and analysis capability with the functionality for data discovery and access. Model integration is possible through a plug-in built on the OpenMI standard and data visualization and analysis is supported by an R plug-in. This presentation will demonstrate HydroDesktop, showing how it provides an analysis environment within which data from multiple sources can be discovered, accessed and integrated.

A quantitative strategy to detect changes in accessibility of protein regions to chemical modification on heterodimerization

PubMed Central

Dreger, Mathias; Leung, Bo Wah; Brownlee, George G; Deng, Tao

2009-01-01

We describe a method for studying quantitative changes in accessibility of surface lysine residues of the PB1 subunit of the influenza RNA polymerase as a result of association with the PA subunit to form a PB1-PA heterodimer. Our method combines two established methods: (i) the chemical modification of surface lysine residues of native proteins by N-hydroxysuccinimidobiotin (NHS-biotin) and (ii) the stable isotope labeling of amino acids in cell culture (SILAC) followed by tryptic digestion and mass spectrometry. By linking the chemical modification with the SILAC methodology for the first time, we obtain quantitative data on chemical modification allowing subtle changes in accessibility to be described. Five regions in the PB1 monomer showed altered reactivity to NHS-biotin when compared with the [PB1-PA] heterodimer. Mutational analysis of residues in two such regions—at K265 and K481 of PB1, which were about three- and twofold, respectively, less accessible to biotinylation in the PB1-PA heterodimer compared with the PB1 monomer, demonstrated that both K265 and K481 were crucial for polymerase function. This novel assay of quantitative profiling of biotinylation patterns (Q-POP assay) highlights likely conformational changes at important functional sites, as observed here for PB1, and may provide information on protein–protein interaction interfaces. The Q-POP assay should be a generally applicable approach and may detect novel functional sites suitable for targeting by drugs. PMID:19517532

"OnTrack" to University: Understanding Mechanisms of Student Retention in an Australian Pre-University Enabling Program

ERIC Educational Resources Information Center

Lisciandro, Joanne G.; Gibbs, Gael

2016-01-01

University-based enabling programs have become an important pathway to university for non-traditional students. There is increasing interest in understanding the mechanisms that facilitate retention and success of enabling pathway students, with the aim of developing effective strategies for maximising opportunities for university access and…

Quantitation of sweet steviol glycosides by means of a HILIC-MS/MS-SIDA approach.

PubMed

Well, Caroline; Frank, Oliver; Hofmann, Thomas

2013-11-27

Meeting the rising consumer demand for natural food ingredients, steviol glycosides, the sweet principle of Stevia rebaudiana Bertoni (Bertoni), have recently been approved as food additives in the European Union. As regulatory constraints require sensitive methods to analyze the sweet-tasting steviol glycosides in foods and beverages, a HILIC-MS/MS method was developed enabling the accurate and reliable quantitation of the major steviol glycosides stevioside, rebaudiosides A-F, steviolbioside, rubusoside, and dulcoside A by using the corresponding deuterated 16,17-dihydrosteviol glycosides as suitable internal standards. This quantitation not only enables the analysis of the individual steviol glycosides in foods and beverages but also can support the optimization of breeding and postharvest downstream processing of Stevia plants to produce preferentially sweet and least bitter tasting Stevia extracts.

Multiple Intimate Partner Violence Experiences: Knowledge, Access, Utilization and Barriers to Utilization of Resources by Women of the African Diaspora.

PubMed

Sabri, Bushra; Huerta, Julia; Alexander, Kamila A; St Vil, Noelle M; Campbell, Jacquelyn C; Callwood, Gloria B

2015-11-01

This study examined knowledge, access, utilization, and barriers to use of resources among Black women exposed to multiple types of intimate partner violence in Baltimore, Maryland and the U.S. Virgin Islands (USVI). We analyzed quantitative survey data collected by 163 women recruited from primary care, prenatal or family planning clinics in Baltimore and the USVI. In addition we analyzed qualitative data from in-depth interviews with 11 women. Quantitative data were analyzed using descriptive statistics and qualitative data were analyzed using thematic analysis. A substantial proportion of Black women with multiple types of violence experiences lacked knowledge of, did not have access to, and did not use resources. Barriers to resource use were identified at the individual, relationship, and community levels. There is need for programs to develop awareness, promote access and utilization of resources, and eliminate barriers to resource use among abused Black women.

Dr. Tulga Ersal at NSF Workshop Accessible Remote Testbeds ART'15

Science.gov Websites

;Enabling High-Fidelity Closed-Loop Integration of Remotely Accessible Testbeds" at the NSF Sponsored project (2010-2013) "Internet-Distributed Hardware-in-the-Loop Simulation". Sponsored by U.S

Virtual Computing Laboratories: A Case Study with Comparisons to Physical Computing Laboratories

ERIC Educational Resources Information Center

Burd, Stephen D.; Seazzu, Alessandro F.; Conway, Christopher

2009-01-01

Current technology enables schools to provide remote or virtual computing labs that can be implemented in multiple ways ranging from remote access to banks of dedicated workstations to sophisticated access to large-scale servers hosting virtualized workstations. This paper reports on the implementation of a specific lab using remote access to…

Achieving Access to the General Curriculum for Students with Mental Retardation.

ERIC Educational Resources Information Center

Wehmeyer, Michael L.; Lattin, Dana; Agran, Martin

2001-01-01

This article reviews requirements in the Individuals with Disabilities Education Act for providing access to the general education curriculum, examines the intent of the language, and proposes a decision-making model to enable Individualized Education Program teams to reach curriculum decisions that provide such access for students with mental…

Achievable Rate Estimation of IEEE 802.11ad Visual Big-Data Uplink Access in Cloud-Enabled Surveillance Applications.

PubMed

Kim, Joongheon; Kim, Jong-Kook

2016-01-01

This paper addresses the computation procedures for estimating the impact of interference in 60 GHz IEEE 802.11ad uplink access in order to construct visual big-data database from randomly deployed surveillance camera sensing devices. The acquired large-scale massive visual information from surveillance camera devices will be used for organizing big-data database, i.e., this estimation is essential for constructing centralized cloud-enabled surveillance database. This performance estimation study captures interference impacts on the target cloud access points from multiple interference components generated by the 60 GHz wireless transmissions from nearby surveillance camera devices to their associated cloud access points. With this uplink interference scenario, the interference impacts on the main wireless transmission from a target surveillance camera device to its associated target cloud access point with a number of settings are measured and estimated under the consideration of 60 GHz radiation characteristics and antenna radiation pattern models.

What do parents perceive are the barriers and facilitators to accessing psychological treatment for mental health problems in children and adolescents? A systematic review of qualitative and quantitative studies.

PubMed

Reardon, Tessa; Harvey, Kate; Baranowska, Magdalena; O'Brien, Doireann; Smith, Lydia; Creswell, Cathy

2017-06-01

A minority of children and adolescents with mental health problems access treatment. The reasons for poor rates of treatment access are not well understood. As parents are a key gatekeeper to treatment access, it is important to establish parents' views of barriers/facilitators to accessing treatment. The aims of this study are to synthesise findings from qualitative and quantitative studies that report parents' perceptions of barriers/facilitators to accessing treatment for mental health problems in children/adolescents. A systematic review and narrative synthesis were conducted. Forty-four studies were included in the review and were assessed in detail. Parental perceived barriers/facilitators relating to (1) systemic/structural issues; (2) views and attitudes towards services and treatment; (3) knowledge and understanding of mental health problems and the help-seeking process; and (4) family circumstances were identified. Findings highlight avenues for improving access to child mental health services, including increased provision that is free to service users and flexible to their needs, with opportunities to develop trusting, supportive relationships with professionals. Furthermore, interventions are required to improve parents' identification of mental health problems, reduce stigma for parents, and increase awareness of how to access services.

PTMScout, a Web Resource for Analysis of High Throughput Post-translational Proteomics Studies*

PubMed Central

Naegle, Kristen M.; Gymrek, Melissa; Joughin, Brian A.; Wagner, Joel P.; Welsch, Roy E.; Yaffe, Michael B.; Lauffenburger, Douglas A.; White, Forest M.

2010-01-01

The rate of discovery of post-translational modification (PTM) sites is increasing rapidly and is significantly outpacing our biological understanding of the function and regulation of those modifications. To help meet this challenge, we have created PTMScout, a web-based interface for viewing, manipulating, and analyzing high throughput experimental measurements of PTMs in an effort to facilitate biological understanding of protein modifications in signaling networks. PTMScout is constructed around a custom database of PTM experiments and contains information from external protein and post-translational resources, including gene ontology annotations, Pfam domains, and Scansite predictions of kinase and phosphopeptide binding domain interactions. PTMScout functionality comprises data set comparison tools, data set summary views, and tools for protein assignments of peptides identified by mass spectrometry. Analysis tools in PTMScout focus on informed subset selection via common criteria and on automated hypothesis generation through subset labeling derived from identification of statistically significant enrichment of other annotations in the experiment. Subset selection can be applied through the PTMScout flexible query interface available for quantitative data measurements and data annotations as well as an interface for importing data set groupings by external means, such as unsupervised learning. We exemplify the various functions of PTMScout in application to data sets that contain relative quantitative measurements as well as data sets lacking quantitative measurements, producing a set of interesting biological hypotheses. PTMScout is designed to be a widely accessible tool, enabling generation of multiple types of biological hypotheses from high throughput PTM experiments and advancing functional assignment of novel PTM sites. PTMScout is available at http://ptmscout.mit.edu. PMID:20631208

Predictive Modeling of Chemical Hazard by Integrating Numerical Descriptors of Chemical Structures and Short-term Toxicity Assay Data

PubMed Central

Rusyn, Ivan; Sedykh, Alexander; Guyton, Kathryn Z.; Tropsha, Alexander

2012-01-01

Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR–like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage. PMID:22387746

Improving organic tandem solar cells based on water-processed nanoparticles by quantitative 3D nanoimaging.

PubMed

Pedersen, E B L; Angmo, D; Dam, H F; Thydén, K T S; Andersen, T R; Skjønsfjell, E T B; Krebs, F C; Holler, M; Diaz, A; Guizar-Sicairos, M; Breiby, D W; Andreasen, J W

2015-08-28

Organic solar cells have great potential for upscaling due to roll-to-roll processing and a low energy payback time, making them an attractive sustainable energy source for the future. Active layers coated with water-dispersible Landfester particles enable greater control of the layer formation and easier access to the printing industry, which has reduced the use of organic solvents since the 1980s. Through ptychographic X-ray computed tomography (PXCT), we image quantitatively a roll-to-roll coated photovoltaic tandem stack consisting of one bulk heterojunction active layer and one Landfester particle active layer. We extract the layered morphology with structural and density information including the porosity present in the various layers and the silver electrode with high resolution in 3D. The Landfester particle layer is found to have an undesired morphology with negatively correlated top- and bottom interfaces, wide thickness distribution and only partial surface coverage causing electric short circuits through the layer. By top coating a polymer material onto the Landfester nanoparticles we eliminate the structural defects of the layer such as porosity and roughness, and achieve the increased performance larger than 1 V expected for a tandem cell. This study highlights that quantitative imaging of weakly scattering stacked layers of organic materials has become feasible by PXCT, and that this information cannot be obtained by other methods. In the present study, this technique specifically reveals the need to improve the coatability and layer formation of Landfester nanoparticles, thus allowing improved solar cells to be produced.

An optimized framework for quantitative magnetization transfer imaging of the cervical spinal cord in vivo.

PubMed

Battiston, Marco; Grussu, Francesco; Ianus, Andrada; Schneider, Torben; Prados, Ferran; Fairney, James; Ourselin, Sebastien; Alexander, Daniel C; Cercignani, Mara; Gandini Wheeler-Kingshott, Claudia A M; Samson, Rebecca S

2018-05-01

To develop a framework to fully characterize quantitative magnetization transfer indices in the human cervical cord in vivo within a clinically feasible time. A dedicated spinal cord imaging protocol for quantitative magnetization transfer was developed using a reduced field-of-view approach with echo planar imaging (EPI) readout. Sequence parameters were optimized based in the Cramer-Rao-lower bound. Quantitative model parameters (i.e., bound pool fraction, free and bound pool transverse relaxation times [ T2F, T2B], and forward exchange rate [k FB ]) were estimated implementing a numerical model capable of dealing with the novelties of the sequence adopted. The framework was tested on five healthy subjects. Cramer-Rao-lower bound minimization produces optimal sampling schemes without requiring the establishment of a steady-state MT effect. The proposed framework allows quantitative voxel-wise estimation of model parameters at the resolution typically used for spinal cord imaging (i.e. 0.75 × 0.75 × 5 mm 3 ), with a protocol duration of ∼35 min. Quantitative magnetization transfer parametric maps agree with literature values. Whole-cord mean values are: bound pool fraction = 0.11(±0.01), T2F = 46.5(±1.6) ms, T2B = 11.0(±0.2) µs, and k FB  = 1.95(±0.06) Hz. Protocol optimization has a beneficial effect on reproducibility, especially for T2B and k FB . The framework developed enables robust characterization of spinal cord microstructure in vivo using qMT. Magn Reson Med 79:2576-2588, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine.

Spatial access disparities to primary health care in rural and remote Australia.

PubMed

McGrail, Matthew Richard; Humphreys, John Stirling

2015-11-04

Poor spatial access to health care remains a key issue for rural populations worldwide. Whilst geographic information systems (GIS) have enabled the development of more sophisticated access measures, they are yet to be adopted into health policy and workforce planning. This paper provides and tests a new national-level approach to measuring primary health care (PHC) access for rural Australia, suitable for use in macro-level health policy. The new index was constructed using a modified two-step floating catchment area method framework and the smallest available geographic unit. Primary health care spatial access was operationalised using three broad components: availability of PHC (general practitioner) services; proximity of populations to PHC services; and PHC needs of the population. Data used in its measurement were specifically chosen for accuracy, reliability and ongoing availability for small areas. The resultant index reveals spatial disparities of access to PHC across rural Australia. While generally more remote areas experienced poorer access than more populated rural areas, there were numerous exceptions to this generalisation, with some rural areas close to metropolitan areas having very poor access and some increasingly remote areas having relatively good access. This new index provides a geographically-sensitive measure of access, which is readily updateable and enables a fine granulation of access disparities. Such an index can underpin national rural health programmes and policies designed to improve rural workforce recruitment and retention, and, importantly, health service planning and resource allocation decisions designed to improve equity of PHC access.

Comparison of Standards for Accessible Design between America and China

NASA Astrophysics Data System (ADS)

Han, Ying; Tao, Xu Feng

2018-06-01

Aiming at the accessibility design and environmental constructions of China, comparing the differences of codes for accessibility design between domestic and abroad. It's including four aspects: the difference in audience of accessible design, content of the facilities, quantitative indexes and vision and hearing accessible design. It analyzed that the early stage of our country is backward in terms of accessibility and construction, mainly based on differences in values and professional education. In the end it put forward three suggestions to improve the construction of barrier-free environment in China.

Barriers to and enablers of implementing antimicrobial stewardship programs in veterinary practices.

PubMed

Hardefeldt, Laura Y; Gilkerson, J R; Billman-Jacobe, H; Stevenson, M A; Thursky, K; Bailey, K E; Browning, G F

2018-03-23

Antimicrobial stewardship (AMS) programs are yet to be widely implemented in veterinary practice and medical programs are unlikely to be directly applicable to veterinary settings. To gain an in-depth understanding of the factors that influence effective AMS in veterinary practices in Australia. A concurrent explanatory mixed methods design was used. The quantitative phase of the study consisted of an online questionnaire to assess veterinarians' attitudes to antimicrobial resistance (AMR) and antimicrobial use in animals, and the extent to which AMS currently is implemented (knowingly or unknowingly). The qualitative phase used semi-structured interviews to gain an understanding of the barriers to and enablers of AMS in veterinary practices. Data were collected and entered into NVivo v.11, openly coded and analyzed according to mixed methods data analysis principles. Companion animal, equine, and bovine veterinarians participated in the study. Veterinary practices rarely had antimicrobial prescribing policies. The key barriers were a lack of AMS governance structures, client expectations and competition between practices, cost of microbiological testing, and lack of access to education, training and AMS resources. The enablers were concern for the role of veterinary antimicrobial use in development of AMR in humans, a sense of pride in the service provided, and preparedness to change prescribing practices. Our study can guide development and establishment of AMS programs in veterinary practices by defining the major issues that influence the prescribing behavior of veterinarians. © 2018 The Authors. Journal of Veterinary Internal Medicine published by Wiley Periodicals, Inc. on behalf of the American College of Veterinary Internal Medicine.

Technology-Enabled and Universally Designed Assessment: Considering Access in Measuring the Achievement of Students with Disabilities--A Foundation for Research

ERIC Educational Resources Information Center

Almond, Patricia; Winter, Phoebe; Cameto, Renee; Russell, Michael; Sato, Edynn; Clarke-Midura, Jody; Torres, Chloe; Haertel, Geneva; Dolan, Robert; Beddow, Peter; Lazarus, Sheryl

2010-01-01

This paper represents one outcome from the "Invitational Research Symposium on Technology-Enabled and Universally Designed Assessments," which examined technology-enabled assessments (TEA) and universal design (UD) as they relate to students with disabilities (SWD). It was developed to stimulate research into TEAs designed to make tests…

Core or Periphery? The Positioning of Language and Literacies in Enabling Programs in Australia

ERIC Educational Resources Information Center

Baker, Sally; Irwin, Evonne

2016-01-01

Enabling education has a respected and established place in Australian higher education as an alternative pathway into university study. While the value of enabling education in providing access to higher education is undeniable, its provision across Australia is necessarily diverse, as individual programs respond to the needs of their local…

Building Strategic Capabilities for Sustained Lunar Exploration

NASA Astrophysics Data System (ADS)

Landgraf, M.; Hufenbach, B.; Houdou, B.

2016-11-01

We discuss a lunar exploration architecture that addresses the strategic objective of providing access to the lunar surface. This access enables the most exciting part of the lunar exploration: building a sustained infrastructure on the lunar surface.

Mobile devices and weak ties: a study of vision impairments and workplace access in Bangalore.

PubMed

Pal, Joyojeet; Lakshmanan, Meera

2015-07-01

To explore ways in which social and economic interactions are changed by access to mobile telephony. This is a mixed-methods study of mobile phone use among 52 urban professionals with vision impairments in Bangalore, India. Interviews and survey results indicated that mobile devices, specifically those with adaptive technology software, play a vital role as multi-purpose devices that enable people with disabilities to navigate economically and socially in an environment where accessibility remains a significant challenge. We found that mobile devices play a central role in enabling and sustaining weak ties, but also that these weak ties have important gender-specific implications. We found that women have less access to weak ties than men, which impacts women's access to assistive technology (AT). This has potential implications for women's sense of safety and independence, both of which are strongly related to AT access. Implications for Rehabilitation Adaptive technologies increase individuals' ability to keep in contact with casual connections or weak ties through phone calls or social media. Men tend to have stronger access to weak ties than women in India due to cultural impediments to independent access to public spaces. Weak ties are an important source of assistive technology (AT) due to the high rate of resale of used AT, typically through informal networks.

A comparative study of quantitative immunohistochemistry and quantum dot immunohistochemistry for mutation carrier identification in Lynch syndrome.

PubMed

Barrow, Emma; Evans, D Gareth; McMahon, Ray; Hill, James; Byers, Richard

2011-03-01

Lynch Syndrome is caused by mutations in DNA mismatch repair (MMR) genes. Mutation carrier identification is facilitated by immunohistochemical detection of the MMR proteins MHL1 and MSH2 in tumour tissue and is desirable as colonoscopic screening reduces mortality. However, protein detection by conventional immunohistochemistry (IHC) is subjective, and quantitative techniques are required. Quantum dots (QDs) are novel fluorescent labels that enable quantitative multiplex staining. This study compared their use with quantitative 3,3'-diaminobenzidine (DAB) IHC for the diagnosis of Lynch Syndrome. Tumour sections from 36 mutation carriers and six controls were obtained. These were stained with DAB on an automated platform using antibodies against MLH1 and MSH2. Multiplex QD immunofluorescent staining of the sections was performed using antibodies against MLH1, MSH2 and smooth muscle actin (SMA). Multispectral analysis of the slides was performed. The staining intensity of DAB and QDs was measured in multiple colonic crypts, and the mean intensity scores calculated. Receiver operating characteristic (ROC) curves of staining performance for the identification of mutation carriers were evaluated. For quantitative DAB IHC, the area under the MLH1 ROC curve was 0.872 (95% CI 0.763 to 0.981), and the area under the MSH2 ROC curve was 0.832 (95% CI 0.704 to 0.960). For quantitative QD IHC, the area under the MLH1 ROC curve was 0.812 (95% CI 0.681 to 0.943), and the area under the MSH2 ROC curve was 0.598 (95% CI 0.418 to 0.777). Despite the advantage of QD staining to enable several markers to be measured simultaneously, it is of lower utility than DAB IHC for the identification of MMR mutation carriers. Automated DAB IHC staining and quantitative slide analysis may enable high-throughput IHC.

Terrain - Umbra Package v. 1.0

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

Oppel, Fred; Hart, Brian; Rigdon, James Brian

This library contains modules that read terrain files (e.g., OpenFlight, Open Scene Graph IVE, GeoTIFF Image) and to read and manage ESRI terrain datasets. All data is stored and managed in Open Scene Graph (OSG). Terrain system accesses OSG and provides elevation data, access to meta-data such as soil types and enables linears, areals and buildings to be placed in a terrain, These geometry objects include boxes, point, path, and polygon (region), and sector modules. Utilities have been made available for clamping objects to the terrain and accessing LOS information. This assertion includes a managed C++ wrapper code (TerrainWrapper) tomore » enable C# applications, such as OpShed and UTU, to incorporate this library.« less

On the Distinction Between Quantitative and Qualitative Research.

ERIC Educational Resources Information Center

Smith, P. L.

Quantitative and qualitative research are differing modes of measurement, one using numbers and the other not. The assignment of numerals to represent properties enables a researcher to distinguish minutely between different properties. The major issue dividing these approaches to empirical research represents a philosophical dispute which has…

Quantitative single-molecule imaging by confocal laser scanning microscopy.

PubMed

Vukojevic, Vladana; Heidkamp, Marcus; Ming, Yu; Johansson, Björn; Terenius, Lars; Rigler, Rudolf

2008-11-25

A new approach to quantitative single-molecule imaging by confocal laser scanning microscopy (CLSM) is presented. It relies on fluorescence intensity distribution to analyze the molecular occurrence statistics captured by digital imaging and enables direct determination of the number of fluorescent molecules and their diffusion rates without resorting to temporal or spatial autocorrelation analyses. Digital images of fluorescent molecules were recorded by using fast scanning and avalanche photodiode detectors. In this way the signal-to-background ratio was significantly improved, enabling direct quantitative imaging by CLSM. The potential of the proposed approach is demonstrated by using standard solutions of fluorescent dyes, fluorescently labeled DNA molecules, quantum dots, and the Enhanced Green Fluorescent Protein in solution and in live cells. The method was verified by using fluorescence correlation spectroscopy. The relevance for biological applications, in particular, for live cell imaging, is discussed.

Naval Oceanography Portal

Science.gov Websites

accessible and usable, working in accordance with the Web Content Accessibility Guidelines (WCAG v1.0). If navigation device enabling you to get around this web site using your keyboard. Available access keys This develop a web site that is clear and simple for everybody to use. Validation We have used XHTML 1.0 and

LOADING AND UNLOADING DEVICE

DOEpatents

Treshow, M.

1960-08-16

A device for loading and unloading fuel rods into and from a reactor tank through an access hole includes parallel links carrying a gripper. These links enable the gripper to go through the access hole and then to be moved laterally from the axis of the access hole to the various locations of the fuel rods in the reactor tank.

Putting a Medical Library Online: Phase III--Remote Access to CD-ROMs.

ERIC Educational Resources Information Center

Kittle, Paul

1989-01-01

Describes the implementation of a project that provides dial-up access to MEDLINE on remote optical data disk (CD-ROM) using software that enables callers to use programs like Wordstar, Lotus, and dBase. Highlights include networking CD-ROM databases, hardware considerations, advantages and disadvantages of remote access, and future plans. A…

Measuring Confidence Levels of Male and Female Students in Open Access Enabling Courses

ERIC Educational Resources Information Center

Atherton, Mirella

2015-01-01

The study of confidence was undertaken at the University of Newcastle with students selecting science courses at two campuses. The students were enrolled in open access programs and aimed to gain access to undergraduate studies in various disciplines at University. The "third person effect" was used to measure the confidence levels of…

76 FR 19357 - Emergency Access Advisory Committee; Announcement of Date of Next Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-07

... Committee will address the status of the national survey of persons with disability and seniors to learn... access to emergency services by individuals with disabilities as part of our nation's migration to a... methods by which to enable access to NG9-1-1 emergency services by individuals with disabilities. In order...

Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis.

PubMed

Lindén, Rolf O; Eronen, Ville-Pekka; Aittokallio, Tero

2011-03-24

High-throughput genetic screening approaches have enabled systematic means to study how interactions among gene mutations contribute to quantitative fitness phenotypes, with the aim of providing insights into the functional wiring diagrams of genetic interaction networks on a global scale. However, it is poorly known how well these quantitative interaction measurements agree across the screening approaches, which hinders their integrated use toward improving the coverage and quality of the genetic interaction maps in yeast and other organisms. Using large-scale data matrices from epistatic miniarray profiling (E-MAP), genetic interaction mapping (GIM), and synthetic genetic array (SGA) approaches, we carried out here a systematic comparative evaluation among these quantitative maps of genetic interactions in yeast. The relatively low association between the original interaction measurements or their customized scores could be improved using a matrix-based modelling framework, which enables the use of single- and double-mutant fitness estimates and measurements, respectively, when scoring genetic interactions. Toward an integrative analysis, we show how the detections from the different screening approaches can be combined to suggest novel positive and negative interactions which are complementary to those obtained using any single screening approach alone. The matrix approximation procedure has been made available to support the design and analysis of the future screening studies. We have shown here that even if the correlation between the currently available quantitative genetic interaction maps in yeast is relatively low, their comparability can be improved by means of our computational matrix approximation procedure, which will enable integrative analysis and detection of a wider spectrum of genetic interactions using data from the complementary screening approaches.

Human genomic DNA quantitation system, H-Quant: development and validation for use in forensic casework.

PubMed

Shewale, Jaiprakash G; Schneida, Elaine; Wilson, Jonathan; Walker, Jerilyn A; Batzer, Mark A; Sinha, Sudhir K

2007-03-01

The human DNA quantification (H-Quant) system, developed for use in human identification, enables quantitation of human genomic DNA in biological samples. The assay is based on real-time amplification of AluYb8 insertions in hominoid primates. The relatively high copy number of subfamily-specific Alu repeats in the human genome enables quantification of very small amounts of human DNA. The oligonucleotide primers present in H-Quant are specific for human DNA and closely related great apes. During the real-time PCR, the SYBR Green I dye binds to the DNA that is synthesized by the human-specific AluYb8 oligonucleotide primers. The fluorescence of the bound SYBR Green I dye is measured at the end of each PCR cycle. The cycle at which the fluorescence crosses the chosen threshold correlates to the quantity of amplifiable DNA in that sample. The minimal sensitivity of the H-Quant system is 7.6 pg/microL of human DNA. The amplicon generated in the H-Quant assay is 216 bp, which is within the same range of the common amplifiable short tandem repeat (STR) amplicons. This size amplicon enables quantitation of amplifiable DNA as opposed to a quantitation of degraded or nonamplifiable DNA of smaller sizes. Development and validation studies were performed on the 7500 real-time PCR system following the Quality Assurance Standards for Forensic DNA Testing Laboratories.

Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry.

PubMed

Gómez, Gabriela E; Mundo, Mariana R; Craig, Patricio O; Delfino, José M

2012-01-01

Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites. © American Society for Mass Spectrometry, 2011

Valued aspects of primary palliative care: content analysis of bereaved carers' descriptions.

PubMed

Grande, Gunn E; Farquhar, Morag C; Barclay, Stephen Ig; Todd, Chris J

2004-10-01

Informal carers provide the bulk of palliative home care. They largely rely on general practitioners (GPs) and district nurses to support them in this role, yet little is known about what carers themselves consider important in this support. To identify what informal carers valued in the palliative support provided by GPs and district nurses by using carers' own descriptions of such support. Retrospective interviews. Primary care in Cambridgeshire. Semi-structured interviews with bereaved carers of 48 patients with cancer and 12 patients with non-cancer diagnoses. Content analysis of carers' evaluative descriptions of GP and district nurse support. The accessibility of the GP and district nurse emerged as the most important aspect of support. Enlistment of help from other agencies was also extensively mentioned, together with provision of equipment. Attitude or approach during interactions, and relationship with the professional were important, particularly regarding GP support, whereas support for the carer, information, and symptom control were mentioned less often. Data suggested that support was not as good for older patients (> or =75 years), but this finding requires further investigation. Results largely confirmed findings of previous, quantitative research and the importance of a patient-centred approach. What emerged most strongly, however, was the central importance of accessibility of support services for lay carers responsible for end-of-life home care. This mainly concerned GP and district nurse support, but accessibility of additional care and equipment were also important. In short, carers' main focus was the basic support that enabled them to sustain care in the home.

Information Power Grid (IPG) Tutorial 2003

NASA Technical Reports Server (NTRS)

Meyers, George

2003-01-01

For NASA and the general community today Grid middleware: a) provides tools to access/use data sources (databases, instruments, ...); b) provides tools to access computing (unique and generic); c) Is an enabler of large scale collaboration. Dynamically responding to needs is a key selling point of a grid. Independent resources can be joined as appropriate to solve a problem. Provide tools to enable the building of a frameworks for application. Provide value added service to the NASA user base for utilizing resources on the grid in new and more efficient ways. Provides tools for development of Frameworks.

The role of CORBA in enabling telemedicine

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

Forslund, D.W.

1997-07-01

One of the most powerful tools available for telemedicine is a multimedia medical record accessible over a wide area and simultaneously editable by multiple physicians. The ability to do this through an intuitive interface linking multiple distributed data repositories while maintaining full data integrity is a fundamental enabling technology in healthcare. The author discusses the role of distributed object technology using CORBA in providing this capability including an example of such a system (TeleMed) which can be accessed through the World Wide Web. Issues of security, scalability, data integrity, and useability are emphasized.

SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes.

PubMed

Mägi, Reedik; Suleimanov, Yury V; Clarke, Geraldine M; Kaakinen, Marika; Fischer, Krista; Prokopenko, Inga; Morris, Andrew P

2017-01-11

Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite the fact that many diseases and quantitative traits are correlated with each other, and often measured in the same sample of individuals. Multivariate analyses of correlated phenotypes have been demonstrated, by simulation, to increase power to detect association with SNPs, and thus may enable improved detection of novel loci contributing to diseases and quantitative traits. We have developed the SCOPA software to enable GWAS analysis of multiple correlated phenotypes. The software implements "reverse regression" methodology, which treats the genotype of an individual at a SNP as the outcome and the phenotypes as predictors in a general linear model. SCOPA can be applied to quantitative traits and categorical phenotypes, and can accommodate imputed genotypes under a dosage model. The accompanying META-SCOPA software enables meta-analysis of association summary statistics from SCOPA across GWAS. Application of SCOPA to two GWAS of high-and low-density lipoprotein cholesterol, triglycerides and body mass index, and subsequent meta-analysis with META-SCOPA, highlighted stronger association signals than univariate phenotype analysis at established lipid and obesity loci. The META-SCOPA meta-analysis also revealed a novel signal of association at genome-wide significance for triglycerides mapping to GPC5 (lead SNP rs71427535, p = 1.1x10 -8 ), which has not been reported in previous large-scale GWAS of lipid traits. The SCOPA and META-SCOPA software enable discovery and dissection of multiple phenotype association signals through implementation of a powerful reverse regression approach.

Safe Grid

NASA Technical Reports Server (NTRS)

Chow, Edward T.; Stewart, Helen; Korsmeyer, David (Technical Monitor)

2003-01-01

The biggest users of GRID technologies came from the science and technology communities. These consist of government, industry and academia (national and international). The NASA GRID is moving into a higher technology readiness level (TRL) today; and as a joint effort among these leaders within government, academia, and industry, the NASA GRID plans to extend availability to enable scientists and engineers across these geographical boundaries collaborate to solve important problems facing the world in the 21 st century. In order to enable NASA programs and missions to use IPG resources for program and mission design, the IPG capabilities needs to be accessible from inside the NASA center networks. However, because different NASA centers maintain different security domains, the GRID penetration across different firewalls is a concern for center security people. This is the reason why some IPG resources are been separated from the NASA center network. Also, because of the center network security and ITAR concerns, the NASA IPG resource owner may not have full control over who can access remotely from outside the NASA center. In order to obtain organizational approval for secured remote access, the IPG infrastructure needs to be adapted to work with the NASA business process. Improvements need to be made before the IPG can be used for NASA program and mission development. The Secured Advanced Federated Environment (SAFE) technology is designed to provide federated security across NASA center and NASA partner's security domains. Instead of one giant center firewall which can be difficult to modify for different GRID applications, the SAFE "micro security domain" provide large number of professionally managed "micro firewalls" that can allow NASA centers to accept remote IPG access without the worry of damaging other center resources. The SAFE policy-driven capability-based federated security mechanism can enable joint organizational and resource owner approved remote access from outside of NASA centers. A SAFE enabled IPG can enable IPG capabilities to be available to NASA mission design teams across different NASA center and partner company firewalls. This paper will first discuss some of the potential security issues for IPG to work across NASA center firewalls. We will then present the SAFE federated security model. Finally we will present the concept of the architecture of a SAFE enabled IPG and how it can benefit NASA mission development.

Virtualising the Quantitative Research Methods Course: An Island-Based Approach

ERIC Educational Resources Information Center

Baglin, James; Reece, John; Baker, Jenalle

2015-01-01

Many recent improvements in pedagogical practice have been enabled by the rapid development of innovative technologies, particularly for teaching quantitative research methods and statistics. This study describes the design, implementation, and evaluation of a series of specialised computer laboratory sessions. The sessions combined the use of an…

Recent Progress in the Remote Detection of Vapours and Gaseous Pollutants.

ERIC Educational Resources Information Center

Moffat, A. J.; And Others

Work has been continuing on the correlation spectrometry techniques described at previous remote sensing symposiums. Advances in the techniques are described which enable accurate quantitative measurements of diffused atmospheric gases to be made using controlled light sources, accurate quantitative measurements of gas clouds relative to…

Droplet microfluidics--a tool for single-cell analysis.

PubMed

Joensson, Haakan N; Andersson Svahn, Helene

2012-12-03

Droplet microfluidics allows the isolation of single cells and reagents in monodisperse picoliter liquid capsules and manipulations at a throughput of thousands of droplets per second. These qualities allow many of the challenges in single-cell analysis to be overcome. Monodispersity enables quantitative control of solute concentrations, while encapsulation in droplets provides an isolated compartment for the single cell and its immediate environment. The high throughput allows the processing and analysis of the tens of thousands to millions of cells that must be analyzed to accurately describe a heterogeneous cell population so as to find rare cell types or access sufficient biological space to find hits in a directed evolution experiment. The low volumes of the droplets make very large screens economically viable. This Review gives an overview of the current state of single-cell analysis involving droplet microfluidics and offers examples where droplet microfluidics can further biological understanding. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Direct determination of the local Hamaker constant of inorganic surfaces based on scanning force microscopy

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

Krajina, Brad A.; Kocherlakota, Lakshmi S.; Overney, René M., E-mail: roverney@u.washington.edu

The energetics involved in the bonding fluctuations between nanometer-sized silicon dioxide (SiO{sub 2}) probes and highly oriented pyrolytic graphite (HOPG) and molybdenum disulfide (MoS{sub 2}) could be quantified directly and locally on the submicron scale via a time-temperature superposition analysis of the lateral forces between scanning force microscopy silicon dioxide probes and inorganic sample surfaces. The so-called “intrinsic friction analysis” (IFA) provided direct access to the Hamaker constants for HOPG and MoS{sub 2}, as well as the control sample, calcium fluoride (CaF{sub 2}). The use of scanning probe enables nanoscopic analysis of bonding fluctuations, thereby overcoming challenges associated with largermore » scale inhomogeneity and surface roughness common to conventional techniques used to determine surface free energies and dielectric properties. A complementary numerical analysis based on optical and electron energy loss spectroscopy and the Lifshitz quantum electrodynamic theory of van der Waals interactions is provided and confirms quantitatively the IFA results.« less

Inkjet-printed point-of-care immunoassay on a nanoscale polymer brush enables subpicomolar detection of analytes in blood

NASA Astrophysics Data System (ADS)

Joh, Daniel Y.; Hucknall, Angus M.; Wei, Qingshan; Mason, Kelly A.; Lund, Margaret L.; Fontes, Cassio M.; Hill, Ryan T.; Blair, Rebecca; Zimmers, Zackary; Achar, Rohan K.; Tseng, Derek; Gordan, Raluca; Freemark, Michael; Ozcan, Aydogan; Chilkoti, Ashutosh

2017-08-01

The ELISA is the mainstay for sensitive and quantitative detection of protein analytes. Despite its utility, ELISA is time-consuming, resource-intensive, and infrastructure-dependent, limiting its availability in resource-limited regions. Here, we describe a self-contained immunoassay platform (the “D4 assay”) that converts the sandwich immunoassay into a point-of-care test (POCT). The D4 assay is fabricated by inkjet printing assay reagents as microarrays on nanoscale polymer brushes on glass chips, so that all reagents are “on-chip,” and these chips show durable storage stability without cold storage. The D4 assay can interrogate multiple analytes from a drop of blood, is compatible with a smartphone detector, and displays analytical figures of merit that are comparable to standard laboratory-based ELISA in whole blood. These attributes of the D4 POCT have the potential to democratize access to high-performance immunoassays in resource-limited settings without sacrificing their performance.

Complementation of biotransformations with chemical C-H oxidation: copper-catalyzed oxidation of tertiary amines in complex pharmaceuticals.

PubMed

Genovino, Julien; Lütz, Stephan; Sames, Dalibor; Touré, B Barry

2013-08-21

The isolation, quantitation, and characterization of drug metabolites in biological fluids remain challenging. Rapid access to oxidized drugs could facilitate metabolite identification and enable early pharmacology and toxicity studies. Herein, we compared biotransformations to classical and new chemical C-H oxidation methods using oxcarbazepine, naproxen, and an early compound hit (phthalazine 1). These studies illustrated the low preparative efficacy of biotransformations and the inability of chemical methods to oxidize complex pharmaceuticals. We also disclose an aerobic catalytic protocole (CuI/air) to oxidize tertiary amines and benzylic CH's in drugs. The reaction tolerates a broad range of functionalities and displays a high level of chemoselectivity, which is not generally explained by the strength of the C-H bonds but by the individual structural chemotype. This study represents a first step toward establishing a chemical toolkit (chemotransformations) that can selectively oxidize C-H bonds in complex pharmaceuticals and rapidly deliver drug metabolites.

Using Aoristic Analysis to Link Remote and Ground-Level Phenological Observations

NASA Astrophysics Data System (ADS)

Henebry, G. M.

2013-12-01

Phenology is about observing events in time and space. With the advent of publically accessible geospatial datastreams and easy to use mapping software, specifying where an event occurs is much less of a challenge than it was just two decades ago. In contrast, specifying when an event occurs remains a nontrivial function of a population of organismal responses, sampling interval, compositing period, and reporting precision. I explore how aoristic analysis can be used to analyzing spatiotemporal events for which the location is known to acceptable levels of precision but for which temporal coordinates are poorly specified or only partially bounded. Aoristic analysis was developed in the late 1990s in the field of quantitative criminology to leverage temporally imprecise geospatial data of crime reports. Here I demonstrate how aoristic analysis can be used to link remotely sensed observations of land surface phenology to ground-level observations of organismal phenophase transitions. Explicit representation of the windows of temporal uncertainty with aoristic weights enables cross-validation exercises and forecasting efforts to avoid false precision.

Shape coexistence from lifetime and branching-ratio measurements in 68,70Ni

DOE PAGES

Crider, B. P.; Prokop, C. J.; Liddick, S. N.; ...

2016-10-15

Shape coexistence near closed-shell nuclei, whereby states associated with deformed shapes appear at relatively low excitation energy alongside spherical ones, is indicative of the rapid change in structure that can occur with the addition or removal of a few protons or neutrons. Near 68Ni (Z=28, N=40), the identification of shape coexistence hinges on hitherto undetermined transition rates to and from low-energy 0 + states. In 68,70Ni, new lifetimes and branching ratios have been measured. These data enable quantitative descriptions of the 0 + states through the deduced transition rates and serve as sensitive probes for characterizing their nuclear wave functions.more » The results are compared to, and consistent with, large-scale shell-model calculations which predict shape coexistence. With the firm identification of this phenomenon near 68Ni, shape coexistence is now observed in all currently accessible regions of the nuclear chart with closed proton shells and mid-shell neutrons.« less

Direct determination of the local Hamaker constant of inorganic surfaces based on scanning force microscopy

NASA Astrophysics Data System (ADS)

Krajina, Brad A.; Kocherlakota, Lakshmi S.; Overney, René M.

2014-10-01

The energetics involved in the bonding fluctuations between nanometer-sized silicon dioxide (SiO2) probes and highly oriented pyrolytic graphite (HOPG) and molybdenum disulfide (MoS2) could be quantified directly and locally on the submicron scale via a time-temperature superposition analysis of the lateral forces between scanning force microscopy silicon dioxide probes and inorganic sample surfaces. The so-called "intrinsic friction analysis" (IFA) provided direct access to the Hamaker constants for HOPG and MoS2, as well as the control sample, calcium fluoride (CaF2). The use of scanning probe enables nanoscopic analysis of bonding fluctuations, thereby overcoming challenges associated with larger scale inhomogeneity and surface roughness common to conventional techniques used to determine surface free energies and dielectric properties. A complementary numerical analysis based on optical and electron energy loss spectroscopy and the Lifshitz quantum electrodynamic theory of van der Waals interactions is provided and confirms quantitatively the IFA results.

Direct determination of the local Hamaker constant of inorganic surfaces based on scanning force microscopy.

PubMed

Krajina, Brad A; Kocherlakota, Lakshmi S; Overney, René M

2014-10-28

The energetics involved in the bonding fluctuations between nanometer-sized silicon dioxide (SiO2) probes and highly oriented pyrolytic graphite (HOPG) and molybdenum disulfide (MoS2) could be quantified directly and locally on the submicron scale via a time-temperature superposition analysis of the lateral forces between scanning force microscopy silicon dioxide probes and inorganic sample surfaces. The so-called "intrinsic friction analysis" (IFA) provided direct access to the Hamaker constants for HOPG and MoS2, as well as the control sample, calcium fluoride (CaF2). The use of scanning probe enables nanoscopic analysis of bonding fluctuations, thereby overcoming challenges associated with larger scale inhomogeneity and surface roughness common to conventional techniques used to determine surface free energies and dielectric properties. A complementary numerical analysis based on optical and electron energy loss spectroscopy and the Lifshitz quantum electrodynamic theory of van der Waals interactions is provided and confirms quantitatively the IFA results.

Automated classification of cell morphology by coherence-controlled holographic microscopy

NASA Astrophysics Data System (ADS)

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity.

Automated classification of cell morphology by coherence-controlled holographic microscopy.

PubMed

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Investigating the Educational Value of Social Learning Networks: A Quantitative Analysis

ERIC Educational Resources Information Center

Dafoulas, Georgios; Shokri, Azam

2016-01-01

Purpose: The emergence of Education 2.0 enabled technology-enhanced learning, necessitating new pedagogical approaches, while e-learning has evolved into an instrumental pedagogy of collaboration through affordances of social media. Social learning networks and ubiquitous learning enabled individual and group learning through social engagement and…

Barriers and enablers to healthcare access and use among Arabic-speaking and Caucasian English-speaking patients with type 2 diabetes mellitus: a qualitative comparative study.

PubMed

Alzubaidi, H; Mc Namara, K; Browning, Colette; Marriott, J

2015-11-17

The objective of this study was to explore the decision-making processes and associated barriers and enablers that determine access and use of healthcare services in Arabic-speaking and English-speaking Caucasian patients with diabetes in Australia. Face-to-face semistructured individual interviews and group interviews were conducted at various healthcare settings-diabetes outpatient clinics in 2 tertiary referral hospitals, 6 primary care practices and 10 community centres in Melbourne, Australia. A total of 100 participants with type 2 diabetes mellitus were recruited into 2 groups: 60 Arabic-speaking and 40 English-speaking Caucasian. Interviews were audio-taped, translated into English when necessary, transcribed and coded thematically. Sociodemographic and clinical information was gathered using a self-completed questionnaire and medical records. Only Arabic-speaking migrants intentionally delayed access to healthcare services when obvious signs of diabetes were experienced, missing opportunities to detect diabetes at an early stage. Four major barriers and enablers to healthcare access and use were identified: influence of significant other(s), unique sociocultural and religious beliefs, experiences with healthcare providers and lack of knowledge about healthcare services. Compared with Arabic-speaking migrants, English-speaking participants had no reluctance to access and use medical services when signs of ill-health appeared; their treatment-seeking behaviours were straightforward. Arabic-speaking migrants appear to intentionally delay access to medical services even when symptomatic. Four barriers to health services access have been identified. Tailored interventions must be developed for Arabic-speaking migrants to improve access to available health services, facilitate timely diagnosis of diabetes and ultimately to improve glycaemic control. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

DEFENSE RTD&E ONLINE SYSTEM (DROLS)

EPA Science Inventory

Web Enabled DROLS (WED) is a free subscription service available to registered users that provides online access to DTIC's Technical Reports and Research Summaries Databases. It replaces the former unclassified dial-up access to DROLS, DTIC's Defense RDT&E Online System. The Defe...

Quantitative Microbial Risk Assessment Tutorial: Installation of Software for Watershed Modeling in Support of QMRA

EPA Science Inventory

This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling:• SDMProjectBuilder (which includes the Microbial Source Module as part...

Assess to Public Meetings [and] Assistive Listening Devices (ALD'S) [and] Access to Printed Information by Visually-Impaired Persons. Technical Assistance Guides.

ERIC Educational Resources Information Center

Department of Justice, Washington, DC. Civil Rights Div.

This item consists of three separate "Technical Assistance Guides" combined into one document because they all are concerned with improving access to information for handicapped people. Specifically, the three guides provide: (1) information to enable hearing impaired, visually impaired, and mobility impaired persons to have access to public…

Accessing Social Grants to Meet Orphan Children School Needs: Namibia and South Africa Perspective

ERIC Educational Resources Information Center

Taukeni, Simon; Matshidiso, Taole

2013-01-01

In this comparative paper we interrogate the access of social grants to meet orphan children school needs in Namibia and South Africa. We noted that the two governments are committed to provide orphan children with social grants to enable them to meet the school needs. However, accessing social grant to benefit most vulnerable orphan children…

Cal OES Internet Home Cal OES Home

Science.gov Websites

Sign In You may be trying to access this site from a secured browser on the server. Please enable scripts and reload this page. Turn on more accessible mode Turn off more accessible mode Skip Ribbon Commands Skip to main content Turn off Animations Turn on Animations image of CA.gov logo image of Cal OES

Space Nuclear Power Systems

NASA Technical Reports Server (NTRS)

Houts, Michael G.

2012-01-01

Fission power and propulsion systems can enable exciting space exploration missions. These include bases on the moon and Mars; and the exploration, development, and utilization of the solar system. In the near-term, fission surface power systems could provide abundant, constant, cost-effective power anywhere on the surface of the Moon or Mars, independent of available sunlight. Affordable access to Mars, the asteroid belt, or other destinations could be provided by nuclear thermal rockets. In the further term, high performance fission power supplies could enable both extremely high power levels on planetary surfaces and fission electric propulsion vehicles for rapid, efficient cargo and crew transfer. Advanced fission propulsion systems could eventually allow routine access to the entire solar system. Fission systems could also enable the utilization of resources within the solar system.

Comfort and Accessibility Evaluation of Light Rail Vehicles

NASA Astrophysics Data System (ADS)

Hirasawa, Takayuki; Matsuoka, Shigeki; Suda, Yoshihiro

A quantitative evaluation method for passenger rooms of light rail vehicles from viewpoint of comfort and accessibility is proposed as the result of physical modeling of in-vehicle behavior of passengers upon Gibson's ecological psychology approach. The model parameters are identified from experiments at real vehicles at the depot of Kumamoto municipal transport and at the full-scale mockup of the University of Tokyo. The developed model has realized quantitative evaluation of floor lowering effects by abolishing internal steps at passenger doorways and door usage restriction scenarios from viewpoint of both passengers and operators in comparison to commuter railway vehicles.

Security in Distributed Collaborative Environments: Limitations and Solutions

NASA Astrophysics Data System (ADS)

Saadi, Rachid; Pierson, Jean-Marc; Brunie, Lionel

The main goal of establishing collaboration between heterogeneous environment is to create such as Pervasive context which provide nomadic users with ubiquitous access to digital information and surrounding resources. However, the constraints of mobility and heterogeneity arise a number of crucial issues related to security, especially authentication access control and privacy. First of all, in this chapter we explore the trust paradigm, specially the transitive capability to enable a trust peer to peer collaboration. In this manner, when each organization sets its own security policy to recognize (authenticate) users members of a trusted community and provide them a local access (access control), the trust transitivity between peers will allows users to gain a broad, larger and controlled access inside the pervasive environment. Next, we study the problem of user's privacy. In fact in pervasive and ubiquitous environments, nomadic users gather and exchange certificates or credential which providing them rights to access by transitivity unknown and trusted environments. These signed documents embeds increasing number of attribute that require to be filtered according to such contextual situation. In this chapter, we propose a new morph signature enabling each certificate owner to preserve his privacy by discloses or blinds some sensitive attributes according to faced situation.

Navigating the poverty of heroin addiction treatment and recovery opportunity in Kenya: access work, self-care and rationed expectations.

PubMed

Rhodes, Tim; Ndimbii, James; Guise, Andy; Cullen, Lucy; Ayon, Sylvia

2015-01-01

Drawing on the analyses of qualitative interview accounts of people who inject heroin in Kenya, we describe the narration of addiction treatment access and recovery desire in conditions characterised by a 'poverty of drug treatment opportunity'. We observe the performance of addiction recovery narrative in the face of heavy social constraints limiting access to care. Fee-based residential rehabilitation ('rehab') is the only treatment locally available and inaccessible to most. Its recovery potential is doubted, given normative expectations of relapse. Treating drug use is a product of tightly bounded agency. Individuals enact strategies to maximise their slim chances of treatment access ('access work'), develop self-care alternatives when these fail to materialise and ration their care expectations. The use of rehab as a primary means of respite and harm reduction rather than recovery and the individuation of care in the absence of an enabling recovery environment are key characteristics of drug treatment experience. The recent incorporation of 'harm reduction' into policy discourses may trouble the primacy of recovery narrative in addiction treatment and in how treatment desires are voiced. The diversification of drug treatments in combination with social interventions enabling their access are fundamental.

Considerations on private human access to space from an institutional point of view

NASA Astrophysics Data System (ADS)

Hufenbach, Bernhard

2013-12-01

Private human access to space as discussed in this article addresses two market segments: suborbital flight and crew flights to Low Earth Orbit. The role of entrepreneurs, the technical complexity, the customers, the market conditions as well as the time to market in these two segments differ significantly. Space agencies take currently a very different approach towards private human access to space in both segments. Analysing the outcome of broader inter-agency deliberations on the future of human spaceflight and exploration, performed e.g. in the framework of the International Space Exploration Coordination Group, enables to derive some common general views on this topic. Various documents developed by inter-agency working groups recognise the general strategic importance for enabling private human access to space for ensuring a sustainable future of human spaceflight, although the specific definition of private human access and approaches vary. ESA has performed some reflections on this subject throughout the last 5 years. While it gained through these reflections a good understanding on the opportunities and implications resulting from the development of capabilities and markets for Private Human Access, limited concrete activities have been initiated in relation to this topic as of today.

EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data.

PubMed

Koulouras, Grigorios; Panagopoulos, Andreas; Rapsomaniki, Maria A; Giakoumakis, Nickolaos N; Taraviras, Stavros; Lygerou, Zoi

2018-06-13

Understanding protein dynamics is crucial in order to elucidate protein function and interactions. Advances in modern microscopy facilitate the exploration of the mobility of fluorescently tagged proteins within living cells. Fluorescence recovery after photobleaching (FRAP) is an increasingly popular functional live-cell imaging technique which enables the study of the dynamic properties of proteins at a single-cell level. As an increasing number of labs generate FRAP datasets, there is a need for fast, interactive and user-friendly applications that analyze the resulting data. Here we present easyFRAP-web, a web application that simplifies the qualitative and quantitative analysis of FRAP datasets. EasyFRAP-web permits quick analysis of FRAP datasets through an intuitive web interface with interconnected analysis steps (experimental data assessment, different types of normalization and estimation of curve-derived quantitative parameters). In addition, easyFRAP-web provides dynamic and interactive data visualization and data and figure export for further analysis after every step. We test easyFRAP-web by analyzing FRAP datasets capturing the mobility of the cell cycle regulator Cdt2 in the presence and absence of DNA damage in cultured cells. We show that easyFRAP-web yields results consistent with previous studies and highlights cell-to-cell heterogeneity in the estimated kinetic parameters. EasyFRAP-web is platform-independent and is freely accessible at: https://easyfrap.vmnet.upatras.gr/.

CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside.

PubMed

Goñi-Moreno, Ángel; Kim, Juhyun; de Lorenzo, Víctor

2017-02-01

Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells. CellShape is entirely coded in Python, a free, open-source programming language with widespread community support. For a developer, CellShape enhances extensibility (ease of software improvements) by acting as an interface to access and use existing Python modules; for an end-user, CellShape presents standalone executable files ready to open without installation. We have adopted this platform to analyse with an unprecedented detail the tridimensional distribution of the constituents of the gene expression flow (DNA, RNA polymerase, mRNA and ribosomal proteins) in individual cells of the industrial platform strain Pseudomonas putida KT2440. While the CellShape first release version (v0.8) is readily operational, users and/or developers are enabled to expand the platform further. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Toolkit to assess health needs for congenital disorders in low- and middle-income countries: an instrument for public health action.

PubMed

Nacul, L C; Stewart, A; Alberg, C; Chowdhury, S; Darlison, M W; Grollman, C; Hall, A; Modell, B; Moorthie, S; Sagoo, G S; Burton, H

2014-06-01

In 2010 the World Health Assembly called for action to improve the care and prevention of congenital disorders, noting that technical guidance would be required for this task, especially in low- and middle-income countries. Responding to this call, we have developed a freely available web-accessible Toolkit for assessing health needs for congenital disorders. Materials for the Toolkit website (http://toolkit.phgfoundation.org) were prepared by an iterative process of writing, discussion and modification by the project team, with advice from external experts. A customized database was developed using epidemiological, demographic, socio-economic and health-services data from a range of validated sources. Document-processing and data integration software combines data from the database with a template to generate topic- and country-specific Calculator documents for quantitative analysis. The Toolkit guides users through selection of topics (including both clinical conditions and relevant health services), assembly and evaluation of qualitative and quantitative information, assessment of the potential effects of selected interventions, and planning and prioritization of actions to reduce the risk or prevalence of congenital disorders. The Toolkit enables users without epidemiological or public health expertise to undertake health needs assessment as a prerequisite for strategic planning in relation to congenital disorders in their country or region. © The Author 2013. Published by Oxford University Press on behalf of Faculty of Public Health.

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR.

PubMed

Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

2011-01-01

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch.

GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

PubMed Central

Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

2011-01-01

The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch. PMID:21917859

Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis.

PubMed

Kooke, Rik; Kruijer, Willem; Bours, Ralph; Becker, Frank; Kuhn, André; van de Geest, Henri; Buntjer, Jaap; Doeswijk, Timo; Guerra, José; Bouwmeester, Harro; Vreugdenhil, Dick; Keurentjes, Joost J B

2016-04-01

Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified. © 2016 American Society of Plant Biologists. All Rights Reserved.

78 FR 63458 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-24

..., access to conduct research involving DoDEA students, staff, parents or data. Additionally will establish researcher accountability, enable future contact with researchers, and support preparation of statistical and... students, staff, parents or data. To establish researcher accountability, enable future contact with...

Social Media, Power, and the Future of VBAC.

PubMed

Romano, Amy M; Gerber, Hilary; Andrews, Desirre

2010-01-01

The Internet has been called a disruptive technology because it has shifted power and altered the economics of doing business, whether that business is selling books or providing health care. Social media have accelerated the pace of disruption by enabling interactive information sharing and blurring the lines between the "producers" and "consumers" of knowledge, goods, and services. In the wake of the National Institutes of Health Consensus Development Conference on Vaginal Birth After Cesarean (VBAC) and major national recommendations for maternity care reform, activated, engaged consumers face an unprecedented opportunity to drive meaningful changes in VBAC access and safety. This article examines the role of social networks in informing women about VBAC, producing low-cost, accessible decision aids, and enabling multi-stakeholder collaborations toward workable solutions that remove barriers women face in accessing VBAC.

Computational neuroanatomy: ontology-based representation of neural components and connectivity.

PubMed

Rubin, Daniel L; Talos, Ion-Florin; Halle, Michael; Musen, Mark A; Kikinis, Ron

2009-02-05

A critical challenge in neuroscience is organizing, managing, and accessing the explosion in neuroscientific knowledge, particularly anatomic knowledge. We believe that explicit knowledge-based approaches to make neuroscientific knowledge computationally accessible will be helpful in tackling this challenge and will enable a variety of applications exploiting this knowledge, such as surgical planning. We developed ontology-based models of neuroanatomy to enable symbolic lookup, logical inference and mathematical modeling of neural systems. We built a prototype model of the motor system that integrates descriptive anatomic and qualitative functional neuroanatomical knowledge. In addition to modeling normal neuroanatomy, our approach provides an explicit representation of abnormal neural connectivity in disease states, such as common movement disorders. The ontology-based representation encodes both structural and functional aspects of neuroanatomy. The ontology-based models can be evaluated computationally, enabling development of automated computer reasoning applications. Neuroanatomical knowledge can be represented in machine-accessible format using ontologies. Computational neuroanatomical approaches such as described in this work could become a key tool in translational informatics, leading to decision support applications that inform and guide surgical planning and personalized care for neurological disease in the future.

Petaminer: Using ROOT for efficient data storage in MySQL database

NASA Astrophysics Data System (ADS)

Cranshaw, J.; Malon, D.; Vaniachine, A.; Fine, V.; Lauret, J.; Hamill, P.

2010-04-01

High Energy and Nuclear Physics (HENP) experiments store Petabytes of event data and Terabytes of calibration data in ROOT files. The Petaminer project is developing a custom MySQL storage engine to enable the MySQL query processor to directly access experimental data stored in ROOT files. Our project is addressing the problem of efficient navigation to PetaBytes of HENP experimental data described with event-level TAG metadata, which is required by data intensive physics communities such as the LHC and RHIC experiments. Physicists need to be able to compose a metadata query and rapidly retrieve the set of matching events, where improved efficiency will facilitate the discovery process by permitting rapid iterations of data evaluation and retrieval. Our custom MySQL storage engine enables the MySQL query processor to directly access TAG data stored in ROOT TTrees. As ROOT TTrees are column-oriented, reading them directly provides improved performance over traditional row-oriented TAG databases. Leveraging the flexible and powerful SQL query language to access data stored in ROOT TTrees, the Petaminer approach enables rich MySQL index-building capabilities for further performance optimization.

Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement.

PubMed

Bohra, Abhishek; Singh, Narendra P

2015-08-01

Unprecedented developments in legume genomics over the last decade have resulted in the acquisition of a wide range of modern genomic resources to underpin genetic improvement of grain legumes. The genome enabled insights direct investigators in various ways that primarily include unearthing novel structural variations, retrieving the lost genetic diversity, introducing novel/exotic alleles from wider gene pools, finely resolving the complex quantitative traits and so forth. To this end, ready availability of cost-efficient and high-density genotyping assays allows genome wide prediction to be increasingly recognized as the key selection criterion in crop breeding. Further, the high-dimensional measurements of agronomically significant phenotypes obtained by using new-generation screening techniques will empower reference based resequencing as well as allele mining and trait mapping methods to comprehensively associate genome diversity with the phenome scale variation. Besides stimulating the forward genetic systems, accessibility to precisely delineated genomic segments reveals novel candidates for reverse genetic techniques like targeted genome editing. The shifting paradigm in plant genomics in turn necessitates optimization of crop breeding strategies to enable the most efficient integration of advanced omics knowledge and tools. We anticipate that the crop improvement schemes will be bolstered remarkably with rational deployment of these genome-guided approaches, ultimately resulting in expanded plant breeding capacities and improved crop performance.

mzStudio: A Dynamic Digital Canvas for User-Driven Interrogation of Mass Spectrometry Data.

PubMed

Ficarro, Scott B; Alexander, William M; Marto, Jarrod A

2017-08-01

Although not yet truly 'comprehensive', modern mass spectrometry-based experiments can generate quantitative data for a meaningful fraction of the human proteome. Importantly for large-scale protein expression analysis, robust data pipelines are in place for identification of un-modified peptide sequences and aggregation of these data to protein-level quantification. However, interoperable software tools that enable scientists to computationally explore and document novel hypotheses for peptide sequence, modification status, or fragmentation behavior are not well-developed. Here, we introduce mzStudio, an open-source Python module built on our multiplierz project. This desktop application provides a highly-interactive graphical user interface (GUI) through which scientists can examine and annotate spectral features, re-search existing PSMs to test different modifications or new spectral matching algorithms, share results with colleagues, integrate other domain-specific software tools, and finally create publication-quality graphics. mzStudio leverages our common application programming interface (mzAPI) for access to native data files from multiple instrument platforms, including ion trap, quadrupole time-of-flight, Orbitrap, matrix-assisted laser desorption ionization, and triple quadrupole mass spectrometers and is compatible with several popular search engines including Mascot, Proteome Discoverer, X!Tandem, and Comet. The mzStudio toolkit enables researchers to create a digital provenance of data analytics and other evidence that support specific peptide sequence assignments.

Evaluation of intensity drift correction strategies using MetaboDrift, a normalization tool for multi-batch metabolomics data.

PubMed

Thonusin, Chanisa; IglayReger, Heidi B; Soni, Tanu; Rothberg, Amy E; Burant, Charles F; Evans, Charles R

2017-11-10

In recent years, mass spectrometry-based metabolomics has increasingly been applied to large-scale epidemiological studies of human subjects. However, the successful use of metabolomics in this context is subject to the challenge of detecting biologically significant effects despite substantial intensity drift that often occurs when data are acquired over a long period or in multiple batches. Numerous computational strategies and software tools have been developed to aid in correcting for intensity drift in metabolomics data, but most of these techniques are implemented using command-line driven software and custom scripts which are not accessible to all end users of metabolomics data. Further, it has not yet become routine practice to assess the quantitative accuracy of drift correction against techniques which enable true absolute quantitation such as isotope dilution mass spectrometry. We developed an Excel-based tool, MetaboDrift, to visually evaluate and correct for intensity drift in a multi-batch liquid chromatography - mass spectrometry (LC-MS) metabolomics dataset. The tool enables drift correction based on either quality control (QC) samples analyzed throughout the batches or using QC-sample independent methods. We applied MetaboDrift to an original set of clinical metabolomics data from a mixed-meal tolerance test (MMTT). The performance of the method was evaluated for multiple classes of metabolites by comparison with normalization using isotope-labeled internal standards. QC sample-based intensity drift correction significantly improved correlation with IS-normalized data, and resulted in detection of additional metabolites with significant physiological response to the MMTT. The relative merits of different QC-sample curve fitting strategies are discussed in the context of batch size and drift pattern complexity. Our drift correction tool offers a practical, simplified approach to drift correction and batch combination in large metabolomics studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Combustion Chemistry of Fuels: Quantitative Speciation Data Obtained from an Atmospheric High-temperature Flow Reactor with Coupled Molecular-beam Mass Spectrometer.

PubMed

Köhler, Markus; Oßwald, Patrick; Krueger, Dominik; Whitside, Ryan

2018-02-19

This manuscript describes a high-temperature flow reactor experiment coupled to the powerful molecular beam mass spectrometry (MBMS) technique. This flexible tool offers a detailed observation of chemical gas-phase kinetics in reacting flows under well-controlled conditions. The vast range of operating conditions available in a laminar flow reactor enables access to extraordinary combustion applications that are typically not achievable by flame experiments. These include rich conditions at high temperatures relevant for gasification processes, the peroxy chemistry governing the low temperature oxidation regime or investigations of complex technical fuels. The presented setup allows measurements of quantitative speciation data for reaction model validation of combustion, gasification and pyrolysis processes, while enabling a systematic general understanding of the reaction chemistry. Validation of kinetic reaction models is generally performed by investigating combustion processes of pure compounds. The flow reactor has been enhanced to be suitable for technical fuels (e.g. multi-component mixtures like Jet A-1) to allow for phenomenological analysis of occurring combustion intermediates like soot precursors or pollutants. The controlled and comparable boundary conditions provided by the experimental design allow for predictions of pollutant formation tendencies. Cold reactants are fed premixed into the reactor that are highly diluted (in around 99 vol% in Ar) in order to suppress self-sustaining combustion reactions. The laminar flowing reactant mixture passes through a known temperature field, while the gas composition is determined at the reactors exhaust as a function of the oven temperature. The flow reactor is operated at atmospheric pressures with temperatures up to 1,800 K. The measurements themselves are performed by decreasing the temperature monotonically at a rate of -200 K/h. With the sensitive MBMS technique, detailed speciation data is acquired and quantified for almost all chemical species in the reactive process, including radical species.

Sociocritical Matters: Migrant Students' College Access

ERIC Educational Resources Information Center

Núñez, Anne-Marie; Gildersleeve, Ryan Evely

2016-01-01

Migrant students face many educational, economic, social, and cultural challenges to college access. Anti-bilingual, anti-affirmative action, and anti-immigrant policies also constrain their postsecondary pathways. With these issues in mind, this article draws on quantitative and qualitative research to examine the influence of a residential…

Gaps in the Digital Divide in Higher Education: Economically Disadvantaged Students and a Lack of Access and Skills

ERIC Educational Resources Information Center

Chappell, Timothy P.

2012-01-01

The digital divide between students who have access to and skills with information technology resources and those who do not is growing wider. This dissertation documents a quantitative study on the effect and relationship between age, gender, ethnicity and low economic status on students' access to computers and the Internet, as well as…

Multiple Intimate Partner Violence Experiences: Knowledge, Access, Utilization and Barriers to Utilization of Resources by Women of the African Diaspora

PubMed Central

Sabri, Bushra; Huerta, Julia; Alexander, Kamila A.; St.Vil, Noelle M.; Campbell, Jacquelyn C.; Callwood, Gloria B.

2016-01-01

Objective This study examined knowledge, access, utilization, and barriers to use of resources among Black women exposed to multiple types of intimate partner violence in Baltimore, Maryland and the U.S. Virgin Islands (USVI). Methods We analyzed quantitative survey data collected by 163 women recruited from primary care, prenatal or family planning clinics in Baltimore and the USVI. In addition we analyzed qualitative data from in-depth interviews with 11 women. Quantitative data were analyzed using descriptive statistics and qualitative data were analyzed using thematic analysis. Results A substantial proportion of Black women with multiple types of violence experiences lacked knowledge of, did not have access to, and did not use resources. Barriers to resource use were identified at the individual, relationship, and community levels. Conclusion There is need for programs to develop awareness, promote access and utilization of resources, and eliminate barriers to resource use among abused Black women. PMID:26548679

Enhancing Return from Lunar Surface Missions via the Deep Space Gateway

NASA Astrophysics Data System (ADS)

Chavers, D. G.; Whitley, R. J.; Percy, T. K.; Needham, D. H.; Polsgrove, T. T.

2018-02-01

The Deep Space Gateway (DSG) will facilitate access to and communication with lunar surface assets. With a science airlock, docking port, and refueling capability in an accessible orbit, the DSG will enable high priority science across the lunar surface.

A concise history of central venous access.

PubMed

Beheshti, Michael V

2011-12-01

Central venous access has become a mainstay of modern interventional radiology practice. Its history has paralleled and enabled many current medical therapies. This short overview provides an interesting historical perspective of these increasingly common interventional procedures. Copyright © 2011 Elsevier Inc. All rights reserved.

Kenai Fjords National Park Over-the-Snow Transportation Feasibility Study.

DOT National Transportation Integrated Search

2012-01-31

Kenai Fjords National Park seeks to expand winter access to the Exit Glacier Area. Year-round access would better enable the park to accomplish its mission related to visitor experience, education, and research. The road to the area is inaccessible t...

Quantitative Microbial Risk Assessment Tutorial Installation of Software for Watershed Modeling in Support of QMRA - Updated 2017

EPA Science Inventory

This tutorial provides instructions for accessing, retrieving, and downloading the following software to install on a host computer in support of Quantitative Microbial Risk Assessment (QMRA) modeling: • QMRA Installation • SDMProjectBuilder (which includes the Microbial ...

Quantitative trait loci associated with the tocochromanol (vitamin E) pathway in barley

USDA-ARS?s Scientific Manuscript database

In this study, the Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- alpha-, beta-, delta-, gamma-tocopherol and tocotrienol- were assayed. We found...

Food insecurity and low self-efficacy are associated with health care access barriers among Puerto-Ricans with type 2 diabetes.

PubMed

Kollannoor-Samuel, Grace; Vega-López, Sonia; Chhabra, Jyoti; Segura-Pérez, Sofia; Damio, Grace; Pérez-Escamilla, Rafael

2012-08-01

Racial/ethnic minorities are disproportionately affected by barriers to health care access and utilization. The primary objective was to test for an independent association between household food insecurity and health care access/utilization. In this cross-sectional survey, 211 Latinos (predominantly, Puerto-Ricans) with type 2 diabetes (T2D) were interviewed at their homes. Factor analyses identified four barriers for health care access/utilization: enabling factor, doctor access, medication access and forgetfulness. Multivariate logistic regression models examined the association between each of the barrier factors and food insecurity controlling for sociodemographic, cultural, psychosocial, and diabetes self-care variables. Higher food insecurity score was a risk factor for experiencing enabling factor (OR = 1.46; 95% CI = 1.17-1.82), medication access (OR = 1.26; 95 CI% = 1.06-1.50), and forgetfulness (OR = 1.22; 95 CI% = 1.04-1.43) barriers. Higher diabetes management self-efficacy was protective against all four barriers. Other variables associated with one or more barriers were health insurance, perceived health, depression, blood glucose, age and education. Findings suggest that addressing barriers such as food insecurity, low self-efficacy, lack of health insurance, and depression could potentially result in better health care access and utilization among low income Puerto-Ricans with T2D.

Enabling Tussle-Agile Inter-networking Architectures by Underlay Virtualisation

NASA Astrophysics Data System (ADS)

Dianati, Mehrdad; Tafazolli, Rahim; Moessner, Klaus

In this paper, we propose an underlay inter-network virtualisation framework in order to enable tussle-agile flexible networking over the existing inter-network infrastructures. The functionalities that inter-networking elements (transit nodes, access networks, etc.) need to support in order to enable virtualisation are discussed. We propose the base architectures of each the abstract elements to support the required inter-network virtualisation functionalities.

A survey of enabling technologies in synthetic biology

PubMed Central

2013-01-01

Background Realizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies. Results We conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants. Conclusions The set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential. PMID:23663447

Proximity-based access control for context-sensitive information provision in SOA-based systems

NASA Astrophysics Data System (ADS)

Rajappan, Gowri; Wang, Xiaofei; Grant, Robert; Paulini, Matthew

2014-06-01

Service Oriented Architecture (SOA) has enabled open-architecture integration of applications within an enterprise. For net-centric Command and Control (C2), this elucidates information sharing between applications and users, a critical requirement for mission success. The Information Technology (IT) access control schemes, which arbitrate who gets access to what information, do not yet have the contextual knowledge to dynamically allow this information sharing to happen dynamically. The access control might prevent legitimate users from accessing information relevant to the current mission context, since this context may be very different from the context for which the access privileges were configured. We evaluate a pair of data relevance measures - proximity and risk - and use these as the basis of dynamic access control. Proximity is a measure of the strength of connection between the user and the resource. However, proximity is not sufficient, since some data might have a negative impact, if leaked, which far outweighs importance to the subject's mission. For this, we use a risk measure to quantify the downside of data compromise. Given these contextual measures of proximity and risk, we investigate extending Attribute-Based Access Control (ABAC), which is used by the Department of Defense, and Role-Based Access Control (RBAC), which is widely used in the civilian market, so that these standards-based access control models are given contextual knowledge to enable dynamic information sharing. Furthermore, we consider the use of such a contextual access control scheme in a SOA-based environment, in particular for net-centric C2.

Dynamic Personal Identity and the Dynamic Identity Grid: How Theory and Concept Can Transform Information into Knowledge and Secure the American Homeland

DTIC Science & Technology

2008-09-01

Research Methods: Qualitative and Quantitative Approaches (Boston: Pearson, 2006), 1-592. 48 This project demanded the use of a primarily...enforcement practices. 200 Neuman, Social Research Methods: Qualitative and Quantitative Approaches, 152...www.socialresearchmethods.net/kb/strucres.php (accessed July 12, 2008). 203 Neuman, Social Research Methods: Qualitative and Quantitative Approaches, 149. 204 Paul

Measurements in quantitative research: how to select and report on research instruments.

PubMed

Hagan, Teresa L

2014-07-01

Measures exist to numerically represent degrees of attributes. Quantitative research is based on measurement and is conducted in a systematic, controlled manner. These measures enable researchers to perform statistical tests, analyze differences between groups, and determine the effectiveness of treatments. If something is not measurable, it cannot be tested.

Parent-identified barriers to pediatric health care: a process-oriented model.

PubMed

Sobo, Elisa J; Seid, Michael; Reyes Gelhard, Leticia

2006-02-01

To further understand barriers to care as experienced by health care consumers, and to demonstrate the importance of conjoining qualitative and quantitative health services research. Transcripts from focus groups conducted in San Diego with English- and Spanish-speaking parents of children with special health care needs. Participants were asked about the barriers to care they had experienced or perceived, and their strategies for overcoming these barriers. Using elementary anthropological discourse analysis techniques, a process-based conceptual model of the parent experience was devised. The analysis revealed a parent-motivated model of barriers to care that enriched our understanding of quantitative findings regarding the population from which the focus group sample was drawn. Parent-identified barriers were grouped into the following six temporally and spatially sequenced categories: necessary skills and prerequisites for gaining access to the system; realizing access once it is gained; front office experiences; interactions with physicians; system arbitrariness and fragmentation; outcomes that affect future interaction with the system. Key to the successful navigation of the system was parents' functional biomedical acculturation; this construct likens the biomedical health services system to a cultural system within which all parents/patients must learn to function competently. Qualitative analysis of focus group data enabled a deeper understanding of barriers to care--one that went beyond the traditional association of marker variables with poor outcomes ("what") to reveal an understanding of the processes by which parents experience the health care system ("how,"why") and by which disparities may arise. Development of such process-oriented models furthers the provision of patient-centered care and the creation of interventions, programs, and curricula to enhance such care. Qualitative discourse analysis, for example using this project's widely applicable protocol for generating experientially based models, can enhance our knowledge of the parent/patient experience and aid in the development of more powerful conceptualizations of key health care constructs.

Web-Enabled Systems for Student Access.

ERIC Educational Resources Information Center

Harris, Chad S.; Herring, Tom

1999-01-01

California State University, Fullerton is developing a suite of server-based, Web-enabled applications that distribute the functionality of its student information system software to external customers without modifying the mainframe applications or databases. The cost-effective, secure, and rapidly deployable business solution involves using the…

In situ quantitative characterisation of the ocean water column using acoustic multibeam backscatter data

NASA Astrophysics Data System (ADS)

Lamarche, G.; Le Gonidec, Y.; Lucieer, V.; Lurton, X.; Greinert, J.; Dupré, S.; Nau, A.; Heffron, E.; Roche, M.; Ladroit, Y.; Urban, P.

2017-12-01

Detecting liquid, solid or gaseous features in the ocean is generating considerable interest in the geoscience community, because of their potentially high economic values (oil & gas, mining), their significance for environmental management (oil/gas leakage, biodiversity mapping, greenhouse gas monitoring) as well as their potential cultural and traditional values (food, freshwater). Enhancing people's capability to quantify and manage the natural capital present in the ocean water goes hand in hand with the development of marine acoustic technology, as marine echosounders provide the most reliable and technologically advanced means to develop quantitative studies of water column backscatter data. This is not developed to its full capability because (i) of the complexity of the physics involved in relation to the constantly changing marine environment, and (ii) the rapid technological evolution of high resolution multibeam echosounder (MBES) water-column imaging systems. The Water Column Imaging Working Group is working on a series of multibeam echosounder (MBES) water column datasets acquired in a variety of environments, using a range of frequencies, and imaging a number of water-column features such as gas seeps, oil leaks, suspended particulate matter, vegetation and freshwater springs. Access to data from different acoustic frequencies and ocean dynamics enables us to discuss and test multifrequency approaches which is the most promising means to develop a quantitative analysis of the physical properties of acoustic scatterers, providing rigorous cross calibration of the acoustic devices. In addition, high redundancy of multibeam data, such as is available for some datasets, will allow us to develop data processing techniques, leading to quantitative estimates of water column gas seeps. Each of the datasets has supporting ground-truthing data (underwater videos and photos, physical oceanography measurements) which provide information on the origin and chemistry of the seep content. This is of first importance when assessing the physical properties of water column scatterers from backscatter acoustic measurement.

Public participation and marginalized groups: the community development model.

PubMed

O'Keefe, Eileen; Hogg, Christine

1999-12-01

OBJECTIVES: To develop ways of reaching house-bound people and enabling them to give their views in planning and monitoring health and social care. STRATEGY: HealthLINK - a project based in a community health council - explored ways of involving older house-bound people in the London Borough of Camden, in planning and monitoring health and social care using community development techniques. RESULTS: HealthLINK set up an infrastructure to enable house-bound people to have access to information and to enable them to give their views. This resulted in access for health and local authorities to the views of house-bound older people and increased the self esteem and quality of life of those who became involved. CONCLUSIONS: Community development approaches that enable an infrastructure to be established may be an effective way of reaching marginalized communities. However, there are tensions in this approach between the different requirements for public involvement of statutory bodies and of users, and between representation of groups and listening to individual voices.

Understanding Knowledge-Sharing Breakdowns: A Meeting of the Quantitative and Qualitative Minds

ERIC Educational Resources Information Center

Soller, Amy

2004-01-01

The rapid advance of distance learning and networking technology has enabled universities and corporations to reach out and educate students across time and space barriers. Although this technology enables structured collaborative learning activities, online groups often do not enjoy the same benefits as face-to-face learners, and their…

ScienceOrganizer System and Interface Summary

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Norvig, Peter (Technical Monitor)

2001-01-01

ScienceOrganizer is a specialized knowledge management tool designed to enhance the information storage, organization, and access capabilities of distributed NASA science teams. Users access ScienceOrganizer through an intuitive Web-based interface that enables them to upload, download, and organize project information - including data, documents, images, and scientific records associated with laboratory and field experiments. Information in ScienceOrganizer is "threaded", or interlinked, to enable users to locate, track, and organize interrelated pieces of scientific data. Linkages capture important semantic relationships among information resources in the repository, and these assist users in navigating through the information related to their projects.

Evaluation of Standards for Access Control Enabling PHR-S Federation.

PubMed

Mense, Alexander; Urbauer, Philipp; Sauermann, Stefan

2017-01-01

The adoption of the Internet of Things (IoT) and mobile applications in the healthcare may transform the healthcare industry by offering better disease tracking and management as well as patient empowerment. Unfortunately, almost all of these new systems set up their own ecosystem and to be really valuable for the care process they need to be integrated or federated with user managed access control services based on international standards and profiles to enable interoperability. Thus, this work presents the results of an evaluation of available specifications for federated authorization, based on a set of basic requirements.

OpenTopography: Addressing Big Data Challenges Using Cloud Computing, HPC, and Data Analytics

NASA Astrophysics Data System (ADS)

Crosby, C. J.; Nandigam, V.; Phan, M.; Youn, C.; Baru, C.; Arrowsmith, R.

2014-12-01

OpenTopography (OT) is a geoinformatics-based data facility initiated in 2009 for democratizing access to high-resolution topographic data, derived products, and tools. Hosted at the San Diego Supercomputer Center (SDSC), OT utilizes cyberinfrastructure, including large-scale data management, high-performance computing, and service-oriented architectures to provide efficient Web based access to large, high-resolution topographic datasets. OT collocates data with processing tools to enable users to quickly access custom data and derived products for their application. OT's ongoing R&D efforts aim to solve emerging technical challenges associated with exponential growth in data, higher order data products, as well as user base. Optimization of data management strategies can be informed by a comprehensive set of OT user access metrics that allows us to better understand usage patterns with respect to the data. By analyzing the spatiotemporal access patterns within the datasets, we can map areas of the data archive that are highly active (hot) versus the ones that are rarely accessed (cold). This enables us to architect a tiered storage environment consisting of high performance disk storage (SSD) for the hot areas and less expensive slower disk for the cold ones, thereby optimizing price to performance. From a compute perspective, OT is looking at cloud based solutions such as the Microsoft Azure platform to handle sudden increases in load. An OT virtual machine image in Microsoft's VM Depot can be invoked and deployed quickly in response to increased system demand. OT has also integrated SDSC HPC systems like the Gordon supercomputer into our infrastructure tier to enable compute intensive workloads like parallel computation of hydrologic routing on high resolution topography. This capability also allows OT to scale to HPC resources during high loads to meet user demand and provide more efficient processing. With a growing user base and maturing scientific user community comes new requests for algorithms and processing capabilities. To address this demand, OT is developing an extensible service based architecture for integrating community-developed software. This "plugable" approach to Web service deployment will enable new processing and analysis tools to run collocated with OT hosted data.

Quantitative prediction of phase transformations in silicon during nanoindentation

NASA Astrophysics Data System (ADS)

Zhang, Liangchi; Basak, Animesh

2013-08-01

This paper establishes the first quantitative relationship between the phases transformed in silicon and the shape characteristics of nanoindentation curves. Based on an integrated analysis using TEM and unit cell properties of phases, the volumes of the phases emerged in a nanoindentation are formulated as a function of pop-out size and depth of nanoindentation impression. This simple formula enables a fast, accurate and quantitative prediction of the phases in a nanoindentation cycle, which has been impossible before.

Army Communicator. Volume 37, Number 2, Summer 2012

DTIC Science & Technology

2012-01-01

solution will have to meet four criteria: FIPS 140-2 validated crypto; approved data-at-rest; Common Access Card enablement; and, enterprise management...Information Grid. Common Access Cards , Federal Information Processing Standard 140-2 certifications, and software compliance are just a few of the...and Evaluation Command BMC – Brigade Modernization Command CAC – Common Access Card FIPS – Federal Information Processing Standard GIG – Global

SAFE: SPARQL Federation over RDF Data Cubes with Access Control.

PubMed

Khan, Yasar; Saleem, Muhammad; Mehdi, Muntazir; Hogan, Aidan; Mehmood, Qaiser; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2017-02-01

Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stakeholders; consequently, privacy is a major concern when federating queries over such datasets. In the Healthcare and Life Sciences (HCLS) domain real-world datasets contain sensitive statistical information: strict ownership is granted to individuals working in hospitals, research labs, clinical trial organisers, etc. Therefore, the legal and ethical concerns on (i) preserving the anonymity of patients (or clinical subjects); and (ii) respecting data ownership through access control; are key challenges faced by the data analytics community working within the HCLS domain. Likewise statistical data play a key role in the domain, where the RDF Data Cube Vocabulary has been proposed as a standard format to enable the exchange of such data. However, to the best of our knowledge, no existing approach has looked to optimise federated queries over such statistical data. We present SAFE: a query federation engine that enables policy-aware access to sensitive statistical datasets represented as RDF data cubes. SAFE is designed specifically to query statistical RDF data cubes in a distributed setting, where access control is coupled with source selection, user profiles and their access rights. SAFE proposes a join-aware source selection method that avoids wasteful requests to irrelevant and unauthorised data sources. In order to preserve anonymity and enforce stricter access control, SAFE's indexing system does not hold any data instances-it stores only predicates and endpoints. The resulting data summary has a significantly lower index generation time and size compared to existing engines, which allows for faster updates when sources change. We validate the performance of the system with experiments over real-world datasets provided by three clinical organisations as well as legacy linked datasets. We show that SAFE enables granular graph-level access control over distributed clinical RDF data cubes and efficiently reduces the source selection and overall query execution time when compared with general-purpose SPARQL query federation engines in the targeted setting.

The Virtual Solar Observatory: What Are We Up To Now?

NASA Technical Reports Server (NTRS)

Gurman, J. B.; Hill, F.; Suarez-Sola, F.; Bogart, R.; Amezcua, A.; Martens, P.; Hourcle, J.; Hughitt, K.; Davey, A.

2012-01-01

In the nearly ten years of a functional Virtual Solar Observatory (VSO), http://virtualsolar.org/ we have made it possible to query and access sixty-seven distinct solar data products and several event lists from nine spacecraft and fifteen observatories or observing networks. We have used existing VSO technology, and developed new software, for a distributed network of sites caching and serving SDO HMI and/ or AlA data. We have also developed an application programming interface (API) that has enabled VSO search and data access capabilities in IDL, Python, and Java. We also have quite a bit of work yet to do, including completion of the implementation of access to SDO EVE data, and access to some nineteen other data sets from space- and ground-based observatories. In addition, we have been developing a new graphic user interface that will enable the saving of user interface and search preferences. We solicit advice from the community input prioritizing our task list, and adding to it

Teaching Mathematics in Primary Schools with Challenging Tasks: The Big (Not So) Friendly Giant

ERIC Educational Resources Information Center

Russo, James

2016-01-01

The use of enabling and extending prompts allows tasks to be both accessible and challenging within a classroom. This article provides an example of how to use enabling and extending prompts effectively when employing a challenging task in Year 2.

Food provision among food relief agencies in rural Australia, and perceived barriers and enablers to provide healthy food.

PubMed

Bortolin, Natalia; Priestly, Jaqueline; Sangster, Janice

2018-04-01

Food insecurity affects 4-14% of Australians, and up to 82% of vulnerable groups. Food relief agencies commonly provide food parcels or food vouchers. Little research has been undertaken on food relief agencies within rural Australia. This study determined the type of food assistance provided by rural food relief agencies, and barriers and enablers to provide healthy food. Cross-sectional study, using telephone questionnaires with qualitative and quantitative aspects. Data were analysed using descriptive statistics and thematic analysis. Rural New South Wales, Australia. Representatives of 10 food relief agencies. Types of food assistance and food provided, and the barriers and enablers to provide healthy food to clients. Most agencies provided food hampers and perishable and non-perishable food. Rural food relief agencies had a greater capacity to provide non-perishable compared to perishable food. Grains, breads and cereals, and canned fruit and vegetables were most popular. Nine key themes emerged including 'Ability to purchase and provide healthy food', 'Ability to regulate food purchased or chosen by clients', 'Financial constraints of the agency' and 'Lack of storage'. There are many variables to consider in order to understand the capacity of rural food relief agencies to provide healthy food. There are also opportunities for food relief agencies to appraise current practices and make changes. Initiatives to improve storage facilities and food availability are key and include networking with local businesses, community organisations and government. Rural food relief agency clients could benefit from accessing food literacy and health programs like FoodREDi, OzHarvest NEST and SecondBite Fresh NED. © 2017 National Rural Health Alliance Inc.

The ICF: International Classification of Functioning, Disability and Health (ICF)--a Swiss army knife? Accessibility and disability in a Scandinavian disability magazine (SDM)--a quantitative content analysis.

PubMed

Lundälv, Jörgen; Larsson, Per-Olof; Törnbom, Marie; Sunnerhagen, Katharina Stibrant

2012-11-01

The study describes the extent to which the concept of accessibility and accessibility issues has been reported in a national Scandinavian disability magazine. In this study particular attention is paid to how the compatibility between the various domains of the international classification - International Classification of Functioning, Disability and Health (ICF) - has been covered in the magazine over a decade. Furthermore, other types of descriptions that the magazine has made of accessibility for people with physical disabilities are considered. The study is based on a quantitative content analysis of a total of 326 articles from the Swedish disability magazine (SDM); 450 text pages published during the years 2000-2009. The magazine's coverage has been comprehensive. More than half of the studied texts were news items about various accessibility issues. Every third article can be characterised as a news article or feature article. The most frequently reported of the ICF domains consist of two perspectives: environmental accessibility and civil rights. Public opinion articles in the form of letters to editors and editorials focused on accessibility have a low frequency. Likewise, research reports are few. The study has included a review of illustrations and photographs. The illustrations are generally of high quality, reinforcing the disability message of the article. Crown Copyright © 2012. Published by Elsevier Ireland Ltd. All rights reserved.

Nuclear Energy for Space Exploration

NASA Technical Reports Server (NTRS)

Houts, Michael G.

2010-01-01

Nuclear power and propulsion systems can enable exciting space exploration missions. These include bases on the moon and Mars; and the exploration, development, and utilization of the solar system. In the near-term, fission surface power systems could provide abundant, constant, cost-effective power anywhere on the surface of the Moon or Mars, independent of available sunlight. Affordable access to Mars, the asteroid belt, or other destinations could be provided by nuclear thermal rockets. In the further term, high performance fission power supplies could enable both extremely high power levels on planetary surfaces and fission electric propulsion vehicles for rapid, efficient cargo and crew transfer. Advanced fission propulsion systems could eventually allow routine access to the entire solar system. Fission systems could also enable the utilization of resources within the solar system. Fusion and antimatter systems may also be viable in the future

Adaptive Visualization for Focused Personalized Information Retrieval

ERIC Educational Resources Information Center

Ahn, Jae-wook

2010-01-01

The new trend on the Web has totally changed today's information access environment. The traditional information overload problem has evolved into the qualitative level beyond the quantitative growth. The mode of producing and consuming information is changing and we need a new paradigm for accessing information. Personalized search is one of…

Academic Administrator Influence on Institutional Commitment to Open Access of Scholarly Research

ERIC Educational Resources Information Center

Reinsfelder, Thomas L.

2012-01-01

This quantitative study investigated the interrelationships among faculty researchers, publishers, librarians, and academic administrators when dealing with the open access of scholarly research. This study sought to identify the nature of any relationship between the perceived attitudes and actions of academic administrators and an…

Assessment and Evaluation Methods for Access Services

ERIC Educational Resources Information Center

Long, Dallas

2014-01-01

This article serves as a primer for assessment and evaluation design by describing the range of methods commonly employed in library settings. Quantitative methods, such as counting and benchmarking measures, are useful for investigating the internal operations of an access services department in order to identify workflow inefficiencies or…

First-Generation College Students: Perceptions, Access, and Participation at Urban University

ERIC Educational Resources Information Center

Lovano McCann, Erica

2017-01-01

This study explores how participation in a first-generation college student sophomore seminar course, a high impact practice, influences students' perceptions of campus climate, access to forms of capital and involvement behaviors. Utilizing a mixed methods approach of quantitative surveys and qualitative interviews to explore the experience of…

Assessment of access to primary health care among children and adolescents hospitalized due to avoidable conditions.

PubMed

Ferrer, Ana Paula Scoleze; Grisi, Sandra Josefina Ferraz Ellero

2016-09-01

Hospitalizations for ambulatory care-sensitive conditions (HACSC) are considered an indicator of the effectiveness of primary health care (PHC). High rates of HACSC represent problems in the access or the quality of health care. In Brazil, HACSC rates are high and there are few studies on the factors associated with it. To evaluate the access to PHC offered to children and adolescents hospitalized due to ACSC and analyze the conditioning factors. Cross-sectional study with a quantitative and qualitative approach. Five hundred and one (501) users (guardians/caregivers) and 42 professionals of PHC units were interviewed over one year. Quantitative data were obtained using Primary Care Assessment Tool validated in Brazil (PCATool-Brazil), while qualitative data were collected by semi-structured interview. The independent variables were: age, maternal education, family income, type of diagnosis, and model of care offered, and the dependent variables were access and its components (accessibility and use of services). Sixty-five percent (65.2%) of hospitalizations were ACSC. From the perspective of both users and professionals, access and its components presented low scores. Age, type of diagnosis, and model of care affected the results. The proportion of HACSC was high in this population. Access to services is inappropriate due to: barriers to access, appreciation of the emergency services, and attitude towards health needs. Professional attitudes and opinions reinforce inadequate ideas of users reflecting on the pattern of service use.

Priorities and strategies for improving disabled women's access to maternity services when they are affected by domestic abuse: a multi-method study using concept maps.

PubMed

Bradbury-Jones, Caroline; Breckenridge, Jenna P; Devaney, John; Duncan, Fiona; Kroll, Thilo; Lazenbatt, Anne; Taylor, Julie

2015-12-28

Domestic abuse is a significant public health issue. It occurs more frequently among disabled women than those without a disability and evidence suggests that a great deal of domestic abuse begins or worsens during pregnancy. All women and their infants are entitled to equal access to high quality maternity care. However, research has shown that disabled women who experience domestic abuse face numerous barriers to accessing care. The aim of the study was to identify the priority areas for improving access to maternity services for this group of women; develop strategies for improved access and utilisation; and explore the feasibility of implementing the identified strategies. This multi-method study was the third and final part of a larger study conducted in the UK between 2012 and 2014. The study used a modified concept mapping approach and was theoretically underpinned by Andersen's model of healthcare use. Seven focus group interviews were conducted with a range of maternity care professionals (n = 45), incorporating quantitative and qualitative components. Participants ranked perceived barriers to women's access and utilisation of maternity services in order of priority using a 5-point Likert scale. Quantitative data exploration used descriptive and non-parametric analyses. In the qualitative component of each focus group, participants discussed the barriers and identified potential improvement strategies (and feasibility of implementing these). Qualitative data were analysed inductively using a framework analysis approach. The three most highly ranked barriers to women's access and utilisation of maternity services identified in the quantitative component were: 1) staff being unaware and not asking about domestic abuse and disability; 2) the impact of domestic abuse on women; 3) women's fear of disclosure. The top two priority strategies were: providing information about domestic abuse to all women and promoting non-judgemental staff attitude. These were also considered very feasible. The qualitative analysis identified a range of psychosocial and environmental barriers experienced by this group of women in accessing maternity care. Congruent with the quantitative results, the main themes were lack of awareness and fear of disclosure. Key strategies were identified as demystifying disclosure and creating physical spaces to facilitate disclosure. The study supports findings of previous research regarding the barriers that women face in accessing and utilising maternity services, particularly regarding the issue of disclosure. But the study provides new evidence on the perceived importance and feasibility of strategies to address such barriers. This is an important step in ensuring practice-based acceptability and ease with which improvement strategies might be implemented in maternity care settings.

Social Media, Power, and the Future of VBAC

PubMed Central

Romano, Amy M.; Gerber, Hilary; Andrews, Desirre

2010-01-01

The Internet has been called a disruptive technology because it has shifted power and altered the economics of doing business, whether that business is selling books or providing health care. Social media have accelerated the pace of disruption by enabling interactive information sharing and blurring the lines between the “producers” and “consumers” of knowledge, goods, and services. In the wake of the National Institutes of Health Consensus Development Conference on Vaginal Birth After Cesarean (VBAC) and major national recommendations for maternity care reform, activated, engaged consumers face an unprecedented opportunity to drive meaningful changes in VBAC access and safety. This article examines the role of social networks in informing women about VBAC, producing low-cost, accessible decision aids, and enabling multi-stakeholder collaborations toward workable solutions that remove barriers women face in accessing VBAC. PMID:21170180

Simple video format for mobile applications

NASA Astrophysics Data System (ADS)

Smith, John R.; Miao, Zhourong; Li, Chung-Sheng

2000-04-01

With the advent of pervasive computing, there is a growing demand for enabling multimedia applications on mobile devices. Large numbers of pervasive computing devices, such as personal digital assistants (PDAs), hand-held computer (HHC), smart phones, portable audio players, automotive computing devices, and wearable computers are gaining access to online information sources. However, the pervasive computing devices are often constrained along a number of dimensions, such as processing power, local storage, display size and depth, connectivity, and communication bandwidth, which makes it difficult to access rich image and video content. In this paper, we report on our initial efforts in designing a simple scalable video format with low-decoding and transcoding complexity for pervasive computing. The goal is to enable image and video access for mobile applications such as electronic catalog shopping, video conferencing, remote surveillance and video mail using pervasive computing devices.

Advancing Precision Nuclear Medicine and Molecular Imaging for Lymphoma.

PubMed

Wright, Chadwick L; Maly, Joseph J; Zhang, Jun; Knopp, Michael V

2017-01-01

PET with fluorodeoxyglucose F 18 ( 18 F FDG-PET) is a meaningful biomarker for the detection, targeted biopsy, and treatment of lymphoma. This article reviews the evolution of 18 F FDG-PET as a putative biomarker for lymphoma and addresses the current capabilities, challenges, and opportunities to enable precision medicine practices for lymphoma. Precision nuclear medicine is driven by new imaging technologies and methodologies to more accurately detect malignant disease. Although quantitative assessment of response is limited, such technologies will enable a more precise metabolic mapping with much higher definition image detail and thus may make it a robust and valid quantitative response assessment methodology. Copyright © 2016 Elsevier Inc. All rights reserved.

Exploring access to care among older people in the last phase of life using the behavioural model of health services use: a qualitative study from the perspective of the next of kin of older persons who had died in a nursing home.

PubMed

Condelius, Anna; Andersson, Magdalena

2015-10-26

There is little investigation into what care older people access during the last phase of their life and what factors enable access to care in this group. Illuminating this from the perspective of the next of kin may provide valuable insights into how the health and social care system operates with reference to providing care for this vulnerable group. The behavioural model of health services use has a wide field of application but has not been tested conceptually regarding access to care from the perspective of the next of kin. The aim of this study was to explore the care accessed by older people during the last phase of their life from the perspective of the next of kin and to conceptually test the behavioural model of health services use. The data collection took place in 2011 by means of qualitative interviews with 14 next of kin of older people who had died in a nursing home. The interviews were analysed using directed content analysis. The behavioural model of health services use was used in deriving the initial coding scheme, including the categories: utilization of health services, consumer satisfaction and characteristics of the population at risk. Utilization of health services in the last phase of life was described in five subcategories named after the type of care accessed i.e. admission to a nursing home, primary healthcare, hospital care, dental care and informal care. The needs were illuminated in the subcategories: general deterioration, medical conditions and acute illness and deterioration when death approaches. Factors that enabled access to care were described in three subcategories: the organisation of care, next of kin and the older person. These factors could also constitute barriers to accessing care. Next of kin's satisfaction with care was illuminated in the subcategories: satisfaction, dissatisfaction and factors influencing satisfaction. One new category was constructed inductively: the situation of the next of kin. A bed in a nursing home was often accessed during what the next of kin regarded as the last phase of life. The needs among older people in the last phase of life can be regarded as complex and worsening over time. Most enabling factors lied within the organisation of care but the next of kin enabled access to care and contributed significantly to care quality. More research is needed regarding ageism and stigmatic attitudes among professionals and informal caregivers acting as a barrier to accessing care for older people in the last phase of their life. The behavioural model of health services use was extended with a new category showing that the situation of the next of kin must be taken into consideration when investigating access to care from their perspective. It may also be appropriate to include informal care as part of the concept of access when investigating access to care among older people in the last phase of their life. The results may not be transferable to older people who have not gained access to a bed in a nursing home or to countries where the healthcare system differs largely from the Swedish.

47 CFR 1.20004 - Maintaining secure and accurate records.

Code of Federal Regulations, 2010 CFR

2010-10-01

... access to call-identifying information, made with or without appropriate authorization, in the form of... that the carrier enables the interception of communications or access to call identifying information; (iii) The identity of the law enforcement officer presenting the authorization; (iv) The name of the...

Enabling Equal Access to Molecular Diagnostics: What Are the Implications for Policy and Health Technology Assessment?

PubMed

Plun-Favreau, Juliette; Immonen-Charalambous, Kaisa; Steuten, Lotte; Strootker, Anja; Rouzier, Roman; Horgan, Denis; Lawler, Mark

2016-01-01

Molecular diagnostics can offer important benefits to patients and are a key enabler of the integration of personalised medicine into health care systems. However, despite their promise, few molecular diagnostics are embedded into clinical practice (especially in Europe) and access to these technologies remains unequal across countries and sometimes even within individual countries. If research translation and the regulatory environments have proven to be more challenging than expected, reimbursement and value assessment remain the main barriers to providing patients with equal access to molecular diagnostics. Unclear or non-existent reimbursement pathways, together with the lack of clear evidence requirements, have led to significant delays in the assessment of molecular diagnostics technologies in certain countries. Additionally, the lack of dedicated diagnostics budgets and the siloed nature of resource allocation within certain health care systems have significantly delayed diagnostics commissioning. This article will consider the perspectives of different stakeholders (patients, health care payers, health care professionals, and manufacturers) on the provision of a research-enabled, patient-focused molecular diagnostics platform that supports optimal patient care. Through the discussion of specific case studies, and building on the experience from countries that have successfully integrated molecular diagnostics into clinical practice, this article will discuss the necessary evolutions in policy and health technology assessment to ensure that patients can have equal access to appropriate molecular diagnostics. © 2016 S. Karger AG, Basel.

Structuring Legacy Pathology Reports by openEHR Archetypes to Enable Semantic Querying.

PubMed

Kropf, Stefan; Krücken, Peter; Mueller, Wolf; Denecke, Kerstin

2017-05-18

Clinical information is often stored as free text, e.g. in discharge summaries or pathology reports. These documents are semi-structured using section headers, numbered lists, items and classification strings. However, it is still challenging to retrieve relevant documents since keyword searches applied on complete unstructured documents result in many false positive retrieval results. We are concentrating on the processing of pathology reports as an example for unstructured clinical documents. The objective is to transform reports semi-automatically into an information structure that enables an improved access and retrieval of relevant data. The data is expected to be stored in a standardized, structured way to make it accessible for queries that are applied to specific sections of a document (section-sensitive queries) and for information reuse. Our processing pipeline comprises information modelling, section boundary detection and section-sensitive queries. For enabling a focused search in unstructured data, documents are automatically structured and transformed into a patient information model specified through openEHR archetypes. The resulting XML-based pathology electronic health records (PEHRs) are queried by XQuery and visualized by XSLT in HTML. Pathology reports (PRs) can be reliably structured into sections by a keyword-based approach. The information modelling using openEHR allows saving time in the modelling process since many archetypes can be reused. The resulting standardized, structured PEHRs allow accessing relevant data by retrieving data matching user queries. Mapping unstructured reports into a standardized information model is a practical solution for a better access to data. Archetype-based XML enables section-sensitive retrieval and visualisation by well-established XML techniques. Focussing the retrieval to particular sections has the potential of saving retrieval time and improving the accuracy of the retrieval.

Metabolite profiling and quantitative genetics of natural variation for flavonoids in Arabidopsis

PubMed Central

Routaboul, Jean-Marc; Dubos, Christian; Beck, Gilles; Marquis, Catherine; Bidzinski, Przemyslaw; Loudet, Olivier; Lepiniec, Loïc

2012-01-01

Little is known about the range and the genetic bases of naturally occurring variation for flavonoids. Using Arabidopsis thaliana seed as a model, the flavonoid content of 41 accessions and two recombinant inbred line (RIL) sets derived from divergent accessions (Cvi-0×Col-0 and Bay-0×Shahdara) were analysed. These accessions and RILs showed mainly quantitative rather than qualitative changes. To dissect the genetic architecture underlying these differences, a quantitative trait locus (QTL) analysis was performed on the two segregating populations. Twenty-two flavonoid QTLs were detected that accounted for 11–64% of the observed trait variations, only one QTL being common to both RIL sets. Sixteen of these QTLs were confirmed and coarsely mapped using heterogeneous inbred families (HIFs). Three genes, namely TRANSPARENT TESTA (TT)7, TT15, and MYB12, were proposed to underlie their variations since the corresponding mutants and QTLs displayed similar specific flavonoid changes. Interestingly, most loci did not co-localize with any gene known to be involved in flavonoid metabolism. This latter result shows that novel functions have yet to be characterized and paves the way for their isolation. PMID:22442426

Barriers and enablers for iron folic acid (IFA) supplementation in pregnant women.

PubMed

Siekmans, Kendra; Roche, Marion; Kung'u, Jacqueline K; Desrochers, Rachelle E; De-Regil, Luz Maria

2017-12-22

In order to inform large scale supplementation programme design, we review and summarize the barriers and enablers for improved coverage and utilization of iron and folic acid (IFA) supplements by pregnant women in 7 countries in Africa and Asia. Mixed methods were used to analyse IFA supplementation programmes in Afghanistan, Bangladesh, Indonesia, Ethiopia, Kenya, Nigeria, and Senegal based on formative research conducted in 2012-2013. Qualitative data from focus-group discussions and interviews with women and service providers were used for content analysis to elicit common themes on barriers and enablers at internal, external, and relational levels. Anaemia symptoms in pregnancy are well known among women and health care providers in all countries, yet many women do not feel personally at risk. Broad awareness and increased coverage of facility-based antenatal care (ANC) make it an efficient delivery channel for IFA; however, first trimester access to IFA is hindered by beliefs about when to first attend ANC and preferences for disclosing pregnancy status. Variable access and poor quality ANC services, including insufficient IFA supplies and inadequate counselling to encourage consumption, are barriers to both coverage and adherence. Community-based delivery of IFA and referral to ANC provides earlier and more frequent access and opportunities for follow-up. Improving ANC access and quality is needed to facilitate IFA supplementation during pregnancy. Community-based delivery and counselling can address problems of timely and continuous access to supplements. Renewed investment in training for service providers and effective behaviour change designs are urgently needed to achieve the desired impact. © 2018 John Wiley & Sons Ltd.

Mixed methods research.

PubMed

Halcomb, Elizabeth; Hickman, Louise

2015-04-08

Mixed methods research involves the use of qualitative and quantitative data in a single research project. It represents an alternative methodological approach, combining qualitative and quantitative research approaches, which enables nurse researchers to explore complex phenomena in detail. This article provides a practical overview of mixed methods research and its application in nursing, to guide the novice researcher considering a mixed methods research project.

Anatomy Drawing Screencasts: Enabling Flexible Learning for Medical Students

ERIC Educational Resources Information Center

Pickering, James D.

2015-01-01

The traditional lecture remains an essential method of disseminating information to medical students. However, due to the constant development of the modern medical curriculum many institutions are embracing novel means for delivering the core anatomy syllabus. Using mobile media devices is one such way, enabling students to access core material…

75 FR 43825 - Exemption to Prohibition on Circumvention of Copyright Protection Systems for Access Control...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-27

... works such as video games and slide presentations). B. Computer programs that enable wireless telephone... enabling interoperability of such applications, when they have been lawfully obtained, with computer... new printer driver to a computer constitutes a `modification' of the operating system already...

Developing Accessible Cyberinfrastructure-Enabled Knowledge Communities in the National Disability Community: Theory, Practice, and Policy

ERIC Educational Resources Information Center

Myhill, William N.; Cogburn, Derrick L.; Samant, Deepti

2008-01-01

Since publication of the Atkins Commission report 2003, the national scientific community has placed significant emphasis on developing cyberinfrastructure-enabled knowledge communities, which are designed to facilitate enhanced efficiency and collaboration in geographically distributed networks of researchers. This article suggests that the new…

[Immigrants' access to health care in Spain: a review].

PubMed

Llop-Gironés, Alba; Vargas Lorenzo, Ingrid; Garcia-Subirats, Irene; Aller, Marta-Beatriz; Vázquez Navarrete, María Luisa

2014-01-01

An important proportion of the population in Spain is immigrant and the international literature indicates their inadequate access to health services. The objective is to contribute to improving the knowledge on access to health care of the immigrant population in Spain. Review of original papers published (1998-2012) on access to health services of the immigrant population in Spain published in Medline and MEDES. Out of 319 studies, 20 were selected, applying predefined criteria. The results were analyzed using the Aday and Andersen framework. Among the publications, 13 quantitative studies analysed differences in health care use between the immigrant and the native population, and 7 studied determinants of access of immigrants. Studies showed less use of specialized care by immigrants, higher use of emergency care and no differences in the use of primary care between groups. Five quantitative articles on determinants of access focused on factors related to the immigrant population (sex, age, educational level and holding private health insurance), but without observing clear patterns. The two qualitative studies analyzed factors related to health services, describing access to healthcare barriers such as the limited provision of information or the requirements for personal health card. Access to health care in immigrants has been scarcely studied, using different approaches and the barely analysed factors related to the services. No clear patterns were observed, as differences depend on the classification of migrants according to country of origin and the level of care. However, studies showed less use of specialized care by immigrants, higher use of emergency care and the existence of determinants of access different to their needs.

Quantitative secondary electron detection

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

Agrawal, Jyoti; Joy, David C.; Nayak, Subuhadarshi

Quantitative Secondary Electron Detection (QSED) using the array of solid state devices (SSD) based electron-counters enable critical dimension metrology measurements in materials such as semiconductors, nanomaterials, and biological samples (FIG. 3). Methods and devices effect a quantitative detection of secondary electrons with the array of solid state detectors comprising a number of solid state detectors. An array senses the number of secondary electrons with a plurality of solid state detectors, counting the number of secondary electrons with a time to digital converter circuit in counter mode.

Generation of High-Quality SWATH® Acquisition Data for Label-free Quantitative Proteomics Studies Using TripleTOF® Mass Spectrometers

PubMed Central

Schilling, Birgit; Gibson, Bradford W.; Hunter, Christie L.

2017-01-01

Data-independent acquisition is a powerful mass spectrometry technique that enables comprehensive MS and MS/MS analysis of all detectable species, providing an information rich data file that can be mined deeply. Here, we describe how to acquire high-quality SWATH® Acquisition data to be used for large quantitative proteomic studies. We specifically focus on using variable sized Q1 windows for acquisition of MS/MS data for generating higher specificity quantitative data. PMID:28188533

High-resolution quantitative determination of dielectric function by using scattering scanning near-field optical microscopy

PubMed Central

Tranca, D. E.; Stanciu, S. G.; Hristu, R.; Stoichita, C.; Tofail, S. A. M.; Stanciu, G. A.

2015-01-01

A new method for high-resolution quantitative measurement of the dielectric function by using scattering scanning near-field optical microscopy (s-SNOM) is presented. The method is based on a calibration procedure that uses the s-SNOM oscillating dipole model of the probe-sample interaction and quantitative s-SNOM measurements. The nanoscale capabilities of the method have the potential to enable novel applications in various fields such as nano-electronics, nano-photonics, biology or medicine. PMID:26138665

Evidence-Based Practice Point-of-Care Resources: A Quantitative Evaluation of Quality, Rigor, and Content.

PubMed

Campbell, Jared M; Umapathysivam, Kandiah; Xue, Yifan; Lockwood, Craig

2015-12-01

Clinicians and other healthcare professionals need access to summaries of evidence-based information in order to provide effective care to their patients at the point-of-care. Evidence-based practice (EBP) point-of-care resources have been developed and are available online to meet this need. This study aimed to develop a comprehensive list of available EBP point-of-care resources and evaluate their processes and policies for the development of content, in order to provide a critical analysis based upon rigor, transparency and measures of editorial quality to inform healthcare providers and promote quality improvement amongst publishers of EBP resources. A comprehensive and systematic search (Pubmed, CINAHL, and Cochrane Central) was undertaken to identify available EBP point-of-care resources, defined as "web-based medical compendia specifically designed to deliver predigested, rapidly accessible, comprehensive, periodically updated, and evidence-based information (and possibly also guidance) to clinicians." A pair of investigators independently extracted information on general characteristics, content presentation, editorial quality, evidence-based methodology, and breadth and volume. Twenty-seven summary resources were identified, of which 22 met the predefined inclusion criteria for EBP point-of-care resources, and 20 could be accessed for description and assessment. Overall, the upper quartile of EBP point-of-care providers was assessed to be UpToDate, Nursing Reference Centre, Mosby's Nursing Consult, BMJ Best Practice, and JBI COnNECT+. The choice of which EBP point-of-care resources are suitable for an organization is a decision that depends heavily on the unique requirements of that organization and the resources it has available. However, the results presented in this study should enable healthcare providers to make that assessment in a clear, evidence-based manner, and provide a comprehensive list of the available options. © 2015 Sigma Theta Tau International.

An Architecture for Enabling Migration of Tactical Networks to Future Flexible Ad Hoc WBWF

DTIC Science & Technology

2010-09-01

Requirements Several multiple access schemes TDMA OFDMA SC-OFDMA, FH- CDMA , DS - CDMA , hybrid access schemes, transitions between them Dynamic...parameters algorithms depend on the multiple access scheme If DS - CDMA : handling of macro-diversity (linked to cooperative routing) TDMA and/of OFDMA...Transport format Ciphering @MAC/RLC level : SCM Physical layer (PHY) : signal processing (mod, FEC, etc) CDMA : macro-diversity CDMA , OFDMA

Effects of network node consolidation in optical access and aggregation networks on costs and power consumption

NASA Astrophysics Data System (ADS)

Lange, Christoph; Hülsermann, Ralf; Kosiankowski, Dirk; Geilhardt, Frank; Gladisch, Andreas

2010-01-01

The increasing demand for higher bit rates in access networks requires fiber deployment closer to the subscriber resulting in fiber-to-the-home (FTTH) access networks. Besides higher access bit rates optical access network infrastructure and related technologies enable the network operator to establish larger service areas resulting in a simplified network structure with a lower number of network nodes. By changing the network structure network operators want to benefit from a changed network cost structure by decreasing in short and mid term the upfront investments for network equipment due to concentration effects as well as by reducing the energy costs due to a higher energy efficiency of large network sites housing a high amount of network equipment. In long term also savings in operational expenditures (OpEx) due to the closing of central office (CO) sites are expected. In this paper different architectures for optical access networks basing on state-of-the-art technology are analyzed with respect to network installation costs and power consumption in the context of access node consolidation. Network planning and dimensioning results are calculated for a realistic network scenario of Germany. All node consolidation scenarios are compared against a gigabit capable passive optical network (GPON) based FTTH access network operated from the conventional CO sites. The results show that a moderate reduction of the number of access nodes may be beneficial since in that case the capital expenditures (CapEx) do not rise extraordinarily and savings in OpEx related to the access nodes are expected. The total power consumption does not change significantly with decreasing number of access nodes but clustering effects enable a more energyefficient network operation and optimized power purchase order quantities leading to benefits in energy costs.

Quantitative force measurements using frequency modulation atomic force microscopy—theoretical foundations

NASA Astrophysics Data System (ADS)

Sader, John E.; Uchihashi, Takayuki; Higgins, Michael J.; Farrell, Alan; Nakayama, Yoshikazu; Jarvis, Suzanne P.

2005-03-01

Use of the atomic force microscope (AFM) in quantitative force measurements inherently requires a theoretical framework enabling conversion of the observed deflection properties of the cantilever to an interaction force. In this paper, the theoretical foundations of using frequency modulation atomic force microscopy (FM-AFM) in quantitative force measurements are examined and rigorously elucidated, with consideration being given to both 'conservative' and 'dissipative' interactions. This includes a detailed discussion of the underlying assumptions involved in such quantitative force measurements, the presentation of globally valid explicit formulae for evaluation of so-called 'conservative' and 'dissipative' forces, discussion of the origin of these forces, and analysis of the applicability of FM-AFM to quantitative force measurements in liquid.

Studying learning in the healthcare setting: the potential of quantitative diary methods.

PubMed

Ciere, Yvette; Jaarsma, Debbie; Visser, Annemieke; Sanderman, Robbert; Snippe, Evelien; Fleer, Joke

2015-08-01

Quantitative diary methods are longitudinal approaches that involve the repeated measurement of aspects of peoples' experience of daily life. In this article, we outline the main characteristics and applications of quantitative diary methods and discuss how their use may further research in the field of medical education. Quantitative diary methods offer several methodological advantages, such as measuring aspects of learning with great detail, accuracy and authenticity. Moreover, they enable researchers to study how and under which conditions learning in the health care setting occurs and in which way learning can be promoted. Hence, quantitative diary methods may contribute to theory development and the optimization of teaching methods in medical education.

Identification and Quantitation of Asparagine and Citrulline Using High-Performance Liquid Chromatography (HPLC)

PubMed Central

Bai, Cheng; Reilly, Charles C.; Wood, Bruce W.

2007-01-01

High-performance liquid chromatography (HPLC) analysis was used for identification of two problematic ureides, asparagine and citrulline. We report here a technique that takes advantage of the predictable delay in retention time of the co-asparagine/citrulline peak to enable both qualitative and quantitative analysis of asparagine and citrulline using the Platinum EPS reverse-phase C18 column (Alltech Associates). Asparagine alone is eluted earlier than citrulline alone, but when both of them are present in biological samples they may co-elute. HPLC retention times for asparagine and citrulline were influenced by other ureides in the mixture. We found that at various asparagines and citrulline ratios [= 3:1, 1:1, and 1:3; corresponding to 75:25, 50:50, and 25:75 (μMol ml−1/μMol ml−1)], the resulting peak exhibited different retention times. Adjustment of ureide ratios as internal standards enables peak identification and quantification. Both chemicals were quantified in xylem sap samples of pecan [Carya illinoinensis (Wangenh.) K. Koch] trees. Analysis revealed that tree nickel nutrition status affects relative concentrations of Urea Cycle intermediates, asparagine and citrulline, present in sap. Consequently, we concluded that the HPLC methods are presented to enable qualitative and quantitative analysis of these metabolically important ureides. PMID:19662174

Identification and quantitation of asparagine and citrulline using high-performance liquid chromatography (HPLC).

PubMed

Bai, Cheng; Reilly, Charles C; Wood, Bruce W

2007-03-28

High-performance liquid chromatography (HPLC) analysis was used for identification of two problematic ureides, asparagine and citrulline. We report here a technique that takes advantage of the predictable delay in retention time of the co-asparagine/citrulline peak to enable both qualitative and quantitative analysis of asparagine and citrulline using the Platinum EPS reverse-phase C18 column (Alltech Associates). Asparagine alone is eluted earlier than citrulline alone, but when both of them are present in biological samples they may co-elute. HPLC retention times for asparagine and citrulline were influenced by other ureides in the mixture. We found that at various asparagines and citrulline ratios [= 3:1, 1:1, and 1:3; corresponding to 75:25, 50:50, and 25:75 (microMol ml(-1)/microMol ml(-1))], the resulting peak exhibited different retention times. Adjustment of ureide ratios as internal standards enables peak identification and quantification. Both chemicals were quantified in xylem sap samples of pecan [Carya illinoinensis (Wangenh.) K. Koch] trees. Analysis revealed that tree nickel nutrition status affects relative concentrations of Urea Cycle intermediates, asparagine and citrulline, present in sap. Consequently, we concluded that the HPLC methods are presented to enable qualitative and quantitative analysis of these metabolically important ureides.

Overview of Sparse Graph for Multiple Access in Future Mobile Networks

NASA Astrophysics Data System (ADS)

Lei, Jing; Li, Baoguo; Li, Erbao; Gong, Zhenghui

2017-10-01

Multiple access via sparse graph, such as low density signature (LDS) and sparse code multiple access (SCMA), is a promising technique for future wireless communications. This survey presents an overview of the developments in this burgeoning field, including transmitter structures, extrinsic information transform (EXIT) chart analysis and comparisons with existing multiple access techniques. Such technique enables multiple access under overloaded conditions to achieve a satisfactory performance. Message passing algorithm is utilized for multi-user detection in the receiver, and structures of the sparse graph are illustrated in detail. Outlooks and challenges of this technique are also presented.

Measurement Invariance: A Foundational Principle for Quantitative Theory Building

ERIC Educational Resources Information Center

Nimon, Kim; Reio, Thomas G., Jr.

2011-01-01

This article describes why measurement invariance is a critical issue to quantitative theory building within the field of human resource development. Readers will learn what measurement invariance is and how to test for its presence using techniques that are accessible to applied researchers. Using data from a LibQUAL+[TM] study of user…

Low-Income Low-Qualified Employees' Access to Workplace Learning

ERIC Educational Resources Information Center

McPherson, Rebecca; Wang, Jia

2014-01-01

Purpose: The purpose of this paper was to investigate the embedded process that enables or constrains low-income low-qualified employees' access to workplace learning in small organizations. Design/methodology/approach: Informed by the sociomaterial approach and cultural historical activity theory, this study adopted a qualitative cross-case study…

A Method for Selection of Appropriate Assistive Technology for Computer Access

ERIC Educational Resources Information Center

Jenko, Mojca

2010-01-01

Assistive technologies (ATs) for computer access enable people with disabilities to be included in the information society. Current methods for assessment and selection of the most appropriate AT for each individual are nonstandardized, lengthy, subjective, and require substantial clinical experience of a multidisciplinary team. This manuscript…

EPAct 2005: A Roadmap for Open Access

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

Morrison, Jay A.

After nine years of negotiation characterized by significant philosophical swings, Congress came together in the middle to support a moderate vision of open access intended primarily to enable load-serving entities to obtain the transmission service they need to meet the long-term needs of their consumers reliably and economically.

Managing intellectual property to develop medicines for the world's poorest.

PubMed

Fonteilles-Drabek, Sylvie; Reddy, David; Wells, Timothy N C

2017-04-01

It has been argued that patents impede the development and access of medicines for tropical diseases such as malaria. However, we believe that intellectual property can be a key tool to enable timely progression of drug development projects involving multiple partners and to ensure equitable access to successful products.

MaizeGDB: enabling access to basic, translational, and applied research information

USDA-ARS?s Scientific Manuscript database

MaizeGDB is the Maize Genetics and Genomics Database (available online at http://www.maizegdb.org). The MaizeGDB project is not simply an online database and website but rather an information service to maize researchers that supports customized data access and analysis needs to individual research...

The Quality of Urban Environments: Mapping Variation in Access to Community Resources.

ERIC Educational Resources Information Center

Witten, Karen; Exeter, Daniel; Field, Adrian

2003-01-01

Discusses the relationship between community infrastructure and health through the development of the Community Resource Accessibility Index (CRAI) research tool.This area-based index of community services, facilities, and amenities enables comparisons between opportunity structures in the local environment and residents' health and wellbeing. It…

--No Title--

Science.gov Websites

You may be trying to access this site from a secured browser on the server. Please enable scripts and utilizing to make their lives easier and access to information literally at their fingertips. To make information readily available, U. S. Fleet Forces developed mobile applications to provide the

Enabling Accessibility Through Model-Based User Interface Development.

PubMed

Ziegler, Daniel; Peissner, Matthias

2017-01-01

Adaptive user interfaces (AUIs) can increase the accessibility of interactive systems. They provide personalized display and interaction modes to fit individual user needs. Most AUI approaches rely on model-based development, which is considered relatively demanding. This paper explores strategies to make model-based development more attractive for mainstream developers.

Provisional Admission Practices: Blending Access and Support to Facilitate Student Success

ERIC Educational Resources Information Center

Nichols, Andrew Howard; Clinedinst, Melissa

2013-01-01

This report examines provisional admission as an initiative that can expand four-year college access and success for students from economically disadvantaged backgrounds. Provisional admission policies and programs enable students to enroll at an institution under specific conditions. Students are often required to meet certain academic…

NIPTE: a multi-university partnership supporting academic drug development.

PubMed

Gurvich, Vadim J; Byrn, Stephen R

2013-10-01

The strategic goal of academic translational research is to accelerate translational science through the improvement and development of resources for moving discoveries across translational barriers through 'first in humans' studies. To achieve this goal, access to drug discovery resources and preclinical IND-enabling infrastructure is crucial. One potential approach of research institutions for coordinating preclinical development, based on a model from the National Institute for Pharmaceutical Technology and Education (NIPTE), can provide academic translational and medical centers with access to a wide variety of enabling infrastructure for developing small molecule clinical candidates in an efficient, cost-effective manner. Copyright © 2013 Elsevier Ltd. All rights reserved.

Computational neuroanatomy: ontology-based representation of neural components and connectivity

PubMed Central

Rubin, Daniel L; Talos, Ion-Florin; Halle, Michael; Musen, Mark A; Kikinis, Ron

2009-01-01

Background A critical challenge in neuroscience is organizing, managing, and accessing the explosion in neuroscientific knowledge, particularly anatomic knowledge. We believe that explicit knowledge-based approaches to make neuroscientific knowledge computationally accessible will be helpful in tackling this challenge and will enable a variety of applications exploiting this knowledge, such as surgical planning. Results We developed ontology-based models of neuroanatomy to enable symbolic lookup, logical inference and mathematical modeling of neural systems. We built a prototype model of the motor system that integrates descriptive anatomic and qualitative functional neuroanatomical knowledge. In addition to modeling normal neuroanatomy, our approach provides an explicit representation of abnormal neural connectivity in disease states, such as common movement disorders. The ontology-based representation encodes both structural and functional aspects of neuroanatomy. The ontology-based models can be evaluated computationally, enabling development of automated computer reasoning applications. Conclusion Neuroanatomical knowledge can be represented in machine-accessible format using ontologies. Computational neuroanatomical approaches such as described in this work could become a key tool in translational informatics, leading to decision support applications that inform and guide surgical planning and personalized care for neurological disease in the future. PMID:19208191

A Quantitative Examination of Factors that Impact Technology Integration in Urban Public Secondary Mathematics Classrooms

ERIC Educational Resources Information Center

Harvey-Buschel, Phyllis

2009-01-01

The problem explored in this study was whether access to technology impacted technology integration in mathematics instruction in urban public secondary schools. Access to technology was measured by availability of computers in the classroom, teacher experience, and teacher professional development. Technology integration was measured by…

Access to Music Education with Regard to Race in Two Urban Areas

ERIC Educational Resources Information Center

Salvador, Karen; Allegood, Kristen

2014-01-01

This quantitative study examined access to school music instruction with regard to race in two urban areas: Detroit, Michigan, and Washington, DC, in 2009-2010. We found significant differences in the provision of music instruction between schools with high and low proportions of nonwhite enrollment, in categories including curricular offerings,…

Does Accelerating Access to Higher Education Lower Its Quality? The Australian Experience

ERIC Educational Resources Information Center

Pitman, Tim; Koshy, Paul; Phillimore, John

2015-01-01

In the pursuit of mass higher education, fears are often expressed that the quality of higher education suffers as access is increased. This quantitative study considers three proxies of educational quality: (1) prior academic achievement of the student, (2) attrition and retention rates and (3) progression rates, to establish whether educational…

Provider imposed restrictions to clients’ access to family planning in urban Uttar Pradesh, India: a mixed methods study

PubMed Central

2013-01-01

Background Medical barriers refer to unnecessary policies or procedures imposed by health care providers that are not necessarily medically advised; these restrictions impede clients’ access to family planning (FP). This mixed methods study investigates provider imposed barriers to provision of FP using recent quantitative and qualitative data from urban Uttar Pradesh, India. Methods Baseline quantitative data were collected in six cities in Uttar Pradesh, India from service delivery points (SDP), using facility audits, exit interviews, and provider surveys; for this study, the focus is on the provider surveys. More than 250 providers were surveyed in each city. Providers were asked about the FP methods they provide, and if they restrict clients’ access to each method based on age, parity, partner consent, or marital status. For the qualitative research, we conducted one-on-one interviews with 21 service providers in four of the six cities in Uttar Pradesh. Each interview lasted approximately 45 minutes. Results The quantitative findings show that providers restrict clients’ access to spacing and long-acting and permanent methods of FP based on age, parity, partner consent and marital status. Qualitative findings reinforce that providers, at times, make judgments about their clients’ education, FP needs and ability to understand FP options thereby imposing unnecessary barriers to FP methods. Conclusions Provider restrictions on FP methods are common in these urban Uttar Pradesh sites. This means that women who are young, unmarried, have few or no children, do not have the support of their partner, or are less educated may not be able to access or use FP or their preferred method. These findings highlight the need for in-service training for staff, with a focus on reviewing current guidelines and eligibility criteria for provision of methods. PMID:24365015

Preserving Smart Objects Privacy through Anonymous and Accountable Access Control for a M2M-Enabled Internet of Things

PubMed Central

Hernández-Ramos, José L.; Bernabe, Jorge Bernal; Moreno, M. Victoria; Skarmeta, Antonio F.

2015-01-01

As we get into the Internet of Things era, security and privacy concerns remain as the main obstacles in the development of innovative and valuable services to be exploited by society. Given the Machine-to-Machine (M2M) nature of these emerging scenarios, the application of current privacy-friendly technologies needs to be reconsidered and adapted to be deployed in such global ecosystem. This work proposes different privacy-preserving mechanisms through the application of anonymous credential systems and certificateless public key cryptography. The resulting alternatives are intended to enable an anonymous and accountable access control approach to be deployed on large-scale scenarios, such as Smart Cities. Furthermore, the proposed mechanisms have been deployed on constrained devices, in order to assess their suitability for a secure and privacy-preserving M2M-enabled Internet of Things. PMID:26140349

Preserving Smart Objects Privacy through Anonymous and Accountable Access Control for a M2M-Enabled Internet of Things.

PubMed

Hernández-Ramos, José L; Bernabe, Jorge Bernal; Moreno, M Victoria; Skarmeta, Antonio F

2015-07-01

As we get into the Internet of Things era, security and privacy concerns remain as the main obstacles in the development of innovative and valuable services to be exploited by society. Given the Machine-to-Machine (M2M) nature of these emerging scenarios, the application of current privacy-friendly technologies needs to be reconsidered and adapted to be deployed in such global ecosystem. This work proposes different privacy-preserving mechanisms through the application of anonymous credential systems and certificateless public key cryptography. The resulting alternatives are intended to enable an anonymous and accountable access control approach to be deployed on large-scale scenarios, such as Smart Cities. Furthermore, the proposed mechanisms have been deployed on constrained devices, in order to assess their suitability for a secure and privacy-preserving M2M-enabled Internet of Things.

Grid workflow validation using ontology-based tacit knowledge: A case study for quantitative remote sensing applications

NASA Astrophysics Data System (ADS)

Liu, Jia; Liu, Longli; Xue, Yong; Dong, Jing; Hu, Yingcui; Hill, Richard; Guang, Jie; Li, Chi

2017-01-01

Workflow for remote sensing quantitative retrieval is the ;bridge; between Grid services and Grid-enabled application of remote sensing quantitative retrieval. Workflow averts low-level implementation details of the Grid and hence enables users to focus on higher levels of application. The workflow for remote sensing quantitative retrieval plays an important role in remote sensing Grid and Cloud computing services, which can support the modelling, construction and implementation of large-scale complicated applications of remote sensing science. The validation of workflow is important in order to support the large-scale sophisticated scientific computation processes with enhanced performance and to minimize potential waste of time and resources. To research the semantic correctness of user-defined workflows, in this paper, we propose a workflow validation method based on tacit knowledge research in the remote sensing domain. We first discuss the remote sensing model and metadata. Through detailed analysis, we then discuss the method of extracting the domain tacit knowledge and expressing the knowledge with ontology. Additionally, we construct the domain ontology with Protégé. Through our experimental study, we verify the validity of this method in two ways, namely data source consistency error validation and parameters matching error validation.

System and method for programmable bank selection for banked memory subsystems

DOEpatents

Blumrich, Matthias A.; Chen, Dong; Gara, Alan G.; Giampapa, Mark E.; Hoenicke, Dirk; Ohmacht, Martin; Salapura, Valentina; Sugavanam, Krishnan

2010-09-07

A programmable memory system and method for enabling one or more processor devices access to shared memory in a computing environment, the shared memory including one or more memory storage structures having addressable locations for storing data. The system comprises: one or more first logic devices associated with a respective one or more processor devices, each first logic device for receiving physical memory address signals and programmable for generating a respective memory storage structure select signal upon receipt of pre-determined address bit values at selected physical memory address bit locations; and, a second logic device responsive to each of the respective select signal for generating an address signal used for selecting a memory storage structure for processor access. The system thus enables each processor device of a computing environment memory storage access distributed across the one or more memory storage structures.

A Bookmarking Service for Organizing and Sharing URLs

NASA Technical Reports Server (NTRS)

Keller, Richard M.; Wolfe, Shawn R.; Chen, James R.; Mathe, Nathalie; Rabinowitz, Joshua L.

1997-01-01

Web browser bookmarking facilities predominate as the method of choice for managing URLs. In this paper, we describe some deficiencies of current bookmarking schemes, and examine an alternative to current approaches. We present WebTagger(TM), an implemented prototype of a personal bookmarking service that provides both individuals and groups with a customizable means of organizing and accessing Web-based information resources. In addition, the service enables users to supply feedback on the utility of these resources relative to their information needs, and provides dynamically-updated ranking of resources based on incremental user feedback. Individuals may access the service from anywhere on the Internet, and require no special software. This service greatly simplifies the process of sharing URLs within groups, in comparison with manual methods involving email. The underlying bookmark organization scheme is more natural and flexible than current hierarchical schemes supported by the major Web browsers, and enables rapid access to stored bookmarks.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

PubMed Central

Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F.; Christie, Cole H.; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S.; Westbrook, John D.; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M.; Bourne, Philip E.; Burley, Stephen K.

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. PMID:25428375

Towards quantitative mass spectrometry-based metabolomics in microbial and mammalian systems.

PubMed

Kapoore, Rahul Vijay; Vaidyanathan, Seetharaman

2016-10-28

Metabolome analyses are a suite of analytical approaches that enable us to capture changes in the metabolome (small molecular weight components, typically less than 1500 Da) in biological systems. Mass spectrometry (MS) has been widely used for this purpose. The key challenge here is to be able to capture changes in a reproducible and reliant manner that is representative of the events that take place in vivo Typically, the analysis is carried out in vitro, by isolating the system and extracting the metabolome. MS-based approaches enable us to capture metabolomic changes with high sensitivity and resolution. When developing the technique for different biological systems, there are similarities in challenges and differences that are specific to the system under investigation. Here, we review some of the challenges in capturing quantitative changes in the metabolome with MS based approaches, primarily in microbial and mammalian systems.This article is part of the themed issue 'Quantitative mass spectrometry'. © 2016 The Author(s).

Attendance at NHS mandatory training sessions.

PubMed

Brand, Darren

2015-02-17

To identify factors that affect NHS healthcare professionals' attendance at mandatory training sessions. A quantitative approach was used, with a questionnaire sent to 400 randomly selected participants. A total of 122 responses were received, providing a mix of qualitative and quantitative data. Quantitative data were analysed using statistical methods. Open-ended responses were reviewed using thematic analysis. Clinical staff value mandatory training sessions highly. They are aware of the requirement to keep practice up-to-date and ensure patient safety remains a priority. However, changes to the delivery format of mandatory training sessions are required to enable staff to participate more easily, as staff are often unable to attend. The delivery of mandatory training should move from classroom-based sessions into the clinical area to maximise participation. Delivery should be assisted by local 'experts' who are able to customise course content to meet local requirements and the requirements of different staff groups. Improved arrangements to provide staff cover, for those attending training, would enable more staff to attend training sessions.

Cloud computing for context-aware enhanced m-Health services.

PubMed

Fernandez-Llatas, Carlos; Pileggi, Salvatore F; Ibañez, Gema; Valero, Zoe; Sala, Pilar

2015-01-01

m-Health services are increasing its presence in our lives due to the high penetration of new smartphone devices. This new scenario proposes new challenges in terms of information accessibility that require new paradigms which enable the new applications to access the data in a continuous and ubiquitous way, ensuring the privacy required depending on the kind of data accessed. This paper proposes an architecture based on cloud computing paradigms in order to empower new m-Health applications to enrich their results by providing secure access to user data.

Enabling the Differently-Abled

ERIC Educational Resources Information Center

Pal, Sonali

2009-01-01

It is perhaps unfortunate that enabling technologies do not come with an "ability warning", as they generally require the user to already have acquired a certain level of IT skills, in a similar way that online courses require users to have a certain level of prior IT knowledge. Accessing a computer and making the most of e-learning…

Micro/nano-computed tomography technology for quantitative dynamic, multi-scale imaging of morphogenesis.

PubMed

Gregg, Chelsea L; Recknagel, Andrew K; Butcher, Jonathan T

2015-01-01

Tissue morphogenesis and embryonic development are dynamic events challenging to quantify, especially considering the intricate events that happen simultaneously in different locations and time. Micro- and more recently nano-computed tomography (micro/nanoCT) has been used for the past 15 years to characterize large 3D fields of tortuous geometries at high spatial resolution. We and others have advanced micro/nanoCT imaging strategies for quantifying tissue- and organ-level fate changes throughout morphogenesis. Exogenous soft tissue contrast media enables visualization of vascular lumens and tissues via extravasation. Furthermore, the emergence of antigen-specific tissue contrast enables direct quantitative visualization of protein and mRNA expression. Micro-CT X-ray doses appear to be non-embryotoxic, enabling longitudinal imaging studies in live embryos. In this chapter we present established soft tissue contrast protocols for obtaining high-quality micro/nanoCT images and the image processing techniques useful for quantifying anatomical and physiological information from the data sets.

Quantitation of Staphylococcus aureus in Seawater Using CHROMagar™ SA

PubMed Central

Pombo, David; Hui, Jennifer; Kurano, Michelle; Bankowski, Matthew J; Seifried, Steven E

2010-01-01

A microbiological algorithm has been developed to analyze beach water samples for the determination of viable colony forming units (CFU) of Staphylococcus aureus (S. aureus). Membrane filtration enumeration of S. aureus from recreational beach waters using the chromogenic media CHROMagar™SA alone yields a positive predictive value (PPV) of 70%. Presumptive CHROMagar™SA colonies were confirmed as S. aureus by 24-hour tube coagulase test. Combined, these two tests yield a PPV of 100%. This algorithm enables accurate quantitation of S. aureus in seawater in 72 hours and could support risk-prediction processes for recreational waters. A more rapid protocol, utilizing a 4-hour tube coagulase confirmatory test, enables a 48-hour turnaround time with a modest false negative rate of less than 10%. PMID:20222490

Quantitative Analysis of the Usage of the COSMOS Science Education Portal

ERIC Educational Resources Information Center

Sotiriou, Sofoklis; Bogner, Franz X.; Neofotistos, George

2011-01-01

A quantitative method of mapping the web usage of an innovative educational portal is applied to analyze the behaviour of users of the COSMOS Science Education Portal. The COSMOS Portal contains user-generated resources (that are uploaded by its users). It has been designed to support a science teacher's search, retrieval and access to both,…

MaizeGDB: Global support for maize research through open access information [abstract

USDA-ARS?s Scientific Manuscript database

MaizeGDB is the open-access global repository for maize genetic and genomic information – from single genes that determine nutritional quality to whole genome-scale data for complex traits including yield and drought tolerance. The data and tools at MaizeGDB enable researchers from Ethiopia to Ghan...

Leading the Way: Access. 2013-18 Master Plan

ERIC Educational Resources Information Center

West Virginia Higher Education Policy Commission, 2013

2013-01-01

The 2013-18 West Virginia Higher Education Policy Commission master plan, "Leading the Way: Access. Success. Impact" was developed to provide a programmatic framework and goals to enable the state's system of public four-year institutions to meet the educational needs of West Virginians. A state economy in flux with declining revenues…

Understanding and Creating Accessible Touch Screen Interactions for Blind People

ERIC Educational Resources Information Center

Kane, Shaun K.

2011-01-01

Using touch screens presents a number of usability and accessibility challenges for blind people. Most touch screen-based user interfaces are optimized for visual interaction, and are therefore difficult or impossible to use without vision. This dissertation presents an approach to redesigning gesture-based user interfaces to enable blind people…

Maximizing Access Technology Tools for the Library of the Future

ERIC Educational Resources Information Center

Pearson, Waynn

2003-01-01

The renovated Cerritos Public Library is a unique blending of traditional and hightech features. One of the key principles in its planning and design was to enable a range of convenient access services. This article summarizes the process of building this library and how it has been received by users. (Contains 5 figures.)

Effects of Practice Type in the Here and Now Mobile Learning Environment

ERIC Educational Resources Information Center

Tutty, Jeremy I.; Martin, Florence

2014-01-01

This generation of technology is characterized by mobile and portable devices such as smartphones and tablet computers with wireless broadband access. Mobile technologies enable a new kind of learning called "here and now learning," where learners have access to information anytime and anywhere to perform authentic activities in the…

Spacecraft Demand Access: Autonomy for Low-Cost Planetary Operations

NASA Technical Reports Server (NTRS)

Sweetnam, Donald

1997-01-01

In this paper we describe a new concept and prototype for dramtically reducing the cost of contact with planetary spacecraft. Known as spacecraft Demand Access, a suite of spacecraft and ground automation technologies, it enables future intelligent spacecraft to act as initiators of cost effective contact with the ground - doing it only when necessary.

SECIMTools: a suite of metabolomics data analysis tools.

PubMed

Kirpich, Alexander S; Ibarra, Miguel; Moskalenko, Oleksandr; Fear, Justin M; Gerken, Joseph; Mi, Xinlei; Ashrafi, Ali; Morse, Alison M; McIntyre, Lauren M

2018-04-20

Metabolomics has the promise to transform the area of personalized medicine with the rapid development of high throughput technology for untargeted analysis of metabolites. Open access, easy to use, analytic tools that are broadly accessible to the biological community need to be developed. While technology used in metabolomics varies, most metabolomics studies have a set of features identified. Galaxy is an open access platform that enables scientists at all levels to interact with big data. Galaxy promotes reproducibility by saving histories and enabling the sharing workflows among scientists. SECIMTools (SouthEast Center for Integrated Metabolomics) is a set of Python applications that are available both as standalone tools and wrapped for use in Galaxy. The suite includes a comprehensive set of quality control metrics (retention time window evaluation and various peak evaluation tools), visualization techniques (hierarchical cluster heatmap, principal component analysis, modular modularity clustering), basic statistical analysis methods (partial least squares - discriminant analysis, analysis of variance, t-test, Kruskal-Wallis non-parametric test), advanced classification methods (random forest, support vector machines), and advanced variable selection tools (least absolute shrinkage and selection operator LASSO and Elastic Net). SECIMTools leverages the Galaxy platform and enables integrated workflows for metabolomics data analysis made from building blocks designed for easy use and interpretability. Standard data formats and a set of utilities allow arbitrary linkages between tools to encourage novel workflow designs. The Galaxy framework enables future data integration for metabolomics studies with other omics data.

In what ways do communities support optimal antiretroviral treatment in Zimbabwe?

PubMed

Scott, K; Campbell, C; Madanhire, C; Skovdal, M; Nyamukapa, C; Gregson, S

2014-12-01

Little research has been conducted on how pre-existing indigenous community resources, especially social networks, affect the success of externally imposed HIV interventions. Antiretroviral treatment (ART), an externally initiated biomedical intervention, is being rolled out across sub-Saharan Africa. Understanding the ways in which community networks are working to facilitate optimal ART access and adherence will enable policymakers to better engage with and bolster these pre-existing resources. We conducted 67 interviews and eight focus group discussions with 127 people from three key population groups in Manicaland, eastern Zimbabwe: healthcare workers, adults on ART and carers of children on ART. We also observed over 100 h of HIV treatment sites at local clinics and hospitals. Our research sought to determine how indigenous resources were enabling people to achieve optimal ART access and adherence. We analysed data transcripts using thematic network technique, coding references to supportive community networks that enable local people to achieve ART access and adherence. People on ART or carers of children on ART in Zimbabwe report drawing support from a variety of social networks that enable them to overcome many obstacles to adherence. Key support networks include: HIV groups; food and income support networks; home-based care, church and women's groups; family networks; and relationships with healthcare providers. More attention to the community context in which HIV initiatives occur will help ensure that interventions work with and benefit from pre-existing social capital. © The Author (2013). Published by Oxford University Press.

Zero-Copy Objects System

NASA Technical Reports Server (NTRS)

Burleigh, Scott C.

2011-01-01

Zero-Copy Objects System software enables application data to be encapsulated in layers of communication protocol without being copied. Indirect referencing enables application source data, either in memory or in a file, to be encapsulated in place within an unlimited number of protocol headers and/or trailers. Zero-copy objects (ZCOs) are abstract data access representations designed to minimize I/O (input/output) in the encapsulation of application source data within one or more layers of communication protocol structure. They are constructed within the heap space of a Simple Data Recorder (SDR) data store to which all participating layers of the stack must have access. Each ZCO contains general information enabling access to the core source data object (an item of application data), together with (a) a linked list of zero or more specific extents that reference portions of this source data object, and (b) linked lists of protocol header and trailer capsules. The concatenation of the headers (in ascending stack sequence), the source data object extents, and the trailers (in descending stack sequence) constitute the transmitted data object constructed from the ZCO. This scheme enables a source data object to be encapsulated in a succession of protocol layers without ever having to be copied from a buffer at one layer of the protocol stack to an encapsulating buffer at a lower layer of the stack. For large source data objects, the savings in copy time and reduction in memory consumption may be considerable.

In what ways do communities support optimal antiretroviral treatment in Zimbabwe?

PubMed Central

Scott, K.; Campbell, C.; Madanhire, C.; Skovdal, M.; Nyamukapa, C.; Gregson, S.

2014-01-01

Little research has been conducted on how pre-existing indigenous community resources, especially social networks, affect the success of externally imposed HIV interventions. Antiretroviral treatment (ART), an externally initiated biomedical intervention, is being rolled out across sub-Saharan Africa. Understanding the ways in which community networks are working to facilitate optimal ART access and adherence will enable policymakers to better engage with and bolster these pre-existing resources. We conducted 67 interviews and eight focus group discussions with 127 people from three key population groups in Manicaland, eastern Zimbabwe: healthcare workers, adults on ART and carers of children on ART. We also observed over 100 h of HIV treatment sites at local clinics and hospitals. Our research sought to determine how indigenous resources were enabling people to achieve optimal ART access and adherence. We analysed data transcripts using thematic network technique, coding references to supportive community networks that enable local people to achieve ART access and adherence. People on ART or carers of children on ART in Zimbabwe report drawing support from a variety of social networks that enable them to overcome many obstacles to adherence. Key support networks include: HIV groups; food and income support networks; home-based care, church and women's groups; family networks; and relationships with healthcare providers. More attention to the community context in which HIV initiatives occur will help ensure that interventions work with and benefit from pre-existing social capital. PMID:23503291

Total centralisation and optimisation of an oncology management suite via Citrix®

NASA Astrophysics Data System (ADS)

James, C.; Frantzis, J.; Ripps, L.; Fenton, P.

2014-03-01

The management of patient information and treatment planning is traditionally an intra-departmental requirement of a radiation oncology service. Epworth Radiation Oncology systems must support the transient nature of Visiting Medical Officers (VMOs). This unique work practice created challenges when implementing the vision of a completely paperless solution that allows for a responsive and efficient service delivery. ARIA® and EclipseTM (Varian Medical Systems, Palo Alto, CA, USA) have been deployed across four dedicated Citrix® (Citrix Systems, Santa Clara, CA, USA) servers allowing VMOs to access these applications remotely. A range of paperless solutions were developed within ARIA® to facilitate clinical and organisational management whilst optimising efficient work practices. The IT infrastructure and paperless workflow has enabled VMOs to securely access the VarianTM (Varian Medical Systems, Palo Alto, CA, USA) oncology software and experience full functionality from any location on multiple devices. This has enhanced access to patient information and improved the responsiveness of the service. Epworth HealthCare has developed a unique solution to enable remote access to a centralised oncology management suite, while maintaining a secure and paperless working environment.

Kokkos: Enabling manycore performance portability through polymorphic memory access patterns

DOE PAGES

Carter Edwards, H.; Trott, Christian R.; Sunderland, Daniel

2014-07-22

The manycore revolution can be characterized by increasing thread counts, decreasing memory per thread, and diversity of continually evolving manycore architectures. High performance computing (HPC) applications and libraries must exploit increasingly finer levels of parallelism within their codes to sustain scalability on these devices. We found that a major obstacle to performance portability is the diverse and conflicting set of constraints on memory access patterns across devices. Contemporary portable programming models address manycore parallelism (e.g., OpenMP, OpenACC, OpenCL) but fail to address memory access patterns. The Kokkos C++ library enables applications and domain libraries to achieve performance portability on diversemore » manycore architectures by unifying abstractions for both fine-grain data parallelism and memory access patterns. In this paper we describe Kokkos’ abstractions, summarize its application programmer interface (API), present performance results for unit-test kernels and mini-applications, and outline an incremental strategy for migrating legacy C++ codes to Kokkos. Furthermore, the Kokkos library is under active research and development to incorporate capabilities from new generations of manycore architectures, and to address a growing list of applications and domain libraries.« less

Digital Health Services and Digital Identity in Alberta.

PubMed

McEachern, Aiden; Cholewa, David

2017-01-01

The Government of Alberta continues to improve delivery of healthcare by allowing Albertans to access their health information online. Alberta is the only province in Canada with provincial electronic health records for all its citizens. These records are currently made available to medical practitioners, but Alberta Health believes that providing Albertans access to their health records will transform the delivery of healthcare in Alberta. It is important to have a high level of assurance that the health records are provided to the correct Albertan. Alberta Health requires a way for Albertans to obtain a digital identity with a high level of identity assurance prior to releasing health records via the Personal Health Portal. Service Alberta developed the MyAlberta Digital ID program to provide a digital identity verification service. The Ministry of Health is leveraging MyAlberta Digital ID to enable Albertans to access their personal health records through the Personal Health Portal. The Government of Alberta is advancing its vision of patient-centred healthcare by enabling Albertans to access a trusted source for health information and their electronic health records using a secure digital identity.

Optimising LAN access to grid enabled storage elements

NASA Astrophysics Data System (ADS)

Stewart, G. A.; Cowan, G. A.; Dunne, B.; Elwell, A.; Millar, A. P.

2008-07-01

When operational, the Large Hadron Collider experiments at CERN will collect tens of petabytes of physics data per year. The worldwide LHC computing grid (WLCG) will distribute this data to over two hundred Tier-1 and Tier-2 computing centres, enabling particle physicists around the globe to access the data for analysis. Although different middleware solutions exist for effective management of storage systems at collaborating institutes, the patterns of access envisaged for Tier-2s fall into two distinct categories. The first involves bulk transfer of data between different Grid storage elements using protocols such as GridFTP. This data movement will principally involve writing ESD and AOD files into Tier-2 storage. Secondly, once datasets are stored at a Tier-2, physics analysis jobs will read the data from the local SE. Such jobs require a POSIX-like interface to the storage so that individual physics events can be extracted. In this paper we consider the performance of POSIX-like access to files held in Disk Pool Manager (DPM) storage elements, a popular lightweight SRM storage manager from EGEE.

Portable and Error-Free DNA-Based Data Storage.

PubMed

Yazdi, S M Hossein Tabatabaei; Gabrys, Ryan; Milenkovic, Olgica

2017-07-10

DNA-based data storage is an emerging nonvolatile memory technology of potentially unprecedented density, durability, and replication efficiency. The basic system implementation steps include synthesizing DNA strings that contain user information and subsequently retrieving them via high-throughput sequencing technologies. Existing architectures enable reading and writing but do not offer random-access and error-free data recovery from low-cost, portable devices, which is crucial for making the storage technology competitive with classical recorders. Here we show for the first time that a portable, random-access platform may be implemented in practice using nanopore sequencers. The novelty of our approach is to design an integrated processing pipeline that encodes data to avoid costly synthesis and sequencing errors, enables random access through addressing, and leverages efficient portable sequencing via new iterative alignment and deletion error-correcting codes. Our work represents the only known random access DNA-based data storage system that uses error-prone nanopore sequencers, while still producing error-free readouts with the highest reported information rate/density. As such, it represents a crucial step towards practical employment of DNA molecules as storage media.

Data management and analysis for the Earth System Grid

NASA Astrophysics Data System (ADS)

Williams, D. N.; Ananthakrishnan, R.; Bernholdt, D. E.; Bharathi, S.; Brown, D.; Chen, M.; Chervenak, A. L.; Cinquini, L.; Drach, R.; Foster, I. T.; Fox, P.; Hankin, S.; Henson, V. E.; Jones, P.; Middleton, D. E.; Schwidder, J.; Schweitzer, R.; Schuler, R.; Shoshani, A.; Siebenlist, F.; Sim, A.; Strand, W. G.; Wilhelmi, N.; Su, M.

2008-07-01

The international climate community is expected to generate hundreds of petabytes of simulation data within the next five to seven years. This data must be accessed and analyzed by thousands of analysts worldwide in order to provide accurate and timely estimates of the likely impact of climate change on physical, biological, and human systems. Climate change is thus not only a scientific challenge of the first order but also a major technological challenge. In order to address this technological challenge, the Earth System Grid Center for Enabling Technologies (ESG-CET) has been established within the U.S. Department of Energy's Scientific Discovery through Advanced Computing (SciDAC)-2 program, with support from the offices of Advanced Scientific Computing Research and Biological and Environmental Research. ESG-CET's mission is to provide climate researchers worldwide with access to the data, information, models, analysis tools, and computational capabilities required to make sense of enormous climate simulation datasets. Its specific goals are to (1) make data more useful to climate researchers by developing Grid technology that enhances data usability; (2) meet specific distributed database, data access, and data movement needs of national and international climate projects; (3) provide a universal and secure web-based data access portal for broad multi-model data collections; and (4) provide a wide-range of Grid-enabled climate data analysis tools and diagnostic methods to international climate centers and U.S. government agencies. Building on the successes of the previous Earth System Grid (ESG) project, which has enabled thousands of researchers to access tens of terabytes of data from a small number of ESG sites, ESG-CET is working to integrate a far larger number of distributed data providers, high-bandwidth wide-area networks, and remote computers in a highly collaborative problem-solving environment.

SkyGlowNet as a Vehicle for STEM Education

NASA Astrophysics Data System (ADS)

Flurchick, K. M.; Craine, E. R.; Culver, R. B.; Deal, S.; Foster, C.

2013-06-01

SkyGlowNet is an emerging network of internet-enabled sky brightness meters (iSBM) that continuously record and log sky brightness at the zenith of each network node site. Also logged are time and weather information. These data are polled at a user-defined frequency, typically about every 45 seconds. The data are uploaded to the SkyGlowNet website, initially to a proprietary area where the data for each institution are embargoed for one or two semesters as students conduct research projects with their data. When released from embargo, the data are moved to another area where they can be accessed by all SkyGlowNet participants. Some of the data are periodically released to a public area on the website. In this presentation we describe the data formats and provide examples of both data content and the structure of the website. Early data from two nodes in the SkyGlowNet have been characterized, both quantitatively and qualitatively, by undergraduate students at NCAT. A summary of their work is presented here. These analyses are of utility in helping those new to looking at these data to understand how to interpret them. In particular, we demonstrate differences between effects on light at night and sky brightness due to astronomical cycles, atmospheric phenomena, and artificial lighting. Quantitative characterization of the data includes statistical analyses of parsed segments of the temporal data stream. An attempt is made to relate statistical metrics to specific types of phenomena.

Laser-induced incandescence measurements in a fired diesel engine at 3 kHz

NASA Astrophysics Data System (ADS)

Boxx, I. G.; Heinold, O.; Geigle, K. P.

2015-01-01

Laser-induced incandescence (LII) was performed at 3 kHz in an optically accessible cylinder of a fired diesel engine using a commercially available diode-pumped solid-state laser and an intensified CMOS camera. The resulting images, acquired every 3° of crank angle, enabled the spatiotemporal tracking of soot structures during the expansion/exhaust stroke of the engine cycle. The image sequences demonstrate that soot tends to form in thin sheets that propagate and interact with the in-cylinder flow. These sheets tend to align parallel to the central axis of the cylinder and are frequently wrapped into conical spirals by aerodynamic swirl. Most of the soot is observed well away from the cylinder walls. Quantitative soot measurements were beyond the scope of this study but the results demonstrate the practical utility of using kHz-rate LII to acquire ensemble-averaged statistical data with high crank angle resolution over a complete engine cycle. Based on semi-quantitative measures of soot distribution, it was possible to identify soot dynamics related to incomplete charge exchange. This study shows that long-duration, multi-kHz acquisition rate LII measurements are viable in a fired diesel engine with currently available laser and camera technology, albeit only in the expansion and exhaust phase of the cycle at present. Furthermore, such measurements yield useful insight into soot dynamics and therefore constitute an important new tool for the development and optimization of diesel engine technology.

Frequency modulation atomic force microscopy in ambient environments utilizing robust feedback tuning

NASA Astrophysics Data System (ADS)

Kilpatrick, J. I.; Gannepalli, A.; Cleveland, J. P.; Jarvis, S. P.

2009-02-01

Frequency modulation atomic force microscopy (FM-AFM) is rapidly evolving as the technique of choice in the pursuit of high resolution imaging of biological samples in ambient environments. The enhanced stability afforded by this dynamic AFM mode combined with quantitative analysis enables the study of complex biological systems, at the nanoscale, in their native physiological environment. The operational bandwidth and accuracy of constant amplitude FM-AFM in low Q environments is heavily dependent on the cantilever dynamics and the performance of the demodulation and feedback loops employed to oscillate the cantilever at its resonant frequency with a constant amplitude. Often researchers use ad hoc feedback gains or instrument default values that can result in an inability to quantify experimental data. Poor choice of gains or exceeding the operational bandwidth can result in imaging artifacts and damage to the tip and/or sample. To alleviate this situation we present here a methodology to determine feedback gains for the amplitude and frequency loops that are specific to the cantilever and its environment, which can serve as a reasonable "first guess," thus making quantitative FM-AFM in low Q environments more accessible to the nonexpert. This technique is successfully demonstrated for the low Q systems of air (Q ˜40) and water (Q ˜1). In addition, we present FM-AFM images of MC3T3-E1 preosteoblast cells acquired using the gains calculated by this methodology demonstrating the effectiveness of this technique.

p-BioSPRE—an information and communication technology framework for transnational biomaterial sharing and access

PubMed Central

Weiler, Gabriele; Schröder, Christina; Schera, Fatima; Dobkowicz, Matthias; Kiefer, Stephan; Heidtke, Karsten R; Hänold, Stefanie; Nwankwo, Iheanyi; Forgó, Nikolaus; Stanulla, Martin; Eckert, Cornelia; Graf, Norbert

2014-01-01

Biobanks represent key resources for clinico-genomic research and are needed to pave the way to personalised medicine. To achieve this goal, it is crucial that scientists can securely access and share high-quality biomaterial and related data. Therefore, there is a growing interest in integrating biobanks into larger biomedical information and communication technology (ICT) infrastructures. The European project p-medicine is currently building an innovative ICT infrastructure to meet this need. This platform provides tools and services for conducting research and clinical trials in personalised medicine. In this paper, we describe one of its main components, the biobank access framework p-BioSPRE (p-medicine Biospecimen Search and Project Request Engine). This generic framework enables and simplifies access to existing biobanks, but also to offer own biomaterial collections to research communities, and to manage biobank specimens and related clinical data over the ObTiMA Trial Biomaterial Manager. p-BioSPRE takes into consideration all relevant ethical and legal standards, e.g., safeguarding donors’ personal rights and enabling biobanks to keep control over the donated material and related data. The framework thus enables secure sharing of biomaterial within open and closed research communities, while flexibly integrating related clinical and omics data. Although the development of the framework is mainly driven by user scenarios from the cancer domain, in this case, acute lymphoblastic leukaemia and Wilms tumour, it can be extended to further disease entities. PMID:24567758

Data governance and stewardship: designing data stewardship entities and advancing data access.

PubMed

Rosenbaum, Sara

2010-10-01

U.S. health policy is engaged in a struggle over access to health information, in particular, the conditions under which information should be accessible for research when appropriate privacy protections and security safeguards are in place. The expanded use of health information-an inevitable step in an information age-is widely considered be essential to health system reform. Models exist for the creation of data-sharing arrangements that promote proper use of information in a safe and secure environment and with attention to ethical standards. Data stewardship is a concept with deep roots in the science and practice of data collection, sharing, and analysis. Reflecting the values of fair information practice, data stewardship denotes an approach to the management of data, particularly data that can identify individuals. The concept of a data steward is intended to convey a fiduciary (or trust) level of responsibility toward the data. Data governance is the process by which responsibilities of stewardship are conceptualized and carried out. As the concept of health information data stewardship advances in a technology-enabled environment, the question is whether legal barriers to data access and use will begin to give way. One possible answer may lie in defining the public interest in certain data uses, tying provider participation in federal health programs to the release of all-payer data to recognized data stewardship entities for aggregation and management, and enabling such entities to foster and enable the creation of knowledge through research. © Health Research and Educational Trust.

Data Governance and Stewardship: Designing Data Stewardship Entities and Advancing Data Access

PubMed Central

Rosenbaum, Sara

2010-01-01

U.S. health policy is engaged in a struggle over access to health information, in particular, the conditions under which information should be accessible for research when appropriate privacy protections and security safeguards are in place. The expanded use of health information—an inevitable step in an information age—is widely considered be essential to health system reform. Models exist for the creation of data-sharing arrangements that promote proper use of information in a safe and secure environment and with attention to ethical standards. Data stewardship is a concept with deep roots in the science and practice of data collection, sharing, and analysis. Reflecting the values of fair information practice, data stewardship denotes an approach to the management of data, particularly data that can identify individuals. The concept of a data steward is intended to convey a fiduciary (or trust) level of responsibility toward the data. Data governance is the process by which responsibilities of stewardship are conceptualized and carried out. As the concept of health information data stewardship advances in a technology-enabled environment, the question is whether legal barriers to data access and use will begin to give way. One possible answer may lie in defining the public interest in certain data uses, tying provider participation in federal health programs to the release of all-payer data to recognized data stewardship entities for aggregation and management, and enabling such entities to foster and enable the creation of knowledge through research. PMID:21054365

Subtitle Synchronization across Multiple Screens and Devices

PubMed Central

Rodriguez-Alsina, Aitor; Talavera, Guillermo; Orero, Pilar; Carrabina, Jordi

2012-01-01

Ambient Intelligence is a new paradigm in which environments are sensitive and responsive to the presence of people. This is having an increasing importance in multimedia applications, which frequently rely on sensors to provide useful information to the user. In this context, multimedia applications must adapt and personalize both content and interfaces in order to reach acceptable levels of context-specific quality of service for the user, and enable the content to be available anywhere and at any time. The next step is to make content available to everybody in order to overcome the existing access barriers to content for users with specific needs, or else to adapt to different platforms, hence making content fully usable and accessible. Appropriate access to video content, for instance, is not always possible due to the technical limitations of traditional video packaging, transmission and presentation. This restricts the flexibility of subtitles and audio-descriptions to be adapted to different devices, contexts and users. New Web standards built around HTML5 enable more featured applications with better adaptation and personalization facilities, and thus would seem more suitable for accessible AmI environments. This work presents a video subtitling system that enables the customization, adaptation and synchronization of subtitles across different devices and multiple screens. The benefits of HTML5 applications for building the solution are analyzed along with their current platform support. Moreover, examples of the use of the application in three different cases are presented. Finally, the user experience of the solution is evaluated. PMID:23012513

Subtitle synchronization across multiple screens and devices.

PubMed

Rodriguez-Alsina, Aitor; Talavera, Guillermo; Orero, Pilar; Carrabina, Jordi

2012-01-01

Ambient Intelligence is a new paradigm in which environments are sensitive and responsive to the presence of people. This is having an increasing importance in multimedia applications, which frequently rely on sensors to provide useful information to the user. In this context, multimedia applications must adapt and personalize both content and interfaces in order to reach acceptable levels of context-specific quality of service for the user, and enable the content to be available anywhere and at any time. The next step is to make content available to everybody in order to overcome the existing access barriers to content for users with specific needs, or else to adapt to different platforms, hence making content fully usable and accessible. Appropriate access to video content, for instance, is not always possible due to the technical limitations of traditional video packaging, transmission and presentation. This restricts the flexibility of subtitles and audio-descriptions to be adapted to different devices, contexts and users. New Web standards built around HTML5 enable more featured applications with better adaptation and personalization facilities, and thus would seem more suitable for accessible AmI environments. This work presents a video subtitling system that enables the customization, adaptation and synchronization of subtitles across different devices and multiple screens. The benefits of HTML5 applications for building the solution are analyzed along with their current platform support. Moreover, examples of the use of the application in three different cases are presented. Finally, the user experience of the solution is evaluated.

XGR software for enhanced interpretation of genomic summary data, illustrated by application to immunological traits.

PubMed

Fang, Hai; Knezevic, Bogdan; Burnham, Katie L; Knight, Julian C

2016-12-13

Biological interpretation of genomic summary data such as those resulting from genome-wide association studies (GWAS) and expression quantitative trait loci (eQTL) studies is one of the major bottlenecks in medical genomics research, calling for efficient and integrative tools to resolve this problem. We introduce eXploring Genomic Relations (XGR), an open source tool designed for enhanced interpretation of genomic summary data enabling downstream knowledge discovery. Targeting users of varying computational skills, XGR utilises prior biological knowledge and relationships in a highly integrated but easily accessible way to make user-input genomic summary datasets more interpretable. We show how by incorporating ontology, annotation, and systems biology network-driven approaches, XGR generates more informative results than conventional analyses. We apply XGR to GWAS and eQTL summary data to explore the genomic landscape of the activated innate immune response and common immunological diseases. We provide genomic evidence for a disease taxonomy supporting the concept of a disease spectrum from autoimmune to autoinflammatory disorders. We also show how XGR can define SNP-modulated gene networks and pathways that are shared and distinct between diseases, how it achieves functional, phenotypic and epigenomic annotations of genes and variants, and how it enables exploring annotation-based relationships between genetic variants. XGR provides a single integrated solution to enhance interpretation of genomic summary data for downstream biological discovery. XGR is released as both an R package and a web-app, freely available at http://galahad.well.ox.ac.uk/XGR .

Nanoelectronics enabled chronic multimodal neural platform in a mouse ischemic model.

PubMed

Luan, Lan; Sullender, Colin T; Li, Xue; Zhao, Zhengtuo; Zhu, Hanlin; Wei, Xiaoling; Xie, Chong; Dunn, Andrew K

2018-02-01

Despite significant advancements of optical imaging techniques for mapping hemodynamics in small animal models, it remains challenging to combine imaging with spatially resolved electrical recording of individual neurons especially for longitudinal studies. This is largely due to the strong invasiveness to the living brain from the penetrating electrodes and their limited compatibility with longitudinal imaging. We implant arrays of ultraflexible nanoelectronic threads (NETs) in mice for neural recording both at the brain surface and intracortically, which maintain great tissue compatibility chronically. By mounting a cranial window atop of the NET arrays that allows for chronic optical access, we establish a multimodal platform that combines spatially resolved electrical recording of neural activity and laser speckle contrast imaging (LSCI) of cerebral blood flow (CBF) for longitudinal studies. We induce peri-infarct depolarizations (PIDs) by targeted photothrombosis, and show the ability to detect its occurrence and propagation through spatiotemporal variations in both extracellular potentials and CBF. We also demonstrate chronic tracking of single-unit neural activity and CBF over days after photothrombosis, from which we observe reperfusion and increased firing rates. This multimodal platform enables simultaneous mapping of neural activity and hemodynamic parameters at the microscale for quantitative, longitudinal comparisons with minimal perturbation to the baseline neurophysiology. The ability to spatiotemporally resolve and chronically track CBF and neural electrical activity in the same living brain region has broad applications for studying the interplay between neural and hemodynamic responses in health and in cerebrovascular and neurological pathologies. Copyright © 2017 Elsevier B.V. All rights reserved.

Optimized protocol for quantitative multiple reaction monitoring-based proteomic analysis of formalin-fixed, paraffin embedded tissues

PubMed Central

Kennedy, Jacob J.; Whiteaker, Jeffrey R.; Schoenherr, Regine M.; Yan, Ping; Allison, Kimberly; Shipley, Melissa; Lerch, Melissa; Hoofnagle, Andrew N.; Baird, Geoffrey Stuart; Paulovich, Amanda G.

2016-01-01

Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin embedded (FFPE) tissues. While the feasibility of using targeted, multiple reaction monitoring-mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e. 9 processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R2 = 0.94) and immuno-MRM (R2 = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens. PMID:27462933

NFFA-Europe: enhancing European competitiveness in nanoscience research and innovation (Conference Presentation)

NASA Astrophysics Data System (ADS)

Carsughi, Flavio; Fonseca, Luis

2017-06-01

NFFA-EUROPE is an European open access resource for experimental and theoretical nanoscience and sets out a platform to carry out comprehensive projects for multidisciplinary research at the nanoscale extending from synthesis to nanocharacterization to theory and numerical simulation. Advanced infrastructures specialized on growth, nano-lithography, nano-characterization, theory and simulation and fine-analysis with Synchrotron, FEL and Neutron radiation sources are integrated in a multi-site combination to develop frontier research on methods for reproducible nanoscience research and to enable European and international researchers from diverse disciplines to carry out advanced proposals impacting science and innovation. NFFA-EUROPE will enable coordinated access to infrastructures on different aspects of nanoscience research that is not currently available at single specialized ones and without duplicating their specific scopes. Approved user projects will have access to the best suited instruments and support competences for performing the research, including access to analytical large scale facilities, theory and simulation and high-performance computing facilities. Access is offered free of charge to European users and users will receive a financial contribution for their travel, accommodation and subsistence costs. The users access will include several "installations" and will be coordinated through a single entry point portal that will activate an advanced user-infrastructure dialogue to build up a personalized access programme with an increasing return on science and innovation production. The own research activity of NFFA-EUROPE will address key bottlenecks of nanoscience research: nanostructure traceability, protocol reproducibility, in-operando nano-manipulation and analysis, open data.

Access to specialty mental health services among women in California.

PubMed

Kimerling, Rachel; Baumrind, Nikki

2005-06-01

The Anderson behavioral model was used to investigate racial and ethnic disparities in access to specialty mental health services among women in California as well as factors that might account for such disparities. The study was a cross-sectional examination of a probability sample of 3,750 California women. The main indicators of access to services were perceived need, service seeking, and service use. Multivariate models were constructed that accounted for need and enabling and demographic variables. Significant racial and ethnic variations in access to specialty mental health services were observed. African-American, Hispanic, and Asian women were significantly less likely to use specialty mental health services than white women. Multivariate analyses showed that Hispanic and Asian women were less likely than white women to report perceived need, even after frequent mental distress had been taken into account. Among women with perceived need, African-American and Asian women were less likely than white women to seek mental health services after differences in insurance status had been taken into account. Among women who sought services, Hispanic women were less likely than white women to obtain services after adjustment for the effects of poverty. Need and enabling factors did not entirely account for the observed disparities in access to services. Additional research is needed to identify gender- and culture-specific models for access to mental health services in order to decrease disparities in access. Factors such as perceived need and decisions to seek services are important factors that should be emphasized in future studies.

Coupling Reagent for UV/vis Absorbing Azobenzene-Based Quantitative Analysis of the Extent of Functional Group Immobilization on Silica.

PubMed

Choi, Ra-Young; Lee, Chang-Hee; Jun, Chul-Ho

2018-05-18

A methallylsilane coupling reagent, containing both a N-hydroxysuccinimidyl(NHS)-ester group and a UV/vis absorbing azobenzene linker undergoes acid-catalyzed immobilization on silica. Analysis of the UV/vis absorption band associated with the azobenzene group in the adduct enables facile quantitative determination of the extent of loading of the NHS groups. Reaction of NHS-groups on the silica surface with amine groups of GOx and rhodamine can be employed to generate enzyme or dye-immobilized silica for quantitative analysis.

A quantitative reconstruction software suite for SPECT imaging

NASA Astrophysics Data System (ADS)

Namías, Mauro; Jeraj, Robert

2017-11-01

Quantitative Single Photon Emission Tomography (SPECT) imaging allows for measurement of activity concentrations of a given radiotracer in vivo. Although SPECT has usually been perceived as non-quantitative by the medical community, the introduction of accurate CT based attenuation correction and scatter correction from hybrid SPECT/CT scanners has enabled SPECT systems to be as quantitative as Positron Emission Tomography (PET) systems. We implemented a software suite to reconstruct quantitative SPECT images from hybrid or dedicated SPECT systems with a separate CT scanner. Attenuation, scatter and collimator response corrections were included in an Ordered Subset Expectation Maximization (OSEM) algorithm. A novel scatter fraction estimation technique was introduced. The SPECT/CT system was calibrated with a cylindrical phantom and quantitative accuracy was assessed with an anthropomorphic phantom and a NEMA/IEC image quality phantom. Accurate activity measurements were achieved at an organ level. This software suite helps increasing quantitative accuracy of SPECT scanners.

Cyberinfrastructure at IRIS: Challenges and Solutions Providing Integrated Data Access to EarthScope and Other Earth Science Data

NASA Astrophysics Data System (ADS)

Ahern, T. K.; Barga, R.; Casey, R.; Kamb, L.; Parastatidis, S.; Stromme, S.; Weertman, B. T.

2008-12-01

While mature methods of accessing seismic data from the IRIS DMC have existed for decades, the demands for improved interdisciplinary data integration call for new approaches. Talented software teams at the IRIS DMC, UNAVCO and the ICDP in Germany, have been developing web services for all EarthScope data including data from USArray, PBO and SAFOD. These web services are based upon SOAP and WSDL. The EarthScope Data Portal was the first external system to access data holdings from the IRIS DMC using Web Services. EarthScope will also draw more heavily upon products to aid in cross-disciplinary data reuse. A Product Management System called SPADE allows archive of and access to heterogeneous data products, presented as XML documents, at the IRIS DMC. Searchable metadata are extracted from the XML and enable powerful searches for products from EarthScope and other data sources. IRIS is teaming with the External Research Group at Microsoft Research to leverage a powerful Scientific Workflow Engine (Trident) and interact with the web services developed at centers such as IRIS to enable access to data services as well as computational services. We believe that this approach will allow web- based control of workflows and the invocation of computational services that transform data. This capability will greatly improve access to data across scientific disciplines. This presentation will review some of the traditional access tools as well as many of the newer approaches that use web services, scientific workflow to improve interdisciplinary data access.

Secure, web-accessible call rosters for academic radiology departments.

PubMed

Nguyen, A V; Tellis, W M; Avrin, D E

2000-05-01

Traditionally, radiology department call rosters have been posted via paper and bulletin boards. Frequently, changes to these lists are made by multiple people independently, but often not synchronized, resulting in confusion among the house staff and technical staff as to who is on call and when. In addition, multiple and disparate copies exist in different sections of the department, and changes made would not be propagated to all the schedules. To eliminate such difficulties, a paperless call scheduling application was developed. Our call scheduling program allowed Java-enabled web access to a database by designated personnel from each radiology section who have privileges to make the necessary changes. Once a person made a change, everyone accessing the database would see the modification. This eliminates the chaos resulting from people swapping shifts at the last minute and not having the time to record or broadcast the change. Furthermore, all changes to the database were logged. Users are given a log-in name and password and can only edit their section; however, all personnel have access to all sections' schedules. Our applet was written in Java 2 using the latest technology in database access. We access our Interbase database through the DataExpress and DB Swing (Borland, Scotts Valley, CA) components. The result is secure access to the call rosters via the web. There are many advantages to the web-enabled access, mainly the ability for people to make changes and have the changes recorded and propagated in a single virtual location and available to all who need to know.

Enhancement of a Virtual Reality Wheelchair Simulator to Include Qualitative and Quantitative Performance Metrics

ERIC Educational Resources Information Center

Harrison, C. S.; Grant, P. M.; Conway, B. A.

2010-01-01

The increasing importance of inclusive design and in particular accessibility guidelines established in the U.K. 1996 Disability Discrimination Act (DDA) has been a prime motivation for the work on wheelchair access, a subset of the DDA guidelines, described in this article. The development of these guidelines mirrors the long-standing provisions…

Examining Stakeholder Perceptions of Accessibility and Utilization of Computer and Internet Technology in the Selinsgrove Area School District

ERIC Educational Resources Information Center

Krause, Lorinda M.

2014-01-01

This study utilized a mixed methods approach to examine the issue of how parents, students, and teachers (stakeholders) perceive accessibility and the utilization of computer and Internet technology within the Selinsgrove, Pennsylvania Area School District. Quantitative data was collected through the use of questionnaires distributed to the…

Automated analysis of timber access road alternatives.

Treesearch

Doyle Burke

1974-01-01

The evaluation of timber access road alternatives is one of the primary tasks in timber harvest planning and design. During the planning stages, it is also one of the most difficult to accomplish quantitatively because a basis for comparison is related to such values as grade, length, horizontal and vertical curvature, and volumes of excavation and embankment. Within...

ICT Accessibility and Usability to Support Learning of Visually-Impaired Students in Tanzania

ERIC Educational Resources Information Center

Eligi, Innosencia; Mwantimwa, Kelefa

2017-01-01

The main objective of this study was to assess the accessibility and usability of Information and Communication Technology facilities to facilitate learning among visually-impaired students at the University of Dar es Salaam (UDSM). The study employed a mixed methods design in gathering, processing and analysing quantitative and qualitative data.…

Improving Access to the Baccalaureate: Articulation Agreements and the National Science Foundation's Advanced Technological Education Program

ERIC Educational Resources Information Center

Zinser, Richard W.; Hanssen, Carl E.

2006-01-01

This article presents an analysis of national data from the Advanced Technological Education (ATE) program regarding articulation agreements for the transfer of 2-year technical degrees to baccalaureate degrees. Quantitative and qualitative data are illustrated to help explain the extent to which ATE projects improve access to universities for…

The Contributions of Economics to the Study of College Access and Success

ERIC Educational Resources Information Center

Long, Bridget Terry

2007-01-01

Background/Context: The essay provides a comprehensive review of work by economists and others in related quantitative disciplines on the transition of students to college. A particular emphasis is given to the role of price and financial aid although issues related to college preparation, access, and persistence are also investigated. The final…

Useful, Used, and Peer Approved: The Importance of Rigor and Accessibility in Postsecondary Research and Evaluation. WISCAPE Viewpoints

ERIC Educational Resources Information Center

Vaade, Elizabeth; McCready, Bo

2012-01-01

Traditionally, researchers, policymakers, and practitioners have perceived a tension between rigor and accessibility in quantitative research and evaluation in postsecondary education. However, this study indicates that both producers and consumers of these studies value high-quality work and clear findings that can reach multiple audiences. The…

Barriers and Delays in Tuberculosis Diagnosis and Treatment Services: Does Gender Matter?

PubMed Central

Yang, Wei-Teng; Gounder, Celine R.; Akande, Tokunbo; De Neve, Jan-Walter; McIntire, Katherine N.; Chandrasekhar, Aditya; de Lima Pereira, Alan; Gummadi, Naveen; Samanta, Santanu; Gupta, Amita

2014-01-01

Background. Tuberculosis (TB) remains a global public health problem with known gender-related disparities. We reviewed the quantitative evidence for gender-related differences in accessing TB services from symptom onset to treatment initiation. Methods. Following a systematic review process, we: searched 12 electronic databases; included quantitative studies assessing gender differences in accessing TB diagnostic and treatment services; abstracted data; and assessed study validity. We defined barriers and delays at the individual and provider/system levels using a conceptual framework of the TB care continuum and examined gender-related differences. Results. Among 13,448 articles, 137 were included: many assessed individual-level barriers (52%) and delays (42%), 76% surveyed persons presenting for care with diagnosed or suspected TB, 24% surveyed community members, and two-thirds were from African and Asian regions. Many studies reported no gender differences. Among studies reporting disparities, women faced greater barriers (financial: 64% versus 36%; physical: 100% versus 0%; stigma: 85% versus 15%; health literacy: 67% versus 33%; and provider-/system-level: 100% versus 0%) and longer delays (presentation to diagnosis: 45% versus 0%) than men. Conclusions. Many studies found no quantitative gender-related differences in barriers and delays limiting access to TB services. When differences were identified, women experienced greater barriers and longer delays than men. PMID:24876956

Barriers and delays in tuberculosis diagnosis and treatment services: does gender matter?

PubMed

Yang, Wei-Teng; Gounder, Celine R; Akande, Tokunbo; De Neve, Jan-Walter; McIntire, Katherine N; Chandrasekhar, Aditya; de Lima Pereira, Alan; Gummadi, Naveen; Samanta, Santanu; Gupta, Amita

2014-01-01

Background. Tuberculosis (TB) remains a global public health problem with known gender-related disparities. We reviewed the quantitative evidence for gender-related differences in accessing TB services from symptom onset to treatment initiation. Methods. Following a systematic review process, we: searched 12 electronic databases; included quantitative studies assessing gender differences in accessing TB diagnostic and treatment services; abstracted data; and assessed study validity. We defined barriers and delays at the individual and provider/system levels using a conceptual framework of the TB care continuum and examined gender-related differences. Results. Among 13,448 articles, 137 were included: many assessed individual-level barriers (52%) and delays (42%), 76% surveyed persons presenting for care with diagnosed or suspected TB, 24% surveyed community members, and two-thirds were from African and Asian regions. Many studies reported no gender differences. Among studies reporting disparities, women faced greater barriers (financial: 64% versus 36%; physical: 100% versus 0%; stigma: 85% versus 15%; health literacy: 67% versus 33%; and provider-/system-level: 100% versus 0%) and longer delays (presentation to diagnosis: 45% versus 0%) than men. Conclusions. Many studies found no quantitative gender-related differences in barriers and delays limiting access to TB services. When differences were identified, women experienced greater barriers and longer delays than men.

The Protein Disease Database of human body fluids: II. Computer methods and data issues.

PubMed

Lemkin, P F; Orr, G A; Goldstein, M P; Creed, G J; Myrick, J E; Merril, C R

1995-01-01

The Protein Disease Database (PDD) is a relational database of proteins and diseases. With this database it is possible to screen for quantitative protein abnormalities associated with disease states. These quantitative relationships use data drawn from the peer-reviewed biomedical literature. Assays may also include those observed in high-resolution electrophoretic gels that offer the potential to quantitate many proteins in a single test as well as data gathered by enzymatic or immunologic assays. We are using the Internet World Wide Web (WWW) and the Web browser paradigm as an access method for wide distribution and querying of the Protein Disease Database. The WWW hypertext transfer protocol and its Common Gateway Interface make it possible to build powerful graphical user interfaces that can support easy-to-use data retrieval using query specification forms or images. The details of these interactions are totally transparent to the users of these forms. Using a client-server SQL relational database, user query access, initial data entry and database maintenance are all performed over the Internet with a Web browser. We discuss the underlying design issues, mapping mechanisms and assumptions that we used in constructing the system, data entry, access to the database server, security, and synthesis of derived two-dimensional gel image maps and hypertext documents resulting from SQL database searches.

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.

Developing accessible cyberinfrastructure-enabled knowledge communities in the national disability community: theory, practice, and policy.

PubMed

Myhill, William N; Cogburn, Derrick L; Samant, Deepti; Addom, Benjamin Kwasi; Blanck, Peter

2008-01-01

Since publication of the Atkins Commission report in 2003, the national scientific community has placed significant emphasis on developing cyberinfrastructure-enabled knowledge communities, which are designed to facilitate enhanced efficiency and collaboration in geographically distributed networks of researchers. This article suggests that the new cyberinfrastructure movement may not fully benefit those participants with disabilities, unless closer attention is paid to legal mandates and universal design principles. Many technology-enhanced learning communities provide geographically distributed collaboration opportunities that expand the inclusion of diverse peoples and help close the digital divide. However, to date, most collaboratory efforts have not emphasized the need for access among people with disabilities nor meeting minimum standards for technological accessibility. To address these concerns, this article reports on two pilot collaboratory studies that explore the role advanced information, communication, and collaboration technologies play in enhancing geographically distributed collaboration among specific research and applied networks within the national disability community. Universal design principles inform the design of the collaboratory and its use and our efforts to ensure access for all. Data for this article come from Web-based surveys, interviews, observations, computer logs, and detailed, mixed-methods accessibility testing. Emerging results suggest that with deliberate and systematic efforts, cyberinfrastructure can be more accessible and generate benefits among persons with disabilities. The authors provide lessons learned and recommendations for future research, policy, law, and practice.

Reducing the risk of HIV infection among South African sex workers: socioeconomic and gender barriers.

PubMed

Karim, Q A; Karim, S S; Soldan, K; Zondi, M

1995-11-01

The social context within which women engaged in sex work at a popular truck stop in South Africa are placed at risk of human immunodeficiency virus (HIV) infection and the factors that influence their ability to reduce their risk were assessed. Using qualitative and quantitative techniques, an elected sex worker from within the group collected all data. Given the various pressing needs for basic survival, the risk of HIV infection is viewed as one more burden imposed on these women by their lack of social, legal, and economic power. Violence, or the threat thereof, plays an important role in their disempowerment. In the few instances in which sex workers were able to insist on condom use, it resulted in a decrease in earnings, loss of clients, and physical abuse. Recommendations to reduce the sex workers' risk for HIV infection include negotiation and communication skills to enable them to persuade their clients to use condoms; development of strategies through which they can maximally use their group strength to facilitate unified action; and accessibility of protective methods they can use and control, such as intravaginal microbicides.

Efficient and Scalable Synthesis of 4-Carboxy-Pennsylvania Green Methyl Ester: A Hydrophobic Building Block for Fluorescent Molecular Probes.

PubMed

Woydziak, Zachary R; Fu, Liqiang; Peterson, Blake R

2014-01-01

Fluorinated fluorophores are valuable tools for studies of biological systems. However, amine-reactive single-isomer derivatives of these compounds are often very expensive. To provide an inexpensive alternative, we report a practical synthesis of 4-carboxy-Pennsylvania Green methyl ester. Derivatives of this hydrophobic fluorinated fluorophore, a hybrid of the dyes Oregon Green and Tokyo Green, are often cell permeable, enabling labeling of intracellular targets and components. Moreover, the low pKa of Pennsylvania Green (4.8) confers bright fluorescence in acidic cellular compartments such as endosomes, enhancing its utility for chemical biology investigations. To improve access to the key intermediate 2,7-difluoro-3,6-dihydroxyxanthen-9-one, we subjected bis-(2,4,5-trifluorophenyl)methanone to iterative nucleophilic aromatic substitution by hydroxide on scales of > 40 g. This intermediate was used to prepare over 15 grams of pure 4-carboxy-Pennsylvania Green methyl ester in 28% overall yield without requiring chromatography. This compound can be converted into the amine reactive N -hydroxysuccinimidyl ester in essentially quantitative yield for the synthesis of a wide variety of fluorescent molecular probes.

Imaging Metastasis Using an Integrin-Targeting Chain-Shaped Nanoparticle

PubMed Central

Peiris, Pubudu M.; Toy, Randall; Doolittle, Elizabeth; Pansky, Jenna; Abramowski, Aaron; Tam, Morgan; Vicente, Peter; Tran, Emily; Hayden, Elliott; Camann, Andrew; Mayer, Aaron; Erokwu, Bernadette O.; Berman, Zachary; Wilson, David; Baskaran, Harihara; Flask, Chris A.; Keri, Ruth A.; Karathanasis, Efstathios

2012-01-01

While the enhanced permeability and retention effect may promote the preferential accumulation of nanoparticles into well-vascularized primary tumors, it is ineffective in the case of metastases hidden within a large population of normal cells. Due to their small size, high dispersion to organs, and low vascularization, metastatic tumors are less accessible to targeted nanoparticles. To tackle these challenges, we designed a nanoparticle for vascular targeting based on an αvβ3 integrin-targeted nanochain particle composed of four iron oxide nanospheres chemically linked in a linear assembly. The chain-shaped nanoparticles enabled enhanced ‘sensing’ of the tumor-associated remodeling of the vascular bed offering increased likelihood of specific recognition of metastatic tumors. Compared to spherical nanoparticles, the chain-shaped nanoparticles resulted in superior targeting of αvβ3 integrin due to geometrically enhanced multivalent docking. We performed multimodal in vivo imaging (Fluorescence Molecular Tomography and Magnetic Resonance Imaging) in a non-invasive and quantitative manner, which showed that the nanoparticles targeted metastases in the liver and lungs with high specificity in a highly aggressive breast tumor model in mice. PMID:23005348

Extraction, detection, and quantification of flavano-ellagitannins and ethylvescalagin in a Bordeaux red wine aged in oak barrels.

PubMed

Saucier, Cedric; Jourdes, Michael; Glories, Yves; Quideau, Stephane

2006-09-20

An extraction procedure and an analytical method have been developed to detect and quantify for the first time a series of ellagitannin derivatives formed in wine during aging in oak barrels. The method involves a preliminary purification step on XAD7 HP resin followed by a second purification step on TSK 40 HW gel. The resulting extract is analyzed for compound identification and quantitative determination by high-performance liquid chromatography-electrospray ionization-mass spectrometry in single ion recording mode. Reference compounds, which are accessible through hemisynthesis from the oak C-glycosidic ellagitannin vescalagin, were used to build calibration curves, and chlorogenic acid was selected as an internal standard. This method enabled us to estimate the content of four flavano-ellagitannins and that of another newly identified wine polyphenol, beta-1-O-ethylvescalagin, in a Bordeaux red wine aged for 18 months in oak barrels. All five ellagitannin derivatives are derived from the nucleophilic substitution reaction of vescalagin with the grape flavan-3-ols catechin and epicatechin or ethanol.

PredPsych: A toolbox for predictive machine learning-based approach in experimental psychology research.

PubMed

Koul, Atesh; Becchio, Cristina; Cavallo, Andrea

2017-12-12

Recent years have seen an increased interest in machine learning-based predictive methods for analyzing quantitative behavioral data in experimental psychology. While these methods can achieve relatively greater sensitivity compared to conventional univariate techniques, they still lack an established and accessible implementation. The aim of current work was to build an open-source R toolbox - "PredPsych" - that could make these methods readily available to all psychologists. PredPsych is a user-friendly, R toolbox based on machine-learning predictive algorithms. In this paper, we present the framework of PredPsych via the analysis of a recently published multiple-subject motion capture dataset. In addition, we discuss examples of possible research questions that can be addressed with the machine-learning algorithms implemented in PredPsych and cannot be easily addressed with univariate statistical analysis. We anticipate that PredPsych will be of use to researchers with limited programming experience not only in the field of psychology, but also in that of clinical neuroscience, enabling computational assessment of putative bio-behavioral markers for both prognosis and diagnosis.

Possible ways for Public Health Surveillance practices evaluation.

PubMed

Vilela, Maria Filomena de Gouveia; Santos, Dario Nunes Dos; Kemp, Brigina

2017-10-01

This is an evaluative and qualitative study that proposes to investigate self-assessment evaluation as a device to analyze Health Surveillance practices through a questionnaire built by researchers, adapted from the Self-Assessment of Improved Access and Primary Care Quality (AMAQ) and available on the FORMSUS platform. Forty-one Health Surveillance workers and managers of a large municipality from São Paulo State evaluated the realms of "management", "teamwork" and their respective sub-realms. Two categories were created to analyze the results: "Management" and "Team" in dialogue with references from Management, Evaluation and Health Surveillance. Most "management" and "teamwork" sub-realms were deemed satisfactory. Self-assessment evaluation through an applied evaluation tool was shown to be a powerful resource for the analysis of Health Surveillance practices in combination with other devices adopted by the Unified Health System (SUS). Unlike usual evaluation processes guided by quantitative markers, this self-assessable evaluative process included subjects and enabled the possibility of incorporating a new look at itself to the way Health Surveillance is carried out and support future management contracts between workers and managers.

Has molecular imaging delivered to drug development?

NASA Astrophysics Data System (ADS)

Murphy, Philip S.; Patel, Neel; McCarthy, Timothy J.

2017-10-01

Pharmaceutical research and development requires a systematic interrogation of a candidate molecule through clinical studies. To ensure resources are spent on only the most promising molecules, early clinical studies must understand fundamental attributes of the drug candidate, including exposure at the target site, target binding and pharmacological response in disease. Molecular imaging has the potential to quantitatively characterize these properties in small, efficient clinical studies. Specific benefits of molecular imaging in this setting (compared to blood and tissue sampling) include non-invasiveness and the ability to survey the whole body temporally. These methods have been adopted primarily for neuroscience drug development, catalysed by the inability to access the brain compartment by other means. If we believe molecular imaging is a technology platform able to underpin clinical drug development, why is it not adopted further to enable earlier decisions? This article considers current drug development needs, progress towards integration of molecular imaging into studies, current impediments and proposed models to broaden use and increase impact. This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.

Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Nanoscale Magnetism in Next Generation Magnetic Nanoparticles

DTIC Science & Technology

2018-03-17

as dextran coated SPIONs were studied. From the measured T1 and T2 relaxation times, a new method called Quantitative Ultra- Short Time-to-Echo...angiograms with high clarity and definition, and enabled quantitative MRI in biological samples. At UCL, the work included (i) fabricating multi-element...distribution unlimited. I. Introduction Compared to flat biosensor devices, 3D engineered biosensors achievemore intimate and conformal interfaces with cells

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform

NASA Astrophysics Data System (ADS)

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-11-01

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05839b

Technical Assessment: Integrated Photonics

DTIC Science & Technology

2015-10-01

in global internet protocol traffic as a function of time by local access technology. Photonics continues to play a critical role in enabling this...communication networks. This has enabled services like the internet , high performance computing, and power-efficient large-scale data centers. The...signal processing, quantum information science, and optics for free space applications. However major obstacles challenge the implementation of

Development of a Web-Enabled Learning Platform for Geospatial Laboratories: Improving the Undergraduate Learning Experience

ERIC Educational Resources Information Center

Mui, Amy B.; Nelson, Sarah; Huang, Bruce; He, Yuhong; Wilson, Kathi

2015-01-01

This paper describes a web-enabled learning platform providing remote access to geospatial software that extends the learning experience outside of the laboratory setting. The platform was piloted in two undergraduate courses, and includes a software server, a data server, and remote student users. The platform was designed to improve the quality…

Enabling Self-Directed Computer Use for Individuals with Cerebral Palsy: A Systematic Review of Assistive Devices and Technologies

ERIC Educational Resources Information Center

Davies, T. Claire; Mudge, Suzie; Ameratunga, Shanthi; Stott, N. Susan

2010-01-01

Aim: The purpose of this study was to systematically review published evidence on the development, use, and effectiveness of devices and technologies that enable or enhance self-directed computer access by individuals with cerebral palsy (CP). Methods: Nine electronic databases were searched using keywords "computer", "software", "spastic",…

USDA Plant Hardiness Zone Map

Science.gov Websites

those with slower Internet access. Users may also simply type in a ZIP Code and find the hardiness zone : Find Javascript is not enabled in this Internet Browser For a better experience throughout this web site, please enable Javascript in your Internet Browser What is a Captcha and why am I seeing one (on

In-depth Qualitative and Quantitative Profiling of Tyrosine Phosphorylation Using a Combination of Phosphopeptide Immunoaffinity Purification and Stable Isotope Dimethyl Labeling*

PubMed Central

Boersema, Paul J.; Foong, Leong Yan; Ding, Vanessa M. Y.; Lemeer, Simone; van Breukelen, Bas; Philp, Robin; Boekhorst, Jos; Snel, Berend; den Hertog, Jeroen; Choo, Andre B. H.; Heck, Albert J. R.

2010-01-01

Several mass spectrometry-based assays have emerged for the quantitative profiling of cellular tyrosine phosphorylation. Ideally, these methods should reveal the exact sites of tyrosine phosphorylation, be quantitative, and not be cost-prohibitive. The latter is often an issue as typically several milligrams of (stable isotope-labeled) starting protein material are required to enable the detection of low abundance phosphotyrosine peptides. Here, we adopted and refined a peptidecentric immunoaffinity purification approach for the quantitative analysis of tyrosine phosphorylation by combining it with a cost-effective stable isotope dimethyl labeling method. We were able to identify by mass spectrometry, using just two LC-MS/MS runs, more than 1100 unique non-redundant phosphopeptides in HeLa cells from about 4 mg of starting material without requiring any further affinity enrichment as close to 80% of the identified peptides were tyrosine phosphorylated peptides. Stable isotope dimethyl labeling could be incorporated prior to the immunoaffinity purification, even for the large quantities (mg) of peptide material used, enabling the quantification of differences in tyrosine phosphorylation upon pervanadate treatment or epidermal growth factor stimulation. Analysis of the epidermal growth factor-stimulated HeLa cells, a frequently used model system for tyrosine phosphorylation, resulted in the quantification of 73 regulated unique phosphotyrosine peptides. The quantitative data were found to be exceptionally consistent with the literature, evidencing that such a targeted quantitative phosphoproteomics approach can provide reproducible results. In general, the combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on. Using this approach, a rather complete qualitative and quantitative picture of tyrosine phosphorylation signaling events can be generated. PMID:19770167

General practice research: attitudes and involvement of Queensland general practitioners.

PubMed

Askew, Deborah A; Clavarino, Alexandra M; Glasziou, Paul P; Del Mar, Christopher B

2002-07-15

To determine general practitioners' (GPs') attitudes towards and involvement in general practice research. Postal survey and semi-structured interviews conducted from May to September 2001. 467 of 631 GPs in four Queensland Divisions of General Practice responded to the survey (74% response rate); 18 selected GPs were interviewed. Survey - attitudes to research; access to information resources; and involvement in research. Interviews - the need for general practice research; barriers against and factors enabling greater participation in research. 389/463 (84%) GPs, especially younger and more recent graduates, had positive attitudes to research, but only 29% wanted more involvement. 223/462 (48%) were aware they had access to MEDLINE, although presumably all those with Internet access (89%) would have free access via PubMed. Barriers included the general practice environment (especially fee-for-service funding), and the culture of general practice. Enabling factors included academic mentors; opportunities to participate in reputable, established research activities relevant to general practice; and access to information resources. Although Australian general practice has a weak research culture, about a third of GPs would like to increase their involvement in research. However, the research must be perceived as relevant, and structured to minimise the inherent barriers in the environment and culture of general practice.

Cafe Variome: general-purpose software for making genotype-phenotype data discoverable in restricted or open access contexts.

PubMed

Lancaster, Owen; Beck, Tim; Atlan, David; Swertz, Morris; Thangavelu, Dhiwagaran; Veal, Colin; Dalgleish, Raymond; Brookes, Anthony J

2015-10-01

Biomedical data sharing is desirable, but problematic. Data "discovery" approaches-which establish the existence rather than the substance of data-precisely connect data owners with data seekers, and thereby promote data sharing. Cafe Variome (http://www.cafevariome.org) was therefore designed to provide a general-purpose, Web-based, data discovery tool that can be quickly installed by any genotype-phenotype data owner, or network of data owners, to make safe or sensitive content appropriately discoverable. Data fields or content of any type can be accommodated, from simple ID and label fields through to extensive genotype and phenotype details based on ontologies. The system provides a "shop window" in front of data, with main interfaces being a simple search box and a powerful "query-builder" that enable very elaborate queries to be formulated. After a successful search, counts of records are reported grouped by "openAccess" (data may be directly accessed), "linkedAccess" (a source link is provided), and "restrictedAccess" (facilitated data requests and subsequent provision of approved records). An administrator interface provides a wide range of options for system configuration, enabling highly customized single-site or federated networks to be established. Current uses include rare disease data discovery, patient matchmaking, and a Beacon Web service. © 2015 WILEY PERIODICALS, INC.

Educational Research: Planning, Conducting, and Evaluating Quantitative and Qualitative Research, Enhanced Pearson eText with Loose-Leaf Version--Access Card Package. Fifth Edition

ERIC Educational Resources Information Center

Creswell, John W.

2015-01-01

"Educational Research: Planning, Conducting, and Evaluating Quantitative and Qualitative Research" offers a truly balanced, inclusive, and integrated overview of the processes involved in educational research. This text first examines the general steps in the research process and then details the procedures for conducting specific types…

Towards a Re-Conceptualization of Teachers' Self-Efficacy Beliefs: Tackling Enduring Problems with the Quantitative Research and Moving On

ERIC Educational Resources Information Center

Wyatt, Mark

2014-01-01

Various commentators have argued for years that the study of teachers' self-efficacy (TSE) beliefs, largely dominated by quantitative research methodologies, has been confused. Contentious issues include the very conceptualization of these beliefs, how they are defined and accessed through research and how the research is used. One of the…

Leveraging Random Number Generation for Mastery of Learning in Teaching Quantitative Research Courses via an E-Learning Method

ERIC Educational Resources Information Center

Boonsathorn, Wasita; Charoen, Danuvasin; Dryver, Arthur L.

2014-01-01

E-Learning brings access to a powerful but often overlooked teaching tool: random number generation. Using random number generation, a practically infinite number of quantitative problem-solution sets can be created. In addition, within the e-learning context, in the spirit of the mastery of learning, it is possible to assign online quantitative…

Math Across the Community College Curriculum (MAC3): A Successful Path to Quantitative Literacy

ERIC Educational Resources Information Center

Hillyard, Cinnamon; Korey, Jane; Leoni, Deann; Hartzler, Rebecca

2010-01-01

In recent years, mathematical and quantitative arguments have become prominent in the media as well as in politics, business, and science conversations. This has led to multiple calls for mathematics to be more accessible and meaningful to a wider range of the population (AMATYC, 2006; Cerrito, 1996; Cheney, 1989; Cohen, 1982; College Board, 1983;…

Conceptualising Knowledge for Access in the Sciences: Academic Development from a Social Realist Perspective

ERIC Educational Resources Information Center

Ellery, Karen

2017-01-01

Whilst arguing from a social realist perspective that knowledge matters in academic development (AD) curricula, this paper addresses the question of what knowledge types and practices are necessary for enabling epistemological access. It presents a single, in-depth, qualitative case study in which the curriculum of a science AD course is…

Essential Skills and Knowledge for Troubleshooting E-Resources Access Issues in a Web-Scale Discovery Environment

ERIC Educational Resources Information Center

Carter, Sunshine; Traill, Stacie

2017-01-01

Electronic resource access troubleshooting is familiar work in most libraries. The added complexity introduced when a library implements a web-scale discovery service, however, creates a strong need for well-organized, rigorous training to enable troubleshooting staff to provide the best service possible. This article outlines strategies, tools,…

Frequently Asked Questions | DOE PAGES

Science.gov Websites

read, download, and analyze at no charge to users. DOE PAGES offers free public access to the best manuscripts are hosted, DOE PAGES enables readers to search them all via a single query. In most cases, free . DOE PAGES offers free public access to the best available full-text version of DOE-funded scholarly

Ask an Anatomist: Identifying Global Trends, Topics and Themes of Academic Anatomists Using Twitter

ERIC Educational Resources Information Center

Marsland, Madeleine J.; Lazarus, Michelle D.

2018-01-01

Social media (SoMe) is increasingly used in higher education (HE) to access knowledge and enable global communication. The SoMe platform Twitter® is particularly beneficial in these contexts because it is readily accessible, easily searchable (via hashtags) and global. Given these advantages, the twitter platform @AskAnatomist was created to…

Mining Social Tagging Data for Enhanced Subject Access for Readers and Researchers

ERIC Educational Resources Information Center

Lawson, Karen G.

2009-01-01

Social tagging enables librarians to partner with users to provide enhanced subject access. This paper quantifies and compares LC subject headings from each of 31 different subject divisions with user tags from Amazon.com and LibraryThing assigned to the same titles. The intersection and integration of these schemas is described and evaluated.…

An Evaluation of a Self-Access Centre through EFL Learners' Eyes

ERIC Educational Resources Information Center

Balcikanli, Cem

2017-01-01

Learner autonomy has become a central concern in the recent history of language learning. Self-Access Centres (SACs) play a critical role in fostering learner autonomy specifically in EFL (English as a Foreign Language) settings. As SACs aim at enabling learning to occur independent of teaching, in these centres, language learners are given more…

Bringing Up Gopher: Access to Local & Remote Electronic Resources for University Library Users.

ERIC Educational Resources Information Center

Brown, Melvin Marlo; And Others

Some of the administrative and organizational issues in creating a gopher, specifically a library gopher for university libraries, are discussed. In 1993 the Electronic Collections Task Force of the New Mexico State University library administration began to develop a library-based gopher system that would enable users to have unlimited access to…

The Role of Boards in College Access Programs: Creating and Maintaining Quality

ERIC Educational Resources Information Center

Center for Higher Education Policy Analysis, University of Southern California, 2006

2006-01-01

Access programs are facing increased scrutiny. Not all programs are equally effective. In an environment in which resources are short, funders increasingly require criteria that enable them to make informed decisions about program quality. As elaborated in this report , one role of a high performance board is to help develop benchmarks of…

From Open Content to Open Course Models: Increasing Access and Enabling Global Participation in Higher Education

ERIC Educational Resources Information Center

Morgan, Tannis; Carey, Stephen

2009-01-01

Two of the major challenges to international students' right of access to higher education are geographical/economic isolation and academic literacy in English (Carey, 1999; Hamel, 2007). The authors propose that adopting open course models in traditional universities, through blended or online delivery, can offer benefits to the institutions and…

Technology-Supported Involvement of Entire Faculties in Examination of Student Data for Instructional Improvement

ERIC Educational Resources Information Center

Wayman, Jeffrey C.; Stringfield, Sam

2006-01-01

Student data are gaining increased attention in education, spurred by accountability policies such as those contained in the federal No Child Left Behind legislation. Student data are useful for informing classroom practice, and user-friendly technologies for organizing and accessing data are enabling access by all teachers. In this study, we…

The Need to Address Mobile Device Security in the Higher Education IT Curriculum

ERIC Educational Resources Information Center

Patten, Karen P.; Harris, Mark A.

2013-01-01

Mobile devices, including smartphones and tablets, enable users to access corporate data from anywhere. In 2013, people will purchase 1.2 billion mobile devices, surpassing personal computers as the most common method for accessing the Internet. However, security of these mobile devices is a major concern for organizations. The two leading…

Internet Activities Using Scientific Data. A Self-Guided Exploration.

ERIC Educational Resources Information Center

Froseth, Stan; Poppe, Barbara

This guide is intended for the secondary school teacher (especially math or science) or the student who wants to access and learn about scientific data on the Internet. It is organized as a self-guided exploration. Nine exercises enable the user to access and analyze on-line information from the National Oceanic and Atmospheric Administration…

Oral health care in remote Kimberley Aboriginal communities: the characteristics and perceptions of dental volunteers.

PubMed

Patel, J; Hearn, L; Slack-Smith, L M

2015-09-01

Aboriginal Australians face significant disparities in oral health and this is particularly the case in remote communities where access to dental services can be difficult. Using volunteers to provide dental care in the remote Kimberley region of Western Australia is a novel approach. This study comprised an anonymous online survey of volunteers working with the Kimberley Dental Team (KDT). The survey had a response fraction of 66% and explored volunteer demographic characteristics, factors that motivated their involvement, perceptions of oral health among Aboriginal communities, and barriers and enablers to oral health in remote Aboriginal communities. Volunteers were more likely to be female, middle-aged and engaged in full-time employment. The two most common reasons reported for volunteering were to assist the community and visit the Kimberley region. Education and access to reliable, culturally appropriate care were perceived as enablers to good oral health for Aboriginal people in the Kimberley while limited access to services, poor nutrition and lack of government support were cited as barriers. Volunteers providing dental services to remote areas in Western Australia had a diverse demographic profile. However, they share similar motivating factors and views on the current barriers and enablers to good oral health in remote Aboriginal communities. © 2015 Australian Dental Association.

Interactive access to LP DAAC satellite data archives through a combination of open-source and custom middleware web services

USGS Publications Warehouse

Davis, Brian N.; Werpy, Jason; Friesz, Aaron M.; Impecoven, Kevin; Quenzer, Robert; Maiersperger, Tom; Meyer, David J.

2015-01-01

Current methods of searching for and retrieving data from satellite land remote sensing archives do not allow for interactive information extraction. Instead, Earth science data users are required to download files over low-bandwidth networks to local workstations and process data before science questions can be addressed. New methods of extracting information from data archives need to become more interactive to meet user demands for deriving increasingly complex information from rapidly expanding archives. Moving the tools required for processing data to computer systems of data providers, and away from systems of the data consumer, can improve turnaround times for data processing workflows. The implementation of middleware services was used to provide interactive access to archive data. The goal of this middleware services development is to enable Earth science data users to access remote sensing archives for immediate answers to science questions instead of links to large volumes of data to download and process. Exposing data and metadata to web-based services enables machine-driven queries and data interaction. Also, product quality information can be integrated to enable additional filtering and sub-setting. Only the reduced content required to complete an analysis is then transferred to the user.

Assisted normality--a grounded theory of adolescent's experiences of living with personal assistance.

PubMed

Hultman, Lill; Forinder, Ulla; Pergert, Pernilla

2016-01-01

The purpose of the study was to explore how adolescents with disabilities experience everyday life with personal assistants. In this qualitative study, individual interviews were conducted at 35 occasions with 16 Swedish adolescents with disabilities, in the ages 16-21. Data were analyzed using grounded theory methodology. The adolescents' main concern was to achieve normality, which is about doing rather than being normal. They try to resolve this by assisted normality utilizing personal assistance. Assisted normality can be obtained by the existing relationship, the cooperation between the assistant and the adolescent and the situational placement of the assistant. Normality is obstructed by physical, social and psychological barriers. This study is from the adolescents' perspective and has implications for understanding the value of having access to personal assistance in order to achieve assisted normality and enable social interaction in everyday life. Access to personal assistance is important to enable social interaction in everyday life. A good and functional relationship is enabled through the existing relation, co-operation and situational placement of the assistant. If the assistant is not properly sensitized, young people risk turning into objects of care. Access to personal assistants cannot compensate for disabling barriers in the society as for example lack of acceptance.

Whole-body PET parametric imaging employing direct 4D nested reconstruction and a generalized non-linear Patlak model

NASA Astrophysics Data System (ADS)

Karakatsanis, Nicolas A.; Rahmim, Arman

2014-03-01

Graphical analysis is employed in the research setting to provide quantitative estimation of PET tracer kinetics from dynamic images at a single bed. Recently, we proposed a multi-bed dynamic acquisition framework enabling clinically feasible whole-body parametric PET imaging by employing post-reconstruction parameter estimation. In addition, by incorporating linear Patlak modeling within the system matrix, we enabled direct 4D reconstruction in order to effectively circumvent noise amplification in dynamic whole-body imaging. However, direct 4D Patlak reconstruction exhibits a relatively slow convergence due to the presence of non-sparse spatial correlations in temporal kinetic analysis. In addition, the standard Patlak model does not account for reversible uptake, thus underestimating the influx rate Ki. We have developed a novel whole-body PET parametric reconstruction framework in the STIR platform, a widely employed open-source reconstruction toolkit, a) enabling accelerated convergence of direct 4D multi-bed reconstruction, by employing a nested algorithm to decouple the temporal parameter estimation from the spatial image update process, and b) enhancing the quantitative performance particularly in regions with reversible uptake, by pursuing a non-linear generalized Patlak 4D nested reconstruction algorithm. A set of published kinetic parameters and the XCAT phantom were employed for the simulation of dynamic multi-bed acquisitions. Quantitative analysis on the Ki images demonstrated considerable acceleration in the convergence of the nested 4D whole-body Patlak algorithm. In addition, our simulated and patient whole-body data in the postreconstruction domain indicated the quantitative benefits of our extended generalized Patlak 4D nested reconstruction for tumor diagnosis and treatment response monitoring.

The craniocaudal extension of posterolateral approaches and their combination: a quantitative anatomic and clinical analysis.

PubMed

Safavi-Abbasi, Sam; de Oliveira, Jean G; Deshmukh, Pushpa; Reis, Cassius V; Brasiliense, Leonardo B C; Crawford, Neil R; Feiz-Erfan, Iman; Spetzler, Robert F; Preul, Mark C

2010-03-01

The aim of this study was to describe quantitatively the properties of the posterolateral approaches and their combination. Six silicone-injected cadaveric heads were dissected bilaterally. Quantitative data were generated with the Optotrak 3020 system (Northern Digital, Waterloo, Canada) and Surgiscope (Elekta Instruments, Inc., Atlanta, GA), including key anatomic points on the skull base and brainstem. All parameters were measured after the basic retrosigmoid craniectomy and then after combination with a basic far-lateral extension. The clinical results of 20 patients who underwent a combined retrosigmoid and far-lateral approach were reviewed. The change in accessibility to the lower clivus was greatest after the far-lateral extension (mean change, 43.62 +/- 10.98 mm2; P = .001). Accessibility to the constant landmarks, Meckel's cave, internal auditory meatus, and jugular foramen did not change significantly between the 2 approaches (P > .05). The greatest change in accessibility to soft tissue between the 2 approaches was to the lower brainstem (mean change, 33.88 +/- 5.25 mm2; P = .0001). Total removal was achieved in 75% of the cases. The average postoperative Glasgow Outcome Scale score of patients who underwent the combined retrosigmoid and far-lateral approach improved significantly, compared with the preoperative scores. The combination of the far-lateral and simple retrosigmoid approaches significantly increases the petroclival working area and access to the cranial nerves. However, risk of injury to neurovascular structures and time needed to extend the craniotomy must be weighed against the increased working area and angles of attack.

A Framework for Context Sensitive Risk-Based Access Control in Medical Information Systems

PubMed Central

Choi, Donghee; Kim, Dohoon; Park, Seog

2015-01-01

Since the access control environment has changed and the threat of insider information leakage has come to the fore, studies on risk-based access control models that decide access permissions dynamically have been conducted vigorously. Medical information systems should protect sensitive data such as medical information from insider threat and enable dynamic access control depending on the context such as life-threatening emergencies. In this paper, we suggest an approach and framework for context sensitive risk-based access control suitable for medical information systems. This approach categorizes context information, estimating and applying risk through context- and treatment-based permission profiling and specifications by expanding the eXtensible Access Control Markup Language (XACML) to apply risk. The proposed framework supports quick responses to medical situations and prevents unnecessary insider data access through dynamic access authorization decisions in accordance with the severity of the context and treatment. PMID:26075013

Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments.

PubMed

Friedman, David B

2012-01-01

All quantitative proteomics experiments measure variation between samples. When performing large-scale experiments that involve multiple conditions or treatments, the experimental design should include the appropriate number of individual biological replicates from each condition to enable the distinction between a relevant biological signal from technical noise. Multivariate statistical analyses, such as principal component analysis (PCA), provide a global perspective on experimental variation, thereby enabling the assessment of whether the variation describes the expected biological signal or the unanticipated technical/biological noise inherent in the system. Examples will be shown from high-resolution multivariable DIGE experiments where PCA was instrumental in demonstrating biologically significant variation as well as sample outliers, fouled samples, and overriding technical variation that would not be readily observed using standard univariate tests.

Neutron multiplicity counting: Confidence intervals for reconstruction parameters

DOE PAGES

Verbeke, Jerome M.

2016-03-09

From nuclear materials accountability to homeland security, the need for improved nuclear material detection, assay, and authentication has grown over the past decades. Starting in the 1940s, neutron multiplicity counting techniques have enabled quantitative evaluation of masses and multiplications of fissile materials. In this paper, we propose a new method to compute uncertainties on these parameters using a model-based sequential Bayesian processor, resulting in credible regions in the fissile material mass and multiplication space. These uncertainties will enable us to evaluate quantitatively proposed improvements to the theoretical fission chain model. Additionally, because the processor can calculate uncertainties in real time,more » it is a useful tool in applications such as portal monitoring: monitoring can stop as soon as a preset confidence of non-threat is reached.« less

Specificity and non-specificity in RNA–protein interactions

PubMed Central

Jankowsky, Eckhard; Harris, Michael E.

2016-01-01

Gene expression is regulated by complex networks of interactions between RNAs and proteins. Proteins that interact with RNA have been traditionally viewed as either specific or non-specific; specific proteins interact preferentially with defined RNA sequence or structure motifs, whereas non-specific proteins interact with RNA sites devoid of such characteristics. Recent studies indicate that the binary “specific vs. non-specific” classification is insufficient to describe the full spectrum of RNA–protein interactions. Here, we review new methods that enable quantitative measurements of protein binding to large numbers of RNA variants, and the concepts aimed as describing resulting binding spectra: affinity distributions, comprehensive binding models and free energy landscapes. We discuss how these new methodologies and associated concepts enable work towards inclusive, quantitative models for specific and non-specific RNA–protein interactions. PMID:26285679

Quantitative aspects of inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Bulska, Ewa; Wagner, Barbara

2016-10-01

Accurate determination of elements in various kinds of samples is essential for many areas, including environmental science, medicine, as well as industry. Inductively coupled plasma mass spectrometry (ICP-MS) is a powerful tool enabling multi-elemental analysis of numerous matrices with high sensitivity and good precision. Various calibration approaches can be used to perform accurate quantitative measurements by ICP-MS. They include the use of pure standards, matrix-matched standards, or relevant certified reference materials, assuring traceability of the reported results. This review critically evaluates the advantages and limitations of different calibration approaches, which are used in quantitative analyses by ICP-MS. Examples of such analyses are provided. This article is part of the themed issue 'Quantitative mass spectrometry'.

Was It Really Worth Pain? Refurbishment of Mercedes-Benz Trucks by Botswana Defence Force

DTIC Science & Technology

2005-12-01

staff, especially those who were involved in rework, was their inability to access the fleet management system Mincom Ellipse database. Access to...CHAPTER IV This chapter analyzes the survey/questionnaires that were sent to the users, the project middle managers, and the CMER. The CMER was a de ...transferred directly to the BDF; they were accessed from a fund set up for the project. This enabled the project manager to have versatility in the

The provision and impact of online patient access to their electronic health records (EHR) and transactional services on the quality and safety of health care: systematic review protocol.

PubMed

Mold, Freda; Ellis, Beverley; de Lusignan, Simon; Sheikh, Aziz; Wyatt, Jeremy C; Cavill, Mary; Michalakidis, Georgios; Barker, Fiona; Majeed, Azeem; Quinn, Tom; Koczan, Phil; Avanitis, Theo; Gronlund, Toto Anne; Franco, Christina; McCarthy, Mary; Renton, Zoë; Chauhan, Umesh; Blakey, Hannah; Kataria, Neha; Jones, Simon; Rafi, Imran

2012-01-01

Innovators have piloted improvements in communication, changed patterns of practice and patient empowerment from online access to electronic health records (EHR). International studies of online services, such as prescription ordering, online appointment booking and secure communications with primary care, show good uptake of email consultations, accessing test results and booking appointments; when technologies and business process are in place. Online access and transactional services are due to be rolled out across England by 2015; this review seeks to explore the impact of online access to health records and other online services on the quality and safety of primary health care. To assess the factors that may affect the provision of online patient access to their EHR and transactional services, and the impact of such access on the quality and safety of health care. Two reviewers independently searched 11 international databases during the period 1999-2012. A range of papers including descriptive studies using qualitative or quantitative methods, hypothesis-testing studies and systematic reviews were included. A detailed eligibility criterion will be used to shape study inclusion. A team of experts will review these papers for eligibility, extract data using a customised extraction form and use the Grading of Recommendations Assessment, Development and Evaluation (GRADE) instrument to determine the quality of the evidence and the strengths of any recommendation. Data will then be descriptively summarised and thematically synthesised. Where feasible, we will perform a quantitative meta-analysis. Prospero (International Prospective Register of Systematic Reviews) registration number: crd42012003091.

Development of a Web Based Simulating System for Earthquake Modeling on the Grid

NASA Astrophysics Data System (ADS)

Seber, D.; Youn, C.; Kaiser, T.

2007-12-01

Existing cyberinfrastructure-based information, data and computational networks now allow development of state- of-the-art, user-friendly simulation environments that democratize access to high-end computational environments and provide new research opportunities for many research and educational communities. Within the Geosciences cyberinfrastructure network, GEON, we have developed the SYNSEIS (SYNthetic SEISmogram) toolkit to enable efficient computations of 2D and 3D seismic waveforms for a variety of research purposes especially for helping to analyze the EarthScope's USArray seismic data in a speedy and efficient environment. The underlying simulation software in SYNSEIS is a finite difference code, E3D, developed by LLNL (S. Larsen). The code is embedded within the SYNSEIS portlet environment and it is used by our toolkit to simulate seismic waveforms of earthquakes at regional distances (<1000km). Architecturally, SYNSEIS uses both Web Service and Grid computing resources in a portal-based work environment and has a built in access mechanism to connect to national supercomputer centers as well as to a dedicated, small-scale compute cluster for its runs. Even though Grid computing is well-established in many computing communities, its use among domain scientists still is not trivial because of multiple levels of complexities encountered. We grid-enabled E3D using our own dialect XML inputs that include geological models that are accessible through standard Web services within the GEON network. The XML inputs for this application contain structural geometries, source parameters, seismic velocity, density, attenuation values, number of time steps to compute, and number of stations. By enabling a portal based access to a such computational environment coupled with its dynamic user interface we enable a large user community to take advantage of such high end calculations in their research and educational activities. Our system can be used to promote an efficient and effective modeling environment to help scientists as well as educators in their daily activities and speed up the scientific discovery process.

Access to Higher Education. Intergovernmental Conference on Policies for Higher Education in the 80s (Paris, France, October 12-14, 1981).

ERIC Educational Resources Information Center

Squires, Geoffrey; And Others

Access to higher education in countries that are members of the Organisation for Economic Co-operation and Development (OECD) is addressed. The following topics are considered: principles for quantitative planning of higher education, admission policies and the institutional framework, changing links between secondary and higher education, access…

Poor Affordability and Low Access to Primary Education with Special Reference to Eastern Uttar Pradesh: Reflections from DISE Data

ERIC Educational Resources Information Center

Sulochana, Rosy

2015-01-01

"Access to basic education" continues to be a matter of serious concern in India. While the quantitative expansion of the system appears to be very impressive, the achievement of the goal of universalisation of primary education has still remained elusive. This is because the government continues its celebration through reflecting on…

Internet Access and Usage by Secondary School Students in Morogoro Municipality, Tanzania

ERIC Educational Resources Information Center

Tarimo, Ronald; Kavishe, George

2017-01-01

The purpose of this paper was to report results of a study on the investigation of the Internet access and usage by secondary school students in Morogoro municipality in Tanzania. A simple random sampling technique was used to select 120 students from six schools. The data was collected through a questionnaire. A quantitative approach using the…

Access to Higher Education at the End of Lower Secondary for "Disadvantaged" Students: The Interplay of Structural, Institutional Frameworks and Student Agency

ERIC Educational Resources Information Center

Danic, Isabelle

2015-01-01

Drawing from quantitative and qualitative data collected by the European research project GOETE in eight European countries, the article focuses on the experiences of so-called "disadvantaged students" at the end of lower secondary and analyzes how access to higher education is negotiated in the interaction of structural/institutional…

Barriers to access to infertility care and assisted reproductive technology within the public health sector in Brazil.

PubMed

Makuch, M Y; Bahamondes, L

2012-01-01

In Brazil, access to infertility care, including assisted reproductive technologies (ARTs), is restricted. This is the third report of a study on access to infertility care and ARTs within the public sector, focusing on the barriers to these services. The study was anchored on quantitative and qualitative methods. For the quantitative study interviews were conducted with health authorities in each of the 26 states, the Federal District, the state capitals and 16 cities with ≥ 500,000 inhabitants and directors of infertility referral centres within the public sector. Qualitative case studies-- were conducted in five ART centres. Overall, 63.5% of the authorities reported that complex infertility treatments were unavailable. Barriers identified consisted of "lack of political decision to implement them", and "lack of financial resources". In addition, 75% reported to have "no plans to implement them over the next 12 months". At the facilities offering ART, the barriers to these procedures were the high costs, long waiting times, complex scheduling processes and lack of initiative to implement low cost ARTs. Infertile couples' access to ART procedures is restricted due to the insufficient services and lack of political commitment to support existing and new services..

The Geodetic Seamless Archive Centers Service Layer: A System Architecture for Federating Geodesy Data Repositories

NASA Astrophysics Data System (ADS)

McWhirter, J.; Boler, F. M.; Bock, Y.; Jamason, P.; Squibb, M. B.; Noll, C. E.; Blewitt, G.; Kreemer, C. W.

2010-12-01

Three geodesy Archive Centers, Scripps Orbit and Permanent Array Center (SOPAC), NASA's Crustal Dynamics Data Information System (CDDIS) and UNAVCO are engaged in a joint effort to define and develop a common Web Service Application Programming Interface (API) for accessing geodetic data holdings. This effort is funded by the NASA ROSES ACCESS Program to modernize the original GPS Seamless Archive Centers (GSAC) technology which was developed in the 1990s. A new web service interface, the GSAC-WS, is being developed to provide uniform and expanded mechanisms through which users can access our data repositories. In total, our respective archives hold tens of millions of files and contain a rich collection of site/station metadata. Though we serve similar user communities, we currently provide a range of different access methods, query services and metadata formats. This leads to a lack of consistency in the userís experience and a duplication of engineering efforts. The GSAC-WS API and its reference implementation in an underlying Java-based GSAC Service Layer (GSL) supports metadata and data queries into site/station oriented data archives. The general nature of this API makes it applicable to a broad range of data systems. The overall goals of this project include providing consistent and rich query interfaces for end users and client programs, the development of enabling technology to facilitate third party repositories in developing these web service capabilities and to enable the ability to perform data queries across a collection of federated GSAC-WS enabled repositories. A fundamental challenge faced in this project is to provide a common suite of query services across a heterogeneous collection of data yet enabling each repository to expose their specific metadata holdings. To address this challenge we are developing a "capabilities" based service where a repository can describe its specific query and metadata capabilities. Furthermore, the architecture of the GSL is based on a model-view paradigm that decouples the underlying data model semantics from particular representations of the data model. This will allow for the GSAC-WS enabled repositories to evolve their service offerings to incorporate new metadata definition formats (e.g., ISO-19115, FGDC, JSON, etc.) and new techniques for accessing their holdings. Building on the core GSAC-WS implementations the project is also developing a federated/distributed query service. This service will seamlessly integrate with the GSAC Service Layer and will support data and metadata queries across a collection of federated GSAC repositories.

The digital divide: Examining socio-demographic factors associated with health literacy, access and use of internet to seek health information.

PubMed

Estacio, Emee Vida; Whittle, Rebecca; Protheroe, Joanne

2017-02-01

This article aims to examine the socio-demographic characteristics associated with access and use of Internet for health-related purposes and its relationship with health literacy. Data were drawn from a health literacy survey ( N = 1046) and analysed using logistic regression. Results show a strong association between health literacy, internet access and use. Socio-demographic characteristics particularly age, education, income, perceived health and social isolation also predict internet access. Thus, in addition to widening access, the movement towards digitisation of health information and services should also consider digital skills development to enable people to utilise digital technology more effectively, especially among traditionally hard-to-reach communities.

Stereological analysis of bacterial load and lung lesions in nonhuman primates (rhesus macaques) experimentally infected with Mycobacterium tuberculosis.

PubMed

Luciw, Paul A; Oslund, Karen L; Yang, Xiao-Wei; Adamson, Lourdes; Ravindran, Resmi; Canfield, Don R; Tarara, Ross; Hirst, Linda; Christensen, Miles; Lerche, Nicholas W; Offenstein, Heather; Lewinsohn, David; Ventimiglia, Frank; Brignolo, Laurie; Wisner, Erik R; Hyde, Dallas M

2011-11-01

Infection with Mycobacterium tuberculosis primarily produces a multifocal distribution of pulmonary granulomas in which the pathogen resides. Accordingly, quantitative assessment of the bacterial load and pathology is a substantial challenge in tuberculosis. Such assessments are critical for studies of the pathogenesis and for the development of vaccines and drugs in animal models of experimental M. tuberculosis infection. Stereology enables unbiased quantitation of three-dimensional objects from two-dimensional sections and thus is suited to quantify histological lesions. We have developed a protocol for stereological analysis of the lung in rhesus macaques inoculated with a pathogenic clinical strain of M. tuberculosis (Erdman strain). These animals exhibit a pattern of infection and tuberculosis similar to that of naturally infected humans. Conditions were optimized for collecting lung samples in a nonbiased, random manner. Bacterial load in these samples was assessed by a standard plating assay, and granulomas were graded and enumerated microscopically. Stereological analysis provided quantitative data that supported a significant correlation between bacterial load and lung granulomas. Thus this stereological approach enables a quantitative, statistically valid analysis of the impact of M. tuberculosis infection in the lung and will serve as an essential tool for objectively comparing the efficacy of drugs and vaccines.

Robust Informatics Infrastructure Required For ICME: Combining Virtual and Experimental Data

NASA Technical Reports Server (NTRS)

Arnold, Steven M.; Holland, Frederic A. Jr.; Bednarcyk, Brett A.

2014-01-01

With the increased emphasis on reducing the cost and time to market of new materials, the need for robust automated materials information management system(s) enabling sophisticated data mining tools is increasing, as evidenced by the emphasis on Integrated Computational Materials Engineering (ICME) and the recent establishment of the Materials Genome Initiative (MGI). This need is also fueled by the demands for higher efficiency in material testing; consistency, quality and traceability of data; product design; engineering analysis; as well as control of access to proprietary or sensitive information. Further, the use of increasingly sophisticated nonlinear, anisotropic and or multi-scale models requires both the processing of large volumes of test data and complex materials data necessary to establish processing-microstructure-property-performance relationships. Fortunately, material information management systems have kept pace with the growing user demands and evolved to enable: (i) the capture of both point wise data and full spectra of raw data curves, (ii) data management functions such as access, version, and quality controls;(iii) a wide range of data import, export and analysis capabilities; (iv) data pedigree traceability mechanisms; (v) data searching, reporting and viewing tools; and (vi) access to the information via a wide range of interfaces. This paper discusses key principles for the development of a robust materials information management system to enable the connections at various length scales to be made between experimental data and corresponding multiscale modeling toolsets to enable ICME. In particular, NASA Glenn's efforts towards establishing such a database for capturing constitutive modeling behavior for both monolithic and composites materials

Exploring educational needs and design aspects of internet-enabled patient education for persons with diabetes: a qualitative interview study

PubMed Central

Jafari, Javad; Karimi Moonaghi, Hosein; Zary, Nabil; Masiello, Italo

2016-01-01

Objective The objective of this article is to explore the educational needs and design aspects of personalised internet-enabled education for patients with diabetes in Iran. Design Data were collected using semistructured interviews and then qualitatively analysed using inductive content analysis. Participants 9 patients with type 2 diabetes were included. Inclusion criteria were access to and knowledge on how to use the internet. The selection ensured representation based on gender, age, occupation and educational background. Setting The sample population was patients with diabetes who were admitted to an outpatient diabetes clinic in Mashhad, a large city of Iran with about 3 million inhabitants. Results 4 core categories emerged from the data: (1) seeking knowledge about diabetes, including specific knowledge acquisition, patient's interactions and learning requirements; (2) teaching and learning, including using different teaching methods and different ways to learn about the disease; (3) facilitators, including internet and mobile phone use to learn about the disease; and (4) barriers, including lack of internet access, uncertainty of access to the internet and lack of website in the local language and also perceived cultural barriers, such as patients' fears of the internet, lack of time and awareness. Conclusions This study provides a better understanding of the patient's educational expectations and technical needs in relation to internet-enabled education. This knowledge will inform the development of functional mock-ups in the next research phase using a design-based research approach in order to design internet-enabled patient education for self-management of diabetes. PMID:27799245

Index of Access: a new innovative and dynamic tool for rural health service and workforce planning.

PubMed

McGrail, Matthew R; Russell, Deborah J; Humphreys, John S

2017-10-01

Objective Improving access to primary health care (PHC) remains a key issue for rural residents and health service planners. This study aims to show that how access to PHC services is measured has important implications for rural health service and workforce planning. Methods A more sophisticated tool to measure access to PHC services is proposed, which can help health service planners overcome the shortcomings of existing measures and long-standing access barriers to PHC. Critically, the proposed Index of Access captures key components of access and uses a floating catchment approach to better define service areas and population accessibility levels. Moreover, as demonstrated through a case study, the Index of Access enables modelling of the effects of workforce supply variations. Results Hypothetical increases in supply are modelled for a range of regional centres, medium and small rural towns, with resulting changes of access scores valuable to informing health service and workforce planning decisions. Conclusions The availability and application of a specific 'fit-for-purpose' access measure enables a more accurate empirical basis for service planning and allocation of health resources. This measure has great potential for improved identification of PHC access inequities and guiding redistribution of PHC services to correct such inequities. What is known about the topic? Resource allocation and health service planning decisions for rural and remote health settings are currently based on either simple measures of access (e.g. provider-to-population ratios) or proxy measures of access (e.g. standard geographical classifications). Both approaches have substantial limitations for informing rural health service planning and decision making. What does this paper add? The adoption of a new improved tool to measure access to PHC services, the Index of Access, is proposed to assist health service and workforce planning. Its usefulness for health service planning is demonstrated using a case study to hypothetically model changes in rural PHC workforce supply. What are the implications for practitioners? The Index of Access has significant potential for identifying how rural and remote primary health care access inequities can be addressed. This critically important information can assist health service planners, for example those working in primary health networks, to determine where and how much redistribution of PHC services is needed to correct existing inequities.

Strategies for P2P connectivity in reconfigurable converged wired/wireless access networks.

PubMed

Puerto, Gustavo; Mora, José; Ortega, Beatriz; Capmany, José

2010-12-06

This paper presents different strategies to define the architecture of a Radio-Over-Fiber (RoF) Access networks enabling Peer-to-Peer (P2P) functionalities. The architectures fully exploit the flexibility of a wavelength router based on the feedback configuration of an Arrayed Waveguide Grating (AWG) and an optical switch to broadcast P2P services among diverse infrastructures featuring dynamic channel allocation and enabling an optical platform for 3G and beyond wireless backhaul requirements. The first architecture incorporates a tunable laser to generate a dedicated wavelength for P2P purposes and the second architecture takes advantage of reused wavelengths to enable the P2P connectivity among Optical Network Units (ONUs) or Base Stations (BS). While these two approaches allow the P2P connectivity in a one at a time basis (1:1), the third architecture enables the broadcasting of P2P sessions among different ONUs or BSs at the same time (1:M). Experimental assessment of the proposed architecture shows approximately 0.6% Error Vector Magnitude (EVM) degradation for wireless services and 1 dB penalty in average for 1 x 10(-12) Bit Error Rate (BER) for wired baseband services.

In-field Access to Geoscientific Metadata through GPS-enabled Mobile Phones

NASA Astrophysics Data System (ADS)

Hobona, Gobe; Jackson, Mike; Jordan, Colm; Butchart, Ben

2010-05-01

Fieldwork is an integral part of much geosciences research. But whilst geoscientists have physical or online access to data collections whilst in the laboratory or at base stations, equivalent in-field access is not standard or straightforward. The increasing availability of mobile internet and GPS-supported mobile phones, however, now provides the basis for addressing this issue. The SPACER project was commissioned by the Rapid Innovation initiative of the UK Joint Information Systems Committee (JISC) to explore the potential for GPS-enabled mobile phones to access geoscientific metadata collections. Metadata collections within the geosciences and the wider geospatial domain can be disseminated through web services based on the Catalogue Service for Web(CSW) standard of the Open Geospatial Consortium (OGC) - a global grouping of over 380 private, public and academic organisations aiming to improve interoperability between geospatial technologies. CSW offers an XML-over-HTTP interface for querying and retrieval of geospatial metadata. By default, the metadata returned by CSW is based on the ISO19115 standard and encoded in XML conformant to ISO19139. The SPACER project has created a prototype application that enables mobile phones to send queries to CSW containing user-defined keywords and coordinates acquired from GPS devices built-into the phones. The prototype has been developed using the free and open source Google Android platform. The mobile application offers views for listing titles, presenting multiple metadata elements and a Google Map with an overlay of bounding coordinates of datasets. The presentation will describe the architecture and approach applied in the development of the prototype.

An efficient General Transit Feed Specification (GTFS) enabled algorithm for dynamic transit accessibility analysis.

PubMed

Fayyaz S, S Kiavash; Liu, Xiaoyue Cathy; Zhang, Guohui

2017-01-01

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George's transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis.

An efficient General Transit Feed Specification (GTFS) enabled algorithm for dynamic transit accessibility analysis

PubMed Central

Fayyaz S., S. Kiavash; Zhang, Guohui

2017-01-01

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George’s transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis. PMID:28981544

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.

PubMed

Gomes, Antonio L C; Wang, Harris H

2016-04-01

ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression. However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions. Furthermore, ChIP-seq data often poorly correlate with in vitro measurements or predicted motifs, highlighting that binding affinity alone is insufficient to explain transcription factor (TF)-binding in vivo. One possibility is that binding sites are not equally accessible across the genome. A more comprehensive biophysical representation of TF-binding is required to improve our ability to understand, predict, and alter gene expression. Here, we show that genome accessibility is a key parameter that impacts TF-binding in bacteria. We developed a thermodynamic model that parameterizes ChIP-seq coverage in terms of genome accessibility and binding affinity. The role of genome accessibility is validated using a large-scale ChIP-seq dataset of the M. tuberculosis regulatory network. We find that accounting for genome accessibility led to a model that explains 63% of the ChIP-seq profile variance, while a model based in motif score alone explains only 35% of the variance. Moreover, our framework enables de novo ChIP-seq peak prediction and is useful for inferring TF-binding peaks in new experimental conditions by reducing the need for additional experiments. We observe that the genome is more accessible in intergenic regions, and that increased accessibility is positively correlated with gene expression and anti-correlated with distance to the origin of replication. Our biophysically motivated model provides a more comprehensive description of TF-binding in vivo from first principles towards a better representation of gene regulation in silico, with promising applications in systems biology.

Apparatus and method for identification of matrix materials in which transuranic elements are embedded using thermal neutron capture gamma-ray emission

DOEpatents

Close, D.A.; Franks, L.A.; Kocimski, S.M.

1984-08-16

An invention is described that enables the quantitative simultaneous identification of the matrix materials in which fertile and fissile nuclides are embedded to be made along with the quantitative assay of the fertile and fissile materials. The invention also enables corrections for any absorption of neutrons by the matrix materials and by the measurement apparatus by the measurement of the prompt and delayed neutron flux emerging from a sample after the sample is interrogated by simultaneously applied neutrons and gamma radiation. High energy electrons are directed at a first target to produce gamma radiation. A second target receives the resulting pulsed gamma radiation and produces neutrons from the interaction with the gamma radiation. These neutrons are slowed by a moderator surrounding the sample and bathe the sample uniformly, generating second gamma radiation in the interaction. The gamma radiation is then resolved and quantitatively detected, providing a spectroscopic signature of the constituent elements contained in the matrix and in the materials within the vicinity of the sample. (LEW)

Self-powered integrated microfluidic point-of-care low-cost enabling (SIMPLE) chip

PubMed Central

Yeh, Erh-Chia; Fu, Chi-Cheng; Hu, Lucy; Thakur, Rohan; Feng, Jeffrey; Lee, Luke P.

2017-01-01

Portable, low-cost, and quantitative nucleic acid detection is desirable for point-of-care diagnostics; however, current polymerase chain reaction testing often requires time-consuming multiple steps and costly equipment. We report an integrated microfluidic diagnostic device capable of on-site quantitative nucleic acid detection directly from the blood without separate sample preparation steps. First, we prepatterned the amplification initiator [magnesium acetate (MgOAc)] on the chip to enable digital nucleic acid amplification. Second, a simplified sample preparation step is demonstrated, where the plasma is separated autonomously into 224 microwells (100 nl per well) without any hemolysis. Furthermore, self-powered microfluidic pumping without any external pumps, controllers, or power sources is accomplished by an integrated vacuum battery on the chip. This simple chip allows rapid quantitative digital nucleic acid detection directly from human blood samples (10 to 105 copies of methicillin-resistant Staphylococcus aureus DNA per microliter, ~30 min, via isothermal recombinase polymerase amplification). These autonomous, portable, lab-on-chip technologies provide promising foundations for future low-cost molecular diagnostic assays. PMID:28345028

Abdo-Man: a 3D-printed anthropomorphic phantom for validating quantitative SIRT.

PubMed

Gear, Jonathan I; Cummings, Craig; Craig, Allison J; Divoli, Antigoni; Long, Clive D C; Tapner, Michael; Flux, Glenn D

2016-12-01

The use of selective internal radiation therapy (SIRT) is rapidly increasing, and the need for quantification and dosimetry is becoming more widespread to facilitate treatment planning and verification. The aim of this project was to develop an anthropomorphic phantom that can be used as a validation tool for post-SIRT imaging and its application to dosimetry. The phantom design was based on anatomical data obtained from a T1-weighted volume-interpolated breath-hold examination (VIBE) on a Siemens Aera 1.5 T MRI scanner. The liver, lungs and abdominal trunk were segmented using the Hermes image processing workstation. Organ volumes were then uploaded to the Delft Visualization and Image processing Development Environment for smoothing and surface rendering. Triangular meshes defining the iso-surfaces were saved as stereo lithography (STL) files and imported into the Autodesk® Meshmixer software. Organ volumes were subtracted from the abdomen and a removable base designed to allow access to the liver cavity. Connection points for placing lesion inserts and filling holes were also included. The phantom was manufactured using a Stratasys Connex3 PolyJet 3D printer. The printer uses stereolithography technology combined with ink jet printing. Print material is a solid acrylic plastic, with similar properties to polymethylmethacrylate (PMMA). Measured Hounsfield units and calculated attenuation coefficients of the material were shown to also be similar to PMMA. Total print time for the phantom was approximately 5 days. Initial scans of the phantom have been performed with Y-90 bremsstrahlung SPECT/CT, Y-90 PET/CT and Tc-99m SPECT/CT. The CT component of these images compared well with the original anatomical reference, and measurements of volume agreed to within 9 %. Quantitative analysis of the phantom was performed using all three imaging techniques. Lesion and normal liver absorbed doses were calculated from the quantitative images in three dimensions using the local deposition method. 3D printing is a flexible and cost-efficient technology for manufacture of anthropomorphic phantom. Application of such phantoms will enable quantitative imaging and dosimetry methodologies to be evaluated, which with optimisation could help improve outcome for patients.