Development, Validation, and Verification of a Self-Assessment Tool to Estimate Agnibala (Digestive Strength).

PubMed

Singh, Aparna; Singh, Girish; Patwardhan, Kishor; Gehlot, Sangeeta

2017-01-01

According to Ayurveda, the traditional system of healthcare of Indian origin, Agni is the factor responsible for digestion and metabolism. Four functional states (Agnibala) of Agni have been recognized: regular, irregular, intense, and weak. The objective of the present study was to develop and validate a self-assessment tool to estimate Agnibala The developed tool was evaluated for its reliability and validity by administering it to 300 healthy volunteers of either gender belonging to 18 to 40-year age group. Besides confirming the statistical validity and reliability, the practical utility of the newly developed tool was also evaluated by recording serum lipid parameters of all the volunteers. The results show that the lipid parameters vary significantly according to the status of Agni The tool, therefore, may be used to screen normal population to look for possible susceptibility to certain health conditions. © The Author(s) 2016.

Development of EUV mask handling technology at MIRAI-Selete

NASA Astrophysics Data System (ADS)

Ota, Kazuya; Amemiya, Mitsuaki; Taguchi, Takao; Kamono, Takashi; Kubo, Hiroyoshi; Takikawa, Tadahiko; Usui, Yoichi; Suga, Osamu

2007-03-01

We, MIRAI-Selete, started a new EUV mask program in April, 2006. Development of EUV mask handling technology is one of the key areas of the program. We plan to develop mask handling technology and to evaluate EUV mask carriers using Lasertec M3350, a particle inspection tool with the defect sensitivity less than 50nm PSL, and Mask Protection Engineering Tool (named "MPE Tool"). M3350 is a newly developed tool based on a conventional M1350 for EUV blanks inspection. Since our M3350 has a blank flipping mechanism in it, we can inspect the front and the back surface of the blank automatically. We plan to use the M3350 for evaluating particle adders during mask shipping, storage and handling. MPE Tool is a special tool exclusively developed for demonstration of pellicleless mask handling. It can handle a mask within a protective enclosure, which Canon and Nikon have been jointly proposing1, and also, can be modified to handle other type of carrier as the need arises.

A Quasi-Universal Nonword Repetition Task as a Diagnostic Tool for Bilingual Children Learning Dutch as a Second Language

ERIC Educational Resources Information Center

Boerma, Tessel; Chiat, Shula; Leseman, Paul; Timmermeister, Mona; Wijnen, Frank; Blom, Elma

2015-01-01

Purpose: This study evaluated a newly developed quasi-universal nonword repetition task (Q-U NWRT) as a diagnostic tool for bilingual children with language impairment (LI) who have Dutch as a 2nd language. The Q-U NWRT was designed to be minimally influenced by knowledge of 1 specific language in contrast to a language-specific NWRT with which it…

Symbols Build Communication and Thought: The Role of Gestures and Words in the Development of Engagement Skills and Social-Emotional Concepts during Toddlerhood

ERIC Educational Resources Information Center

Vallotton, Claire D.; Ayoub, Catherine C.

2010-01-01

Social skills and symbol skills are positively associated in middle childhood, but the relation between these domains is less clear in newly verbal toddlers. Vygotsky proposed that symbols are both tools for interaction and mental tools for thought. Do symbols help even very young children build skills for interacting with and conceptualizing the…

The MAT-sf: identifying risk for major mobility disability

USDA-ARS?s Scientific Manuscript database

BACKGROUND: The assessment of mobility is essential to both aging research and clinical geriatric practice. A newly developed self-report measure of mobility, the mobility assessment tool-short form (MAT-sf), uses video animations as an innovative method to improve measurement accuracy/precision. Th...

Concept mapping in a critical care orientation program: a pilot study to develop critical thinking and decision-making skills in novice nurses.

PubMed

Wahl, Stacy E; Thompson, Anita M

2013-10-01

Newly graduated registered nurses who were hired into a critical care intensive care unit showed a lack of critical thinking skills to inform their clinical decision-making abilities. This study evaluated the effectiveness of concept mapping as a teaching tool to improve critical thinking and clinical decision-making skills in novice nurses. A self-evaluation tool was administered before and after the learning intervention. The 25-item tool measured five key indicators of the development of critical thinking skills: problem recognition, clinical decision-making, prioritization, clinical implementation, and reflection. Statistically significant improvements were seen in 10 items encompassing all five indicators. Concept maps are an effective tool for educators to use in assisting novice nurses to develop their critical thinking and clinical decision-making skills. Copyright 2013, SLACK Incorporated.

Toward the development of survey trapping technology for the emerald ash borer

Treesearch

Therese Poland; Damon Crook; Joseph Francese; Jason Oliver; Gard Otis; Peter De Groot; Gary Grant; Linda MacDonald; Deborah McCullough; Ivich Fraser; David Lance; Victor Mastro; Nadeer Youssef; Tanya Turk; Melodie Youngs

2007-01-01

Improved survey tools are essential for accurately delimiting the infestation of emerald ash borer (EAB), Agrilus planipennis Fairmaire (Coleoptera: Buprestidae) and for detecting new infestations. Current survey methods including visual surveys for damage, girdled trap trees, and trunk dissections are less than ideal because newly infested trees...

Electromagnetic Particle-In-Cell simulation on the impedance of a dipole antenna surrounded by an ion sheath

NASA Astrophysics Data System (ADS)

Miyake, Y.; Usui, H.; Kojima, H.; Omura, Y.; Matsumoto, H.

2008-06-01

We have newly developed a numerical tool for the analysis of antenna impedance in plasma environment by making use of electromagnetic Particle-In-Cell (PIC) plasma simulations. To validate the developed tool, we first examined the antenna impedance in a homogeneous kinetic plasma and confirmed that the obtained results basically agree with the conventional theories. We next applied the tool to examine an ion-sheathed dipole antenna. The results confirmed that the inclusion of the ion-sheath effects reduces the capacitance below the electron plasma frequency. The results also revealed that the signature of impedance resonance observed at the plasma frequency is modified by the presence of the sheath. Since the sheath dynamics can be solved by the PIC scheme throughout the antenna analysis in a self-consistent manner, the developed tool has feasibility to perform more practical and complicated antenna analyses that will be necessary in real space missions.

Multidisciplinary Shape Optimization of a Composite Blended Wing Body Aircraft

NASA Astrophysics Data System (ADS)

Boozer, Charles Maxwell

A multidisciplinary shape optimization tool coupling aerodynamics, structure, and performance was developed for battery powered aircraft. Utilizing high-fidelity computational fluid dynamics analysis tools and a structural wing weight tool, coupled based on the multidisciplinary feasible optimization architecture; aircraft geometry is modified in the optimization of the aircraft's range or endurance. The developed tool is applied to three geometries: a hybrid blended wing body, delta wing UAS, the ONERA M6 wing, and a modified ONERA M6 wing. First, the optimization problem is presented with the objective function, constraints, and design vector. Next, the tool's architecture and the analysis tools that are utilized are described. Finally, various optimizations are described and their results analyzed for all test subjects. Results show that less computationally expensive inviscid optimizations yield positive performance improvements using planform, airfoil, and three-dimensional degrees of freedom. From the results obtained through a series of optimizations, it is concluded that the newly developed tool is both effective at improving performance and serves as a platform ready to receive additional performance modules, further improving its computational design support potential.

Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing.

PubMed

Walder, Florian; Schlaeppi, Klaus; Wittwer, Raphaël; Held, Alain Y; Vogelgsang, Susanne; van der Heijden, Marcel G A

2017-01-01

Fusarium head blight, caused by fungi from the genus Fusarium , is one of the most harmful cereal diseases, resulting not only in severe yield losses but also in mycotoxin contaminated and health-threatening grains. Fusarium head blight is caused by a diverse set of species that have different host ranges, mycotoxin profiles and responses to agricultural practices. Thus, understanding the composition of Fusarium communities in the field is crucial for estimating their impact and also for the development of effective control measures. Up to now, most molecular tools that monitor Fusarium communities on plants are limited to certain species and do not distinguish other plant associated fungi. To close these gaps, we developed a sequencing-based community profiling methodology for crop-associated fungi with a focus on the genus Fusarium . By analyzing a 1600 bp long amplicon spanning the highly variable segments ITS and D1-D3 of the ribosomal operon by PacBio SMRT sequencing, we were able to robustly quantify Fusarium down to species level through clustering against reference sequences. The newly developed methodology was successfully validated in mock communities and provided similar results as the culture-based assessment of Fusarium communities by seed health tests in grain samples from different crop species. Finally, we exemplified the newly developed methodology in a field experiment with a wheat-maize crop sequence under different cover crop and tillage regimes. We analyzed wheat straw residues, cover crop shoots and maize grains and we could reveal that the cover crop hairy vetch ( Vicia villosa ) acts as a potent alternative host for Fusarium (OTU F.ave/tri ) showing an eightfold higher relative abundance compared with other cover crop treatments. Moreover, as the newly developed methodology also allows to trace other crop-associated fungi, we found that vetch and green fallow hosted further fungal plant pathogens including Zymoseptoria tritici . Thus, besides their beneficial traits, cover crops can also entail phytopathological risks by acting as alternative hosts for Fusarium and other noxious plant pathogens. The newly developed sequencing based methodology is a powerful diagnostic tool to trace Fusarium in combination with other fungi associated to different crop species.

Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing

PubMed Central

Walder, Florian; Schlaeppi, Klaus; Wittwer, Raphaël; Held, Alain Y.; Vogelgsang, Susanne; van der Heijden, Marcel G. A.

2017-01-01

Fusarium head blight, caused by fungi from the genus Fusarium, is one of the most harmful cereal diseases, resulting not only in severe yield losses but also in mycotoxin contaminated and health-threatening grains. Fusarium head blight is caused by a diverse set of species that have different host ranges, mycotoxin profiles and responses to agricultural practices. Thus, understanding the composition of Fusarium communities in the field is crucial for estimating their impact and also for the development of effective control measures. Up to now, most molecular tools that monitor Fusarium communities on plants are limited to certain species and do not distinguish other plant associated fungi. To close these gaps, we developed a sequencing-based community profiling methodology for crop-associated fungi with a focus on the genus Fusarium. By analyzing a 1600 bp long amplicon spanning the highly variable segments ITS and D1–D3 of the ribosomal operon by PacBio SMRT sequencing, we were able to robustly quantify Fusarium down to species level through clustering against reference sequences. The newly developed methodology was successfully validated in mock communities and provided similar results as the culture-based assessment of Fusarium communities by seed health tests in grain samples from different crop species. Finally, we exemplified the newly developed methodology in a field experiment with a wheat-maize crop sequence under different cover crop and tillage regimes. We analyzed wheat straw residues, cover crop shoots and maize grains and we could reveal that the cover crop hairy vetch (Vicia villosa) acts as a potent alternative host for Fusarium (OTU F.ave/tri) showing an eightfold higher relative abundance compared with other cover crop treatments. Moreover, as the newly developed methodology also allows to trace other crop-associated fungi, we found that vetch and green fallow hosted further fungal plant pathogens including Zymoseptoria tritici. Thus, besides their beneficial traits, cover crops can also entail phytopathological risks by acting as alternative hosts for Fusarium and other noxious plant pathogens. The newly developed sequencing based methodology is a powerful diagnostic tool to trace Fusarium in combination with other fungi associated to different crop species. PMID:29234337

Developing a "toolkit" to measure implementation of concurrent palliative care in rural community cancer centers.

PubMed

Zubkoff, Lisa; Dionne-Odom, J Nicholas; Pisu, Maria; Babu, Dilip; Akyar, Imatullah; Smith, Tasha; Mancarella, Gisella A; Gansauer, Lucy; Sullivan, Margaret Murray; Swetz, Keith M; Azuero, Andres; Bakitas, Marie A

2018-02-01

Despite national guidelines recommending early concurrent palliative care for individuals newly diagnosed with metastatic cancer, few community cancer centers, especially those in underserved rural areas do so. We are implementing an early concurrent palliative care model, ENABLE (Educate, Nurture, Advise, Before Life Ends) in four, rural-serving community cancer centers. Our objective was to develop a "toolkit" to assist community cancer centers that wish to integrate early palliative care for patients with newly diagnosed advanced cancer and their family caregivers. Guided by the RE-AIM (Reach, Effectiveness-Adoption, Implementation, Maintenance) framework, we undertook an instrument-development process based on the literature, expert and site stakeholder review and feedback, and pilot testing during site visits. We developed four instruments to measure ENABLE implementation: (1) the ENABLE RE-AIM Self-Assessment Tool to assess reach, adoption, implementation, and maintenance; (2) the ENABLE General Organizational Index to assess institutional implementation; (3) an Implementation Costs Tool; and (4) an Oncology Clinicians' Perceptions of Early Concurrent Oncology Palliative Care survey. We developed four measures to determine early palliative care implementation. These measures have been pilot-tested, and will be integrated into a comprehensive "toolkit" to assist community cancer centers to measure implementation outcomes. We describe the lessons learned and recommend strategies for promoting long-term program sustainability.

Inflammation-driven malnutrition: a new screening tool predicts outcome in Crohn's disease.

PubMed

Jansen, Irene; Prager, Matthias; Valentini, Luzia; Büning, Carsten

2016-09-01

Malnutrition is a frequent feature in Crohn's disease (CD), affects patient outcome and must be recognised. For chronic inflammatory diseases, recent guidelines recommend the development of combined malnutrition and inflammation risk scores. We aimed to design and evaluate a new screening tool that combines both malnutrition and inflammation parameters that might help predict clinical outcome. In a prospective cohort study, we examined fifty-five patients with CD in remission (Crohn's disease activity index (CDAI) <200) at 0 and 6 months. We assessed disease activity (CDAI, Harvey-Bradshaw index), inflammation (C-reactive protein (CRP), faecal calprotectin (FC)), malnutrition (BMI, subjective global assessment (SGA), serum albumin, handgrip strength), body composition (bioelectrical impedance analysis) and administered the newly developed 'Malnutrition Inflammation Risk Tool' (MIRT; containing BMI, unintentional weight loss over 3 months and CRP). All parameters were evaluated regarding their ability to predict disease outcome prospectively at 6 months. At baseline, more than one-third of patients showed elevated inflammatory markers despite clinical remission (36·4 % CRP ≥5 mg/l, 41·5 % FC ≥100 µg/g). Prevalence of malnutrition at baseline according to BMI, SGA and serum albumin was 2-16 %. At 6 months, MIRT significantly predicted outcome in numerous nutritional and clinical parameters (SGA, CD-related flares, hospitalisations and surgeries). In contrast, SGA, handgrip strength, BMI, albumin and body composition had no influence on the clinical course. The newly developed MIRT was found to reliably predict clinical outcome in CD patients. This screening tool might be used to facilitate clinical decision making, including treatment of both inflammation and malnutrition in order to prevent complications.

Emotioncy: A Potential Measure of Readability

ERIC Educational Resources Information Center

Pishghadamn, Reza; Abbasnejad, Hannaheh

2016-01-01

Given the deficiencies of readability formulae as reliable tools for measuring text readability in educational settings, this study aims to offer a new measure to improve the current methods of testing the readability levels of texts through the incorporation of the newly-developed concept of emotioncy. To this end, a group of 221 students were…

Learning Geometry by Designing Persian Mosaics

ERIC Educational Resources Information Center

Karssenberg, Goossen

2014-01-01

To encourage students to do geometry, the art of Islamic geometric ornamentation was chosen as the central theme of a lesson strand which was developed using the newly presented didactical tool called "Learning by Acting". The Dutch students who took these lessons in 2010 to 2013 were challenged to act as if they themselves were Persian…

EXISTING AND NEWLY DEVELOPED ASSESSMENT TOOLS AND BIOCRITERIA FOR THE U.S. EPA'S NEW ENGLAND AND MID-ATLANTIC REGIONS

EPA Science Inventory

This poster offers an overview of biological assessment programs for wadeable streams and rivers within states in the U.S. EPA Regions 1 (Connecticut, Maine, Massachusetts, New Hampshire, Rhode Island and Vermont) and Region 3 (Delaware, Maryland, Pennsylvania, Virginia and West ...

Effects of Web-Based Interactive Modules on Engineering Students' Learning Motivations

ERIC Educational Resources Information Center

Bai, Haiyan; Aman, Amjad; Xu, Yunjun; Orlovskaya, Nina; Zhou, Mingming

2016-01-01

The purpose of this study is to assess the impact of a newly developed modules, Interactive Web-Based Visualization Tools for Gluing Undergraduate Fuel Cell Systems Courses system (IGLU), on learning motivations of engineering students using two samples (n[subscript 1] = 144 and n[subscript 2] = 135) from senior engineering classes. The…

Current knowledge on effects of forest silvicultural operations on carbon sequestration in southern forests

Treesearch

John D. Cason; Donald L. Grebner; Andrew J. Londo; Stephen C. Grado

2006-01-01

Incentive programs to reduce carbon dioxide (CO2) emissions are increasing in number with the growing threat of global warming. Terrestrial sequestration of CO2 through forestry practices on newly established forests is a potential mitigation tool for developing carbon markets in the United States. The extent of industrial...

Clinical Prediction Model for Time in Therapeutic Range While on Warfarin in Newly Diagnosed Atrial Fibrillation.

PubMed

Williams, Brent A; Evans, Michael A; Honushefsky, Ashley M; Berger, Peter B

2017-10-12

Though warfarin has historically been the primary oral anticoagulant for stroke prevention in newly diagnosed atrial fibrillation (AF), several new direct oral anticoagulants may be preferred when anticoagulation control with warfarin is expected to be poor. This study developed a prediction model for time in therapeutic range (TTR) among newly diagnosed AF patients on newly initiated warfarin as a tool to assist decision making between warfarin and direct oral anticoagulants. This electronic medical record-based, retrospective study included newly diagnosed, nonvalvular AF patients with no recent warfarin exposure receiving primary care services through a large healthcare system in rural Pennsylvania. TTR was estimated as the percentage of time international normalized ratio measurements were between 2.0 and 3.0 during the first year following warfarin initiation. Candidate predictors of TTR were chosen from data elements collected during usual clinical care. A TTR prediction model was developed and temporally validated and its predictive performance was compared with the SAMe-TT 2 R 2 score (sex, age, medical history, treatment, tobacco, race) using R 2 and c-statistics. A total of 7877 newly diagnosed AF patients met study inclusion criteria. Median (interquartile range) TTR within the first year of starting warfarin was 51% (32, 67). Of 85 candidate predictors evaluated, 15 were included in the final validated model with an R 2 of 15.4%. The proposed model showed better predictive performance than the SAMe-TT 2 R 2 score ( R 2 =3.0%). The proposed prediction model may assist decision making on the proper mode of oral anticoagulant among newly diagnosed AF patients. However, predicting TTR on warfarin remains challenging. © 2017 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

Phytophthora database 2.0: update and future direction.

PubMed

Park, Bongsoo; Martin, Frank; Geiser, David M; Kim, Hye-Seon; Mansfield, Michele A; Nikolaeva, Ekaterina; Park, Sook-Young; Coffey, Michael D; Russo, Joseph; Kim, Seong H; Balci, Yilmaz; Abad, Gloria; Burgess, Treena; Grünwald, Niklaus J; Cheong, Kyeongchae; Choi, Jaeyoung; Lee, Yong-Hwan; Kang, Seogchan

2013-12-01

The online community resource Phytophthora database (PD) was developed to support accurate and rapid identification of Phytophthora and to help characterize and catalog the diversity and evolutionary relationships within the genus. Since its release in 2008, the sequence database has grown to cover 1 to 12 loci for ≈2,600 isolates (representing 138 described and provisional species). Sequences of multiple mitochondrial loci were added to complement nuclear loci-based phylogenetic analyses and diagnostic tool development. Key characteristics of most newly described and provisional species have been summarized. Other additions to improve the PD functionality include: (i) geographic information system tools that enable users to visualize the geographic origins of chosen isolates on a global-scale map, (ii) a tool for comparing genetic similarity between isolates via microsatellite markers to support population genetic studies, (iii) a comprehensive review of molecular diagnostics tools and relevant references, (iv) sequence alignments used to develop polymerase chain reaction-based diagnostics tools to support their utilization and new diagnostic tool development, and (v) an online community forum for sharing and preserving experience and knowledge accumulated in the global Phytophthora community. Here we present how these improvements can support users and discuss the PD's future direction.

Using Web 2.0 for Learning in the Community

ERIC Educational Resources Information Center

Mason, Robin; Rennie, Frank

2007-01-01

This paper describes the use of a range of Web 2.0 technologies to support the development of community for a newly formed Land Trust on the Isle of Lewis, in NW Scotland. The application of social networking tools in text, audio and video has several purposes: informal learning about the area to increase tourism, community interaction,…

Multilingualism as Policy and Practices in Elementary School: Powerful Tools for Inclusion of Newly Arrived Pupils

ERIC Educational Resources Information Center

Wedin, Åsa; Wessman, Anneli

2017-01-01

In this article, language policy is analysed in relation to multilingual practices in primary school through an understanding of the policy on different levels--as management, perception and practice. The article is based on longitudinal ethnographic action research that was conducted parallel to local school development. Here we draw on material…

Effects of Learning Analytics Dashboard: Analyzing the Relations among Dashboard Utilization, Satisfaction, and Learning Achievement

ERIC Educational Resources Information Center

Kim, Jeonghyun; Jo, Il-Hyun; Park, Yeonjeong

2016-01-01

The learning analytics dashboard (LAD) is a newly developed learning support tool for virtual classrooms that is believed to allow students to review their online learning behavior patterns intuitively through the provision of visual information. The purpose of this study was to empirically validate the effects of LAD. An experimental study was…

Molecular HIV screening.

PubMed

Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

2013-09-01

Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

NASA Electronic Parts and Packaging Program

NASA Technical Reports Server (NTRS)

Kayali, Sammy

2000-01-01

NEPP program objectives are to: (1) Access the reliability of newly available electronic parts and packaging technologies for usage on NASA projects through validations, assessments, and characterizations, and the development of test methods/tools; (2)Expedite infusion paths for advanced (emerging) electronic parts and packaging technologies by evaluations of readiness for manufacturability and project usage consideration; (3) Provide NASA projects with technology selection, application, and validation guidelines for electronic parts and packaging hardware and processes; nd (4) Retain and disseminate electronic parts and packaging quality assurance, reliability validations, tools, and availability information to the NASA community.

deepTools: a flexible platform for exploring deep-sequencing data.

PubMed

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

2014-07-01

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Anthropomorphic Telemanipulation System in Terminus Control Mode

NASA Technical Reports Server (NTRS)

Jau, Bruno M.; Lewis, M. Anthony; Bejczy, Antal K.

1994-01-01

This paper describes a prototype anthropomorphic kinesthetic telepresence system that is being developed at JPL. It utilizes dexterous terminus devices in the form of an exoskeleton force-sensing master glove worn by the operator and a replica four finger anthropomorphic slave hand. The newly developed master glove is integrated with our previously developed non-anthropomorphic six degree of freedom (DOF) universal force-reflecting hand controller (FRHC). The mechanical hand and forearm are mounted to an industrial robot (PUMA 560), replacing its standard forearm. The notion of 'terminus control mode' refers to the fact that only the terminus devices (glove and robot hand) are of anthropomorphic nature, and the master and slave arms are non-anthropomorphic. The system is currently being evaluated, focusing on tool handling and astronaut equivalent task executions. The evaluation revealed the system's potential for tool handling but it also became evident that hand tool manipulations and space operations require a dual arm robot. This paper describes the system's principal components, its control and computing architecture, discusses findings of the tool handling evaluation, and explains why common tool handling and EVA space tasks require dual arm robots.

An Observation Analysis Tool for time-series analysis and sensor management in the FREEWAT GIS environment for water resources management

NASA Astrophysics Data System (ADS)

Cannata, Massimiliano; Neumann, Jakob; Cardoso, Mirko; Rossetto, Rudy; Foglia, Laura; Borsi, Iacopo

2017-04-01

In situ time-series are an important aspect of environmental modelling, especially with the advancement of numerical simulation techniques and increased model complexity. In order to make use of the increasing data available through the requirements of the EU Water Framework Directive, the FREEWAT GIS environment incorporates the newly developed Observation Analysis Tool for time-series analysis. The tool is used to import time-series data into QGIS from local CSV files, online sensors using the istSOS service, or MODFLOW model result files and enables visualisation, pre-processing of data for model development, and post-processing of model results. OAT can be used as a pre-processor for calibration observations, integrating the creation of observations for calibration directly from sensor time-series. The tool consists in an expandable Python library of processing methods and an interface integrated in the QGIS FREEWAT plug-in which includes a large number of modelling capabilities, data management tools and calibration capacity.

[Development of a Text-Data Based Learning Tool That Integrates Image Processing and Displaying].

PubMed

Shinohara, Hiroyuki; Hashimoto, Takeyuki

2015-01-01

We developed a text-data based learning tool that integrates image processing and displaying by Excel. Knowledge required for programing this tool is limited to using absolute, relative, and composite cell references and learning approximately 20 mathematical functions available in Excel. The new tool is capable of resolution translation, geometric transformation, spatial-filter processing, Radon transform, Fourier transform, convolutions, correlations, deconvolutions, wavelet transform, mutual information, and simulation of proton density-, T1-, and T2-weighted MR images. The processed images of 128 x 128 pixels or 256 x 256 pixels are observed directly within Excel worksheets without using any particular image display software. The results of image processing using this tool were compared with those using C language and the new tool was judged to have sufficient accuracy to be practically useful. The images displayed on Excel worksheets were compared with images using binary-data display software. This comparison indicated that the image quality of the Excel worksheets was nearly equal to the latter in visual impressions. Since image processing is performed by using text-data, the process is visible and facilitates making contrasts by using mathematical equations within the program. We concluded that the newly developed tool is adequate as a computer-assisted learning tool for use in medical image processing.

A framework for measurement and harmonization of pediatric multiple sclerosis etiologic research studies: The Pediatric MS Tool-Kit.

PubMed

Magalhaes, Sandra; Banwell, Brenda; Bar-Or, Amit; Fortier, Isabel; Hanwell, Heather E; Lim, Ming; Matt, Georg E; Neuteboom, Rinze F; O'Riordan, David L; Schneider, Paul K; Pugliatti, Maura; Shatenstein, Bryna; Tansey, Catherine M; Wassmer, Evangeline; Wolfson, Christina

2018-06-01

While studying the etiology of multiple sclerosis (MS) in children has several methodological advantages over studying etiology in adults, studies are limited by small sample sizes. Using a rigorous methodological process, we developed the Pediatric MS Tool-Kit, a measurement framework that includes a minimal set of core variables to assess etiological risk factors. We solicited input from the International Pediatric MS Study Group to select three risk factors: environmental tobacco smoke (ETS) exposure, sun exposure, and vitamin D intake. To develop the Tool-Kit, we used a Delphi study involving a working group of epidemiologists, neurologists, and content experts from North America and Europe. The Tool-Kit includes six core variables to measure ETS, six to measure sun exposure, and six to measure vitamin D intake. The Tool-Kit can be accessed online ( www.maelstrom-research.org/mica/network/tool-kit ). The goals of the Tool-Kit are to enhance exposure measurement in newly designed pediatric MS studies and comparability of results across studies, and in the longer term to facilitate harmonization of studies, a methodological approach that can be used to circumvent issues of small sample sizes. We believe the Tool-Kit will prove to be a valuable resource to guide pediatric MS researchers in developing study-specific questionnaire.

Teacher Reporting Attitudes Scale (TRAS): Confirmatory and Exploratory Factor Analyses with a Malaysian Sample

ERIC Educational Resources Information Center

Choo, Wan Yuen; Walsh, Kerryann; Chinna, Karuthan; Tey, Nai Peng

2013-01-01

The Teacher Reporting Attitude Scale (TRAS) is a newly developed tool to assess teachers' attitudes toward reporting child abuse and neglect. This article reports on an investigation of the factor structure and psychometric properties of the short form Malay version of the TRAS. A self-report cross-sectional survey was conducted with 667 teachers…

Logistics Force Planner Assistant (Log Planner)

DTIC Science & Technology

1989-09-01

elements. The system is implemented on a MS-DOS based microcomputer, using the "Knowledge Pro’ software tool., 20 DISTRIBUTION/AVAILABILITY OF... service support structure. 3. A microcomputer-based knowledge system was developed and successfully demonstrated. Four modules of information are...combat service support (CSS) units planning process to Army Staff logistics planners. Personnel newly assigned to logistics planning need an

Feasibility and fidelity of practising surgical fixation on a virtual ulna bone

PubMed Central

LeBlanc, Justin; Hutchison, Carol; Hu, Yaoping; Donnon, Tyrone

2013-01-01

Background Surgical simulators provide a safe environment to learn and practise psychomotor skills. A goal for these simulators is to achieve high levels of fidelity. The purpose of this study was to develop a reliable surgical simulator fidelity questionnaire and to assess whether a newly developed virtual haptic simulator for fixation of an ulna has comparable levels of fidelity as Sawbones. Methods Simulator fidelity questionnaires were developed. We performed a stratified randomized study with surgical trainees. They performed fixation of the ulna using a virtual simulator and Sawbones. They completed the fidelity questionnaires after each procedure. Results Twenty-two trainees participated in the study. The reliability of the fidelity questionnaire for each separate domain (environment, equipment, psychological) was Cronbach α greater than 0.70, except for virtual environment. The Sawbones had significantly higher levels of fidelity than the virtual simulator (p < 0.001) with a large effect size difference (Cohen d < 1.3). Conclusion The newly developed fidelity questionnaire is a reliable tool that can potentially be used to determine the fidelity of other surgical simulators. Increasing the fidelity of this virtual simulator is required before its use as a training tool for surgical fixation. The virtual simulator brings with it the added benefits of repeated, independent safe use with immediate, objective feedback and the potential to alter the complexity of the skill. PMID:23883510

A GIS Tool for evaluating and improving NEXRAD and its application in distributed hydrologic modeling

NASA Astrophysics Data System (ADS)

Zhang, X.; Srinivasan, R.

2008-12-01

In this study, a user friendly GIS tool was developed for evaluating and improving NEXRAD using raingauge data. This GIS tool can automatically read in raingauge and NEXRAD data, evaluate the accuracy of NEXRAD for each time unit, implement several geostatistical methods to improve the accuracy of NEXRAD through raingauge data, and output spatial precipitation map for distributed hydrologic model. The geostatistical methods incorporated in this tool include Simple Kriging with varying local means, Kriging with External Drift, Regression Kriging, Co-Kriging, and a new geostatistical method that was newly developed by Li et al. (2008). This tool was applied in two test watersheds at hourly and daily temporal scale. The preliminary cross-validation results show that incorporating raingauge data to calibrate NEXRAD can pronouncedly change the spatial pattern of NEXRAD and improve its accuracy. Using different geostatistical methods, the GIS tool was applied to produce long term precipitation input for a distributed hydrologic model - Soil and Water Assessment Tool (SWAT). Animated video was generated to vividly illustrate the effect of using different precipitation input data on distributed hydrologic modeling. Currently, this GIS tool is developed as an extension of SWAT, which is used as water quantity and quality modeling tool by USDA and EPA. The flexible module based design of this tool also makes it easy to be adapted for other hydrologic models for hydrological modeling and water resources management.

Low Cost Electroencephalographic Acquisition Amplifier to serve as Teaching and Research Tool

PubMed Central

Jain, Ankit; Kim, Insoo; Gluckman, Bruce J.

2012-01-01

We describe the development and testing of a low cost, easily constructed electroencephalographic acquisition amplifier for noninvasive Brain Computer Interface (BCI) education and research. The acquisition amplifier is constructed from newly available off-the-shelf integrated circuit components, and readily sends a 24-bit data stream via USB bus to a computer platform. We demonstrate here the hardware’s use in the analysis of a visually evoked P300 paradigm for a choose one-of-eight task. This clearly shows the applicability of this system as a low cost teaching and research tool. PMID:22254699

SpecTracer: A Python-Based Interactive Solution for Echelle Spectra Reduction

NASA Astrophysics Data System (ADS)

Romero Matamala, Oscar Fernando; Petit, Véronique; Caballero-Nieves, Saida Maria

2018-01-01

SpecTracer is a newly developed interactive solution to reduce cross dispersed echelle spectra. The use of widgets saves the user the steep learning curves of currently available reduction software. SpecTracer uses well established image processing techniques based on IRAF to succesfully extract the stellar spectra. Comparisons with other reduction software, like IRAF, show comparable results, with the added advantages of ease of use, platform independence and portability. This tool can obtain meaningful scientific data and serve also as a training tool, especially for undergraduates doing research, in the procedure for spectroscopic analysis.

Risk-Aware Planetary Rover Operation: Autonomous Terrain Classification and Path Planning

NASA Technical Reports Server (NTRS)

Ono, Masahiro; Fuchs, Thoams J.; Steffy, Amanda; Maimone, Mark; Yen, Jeng

2015-01-01

Identifying and avoiding terrain hazards (e.g., soft soil and pointy embedded rocks) are crucial for the safety of planetary rovers. This paper presents a newly developed groundbased Mars rover operation tool that mitigates risks from terrain by automatically identifying hazards on the terrain, evaluating their risks, and suggesting operators safe paths options that avoids potential risks while achieving specified goals. The tool will bring benefits to rover operations by reducing operation cost, by reducing cognitive load of rover operators, by preventing human errors, and most importantly, by significantly reducing the risk of the loss of rovers.

Two New Tools for Glycopeptide Analysis Researchers: A Glycopeptide Decoy Generator and a Large Data Set of Assigned CID Spectra of Glycopeptides.

PubMed

Lakbub, Jude C; Su, Xiaomeng; Zhu, Zhikai; Patabandige, Milani W; Hua, David; Go, Eden P; Desaire, Heather

2017-08-04

The glycopeptide analysis field is tightly constrained by a lack of effective tools that translate mass spectrometry data into meaningful chemical information, and perhaps the most challenging aspect of building effective glycopeptide analysis software is designing an accurate scoring algorithm for MS/MS data. We provide the glycoproteomics community with two tools to address this challenge. The first tool, a curated set of 100 expert-assigned CID spectra of glycopeptides, contains a diverse set of spectra from a variety of glycan types; the second tool, Glycopeptide Decoy Generator, is a new software application that generates glycopeptide decoys de novo. We developed these tools so that emerging methods of assigning glycopeptides' CID spectra could be rigorously tested. Software developers or those interested in developing skills in expert (manual) analysis can use these tools to facilitate their work. We demonstrate the tools' utility in assessing the quality of one particular glycopeptide software package, GlycoPep Grader, which assigns glycopeptides to CID spectra. We first acquired the set of 100 expert assigned CID spectra; then, we used the Decoy Generator (described herein) to generate 20 decoys per target glycopeptide. The assigned spectra and decoys were used to test the accuracy of GlycoPep Grader's scoring algorithm; new strengths and weaknesses were identified in the algorithm using this approach. Both newly developed tools are freely available. The software can be downloaded at http://glycopro.chem.ku.edu/GPJ.jar.

Validation of an Adapted French Form of the Career Adapt-Abilities Scale in Four Francophone Countries

ERIC Educational Resources Information Center

Johnston, Claire S.; Broonen, Jean-Paul; Stauffer, Sarah D.; Hamtiaux, Armanda; Pouyaud, Jacques; Zecca, Gregory; Houssemand, Claude; Rossier, Jerome

2013-01-01

This study presents the validation of a French version of the Career Adapt-Abilities Scale in four Francophone countries. The aim was to re-analyze the item selection and then compare this newly developed French-language form with the international form 2.0. Exploratory factor analysis was used as a tool for item selection, and confirmatory factor…

Fully automated muscle quality assessment by Gabor filtering of second harmonic generation images

NASA Astrophysics Data System (ADS)

Paesen, Rik; Smolders, Sophie; Vega, José Manolo de Hoyos; Eijnde, Bert O.; Hansen, Dominique; Ameloot, Marcel

2016-02-01

Although structural changes on the sarcomere level of skeletal muscle are known to occur due to various pathologies, rigorous studies of the reduced sarcomere quality remain scarce. This can possibly be explained by the lack of an objective tool for analyzing and comparing sarcomere images across biological conditions. Recent developments in second harmonic generation (SHG) microscopy and increasing insight into the interpretation of sarcomere SHG intensity profiles have made SHG microscopy a valuable tool to study microstructural properties of sarcomeres. Typically, sarcomere integrity is analyzed by fitting a set of manually selected, one-dimensional SHG intensity profiles with a supramolecular SHG model. To circumvent this tedious manual selection step, we developed a fully automated image analysis procedure to map the sarcomere disorder for the entire image at once. The algorithm relies on a single-frequency wavelet-based Gabor approach and includes a newly developed normalization procedure allowing for unambiguous data interpretation. The method was validated by showing the correlation between the sarcomere disorder, quantified by the M-band size obtained from manually selected profiles, and the normalized Gabor value ranging from 0 to 1 for decreasing disorder. Finally, to elucidate the applicability of our newly developed protocol, Gabor analysis was used to study the effect of experimental autoimmune encephalomyelitis on the sarcomere regularity. We believe that the technique developed in this work holds great promise for high-throughput, unbiased, and automated image analysis to study sarcomere integrity by SHG microscopy.

Physicians’ experience adopting the electronic transfer of care communication tool: barriers and opportunities

PubMed Central

de Grood, Chloe; Eso, Katherine; Santana, Maria Jose

2015-01-01

Purpose The purpose of this study was to assess physicians’ perceptions on a newly developed electronic transfer of care (e-TOC) communication tool and identify barriers and opportunities toward its adoption. Participants and methods The study was conducted in a tertiary care teaching center as part of a randomized controlled trial assessing the efficacy of an e-TOC communication tool. The e-TOC technology was developed through iterative consultation with stakeholders. This e-TOC summary was populated by acute care physicians (AcPs) and communicated electronically to community care physicians (CcPs). The AcPs consisted of attending physicians, resident trainees, and medical students rotating through the Medical Teaching Unit. The CcPs were health care providers caring for patients discharged from hospital to the community. AcPs and CcPs completed validated surveys assessing their experience with the newly developed e-TOC tool. Free text questions were added to gather general comments from both groups of physicians. Units of analysis were individual physicians. Data from the surveys were analyzed using mixed methods. Results AcPs completed 138 linked pre- and post-rotation surveys. At post-rotation, each AcP completed an average of six e-TOC summaries, taking an average of 37 minutes per e-TOC summary. Over 100 CcPs assessed the quality of the TOC summaries, with an overall rating of 8.3 (standard deviation: 1.48; on a scale of 1–10). Thematic analyses revealed barriers and opportunities encountered by physicians toward the adoption of the e-TOC tool. While the AcPs highlighted issues with timeliness, usability, and presentation, the CcPs identified barriers accessing the web-based TOC summaries, emphasizing that the summaries were timely and the quality of information supported continuity of care. Conclusion Despite the barriers identified by both groups of physicians, the e-TOC communication tool was well received. Our experience can serve as a template for other health research teams considering the implementation of e-health technologies into health care systems. PMID:25609977

Assessment of competence in video-assisted thoracoscopic surgery lobectomy: A Danish nationwide study.

PubMed

Petersen, René Horsleben; Gjeraa, Kirsten; Jensen, Katrine; Møller, Lars Borgbjerg; Hansen, Henrik Jessen; Konge, Lars

2018-04-18

Competence in video-assisted thoracoscopic surgery lobectomy has previously been established on the basis of numbers of procedures performed, but this approach does not ensure competence. Specific assessment tools, such as the newly developed video-assisted thoracoscopic surgery lobectomy assessment tool, allow for structured and objective assessment of competence. Our aim was to provide validity evidence for the video-assisted thoracoscopic surgery lobectomy assessment tool. Video recordings of 60 video-assisted thoracoscopic surgery lobectomies performed by 18 thoracic surgeons were rated using the video-assisted thoracoscopic surgery lobectomy assessment tool. All 4 centers of thoracic surgery in Denmark participated in the study. Two video-assisted thoracoscopic surgery experts rated the videos. They were blinded to surgeon and center. The total internal consistency reliability Cronbach's alpha was 0.93. Inter-rater reliability between the 2 raters was Pearson's r = 0.71 (P < .001). The mean video-assisted thoracoscopic surgery lobectomy assessment tool scores for the 10 procedures performed by beginners were 22.1 (standard deviation [SD], 8.6) for the 28 procedures performed by the intermediate surgeons, 31.2 (SD, 4.4), and for the 20 procedures performed by experts 35.9 (SD, 2.9) (P < .001). Bonferroni post hoc tests showed that experts were significantly better than intermediates (P < .008) and beginners (P < .001). Intermediates' mean scores were significantly better than beginners (P < .001). The pass/fail standard calculated using the contrasting group's method was 31 points. One of the beginners passed, and 2 experts failed the test. Validity evidence was provided for a newly developed assessment tool for video-assisted thoracoscopic surgery lobectomy (video-assisted thoracoscopic surgery lobectomy assessment tool) in a clinical setting. The discriminatory ability among expert surgeons, intermediate surgeons, and beginners proved highly significant. The video-assisted thoracoscopic surgery lobectomy assessment tool could be an important aid in the future training and certification of thoracic surgeons. Copyright © 2018 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

Cas9-based tools for targeted genome editing and transcriptional control.

PubMed

Xu, Tao; Li, Yongchao; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong

2014-03-01

Development of tools for targeted genome editing and regulation of gene expression has significantly expanded our ability to elucidate the mechanisms of interesting biological phenomena and to engineer desirable biological systems. Recent rapid progress in the study of a clustered, regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) protein system in bacteria has facilitated the development of newly facile and programmable platforms for genome editing and transcriptional control in a sequence-specific manner. The core RNA-guided Cas9 endonuclease in the type II CRISPR system has been harnessed to realize gene mutation and DNA deletion and insertion, as well as transcriptional activation and repression, with multiplex targeting ability, just by customizing 20-nucleotide RNA components. Here we describe the molecular basis of the type II CRISPR/Cas system and summarize applications and factors affecting its utilization in model organisms. We also discuss the advantages and disadvantages of Cas9-based tools in comparison with widely used customizable tools, such as Zinc finger nucleases and transcription activator-like effector nucleases.

CAST: a new program package for the accurate characterization of large and flexible molecular systems.

PubMed

Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

2014-09-15

The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

Time-Series Analysis: A Cautionary Tale

NASA Technical Reports Server (NTRS)

Damadeo, Robert

2015-01-01

Time-series analysis has often been a useful tool in atmospheric science for deriving long-term trends in various atmospherically important parameters (e.g., temperature or the concentration of trace gas species). In particular, time-series analysis has been repeatedly applied to satellite datasets in order to derive the long-term trends in stratospheric ozone, which is a critical atmospheric constituent. However, many of the potential pitfalls relating to the non-uniform sampling of the datasets were often ignored and the results presented by the scientific community have been unknowingly biased. A newly developed and more robust application of this technique is applied to the Stratospheric Aerosol and Gas Experiment (SAGE) II version 7.0 ozone dataset and the previous biases and newly derived trends are presented.

IgSimulator: a versatile immunosequencing simulator.

PubMed

Safonova, Yana; Lapidus, Alla; Lill, Jennie

2015-10-01

The recent introduction of next-generation sequencing technologies to antibody studies have resulted in a growing number of immunoinformatics tools for antibody repertoire analysis. However, benchmarking these newly emerging tools remains problematic since the gold standard datasets that are needed to validate these tools are typically not available. Since simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools, we developed the IgSimulator tool that addresses various complications in generating realistic antibody repertoires. IgSimulator's code has modular structure and can be easily adapted to new requirements to simulation. IgSimulator is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from yana-safonova.github.io/ig_simulator. safonova.yana@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Automatic alternative phase-shift mask CAD layout tool for gate shrinkage of embedded DRAM in logic below 0.18 μm

NASA Astrophysics Data System (ADS)

Ohnuma, Hidetoshi; Kawahira, Hiroichi

1998-09-01

An automatic alternative phase shift mask (PSM) pattern layout tool has been newly developed. This tool is dedicated for embedded DRAM in logic device to shrink gate line width with improving line width controllability in lithography process with a design rule below 0.18 micrometers by the KrF excimer laser exposure. The tool can crete Levenson type PSM used being coupled with a binary mask adopting a double exposure method for positive photo resist. By using graphs, this tool automatically creates alternative PSM patterns. Moreover, it does not give any phase conflicts. By adopting it to actual embedded DRAM in logic cells, we have provided 0.16 micrometers gate resist patterns at both random logic and DRAM areas. The patterns were fabricated using two masks with the double exposure method. Gate line width has been well controlled under a practical exposure-focus window.

New educational tools to encourage high-school students' activity in stem

NASA Astrophysics Data System (ADS)

Mayorova, Vera; Grishko, Dmitriy; Leonov, Victor

2018-01-01

Many students have to choose their future profession during their last years in the high school and therefore to choose a university where they will get proper education. That choice may define their professional life for many years ahead or probably for the rest of their lives. Bauman Moscow State Technical University conducts various events to introduce future professions to high-school students. Such activity helps them to pick specialization in line with their interests and motivates them to study key scientific subjects. The paper focuses on newly developed educational tools to encourage high school students' interest in STEM disciplines. These tools include laboratory courses developed in the fields of physics, information technologies and mathematics. More than 2000 high school students already participated in these experimental courses. These activities are aimed at increasing the quality of STEM disciplines learning which will result in higher quality of training of future engineers.

Studienlandschaft Schwingbachtal: an out-door full-scale learning tool newly equipped with augmented reality

NASA Astrophysics Data System (ADS)

Aubert, A. H.; Schnepel, O.; Kraft, P.; Houska, T.; Plesca, I.; Orlowski, N.; Breuer, L.

2015-11-01

This paper addresses education and communication in hydrology and geosciences. Many approaches can be used, such as the well-known seminars, modelling exercises and practical field work but out-door learning in our discipline is a must, and this paper focuses on the recent development of a new out-door learning tool at the landscape scale. To facilitate improved teaching and hands-on experience, we designed the Studienlandschaft Schwingbachtal. Equipped with field instrumentation, education trails, and geocache, we now implemented an augmented reality App, adding virtual teaching objects on the real landscape. The App development is detailed, to serve as methodology for people wishing to implement such a tool. The resulting application, namely the Schwingbachtal App, is described as an example. We conclude that such an App is useful for communication and education purposes, making learning pleasant, and offering personalized options.

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

We present a newly developed software package which implements a wide range of routines frequently used in Weak Gravitational Lensing (WL). With the continuously increasing size of the WL scientific community we feel that easy to use Application Program Interfaces (APIs) for common calculations are a necessity to ensure efficiency and coordination across different working groups. Coupled with existing open source codes, such as CAMB (Lewis et al., 2000) and Gadget2 (Springel, 2005), LensTools brings together a cosmic shear simulation pipeline which, complemented with a variety of WL feature measurement tools and parameter sampling routines, provides easy access to the numerics for theoretical studies of WL as well as for experiment forecasts. Being implemented in PYTHON (Rossum, 1995), LensTools takes full advantage of a range of state-of-the art techniques developed by the large and growing open-source software community (Jones et al., 2001; McKinney, 2010; Astrophy Collaboration, 2013; Pedregosa et al., 2011; Foreman-Mackey et al., 2013). We made the LensTools code available on the Python Package Index and published its documentation on http://lenstools.readthedocs.io.

Decision-making and referral processes for patients with motor neurone disease: a qualitative study of GP experiences and evaluation of a new decision-support tool.

PubMed

Baxter, Susan; McDermott, Christopher J

2017-05-08

The diagnosis of motor neurone disease (MND) is known to be challenging and there may be delay in patients receiving a correct diagnosis. This study investigated the referral process for patients who had been diagnosed with MND, and whether a newly-developed tool (The Red Flags checklist) might help General Practitioners (GPs) in making referral decisions. We carried out interviews with GPs who had recently referred a patient diagnosed with MND, and interviews/surveys with GPs who had not recently referred a patient with suspected MND. We collected data before the Red Flags checklist was introduced; and again one year later. We analysed the data to identify key recurring themes. Forty two GPs took part in the study. The presence of fasciculation was the clinical feature that most commonly led to consideration of a potential MND diagnosis. GPs perceived that their role was to make onward referrals rather than attempting to make a diagnosis, and delays in correct diagnosis tended to occur at the specialist level. A quarter of participants had some awareness of the newly-developed tool; most considered it useful, if incorporated into existing systems. While fasciculation is the most common symptom associated with MND, other bulbar, limb or respiratory features, together with progression should be considered. There is a need for further research into how decision-support tools should be designed and provided, in order to best assist GPs with referral decisions. There is also a need for further work at the level of secondary care, in order that referrals made are re-directed appropriately.

Robotic digital subtraction angiography systems within the hybrid operating room.

PubMed

Murayama, Yuichi; Irie, Koreaki; Saguchi, Takayuki; Ishibashi, Toshihiro; Ebara, Masaki; Nagashima, Hiroyasu; Isoshima, Akira; Arakawa, Hideki; Takao, Hiroyuki; Ohashi, Hiroki; Joki, Tatsuhiro; Kato, Masataka; Tani, Satoshi; Ikeuchi, Satoshi; Abe, Toshiaki

2011-05-01

Fully equipped high-end digital subtraction angiography (DSA) within the operating room (OR) environment has emerged as a new trend in the fields of neurosurgery and vascular surgery. To describe initial clinical experience with a robotic DSA system in the hybrid OR. A newly designed robotic DSA system (Artis zeego; Siemens AG, Forchheim, Germany) was installed in the hybrid OR. The system consists of a multiaxis robotic C arm and surgical OR table. In addition to conventional neuroendovascular procedures, the system was used as an intraoperative imaging tool for various neurosurgical procedures such as aneurysm clipping and spine instrumentation. Five hundred one neurosurgical procedures were successfully conducted in the hybrid OR with the robotic DSA. During surgical procedures such as aneurysm clipping and arteriovenous fistula treatment, intraoperative 2-/3-dimensional angiography and C-arm-based computed tomographic images (DynaCT) were easily performed without moving the OR table. Newly developed virtual navigation software (syngo iGuide; Siemens AG) can be used in frameless navigation and in access to deep-seated intracranial lesions or needle placement. This newly developed robotic DSA system provides safe and precise treatment in the fields of endovascular treatment and neurosurgery.

Development and evaluation of low cost game-based balance rehabilitation tool using the Microsoft Kinect sensor.

PubMed

Lange, Belinda; Chang, Chien-Yen; Suma, Evan; Newman, Bradley; Rizzo, Albert Skip; Bolas, Mark

2011-01-01

The use of the commercial video games as rehabilitation tools, such as the Nintendo WiiFit, has recently gained much interest in the physical therapy arena. Motion tracking controllers such as the Nintendo Wiimote are not sensitive enough to accurately measure performance in all components of balance. Additionally, users can figure out how to "cheat" inaccurate trackers by performing minimal movement (e.g. wrist twisting a Wiimote instead of a full arm swing). Physical rehabilitation requires accurate and appropriate tracking and feedback of performance. To this end, we are developing applications that leverage recent advances in commercial video game technology to provide full-body control of animated virtual characters. A key component of our approach is the use of newly available low cost depth sensing camera technology that provides markerless full-body tracking on a conventional PC. The aim of this research was to develop and assess an interactive game-based rehabilitation tool for balance training of adults with neurological injury.

Development of an e-VLBI Data Transport Software Suite with VDIF

NASA Technical Reports Server (NTRS)

Sekido, Mamoru; Takefuji, Kazuhiro; Kimura, Moritaka; Hobiger, Thomas; Kokado, Kensuke; Nozawa, Kentarou; Kurihara, Shinobu; Shinno, Takuya; Takahashi, Fujinobu

2010-01-01

We have developed a software library (KVTP-lib) for VLBI data transmission over the network with the VDIF (VLBI Data Interchange Format), which is the newly proposed standard VLBI data format designed for electronic data transfer over the network. The software package keeps the application layer (VDIF frame) and the transmission layer separate, so that each layer can be developed efficiently. The real-time VLBI data transmission tool sudp-send is an application tool based on the KVTP-lib library. sudp-send captures the VLBI data stream from the VSI-H interface with the K5/VSI PC-board and writes the data to file in standard Linux file format or transmits it to the network using the simple- UDP (SUDP) protocol. Another tool, sudp-recv , receives the data stream from the network and writes the data to file in a specific VLBI format (K5/VSSP, VDIF, or Mark 5B). This software system has been implemented on the Wettzell Tsukuba baseline; evaluation before operational employment is under way.

Development of the public information and communication technology assessment tool.

PubMed

Ripat, Jacquie; Watzke, James; Birch, Gary

2008-09-01

Public information and communication technologies, such as information kiosks, automated banking machines and ticket dispensers, allow people to access services in a convenient and timely manner. However, the development of these technologies has occurred largely without consideration of access by people with disabilities. Inaccessible technical features make operation of a public technology difficult and barriers in the environment create navigational challenges, limiting the opportunity of people with disabilities to use these devices and access the services they provide. This paper describes the development of a tool that individuals, disability advocacy groups, business owners, healthcare providers, and urban planners can use to evaluate the accessibility of public technologies and the surrounding environment. Evaluation results can then be used to develop recommendations and advocate for technical and environmental changes to improve access. Tool development consisted of a review of the literature and key Canadian Standards Association documents, task analysis, and consultation with accessibility experts. Studies of content validity, tool usability, inter-rater and test-retest reliability were conducted in sites across Canada. Accessibility experts verified the content validity of the tool. The current version of the tool has incorporated the findings of a usability study. Initial testing indicated excellent agreement for inter-rater and test-retest reliability scores. Social exclusion can arise when public technologies are not accessible. This newly developed instrument provides detailed information that can be used to advocate for more accessible and inclusive public information and communication technologies.

New diagnostic tool for robotic psychology and robotherapy studies.

PubMed

Libin, Elena; Libin, Alexander

2003-08-01

Robotic psychology and robotherapy as a new research area employs a systematic approach in studying psycho-physiological, psychological, and social aspects of person-robot communication. An analysis of the mechanisms underlying different forms of computer-mediated behavior requires both an adequate methodology and research tools. In the proposed article we discuss the concept, basic principles, structure, and contents of the newly designed Person-Robot Complex Interactive Scale (PRCIS), proposed for the purpose of investigating psychological specifics and therapeutic potentials of multilevel person-robot interactions. Assuming that human-robot communication has symbolic meaning, each interactive pattern evaluated via the newly developed scale is assigned certain psychological value associated with the person's past life experiences, likes and dislikes, emotional, cognitive, and behavioral traits or states. PRCIS includes (1) assessment of a person's individual style of communication with the robotic creature based on direct observations; (2) the participant's evaluation of his/her new experiences with an interactive robot and evaluation of its features, advantages and disadvantages, as well as past experiences with modern technology; and (3) the instructor's overall evaluation of the session.

Correlative 3D imaging of Whole Mammalian Cells with Light and Electron Microscopy

PubMed Central

Murphy, Gavin E.; Narayan, Kedar; Lowekamp, Bradley C.; Hartnell, Lisa M.; Heymann, Jurgen A. W.; Fu, Jing; Subramaniam, Sriram

2011-01-01

We report methodological advances that extend the current capabilities of ion-abrasion scanning electron microscopy (IA–SEM), also known as focused ion beam scanning electron microscopy, a newly emerging technology for high resolution imaging of large biological specimens in 3D. We establish protocols that enable the routine generation of 3D image stacks of entire plastic-embedded mammalian cells by IA-SEM at resolutions of ~10 to 20 nm at high contrast and with minimal artifacts from the focused ion beam. We build on these advances by describing a detailed approach for carrying out correlative live confocal microscopy and IA–SEM on the same cells. Finally, we demonstrate that by combining correlative imaging with newly developed tools for automated image processing, small 100 nm-sized entities such as HIV-1 or gold beads can be localized in SEM image stacks of whole mammalian cells. We anticipate that these methods will add to the arsenal of tools available for investigating mechanisms underlying host-pathogen interactions, and more generally, the 3D subcellular architecture of mammalian cells and tissues. PMID:21907806

Technical Training on High-Order Spectral Analysis and Thermal Anemometry Applications

NASA Technical Reports Server (NTRS)

Maslov, A. A.; Shiplyuk, A. N.; Sidirenko, A. A.; Bountin, D. A.

2003-01-01

The topics of thermal anemometry and high-order spectral analyses were the subject of the technical training. Specifically, the objective of the technical training was to study: (i) the recently introduced constant voltage anemometer (CVA) for high-speed boundary layer; and (ii) newly developed high-order spectral analysis techniques (HOSA). Both CVA and HOSA are relevant tools for studies of boundary layer transition and stability.

Teacher Reporting Attitudes Scale (TRAS): confirmatory and exploratory factor analyses with a Malaysian sample.

PubMed

Choo, Wan Yuen; Walsh, Kerryann; Chinna, Karuthan; Tey, Nai Peng

2013-01-01

The Teacher Reporting Attitude Scale (TRAS) is a newly developed tool to assess teachers' attitudes toward reporting child abuse and neglect. This article reports on an investigation of the factor structure and psychometric properties of the short form Malay version of the TRAS. A self-report cross-sectional survey was conducted with 667 teachers in 14 randomly selected schools in Selangor state, Malaysia. Analyses were conducted in a 3-stage process using both confirmatory (stages 1 and 3) and exploratory factor analyses (stage 2) to test, modify, and confirm the underlying factor structure of the TRAS in a non-Western teacher sample. Confirmatory factor analysis did not support a 3-factor model previously reported in the original TRAS study. Exploratory factor analysis revealed an 8-item, 4-factor structure. Further confirmatory factor analysis demonstrated appropriateness of the 4-factor structure. Reliability estimates for the four factors-commitment, value, concern, and confidence-were moderate. The modified short form TRAS (Malay version) has potential to be used as a simple tool for relatively quick assessment of teachers' attitudes toward reporting child abuse and neglect. Cross-cultural differences in attitudes toward reporting may exist and the transferability of newly developed instruments to other populations should be evaluated.

Improvements in Spectrum's fit to program data tool.

PubMed

Mahiane, Severin G; Marsh, Kimberly; Grantham, Kelsey; Crichlow, Shawna; Caceres, Karen; Stover, John

2017-04-01

The Joint United Nations Program on HIV/AIDS-supported Spectrum software package (Glastonbury, Connecticut, USA) is used by most countries worldwide to monitor the HIV epidemic. In Spectrum, HIV incidence trends among adults (aged 15-49 years) are derived by either fitting to seroprevalence surveillance and survey data or generating curves consistent with program and vital registration data, such as historical trends in the number of newly diagnosed infections or people living with HIV and AIDS related deaths. This article describes development and application of the fit to program data (FPD) tool in Joint United Nations Program on HIV/AIDS' 2016 estimates round. In the FPD tool, HIV incidence trends are described as a simple or double logistic function. Function parameters are estimated from historical program data on newly reported HIV cases, people living with HIV or AIDS-related deaths. Inputs can be adjusted for proportions undiagnosed or misclassified deaths. Maximum likelihood estimation or minimum chi-squared distance methods are used to identify the best fitting curve. Asymptotic properties of the estimators from these fits are used to estimate uncertainty. The FPD tool was used to fit incidence for 62 countries in 2016. Maximum likelihood and minimum chi-squared distance methods gave similar results. A double logistic curve adequately described observed trends in all but four countries where a simple logistic curve performed better. Robust HIV-related program and vital registration data are routinely available in many middle-income and high-income countries, whereas HIV seroprevalence surveillance and survey data may be scarce. In these countries, the FPD tool offers a simpler, improved approach to estimating HIV incidence trends.

Flight test validation of a design procedure for digital autopilots

NASA Technical Reports Server (NTRS)

Bryant, W. H.

1983-01-01

Commercially available general aviation autopilots are currently in transition from an analogue circuit system to a computer implemented digital flight control system. Well known advantages of the digital autopilot include enhanced modes, self-test capacity, fault detection, and greater computational capacity. A digital autopilot's computational capacity can be used to full advantage by increasing the sophistication of the digital autopilot's chief function, stability and control. NASA's Langley Research Center has been pursuing the development of direct digital design tools for aircraft stabilization systems for several years. This effort has most recently been directed towards the development and realization of multi-mode digital autopilots for GA aircraft, conducted under a SPIFR-related program called the General Aviation Terminal Operations Research (GATOR) Program. This presentation focuses on the implementation and testing of a candidate multi-mode autopilot designed using these newly developed tools.

Building Efficiency Evaluation and Uncertainty Analysis with DOE's Asset Score Preview

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

None

2016-08-12

Building Energy Asset Score Tool, developed by the U.S. Department of Energy (DOE), is a program to encourage energy efficiency improvement by helping building owners and managers assess a building's energy-related systems independent of operations and maintenance. Asset Score Tool uses a simplified EnergyPlus model to provide an assessment of building systems, through minimum user inputs of basic building characteristics. Asset Score Preview is a newly developed option that allows users to assess their building's systems and the potential value of a more in-depth analysis via an even more simplified approach. This methodology provides a preliminary approach to estimating amore » building's energy efficiency and potential for improvement. This paper provides an overview of the methodology used for the development of Asset Score Preview and the scoring methodology.« less

Audio signal analysis for tool wear monitoring in sheet metal stamping

NASA Astrophysics Data System (ADS)

Ubhayaratne, Indivarie; Pereira, Michael P.; Xiang, Yong; Rolfe, Bernard F.

2017-02-01

Stamping tool wear can significantly degrade product quality, and hence, online tool condition monitoring is a timely need in many manufacturing industries. Even though a large amount of research has been conducted employing different sensor signals, there is still an unmet demand for a low-cost easy to set up condition monitoring system. Audio signal analysis is a simple method that has the potential to meet this demand, but has not been previously used for stamping process monitoring. Hence, this paper studies the existence and the significance of the correlation between emitted sound signals and the wear state of sheet metal stamping tools. The corrupting sources generated by the tooling of the stamping press and surrounding machinery have higher amplitudes compared to that of the sound emitted by the stamping operation itself. Therefore, a newly developed semi-blind signal extraction technique was employed as a pre-processing technique to mitigate the contribution of these corrupting sources. The spectral analysis results of the raw and extracted signals demonstrate a significant qualitative relationship between wear progression and the emitted sound signature. This study lays the basis for employing low-cost audio signal analysis in the development of a real-time industrial tool condition monitoring system.

Validity and reliability of smartphone magnetometer-based goniometer evaluation of shoulder abduction--A pilot study.

PubMed

Johnson, Linda B; Sumner, Sean; Duong, Tina; Yan, Posu; Bajcsy, Ruzena; Abresch, R Ted; de Bie, Evan; Han, Jay J

2015-12-01

Goniometers are commonly used by physical therapists to measure range-of-motion (ROM) in the musculoskeletal system. These measurements are used to assist in diagnosis and to help monitor treatment efficacy. With newly emerging technologies, smartphone-based applications are being explored for measuring joint angles and movement. This pilot study investigates the intra- and inter-rater reliability as well as concurrent validity of a newly-developed smartphone magnetometer-based goniometer (MG) application for measuring passive shoulder abduction in both sitting and supine positions, and compare against the traditional universal goniometer (UG). This is a comparative study with repeated measurement design. Three physical therapists utilized both the smartphone MG and a traditional UG to measure various angles of passive shoulder abduction in a healthy subject, whose shoulder was positioned in eight different positions with pre-determined degree of abduction while seated or supine. Each therapist was blinded to the measured angles. Concordance correlation coefficients (CCCs), Bland-Altman plotting methods, and Analysis of Variance (ANOVA) were used for statistical analyses. Both traditional UG and smartphone MG were reliable in repeated measures of standardized joint angle positions (average CCC > 0.997) with similar variability in both measurement tools (standard deviation (SD) ± 4°). Agreement between the UG and MG measurements was greater than 0.99 in all positions. Our results show that the smartphone MG has equivalent reliability compared to the traditional UG when measuring passive shoulder abduction ROM. With concordant measures and comparable reliability to the UG, the newly developed MG application shows potential as a useful tool to assess joint angles. Published by Elsevier Ltd.

Evaluation of an existing screening tool for psoriatic arthritis in people with psoriasis and the development of a new instrument: the Psoriasis Epidemiology Screening Tool (PEST) questionnaire.

PubMed

Ibrahim, G H; Buch, M H; Lawson, C; Waxman, R; Helliwell, P S

2009-01-01

To evaluate an existing tool (the Swedish modification of the Psoriasis Assessment Questionnaire) and to develop a new instrument to screen for psoriatic arthritis in people with psoriasis. The starting point was a community-based survey of people with psoriasis using questionnaires developed from the literature. Selected respondents were examined and additional known cases of psoriatic arthritis were included in the analysis. The new instrument was developed using univariate statistics and a logistic regression model, comparing people with and without psoriatic arthritis. The instruments were compared using receiver operating curve (ROC) curve analysis. 168 questionnaires were returned (response rate 27%) and 93 people attended for examination (55% of questionnaire respondents). Of these 93, twelve were newly diagnosed with psoriatic arthritis during this study. These 12 were supplemented by 21 people with known psoriatic arthritis. Just 5 questions were found to be significant predictors of psoriatic arthritis in this population. Figures for sensitivity and specificity were 0.92 and 0.78 respectively, an improvement on the Alenius tool (sensitivity and specificity, 0.63 and 0.72 respectively). A new screening tool for identifying people with psoriatic arthritis has been developed. Five simple questions demonstrated good sensitivity and specificity in this population but further validation is required.

Performance profiling for brachytherapy applications

NASA Astrophysics Data System (ADS)

Choi, Wonqook; Cho, Kihyeon; Yeo, Insung

2018-05-01

In many physics applications, a significant amount of software (e.g. R, ROOT and Geant4) is developed on novel computing architectures, and much effort is expended to ensure the software is efficient in terms of central processing unit (CPU) time and memory usage. Profiling tools are used during the evaluation process to evaluate the efficiency; however, few such tools are able to accommodate low-energy physics regions. To address this limitation, we developed a low-energy physics profiling system in Geant4 to profile the CPU time and memory of software applications in brachytherapy applications. This paper describes and evaluates specific models that are applied to brachytherapy applications in Geant4, such as QGSP_BIC_LIV, QGSP_BIC_EMZ, and QGSP_BIC_EMY. The physics range in this tool allows it to be used to generate low energy profiles in brachytherapy applications. This was a limitation in previous studies, which caused us to develop a new profiling tool that supports profiling in the MeV range, in contrast to the TeV range that is supported by existing high-energy profiling tools. In order to easily compare the profiling results between low-energy and high-energy modes, we employed the same software architecture as that in the SimpliCarlo tool developed at the Fermilab National Accelerator Laboratory (FNAL) for the Large Hadron Collider (LHC). The results show that the newly developed profiling system for low-energy physics (less than MeV) complements the current profiling system used for high-energy physics (greater than TeV) applications.

Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

PubMed Central

Cuesta, Jose Antonio; Drake, Pilar; Macpherson, Enrique; Bernatchez, Louis

2017-01-01

Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations. PMID:28439464

Educational Research in the United States: A Survey of Pre-K-12 Teachers' Perceptions Regarding the Purpose, Conceptions, Use, Impact, and Dissemination

ERIC Educational Resources Information Center

Mahoney, Shawn

2013-01-01

The purpose of this survey study was to collect data from pre-K-12 educators in the U.S. regarding their perceptions of the purpose, conceptions, use, impact, and results of educational research. The survey tool was based on existing questionnaires and case studies in the literature, as well as newly developed items. 3,908 educators in a database…

Modeling Tool for Decision Support during Early Days of an Anthrax Event.

PubMed

Rainisch, Gabriel; Meltzer, Martin I; Shadomy, Sean; Bower, William A; Hupert, Nathaniel

2017-01-01

Health officials lack field-implementable tools for forecasting the effects that a large-scale release of Bacillus anthracis spores would have on public health and hospitals. We created a modeling tool (combining inhalational anthrax caseload projections based on initial case reports, effects of variable postexposure prophylaxis campaigns, and healthcare facility surge capacity requirements) to project hospitalizations and casualties from a newly detected inhalation anthrax event, and we examined the consequences of intervention choices. With only 3 days of case counts, the model can predict final attack sizes for simulated Sverdlovsk-like events (1979 USSR) with sufficient accuracy for decision making and confirms the value of early postexposure prophylaxis initiation. According to a baseline scenario, hospital treatment volume peaks 15 days after exposure, deaths peak earlier (day 5), and recovery peaks later (day 23). This tool gives public health, hospital, and emergency planners scenario-specific information for developing quantitative response plans for this threat.

Judgment skills, a missing component in health literacy: development of a tool for asthma patients in the Italian-speaking region of Switzerland.

PubMed

Moreno Londoño, Ana Maria; Schulz, Peter J

2014-04-01

Health literacy has been recognized as an important factor influencing health behaviors and health outcomes. However, its definition is still evolving, and the tools available for its measurement are limited in scope. Based on the conceptualization of health literacy within the Health Empowerment Model, the present study developed and validated a tool to assess patient's health knowledge use, within the context of asthma self-management. A review of scientific literature on asthma self-management, and several interviews with pulmonologists and asthma patients were conducted. From these, 19 scenarios with 4 response options each were drafted and assembled in a scenario-based questionnaire. Furthermore, a three round Delphi procedure was carried out, to validate the tool with the participation of 12 specialists in lung diseases. The face and content validity of the tool were achieved by face-to-face interviews with 2 pulmonologists and 5 patients. Consensus among the specialists on the adequacy of the response options was achieved after the three round Delphi procedure. The final tool has a 0.97 intra-class correlation coefficient (ICC), indicating a strong level of agreement among experts on the ratings of the response options. The ICC for single scenarios, range from 0.92 to 0.99. The newly developed tool provides a final score representing patient's health knowledge use, based on the specialist's consensus. This tool contributes to enriching the measurement of a more advanced health literacy dimension.

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

PubMed

Rauscher, Gilda; Simko, Ivan

2013-01-22

Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes

PubMed Central

2013-01-01

Background Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Results Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. Conclusions The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes. PMID:23339733

XML schemas for common bioinformatic data types and their application in workflow systems

PubMed Central

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

Investigating the need for clinicians to use tablet computers with a newly envisioned electronic health record.

PubMed

Saleem, Jason J; Savoy, April; Etherton, Gale; Herout, Jennifer

2018-02-01

The Veterans Health Administration (VHA) has deployed a large number of tablet computers in the last several years. However, little is known about how clinicians may use these devices with a newly planned Web-based electronic health record (EHR), as well as other clinical tools. The objective of this study was to understand the types of use that can be expected of tablet computers versus desktops. Semi-structured interviews were conducted with 24 clinicians at a Veterans Health Administration (VHA) Medical Center. An inductive qualitative analysis resulted in findings organized around recurrent themes of: (1) Barriers, (2) Facilitators, (3) Current Use, (4) Anticipated Use, (5) Patient Interaction, and (6) Connection. Our study generated several recommendations for the use of tablet computers with new health information technology tools being developed. Continuous connectivity for the mobile device is essential to avoid interruptions and clinician frustration. Also, making a physical keyboard available as an option for the tablet was a clear desire from the clinicians. Larger tablets (e.g., regular size iPad as compared to an iPad mini) were preferred. Being able to use secure messaging tools with the tablet computer was another consistent finding. Finally, more simplicity is needed for accessing patient data on mobile devices, while balancing the important need for adequate security. Published by Elsevier B.V.

Evaluation of a computerized aid for creating human behavioral representations of human-computer interaction.

PubMed

Williams, Kent E; Voigt, Jeffrey R

2004-01-01

The research reported herein presents the results of an empirical evaluation that focused on the accuracy and reliability of cognitive models created using a computerized tool: the cognitive analysis tool for human-computer interaction (CAT-HCI). A sample of participants, expert in interacting with a newly developed tactical display for the U.S. Army's Bradley Fighting Vehicle, individually modeled their knowledge of 4 specific tasks employing the CAT-HCI tool. Measures of the accuracy and consistency of task models created by these task domain experts using the tool were compared with task models created by a double expert. The findings indicated a high degree of consistency and accuracy between the different "single experts" in the task domain in terms of the resultant models generated using the tool. Actual or potential applications of this research include assessing human-computer interaction complexity, determining the productivity of human-computer interfaces, and analyzing an interface design to determine whether methods can be automated.

Asthma 1-2-3: a low literacy multimedia tool to educate African American adults about asthma.

PubMed

Sobel, Rina M; Paasche-Orlow, Michael K; Waite, Katherine R; Rittner, Sarah S; Wilson, Elizabeth A H; Wolf, Michael S

2009-08-01

Asthma 1-2-3 is a newly-developed low-literacy multimedia education tool designed to promote asthma self-care concepts among African American adults. An expert panel (n = 10) informed content development for the tool. The video script and storyboard imagery were shown to 30 African Americans recruited from the American Lung Association, whose reactions and comments guided further revisions. The final version was pilot tested in three diverse community settings in Chicago to determine the efficacy of Asthma 1-2-3 at improving patient understanding of asthma and its symptoms. In all, 130 adults participated in the pilot test. Knowledge scores significantly improved from pretest to posttest following presentation of the developed tool for subjects across all literacy levels (Pretest: Mean = 4.2 [SD = 1.6]; Posttest: M = 6.8 [SD = 2.0], P < 0.001). Symptom pathophysiology concepts were the least understood. Individuals with low literacy had less total knowledge score gains compared to those with marginal and adequate literacy (1.8, 2.6, and 3.2 respectively; P = 0.002). The multimedia tool significantly improved understanding of asthma. Individuals with limited literacy may require additional instruction, repeated viewing, or added tangible cues (i.e. supplementary print materials) to support knowledge retention. In general, feedback from the target population was particularly helpful in the development of the tool and its initial evaluation, and should be considered as a necessary step in the creation of other patient education materials.

Cellular automata and its applications in protein bioinformatics.

PubMed

Xiao, Xuan; Wang, Pu; Chou, Kuo-Chen

2011-09-01

With the explosion of protein sequences generated in the postgenomic era, it is highly desirable to develop high-throughput tools for rapidly and reliably identifying various attributes of uncharacterized proteins based on their sequence information alone. The knowledge thus obtained can help us timely utilize these newly found protein sequences for both basic research and drug discovery. Many bioinformatics tools have been developed by means of machine learning methods. This review is focused on the applications of a new kind of science (cellular automata) in protein bioinformatics. A cellular automaton (CA) is an open, flexible and discrete dynamic model that holds enormous potentials in modeling complex systems, in spite of the simplicity of the model itself. Researchers, scientists and practitioners from different fields have utilized cellular automata for visualizing protein sequences, investigating their evolution processes, and predicting their various attributes. Owing to its impressive power, intuitiveness and relative simplicity, the CA approach has great potential for use as a tool for bioinformatics.

Neural Cell Chip Based Electrochemical Detection of Nanotoxicity

PubMed Central

Kafi, Md. Abdul; Cho, Hyeon-Yeol; Choi, Jeong Woo

2015-01-01

Development of a rapid, sensitive and cost-effective method for toxicity assessment of commonly used nanoparticles is urgently needed for the sustainable development of nanotechnology. A neural cell with high sensitivity and conductivity has become a potential candidate for a cell chip to investigate toxicity of environmental influences. A neural cell immobilized on a conductive surface has become a potential tool for the assessment of nanotoxicity based on electrochemical methods. The effective electrochemical monitoring largely depends on the adequate attachment of a neural cell on the chip surfaces. Recently, establishment of integrin receptor specific ligand molecules arginine-glycine-aspartic acid (RGD) or its several modifications RGD-Multi Armed Peptide terminated with cysteine (RGD-MAP-C), C(RGD)4 ensure farm attachment of neural cell on the electrode surfaces either in their two dimensional (dot) or three dimensional (rod or pillar) like nano-scale arrangement. A three dimensional RGD modified electrode surface has been proven to be more suitable for cell adhesion, proliferation, differentiation as well as electrochemical measurement. This review discusses fabrication as well as electrochemical measurements of neural cell chip with particular emphasis on their use for nanotoxicity assessments sequentially since inception to date. Successful monitoring of quantum dot (QD), graphene oxide (GO) and cosmetic compound toxicity using the newly developed neural cell chip were discussed here as a case study. This review recommended that a neural cell chip established on a nanostructured ligand modified conductive surface can be a potential tool for the toxicity assessments of newly developed nanomaterials prior to their use on biology or biomedical technologies. PMID:28347059

Concentration of carp edema virus (CEV) DNA in koi tissues affected by koi sleepy disease (KSD).

PubMed

Adamek, Mikolaj; Jung-Schroers, Verena; Hellmann, John; Teitge, Felix; Bergmann, Sven Michael; Runge, Martin; Kleingeld, Dirk Willem; Way, Keith; Stone, David Michael; Steinhagen, Dieter

2016-05-26

Carp edema virus (CEV), the causative agent of 'koi sleepy disease' (KSD), appears to be spreading worldwide and to be responsible for losses in koi, ornamental varieties of the common carp Cyprinus carpio. Clinical signs of KSD include lethargic behaviour, swollen gills, sunken eyes and skin alterations and can easily be mistaken for other diseases, such as infection with cyprinid herpesvirus 3 (CyHV-3). To improve the future diagnosis of CEV infection and to provide a tool to better explore the relationship between viral load and clinical disease, we developed a specific quantitative PCR (qPCR) for strains of the virus known to infect koi carp. In samples from several clinically affected koi, CEV-specific DNA was present in a range from 1 to 2,046,000 copies, with a mean of 129,982 copies and a median of 45 copies per 250 ng of isolated DNA, but virus DNA could not be detected in all clinically affected koi. A comparison of the newly developed qPCR, which is based on a dual-labelled probe, to an existing end-point PCR procedure revealed higher specificity and sensitivity of the qPCR and demonstrated that the new protocol could improve CEV detection in koi. In addition to improved diagnosis, the newly developed qPCR test would be a useful research tool. For example, studies on the pathobiology of CEV could employ controlled infection experiments in which the development of clinical signs could be examined in parallel with a quantitative determination of virus load.

A newly developed tool for intra-tracheal temperature and humidity assessment in laryngectomized individuals: the Airway Climate Explorer (ACE)

PubMed Central

Zuur, J. K.; Muller, S. H.; de Jongh, F. H. C.; van der Horst, M. J.; Shehata, M.; van Leeuwen, J.; Sinaasappel, M.

2007-01-01

The aim of this study is to develop a postlaryngectomy airway climate explorer (ACE) for assessment of intratracheal temperature and humidity and of influence of heat and moisture exchangers (HMEs). Engineering goals were within-device condensation prevention and fast response time characteristics. The ACE consists of a small diameter, heated air-sampling catheter connected to a heated sensor house, containing a humidity sensor. Air is sucked through the catheter by a controlled-flow pump. Validation was performed in a climate chamber using a calibrated reference sensor and in a two-flow system. Additionally, the analyser was tested in vivo. Over the clinically relevant range of humidity values (5–42 mg H2O/l air) the sensor output highly correlates with the reference sensor readings (R2 > 0.99). The 1–1/e response times are all <0.5 s. A first in vivo pilot measurement was successful. The newly developed, verified, fast-responding ACE is suitable for postlaryngectomy airway climate assessment. PMID:17629761

Development of materials for the rapid manufacture of die cast tooling

NASA Astrophysics Data System (ADS)

Hardro, Peter Jason

The focus of this research is to develop a material composition that can be processed by rapid prototyping (RP) in order to produce tooling for the die casting process. Where these rapidly produced tools will be superior to traditional tooling production methods by offering one or more of the following advantages: reduced tooling cost, shortened tooling creation time, reduced man-hours for tool creation, increased tool life, and shortened die casting cycle time. By utilizing RP's additive build process and vast material selection, there was a prospect that die cast tooling may be produced quicker and with superior material properties. To this end, the material properties that influence die life and cycle time were determined, and a list of materials that fulfill these "optimal" properties were highlighted. Physical testing was conducted in order to grade the processability of each of the material systems and to optimize the manufacturing process for the downselected material system. Sample specimens were produced and microscopy techniques were utilized to determine a number of physical properties of the material system. Additionally, a benchmark geometry was selected and die casting dies were produced from traditional tool materials (H13 steel) and techniques (machining) and from the newly developed materials and RP techniques (selective laser sintering (SLS) and laser engineered net shaping (LENS)). Once the tools were created, a die cast alloy was selected and a preset number of parts were shot into each tool. During tool creation, the manufacturing time and cost was closely monitored and an economic model was developed to compare traditional tooling to RP tooling. This model allows one to determine, in the early design stages, when it is advantageous to implement RP tooling and when traditional tooling would be best. The results of the physical testing and economic analysis has shown that RP tooling is able to achieve a number of the research objectives, namely, reduce tooling cost, shorten tooling creation time, and reduce the man-hours needed for tool creation. Though identifying the appropriate time to use RP tooling appears to be the most important aspect in achieving successful implementation.

State of the art techniques for preservation and reuse of hard copy electrocardiograms.

PubMed

Lobodzinski, Suave M; Teppner, Ulrich; Laks, Michael

2003-01-01

Baseline examinations and periodic reexaminations in longitudinal population studies, together with ongoing surveillance for morbidity and mortality, provide unique opportunities for seeking ways to enhance the value of electrocardiography (ECG) as an inexpensive and noninvasive tool for prognosis and diagnosis. We used newly developed optical ECG waveform recognition (OEWR) technique capable of extracting raw waveform data from legacy hard copy ECG recording. Hardcopy ECG recordings were scanned and processed by the OEWR algorithm. The extracted ECG datasets were formatted into a newly proposed, vendor-neutral, ECG XML data format. Oracle database was used as a repository for ECG records in XML format. The proposed technique for XML encapsulation of OEWR processed hard copy records resulted in an efficient method for inclusion of paper ECG records into research databases, thus providing their preservation, reuse and accession.

Remote Patient Management in Automated Peritoneal Dialysis: A Promising New Tool.

PubMed

Drepper, Valérie Jotterand; Martin, Pierre-Yves; Chopard, Catherine Stoermann; Sloand, James A

2018-01-01

Remote patient management (RPM) has the potential to help clinicians detect early issues, allowing intervention prior to development of more significant problems. A 23-year-old end-stage kidney disease patient required urgent start of renal replacement therapy. A newly available automated peritoneal dialysis (APD) RPM system with cloud-based connectivity was implemented in her care. Pre-defined RPM threshold parameters were set to identify clinically relevant issues. Red flag dashboard alerts heralded prolonged drain times leading to clinical evaluation with subsequent diagnosis of and surgical repositioning for catheter displacement, although it took several days for newly-RPM-exposed staff to recognize this issue. Post-PD catheter repositioning, drain times were again normal as indicated by disappearance of flag alerts and unremarkable cycle volume profiles. Identification of < 90% adherence to prescribed PD therapy was then documented with the RPM system, alerting the clinical staff to address this important issue given its association with significant negative clinical outcomes. Healthcare providers face a "learning curve" to effect optimal utilization of the RPM tool. Larger scale observational studies will determine the impact of RPM on APD technique survival and resource utilization. Copyright © 2018 International Society for Peritoneal Dialysis.

A patient and public involvement (PPI) toolkit for meaningful and flexible involvement in clinical trials - a work in progress.

PubMed

Bagley, Heather J; Short, Hannah; Harman, Nicola L; Hickey, Helen R; Gamble, Carrol L; Woolfall, Kerry; Young, Bridget; Williamson, Paula R

2016-01-01

Funders of research are increasingly requiring researchers to involve patients and the public in their research. Patient and public involvement (PPI) in research can potentially help researchers make sure that the design of their research is relevant, that it is participant friendly and ethically sound. Using and sharing PPI resources can benefit those involved in undertaking PPI, but existing PPI resources are not used consistently and this can lead to duplication of effort. This paper describes how we are developing a toolkit to support clinical trials teams in a clinical trials unit. The toolkit will provide a key 'off the shelf' resource to support trial teams with limited resources, in undertaking PPI. Key activities in further developing and maintaining the toolkit are to: ● listen to the views and experience of both research teams and patient and public contributors who use the tools; ● modify the tools based on our experience of using them; ● identify the need for future tools; ● update the toolkit based on any newly identified resources that come to light; ● raise awareness of the toolkit and ● work in collaboration with others to either develop or test out PPI resources in order to reduce duplication of work in PPI. Background Patient and public involvement (PPI) in research is increasingly a funder requirement due to the potential benefits in the design of relevant, participant friendly, ethically sound research. The use and sharing of resources can benefit PPI, but available resources are not consistently used leading to duplication of effort. This paper describes a developing toolkit to support clinical trials teams to undertake effective and meaningful PPI. Methods The first phase in developing the toolkit was to describe which PPI activities should be considered in the pathway of a clinical trial and at what stage these activities should take place. This pathway was informed through review of the type and timing of PPI activities within trials coordinated by the Clinical Trials Research Centre and previously described areas of potential PPI impact in trials. In the second phase, key websites around PPI and identification of resources opportunistically, e.g. in conversation with other trialists or social media, were used to identify resources. Tools were developed where gaps existed. Results A flowchart was developed describing PPI activities that should be considered in the clinical trial pathway and the point at which these activities should happen. Three toolkit domains were identified: planning PPI; supporting PPI; recording and evaluating PPI. Four main activities and corresponding tools were identified under the planning for PPI: developing a plan; identifying patient and public contributors; allocating appropriate costs; and managing expectations. In supporting PPI, tools were developed to review participant information sheets. These tools, which require a summary of potential trial participant characteristics and circumstances help to clarify requirements and expectations of PPI review. For recording and evaluating PPI, the planned PPI interventions should be monitored in terms of impact, and a tool to monitor public contributor experience is in development. Conclusions This toolkit provides a developing 'off the shelf' resource to support trial teams with limited resources in undertaking PPI. Key activities in further developing and maintaining the toolkit are to: listen to the views and experience of both research teams and public contributors using the tools, to identify the need for future tools, to modify tools based on experience of their use; to update the toolkit based on any newly identified resources that come to light; to raise awareness of the toolkit and to work in collaboration with others to both develop and test out PPI resources in order to reduce duplication of work in PPI.

DNA-binding specificity prediction with FoldX.

PubMed

Nadra, Alejandro D; Serrano, Luis; Alibés, Andreu

2011-01-01

With the advent of Synthetic Biology, a field between basic science and applied engineering, new computational tools are needed to help scientists reach their goal, their design, optimizing resources. In this chapter, we present a simple and powerful method to either know the DNA specificity of a wild-type protein or design new specificities by using the protein design algorithm FoldX. The only basic requirement is having a good resolution structure of the complex. Protein-DNA interaction design may aid the development of new parts designed to be orthogonal, decoupled, and precise in its target. Further, it could help to fine-tune the systems in terms of specificity, discrimination, and binding constants. In the age of newly developed devices and invented systems, computer-aided engineering promises to be an invaluable tool. Copyright © 2011 Elsevier Inc. All rights reserved.

The development and evaluation of the Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP©) for use by healthcare staff.

PubMed

McCarthy, H; Dixon, M; Crabtree, I; Eaton-Evans, M J; McNulty, H

2012-08-01

The early identification of malnutrition and nutrition risk through nutrition screening is common practice in adult clinical care but, in children, this has been hampered by the lack of an appropriate nutrition screening tool. The present study aimed to develop and evaluate a simple, child-specific nutrition screening tool for administration by non-nutrition healthcare professionals. In a two-phase observational study, significant predictors of nutrition risk were identified using a structured questionnaire. These were then combined to produce a nutrition screening tool. For evaluation purposes, the reliability, sensitivity and specificity of the newly-developed Screening Tool for the Assessment of Malnutrition in Paediatrics (STAMP(©)) were estimated by comparing the classification of nutrition risk using the tool with that determined by a full nutritional assessment by a registered dietitian. A total of 122 children were recruited for development phase and a separate cohort of 238 children was recruited for the evaluation phase. Low percentile weight for age, reported weight loss, discrepancy between weight and height percentile and recently changed appetite were all identified as predictors of nutrition risk. These predictors, together with the expected nutrition risk of clinical diagnoses, were combined to produce STAMP(©). Evaluation of STAMP(©) demonstrated fair to moderate reliability in identifying nutrition risk compared to the nutrition risk classification determined by a registered dietitian (κ = 0.541; 95% confidence interval = 0.461-0.621). Sensitivity and specificity were estimated at 70% (51-84%) and 91% (86-94%), respectively. The present study describes the development and evaluation of a new nutrition screening tool specifically for use in a UK general paediatric inpatient population. © 2012 The Authors. Journal of Human Nutrition and Dietetics © 2012 The British Dietetic Association Ltd.

Inferring transposons activity chronology by TRANScendence - TEs database and de-novo mining tool.

PubMed

Startek, Michał Piotr; Nogły, Jakub; Gromadka, Agnieszka; Grzebelus, Dariusz; Gambin, Anna

2017-10-16

The constant progress in sequencing technology leads to ever increasing amounts of genomic data. In the light of current evidence transposable elements (TEs for short) are becoming useful tools for learning about the evolution of host genome. Therefore the software for genome-wide detection and analysis of TEs is of great interest. Here we describe the computational tool for mining, classifying and storing TEs from newly sequenced genomes. This is an online, web-based, user-friendly service, enabling users to upload their own genomic data, and perform de-novo searches for TEs. The detected TEs are automatically analyzed, compared to reference databases, annotated, clustered into families, and stored in TEs repository. Also, the genome-wide nesting structure of found elements are detected and analyzed by new method for inferring evolutionary history of TEs. We illustrate the functionality of our tool by performing a full-scale analyses of TE landscape in Medicago truncatula genome. TRANScendence is an effective tool for the de-novo annotation and classification of transposable elements in newly-acquired genomes. Its streamlined interface makes it well-suited for evolutionary studies.

The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit.

PubMed

Murugan, Karthik; Babu, Kesavan; Sundaresan, Ramya; Rajan, Rakhi; Sashital, Dipali G

2017-10-05

CRISPR-Cas systems defend prokaryotes against bacteriophages and mobile genetic elements and serve as the basis for revolutionary tools for genetic engineering. Class 2 CRISPR-Cas systems use single Cas endonucleases paired with guide RNAs to cleave complementary nucleic acid targets, enabling programmable sequence-specific targeting with minimal machinery. Recent discoveries of previously unidentified CRISPR-Cas systems have uncovered a deep reservoir of potential biotechnological tools beyond the well-characterized Type II Cas9 systems. Here we review the current mechanistic understanding of newly discovered single-protein Cas endonucleases. Comparison of these Cas effectors reveals substantial mechanistic diversity, underscoring the phylogenetic divergence of related CRISPR-Cas systems. This diversity has enabled further expansion of CRISPR-Cas biotechnological toolkits, with wide-ranging applications from genome editing to diagnostic tools based on various Cas endonuclease activities. These advances highlight the exciting prospects for future tools based on the continually expanding set of CRISPR-Cas systems. Copyright © 2017 Elsevier Inc. All rights reserved.

Engineering Education Development to Enhance Human Skill in DENSO

NASA Astrophysics Data System (ADS)

Isogai, Emiko; Nuka, Takeji

Importance of human skills such as communication or instruction capability to their staff members has recently been highlighted in a workplace, due to decreasing opportunity of face-to-face communication between supervisors and their staff, or Instruction capability through OJT (On the Job Training) . Currently, communication skills are being reinforced mainly through OJT at DENSO. Therefore, as part of supplemental support tools, DENSO has established comprehensive engineers training program on off-JT basis for developing human skills, covering from newly employeed enginners up to managerial class since 2003. This paper describes education activities and reports the results.

Assembly of cucumber (Cucumis sativus L.) somaclones

NASA Astrophysics Data System (ADS)

Skarzyńska, Agnieszka; Kuśmirek, Wiktor; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Nowak, Robert M.

2017-08-01

The development of next generation sequencing opens the possibility of using sequencing in various plant studies, such as finding structural changes and small polymorphisms between species and within them. Most analyzes rely on genomic sequences and it is crucial to use well-assembled genomes of high quality and completeness. Herein we compare commonly available programs for genomic assembling and newly developed software - dnaasm. Assemblies were tested on cucumber (Cucumis sativus L.) lines obtained by in vitro regeneration (somaclones), showing different phenotypes. Obtained results shows that dnaasm assembler is a good tool for short read assembly, which allows obtaining genomes of high quality and completeness.

Development of a SCALE Tool for Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations

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

Perfetti, Christopher M; Rearden, Bradley T

2013-01-01

Two methods for calculating eigenvalue sensitivity coefficients in continuous-energy Monte Carlo applications were implemented in the KENO code within the SCALE code package. The methods were used to calculate sensitivity coefficients for several criticality safety problems and produced sensitivity coefficients that agreed well with both reference sensitivities and multigroup TSUNAMI-3D sensitivity coefficients. The newly developed CLUTCH method was observed to produce sensitivity coefficients with high figures of merit and low memory requirements, and both continuous-energy sensitivity methods met or exceeded the accuracy of the multigroup TSUNAMI-3D calculations.

Development of Waypoint Planning Tool in Response to NASA Field Campaign Challenges

NASA Technical Reports Server (NTRS)

He, Matt; Hardin, Danny; Conover, Helen; Graves, Sara; Meyer, Paul; Blakeslee, Richard; Goodman, Michael

2012-01-01

Airborne real time observations are a major component of NASA's Earth Science research and satellite ground validation studies. For mission scientists, planning a research aircraft mission within the context of meeting the science objectives is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. Multiple aircrafts are often involved in NASA field campaigns. The coordination of the aircrafts with satellite overpasses, other airplanes and the constantly evolving, dynamic weather conditions often determines the success of the campaign. A flight planning tool is needed to provide situational awareness information to the mission scientists, and help them plan and modify the flight tracks. Scientists at the University of Alabama-Huntsville and the NASA Marshall Space Flight Center developed the Waypoint Planning Tool, an interactive software tool that enables scientists to develop their own flight plans (also known as waypoints) with point -and-click mouse capabilities on a digital map filled with real time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analysis during and after each campaign helped identify both issues and new requirements, and initiated the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities, to Google Earth Plugin and Java Web Start/Applet on web platform, and to the rising open source GIS tools with new JavaScript frameworks, the Waypoint Planning Tool has entered its third phase of technology advancement. The newly innovated, cross ]platform, modular designed JavaScript ]controlled Way Point Tool is planned to be integrated with NASA Airborne Science Mission Tool Suite. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientists reach their mission objectives. This presentation will discuss the development processes of the Waypoint Planning Tool in responding to field campaign challenges, identify new information technologies, and describe the capabilities and features of the Waypoint Planning Tool with the real time aspect, interactive nature, and the resultant benefits to the airborne science community.

Development of Way Point Planning Tool in Response to NASA Field Campaign Challenges

NASA Astrophysics Data System (ADS)

He, M.; Hardin, D. M.; Conover, H.; Graves, S. J.; Meyer, P.; Blakeslee, R. J.; Goodman, M. L.

2012-12-01

Airborne real time observations are a major component of NASA's Earth Science research and satellite ground validation studies. For mission scientists, planning a research aircraft mission within the context of meeting the science objectives is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. Multiple aircrafts are often involved in NASA field campaigns. The coordination of the aircrafts with satellite overpasses, other airplanes and the constantly evolving, dynamic weather conditions often determines the success of the campaign. A flight planning tool is needed to provide situational awareness information to the mission scientists, and help them plan and modify the flight tracks. Scientists at the University of Alabama-Huntsville and the NASA Marshall Space Flight Center developed the Waypoint Planning Tool, an interactive software tool that enables scientists to develop their own flight plans (also known as waypoints) with point-and-click mouse capabilities on a digital map filled with real time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analysis during and after each campaign helped identify both issues and new requirements, and initiated the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities, to Google Earth Plugin and Java Web Start/Applet on web platform, and to the rising open source GIS tools with new JavaScript frameworks, the Waypoint Planning Tool has entered its third phase of technology advancement. The newly innovated, cross-platform, modular designed JavaScript-controlled Way Point Tool is planned to be integrated with NASA Airborne Science Mission Tool Suite. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientists reach their mission objectives. This presentation will discuss the development processes of the Waypoint Planning Tool in responding to field campaign challenges, identify new information technologies, and describe the capabilities and features of the Waypoint Planning Tool with the real time aspect, interactive nature, and the resultant benefits to the airborne science community.

From Chaos to Content: An Integrated Approach to Government Web Sites

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

Demuth, Nora H.; Knudson, Christa K.

2005-01-03

The web development team of the Environmental Technology Directorate (ETD) at the U.S. Department of Energy’s Pacific Northwest National Laboratory (PNNL) redesigned the ETD website as a database-driven system, powered by the newly designed ETD Common Information System (ETD-CIS). The ETD website was redesigned in response to an analysis that showed the previous ETD websites were inefficient, costly, and lacking in a consistent focus. Redesigned and newly created websites based on a new ETD template provide a consistent image, meet or exceed accessibility standards, and are linked through a common database. The protocols used in developing the ETD website supportmore » integration of further organizational sites and facilitate internal use by staff and training on ETD website development and maintenance. Other PNNL organizations have approached the ETD web development team with an interest in applying the methods established by the ETD system. The ETD system protocol could potentially be used by other DOE laboratories to improve their website efficiency and content focus. “The tools by which we share science information must be as extraordinary as the information itself.[ ]” – DOE Science Director Raymond Orbach« less

Evaluation of the reliability, usability, and applicability of AMSTAR, AMSTAR 2, and ROBIS: protocol for a descriptive analytic study.

PubMed

Gates, Allison; Gates, Michelle; Duarte, Gonçalo; Cary, Maria; Becker, Monika; Prediger, Barbara; Vandermeer, Ben; Fernandes, Ricardo M; Pieper, Dawid; Hartling, Lisa

2018-06-13

Systematic reviews (SRs) of randomised controlled trials (RCTs) can provide the best evidence to inform decision-making, but their methodological and reporting quality varies. Tools exist to guide the critical appraisal of quality and risk of bias in SRs, but evaluations of their measurement properties are limited. We will investigate the interrater reliability (IRR), usability, and applicability of A MeaSurement Tool to Assess systematic Reviews (AMSTAR), AMSTAR 2, and Risk Of Bias In Systematic reviews (ROBIS) for SRs in the fields of biomedicine and public health. An international team of researchers at three collaborating centres will undertake the study. We will use a random sample of 30 SRs of RCTs investigating therapeutic interventions indexed in MEDLINE in February 2014. Two reviewers at each centre will appraise the quality and risk of bias in each SR using AMSTAR, AMSTAR 2, and ROBIS. We will record the time to complete each assessment and for the two reviewers to reach consensus for each SR. We will extract the descriptive characteristics of each SR, the included studies, participants, interventions, and comparators. We will also extract the direction and strength of the results and conclusions for the primary outcome. We will summarise the descriptive characteristics of the SRs using means and standard deviations, or frequencies and proportions. To test for interrater reliability between reviewers and between the consensus agreements of reviewer pairs, we will use Gwet's AC 1 statistic. For comparability to previous evaluations, we will also calculate weighted Cohen's kappa and Fleiss' kappa statistics. To estimate usability, we will calculate the mean time to complete the appraisal and to reach consensus for each tool. To inform applications of the tools, we will test for statistical associations between quality scores and risk of bias judgments, and the results and conclusions of the SRs. Appraising the methodological and reporting quality of SRs is necessary to determine the trustworthiness of their conclusions. Which tool may be most reliably applied and how the appraisals should be used is uncertain; the usability of newly developed tools is unknown. This investigation of common (AMSTAR) and newly developed (AMSTAR 2, ROBIS) tools will provide empiric data to inform their application, interpretation, and refinement.

Practical quality control tools for curves and surfaces

NASA Technical Reports Server (NTRS)

Small, Scott G.

1992-01-01

Curves (geometry) and surfaces created by Computer Aided Geometric Design systems in the engineering environment must satisfy two basic quality criteria: the geometric shape must have the desired engineering properties; and the objects must be parameterized in a way which does not cause computational difficulty for geometric processing and engineering analysis. Interactive techniques are described which are in use at Boeing to evaluate the quality of aircraft geometry prior to Computational Fluid Dynamic analysis, including newly developed methods for examining surface parameterization and its effects.

Dry rotary swaging with structured and coated tools

NASA Astrophysics Data System (ADS)

Herrmann, Marius; Schenck, Christian; Kuhfuss, Bernd

2018-05-01

Rotary swaging is a cold bulk forming process for manufacturing of complex bar and tube profiles like axles and gear shafts in the automotive industry. Conventional rotary swaging is carried out under intense use of lubricant usually based on mineral oil. Besides lubrication the lubricant fulfills necessary functions like lubrication, flushing and cooling, but generates costs for recycling, replacement and cleaning of the workpieces. Hence, the development of a dry process design is highly desirable, both under economic and ecological points of view. Therefore, it is necessary to substitute the functions of the lubricant. This was realized by the combination of newly developed a-C:H:W coating systems on the tools to minimize the friction and to avoid adhesion effects. With the application of a deterministic structure in the forging zone of the tools the friction conditions are modified to control the axial process forces. In this study infeed rotary swaging with functionalized tools was experimentally investigated. Therefore, steel and aluminum tubes were formed with and without lubricant. Different structures which were coated and uncoated were implemented in the reduction zone of the tools. The antagonistic effects of coating and structuring were characterized by measuring the axial process force and the produced workpiece quality in terms of roundness and surface roughness. Thus, the presented results allow for further developments towards a dry rotary swaging process.

The Way Point Planning Tool: Real Time Flight Planning for Airborne Science

NASA Technical Reports Server (NTRS)

He, Yubin; Blakeslee, Richard; Goodman, Michael; Hall, John

2012-01-01

Airborne real time observation are a major component of NASA's Earth Science research and satellite ground validation studies. For mission scientist, planning a research aircraft mission within the context of meeting the science objective is a complex task because it requires real time situational awareness of the weather conditions that affect the aircraft track. Multiple aircraft are often involved in the NASA field campaigns the coordination of the aircraft with satellite overpasses, other airplanes and the constantly evolving dynamic weather conditions often determine the success of the campaign. A flight planning tool is needed to provide situational awareness information to the mission scientist and help them plan and modify the flight tracks successfully. Scientists at the University of Alabama Huntsville and the NASA Marshal Space Flight Center developed the Waypoint Planning Tool (WPT), an interactive software tool that enables scientist to develop their own flight plans (also known as waypoints), with point and click mouse capabilities on a digital map filled with time raster and vector data. The development of this Waypoint Planning Tool demonstrates the significance of mission support in responding to the challenges presented during NASA field campaigns. Analyses during and after each campaign helped identify both issues and new requirements, initiating the next wave of development. Currently the Waypoint Planning Tool has gone through three rounds of development and analysis processes. The development of this waypoint tool is directly affected by the technology advances on GIS/Mapping technologies. From the standalone Google Earth application and simple KML functionalities to the Google Earth Plugin and Java Web Start/Applet on web platform, as well as to the rising open source GIS tools with new JavaScript frameworks, the Waypoint planning Tool has entered its third phase of technology advancement. The newly innovated, cross-platform, modular designed JavaScript-controled Waypoint tool is planned to be integrated with the NASA Airborne Science Mission Tool Suite. Adapting new technologies for the Waypoint Planning Tool ensures its success in helping scientist reach their mission objectives. This presentation will discuss the development process of the Waypoint Planning Tool in responding to field campaign challenges, identifying new information technologies, and describing the capabilities and features of the Waypoint Planning Tool with the real time aspect, interactive nature, and the resultant benefits to the airborne science community.

A novel VIGS method by agroinoculation of cotton seeds and application for elucidating functions of GhBI-1 in salt-stress response.

PubMed

Zhang, Jingxia; Wang, Furong; Zhang, Chuanyun; Zhang, Junhao; Chen, Yu; Liu, Guodong; Zhao, Yanxiu; Hao, Fushun; Zhang, Jun

2018-06-04

A VIGS method by agroinoculation of cotton seeds was developed for gene silencing in young seedlings and roots, and applied in functional analysis of GhBI-1 in response to salt stress. Virus-induced gene silencing (VIGS) has been widely used to investigate the functions of genes expressed in mature leaves, but not yet in young seedlings or roots of cotton (Gossypium hirsutum L.). Here, we developed a simple and effective VIGS method for silencing genes in young cotton seedlings and roots by soaking naked seeds in Agrobacterium cultures carrying tobacco rattle virus (TRV)-VIGS vectors. When the naked seeds were soaked in Agrobacterium cultures with an OD600 of 1.5 for 90 min, it was optimal for silencing genes effectively in young seedlings as clear photo-bleaching phenotype in the newly emerging leaves of pTRV:GhCLA1 seedlings were observed at 12-14 days post inoculation. Silencing of GhPGF (cotton pigment gland formation) by this method resulted in a 90% decrease in transcript abundances of the gene in roots at the early development stage. We further used the tool to investigate function of GhBI-1 (cotton Bax inhibitor-1) gene in response to salt stress and demonstrated that GhBI-1 might play a protective role under salt stress by suppressing stress-induced cell death in cotton. Our results showed that the newly established VIGS method is a powerful tool for elucidating functions of genes in cotton, especially the genes expressed in young seedlings and roots.

XML schemas for common bioinformatic data types and their application in workflow systems.

PubMed

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-11-06

Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data--therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at http://bioschemas.sourceforge.net, the BioDOM library can be obtained at http://biodom.sourceforge.net. The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.

Critical choices in financing the response to the global HIV/AIDS pandemic.

PubMed

Hecht, Robert; Bollinger, Lori; Stover, John; McGreevey, William; Muhib, Farzana; Madavo, Callisto Emas; de Ferranti, David

2009-01-01

The AIDS pandemic will enter its fiftieth year in 2031. Despite much progress, there are thirty-three million infected people worldwide, and 2.3 million adults were newly infected in 2007. Without a change in approach, a major pandemic will still be with us in 2031. Modeling carried out for the AIDS 2031 project suggests that funding required for developing countries to address the pandemic could reach $35 billion annually by 2031-three times the current level. Even then, more than a million people will still be newly infected each year. However, wise policy choices focusing on high-impact prevention and efficient treatment could cut costs by half. Investments in new prevention tools and major behavior-change efforts are needed to spur more rapid advances. Existing donors, middle-income countries with contained epidemics, philanthropists, and innovative financing could help bridge the likely funding gap.

Serum ferritin: Past, present and future.

PubMed

Wang, Wei; Knovich, Mary Ann; Coffman, Lan G; Torti, Frank M; Torti, Suzy V

2010-08-01

Serum ferritin was discovered in the 1930s, and was developed as a clinical test in the 1970s. Many diseases are associated with iron overload or iron deficiency. Serum ferritin is widely used in diagnosing and monitoring these diseases. In this chapter, we discuss the role of serum ferritin in physiological and pathological processes and its use as a clinical tool. Although many aspects of the fundamental biology of serum ferritin remain surprisingly unclear, a growing number of roles have been attributed to extracellular ferritin, including newly described roles in iron delivery, angiogenesis, inflammation, immunity, signaling and cancer. Serum ferritin remains a clinically useful tool. Further studies on the biology of this protein may provide new biological insights. Copyright 2010 Elsevier B.V. All rights reserved.

Testing framework for embedded languages

NASA Astrophysics Data System (ADS)

Leskó, Dániel; Tejfel, Máté

2012-09-01

Embedding a new programming language into an existing one is a widely used technique, because it fastens the development process and gives a part of a language infrastructure for free (e.g. lexical, syntactical analyzers). In this paper we are presenting a new advantage of this development approach regarding to adding testing support for these new languages. Tool support for testing is a crucial point for a newly designed programming language. It could be done in the hard way by creating a testing tool from scratch, or we could try to reuse existing testing tools by extending them with an interface to our new language. The second approach requires less work, and also it fits very well for the embedded approach. The problem is that the creation of such interfaces is not straightforward at all, because the existing testing tools were mostly not designed to be extendable and to be able to deal with new languages. This paper presents an extendable and modular model of a testing framework, in which the most basic design decision was to keep the - previously mentioned - interface creation simple and straightforward. Other important aspects of our model are the test data generation, the oracle problem and the customizability of the whole testing phase.

The Microbial Fuel Cell as an Education Tool

ERIC Educational Resources Information Center

Dewan, Alim; Van Wie, Bernard; Beyenal, Haluk; Lewandowski, Zbigniew

2010-01-01

Many chemical engineering programs offer courses from a variety of disciplines to teach their students multidisciplinary concepts, but often these courses lack appropriate tools for linking newly learned concepts to principles learned in the core courses. This paper describes our experience of incorporating a microbial fuel cell education module…

Structural Optimization for Reliability Using Nonlinear Goal Programming

NASA Technical Reports Server (NTRS)

El-Sayed, Mohamed E.

1999-01-01

This report details the development of a reliability based multi-objective design tool for solving structural optimization problems. Based on two different optimization techniques, namely sequential unconstrained minimization and nonlinear goal programming, the developed design method has the capability to take into account the effects of variability on the proposed design through a user specified reliability design criterion. In its sequential unconstrained minimization mode, the developed design tool uses a composite objective function, in conjunction with weight ordered design objectives, in order to take into account conflicting and multiple design criteria. Multiple design criteria of interest including structural weight, load induced stress and deflection, and mechanical reliability. The nonlinear goal programming mode, on the other hand, provides for a design method that eliminates the difficulty of having to define an objective function and constraints, while at the same time has the capability of handling rank ordered design objectives or goals. For simulation purposes the design of a pressure vessel cover plate was undertaken as a test bed for the newly developed design tool. The formulation of this structural optimization problem into sequential unconstrained minimization and goal programming form is presented. The resulting optimization problem was solved using: (i) the linear extended interior penalty function method algorithm; and (ii) Powell's conjugate directions method. Both single and multi-objective numerical test cases are included demonstrating the design tool's capabilities as it applies to this design problem.

Clinical results of HIS, RIS, PACS integration using data integration CASE tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Chan, Hing-Ming; Breant, Claudine M.; Huang, Lu J.; Valentino, Daniel J.

1995-05-01

Current infrastructure research in PACS is dominated by the development of communication networks (local area networks, teleradiology, ATM networks, etc.), multimedia display workstations, and hierarchical image storage architectures. However, limited work has been performed on developing flexible, expansible, and intelligent information processing architectures for the vast decentralized image and text data repositories prevalent in healthcare environments. Patient information is often distributed among multiple data management systems. Current large-scale efforts to integrate medical information and knowledge sources have been costly with limited retrieval functionality. Software integration strategies to unify distributed data and knowledge sources is still lacking commercially. Systems heterogeneity (i.e., differences in hardware platforms, communication protocols, database management software, nomenclature, etc.) is at the heart of the problem and is unlikely to be standardized in the near future. In this paper, we demonstrate the use of newly available CASE (computer- aided software engineering) tools to rapidly integrate HIS, RIS, and PACS information systems. The advantages of these tools include fast development time (low-level code is generated from graphical specifications), and easy system maintenance (excellent documentation, easy to perform changes, and centralized code repository in an object-oriented database). The CASE tools are used to develop and manage the `middle-ware' in our client- mediator-serve architecture for systems integration. Our architecture is scalable and can accommodate heterogeneous database and communication protocols.

User Guidelines for the Brassica Database: BRAD.

PubMed

Wang, Xiaobo; Cheng, Feng; Wang, Xiaowu

2016-01-01

The genome sequence of Brassica rapa was first released in 2011. Since then, further Brassica genomes have been sequenced or are undergoing sequencing. It is therefore necessary to develop tools that help users to mine information from genomic data efficiently. This will greatly aid scientific exploration and breeding application, especially for those with low levels of bioinformatic training. Therefore, the Brassica database (BRAD) was built to collect, integrate, illustrate, and visualize Brassica genomic datasets. BRAD provides useful searching and data mining tools, and facilitates the search of gene annotation datasets, syntenic or non-syntenic orthologs, and flanking regions of functional genomic elements. It also includes genome-analysis tools such as BLAST and GBrowse. One of the important aims of BRAD is to build a bridge between Brassica crop genomes with the genome of the model species Arabidopsis thaliana, thus transferring the bulk of A. thaliana gene study information for use with newly sequenced Brassica crops.

Bioinformatics and molecular modeling in glycobiology

PubMed Central

Schloissnig, Siegfried

2010-01-01

The field of glycobiology is concerned with the study of the structure, properties, and biological functions of the family of biomolecules called carbohydrates. Bioinformatics for glycobiology is a particularly challenging field, because carbohydrates exhibit a high structural diversity and their chains are often branched. Significant improvements in experimental analytical methods over recent years have led to a tremendous increase in the amount of carbohydrate structure data generated. Consequently, the availability of databases and tools to store, retrieve and analyze these data in an efficient way is of fundamental importance to progress in glycobiology. In this review, the various graphical representations and sequence formats of carbohydrates are introduced, and an overview of newly developed databases, the latest developments in sequence alignment and data mining, and tools to support experimental glycan analysis are presented. Finally, the field of structural glycoinformatics and molecular modeling of carbohydrates, glycoproteins, and protein–carbohydrate interaction are reviewed. PMID:20364395

Magnetic Resonance Imaging of Adipose Tissue in Metabolic Dysfunction.

PubMed

Franz, Daniela; Syväri, Jan; Weidlich, Dominik; Baum, Thomas; Rummeny, Ernst J; Karampinos, Dimitrios C

2018-06-06

 Adipose tissue has become an increasingly important tissue target in medicine. It plays a central role in the storage and release of energy throughout the human body and has recently gained interest for its endocrinologic function. Magnetic resonance imaging (MRI) is an established method for quantitative direct evaluation of adipose tissue distribution, and is used increasingly as the modality of choice for metabolic phenotyping. The purpose of this review was the identification and presentation of the currently available literature on MRI of adipose tissue in metabolic dysfunction.  A PubMed (http://www.ncbi.nlm.nih.gov/pubmed) keyword search up to August 2017 without starting date limitation was performed and reference lists of relevant articles were searched.  MRI provides excellent tools for the evaluation of adipose tissue distribution and further characterization of the tissue. Standard as well as newly developed MRI techniques allow a risk stratification for the development of metabolic dysfunction and enable monitoring without the use of ionizing radiation or contrast material.   · Different types of adipose tissue play a crucial role in various types of metabolic dysfunction.. · Magnetic resonance imaging (MRI) is an excellent tool for noninvasive adipose tissue evaluation with respect to distribution, composition and metabolic activity.. · Both standard and newly developed MRI techniques can be used for risk stratification for the development of metabolic dysfunction and allow monitoring without the use of ionizing radiation or contrast material.. · Franz D, Syväri J, Weidlich D et al. Magnetic Resonance Imaging of Adipose Tissue in Metabolic Dysfunction. Fortschr Röntgenstr 2018; DOI: 10.1055/a-0612-8006. © Georg Thieme Verlag KG Stuttgart · New York.

Classification and assessment tools for structural motif discovery algorithms.

PubMed

Badr, Ghada; Al-Turaiki, Isra; Mathkour, Hassan

2013-01-01

Motif discovery is the problem of finding recurring patterns in biological data. Patterns can be sequential, mainly when discovered in DNA sequences. They can also be structural (e.g. when discovering RNA motifs). Finding common structural patterns helps to gain a better understanding of the mechanism of action (e.g. post-transcriptional regulation). Unlike DNA motifs, which are sequentially conserved, RNA motifs exhibit conservation in structure, which may be common even if the sequences are different. Over the past few years, hundreds of algorithms have been developed to solve the sequential motif discovery problem, while less work has been done for the structural case. In this paper, we survey, classify, and compare different algorithms that solve the structural motif discovery problem, where the underlying sequences may be different. We highlight their strengths and weaknesses. We start by proposing a benchmark dataset and a measurement tool that can be used to evaluate different motif discovery approaches. Then, we proceed by proposing our experimental setup. Finally, results are obtained using the proposed benchmark to compare available tools. To the best of our knowledge, this is the first attempt to compare tools solely designed for structural motif discovery. Results show that the accuracy of discovered motifs is relatively low. The results also suggest a complementary behavior among tools where some tools perform well on simple structures, while other tools are better for complex structures. We have classified and evaluated the performance of available structural motif discovery tools. In addition, we have proposed a benchmark dataset with tools that can be used to evaluate newly developed tools.

Newly developed vaginal atrophy symptoms II and vaginal pH: a better correlation in vaginal atrophy?

PubMed

Tuntiviriyapun, P; Panyakhamlerd, K; Triratanachat, S; Chatsuwan, T; Chaikittisilpa, S; Jaisamrarn, U; Taechakraichana, N

2015-04-01

The primary objective of this study was to evaluate the correlation among symptoms, signs, and the number of lactobacilli in postmenopausal vaginal atrophy. The secondary objective was to develop a new parameter to improve the correlation. A cross-sectional descriptive study. Naturally postmenopausal women aged 45-70 years with at least one clinical symptom of vaginal atrophy of moderate to severe intensity were included in this study. All of the objective parameters (vaginal atrophy score, vaginal pH, the number of lactobacilli, vaginal maturation index, and vaginal maturation value) were evaluated and correlated with vaginal atrophy symptoms. A new parameter of vaginal atrophy, vaginal atrophy symptoms II, was developed and consists of the two most bothersome symptoms (vaginal dryness and dyspareunia). Vaginal atrophy symptoms II was analyzed for correlation with the objective parameters. A total of 132 naturally postmenopausal women were recruited for analysis. Vaginal pH was the only objective parameter found to have a weak correlation with vaginal atrophy symptoms (r = 0.273, p = 0.002). The newly developed vaginal atrophy symptoms II parameter showed moderate correlation with vaginal pH (r = 0.356, p < 0.001) and a weak correlation with the vaginal atrophy score (r = 0.230, p < 0.001). History of sexual intercourse within 3 months was associated with a better correlation between vaginal atrophy symptoms and the objective parameters. Vaginal pH was significantly correlated with vaginal atrophy symptoms. The newly developed vaginal atrophy symptoms II was associated with a better correlation. The vaginal atrophy symptoms II and vaginal pH may be better tools for clinical evaluation and future study of the vaginal ecosystem.

Experiments with a novel content-based image retrieval software: can we eliminate classification systems in adolescent idiopathic scoliosis?

PubMed

Menon, K Venugopal; Kumar, Dinesh; Thomas, Tessamma

2014-02-01

Study Design Preliminary evaluation of new tool. Objective To ascertain whether the newly developed content-based image retrieval (CBIR) software can be used successfully to retrieve images of similar cases of adolescent idiopathic scoliosis (AIS) from a database to help plan treatment without adhering to a classification scheme. Methods Sixty-two operated cases of AIS were entered into the newly developed CBIR database. Five new cases of different curve patterns were used as query images. The images were fed into the CBIR database that retrieved similar images from the existing cases. These were analyzed by a senior surgeon for conformity to the query image. Results Within the limits of variability set for the query system, all the resultant images conformed to the query image. One case had no similar match in the series. The other four retrieved several images that were matching with the query. No matching case was left out in the series. The postoperative images were then analyzed to check for surgical strategies. Broad guidelines for treatment could be derived from the results. More precise query settings, inclusion of bending films, and a larger database will enhance accurate retrieval and better decision making. Conclusion The CBIR system is an effective tool for accurate documentation and retrieval of scoliosis images. Broad guidelines for surgical strategies can be made from the postoperative images of the existing cases without adhering to any classification scheme.

Development of siRNA expression vector utilizing rock bream beta-actin promoter: a potential therapeutic tool against viral infection in fish.

PubMed

Zenke, Kosuke; Nam, Yoon Kwon; Kim, Ki Hong

2010-01-01

In the present study, we have developed short interfering RNA (siRNA) expression vector utilizing rock bream beta-actin promoter and examined the possible use for the inhibition of highly pathogenic fish virus, rock bream iridovirus (RBIV), replication in vitro. Initially, in order to express siRNA effectively, we added several modifications to wild-type rock bream beta-actin promoter. Next, we succeeded in knocking down the expression of enhanced green fluorescent protein reporter gene expression in fish cells using newly developed vector more effectively than the fugu U6 promoter-driven vector we described previously. Finally, we could observe that cells transfected with modified rock bream beta-actin promoter-driven siRNA expression vector targeting major capsid protein (MCP) gene of RBIV exhibited more resistance to RBIV challenge than other control cells. Our results indicate that this novel siRNA expression vector can be used as a new tool for therapeutics in virus infection in fish species.

Chiropractic chronic low back pain sufferers and self-report assessment methods. Part II. A reliability study of the Middlesex Hospital Questionnaire and the VAS Disability Scales Questionnaire.

PubMed

Leboeuf, C; Love, A; Crisp, T C

1989-04-01

The subjective complaints of 41 chronic low back pain sufferers attending a chiropractic clinic were assessed twice prior to therapy with a widely used psychological self-report assessment tool, the Middlesex Hospital Questionnaire (MHQ) and a newly developed VAS Disability Scales Questionnaire (DISQ), both of which investigate various aspects of certain basic positions and activities. Reliability was generally acceptable with these two questionnaires. Subjects participating in the study were commonly found to score within the normal range on the MHQ, indicating that psychological disturbance was not a major feature of their presentation. However, mild mood disturbance was commonly reported, and a more sensitive tool may need to be developed for this type of mildly affected chronic low back pain sufferers. The DISQ generally indicated subjects were mildly to moderately affected by their low back trouble and that sitting and leisure activities were the most pain provoking. Recommendations for further development of the disability scale are made.

A Framework for Assessing High School Students' Statistical Reasoning.

PubMed

Chan, Shiau Wei; Ismail, Zaleha; Sumintono, Bambang

2016-01-01

Based on a synthesis of literature, earlier studies, analyses and observations on high school students, this study developed an initial framework for assessing students' statistical reasoning about descriptive statistics. Framework descriptors were established across five levels of statistical reasoning and four key constructs. The former consisted of idiosyncratic reasoning, verbal reasoning, transitional reasoning, procedural reasoning, and integrated process reasoning. The latter include describing data, organizing and reducing data, representing data, and analyzing and interpreting data. In contrast to earlier studies, this initial framework formulated a complete and coherent statistical reasoning framework. A statistical reasoning assessment tool was then constructed from this initial framework. The tool was administered to 10 tenth-grade students in a task-based interview. The initial framework was refined, and the statistical reasoning assessment tool was revised. The ten students then participated in the second task-based interview, and the data obtained were used to validate the framework. The findings showed that the students' statistical reasoning levels were consistent across the four constructs, and this result confirmed the framework's cohesion. Developed to contribute to statistics education, this newly developed statistical reasoning framework provides a guide for planning learning goals and designing instruction and assessments.

A Framework for Assessing High School Students' Statistical Reasoning

PubMed Central

2016-01-01

Based on a synthesis of literature, earlier studies, analyses and observations on high school students, this study developed an initial framework for assessing students’ statistical reasoning about descriptive statistics. Framework descriptors were established across five levels of statistical reasoning and four key constructs. The former consisted of idiosyncratic reasoning, verbal reasoning, transitional reasoning, procedural reasoning, and integrated process reasoning. The latter include describing data, organizing and reducing data, representing data, and analyzing and interpreting data. In contrast to earlier studies, this initial framework formulated a complete and coherent statistical reasoning framework. A statistical reasoning assessment tool was then constructed from this initial framework. The tool was administered to 10 tenth-grade students in a task-based interview. The initial framework was refined, and the statistical reasoning assessment tool was revised. The ten students then participated in the second task-based interview, and the data obtained were used to validate the framework. The findings showed that the students’ statistical reasoning levels were consistent across the four constructs, and this result confirmed the framework’s cohesion. Developed to contribute to statistics education, this newly developed statistical reasoning framework provides a guide for planning learning goals and designing instruction and assessments. PMID:27812091

Virtual Exercise Training Software System

NASA Technical Reports Server (NTRS)

Vu, L.; Kim, H.; Benson, E.; Amonette, W. E.; Barrera, J.; Perera, J.; Rajulu, S.; Hanson, A.

2018-01-01

The purpose of this study was to develop and evaluate a virtual exercise training software system (VETSS) capable of providing real-time instruction and exercise feedback during exploration missions. A resistive exercise instructional system was developed using a Microsoft Kinect depth-camera device, which provides markerless 3-D whole-body motion capture at a small form factor and minimal setup effort. It was hypothesized that subjects using the newly developed instructional software tool would perform the deadlift exercise with more optimal kinematics and consistent technique than those without the instructional software. Following a comprehensive evaluation in the laboratory, the system was deployed for testing and refinement in the NASA Extreme Environment Mission Operations (NEEMO) analog.

Comparison of de novo assembly statistics of Cucumis sativus L.

NASA Astrophysics Data System (ADS)

Wojcieszek, Michał; Kuśmirek, Wiktor; Pawełkowicz, Magdalena; PlÄ der, Wojciech; Nowak, Robert M.

2017-08-01

Genome sequencing is the core of genomic research. With the development of NGS and lowering the cost of procedure there is another tight gap - genome assembly. Developing the proper tool for this task is essential as quality of genome has important impact on further research. Here we present comparison of several de Bruijn assemblers tested on C. sativus genomic reads. The assessment shows that newly developed software - dnaasm provides better results in terms of quantity and quality. The number of generated sequences is lower by 5 - 33% with even two fold higher N50. Quality check showed reliable results were generated by dnaasm. This provides us with very strong base for future genomic analysis.

Modeling NIF experimental designs with adaptive mesh refinement and Lagrangian hydrodynamics

NASA Astrophysics Data System (ADS)

Koniges, A. E.; Anderson, R. W.; Wang, P.; Gunney, B. T. N.; Becker, R.; Eder, D. C.; MacGowan, B. J.; Schneider, M. B.

2006-06-01

Incorporation of adaptive mesh refinement (AMR) into Lagrangian hydrodynamics algorithms allows for the creation of a highly powerful simulation tool effective for complex target designs with three-dimensional structure. We are developing an advanced modeling tool that includes AMR and traditional arbitrary Lagrangian-Eulerian (ALE) techniques. Our goal is the accurate prediction of vaporization, disintegration and fragmentation in National Ignition Facility (NIF) experimental target elements. Although our focus is on minimizing the generation of shrapnel in target designs and protecting the optics, the general techniques are applicable to modern advanced targets that include three-dimensional effects such as those associated with capsule fill tubes. Several essential computations in ordinary radiation hydrodynamics need to be redesigned in order to allow for AMR to work well with ALE, including algorithms associated with radiation transport. Additionally, for our goal of predicting fragmentation, we include elastic/plastic flow into our computations. We discuss the integration of these effects into a new ALE-AMR simulation code. Applications of this newly developed modeling tool as well as traditional ALE simulations in two and three dimensions are applied to NIF early-light target designs.

Benchmarking short sequence mapping tools

PubMed Central

2013-01-01

Background The development of next-generation sequencing instruments has led to the generation of millions of short sequences in a single run. The process of aligning these reads to a reference genome is time consuming and demands the development of fast and accurate alignment tools. However, the current proposed tools make different compromises between the accuracy and the speed of mapping. Moreover, many important aspects are overlooked while comparing the performance of a newly developed tool to the state of the art. Therefore, there is a need for an objective evaluation method that covers all the aspects. In this work, we introduce a benchmarking suite to extensively analyze sequencing tools with respect to various aspects and provide an objective comparison. Results We applied our benchmarking tests on 9 well known mapping tools, namely, Bowtie, Bowtie2, BWA, SOAP2, MAQ, RMAP, GSNAP, Novoalign, and mrsFAST (mrFAST) using synthetic data and real RNA-Seq data. MAQ and RMAP are based on building hash tables for the reads, whereas the remaining tools are based on indexing the reference genome. The benchmarking tests reveal the strengths and weaknesses of each tool. The results show that no single tool outperforms all others in all metrics. However, Bowtie maintained the best throughput for most of the tests while BWA performed better for longer read lengths. The benchmarking tests are not restricted to the mentioned tools and can be further applied to others. Conclusion The mapping process is still a hard problem that is affected by many factors. In this work, we provided a benchmarking suite that reveals and evaluates the different factors affecting the mapping process. Still, there is no tool that outperforms all of the others in all the tests. Therefore, the end user should clearly specify his needs in order to choose the tool that provides the best results. PMID:23758764

Bioluminescence imaging of c-fos gene expression accompanying filial imprinting in the newly hatched chick brain.

PubMed

Yamaguchi, Shinji; Iikubo, Eiji; Hirose, Naoki; Kitajima, Takaaki; Katagiri, Sachiko; Kawamori, Ai; Fujii-Taira, Ikuko; Matsushima, Toshiya; Homma, Koichi J

2010-06-01

Bioluminescence imaging is a powerful tool for examining gene expression in living animals. Previously, we reported that exogenous DNA could be successfully delivered into neurons in the newly hatched chick brain using electroporation. Here, we show the in vivo bioluminescence imaging of c-fos promoter activity and its upregulation, which is associated with filial imprinting. The upregulation of c-fos gene expression correlated with both the strength of the chicks' approach activity to the training object and the acquisition of memory. The present technique should be a powerful tool for analyzing the time changes in neural activity of certain brain areas in real-time during memory formation, using brains of living animals.

The Power of Influence: School Nurse Stories.

PubMed

Mazyck, Donna; Cellucci, Margaret; Largent, Piper

2015-07-01

School nurses have influence, and this influence is ignited with school nurse stories. School nurses must tell school staff, leaders, families, and students what they do to help students access their education. School boards, city councils, and legislators need to know the knowledge, skills, and judgment school nurses use daily. NASN understands that school nurses benefit from a "how to" kit and has developed tools to empower school nurses in advocating for their important role in supporting the health and learning of students. This article provides an overview this newly developed electronic toolkit while at the same time reinforcing the power of influence when sharing your stories. © 2015 The Author(s).

Evidence for a distributed respiratory rhythm generating network in the goldfish (Carsssius auratus).

PubMed

Duchcherer, Maryana; Kottick, Andrew; Wilson, R J A

2010-01-01

Central pattern generators located in the brainstem regulate ventilatory behaviors in vertebrates. The development of the isolated brainstem preparation has allowed these neural networks to be characterized in a number of aquatic species. The aim of this study was to explore the architecture of the respiratory rhythm-generating site in the goldfish (Carassius auratus) and to determine the utility of a newly developed isolated brainstem preparation, the Sheep Dip. Here we provide evidence for a distributed organization of respiratory rhythm generating neurons along the rostrocaudal axis of the goldfish brainstem and outline the advantages of the Sheep Dip as a tool used to survey neural networks.

Ramathibodi Language Development Questionnaire: A Newly Developed Screening Tool for Detection of Delayed Language Development in Children Aged 18-30 Months.

PubMed

Chuthapisith, Jariya; Wantanakorn, Pornchanok; Roongpraiwan, Rawiwan

2015-08-01

To develop a parental questionnaire for screening children with delayed language development in primary care settings. Ramathibodi Language Development (RLD) questionnaire was developed and completed by groups of 40 typically developing children age 18 to 30 months old and 30 children with delayed language development. The mean score was significantly lower in the delay language group (6.7 ± 1.9), comparing with the typically developing group (9.6 ± 0.7). The optimal ROC curve cut-off score was 8 with corresponding sensitivity and specificity were 98% and 72%, respectively. The corresponding area under the curve was 0.96 (95% CI = 0.92-0.99). The RLD questionnaire was the promising language developmental screening instrument that easily utilized in well-child examination settings.

Development of a novel cold forging process to manufacture eccentric shafts

NASA Astrophysics Data System (ADS)

Pasler, Lukas; Liewald, Mathias

2018-05-01

Since the commercial usage of compact combustion engines, eccentric shafts have been used to transform translational into rotational motion. Over the years, several processes to manufacture these eccentric shafts or crankshafts have been developed. Especially for single-cylinder engines manufactured in small quantities, built crankshafts disclose advantages regarding tooling costs and performance. Those manufacturing processes do have one thing in common: They are all executed at elevated temperatures to enable the material to be formed to high forming degree. In this paper, a newly developed cold forging process is presented, which combines lateral extrusion and shifting for manufacturing a crank in one forming operation at room temperature. In comparison to the established upsetting and shifting methods to manufacture such components, the tool cavity or crank web thickness remains constant. Therefore, the developed new process presented in this paper consists of a combination of shifting and extrusion of the billet, which allows pushing material into the forming zone during shifting. In order to reduce the tensile stresses induced by the shifting process, compressive stresses are superimposed. It is expected that the process limits will be expanded regarding the horizontal displacement and form filling. In the following report, the simulation and design of the tooling concept are presented. Experiments were conducted and compared with corresponding simulation results afterwards.

Facilitating participatory multilevel decision-making by using interactive mental maps.

PubMed

Pfeiffer, Constanze; Glaser, Stephanie; Vencatesan, Jayshree; Schliermann-Kraus, Elke; Drescher, Axel; Glaser, Rüdiger

2008-11-01

Participation of citizens in political, economic or social decisions is increasingly recognized as a precondition to foster sustainable development processes. Since spatial information is often important during planning and decision making, participatory mapping gains in popularity. However, little attention has been paid to the fact that information must be presented in a useful way to reach city planners and policy makers. Above all, the importance of visualisation tools to support collaboration, analytical reasoning, problem solving and decision-making in analysing and planning processes has been underestimated. In this paper, we describe how an interactive mental map tool has been developed in a highly interdisciplinary disaster management project in Chennai, India. We moved from a hand drawn mental maps approach to an interactive mental map tool. This was achieved by merging socio-economic and geospatial data on infrastructure, local perceptions, coping and adaptation strategies with remote sensing data and modern technology of map making. This newly developed interactive mapping tool allowed for insights into different locally-constructed realities and facilitated the communication of results to the wider public and respective policy makers. It proved to be useful in visualising information and promoting participatory decision-making processes. We argue that the tool bears potential also for health research projects. The interactive mental map can be used to spatially and temporally assess key health themes such as availability of, and accessibility to, existing health care services, breeding sites of disease vectors, collection and storage of water, waste disposal, location of public toilets or defecation sites.

Saliva diagnostics – Current views and directions

PubMed Central

Kaczor-Urbanowicz, Karolina Elżbieta; Martin Carreras-Presas, Carmen; Aro, Katri; Tu, Michael; Wong, David TW

2016-01-01

In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a “mirror of the body,” can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term “Salivaomics” aimed to highlight the rapid development of knowledge about various “omics” constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome. In the last few years, researchers have developed new technologies and validated a wide range of salivary biomarkers that will soon make the use of saliva a clinical reality. However, a great need still exists for convenient and accurate point-of-care devices that can serve as a non-invasive diagnostic tool. In addition, there is an urgent need to decipher the scientific rationale and mechanisms that convey systemic diseases to saliva. Another promising technology called liquid biopsy enables detection of circulating tumor cells (CTCs) and fragments of tumor DNA in saliva, thus enabling non-invasive early detection of various cancers. The newly developed technology—electric field-induced release and measurement (EFIRM) provides near perfect detection of actionable mutations in lung cancer patients. These recent advances widened the salivary diagnostic approach from the oral cavity to the whole physiological system, and thus point towards a promising future of salivary diagnostics for personalized individual medicine applications including clinical decisions and post-treatment outcome predictions. Impact statement The purpose of this mini-review is to make an update about the present and future applications of saliva as a diagnostic biofluid in many fields of science such as dentistry, medicine and pharmacotherapy. Using saliva as a fluid for diagnostic purposes would be a huge breakthrough for both patients and healthcare providers since saliva collection is easy, non-invasive and inexpensive. We will go through the current main diagnostic applications of saliva, and provide a highlight on the emerging, newly developing technologies and tools for cancer screening, detection and monitoring. PMID:27903834

New Technologies: Real-time Telepathology Systems-Novel Cost-effective Tools for Real-time Consultation and Data Sharing.

PubMed

Siegel, Gabriel; Regelman, Dan; Maronpot, Robert; Rosenstock, Moti; Nyska, Abraham

2017-12-01

Real-time telepathology for use in investigative and regulated preclinical toxicology studies is now feasible. Newly developed microscope-integrated telepathology systems enable geographically remote stakeholders to view the live histopathology slide as seen by the study pathologist within the microscope. Simultaneous online viewing and dialog between study pathologist and remote colleagues is an efficient and cost-effective means for consultation, pathology working groups, and peer review, facilitating good science and economic benefits by enabling more timely and informed clinical decisions.

Emerging Tools for Synthetic Genome Design

PubMed Central

Lee, Bo-Rahm; Cho, Suhyung; Song, Yoseb; Kim, Sun Chang; Cho, Byung-Kwan

2013-01-01

Synthetic biology is an emerging discipline for designing and synthesizing predictable, measurable, controllable, and transformable biological systems. These newly designed biological systems have great potential for the development of cheaper drugs, green fuels, biodegradable plastics, and targeted cancer therapies over the coming years. Fortunately, our ability to quickly and accurately engineer biological systems that behave predictably has been dramatically expanded by significant advances in DNA-sequencing, DNA-synthesis, and DNA-editing technologies. Here, we review emerging technologies and methodologies in the field of building designed biological systems, and we discuss their future perspectives. PMID:23708771

Characterization and application of newly developed polymorphic microsatellite markers in the Ezo red fox (Vulpes vulpes schrencki).

PubMed

Tada, T; Seki, Y; Kameyama, Y; Kikkawa, Y; Wada, K

2016-12-19

The Ezo red fox (Vulpes vulpes schrencki), a subspecies endemic to Hokkaido island, Japan, is a known host species for the tapeworm Echinococcus multilocularis. To develop tools for molecular ecological studies, we isolated 28 microsatellite regions from the genome of Ezo red fox, and developed 18 polymorphic microsatellite markers. These markers were characterized using 7 individuals and 22 fecal samples of the Ezo red fox. The number of alleles for these markers ranged from 1 to 7, and the observed heterozygosity, estimated on the basis of the genotypes of 7 individuals, ranged from 0.29 to 1.00. All markers, except DvNok5, were in Hardy-Weinberg equilibrium (P > 0.05), and no linkage disequilibrium was detected among these loci, except between DvNok14 and DvNok28 (P = 0.01). Moreover, six microsatellite loci were successfully genotyped using feces-derived DNA from the Ezo red fox. The markers developed in our study might serve as a useful tool for molecular ecological studies of the Ezo red fox.

Serum Ferritin: Past, Present and Future

PubMed Central

Wang, Wei; Knovich, Mary Ann; Coffman, Lan G.; Torti, Frank M.; Torti, Suzy V.

2010-01-01

Background Serum ferritin was discovered in the 1930’s, and was developed as a clinical test in the 1970’s. Many diseases are associated with iron overload or iron deficiency. Serum ferritin is widely used in diagnosing and monitoring these diseases. Scope of Review In this chapter, we discuss the role of serum ferritin in physiological and pathological processes and its use as a clinical tool. Major Conclusions Although many aspects of the fundamental biology of serum ferritin remain surprisingly unclear, a growing number of roles have been attributed to extracellular ferritin, including newly described roles in iron delivery, angiogenesis, inflammation, immunity, signaling and cancer. General Significance Serum ferritin remains a clinically useful tool. Further studies on the biology of this protein may provide new biological insights. PMID:20304033

Computer-Controlled Cylindrical Polishing Process for Large X-Ray Mirror Mandrels

NASA Technical Reports Server (NTRS)

Khan, Gufran S.; Gubarev, Mikhail; Speegle, Chet; Ramsey, Brian

2010-01-01

We are developing high-energy grazing incidence shell optics for hard-x-ray telescopes. The resolution of a mirror shells depends on the quality of cylindrical mandrel from which they are being replicated. Mid-spatial-frequency axial figure error is a dominant contributor in the error budget of the mandrel. This paper presents our efforts to develop a deterministic cylindrical polishing process in order to keep the mid-spatial-frequency axial figure errors to a minimum. Simulation software is developed to model the residual surface figure errors of a mandrel due to the polishing process parameters and the tools used, as well as to compute the optical performance of the optics. The study carried out using the developed software was focused on establishing a relationship between the polishing process parameters and the mid-spatial-frequency error generation. The process parameters modeled are the speeds of the lap and the mandrel, the tool s influence function, the contour path (dwell) of the tools, their shape and the distribution of the tools on the polishing lap. Using the inputs from the mathematical model, a mandrel having conical approximated Wolter-1 geometry, has been polished on a newly developed computer-controlled cylindrical polishing machine. The preliminary results of a series of polishing experiments demonstrate a qualitative agreement with the developed model. We report our first experimental results and discuss plans for further improvements in the polishing process. The ability to simulate the polishing process is critical to optimize the polishing process, improve the mandrel quality and significantly reduce the cost of mandrel production

Technical Note: Development and performance of a software tool for quality assurance of online replanning with a conventional Linac or MR-Linac.

PubMed

Chen, Guang-Pei; Ahunbay, Ergun; Li, X Allen

2016-04-01

To develop an integrated quality assurance (QA) software tool for online replanning capable of efficiently and automatically checking radiation treatment (RT) planning parameters and gross plan quality, verifying treatment plan data transfer from treatment planning system (TPS) to record and verify (R&V) system, performing a secondary monitor unit (MU) calculation with or without a presence of a magnetic field from MR-Linac, and validating the delivery record consistency with the plan. The software tool, named ArtQA, was developed to obtain and compare plan and treatment parameters from both the TPS and the R&V system database. The TPS data are accessed via direct file reading and the R&V data are retrieved via open database connectivity and structured query language. Plan quality is evaluated with both the logical consistency of planning parameters and the achieved dose-volume histograms. Beams in between the TPS and R&V system are matched based on geometry configurations. To consider the effect of a 1.5 T transverse magnetic field from MR-Linac in the secondary MU calculation, a method based on modified Clarkson integration algorithm was developed and tested for a series of clinical situations. ArtQA has been used in their clinic and can quickly detect inconsistencies and deviations in the entire RT planning process. With the use of the ArtQA tool, the efficiency for plan check including plan quality, data transfer, and delivery check can be improved by at least 60%. The newly developed independent MU calculation tool for MR-Linac reduces the difference between the plan and calculated MUs by 10%. The software tool ArtQA can be used to perform a comprehensive QA check from planning to delivery with conventional Linac or MR-Linac and is an essential tool for online replanning where the QA check needs to be performed rapidly.

Technical Note: Development and performance of a software tool for quality assurance of online replanning with a conventional Linac or MR-Linac

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

Chen, Guang-Pei, E-mail: gpchen@mcw.edu; Ahunbay, Ergun; Li, X. Allen

Purpose: To develop an integrated quality assurance (QA) software tool for online replanning capable of efficiently and automatically checking radiation treatment (RT) planning parameters and gross plan quality, verifying treatment plan data transfer from treatment planning system (TPS) to record and verify (R&V) system, performing a secondary monitor unit (MU) calculation with or without a presence of a magnetic field from MR-Linac, and validating the delivery record consistency with the plan. Methods: The software tool, named ArtQA, was developed to obtain and compare plan and treatment parameters from both the TPS and the R&V system database. The TPS data aremore » accessed via direct file reading and the R&V data are retrieved via open database connectivity and structured query language. Plan quality is evaluated with both the logical consistency of planning parameters and the achieved dose–volume histograms. Beams in between the TPS and R&V system are matched based on geometry configurations. To consider the effect of a 1.5 T transverse magnetic field from MR-Linac in the secondary MU calculation, a method based on modified Clarkson integration algorithm was developed and tested for a series of clinical situations. Results: ArtQA has been used in their clinic and can quickly detect inconsistencies and deviations in the entire RT planning process. With the use of the ArtQA tool, the efficiency for plan check including plan quality, data transfer, and delivery check can be improved by at least 60%. The newly developed independent MU calculation tool for MR-Linac reduces the difference between the plan and calculated MUs by 10%. Conclusions: The software tool ArtQA can be used to perform a comprehensive QA check from planning to delivery with conventional Linac or MR-Linac and is an essential tool for online replanning where the QA check needs to be performed rapidly.« less

Tailored tools to improve pharmacotherapy in infants.

PubMed

Allegaert, Karel

2014-08-01

Extensive within-population variability is the essence of neonatal pharmacology. Despite this, infants remain one of the last therapeutic orphans. Together with additional legal initiatives, tailoring of already available tools (modeling, covariates, pharmacovigilance) may significantly improve pharmacotherapy in infants. Modeling approaches that hold the promise to improve pharmacotherapy in infants are between-compound extrapolation for compounds that undergo the same route of elimination and integration of time-varying physiology to adapt for the fast maturational changes. Besides these maturational covariates (size, age), newly emerging covariates relate to novel treatment modalities (extracorporeal circulation, hypothermia), environmental issues (microbiome, critical illness) or pharmacogenetics. All these covariates interact with the maturational variation. Finally, pharmacovigilance also needs to be tailored to the characteristics of this population. This relates to preventive strategies, signal detection and assessment of causality. Knowledge on pharmacotherapy in infants is lagging. Tailoring available tools to the specific characteristics (maturation) and clinical needs (newly emerging covariates) of infants is feasible but needs creativity and a multidisciplinary collaboration between modelers, academia, clinical researchers and, obviously, the public, including parents.

Development and process evaluation of the participatory and action-oriented empowerment model facilitated by occupational health nurses for workplace health promotion in small and medium-sized enterprises.

PubMed

Nishikido, Noriko; Matsuda, Kazumi; Fukuda, Eiko; Motoki, Chiharu; Tsutaki, Miho; Kawakami, Yuko; Yuasa, Akiko; Iijima, Miyoko; Tanaka, Mika; Hirata, Mamoru; Hojoh, Minoru; Ikeda, Tomoko; Maeda, Kazutoshi; Miyoshi, Yukari; Arai, Sumiko; Mitsuhashi, Hiroyuki

2007-01-01

The objective of this study is to develop an available empowerment model for workplace health promotion (WHP) in small and medium-sized enterprises (SMEs) and to evaluate its applicability and feasibility. Semi-structured interviews with employers and workers in SMEs were conducted to assess their actual requirements for support. The structure of our new empowerment model was discussed and established through several rounds of focus group meetings with occupational safety and health researchers and practitioners on the basis of results of our interviews. We developed a new participatory and action-oriented empowerment model based on needs for support of employers and workers in SMEs. This new model consists of three originally developed tools: an action checklist, an information guidebook, and a book of good practices. As the facilitators, occupational health nurses (OHNs) from health insurance associations were trained to empower employers and workers using these tools. Approximately 80 SMEs (with less than 300 employees) were invited to participate in the model project. With these tools and continued empowerment by OHNs, employers and workers were able to smoothly work on WHP. This newly developed participatory and action-oriented empowerment model that was facilitated by trained OHNs appears to be both applicable and feasible for WHP in SMEs in Japan.

Astronaut Office Scheduling System Software

NASA Technical Reports Server (NTRS)

Brown, Estevancio

2010-01-01

AOSS is a highly efficient scheduling application that uses various tools to schedule astronauts weekly appointment information. This program represents an integration of many technologies into a single application to facilitate schedule sharing and management. It is a Windows-based application developed in Visual Basic. Because the NASA standard office automation load environment is Microsoft-based, Visual Basic provides AO SS developers with the ability to interact with Windows collaboration components by accessing objects models from applications like Outlook and Excel. This also gives developers the ability to create newly customizable components that perform specialized tasks pertaining to scheduling reporting inside the application. With this capability, AOSS can perform various asynchronous tasks, such as gathering/ sending/ managing astronauts schedule information directly to their Outlook calendars at any time.

hydropower biological evaluation tools

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

This software is a set of analytical tools to evaluate the physical and biological performance of existing, refurbished, or newly installed conventional hydro-turbines nationwide where fish passage is a regulatory concern. The current version is based on information collected by the Sensor Fish. Future version will include other technologies. The tool set includes data acquisition, data processing, and biological response tools with applications to various turbine designs and other passage alternatives. The associated database is centralized, and can be accessed remotely. We have demonstrated its use for various applications including both turbines and spillways

Characterization of Newly Developed Semisolid Stir Joining Method for Cast Cu Base Alloy (Cu-Al-Si-Fe) and Effect of Stirrer Type on Uniformity of Microstructure

NASA Astrophysics Data System (ADS)

Ferasat, Keyvan; Aashuri, Hossein; Kokabi, Amir Hossein; Nikzad, Siamak; Shafizadeh, Mahdi

2015-02-01

In this research, the semisolid stir joining method was used to overcome the problem of hot cracking in welding aluminum and silicon bronzes. Moreover, the effects of grooved and cylindrical tools on the microstructure and mechanical properties of samples were examined. After welding specimens, mechanical tests were carried out to find differences between the cast and welded samples. Optical microscopy and scanning electron microscopy were used to study microstructure. X-ray diffraction was used to investigate compounds formed during casting and welding. The solidus and liquidus temperatures of the alloy were measured by differential scanning calorimetry. In this study, the temperature of the work pieces was raised to 1203 K (930 °C) that is in the semisolid region, and the weld seams were stirred by two different types of tools at the speed of 1600 rpm. Macro and micro-structural analyses show uniformity in the phase distribution for specimens welded by cylindrical tool. Desirable and uniform mechanical properties obtained when the cylindrical tool was used.

Early craniometric tools as a predecessor to neurosurgical stereotaxis.

PubMed

Serletis, Demitre; Pait, T Glenn

2016-06-01

In this paper the authors trace the history of early craniometry, referring to the technique of obtaining cranial measurements for the accurate correlation of external skull landmarks to specific brain regions. Largely drawing on methods from the newly emerging fields of physical anthropology and phrenology in the late 19th and early 20th centuries, basic mathematical concepts were combined with simplistic (yet at the time, innovative) mechanical tools, leading to the first known attempts at craniocerebral topography. It is important to acknowledge the pioneers of this pre-imaging epoch, who applied creativity and ingenuity to tackle the challenge of reproducibly and reliably accessing a specific target in the brain. In particular, with the emergence of Broca's theory of cortical localization, in vivo craniometric tools, and the introduction of 3D coordinate systems, several innovative devices were conceived that subsequently paved the way for modern-day stereotactic techniques. In this context, the authors present a comprehensive and systematic review of the most popular craniometric tools developed during this time period (prior to the stereotactic era) for the purposes of craniocerebral measurement and target localization.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome.

PubMed

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-11-27

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs.

Mi-DISCOVERER: A bioinformatics tool for the detection of mi-RNA in human genome

PubMed Central

Arshad, Saadia; Mumtaz, Asia; Ahmad, Freed; Liaquat, Sadia; Nadeem, Shahid; Mehboob, Shahid; Afzal, Muhammad

2010-01-01

MicroRNAs (miRNAs) are 22 nucleotides non-coding RNAs that play pivotal regulatory roles in diverse organisms including the humans and are difficult to be identified due to lack of either sequence features or robust algorithms to efficiently identify. Therefore, we made a tool that is Mi-Discoverer for the detection of miRNAs in human genome. The tools used for the development of software are Microsoft Office Access 2003, the JDK version 1.6.0, BioJava version 1.0, and the NetBeans IDE version 6.0. All already made miRNAs softwares were web based; so the advantage of our project was to make a desktop facility to the user for sequence alignment search with already identified miRNAs of human genome present in the database. The user can also insert and update the newly discovered human miRNA in the database. Mi-Discoverer, a bioinformatics tool successfully identifies human miRNAs based on multiple sequence alignment searches. It's a non redundant database containing a large collection of publicly available human miRNAs. PMID:21364831

Automated benchmarking of peptide-MHC class I binding predictions.

PubMed

Trolle, Thomas; Metushi, Imir G; Greenbaum, Jason A; Kim, Yohan; Sidney, John; Lund, Ole; Sette, Alessandro; Peters, Bjoern; Nielsen, Morten

2015-07-01

Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study. The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB. Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto_bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto_bench/mhci/join. mniel@cbs.dtu.dk or bpeters@liai.org Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Automated benchmarking of peptide-MHC class I binding predictions

PubMed Central

Trolle, Thomas; Metushi, Imir G.; Greenbaum, Jason A.; Kim, Yohan; Sidney, John; Lund, Ole; Sette, Alessandro; Peters, Bjoern; Nielsen, Morten

2015-01-01

Motivation: Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study. Results: The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB. Availability and implementation: Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto_bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto_bench/mhci/join. Contact: mniel@cbs.dtu.dk or bpeters@liai.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25717196

A peer-led teaching initiative for foundation doctors.

PubMed

Ramsden, Sophie; Abidogun, Abiola; Stringer, Emma; Mahgoub, Sara; Kastrissianakis, Artemis; Baker, Paul

2015-08-01

Peer teaching has been used informally throughout the history of medical education. Formal studies within the medical student and allied health care professional communities have found it to be a popular, and highly effective, method of teaching. Newly qualified doctors are currently an underused resource in terms of teaching one another. A committee, made up of newly qualified doctors and postgraduate education staff, was established. Using only a few resources, this committee organised regular, peer-led tutorials and used educational needs assessment tools, such as questionnaires, to make improvements to early postgraduate training. A realistic and well-received intervention to improve the teaching of newly qualified doctors, which is feasible in the modern, busy health care setting. Other institutions may find this method and its resources valuable. Newly qualified doctors are currently an underused resource in terms of teaching one another. © 2015 John Wiley & Sons Ltd.

Adaptive scallop height tool path generation for robot-based incremental sheet metal forming

NASA Astrophysics Data System (ADS)

Seim, Patrick; Möllensiep, Dennis; Störkle, Denis Daniel; Thyssen, Lars; Kuhlenkötter, Bernd

2016-10-01

Incremental sheet metal forming is an emerging process for the production of individualized products or prototypes in low batch sizes and with short times to market. In these processes, the desired shape is produced by the incremental inward motion of the workpiece-independent forming tool in depth direction and its movement along the contour in lateral direction. Based on this shape production, the tool path generation is a key factor on e.g. the resulting geometric accuracy, the resulting surface quality, and the working time. This paper presents an innovative tool path generation based on a commercial milling CAM package considering the surface quality and working time. This approach offers the ability to define a specific scallop height as an indicator of the surface quality for specific faces of a component. Moreover, it decreases the required working time for the production of the entire component compared to the use of a commercial software package without this adaptive approach. Different forming experiments have been performed to verify the newly developed tool path generation. Mainly, this approach serves to solve the existing conflict of combining the working time and the surface quality within the process of incremental sheet metal forming.

Fan Noise Prediction with Applications to Aircraft System Noise Assessment

NASA Technical Reports Server (NTRS)

Nark, Douglas M.; Envia, Edmane; Burley, Casey L.

2009-01-01

This paper describes an assessment of current fan noise prediction tools by comparing measured and predicted sideline acoustic levels from a benchmark fan noise wind tunnel test. Specifically, an empirical method and newly developed coupled computational approach are utilized to predict aft fan noise for a benchmark test configuration. Comparisons with sideline noise measurements are performed to assess the relative merits of the two approaches. The study identifies issues entailed in coupling the source and propagation codes, as well as provides insight into the capabilities of the tools in predicting the fan noise source and subsequent propagation and radiation. In contrast to the empirical method, the new coupled computational approach provides the ability to investigate acoustic near-field effects. The potential benefits/costs of these new methods are also compared with the existing capabilities in a current aircraft noise system prediction tool. The knowledge gained in this work provides a basis for improved fan source specification in overall aircraft system noise studies.

Improving sustainability by technology assessment and systems analysis: the case of IWRM Indonesia

NASA Astrophysics Data System (ADS)

Nayono, S.; Lehmann, A.; Kopfmüller, J.; Lehn, H.

2016-09-01

To support the implementation of the IWRM-Indonesia process in a water scarce and sanitation poor region of Central Java (Indonesia), sustainability assessments of several technology options of water supply and sanitation were carried out based on the conceptual framework of the integrative sustainability concept of the German Helmholtz association. In the case of water supply, the assessment was based on the life-cycle analysis and life-cycle-costing approach. In the sanitation sector, the focus was set on developing an analytical tool to improve planning procedures in the area of investigation, which can be applied in general to developing and newly emerging countries. Because sanitation systems in particular can be regarded as socio-technical systems, their permanent operability is closely related to cultural or religious preferences which influence acceptability. Therefore, the design of the tool and the assessment of sanitation technologies took into account the views of relevant stakeholders. The key results of the analyses are presented in this article.

The adverse outcome pathway concept: a pragmatic tool in toxicology.

PubMed

Vinken, Mathieu

2013-10-04

Adverse outcome pathways (AOPs) are novel tools in toxicology and human risk assessment with broad potential. AOPs are designed to provide a clear-cut mechanistic representation of critical toxicological effects that span over different layers of biological organization. AOPs share a common structure consisting of a molecular initiating event, a series of intermediate steps and key events, and an adverse outcome. Development of AOPs ideally complies with OECD guidelines. This also holds true for AOP evaluation, which includes consideration of the Bradford Hill criteria for weight-of-evidence assessment and meeting a set of key questions defined by the OECD. Elaborate AOP frameworks have yet been proposed for chemical-induced skin sensitization, cholestasis, liver fibrosis and liver steatosis. These newly postulated AOPs can serve a number of ubiquitous purposes, including the establishment of (quantitative) structure-activity relationships, the development of novel in vitro toxicity screening tests and the elaboration of prioritization strategies. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Fast interactive real-time volume rendering of real-time three-dimensional echocardiography: an implementation for low-end computers

NASA Technical Reports Server (NTRS)

Saracino, G.; Greenberg, N. L.; Shiota, T.; Corsi, C.; Lamberti, C.; Thomas, J. D.

2002-01-01

Real-time three-dimensional echocardiography (RT3DE) is an innovative cardiac imaging modality. However, partly due to lack of user-friendly software, RT3DE has not been widely accepted as a clinical tool. The object of this study was to develop and implement a fast and interactive volume renderer of RT3DE datasets designed for a clinical environment where speed and simplicity are not secondary to accuracy. Thirty-six patients (20 regurgitation, 8 normal, 8 cardiomyopathy) were imaged using RT3DE. Using our newly developed software, all 3D data sets were rendered in real-time throughout the cardiac cycle and assessment of cardiac function and pathology was performed for each case. The real-time interactive volume visualization system is user friendly and instantly provides consistent and reliable 3D images without expensive workstations or dedicated hardware. We believe that this novel tool can be used clinically for dynamic visualization of cardiac anatomy.

Risk and Vulnerability Analysis of Satellites Due to MM/SD with PIRAT

NASA Astrophysics Data System (ADS)

Kempf, Scott; Schafer, Frank Rudolph, Martin; Welty, Nathan; Donath, Therese; Destefanis, Roberto; Grassi, Lilith; Janovsky, Rolf; Evans, Leanne; Winterboer, Arne

2013-08-01

Until recently, the state-of-the-art assessment of the threat posed to spacecraft by micrometeoroids and space debris was limited to the application of ballistic limit equations to the outer hull of a spacecraft. The probability of no penetration (PNP) is acceptable for assessing the risk and vulnerability of manned space mission, however, for unmanned missions, whereby penetrations of the spacecraft exterior do not necessarily constitute satellite or mission failure, these values are overly conservative. The newly developed software tool PIRAT (Particle Impact Risk and Vulnerability Analysis Tool) has been developed based on the Schäfer-Ryan-Lambert (SRL) triple-wall ballistic limit equation (BLE), applicable for various satellite components. As a result, it has become possible to assess the individual failure rates of satellite components. This paper demonstrates the modeling of an example satellite, the performance of a PIRAT analysis and the potential for subsequent design optimizations with respect of micrometeoroid and space debris (MM/SD) impact risk.

Integrating spatial support tools into strategic planning-SEA of the GMS North-South Economic Corridor Strategy and Action Plan

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

Ramachandran, Pavit, E-mail: pramachandran@adb.org; Linde, Lothar, E-mail: lothar.linde@yahoo.de

The GMS countries, supported by the Asian Development Bank, have adopted a holistic, multidimensional approach to strengthen infrastructural linkages and facilitate cross border trade through (i) the establishment of a trans-boundary road connecting two economic nodes across marginalised areas, followed by 2) facilitation of environmentally and socially sound investments in these newly connected areas as a means to develop livelihoods. The North-South Economic Corridor is currently in its second phase of development, with investment opportunities to be laid out in the NSEC Strategy and Action Plan (SAP). It targets the ecologically and culturally sensitive border area between PR China's Yunnanmore » Province, Northern Lao PDR, and Thailand. A trans-boundary, cross-sectoral Strategic Environmental Assessment was conducted to support the respective governments in assessing potential environmental and social impacts, developing alternatives and mitigation options, and feeding the findings back into the SAP writing process. Given the spatial dimension of corridor development-both with regard to opportunities and risks-particular emphasis was put in the application of spatial modelling tools to help geographically locate and quantify impacts as a means to guide interventions and set priorities.« less

CFGP: a web-based, comparative fungal genomics platform.

PubMed

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F; Blair, Jaime E; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the 'fill-in-the-form-and-press-SUBMIT' user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI.

Development and psychometric evaluation of the "Neurosurgical Evaluation of Attitudes towards simulation Training" (NEAT) tool for use in neurosurgical education and training.

PubMed

Kirkman, Matthew A; Muirhead, William; Nandi, Dipankar; Sevdalis, Nick

2014-01-01

Neurosurgical simulation training is becoming increasingly popular. Attitudes toward simulation among residents can contribute to the effectiveness of simulation training, but such attitudes remain poorly explored in neurosurgery with no psychometrically proven measure in the literature. The aim of the present study was to evaluate prospectively a newly developed tool for this purpose: the Neurosurgical Evaluation of Attitudes towards simulation Training (NEAT). The NEAT tool was prospectively developed in 2 stages and psychometrically evaluated (validity and reliability) in 2 administrations with the same participants. The tool comprises a questionnaire with 9 Likert scale items and 2 free-text sections assessing attitudes toward simulation in neurosurgery. The evaluation was completed with 31 neurosurgery residents in London, United Kingdom, who were generally favorable toward neurosurgical simulation. The internal consistency of the questionnaire was high, as demonstrated by the overall Cronbach α values (α=0.899 and α=0.955). All but 2 questionnaire items had "substantial" or "almost perfect" test-retest reliability following repeated survey administrations (median Pearson r correlation=0.688; range, 0.248-0.841). NEAT items were well correlated with each other on both occasions, showing good validity of content within the NEAT tool. There was no significant relationship between either gender or length of neurosurgical experience and item ratings. NEAT is the first psychometrically evaluated tool for evaluating attitudes toward simulation in neurosurgery. Further implementation of NEAT is required in wider neurosurgical populations to establish whether specific population groups differ. Use of NEAT in studies of neurosurgical simulation could offer an additional outcome measure to performance metrics, permitting evaluation of the impact of neurosurgical simulation on attitudes toward simulation both between participants and within the same participants over time. Copyright © 2014 Elsevier Inc. All rights reserved.

Measuring antimicrobial prescribing quality in Australian hospitals: development and evaluation of a national antimicrobial prescribing survey tool.

PubMed

James, Rodney; Upjohn, Lydia; Cotta, Menino; Luu, Susan; Marshall, Caroline; Buising, Kirsty; Thursky, Karin

2015-01-01

Antimicrobial stewardship (AMS) programmes have been developed with the intention of reducing inappropriate and unnecessary use of antimicrobials, while improving the quality of patient care and locally helping prevent the development of antimicrobial resistance. An important aspect of AMS programmes is the qualitative assessment of prescribing through antimicrobial prescribing surveys (APS), which are able to provide information about the prescribing behaviour within institutions. Owing to lack of standardization of audit tools and the resources required, qualitative methods for the assessment of antimicrobial use are not often performed. The aim of this study was to design an audit tool that was appropriate for use in all Australian hospitals, suited to local user requirements and included an assessment of the overall appropriateness of the prescription. In November 2011, a pilot APS was conducted across 32 hospitals to assess the usability and generalizability of a newly designed audit tool. Following participant feedback, this tool was revised to reflect the requirements of the respondents. A second pilot study was then performed in November 2012 across 85 hospitals. These surveys identified several areas that can be targets for quality improvement at a national level, including: documentation of indication; surgical prophylaxis prescribed for >24 h; compliance with prescribing guidelines; and the appropriateness of the prescription. By involving the end users in the design and evaluation, we have been able to provide a practical and relevant APS tool for quantitative and qualitative data collection in a wide range of Australian hospital settings. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Development of an Influenza virus protein array using Sortagging technology

PubMed Central

Sinisi, Antonia; Popp, Maximilian Wei-Lin; Antos, John M.; Pansegrau, Werner; Savino, Silvana; Nissum, Mikkel; Rappuoli, Rino; Ploegh, Hidde L.; Buti, Ludovico

2013-01-01

Protein array technology is an emerging tool that enables high throughput screening of protein-protein or protein-lipid interactions and identification of immunodominant antigens during the course of a bacterial or viral infection. In this work we developed an Influenza virus protein array using the sortase-mediated transpeptidation reaction known as “Sortagging”. LPETG-tagged Influenza virus proteins from bacterial and eukaryotic cellular extracts were immobilized at their carboxyl-termini onto a pre-activated amine-glass slide coated with a Gly3 linker. Immobilized proteins were revealed by specific antibodies and the newly generated Sortag-protein chip can be used as a device for antigen and/or antibody screening. The specificity of the Sortase A (SrtA) reaction avoids purification steps in array building and allows immobilization of proteins in an oriented fashion. Previously, this versatile technology has been successfully employed for protein labeling and protein conjugation. Here, the tool is implemented to covalently link proteins of a viral genome onto a solid support. The system could readily be scaled up to proteins of larger genomes in order to develop protein arrays for high throughput screening. PMID:22594688

Use of cloud computing technology in natural hazard assessment and emergency management

NASA Astrophysics Data System (ADS)

Webley, P. W.; Dehn, J.

2015-12-01

During a natural hazard event, the most up-to-date data needs to be in the hands of those on the front line. Decision support system tools can be developed to provide access to pre-made outputs to quickly assess the hazard and potential risk. However, with the ever growing availability of new satellite data as well as ground and airborne data generated in real-time there is a need to analyze the large volumes of data in an easy-to-access and effective environment. With the growth in the use of cloud computing, where the analysis and visualization system can grow with the needs of the user, then these facilities can used to provide this real-time analysis. Think of a central command center uploading the data to the cloud compute system and then those researchers in-the-field connecting to a web-based tool to view the newly acquired data. New data can be added by any user and then viewed instantly by anyone else in the organization through the cloud computing interface. This provides the ideal tool for collaborative data analysis, hazard assessment and decision making. We present the rationale for developing a cloud computing systems and illustrate how this tool can be developed for use in real-time environments. Users would have access to an interactive online image analysis tool without the need for specific remote sensing software on their local system therefore increasing their understanding of the ongoing hazard and mitigate its impact on the surrounding region.

Feasibility and effects of newly developed balance control trainer for mobility and balance in chronic stroke patients: a randomized controlled trial.

PubMed

Lee, So Hyun; Byun, Seung Deuk; Kim, Chul Hyun; Go, Jin Young; Nam, Hyeon Uk; Huh, Jin Seok; Jung, Tae Du

2012-08-01

To investigate the feasibility and effects of balance training with a newly developed Balance Control Trainer (BCT) that applied the concept of vertical movement for the improvements of mobility and balance in chronic stroke patients. Forty chronic stroke patients were randomly assigned to an experimental or a control group. The experimental group (n=20) underwent training with a BCT for 20 minutes a day, 5 days a week for 4 weeks, in addition to concurrent conventional physical therapy. The control group (n=20) underwent only conventional therapy for 4 weeks. All participants were assessed by: the Functional Ambulation Categories (FAC), 10-meter Walking Test (10mWT), Timed Up and Go test (TUG), Berg Balance Scale (BBS), Korean Modified Barthel Index (MBI), and Manual Muscle Test (MMT) before training, and at 2 and 4 weeks of training. There were statistically significant improvements in all parameters except knee extensor power at 2 weeks of treatment, and in all parameters except MBI which showed further statistically significant progress in the experimental group over the next two weeks (p<0.05). Statistically significant improvements on all measurements were observed in the experimental group after 4 weeks total. Comparing the two groups at 2 and 4 weeks of training respectively, 10mWT, TUG, and BBS showed statistically more significant improvements in the experimental group (p<0.05). Balance training with a newly developed BCT is feasible and may be an effective tool to improve balance and gait in ambulatory chronic stroke patients. Furthermore, it may provide additional benefits when used in conjunction with conventional therapies.

First clinical trial of a newly developed capsule endoscope with panoramic side view for small bowel: a pilot study.

PubMed

Friedrich, Kilian; Gehrke, Sven; Stremmel, Wolfgang; Sieg, Andreas

2013-09-01

Capsule endoscopy is the first-line diagnostic technique for the small bowel. However, the inability to visualize the duodenal papilla is an inherent limitation of this method. In the present study, we evaluated feasibility of a newly developed CapsoCam SV1 capsule. This is a prospective dual center study of a newly developed video capsule CapsoCam SV1 from Capsovision, CA, providing panoramic 360° imaging. A high frequency of 20 frames occurs per second for the first 2 h and thereafter 12 frames/s, with a battery life of 15 h. We evaluated feasibility and completeness of small bowel examination together with secondary endpoints of duodenal papilla detection in 33 patients. Patients swallowed the capsules following colonoscopy or were prepared with 2 L of polyethylene glycol solution prior to the examination. All patients swallowed 20 mg of metoclopramide and 160 mg of simethicone 30 min before ingestion of the capsule. Thirty-one of the 33 patients' data could be evaluated. Small bowel examination was complete in all procedures. Mean time to pass the small bowel was 258 ± 136 min. Average small bowel cleanliness was 3.3 ± 0.5. In 71% of the patients, we identified the duodenal papilla. No adverse reaction in relation to the capsule examination was observed. CapsoCam SV1 is a safe and efficient tool in small bowel examination. The duodenal papilla as the only landmark in small bowel is detected in more than 70% of the patients. © 2013 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

[Innovations in medical undergraduate pathology education: The Paris Descartes medicine faculty experience].

PubMed

Just, Pierre-Alexandre; Verkarre, Virginie; Mansuet-Lupo, Audrey; Rabant, Marion; Daniliuc, Cristina; Radenen, Brigitte; Harent, Marion; Cassanelli, Lucien; Cherel, Éric; Javaux, Hubert; Tesniere, Antoine; Terris, Benoît; Badoual, Cécile

2016-08-01

At the Paris Descartes medicine faculty, we tested some newly developed tools to enhance the pedagogic value of the pathology teaching. In our faculty, this teaching is largely multidisciplinary and integrated in various teaching units; a large part is dedicated to practice works with thirteen 90min sessions. Virtual slides have been used for years in numerous medicine faculties; we successfully implemented this tool by adding contextual annotations, which facilitate students revising. We showed that rewarding students' assiduity enhanced their exam success. To do so, we now propose a short continuous assessment exam at the beginning of each practice session in the form of electronic multi-choice questions. Finally, we now propose a completely computerized final exam, on touchpads, that enhanced its docimologic value. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

[The primary research and development of software oversampling mapping system for electrocardiogram].

PubMed

Zhou, Yu; Ren, Jie

2011-04-01

We put forward a new concept of software oversampling mapping system for electrocardiogram (ECG) to assist the research of the ECG inverse problem to improve the generality of mapping system and the quality of mapping signals. We then developed a conceptual system based on the traditional ECG detecting circuit, Labview and DAQ card produced by National Instruments, and at the same time combined the newly-developed oversampling method into the system. The results indicated that the system could map ECG signals accurately and the quality of the signals was good. The improvement of hardware and enhancement of software made the system suitable for mapping in different situations. So the primary development of the software for oversampling mapping system was successful and further research and development can make the system a powerful tool for researching ECG inverse problem.

Healthcare provider cultural competency: development and initial validation of a patient report measure.

PubMed

Lucas, Todd; Michalopoulou, Georgia; Falzarano, Pamela; Menon, Shanti; Cunningham, Windy

2008-03-01

Health researchers have proposed that provider cultural competency may contribute to health disparities. Yet, this belief continues to lack empirical support, and this is due in part to measurement issues that have plagued the cultural competency construct. In the present research, we report on the development of a theoretically grounded, generally applicable, and patient report measure of provider cultural competency. Samples of predominantly African American patients (N=310) were recruited from three urban medical clinics to complete a survey about their relationship with their physician. We examined the factor structure, validity and other psychometric characteristics of a newly proposed patient report measure of provider cultural competency. Psychometric analyses supported a tripartite model of cultural competency that was comprised of patient judgments of their physician's cultural knowledge, awareness, and skill. In addition, this result was replicated across multiple clinical contexts, while also demonstrating convergent and incremental validity when correlated with measures of trust, satisfaction and discrimination. This newly proposed measure addresses prior limitations in cultural competency measurement and may enhance future research by providing a standardized tool for use in multiple clinical and cultural contexts. Copyright (c) 2008 APA, all rights reserved.

The ecological and construct validity of a newly developed measure of executive function: the Virtual Library Task.

PubMed

Renison, Belinda; Ponsford, Jennie; Testa, Renee; Richardson, Barry; Brownfield, Kylie

2012-05-01

Virtual reality (VR) assessment paradigms have the potential to address the limited ecological validity of pen and paper measures of executive function (EF) and the pragmatic and reliability issues associated with functional measures. To investigate the ecological validity and construct validity of a newly developed VR measure of EF, the Virtual Library Task (VLT); a real life analogous task--the Real Library Task (RLT); and five neuropsychological measures of EF were administered to 30 patients with traumatic brain injury (TBI) and 30 healthy Controls. Significant others for each participant also completed the Dysexecutive Questionnaire (DEX), which is a behavioral rating scale of everyday EF. Performances on the VLT and the RLT were significantly positively correlated indicating that VR performance is similar to real world performance. The TBI group performed significantly worse than the Control group on the VLT and the Modified Six Elements Test (MSET) but the other four neuropsychological measures of EF failed to differentiate the groups. Both the MSET and the VLT significantly predicted everyday EF suggesting that they are both ecologically valid tools for the assessment of EF. The VLT has the advantage over the MSET of providing objective measurement of individual components of EF.

High Thermal Conductivity and High Wear Resistance Tool Steels for cost-effective Hot Stamping Tools

NASA Astrophysics Data System (ADS)

Valls, I.; Hamasaiid, A.; Padré, A.

2017-09-01

In hot stamping/press hardening, in addition to its shaping function, the tool controls the cycle time, the quality of the stamped components through determining the cooling rate of the stamped blank, the production costs and the feasibility frontier for stamping a given component. During the stamping, heat is extracted from the stamped blank and transported through the tool to the cooling medium in the cooling lines. Hence, the tools’ thermal properties determine the cooling rate of the blank, the heat transport mechanism, stamping times and temperature distribution. The tool’s surface resistance to adhesive and abrasive wear is also an important cost factor, as it determines the tool durability and maintenance costs. Wear is influenced by many tool material parameters, such as the microstructure, composition, hardness level and distribution of strengthening phases, as well as the tool’s working temperature. A decade ago, Rovalma developed a hot work tool steel for hot stamping that features a thermal conductivity of more than double that of any conventional hot work tool steel. Since that time, many complimentary grades have been developed in order to provide tailored material solutions as a function of the production volume, degree of blank cooling and wear resistance requirements, tool geometries, tool manufacturing method, type and thickness of the blank material, etc. Recently, Rovalma has developed a new generation of high thermal conductivity, high wear resistance tool steel grades that enable the manufacture of cost effective tools for hot stamping to increase process productivity and reduce tool manufacturing costs and lead times. Both of these novel grades feature high wear resistance and high thermal conductivity to enhance tool durability and cut cycle times in the production process of hot stamped components. Furthermore, one of these new grades reduces tool manufacturing costs through low tool material cost and hardening through readily available gas-quenching, whereas the other new grade enables a faster manufacturing of the tool at reduced cost by eliminating the time and money consuming high temperature hardening altogether. The latter newly developed grade can be hardened from a soft delivery state for easy machining to 52 HRc by way of a simple low temperature precipitation hardening. In this work, these new grades and the role of the tool material’s thermal, mechanical and tribological properties as well as their processing features will be discussed in light of enabling the manufacture of intelligent hot stamping tools.

AnyWave: a cross-platform and modular software for visualizing and processing electrophysiological signals.

PubMed

Colombet, B; Woodman, M; Badier, J M; Bénar, C G

2015-03-15

The importance of digital signal processing in clinical neurophysiology is growing steadily, involving clinical researchers and methodologists. There is a need for crossing the gap between these communities by providing efficient delivery of newly designed algorithms to end users. We have developed such a tool which both visualizes and processes data and, additionally, acts as a software development platform. AnyWave was designed to run on all common operating systems. It provides access to a variety of data formats and it employs high fidelity visualization techniques. It also allows using external tools as plug-ins, which can be developed in languages including C++, MATLAB and Python. In the current version, plug-ins allow computation of connectivity graphs (non-linear correlation h2) and time-frequency representation (Morlet wavelets). The software is freely available under the LGPL3 license. AnyWave is designed as an open, highly extensible solution, with an architecture that permits rapid delivery of new techniques to end users. We have developed AnyWave software as an efficient neurophysiological data visualizer able to integrate state of the art techniques. AnyWave offers an interface well suited to the needs of clinical research and an architecture designed for integrating new tools. We expect this software to strengthen the collaboration between clinical neurophysiologists and researchers in biomedical engineering and signal processing. Copyright © 2015 Elsevier B.V. All rights reserved.

Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

PubMed Central

IJspeert, Hanna; van Schouwenburg, Pauline A.; van Zessen, David; Pico-Knijnenburg, Ingrid

2017-01-01

Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection. PMID:28416602

Alternative polyadenylation: New insights from global analyses

PubMed Central

Shi, Yongsheng

2012-01-01

Recent studies have revealed widespread mRNA alternative polyadenylation (APA) in eukaryotes and its dynamic spatial and temporal regulation. APA not only generates proteomic and functional diversity, but also plays important roles in regulating gene expression. Global deregulation of APA has been demonstrated in a variety of human diseases. Recent exciting advances in the field have been made possible in a large part by high throughput analyses using newly developed experimental tools. Here I review the recent progress in global studies of APA and the insights that have emerged from these and other studies that use more conventional methods. PMID:23097429

Algorithmic tools for interpreting vital signs.

PubMed

Rathbun, Melina C; Ruth-Sahd, Lisa A

2009-07-01

Today's complex world of nursing practice challenges nurse educators to develop teaching methods that promote critical thinking skills and foster quick problem solving in the novice nurse. Traditional pedagogies previously used in the classroom and clinical setting are no longer adequate to prepare nursing students for entry into practice. In addition, educators have expressed frustration when encouraging students to apply newly learned theoretical content to direct the care of assigned patients in the clinical setting. This article presents algorithms as an innovative teaching strategy to guide novice student nurses in the interpretation and decision making related to vital sign assessment in an acute care setting.

Intrinsically Disordered Protein Specific Force Field CHARMM36IDPSFF.

PubMed

Liu, Hao; Song, Dong; Lu, Hui; Luo, Ray; Chen, Hai-Feng

2018-05-28

Intrinsically disordered proteins (IDPs) are closely related to various human diseases. Because IDPs lack certain tertiary structure, it is difficult to use X-ray and NMR methods to measure their structures. Therefore, molecular dynamics simulation is a useful tool to study the conformer distribution of IDPs. However, most generic protein force fields were found to be insufficient in simulations of IDPs. Here we report our development for the CHARMM community. Our residue-specific IDP force field (CHARMM36IDPSFF) was developed based on the base generic force field with CMAP corrections of for all 20 naturally occurring amino acids. Multiple tests show that the simulated chemical shifts with the newly developed force field are in quantitative agreement with NMR experiment and are more accurate than the base generic force field. Comparison of J-couplings with previous work shows that CHARMM36IDPSFF and its corresponding base generic force field have their own advantages. In addition, CHARMM36IDPSFF simulations also agree with experiment for SAXS profiles and radii of gyration of IDPs. Detailed analysis shows that CHARMM36IDPSFF can sample more diverse and disordered conformers. These findings confirm that the newly developed force field can improve the balance of accuracy and efficiency for the conformer sampling of IDPs. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Agile Model Driven Development of Electronic Health Record-Based Specialty Population Registries

PubMed Central

Kannan, Vaishnavi; Fish, Jason C.; Willett, DuWayne L.

2018-01-01

The transformation of the American healthcare payment system from fee-for-service to value-based care increasingly makes it valuable to develop patient registries for specialized populations, to better assess healthcare quality and costs. Recent widespread adoption of Electronic Health Records (EHRs) in the U.S. now makes possible construction of EHR-based specialty registry data collection tools and reports, previously unfeasible using manual chart abstraction. But the complexities of specialty registry EHR tools and measures, along with the variety of stakeholders involved, can result in misunderstood requirements and frequent product change requests, as users first experience the tools in their actual clinical workflows. Such requirements churn could easily stall progress in specialty registry rollout. Modeling a system’s requirements and solution design can be a powerful way to remove ambiguities, facilitate shared understanding, and help evolve a design to meet newly-discovered needs. “Agile Modeling” retains these values while avoiding excessive unused up-front modeling in favor of iterative incremental modeling. Using Agile Modeling principles and practices, in calendar year 2015 one institution developed 58 EHR-based specialty registries, with 111 new data collection tools, supporting 134 clinical process and outcome measures, and enrolling over 16,000 patients. The subset of UML and non-UML models found most consistently useful in designing, building, and iteratively evolving EHR-based specialty registries included User Stories, Domain Models, Use Case Diagrams, Decision Trees, Graphical User Interface Storyboards, Use Case text descriptions, and Solution Class Diagrams. PMID:29750222

Agile Model Driven Development of Electronic Health Record-Based Specialty Population Registries.

PubMed

Kannan, Vaishnavi; Fish, Jason C; Willett, DuWayne L

2016-02-01

The transformation of the American healthcare payment system from fee-for-service to value-based care increasingly makes it valuable to develop patient registries for specialized populations, to better assess healthcare quality and costs. Recent widespread adoption of Electronic Health Records (EHRs) in the U.S. now makes possible construction of EHR-based specialty registry data collection tools and reports, previously unfeasible using manual chart abstraction. But the complexities of specialty registry EHR tools and measures, along with the variety of stakeholders involved, can result in misunderstood requirements and frequent product change requests, as users first experience the tools in their actual clinical workflows. Such requirements churn could easily stall progress in specialty registry rollout. Modeling a system's requirements and solution design can be a powerful way to remove ambiguities, facilitate shared understanding, and help evolve a design to meet newly-discovered needs. "Agile Modeling" retains these values while avoiding excessive unused up-front modeling in favor of iterative incremental modeling. Using Agile Modeling principles and practices, in calendar year 2015 one institution developed 58 EHR-based specialty registries, with 111 new data collection tools, supporting 134 clinical process and outcome measures, and enrolling over 16,000 patients. The subset of UML and non-UML models found most consistently useful in designing, building, and iteratively evolving EHR-based specialty registries included User Stories, Domain Models, Use Case Diagrams, Decision Trees, Graphical User Interface Storyboards, Use Case text descriptions, and Solution Class Diagrams.

Rapid detection of newly isolated Tembusu-related Flavivirus by reverse-transcription loop-mediated isothermal amplification assay

PubMed Central

2011-01-01

Background From April 2010 to January 2011, a severe new viral disease had devastated most duck-farming regions in China. This disease affected not only laying ducks but also meat ducks, causing huge economic losses for the poultry industry. The objective of this study is to develop a one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of the new virus related to Tembusu-related Flavivirus. Results The RT-LAMP assay is very simple and rapid, and the amplification can be completed within 50 min under isothermal conditions at 63°C by a set of 6 primers targeting the E gene based on the sequences analysis of the newly isolated viruses and other closely related Flavivirus.The monitoring of gene amplification can also be visualized by using SYBR green I fluorescent dye. In addition, the RT-LAMP assay for newly isolated Tembusu-related Flavivirus showed higher sensitivity with an RNA detection-limit of 2 copies/μL compared with 190 copies/μL of the conventional RT-PCR method. The specificity was identified without cross reaction to other common avian pathogens. By screening a panel of clinical samples this method was more feasible in clinical settings and there was higher positive coincidence rate than conventional RT-PCR and virus isolation. Conclusion The RT-LAMP assay for newly isolated Tembusu-related Flavivirus is a valuable tool for the rapid and real-time detection not only in well-equipped laboratories but also in general conditions. PMID:22185513

Preliminary clinical results: an analyzing tool for 2D optical imaging in detection of active inflammation in rheumatoid arthritis

NASA Astrophysics Data System (ADS)

Adi Aizudin Bin Radin Nasirudin, Radin; Meier, Reinhard; Ahari, Carmen; Sievert, Matti; Fiebich, Martin; Rummeny, Ernst J.; No"l, Peter B.

2011-03-01

Optical imaging (OI) is a relatively new method in detecting active inflammation of hand joints of patients suffering from rheumatoid arthritis (RA). With the high number of people affected by this disease especially in western countries, the availability of OI as an early diagnostic imaging method is clinically highly relevant. In this paper, we present a newly in-house developed OI analyzing tool and a clinical evaluation study. Our analyzing tool extends the capability of existing OI tools. We include many features in the tool, such as region-based image analysis, hyper perfusion curve analysis, and multi-modality image fusion to aid clinicians in localizing and determining the intensity of inflammation in joints. Additionally, image data management options, such as the full integration of PACS/RIS, are included. In our clinical study we demonstrate how OI facilitates the detection of active inflammation in rheumatoid arthritis. The preliminary clinical results indicate a sensitivity of 43.5%, a specificity of 80.3%, an accuracy of 65.7%, a positive predictive value of 76.6%, and a negative predictive value of 64.9% in relation to clinical results from MRI. The accuracy of inflammation detection serves as evidence to the potential of OI as a useful imaging modality for early detection of active inflammation in patients with rheumatoid arthritis. With our in-house developed tool we extend the usefulness of OI imaging in the clinical arena. Overall, we show that OI is a fast, inexpensive, non-invasive and nonionizing yet highly sensitive and accurate imaging modality.-

Tool development in threat assessment: syntax regularization and correlative analysis. Final report Task I and Task II, November 21, 1977-May 21, 1978. [Linguistic analysis

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

Miron, M.S.; Christopher, C.; Hirshfield, S.

1978-05-01

Psycholinguistics provides crisis managers in nuclear threat incidents with a quantitative methodology which can aid in the determination of threat credibility, authorship identification and perpetrator apprehension. The objective of this contract is to improve and enhance present psycholinguistic software systems by means of newly-developed, computer-automated techniques which significantly extend the technology of automated content and stylistic analysis of nuclear threat. In accordance with this overall objective, the first two contract Tasks have been completed and are reported on in this document. The first Task specifies the development of software support for the purpose of syntax regularization of vocabulary to rootmore » form. The second calls for the exploration and development of alternative approaches to correlative analysis of vocabulary usage.« less

Use of microwave satellite data to study variations in rainfall over the Indian Ocean

NASA Technical Reports Server (NTRS)

Hinton, Barry B.; Martin, David W.; Auvine, Brian; Olson, William S.

1990-01-01

The University of Wisconsin Space Science and Engineering Center mapped rainfall over the Indian Ocean using a newly developed Scanning Multichannel Microwave Radiometer (SMMR) rain-retrieval algorithm. The short-range objective was to characterize the distribution and variability of Indian Ocean rainfall on seasonal and annual scales. In the long-range, the objective is to clarify differences between land and marine regimes of monsoon rain. Researchers developed a semi-empirical algorithm for retrieving Indian Ocean rainfall. Tools for this development have come from radiative transfer and cloud liquid water models. Where possible, ground truth information from available radars was used in development and testing. SMMR rainfalls were also compared with Indian Ocean gauge rainfalls. Final Indian Ocean maps were produced for months, seasons, and years and interpreted in terms of historical analysis over the sub-continent.

New Coleoptera records from New Brunswick, Canada: Buprestidae

PubMed Central

Webster, Reginald P.; DeMerchant, Ian

2012-01-01

Abstract Nine species of Buprestidae; Agrilus bilineatus (Weber), Agrilus crinicornis Horn, Agrilus obsoletoguttatus Gory, Agrilus putillus putillus Say, Brachys ovatus (Weber), Buprestis sulcicollis (LeConte), Chalcophora liberta (Germar), Phaenops aeneola (Melsheimer), and Taphrocerus gracilis (Say) are newly recorded for New Brunswick, Canada. Agrilus bilineatus, A. crinicornis, A. obsoletoguttatus,and B. ovatus are also newly reported for the Maritime provinces. Lindgren 12-funnel traps do not appear to be an effective tool for sampling the Bupresidae. Collection, habitat notes, and distribution maps are presented for each species. PMID:22539885

A Multiagent Modeling Environment for Simulating Work Practice in Organizations

NASA Technical Reports Server (NTRS)

Sierhuis, Maarten; Clancey, William J.; vanHoof, Ron

2004-01-01

In this paper we position Brahms as a tool for simulating organizational processes. Brahms is a modeling and simulation environment for analyzing human work practice, and for using such models to develop intelligent software agents to support the work practice in organizations. Brahms is the result of more than ten years of research at the Institute for Research on Learning (IRL), NYNEX Science & Technology (the former R&D institute of the Baby Bell telephone company in New York, now Verizon), and for the last six years at NASA Ames Research Center, in the Work Systems Design and Evaluation group, part of the Computational Sciences Division (Code IC). Brahms has been used on more than ten modeling and simulation research projects, and recently has been used as a distributed multiagent development environment for developing work practice support tools for human in-situ science exploration on planetary surfaces, in particular a human mission to Mars. Brahms was originally conceived of as a business process modeling and simulation tool that incorporates the social systems of work, by illuminating how formal process flow descriptions relate to people s actual located activities in the workplace. Our research started in the early nineties as a reaction to experiences with work process modeling and simulation . Although an effective tool for convincing management of the potential cost-savings of the newly designed work processes, the modeling and simulation environment was only able to describe work as a normative workflow. However, the social systems, uncovered in work practices studied by the design team played a significant role in how work actually got done-actual lived work. Multi- tasking, informal assistance and circumstantial work interactions could not easily be represented in a tool with a strict workflow modeling paradigm. In response, we began to develop a tool that would have the benefits of work process modeling and simulation, but be distinctively able to represent the relations of people, locations, systems, artifacts, communication and information content.

Systemic regulation of leaf anatomical structure, photosynthetic performance, and high-light tolerance in sorghum.

PubMed

Jiang, Chuang-Dao; Wang, Xin; Gao, Hui-Yuan; Shi, Lei; Chow, Wah Soon

2011-03-01

Leaf anatomy of C3 plants is mainly regulated by a systemic irradiance signal. Since the anatomical features of C4 plants are different from that of C3 plants, we investigated whether the systemic irradiance signal regulates leaf anatomical structure and photosynthetic performance in sorghum (Sorghum bicolor), a C4 plant. Compared with growth under ambient conditions (A), no significant changes in anatomical structure were observed in newly developed leaves by shading young leaves alone (YS). Shading mature leaves (MS) or whole plants (S), on the other hand, caused shade-leaf anatomy in newly developed leaves. By contrast, chloroplast ultrastructure in developing leaves depended only on their local light conditions. Functionally, shading young leaves alone had little effect on their net photosynthetic capacity and stomatal conductance, but shading mature leaves or whole plants significantly decreased these two parameters in newly developed leaves. Specifically, the net photosynthetic rate in newly developed leaves exhibited a positive linear correlation with that of mature leaves, as did stomatal conductance. In MS and S treatments, newly developed leaves exhibited severe photoinhibition under high light. By contrast, newly developed leaves in A and YS treatments were more resistant to high light relative to those in MS- and S-treated seedlings. We suggest that (1) leaf anatomical structure, photosynthetic capacity, and high-light tolerance in newly developed sorghum leaves were regulated by a systemic irradiance signal from mature leaves; and (2) chloroplast ultrastructure only weakly influenced the development of photosynthetic capacity and high-light tolerance. The potential significance of the regulation by a systemic irradiance signal is discussed.

Measuring Patient-Reported Outcomes: Key Metrics in Reconstructive Surgery.

PubMed

Voineskos, Sophocles H; Nelson, Jonas A; Klassen, Anne F; Pusic, Andrea L

2018-01-29

Satisfaction and improved quality of life are among the most important outcomes for patients undergoing plastic and reconstructive surgery for a variety of diseases and conditions. Patient-reported outcome measures (PROMs) are essential tools for evaluating the benefits of newly developed surgical techniques. Modern PROMs are being developed with new psychometric approaches, such as Rasch Measurement Theory, and their measurement properties (validity, reliability, responsiveness) are rigorously tested. These advances have resulted in the availability of PROMs that provide clinically meaningful data and effectively measure functional as well as psychosocial outcomes. This article guides the reader through the steps of creating a PROM and highlights the potential research and clinical uses of such instruments. Limitations of PROMs and anticipated future directions in this field are discussed.

Quantitative 1H NMR: Development and Potential of an Analytical Method – an Update

PubMed Central

Pauli, Guido F.; Gödecke, Tanja; Jaki, Birgit U.; Lankin, David C.

2012-01-01

Covering the literature from mid-2004 until the end of 2011, this review continues a previous literature overview on quantitative 1H NMR (qHNMR) methodology and its applications in the analysis of natural products (NPs). Among the foremost advantages of qHNMR is its accurate function with external calibration, the lack of any requirement for identical reference materials, a high precision and accuracy when properly validated, and an ability to quantitate multiple analytes simultaneously. As a result of the inclusion of over 170 new references, this updated review summarizes a wealth of detailed experiential evidence and newly developed methodology that supports qHNMR as a valuable and unbiased analytical tool for natural product and other areas of research. PMID:22482996

Newly developed double neural network concept for reliable fast plasma position control

NASA Astrophysics Data System (ADS)

Jeon, Young-Mu; Na, Yong-Su; Kim, Myung-Rak; Hwang, Y. S.

2001-01-01

Neural network is considered as a parameter estimation tool in plasma controls for next generation tokamak such as ITER. The neural network has been reported to be so accurate and fast for plasma equilibrium identification that it may be applied to the control of complex tokamak plasmas. For this application, the reliability of the conventional neural network needs to be improved. In this study, a new idea of double neural network is developed to achieve this. The new idea has been applied to simple plasma position identification of KSTAR tokamak for feasibility test. Characteristics of the concept show higher reliability and fault tolerance even in severe faulty conditions, which may make neural network applicable to plasma control reliably and widely in future tokamaks.

Brief Report: Predicting Functional Disability: One-Year Results From the Scottish Early Rheumatoid Arthritis Inception Cohort.

PubMed

Kronisch, Caroline; McLernon, David J; Dale, James; Paterson, Caron; Ralston, Stuart H; Reid, David M; Tierney, Ann; Harvie, John; McKay, Neil; Wilson, Hilary E; Munro, Robin; Saunders, Sarah; Richmond, Ruth; Baxter, Derek; McMahon, Mike; Kumar, Vinod; McLaren, John; Siebert, Stefan; McInnes, Iain B; Porter, Duncan; Macfarlane, Gary J; Basu, Neil

2016-07-01

To identify baseline prognostic indicators of disability at 1 year within a contemporary early inflammatory arthritis inception cohort and then develop a clinically useful tool to support early patient education and decision-making. The Scottish Early Rheumatoid Arthritis (SERA) inception cohort is a multicenter, prospective study of patients with newly presenting RA or undifferentiated arthritis. SERA data were analyzed to determine baseline predictors of disability (defined as a Health Assessment Questionnaire [HAQ] score of ≥1) at 1 year. Clinical and psychosocial baseline exposures were entered into a forward stepwise logistic regression model. The model was externally validated using newly accrued SERA data and subsequently converted into a prediction tool. Of the 578 participants (64.5% female), 36.7% (n = 212) reported functional disability at 1 year. Functional disability was independently predicted by baseline disability (odds ratio [OR] 2.67 [95% confidence interval (95% CI) 1.98, 3.59]), depression (OR 2.52 [95% CI 1.18, 5.37]), anxiety (OR 2.37 [95% CI 1.33, 4.21]), being in paid employment with absenteeism during the last week (OR 1.19 [95% CI 0.63, 2.23]), not being in paid employment (OR 2.36 [95% CI 1.38, 4.03]), and being overweight (OR 1.61 [95% CI 1.04, 2.50]). External validation (using 113 newly acquired patients) evidenced good discriminative performance with a C statistic of 0.74, and the calibration slope showed no evidence of model overfit (P = 0.31). In the context of modern early inflammatory arthritis treatment paradigms, predictors of disability at 1 year appear to be dominated by psychosocial rather than more traditional clinical measures. This indicates the potential benefit of early access to nonpharmacologic interventions targeting key psychosocial factors, such as mental health and work disability. © 2016, American College of Rheumatology.

Drug-Induced Liver Injury: Pattern Recognition and Future Directions

PubMed Central

Haque, Tanvir; Sasatomi, Eizaburo; Hayashi, Paul H.

2016-01-01

Drug-induced liver injury (DILI) remains a significant clinical challenge and is the leading cause of acute liver failure in most countries. An aging population that uses more medications, a constant influx of newly developed drugs and a growing risk from unfamiliar herbal and dietary supplements will make DILI an increasing part of clinical practice. Currently, the most effective strategy for disease management is rapid identification, withholding the inciting agents, supportive care and having a firm understanding of the expected natural history. There are resources available to aid the clinician, including a new online “textbook” as well as causality assessment tools, but a heightened awareness of risk and the disease’s varying phenotypes and good history-taking remain cornerstones to diagnosis. Looking ahead, growing registries of cases, pharmacoepidemiology studies and translational research into the mechanisms of injury may produce better diagnostic tools, markers for risk and disease, and prevention and therapeutics. PMID:26696029

Mechanisms of yeast stress tolerance and its manipulation for efficient fuel ethanol production.

PubMed

Zhao, X Q; Bai, F W

2009-10-12

Yeast strains of Saccharomyces cerevisiae have been extensively studied in recent years for fuel ethanol production, in which yeast cells are exposed to various stresses such as high temperature, ethanol inhibition, and osmotic pressure from product and substrate sugars as well as the inhibitory substances released from the pretreatment of lignocellulosic biomass. An in-depth understanding of the mechanism of yeast stress tolerance contributes to breeding more robust strains for ethanol production, especially under very high gravity conditions. Taking advantage of the "omics" technology, the stress response and defense mechanism of yeast cells during ethanol fermentation were further explored, and the newly emerged tools such as genome shuffling and global transcription machinery engineering have been applied to breed stress resistant yeast strains for ethanol production. In this review, the latest development of stress tolerance mechanisms was focused, and improvement of yeast stress tolerance by both random and rational tools was presented.

Stable-isotope analysis: a neglected tool for placing parasites in food webs.

PubMed

Sabadel, A J M; Stumbo, A D; MacLeod, C D

2018-02-28

Parasites are often overlooked in the construction of food webs, despite their ubiquitous presence in almost every type of ecosystem. Researchers who do recognize their importance often struggle to include parasites using classical food-web theory, mainly due to the parasites' multiple hosts and life stages. A novel approach using compound-specific stable-isotope analysis promises to provide considerable insight into the energetic exchanges of parasite and host, which may solve some of the issues inherent in incorporating parasites using a classical approach. Understanding the role of parasites within food webs, and tracing the associated biomass transfers, are crucial to constructing new models that will expand our knowledge of food webs. This mini-review focuses on stable-isotope studies published in the past decade, and introduces compound-specific stable-isotope analysis as a powerful, but underutilized, newly developed tool that may answer many unresolved questions regarding the role of parasites in food webs.

URDME: a modular framework for stochastic simulation of reaction-transport processes in complex geometries.

PubMed

Drawert, Brian; Engblom, Stefan; Hellander, Andreas

2012-06-22

Experiments in silico using stochastic reaction-diffusion models have emerged as an important tool in molecular systems biology. Designing computational software for such applications poses several challenges. Firstly, realistic lattice-based modeling for biological applications requires a consistent way of handling complex geometries, including curved inner- and outer boundaries. Secondly, spatiotemporal stochastic simulations are computationally expensive due to the fast time scales of individual reaction- and diffusion events when compared to the biological phenomena of actual interest. We therefore argue that simulation software needs to be both computationally efficient, employing sophisticated algorithms, yet in the same time flexible in order to meet present and future needs of increasingly complex biological modeling. We have developed URDME, a flexible software framework for general stochastic reaction-transport modeling and simulation. URDME uses Unstructured triangular and tetrahedral meshes to resolve general geometries, and relies on the Reaction-Diffusion Master Equation formalism to model the processes under study. An interface to a mature geometry and mesh handling external software (Comsol Multiphysics) provides for a stable and interactive environment for model construction. The core simulation routines are logically separated from the model building interface and written in a low-level language for computational efficiency. The connection to the geometry handling software is realized via a Matlab interface which facilitates script computing, data management, and post-processing. For practitioners, the software therefore behaves much as an interactive Matlab toolbox. At the same time, it is possible to modify and extend URDME with newly developed simulation routines. Since the overall design effectively hides the complexity of managing the geometry and meshes, this means that newly developed methods may be tested in a realistic setting already at an early stage of development. In this paper we demonstrate, in a series of examples with high relevance to the molecular systems biology community, that the proposed software framework is a useful tool for both practitioners and developers of spatial stochastic simulation algorithms. Through the combined efforts of algorithm development and improved modeling accuracy, increasingly complex biological models become feasible to study through computational methods. URDME is freely available at http://www.urdme.org.

Timely Reporting and Interactive Visualization of Animal Health and Slaughterhouse Surveillance Data in Switzerland.

PubMed

Muellner, Ulrich J; Vial, Flavie; Wohlfender, Franziska; Hadorn, Daniela; Reist, Martin; Muellner, Petra

2015-01-01

The reporting of outputs from health surveillance systems should be done in a near real-time and interactive manner in order to provide decision makers with powerful means to identify, assess, and manage health hazards as early and efficiently as possible. While this is currently rarely the case in veterinary public health surveillance, reporting tools do exist for the visual exploration and interactive interrogation of health data. In this work, we used tools freely available from the Google Maps and Charts library to develop a web application reporting health-related data derived from slaughterhouse surveillance and from a newly established web-based equine surveillance system in Switzerland. Both sets of tools allowed entry-level usage without or with minimal programing skills while being flexible enough to cater for more complex scenarios for users with greater programing skills. In particular, interfaces linking statistical softwares and Google tools provide additional analytical functionality (such as algorithms for the detection of unusually high case occurrences) for inclusion in the reporting process. We show that such powerful approaches could improve timely dissemination and communication of technical information to decision makers and other stakeholders and could foster the early-warning capacity of animal health surveillance systems.

rVISTA 2.0: Evolutionary Analysis of Transcription Factor Binding Sites

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

Loots, G G; Ovcharenko, I

2004-01-28

Identifying and characterizing the patterns of DNA cis-regulatory modules represents a challenge that has the potential to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and therefore are often conserved between related species. Using this evolutionary principle we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. The rVISTA tool combines transcription factor binding site (TFBS) predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are highly conserved and present in a specific configuration within an alignment. Heremore » we present the newly developed version 2.0 of the rVISTA tool that can process alignments generated by both zPicture and PipMaker alignment programs or use pre-computed pairwise alignments of seven vertebrate genomes available from the ECR Browser. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. rVISTA tool is publicly available at http://rvista.dcode.org/.« less

Screening for psychological late effects in childhood, adolescent and young adult cancer survivors: a systematic review.

PubMed

Michel, Gisela; Vetsch, Janine

2015-07-01

In the past years, increasing evidence showed that many childhood cancer survivors suffer from psychological distress long after treatment ended. However, psychosocial issues are often neglected during follow-up care. Including screening for psychological distress before follow-up appointments might help addressing the topic in survivors who need support. Our aim was to systematically review the available evidence on screening for psychological distress in childhood cancer survivors. We found eight studies that investigated different screening tools for their utility in detecting psychological distress in childhood cancer survivors. The Brief Symptom Inventory-18 with an adapted cutoff score for childhood cancer survivors, and the newly developed short form of the Beck Depression Index were both shown to be of a potential benefit as brief screening tools in follow-up care. We identified promising screening tools to be used to detect psychological distress in childhood cancer survivors. However, there is still a lack of studies addressing applicability and effectiveness when screening is routinely implemented into follow-up care. To improve quality of follow-up care, and identify and treat survivors with psychological distress, screening tools should now be implemented and their adequacy further tested in day-to-day clinic life.

A community resource benchmarking predictions of peptide binding to MHC-I molecules.

PubMed

Peters, Bjoern; Bui, Huynh-Hoa; Frankild, Sune; Nielson, Morten; Lundegaard, Claus; Kostem, Emrah; Basch, Derek; Lamberth, Kasper; Harndahl, Mikkel; Fleri, Ward; Wilson, Stephen S; Sidney, John; Lund, Ole; Buus, Soren; Sette, Alessandro

2006-06-09

Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide binding preference, which can be captured in prediction algorithms, allowing for the rapid scan of entire pathogen proteomes for peptide likely to bind MHC. Here we make public a large set of 48,828 quantitative peptide-binding affinity measurements relating to 48 different mouse, human, macaque, and chimpanzee MHC class I alleles. We use this data to establish a set of benchmark predictions with one neural network method and two matrix-based prediction methods extensively utilized in our groups. In general, the neural network outperforms the matrix-based predictions mainly due to its ability to generalize even on a small amount of data. We also retrieved predictions from tools publicly available on the internet. While differences in the data used to generate these predictions hamper direct comparisons, we do conclude that tools based on combinatorial peptide libraries perform remarkably well. The transparent prediction evaluation on this dataset provides tool developers with a benchmark for comparison of newly developed prediction methods. In addition, to generate and evaluate our own prediction methods, we have established an easily extensible web-based prediction framework that allows automated side-by-side comparisons of prediction methods implemented by experts. This is an advance over the current practice of tool developers having to generate reference predictions themselves, which can lead to underestimating the performance of prediction methods they are not as familiar with as their own. The overall goal of this effort is to provide a transparent prediction evaluation allowing bioinformaticians to identify promising features of prediction methods and providing guidance to immunologists regarding the reliability of prediction tools.

Health-related quality of life in children with newly diagnosed immune thrombocytopenia

PubMed Central

Heitink-Pollé, Katja M.J.; Haverman, Lotte; Annink, Kim V.; Schep, Sarah J.; de Haas, Masja; Bruin, Marrie C.A.

2014-01-01

Despite its generally transient and benign course, childhood immune thrombocytopenia has a large impact on health-related quality of life. Recently published guidelines state that quality of life should be taken into account while making decisions on management in childhood immune thrombocytopenia. We, therefore, assessed health-related quality of life in children with newly diagnosed immune thrombocytopenia in a prospective multicenter study. One hundred and seven children aged 6 months-16 years (mean age 5.57 years) were included. We used Pediatric Quality of Life Inventory™ and Kids’ ITP Tools questionnaires at diagnosis and during standardized follow-up. Scores on the Pediatric Quality of Life Inventory™ Core Scales were compared with those of healthy children. Relationships between health-related quality of life scores and treatment modality, bleeding tendency and course of the disease were examined. Kids’ ITP Tools proxy reports and parent self-reports showed significant higher health-related quality of life scores in children who recovered than in children with persistent immune thrombocytopenia (at 3 months: Kids’ ITP Tools parent self-report score 80.85 for recovered patients (n=69) versus 58.98 for patients with persistent disease (n=21), P<0.001). No significant differences in health-related quality of life were found between children with mild or moderate bleeding or between children who received intravenous immunoglobulin or children who were carefully observed. In conclusion, health-related quality of life of children with newly diagnosed immune thrombocytopenia is not influenced by treatment modality or bleeding severity, but only by clinical course of the disease. (Dutch Trial Register identifier: NTR TC1563) PMID:24951468

Rapid Prototyping of Hydrologic Model Interfaces with IPython

NASA Astrophysics Data System (ADS)

Farthing, M. W.; Winters, K. D.; Ahmadia, A. J.; Hesser, T.; Howington, S. E.; Johnson, B. D.; Tate, J.; Kees, C. E.

2014-12-01

A significant gulf still exists between the state of practice and state of the art in hydrologic modeling. Part of this gulf is due to the lack of adequate pre- and post-processing tools for newly developed computational models. The development of user interfaces has traditionally lagged several years behind the development of a particular computational model or suite of models. As a result, models with mature interfaces often lack key advancements in model formulation, solution methods, and/or software design and technology. Part of the problem has been a focus on developing monolithic tools to provide comprehensive interfaces for the entire suite of model capabilities. Such efforts require expertise in software libraries and frameworks for creating user interfaces (e.g., Tcl/Tk, Qt, and MFC). These tools are complex and require significant investment in project resources (time and/or money) to use. Moreover, providing the required features for the entire range of possible applications and analyses creates a cumbersome interface. For a particular site or application, the modeling requirements may be simplified or at least narrowed, which can greatly reduce the number and complexity of options that need to be accessible to the user. However, monolithic tools usually are not adept at dynamically exposing specific workflows. Our approach is to deliver highly tailored interfaces to users. These interfaces may be site and/or process specific. As a result, we end up with many, customized interfaces rather than a single, general-use tool. For this approach to be successful, it must be efficient to create these tailored interfaces. We need technology for creating quality user interfaces that is accessible and has a low barrier for integration into model development efforts. Here, we present efforts to leverage IPython notebooks as tools for rapid prototyping of site and application-specific user interfaces. We provide specific examples from applications in near-shore environments as well as levee analysis. We discuss our design decisions and methodology for developing customized interfaces, strategies for delivery of the interfaces to users in various computing environments, as well as implications for the design/implementation of simulation models.

Identification of two novel mutations in the SLC45A2 gene in a Hungarian pedigree affected by unusual OCA type 4.

PubMed

Tóth, Lola; Fábos, Beáta; Farkas, Katalin; Sulák, Adrienn; Tripolszki, Kornélia; Széll, Márta; Nagy, Nikoletta

2017-03-15

Oculocutaneous albinism (OCA) is a clinically and genetically heterogenic group of pigmentation abnormalities. OCA type IV (OCA4, OMIM 606574) develops due to homozygous or compound heterozygous mutations in the solute carrier family 45, member 2 (SLC45A2) gene. This gene encodes a membrane-associated transport protein, which regulates tyrosinase activity and, thus, melanin content by changing melanosomal pH and disrupting the incorporation of copper into tyrosinase. Here we report two Hungarian siblings affected by an unusual OCA4 phenotype. After genomic DNA was isolated from peripheral blood of the patients, the coding regions of the SLC45A2 gene were sequenced. In silico tools were applied to identify the functional impact of the newly detected mutations. Direct sequencing of the SLC45A2 gene revealed two novel, heterozygous mutations, one missense (c.1226G > A, p.Gly409Asp) and one nonsense (c.1459C > T, p.Gln437*), which were present in both patients, suggesting the mutations were compound heterozygous. In silico tools suggest that these variations are disease causing mutations. The newly identified mutations may affect the transmembrane domains of the protein, and could impair transport function, resulting in decreases in both melanosomal pH and tyrosinase activity. Our study provides expands on the mutation spectrum of the SLC45A2 gene and the genetic background of OCA4.

Workflow and web application for annotating NCBI BioProject transcriptome data

PubMed Central

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A.; Barrero, Luz S.; Landsman, David

2017-01-01

Abstract The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. Database URL: http://www.ncbi.nlm.nih.gov/projects/physalis/ PMID:28605765

Assessing hand hygiene resources and practices at a large african teaching hospital.

PubMed

Owusu-Ofori, Alex; Jennings, Rebecca; Burgess, Jennifer; Prasad, Priya A; Acheampong, Faustina; Coffin, Susan E

2010-08-01

To gather baseline data on hand hygiene (HH) practices in an African hospital with a newly established infection prevention and control team. Cross-sectional, observational study. Setting. Komfo Anokye Teaching Hospital, a large teaching hospital in Ghana with approximately 1,000 beds. All hospital staff with patient contact were eligible for assessment of HH practices. HH observations were conducted using a standardized data collection tool and method based on the World Health Organization's "5 Moments of Hand Hygiene." Small-group interviews were conducted to gather additional information on perceptions of HH and barriers to its use. HH resource needs were also assessed using a standardized tool. HH was attempted in 12% of the opportunities and was performed appropriately in 4% of the opportunities. Most main wards (89%) had at least 1 functional HH station. The most commonly identified barriers to HH were limited resources and lack of knowledge on appropriate times to perform HH. We developed and applied tools to evaluate HH resources and practices in a large African hospital. These assessments were undertaken to guide future efforts to improve HH at this hospital but can also serve as a model of the way to perform a systematic assessment at acute care hospitals in developing countries.

Enabling Efficient Climate Science Workflows in High Performance Computing Environments

NASA Astrophysics Data System (ADS)

Krishnan, H.; Byna, S.; Wehner, M. F.; Gu, J.; O'Brien, T. A.; Loring, B.; Stone, D. A.; Collins, W.; Prabhat, M.; Liu, Y.; Johnson, J. N.; Paciorek, C. J.

2015-12-01

A typical climate science workflow often involves a combination of acquisition of data, modeling, simulation, analysis, visualization, publishing, and storage of results. Each of these tasks provide a myriad of challenges when running on a high performance computing environment such as Hopper or Edison at NERSC. Hurdles such as data transfer and management, job scheduling, parallel analysis routines, and publication require a lot of forethought and planning to ensure that proper quality control mechanisms are in place. These steps require effectively utilizing a combination of well tested and newly developed functionality to move data, perform analysis, apply statistical routines, and finally, serve results and tools to the greater scientific community. As part of the CAlibrated and Systematic Characterization, Attribution and Detection of Extremes (CASCADE) project we highlight a stack of tools our team utilizes and has developed to ensure that large scale simulation and analysis work are commonplace and provide operations that assist in everything from generation/procurement of data (HTAR/Globus) to automating publication of results to portals like the Earth Systems Grid Federation (ESGF), all while executing everything in between in a scalable environment in a task parallel way (MPI). We highlight the use and benefit of these tools by showing several climate science analysis use cases they have been applied to.

"Survivor" torches "Who Wants to Be a Physician?" in the educational games ratings war.

PubMed

Howard, Mary G; Collins, Heidi L; DiCarlo, Stephen E

2002-12-01

We recently developed an educational game for reviewing respiratory physiology in a large classroom. The "Who Wants to be a Physician?" game encouraged medical students to be active participants in the learning process. An evaluation of the game documented that students enjoyed the active format, and the students reported that the game enhanced their ability to understand and retain information. However, the evaluation also revealed that the game had limitations. Specifically, the students recommended the use of multiple-choice questions to match the Medical Board Examination format and to speed up the game (i.e., cover more topics). The students also wanted to increase their level of participation and interaction. Finally, we wanted to emphasize the benefits of peer instruction as a collaborative learning tool. To address these limitations, we designed a new game, "Survivor." Survivor incorporated multiple-choice questions and emphasized peer instruction and a capacity to gather information and solve novel problems. In addition, participation was increased by including the student audience in the game. Finally, an evaluation instrument was utilized to assess the effectiveness of this instructional tool in an academic setting. As a result of these improvements, the evaluation documents that the newly developed tool is a more effective educational game that couples fun and creative excitement with proven and effective educational concepts.

Development and validation of a patient symptom questionnaire to facilitate early diagnosis of thyroid-associated orbitopathy in graves' disease.

PubMed

Mohaseb, Kam; Linder, Mark; Rootman, Jack; Wilkins, G E; Schechter, Martin T; Dolman, Peter J; Singer, Joel

2008-01-01

To construct a patient-based symptom questionnaire to facilitate early referral of thyroid-associated orbitopathy (TAO) in Graves' hyperthyroidism (GH). Phase I of our study involved developing a symptomatology-based questionnaire for the self-reporting of TAO symptoms in patients recently diagnosed with GH. Phase II involved administering the questionnaire along with a standard ophthalmic examination to a screening cohort of patients newly diagnosed with GH. Symptoms highly associated with the clinical diagnosis of TAO were used to construct a tool with the highest possible sensitivity. Phase III involved validation of this tool in a new cohort of patients recently diagnosed with GH. For each patient, the diagnosis of TAO was made by both a standardized orbital ophthalmic exam and the questionnaire. Results from the questionnaire were then compared to the clinical examination. The questionnaire was compared to the standardized examination and found to have a sensitivity of 0.76 and a specificity of 0.82 in the validation phase of the study. This questionnaire may be a useful tool in clinical practice to allow identification of patients with TAO secondary to GH. Future studies using this questionnaire are needed to determine whether earlier identification and management of these patients is associated with reduced morbidity from TAO.

CFGP: a web-based, comparative fungal genomics platform

PubMed Central

Park, Jongsun; Park, Bongsoo; Jung, Kyongyong; Jang, Suwang; Yu, Kwangyul; Choi, Jaeyoung; Kong, Sunghyung; Park, Jaejin; Kim, Seryun; Kim, Hyojeong; Kim, Soonok; Kim, Jihyun F.; Blair, Jaime E.; Lee, Kwangwon; Kang, Seogchan; Lee, Yong-Hwan

2008-01-01

Since the completion of the Saccharomyces cerevisiae genome sequencing project in 1996, the genomes of over 80 fungal species have been sequenced or are currently being sequenced. Resulting data provide opportunities for studying and comparing fungal biology and evolution at the genome level. To support such studies, the Comparative Fungal Genomics Platform (CFGP; http://cfgp.snu.ac.kr), a web-based multifunctional informatics workbench, was developed. The CFGP comprises three layers, including the basal layer, middleware and the user interface. The data warehouse in the basal layer contains standardized genome sequences of 65 fungal species. The middleware processes queries via six analysis tools, including BLAST, ClustalW, InterProScan, SignalP 3.0, PSORT II and a newly developed tool named BLASTMatrix. The BLASTMatrix permits the identification and visualization of genes homologous to a query across multiple species. The Data-driven User Interface (DUI) of the CFGP was built on a new concept of pre-collecting data and post-executing analysis instead of the ‘fill-in-the-form-and-press-SUBMIT’ user interfaces utilized by most bioinformatics sites. A tool termed Favorite, which supports the management of encapsulated sequence data and provides a personalized data repository to users, is another novel feature in the DUI. PMID:17947331

How we used a patient visit tracker tool to advance experiential learning in systems-based practice and quality improvement in a medical student clinic.

PubMed

Chen, Chen Amy; Park, Ryan J; Hegde, John V; Jun, Tomi; Christman, Mitalee P; Yoo, Sun M; Yamasaki, Alisa; Berhanu, Aaron; Vohra-Khullar, Pamela; Remus, Kristin; Schwartzstein, Richard M; Weinstein, Amy R

2016-01-01

Poorly designed healthcare systems increase costs and preventable medical errors. To address these issues, systems-based practice (SBP) education provides future physicians with the tools to identify systemic errors and implement quality improvement (QI) initiatives to enhance the delivery of cost-effective, safe and multi-disciplinary care. Although SBP education is being implemented in residency programs and is mandated by the Accreditation Council for Graduate Medical Education (ACGME) as one of its core competencies, it has largely not been integrated into undergraduate medical education. We propose that Medical Student-Faculty Collaborative Clinics (MSFCCs) may be the ideal environment in which to train medical students in SBPs and QI initiatives, as they allow students to play pivotal roles in project development, administration, and management. Here we describe a process of experiential learning that was developed within a newly established MSFCC, which challenged students to identify inefficiencies, implement interventions, and track the results. After identifying bottlenecks in clinic operations, our students designed a patient visit tracker tool to monitor clinic flow and implemented solutions to decrease patient visit times. Our model allowed students to drive their own active learning in a practical clinical setting, providing early and unique training in crucial QI skills.

The Computerized Perceptual Motor Skills Assessment: A new visual perceptual motor skills evaluation tool for children in early elementary grades.

PubMed

Howe, Tsu-Hsin; Chen, Hao-Ling; Lee, Candy Chieh; Chen, Ying-Dar; Wang, Tien-Ni

2017-10-01

Visual perceptual motor skills have been proposed as underlying courses of handwriting difficulties. However, there is no evaluation tool currently available to assess these skills comprehensively and to serve as a sensitive measure. The purpose of this study was to validate the Computerized Perceptual Motor Skills Assessment (CPMSA), a newly developed evaluation tool for children in early elementary grades. Its test-retest reliability, concurrent validity, discriminant validity, and responsiveness were examined in 43 typically developing children and 26 children with handwriting difficulty. The CPMSA demonstrated excellent reliability across all subtests with intra-class correlation coefficients (ICCs)≥0.80. Significant moderate correlations between the domains of the CPMSA and corresponding gold standards including Beery VMI, the TVPS-3, and the eye-hand coordination subtest of the DTVP-2 demonstrated good concurrent validity. In addition, the CPMSA showed evidence of discriminant validity in samples of children with and without handwriting difficulty. This article provides evidence in support of the CPMSA. The CPMSA is a reliable, valid, and promising measure of visual perceptual motor skills for children in early elementary grades. Directions for future study and improvements to the assessment are discussed. Copyright © 2017. Published by Elsevier Ltd.

SEPEM: A tool for statistical modeling the solar energetic particle environment

NASA Astrophysics Data System (ADS)

Crosby, Norma; Heynderickx, Daniel; Jiggens, Piers; Aran, Angels; Sanahuja, Blai; Truscott, Pete; Lei, Fan; Jacobs, Carla; Poedts, Stefaan; Gabriel, Stephen; Sandberg, Ingmar; Glover, Alexi; Hilgers, Alain

2015-07-01

Solar energetic particle (SEP) events are a serious radiation hazard for spacecraft as well as a severe health risk to humans traveling in space. Indeed, accurate modeling of the SEP environment constitutes a priority requirement for astrophysics and solar system missions and for human exploration in space. The European Space Agency's Solar Energetic Particle Environment Modelling (SEPEM) application server is a World Wide Web interface to a complete set of cross-calibrated data ranging from 1973 to 2013 as well as new SEP engineering models and tools. Both statistical and physical modeling techniques have been included, in order to cover the environment not only at 1 AU but also in the inner heliosphere ranging from 0.2 AU to 1.6 AU using a newly developed physics-based shock-and-particle model to simulate particle flux profiles of gradual SEP events. With SEPEM, SEP peak flux and integrated fluence statistics can be studied, as well as durations of high SEP flux periods. Furthermore, effects tools are also included to allow calculation of single event upset rate and radiation doses for a variety of engineering scenarios.

Application of the Repetitions in Reserve-Based Rating of Perceived Exertion Scale for Resistance Training

PubMed Central

Cronin, John; Storey, Adam; Zourdos, Michael C.

2016-01-01

ABSTRACT RATINGS OF PERCEIVED EXERTION ARE A VALID METHOD OF ESTIMATING THE INTENSITY OF A RESISTANCE TRAINING EXERCISE OR SESSION. SCORES ARE GIVEN AFTER COMPLETION OF AN EXERCISE OR TRAINING SESSION FOR THE PURPOSES OF ATHLETE MONITORING. HOWEVER, A NEWLY DEVELOPED SCALE BASED ON HOW MANY REPETITIONS ARE REMAINING AT THE COMPLETION OF A SET MAY BE A MORE PRECISE TOOL. THIS APPROACH ADJUSTS LOADS AUTOMATICALLY TO MATCH ATHLETE CAPABILITIES ON A SET-TO-SET BASIS AND MAY MORE ACCURATELY GAUGE INTENSITY AT NEAR-LIMIT LOADS. THIS ARTICLE OUTLINES HOW TO INCORPORATE THIS NOVEL SCALE INTO A TRAINING PLAN. PMID:27531969

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

A. Alfonsi; C. Rabiti; D. Mandelli

The Reactor Analysis and Virtual control ENviroment (RAVEN) code is a software tool that acts as the control logic driver and post-processing engine for the newly developed Thermal-Hydraulic code RELAP-7. RAVEN is now a multi-purpose Probabilistic Risk Assessment (PRA) software framework that allows dispatching different functionalities: Derive and actuate the control logic required to simulate the plant control system and operator actions (guided procedures), allowing on-line monitoring/controlling in the Phase Space Perform both Monte-Carlo sampling of random distributed events and Dynamic Event Tree based analysis Facilitate the input/output handling through a Graphical User Interface (GUI) and a post-processing data miningmore » module« less

Training for laparoscopic Nissen fundoplication with a newly designed model: a replacement for animal tissue models?

PubMed Central

Christie, Lorna; Goossens, Richard; Jakimowicz, Jack J.

2010-01-01

Background To bridge the early learning curve for laparoscopic Nissen fundoplication from the clinical setting to a safe environment, training models can be used. This study aimed to develop a reusable, low-cost model to be used for training in laparoscopic Nissen fundoplication procedure as an alternative to the use of animal tissue models. Methods From artificial organs and tissue, an anatomic model of the human upper abdomen was developed for training in performing laparoscopic Nissen fundoplication. The 20 participants and tutors in the European Association for Endoscopic Surgery (EAES) upper gastrointestinal surgery course completed four complementary tasks of laparoscopic Nissen fundoplication with the artificial model, then compared the realism, haptic feedback, and training properties of the model with those of animal tissue models. Results The main difference between the two training models was seen in the properties of the stomach. The wrapping of the stomach in the artificial model was rated significantly lower than that in the animal tissue model (mean, 3.6 vs. 4.2; p = 0.010). The main criticism of the stomach of the artificial model was that it was too rigid for making a proper wrap. The suturing of the stomach wall, however, was regarded as fairly realistic (mean, 3.6). The crura on the artificial model were rated better (mean, 4.3) than those on the animal tissue (mean, 4.0), although the difference was not significant. The participants regarded the model as a good to excellent (mean, 4.3) training tool. Conclusion The newly developed model is regarded as a good tool for training in laparoscopic Nissen fundoplication procedure. It is cheaper, more durable, and more readily available for training and can therefore be used in every training center. The stomach of this model, however, still needs improvement because it is too rigid for making the wrap. PMID:20526629

First results from the in-situ temperature measurements by the newly developed downhole tool during the drilling cruise in the hydrothermal fields of the mid-Okinawa Trough

NASA Astrophysics Data System (ADS)

Kitada, K.; Wu, H. Y.; Miyazaki, J.; Akiyama, K.; Nozaki, T.; Ishibashi, J. I.; Kumagai, H.; Maeda, L.

2016-12-01

The Okinawa trough is an active backarc basin behind the Ryukyu subduction zone and exhibits active rifting associated with extension of the continental margin. The temperature measurement in this area is essential for understanding hydrothermal system and hydraulic structure. During the CK16-01 cruise this March, we have conducted the in-situ temperature measurements by the newly developed downhole tool, TRDT (Thermo-Resistant Downhole Thermometer) in hydrothermal fields of the mid-Okinawa Trough. The purpose of this measurement is to investigate the in-situ temperature structure in deep-hot zones and its variation after coring and/or drilling. TRDT was designed by JAMSTEC as a memory downhole tool to measure in-situ borehole temperature under the extreme high temperature environment. First trial was conducted in the CK14-04 cruise by the free fall deployment to reduce the operation time. However, there was no temperature data recorded due to the strong vibration during the operation. After CK14-04 cruise, TRDT was modified to improve the function against vibration and shock. The improved TRDT passed the high temperature, vibration and shock tests to ensure the data acquisition of borehole logging. During the CK16-01 cruise, we have first successfully collected the in-situ temperature data from hydrothermal borehole in the Iheya North Knoll with wireline system. The temperature at depth of 187mbsf continued to increase almost linearly from 220 to 245°C during the 20 minute measurements time. This suggests that the inside borehole was cooled down by pumping seawater through drill pipes during the coring and lowering down the TRDT tool to the bottom hole. The in-situ temperature were extrapolated with exponential curve using nonlinear least squares fitting and the estimated equilibrium temperature was 278°C. To recover the in-situ temperature more precisely, the measurement time should kept as long as possible by considering the temperature rating. The operational procedure is also important to succeed in temperature logging. TRDT was deployed by wireline system to avoid damage from the strong vibration and shock. In order to get in-situ temperature data, the key factors are: 1) keeping the borehole for recovering the in-situ temperature after the coring; 2) TRDT sensor deployment without pumping seawater.

[Characteristics of case management programs and their potential for patient empowerment].

PubMed

Grün, Oskar; Maier, Manfred

2008-01-01

Different types of case management programs have been increasingly developed for health care systems. This study, therefore, aimed to identify similarities and differences of case management programs, to estimate their shaping with special emphasis on patient empowerment, and to develop an instrument for their differentiation. During an interdisciplinary seminar for students, eight different case management programs were selected and analyzed. Five characteristics of case management programs were identified: type of case, extent of functions, players involved, limits of availability and need for resources. The programs were categorized into information-, provider-, disease- or patient centred. With these characteristics the selected programs could be exactly described and their potential for patient empowerment could be assessed. This newly developed tool for describing case management programs allows for their sufficient differentiation. The potential for patient empowerment apparently is most prominent in patient centred programs.

Efficient Feature Selection and Classification of Protein Sequence Data in Bioinformatics

PubMed Central

Faye, Ibrahima; Samir, Brahim Belhaouari; Md Said, Abas

2014-01-01

Bioinformatics has been an emerging area of research for the last three decades. The ultimate aims of bioinformatics were to store and manage the biological data, and develop and analyze computational tools to enhance their understanding. The size of data accumulated under various sequencing projects is increasing exponentially, which presents difficulties for the experimental methods. To reduce the gap between newly sequenced protein and proteins with known functions, many computational techniques involving classification and clustering algorithms were proposed in the past. The classification of protein sequences into existing superfamilies is helpful in predicting the structure and function of large amount of newly discovered proteins. The existing classification results are unsatisfactory due to a huge size of features obtained through various feature encoding methods. In this work, a statistical metric-based feature selection technique has been proposed in order to reduce the size of the extracted feature vector. The proposed method of protein classification shows significant improvement in terms of performance measure metrics: accuracy, sensitivity, specificity, recall, F-measure, and so forth. PMID:25045727

Development and evaluation of specific PCR primers targeting the ribosomal DNA-internal transcribed spacer (ITS) region of peritrich ciliates in environmental samples

NASA Astrophysics Data System (ADS)

Su, Lei; Zhang, Qianqian; Gong, Jun

2017-07-01

Peritrich ciliates are highly diverse and can be important bacterial grazers in aquatic ecosystems. Morphological identifications of peritrich species and assemblages in the environment are time-consuming and expertise-demanding. In this study, two peritrich-specific PCR primers were newly designed to amplify a fragment including the internal transcribed spacer (ITS) region of ribosomal rDNA from environmental samples. The primers showed high specificity in silico, and in tests with peritrich isolates and environmental DNA. Application of these primers in clone library construction and sequencing yielded exclusively sequences of peritrichs for water and sediment samples. We also found the ITS1, ITS2, ITS, D1 region of 28S rDNA, and ITS+D1 region co-varied with, and generally more variable than, the V9 region of 18S rDNA in peritrichs. The newly designed specific primers thus provide additional tools to study the molecular diversity, community composition, and phylogeography of these ecologically important protists in different systems.

CE-BLAST makes it possible to compute antigenic similarity for newly emerging pathogens.

PubMed

Qiu, Tianyi; Yang, Yiyan; Qiu, Jingxuan; Huang, Yang; Xu, Tianlei; Xiao, Han; Wu, Dingfeng; Zhang, Qingchen; Zhou, Chen; Zhang, Xiaoyan; Tang, Kailin; Xu, Jianqing; Cao, Zhiwei

2018-05-02

Major challenges in vaccine development include rapidly selecting or designing immunogens for raising cross-protective immunity against different intra- or inter-subtypic pathogens, especially for the newly emerging varieties. Here we propose a computational method, Conformational Epitope (CE)-BLAST, for calculating the antigenic similarity among different pathogens with stable and high performance, which is independent of the prior binding-assay information, unlike the currently available models that heavily rely on the historical experimental data. Tool validation incorporates influenza-related experimental data sufficient for stability and reliability determination. Application to dengue-related data demonstrates high harmonization between the computed clusters and the experimental serological data, undetectable by classical grouping. CE-BLAST identifies the potential cross-reactive epitope between the recent zika pathogen and the dengue virus, precisely corroborated by experimental data. The high performance of the pathogens without the experimental binding data suggests the potential utility of CE-BLAST to rapidly design cross-protective vaccines or promptly determine the efficacy of the currently marketed vaccine against emerging pathogens, which are the critical factors for containing emerging disease outbreaks.

Breast cancer navigation and patient satisfaction: exploring a community-based patient navigation model in a rural setting.

PubMed

Hook, Ann; Ware, Laurie; Siler, Bobbie; Packard, Abbot

2012-07-01

To explore patient satisfaction among newly diagnosed patients with breast cancer in a rural community setting using a nurse navigation model. Nonexperimental, descriptive study. Large, multispecialty physician outpatient clinic serving about 150 newly diagnosed patients with breast cancer annually at the time of the study. 103 patients using nurse navigation services during a two-year period. A researcher-developed 14-item survey tool using a Likert-type scale was mailed to about 300 navigated patients. Nurse navigation and patient satisfaction. The majority of participants (n = 73, 72%) selected "strongly agree" in each survey statement when questioned about the benefits of nurse navigation. Patients receiving nurse navigation for breast cancer are highly satisfied with the services offered in this setting. Findings from this study offer insight regarding the effectiveness of an individualized supportive care approach to nurses and providers of oncology care. That information can be used to guide the implementation of future nurse navigation programs, determine effective methods of guiding patients through the cancer experience, and aid in promoting the highest standard of oncology care.

Developing person-centred analysis of harm in a paediatric hospital: a quality improvement report.

PubMed

Lachman, Peter; Linkson, Lynette; Evans, Trish; Clausen, Henning; Hothi, Daljit

2015-05-01

The provision of safe care is complex and difficult to achieve. Awareness of what happens in real time is one of the ways to develop a safe system within a culture of safety. At Great Ormond Street Hospital, we developed and tested a tool specifically designed for patients and families to report harm, with the aim of raising awareness and opportunities for staff to continually improve and provide safe care. Over a 10-month period, we developed processes to report harm. We used the Model for Improvement and multiple Plan, Do, Study, Act cycles for testing. We measured changes using culture surveys as well as analysis of the reports. The tool was tested in different formats and moved from a provider centric to a person-centred tool analysed in real time. An independent person working with the families was best placed to support reporting. Immediate feedback to families was managed by senior staff, and provided the opportunity for clarification, transparency and apologies. Feedback to staff provided learning opportunities. Improvements in culture climate and staff reporting were noted in the short term. The integration of patient involvement in safety monitoring systems is essential to achieve safety. The high number of newly identified 'near-misses' and 'critical incidents' by families demonstrated an underestimation of potentially harmful events. This testing and introduction of a self-reporting, real-time bedside tool has led to active engagement with families and patients and raised situation awareness. We believe that this will lead to improved and safer care in the longer term. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Usability Testing of the iPhone App to Improve Pain Assessment for Older Adults with Cognitive Impairment (Prehospital Setting): A Qualitative Study.

PubMed

Docking, Rachael E; Lane, Matthew; Schofield, Pat A

2017-03-15

Pain assessment in older adults with cognitive impairment is often challenging, and paramedics are not given sufficient tools/training to assess pain. The development of a mobile app may improve pain assessment and management in this vulnerable population. We conducted usability testing of a newly developed iPhone pain assessment application with potential users, in this case as a tool for clinical paramedic practice to improve pain assessment of older adults with cognitive impairment. We conducted usability testing with paramedic students and a Delphi panel of qualified paramedics. Participants studied the app and paper-based algorithm from which the app was developed. The potential use for the app was discussed. Usability testing focus groups were recorded, transcribed verbatim, and analyzed using a thematic approach. Proposed recommendations were disseminated to the Delphi panel that reviewed and confirmed them. Twenty-four paramedic students from two UK ambulance services participated in the focus groups. Usability of the app and its potential were viewed positively. Four major themes were identified: 1) overall opinion of the app for use in paramedic services; 2) incorporating technological applications into the health care setting; 3) improving knowledge and governance; and 4) alternative uses for the app. Subthemes were identified and are presented. Our results indicate that the pain assessment app constitutes a potentially useful tool in the prehospital setting. By providing access to a tool specifically developed to help identify/assess pain in a user-friendly format, paramedics are likely to have increased knowledge and confidence in assessing pain in patients with dementia. © 2017 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Data-driven Applications for the Sun-Earth System

NASA Astrophysics Data System (ADS)

Kondrashov, D. A.

2016-12-01

Advances in observational and data mining techniques allow extracting information from the large volume of Sun-Earth observational data that can be assimilated into first principles physical models. However, equations governing Sun-Earth phenomena are typically nonlinear, complex, and high-dimensional. The high computational demand of solving the full governing equations over a large range of scales precludes the use of a variety of useful assimilative tools that rely on applied mathematical and statistical techniques for quantifying uncertainty and predictability. Effective use of such tools requires the development of computationally efficient methods to facilitate fusion of data with models. This presentation will provide an overview of various existing as well as newly developed data-driven techniques adopted from atmospheric and oceanic sciences that proved to be useful for space physics applications, such as computationally efficient implementation of Kalman Filter in radiation belts modeling, solar wind gap-filling by Singular Spectrum Analysis, and low-rank procedure for assimilation of low-altitude ionospheric magnetic perturbations into the Lyon-Fedder-Mobarry (LFM) global magnetospheric model. Reduced-order non-Markovian inverse modeling and novel data-adaptive decompositions of Sun-Earth datasets will be also demonstrated.

[Observation of Attachment Disorder Symptoms in Middle Childhood].

PubMed

Iwanski, Alexandra; Zimmermann, Peter

2018-05-01

Observation of Attachment Disorder Symptoms in Middle Childhood Attachment in childhood is mainly assessed by observation. In contrast, assessment of attachment disorder symptoms (RAD) is mainly based on caregiver reports. The present study uses a newly developed observation tool (Coding of Attachment Disorder Behavior in Children; Iwanski u. Zimmermann, 2013) to assess attachment disorder symptoms in a group of school-aged children from a risk group for the development of attachment disorder symptoms and non-clinical controls. In addition, caregiver reports on RAD symptoms are also assessed (Relationship Problems Questionnaire; Minnis, Rabe-Hesketh, Wolkind, 2002; Disturbances of Attachment Interview; Smyke u. Zeanah, 1999). Moreover, associations with children's self-concept (Harter, 2012) were studied. Results reveal that children at risk showed more inhibited and disinhibited attachment disorder symptoms and a more negative self-concept compared to non-clinical controls. RAD symptoms are shown in interaction with both the caregiver and a stranger. The use of a reliable and valid observation tool for the diagnostic of attachment disorder symptoms besides ratings of caregivers is recommended for clinical practice and research.

HTTP-based remote operational options for the Vacuum Tower Telescope, Tenerife

NASA Astrophysics Data System (ADS)

Staiger, J.

2012-09-01

We are currently developing network based tools for the Vacuum Tower Telescope (VTT), Tenerife which will allow to operate the telescope together with the newly developed 2D-spectrometer HELLRIDE under remote control conditions. The computational configuration can be viewed as a distributed system linking hardware components of various functionality from different locations. We have developed a communication protocol which is basically an extension of the HTTP standard. It will serve as a carrier for command- and data-transfers. The server-client software is based on Berkley-Unix sockets in a C++ programming environment. A customized CMS will allow to create browser accessible information on-the-fly. Java-based applet pages have been tested as optional user access GUI's. An access tool has been implemented to download near-realtime, web-based target information from NASA/SDO. Latency tests have been carried out at the VTT and the Swedish STT at La Palma for concept verification. Short response times indicate that under favorable network conditions remote interactive telescope handling may be possible. The scientific focus of possible future remote operations will be set on the helioseismology of the solar atmosphere, the monitoring of flares and the footpoint analysis of coronal loops and chromospheric events.

Zebrafish: A Model for the Study of Toxicants Affecting Muscle Development and Function

PubMed Central

Dubińska-Magiera, Magda; Daczewska, Małgorzata; Lewicka, Anna; Migocka-Patrzałek, Marta; Niedbalska-Tarnowska, Joanna; Jagla, Krzysztof

2016-01-01

The rapid progress in medicine, agriculture, and allied sciences has enabled the development of a large amount of potentially useful bioactive compounds, such as drugs and pesticides. However, there is another side of this phenomenon, which includes side effects and environmental pollution. To avoid or minimize the uncontrollable consequences of using the newly developed compounds, researchers seek a quick and effective means of their evaluation. In achieving this goal, the zebrafish (Danio rerio) has proven to be a highly useful tool, mostly because of its fast growth and development, as well as the ability to absorb the molecules diluted in water through its skin and gills. In this review, we focus on the reports concerning the application of zebrafish as a model for assessing the impact of toxicants on skeletal muscles, which share many structural and functional similarities among vertebrates, including zebrafish and humans. PMID:27869769

LAMP detection assays for boxwood blight pathogens: A comparative genomics approach

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

Malapi-Wight, Martha; Demers, Jill E.; Veltri, Daniel

Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well asmore » three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. In conclusion, this comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.« less

LAMP detection assays for boxwood blight pathogens: A comparative genomics approach

DOE PAGES

Malapi-Wight, Martha; Demers, Jill E.; Veltri, Daniel; ...

2016-05-20

Rapid and accurate molecular diagnostic tools are critical to efforts to minimize the impact and spread of emergent pathogens. The identification of diagnostic markers for novel pathogens presents several challenges, especially in the absence of information about population diversity and where genetic resources are limited. The objective of this study was to use comparative genomics datasets to find unique target regions suitable for the diagnosis of two fungal species causing a newly emergent blight disease of boxwood. Candidate marker regions for loop-mediated isothermal amplification (LAMP) assays were identified from draft genomes of Calonectria henricotiae and C. pseudonaviculata, as well asmore » three related species not associated with this disease. To increase the probability of identifying unique targets, we used three approaches to mine genome datasets, based on (i) unique regions, (ii) polymorphisms, and (iii) presence/absence of regions across datasets. From a pool of candidate markers, we demonstrate LAMP assay specificity by testing related fungal species, common boxwood pathogens, and environmental samples containing 445 diverse fungal taxa. In conclusion, this comparative-genomics-based approach to the development of LAMP diagnostic assays is the first of its kind for fungi and could be easily applied to diagnostic marker development for other newly emergent plant pathogens.« less

SGRAPH (SeismoGRAPHer): Seismic waveform analysis and integrated tools in seismology

NASA Astrophysics Data System (ADS)

Abdelwahed, Mohamed F.

2012-03-01

Although numerous seismological programs are currently available, most of them suffer from the inability to manipulate different data formats and the lack of embedded seismological tools. SeismoGRAPHer, or simply SGRAPH, is a new system for maintaining and analyzing seismic waveform data in a stand-alone, Windows-based application that manipulates a wide range of data formats. SGRAPH was intended to be a tool sufficient for performing basic waveform analysis and solving advanced seismological problems. The graphical user interface (GUI) utilities and the Windows functionalities, such as dialog boxes, menus, and toolbars, simplify the user interaction with the data. SGRAPH supports common data formats, such as SAC, SEED, GSE, ASCII, and Nanometrics Y-format, and provides the ability to solve many seismological problems with built-in inversion tools. Loaded traces are maintained, processed, plotted, and saved as SAC, ASCII, or PS (post script) file formats. SGRAPH includes Generalized Ray Theory (GRT), genetic algorithm (GA), least-square fitting, auto-picking, fast Fourier transforms (FFT), and many additional tools. This program provides rapid estimation of earthquake source parameters, location, attenuation, and focal mechanisms. Advanced waveform modeling techniques are provided for crustal structure and focal mechanism estimation. SGRAPH has been employed in the Egyptian National Seismic Network (ENSN) as a tool assisting with routine work and data analysis. More than 30 users have been using previous versions of SGRAPH in their research for more than 3 years. The main features of this application are ease of use, speed, small disk space requirements, and the absence of third-party developed components. Because of its architectural structure, SGRAPH can be interfaced with newly developed methods or applications in seismology. A complete setup file, including the SGRAPH package with the online user guide, is available.

Share2Quit: Web-Based Peer-Driven Referrals for Smoking Cessation

PubMed Central

2013-01-01

Background Smoking is the number one preventable cause of death in the United States. Effective Web-assisted tobacco interventions are often underutilized and require new and innovative engagement approaches. Web-based peer-driven chain referrals successfully used outside health care have the potential for increasing the reach of Internet interventions. Objective The objective of our study was to describe the protocol for the development and testing of proactive Web-based chain-referral tools for increasing the access to Decide2Quit.org, a Web-assisted tobacco intervention system. Methods We will build and refine proactive chain-referral tools, including email and Facebook referrals. In addition, we will implement respondent-driven sampling (RDS), a controlled chain-referral sampling technique designed to remove inherent biases in chain referrals and obtain a representative sample. We will begin our chain referrals with an initial recruitment of former and current smokers as seeds (initial participants) who will be trained to refer current smokers from their social network using the developed tools. In turn, these newly referred smokers will also be provided the tools to refer other smokers from their social networks. We will model predictors of referral success using sample weights from the RDS to estimate the success of the system in the targeted population. Results This protocol describes the evaluation of proactive Web-based chain-referral tools, which can be used in tobacco interventions to increase the access to hard-to-reach populations, for promoting smoking cessation. Conclusions Share2Quit represents an innovative advancement by capitalizing on naturally occurring technology trends to recruit smokers to Web-assisted tobacco interventions. PMID:24067329

A rapid and efficient newly established method to detect COL1A1-PDGFB gene fusion in dermatofibrosarcoma protuberans

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

Yokoyama, Yoko; Shimizu, Akira; Okada, Etsuko

Highlights: Black-Right-Pointing-Pointer We developed new method to rapidly identify COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer New PCR method using a single primer pair detected COL1A1-PDGFB fusion in DFSP. Black-Right-Pointing-Pointer This is the first report of DFSP with a novel COL1A1 breakpoint in exon 5. -- Abstract: The detection of fusion transcripts of the collagen type 1{alpha}1 (COL1A1) and platelet-derived growth factor-BB (PDGFB) genes by genetic analysis has recognized as a reliable and valuable molecular tool for the diagnosis of dermatofibrosarcoma protuberans (DFSP). To detect the COL1A1-PDGFB fusion, almost previous reports performed reverse transcription polymerase chain reaction (RT-PCR) using multiplex forward primersmore » from COL1A1. However, it has possible technical difficulties with respect to the handling of multiple primers and reagents in the procedure. The objective of this study is to establish a rapid, easy, and efficient one-step method of PCR using only a single primer pair to detect the fusion transcripts of the COL1A1 and PDGFB in DFSP. To validate new method, we compared the results of RT-PCR in five patients of DFSP between the previous method using multiplex primers and our established one-step RT-PCR using a single primer pair. In all cases of DFSP, the COL1A1-PDGFB fusion was detected by both previous method and newly established one-step PCR. Importantly, we detected a novel COL1A1 breakpoint in exon 5. The newly developed method is valuable to rapidly identify COL1A1-PDGFB fusion transcripts in DFSP.« less

New clustered regularly interspaced short palindromic repeat locus spacer pair typing method based on the newly incorporated spacer for Salmonella enterica.

PubMed

Li, Hao; Li, Peng; Xie, Jing; Yi, Shengjie; Yang, Chaojie; Wang, Jian; Sun, Jichao; Liu, Nan; Wang, Xu; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Wang, Yong; Jia, Leili; Li, Kaiqin; Qiu, Shaofu; Song, Hongbin

2014-08-01

A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Decision-making tools in prostate cancer: from risk grouping to nomograms.

PubMed

Fontanella, Paolo; Benecchi, Luigi; Grasso, Angelica; Patel, Vipul; Albala, David; Abbou, Claude; Porpiglia, Francesco; Sandri, Marco; Rocco, Bernardo; Bianchi, Giampaolo

2017-12-01

Prostate cancer (PCa) is the most common solid neoplasm and the second leading cause of cancer death in men. After the Partin tables were developed, a number of predictive and prognostic tools became available for risk stratification. These tools have allowed the urologist to better characterize this disease and lead to more confident treatment decisions for patients. The purpose of this study is to critically review the decision-making tools currently available to the urologist, from the moment when PCa is first diagnosed until patients experience metastatic progression and death. A systematic and critical analysis through Medline, EMBASE, Scopus and Web of Science databases was carried out in February 2016 as per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The search was conducted using the following key words: "prostate cancer," "prediction tools," "nomograms." Seventy-two studies were identified in the literature search. We summarized the results into six sections: Tools for prediction of life expectancy (before treatment), Tools for prediction of pathological stage (before treatment), Tools for prediction of survival and cancer-specific mortality (before/after treatment), Tools for prediction of biochemical recurrence (before/after treatment), Tools for prediction of metastatic progression (after treatment) and in the last section biomarkers and genomics. The management of PCa patients requires a tailored approach to deliver a truly personalized treatment. The currently available tools are of great help in helping the urologist in the decision-making process. These tests perform very well in high-grade and low-grade disease, while for intermediate-grade disease further research is needed. Newly discovered markers, genomic tests, and advances in imaging acquisition through mpMRI will help in instilling confidence that the appropriate treatments are being offered to patients with prostate cancer.

New developments in optical coherence tomography

PubMed Central

Kostanyan, Tigran; Wollstein, Gadi; Schuman, Joel S.

2017-01-01

Purpose of review Optical coherence tomography (OCT) has become the cornerstone technology for clinical ocular imaging in the past few years. The technology is still rapidly evolving with newly developed applications. This manuscript reviews recent innovative OCT applications for glaucoma diagnosis and management. Recent findings The improvements made in the technology have resulted in increased scanning speed, axial and transverse resolution, and more effective use of the OCT technology as a component of multimodal imaging tools. At the same time, the parallel evolution in novel algorithms makes it possible to efficiently analyze the increased volume of acquired data. Summary The innovative iterations of OCT technology have the potential to further improve the performance of the technology in evaluating ocular structural and functional characteristics and longitudinal changes in glaucoma. PMID:25594766

Numerical Simulation of Transient Liquid Phase Bonding under Temperature Gradient

NASA Astrophysics Data System (ADS)

Ghobadi Bigvand, Arian

Transient Liquid Phase bonding under Temperature Gradient (TG-TLP bonding) is a relatively new process of TLP diffusion bonding family for joining difficult-to-weld aerospace materials. Earlier studies have suggested that in contrast to the conventional TLP bonding process, liquid state diffusion drives joint solidification in TG-TLP bonding process. In the present work, a mass conservative numerical model that considers asymmetry in joint solidification is developed using finite element method to properly study the TG-TLP bonding process. The numerical results, which are experimentally verified, show that unlike what has been previously reported, solid state diffusion plays a major role in controlling the solidification behavior during TG-TLP bonding process. The newly developed model provides a vital tool for further elucidation of the TG-TLP bonding process.

A Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1997-01-01

This paper describes a gas turbine simulation system which utilizes the newly developed Java language environment software system. The system provides an interactive graphical environment which allows the quick and efficient construction and analysis of arbitrary gas turbine propulsion systems. The simulation system couples a graphical user interface, developed using the Java Abstract Window Toolkit, and a transient, space- averaged, aero-thermodynamic gas turbine analysis method, both entirely coded in the Java language. The combined package provides analytical, graphical and data management tools which allow the user to construct and control engine simulations by manipulating graphical objects on the computer display screen. Distributed simulations, including parallel processing and distributed database access across the Internet and World-Wide Web (WWW), are made possible through services provided by the Java environment.

Development and verification of ground-based tele-robotics operations concept for Dextre

NASA Astrophysics Data System (ADS)

Aziz, Sarmad

2013-05-01

The Special Purpose Dextreous Manipulator (Dextre) is the latest addition to the on-orbit segment of the Mobile Servicing System (MSS); Canada's contribution to the International Space Station (ISS). Launched in March 2008, the advanced two-armed robot is designed to perform various ISS maintenance tasks on robotically compatible elements and on-orbit replaceable units using a wide variety of tools and interfaces. The addition of Dextre has increased the capabilities of the MSS, and has introduced significant complexity to ISS robotics operations. While the initial operations concept for Dextre was based on human-in-the-loop control by the on-orbit astronauts, the complexities of robotic maintenance and the associated costs of training and maintaining the operator skills required for Dextre operations demanded a reexamination of the old concepts. A new approach to ISS robotic maintenance was developed in order to utilize the capabilities of Dextre safely and efficiently, while at the same time reducing the costs of on-orbit operations. This paper will describe the development, validation, and on-orbit demonstration of the operations concept for ground-based tele-robotics control of Dextre. It will describe the evolution of the new concepts from the experience gained from the development and implementation of the ground control capability for the Space Station Remote Manipulator System; Canadarm 2. It will discuss the various technical challenges faced during the development effort, such as requirements for high positioning accuracy, force/moment sensing and accommodation, failure tolerance, complex tool operations, and the novel operational tools and techniques developed to overcome them. The paper will also describe the work performed to validate the new concepts on orbit and will discuss the results and lessons learned from the on-orbit checkout and commissioning of Dextre using the newly developed tele-robotics techniques and capabilities.

Extreme ultraviolet patterned mask inspection performance of advanced projection electron microscope system for 11nm half-pitch generation

NASA Astrophysics Data System (ADS)

Hirano, Ryoichi; Iida, Susumu; Amano, Tsuyoshi; Watanabe, Hidehiro; Hatakeyama, Masahiro; Murakami, Takeshi; Suematsu, Kenichi; Terao, Kenji

2016-03-01

Novel projection electron microscope optics have been developed and integrated into a new inspection system named EBEYE-V30 ("Model EBEYE" is an EBARA's model code) , and the resulting system shows promise for application to half-pitch (hp) 16-nm node extreme ultraviolet lithography (EUVL) patterned mask inspection. To improve the system's inspection throughput for 11-nm hp generation defect detection, a new electron-sensitive area image sensor with a high-speed data processing unit, a bright and stable electron source, and an image capture area deflector that operates simultaneously with the mask scanning motion have been developed. A learning system has been used for the mask inspection tool to meet the requirements of hp 11-nm node EUV patterned mask inspection. Defects are identified by the projection electron microscope system using the "defectivity" from the characteristics of the acquired image. The learning system has been developed to reduce the labor and costs associated with adjustment of the detection capability to cope with newly-defined mask defects. We describe the integration of the developed elements into the inspection tool and the verification of the designed specification. We have also verified the effectiveness of the learning system, which shows enhanced detection capability for the hp 11-nm node.

The subject of pedagogy from theory to practice--the view of newly registered nurses.

PubMed

Ivarsson, Bodil; Nilsson, Gunilla

2009-07-01

The aim was to describe, from the newly registered nurses' perspective, specific events when using their pedagogical knowledge in their everyday clinical practice. The design was qualitative and the critical incident technique was used. Data was collected via interviews with ten newly registered nurses who graduated from the same University program 10 months earlier and are now employed at a university hospital. Two categories emerged in the analyses. The first category was "Pedagogical methods in theory" with the sub-categories Theory and the application of the course in practice, Knowledge of pedagogy and Information as a professional competence. The second category was "Pedagogical methods in everyday clinical practice" with sub-categories Factual knowledge versus pedagogical knowledge, Information and relatives, Difficulties when giving information, Understanding information received, Pedagogical tools, Collaboration in teams in pedagogical situations, and Time and giving information. By identifying specific events regarding pedagogical methods the findings can be useful for everyone from teachers and health-care managers to nurse students and newly registered nurses, to improve teaching methods in nurse education.

Implementation of SAP Waste Management System

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

Frost, M.L.; LaBorde, C.M.; Nichols, C.D.

2008-07-01

The Y-12 National Security Complex (Y-12) assumed responsibility for newly generated waste on October 1, 2005. To ensure effective management and accountability of newly generated waste, Y-12 has opted to utilize SAP, Y-12's Enterprise Resource Planning (ERP) tool, to track low-level radioactive waste (LLW), mixed waste (MW), hazardous waste, and non-regulated waste from generation through acceptance and disposal. SAP Waste will include the functionality of the current waste tracking system and integrate with the applicable modules of SAP already in use. The functionality of two legacy systems, the Generator Entry System (GES) and the Waste Information Tracking System (WITS), andmore » peripheral spreadsheets, databases, and e-mail/fax communications will be replaced by SAP Waste. Fundamentally, SAP Waste will promote waste acceptance for certification and disposal, not storage. SAP Waste will provide a one-time data entry location where waste generators can enter waste container information, track the status of their waste, and maintain documentation. A benefit of the new system is that it will provide a single data repository where Y-12's Waste Management organization can establish waste profiles, verify and validate data, maintain inventory control utilizing hand-held data transfer devices, schedule and ship waste, manage project accounting, and report on waste handling activities. This single data repository will facilitate the production of detailed waste generation reports for use in forecasting and budgeting, provide the data for required regulatory reports, and generate metrics to evaluate the performance of the Waste Management organization and its subcontractors. SAP Waste will replace the outdated and expensive legacy system, establish tools the site needs to manage newly generated waste, and optimize the use of the site's ERP tool for integration with related business processes while promoting disposition of waste. (authors)« less

Policy Transfer Among Regional-Level Organizations: Insights from Source Water Protection in Ontario.

PubMed

de Loë, R C; Murray, D; Michaels, S; Plummer, R

2016-07-01

Organizations at the local and regional scales often face the challenge of developing policy mechanisms rapidly and concurrently, whether in response to expanding mandates, newly identified threats, or changes in the political environment. In the Canadian Province of Ontario, rapid, concurrent policy development was considered desirable by 19 regional organizations tasked with developing policies for protection of drinking water sources under very tight and highly prescribed mandates. An explicit policy transfer approach was used by these organizations. Policy transfer refers to using knowledge of policies, programs, and institutions in one context in the development of policies, programs, and institutions in another. This paper assesses three online mechanisms developed to facilitate policy transfer for source water protection in Ontario. Insights are based on a survey of policy planners from the 19 regional organizations who used the three policy transfer tools, supplemented by an analysis of three policies created and transferred among the 19 regional source water protection organizations. Policy planners in the study indicated they had used policy transfer to develop source protection policies for their regions-a finding confirmed by analysis of the text of policies. While the online policy transfer tools clearly facilitated systematic policy transfer, participants still preferred informal, direct exchanges with their peers in other regions over the use of the internet-based policy transfer mechanisms created on their behalf.

Evolving with Evidence: Leveraging New Tools for EBP

ERIC Educational Resources Information Center

Valenza, Joyce Kasman

2015-01-01

Focusing on evidence-based practice (EBP) aligns with the school librarian's leadership role acknowledged by the American Association of School Librarians (AASL) in "Empowering Learners: Guidelines for School Library Programs" (2009) and in AASL's newly adopted mission statement. "The American Association of School Librarians…

The risk of bias in systematic reviews tool showed fair reliability and good construct validity.

PubMed

Bühn, Stefanie; Mathes, Tim; Prengel, Peggy; Wegewitz, Uta; Ostermann, Thomas; Robens, Sibylle; Pieper, Dawid

2017-11-01

There is a movement from generic quality checklists toward a more domain-based approach in critical appraisal tools. This study aimed to report on a first experience with the newly developed risk of bias in systematic reviews (ROBIS) tool and compare it with A Measurement Tool to Assess Systematic Reviews (AMSTAR), that is, the most common used tool to assess methodological quality of systematic reviews while assessing validity, reliability, and applicability. Validation study with four reviewers based on 16 systematic reviews in the field of occupational health. Interrater reliability (IRR) of all four raters was highest for domain 2 (Fleiss' kappa κ = 0.56) and lowest for domain 4 (κ = 0.04). For ROBIS, median IRR was κ = 0.52 (range 0.13-0.88) for the experienced pair of raters compared to κ = 0.32 (range 0.12-0.76) for the less experienced pair of raters. The percentage of "yes" scores of each review of ROBIS ratings was strongly correlated with the AMSTAR ratings (r s  = 0.76; P = 0.01). ROBIS has fair reliability and good construct validity to assess the risk of bias in systematic reviews. More validation studies are needed to investigate reliability and applicability, in particular. Copyright © 2017 Elsevier Inc. All rights reserved.

A tool and index to assess surgical capacity in low income countries: an initial implementation in Sierra Leone.

PubMed

Groen, Reinou S; Kamara, Thaim B; Dixon-Cole, Richmond; Kwon, Steven; Kingham, T Peter; Kushner, Adam L

2012-08-01

A first step toward improving surgical care in many low and middle income countries is to document the need. To facilitate the collection and analysis of surgical capacity data and measure changes over time, Surgeons OverSeas (SOS) developed a tool and index based on personnel, infrastructure, procedures, equipment, and supplies (PIPES). A follow-up assessment of 10 government hospitals in Sierra Leone was completed 42 months after an initial survey in 2008 using the PIPES tool. An index based on number of operating rooms, personnel, infrastructure, procedures, equipment, and supplies was calculated. An index was also calculated, using the 2008 data for comparison. Most hospitals demonstrated an increased index that correlated with site visits that verified improved conditions. Connaught Hospital in Sierra Leone had the highest score (9.2), consistent with its being the best equipped and staffed Ministry of Health and Sanitation facility. Makeni District Hospital had the greatest increase, from 3.8 to 7.5, consistent with a newly constructed facility. The PIPES tool was easily administered at hospitals in Sierra Leone and an index was found useful. Surgical capacity in Sierra Leone improved between 2008 and 2011, as demonstrated by an increase in the overall PIPES indices.

The use of anti-Müllerian hormone as diagnostic for gonadectomy status in dogs.

PubMed

Themmen, Axel P N; Kalra, Bhanu; Visser, Jenny A; Kumar, Ajay; Savjani, Gopal; de Gier, Jeffrey; Jaques, Scott

2016-10-01

In the veterinary practice, there is a need for a diagnostic tool to check the gonadal status in female dogs because it may be difficult to determine whether a female animal has been spayed or whether there are ovarian remnants. Although less prevalent, a similar situation pertains to male dogs. Anti-Müllerian hormone (AMH) is an important regulator of gonadal function and is a specific gonadal product that can be determined in circulation. The objective of this study was to develop and test a canine blood AMH assay as a diagnostic tool to determine the presence of functional gonadal tissue in dogs. A prospective study with a training-validation set paradigm was used. A canine AMH assay was developed and serum and plasma AMH concentrations were determined in blood samples from 46 intact female dogs, 48 spayed females, 50 intact males, and 48 castrated males collected at two separate institutes. Using a training-validation set paradigm, it was found that using cutoff values of 1.1 ng/mL (female) and 5.5 ng/mL (male) AMH, the assay reported excellent specificity and sensitivity of 100% and 90% in female dogs, and good specificity and sensitivity of 100% and 76%, in male dogs, respectively. The sensitivity in male dogs could be further enhanced by including a serum testosterone determination. This newly developed canine AMH assay is a valuable diagnostic tool to determine gonadal status in veterinary medicine. Copyright © 2016 Elsevier Inc. All rights reserved.

Innovative financing for late-stage global health research and development: the Global Health Investment Fund.

PubMed

Fitchett, Joseph Robert; Fan Li, Julia; Atun, Rifat

2016-01-01

Innovative financing strategies for global health are urgently needed to reinvigorate investment and new tools for impact. Bottleneck areas along the research and development (R&D) pipeline require particular attention, such as the transitions from preclinical discovery to clinical study, and product development to implementation and delivery. Successful organizations mobilizing and disbursing resources through innovating financing mechanisms include UNITAID, the Global Fund, and Gavi, the Vaccine Alliance. Although precise numbers are poorly documented, estimated investment in low-income settings falls seriously short of local need. This commentary discusses the newly established Global Health Investment Fund as a case study to support late-stage global health R&D. © The Author 2015. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Needle and catheter navigation using electromagnetic tracking for computer-assisted C-arm CT interventions

NASA Astrophysics Data System (ADS)

Nagel, Markus; Hoheisel, Martin; Petzold, Ralf; Kalender, Willi A.; Krause, Ulrich H. W.

2007-03-01

Integrated solutions for navigation systems with CT, MR or US systems become more and more popular for medical products. Such solutions improve the medical workflow, reduce hardware, space and costs requirements. The purpose of our project was to develop a new electromagnetic navigation system for interventional radiology which is integrated into C-arm CT systems. The application is focused on minimally invasive percutaneous interventions performed under local anaesthesia. Together with a vacuum-based patient immobilization device and newly developed navigation tools (needles, panels) we developed a safe and fully automatic navigation system. The radiologist can directly start with navigated interventions after loading images without any prior user interaction. The complete system is adapted to the requirements of the radiologist and to the clinical workflow. For evaluation of the navigation system we performed different phantom studies and achieved an average accuracy of better than 2.0 mm.

Validation of a Magnetic Resonance Imaging-based Auto-contouring Software Tool for Gross Tumour Delineation in Head and Neck Cancer Radiotherapy Planning.

PubMed

Doshi, T; Wilson, C; Paterson, C; Lamb, C; James, A; MacKenzie, K; Soraghan, J; Petropoulakis, L; Di Caterina, G; Grose, D

2017-01-01

To carry out statistical validation of a newly developed magnetic resonance imaging (MRI) auto-contouring software tool for gross tumour volume (GTV) delineation in head and neck tumours to assist in radiotherapy planning. Axial MRI baseline scans were obtained for 10 oropharyngeal and laryngeal cancer patients. GTV was present on 102 axial slices and auto-contoured using the modified fuzzy c-means clustering integrated with the level set method (FCLSM). Peer-reviewed (C-gold) manual contours were used as the reference standard to validate auto-contoured GTVs (C-auto) and mean manual contours (C-manual) from two expert clinicians (C1 and C2). Multiple geometric metrics, including the Dice similarity coefficient (DSC), were used for quantitative validation. A DSC≥0.7 was deemed acceptable. Inter- and intra-variabilities among the manual contours were also validated. The two-dimensional contours were then reconstructed in three dimensions for GTV volume calculation, comparison and three-dimensional visualisation. The mean DSC between C-gold and C-auto was 0.79. The mean DSC between C-gold and C-manual was 0.79 and that between C1 and C2 was 0.80. The average time for GTV auto-contouring per patient was 8 min (range 6-13 min; mean 45 s per axial slice) compared with 15 min (range 6-23 min; mean 88 s per axial slice) for C1. The average volume concordance between C-gold and C-auto volumes was 86.51% compared with 74.16% between C-gold and C-manual. The average volume concordance between C1 and C2 volumes was 86.82%. This newly designed MRI-based auto-contouring software tool shows initial acceptable results in GTV delineation of oropharyngeal and laryngeal tumours using FCLSM. This auto-contouring software tool may help reduce inter- and intra-variability and can assist clinical oncologists with time-consuming, complex radiotherapy planning. Copyright © 2016 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

A 5.8S nuclear ribosomal RNA gene sequence database: applications to ecology and evolution

NASA Technical Reports Server (NTRS)

Cullings, K. W.; Vogler, D. R.

1998-01-01

We complied a 5.8S nuclear ribosomal gene sequence database for animals, plants, and fungi using both newly generated and GenBank sequences. We demonstrate the utility of this database as an internal check to determine whether the target organism and not a contaminant has been sequenced, as a diagnostic tool for ecologists and evolutionary biologists to determine the placement of asexual fungi within larger taxonomic groups, and as a tool to help identify fungi that form ectomycorrhizae.

Workflow and web application for annotating NCBI BioProject transcriptome data.

PubMed

Vera Alvarez, Roberto; Medeiros Vidal, Newton; Garzón-Martínez, Gina A; Barrero, Luz S; Landsman, David; Mariño-Ramírez, Leonardo

2017-01-01

The volume of transcriptome data is growing exponentially due to rapid improvement of experimental technologies. In response, large central resources such as those of the National Center for Biotechnology Information (NCBI) are continually adapting their computational infrastructure to accommodate this large influx of data. New and specialized databases, such as Transcriptome Shotgun Assembly Sequence Database (TSA) and Sequence Read Archive (SRA), have been created to aid the development and expansion of centralized repositories. Although the central resource databases are under continual development, they do not include automatic pipelines to increase annotation of newly deposited data. Therefore, third-party applications are required to achieve that aim. Here, we present an automatic workflow and web application for the annotation of transcriptome data. The workflow creates secondary data such as sequencing reads and BLAST alignments, which are available through the web application. They are based on freely available bioinformatics tools and scripts developed in-house. The interactive web application provides a search engine and several browser utilities. Graphical views of transcript alignments are available through SeqViewer, an embedded tool developed by NCBI for viewing biological sequence data. The web application is tightly integrated with other NCBI web applications and tools to extend the functionality of data processing and interconnectivity. We present a case study for the species Physalis peruviana with data generated from BioProject ID 67621. URL: http://www.ncbi.nlm.nih.gov/projects/physalis/. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Patient-Reported Outcomes and Fatigue in Patients with Chronic Hepatitis C Infection.

PubMed

Golabi, Pegah; Sayiner, Mehmet; Bush, Haley; Gerber, Lynn H; Younossi, Zobair M

2017-08-01

Fatigue is a common symptom. Diagnosis is difficult. Fatigue is often a complex symptom. In the recent years, fatigue has gained considerable amount of attention. It has 2 major types, central and peripheral, which may occur together or alone. Although fatigue has many strong relations with depression and sleep disorders, it is a separate entity. For the diagnosis of fatigue, self-reports and patient-reported outcomes are highly valuable tools because these methods can reflect patients' perceptions. Treating the underlying disease with newly developed direct-acting antivirals often improves the perceived fatigue. Healthy lifestyle changes are the cornerstone of the treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

Stormwater Management Plan for the Arden Hills Army Training Site, Arden Hills, Minnesota

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

Carr, Adrianne E.; Wuthrich, Kelsey K.; Ziech, Angela M.

2013-03-01

This stormwater management plan focuses on the cantonment and training areas of the Arden Hills Army Training Site (AHATS). The plan relates the site stormwater to the regulatory framework, and it summarizes best management practices to aide site managers in promoting clean site runoff. It includes documentation for a newly developed, detailed model of stormwater flow retention for the entire AHATS property and adjacent upgradient areas. The model relies on established modeling codes integrated in a U.S. Department of Defense-sponsored software tool, the Watershed Modeling System (WMS), and it can be updated with data on changes in land use ormore » with monitoring data.« less

Single-cell cloning and expansion of human induced pluripotent stem cells by a microfluidic culture device.

PubMed

Matsumura, Taku; Tatsumi, Kazuya; Noda, Yuichiro; Nakanishi, Naoyuki; Okonogi, Atsuhito; Hirano, Kunio; Li, Liu; Osumi, Takashi; Tada, Takashi; Kotera, Hidetoshi

2014-10-10

The microenvironment of cells, which includes basement proteins, shear stress, and extracellular stimuli, should be taken into consideration when examining physiological cell behavior. Although microfluidic devices allow cellular responses to be analyzed with ease at the single-cell level, few have been designed to recover cells. We herein demonstrated that a newly developed microfluidic device helped to improve culture conditions and establish a clonality-validated human pluripotent stem cell line after tracing its growth at the single-cell level. The device will be a helpful tool for capturing various cell types in the human body that have not yet been established in vitro. Copyright © 2014 Elsevier Inc. All rights reserved.

Modified wound dressing with phyto-nanostructured coating to prevent staphylococcal and pseudomonal biofilm development

NASA Astrophysics Data System (ADS)

Anghel, Ion; Holban, Alina Maria; Grumezescu, Alexandru Mihai; Andronescu, Ecaterina; Ficai, Anton; Anghel, Alina Georgiana; Maganu, Maria; Lazǎr, Veronica; Chifiriuc, Mariana Carmen

2012-12-01

This paper reports a newly fabricated nanophyto-modified wound dressing with microbicidal and anti-adherence properties. Nanofluid-based magnetite doped with eugenol or limonene was used to fabricate modified wound dressings. Nanostructure coated materials were characterized by TEM, XRD, and FT-IR. For the quantitative measurement of biofilm-embedded microbial cells, a culture-based method for viable cell count was used. The optimized textile dressing samples proved to be more resistant to staphylococcal and pseudomonal colonization and biofilm formation compared to the uncoated controls. The functionalized surfaces for wound dressing seems to be a very useful tool for the prevention of wound microbial contamination on viable tissues.

Modified wound dressing with phyto-nanostructured coating to prevent staphylococcal and pseudomonal biofilm development

PubMed Central

2012-01-01

This paper reports a newly fabricated nanophyto-modified wound dressing with microbicidal and anti-adherence properties. Nanofluid-based magnetite doped with eugenol or limonene was used to fabricate modified wound dressings. Nanostructure coated materials were characterized by TEM, XRD, and FT-IR. For the quantitative measurement of biofilm-embedded microbial cells, a culture-based method for viable cell count was used. The optimized textile dressing samples proved to be more resistant to staphylococcal and pseudomonal colonization and biofilm formation compared to the uncoated controls. The functionalized surfaces for wound dressing seems to be a very useful tool for the prevention of wound microbial contamination on viable tissues. PMID:23272823

Modified wound dressing with phyto-nanostructured coating to prevent staphylococcal and pseudomonal biofilm development.

PubMed

Anghel, Ion; Holban, Alina Maria; Grumezescu, Alexandru Mihai; Andronescu, Ecaterina; Ficai, Anton; Anghel, Alina Georgiana; Maganu, Maria; Laz R, Veronica; Chifiriuc, Mariana Carmen

2012-12-31

This paper reports a newly fabricated nanophyto-modified wound dressing with microbicidal and anti-adherence properties. Nanofluid-based magnetite doped with eugenol or limonene was used to fabricate modified wound dressings. Nanostructure coated materials were characterized by TEM, XRD, and FT-IR. For the quantitative measurement of biofilm-embedded microbial cells, a culture-based method for viable cell count was used. The optimized textile dressing samples proved to be more resistant to staphylococcal and pseudomonal colonization and biofilm formation compared to the uncoated controls. The functionalized surfaces for wound dressing seems to be a very useful tool for the prevention of wound microbial contamination on viable tissues.

The role of fMRI in cognitive neuroscience: where do we stand?

PubMed

Poldrack, Russell A

2008-04-01

Functional magnetic resonance imaging (fMRI) has quickly become the most prominent tool in cognitive neuroscience. In this article, I outline some of the limits on the kinds of inferences that can be supported by fMRI, focusing particularly on reverse inference, in which the engagement of specific mental processes is inferred from patterns of brain activation. Although this form of inference is weak, newly developed methods from the field of machine learning offer the potential to formalize and strengthen reverse inferences. I conclude by discussing the increasing presence of fMRI results in the popular media and the ethical implications of the increasing predictive power of fMRI.

The development of a revised version of multi-center molecular Ornstein-Zernike equation

NASA Astrophysics Data System (ADS)

Kido, Kentaro; Yokogawa, Daisuke; Sato, Hirofumi

2012-04-01

Ornstein-Zernike (OZ)-type theory is a powerful tool to obtain 3-dimensional solvent distribution around solute molecule. Recently, we proposed multi-center molecular OZ method, which is suitable for parallel computing of 3D solvation structure. The distribution function in this method consists of two components, namely reference and residue parts. Several types of the function were examined as the reference part to investigate the numerical robustness of the method. As the benchmark, the method is applied to water, benzene in aqueous solution and single-walled carbon nanotube in chloroform solution. The results indicate that fully-parallelization is achieved by utilizing the newly proposed reference functions.

Live Cell Visualization of Multiple Protein-Protein Interactions with BiFC Rainbow.

PubMed

Wang, Sheng; Ding, Miao; Xue, Boxin; Hou, Yingping; Sun, Yujie

2018-05-18

As one of the most powerful tools to visualize PPIs in living cells, bimolecular fluorescence complementation (BiFC) has gained great advancement during recent years, including deep tissue imaging with far-red or near-infrared fluorescent proteins or super-resolution imaging with photochromic fluorescent proteins. However, little progress has been made toward simultaneous detection and visualization of multiple PPIs in the same cell, mainly due to the spectral crosstalk. In this report, we developed novel BiFC assays based on large-Stokes-shift fluorescent proteins (LSS-FPs) to detect and visualize multiple PPIs in living cells. With the large excitation/emission spectral separation, LSS-FPs can be imaged together with normal Stokes shift fluorescent proteins to realize multicolor BiFC imaging using a simple illumination scheme. We also further demonstrated BiFC rainbow combining newly developed BiFC assays with previously established mCerulean/mVenus-based BiFC assays to achieve detection and visualization of four PPI pairs in the same cell. Additionally, we prove that with the complete spectral separation of mT-Sapphire and CyOFP1, LSS-FP-based BiFC assays can be readily combined with intensity-based FRET measurement to detect ternary protein complex formation with minimal spectral crosstalk. Thus, our newly developed LSS-FP-based BiFC assays not only expand the fluorescent protein toolbox available for BiFC but also facilitate the detection and visualization of multiple protein complex interactions in living cells.

Korean guidelines for the diagnosis and management of dry eye: development and validation of clinical efficacy.

PubMed

Hyon, Joon Young; Kim, Hyo-Myung; Lee, Doh; Chung, Eui-Sang; Song, Jong-Suk; Choi, Chul Young; Lee, Jungbok

2014-06-01

To evaluate the clinical efficacy of newly developed guidelines for the diagnosis and management of dry eye. This retrospective, multi-center, non-randomized, observational study included a total of 1,612 patients with dry eye disease who initially visited the clinics from March 2010 to August 2010. Korean guidelines for the diagnosis and management of dry eye were newly developed from concise, expert-consensus recommendations. Severity levels at initial and final visits were determined using the guidelines in patients with 90 ± 7 days of follow-up visits (n = 526). Groups with different clinical outcomes were compared with respect to clinical parameters, treatment modalities, and guideline compliance. Main outcome measures were ocular and visual symptoms, ocular surface disease index, global assessment by patient and physician, tear film break-up time, Schirmer-1 test score, ocular surface staining score at initial and final visits, clinical outcome after three months of treatment, and guideline compliance. Severity level was reduced in 47.37% of patients treated as recommended by the guidelines. Younger age (odd ratio [OR], 0.984; p = 0.044), higher severity level at initial visit, compliance to treatment recommendation (OR, 1.832; p = 0.047), and use of topical cyclosporine (OR, 1.838; p = 0.011) were significantly associated with improved clinical outcomes. Korean guidelines for the diagnosis and management of dry eye can be used as a valid and effective tool for the treatment of dry eye disease.

Mining secreted proteins that function in pepper fruit development and ripening using a yeast secretion trap (YST)

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

Lee, Je Min, E-mail: jemin@knu.ac.kr; Department of Horticultural Science, Kyungpook National University, Daegu; Lee, Sang-Jik

Highlights: • Yeast secretion trap (YST) is a valuable tool for mining secretome. • A total of 80 secreted proteins are newly identified via YST in pepper fruits. • The secreted proteins are differentially regulated during pepper development and ripening. • Transient GFP-fusion assay and in planta secretion trap can effectively validate the secretion of proteins. - Abstract: Plant cells secrete diverse sets of constitutively- and conditionally-expressed proteins under various environmental and developmental states. Secreted protein populations, or secretomes have multiple functions, including defense responses, signaling, metabolic processes, and developmental regulation. To identify genes encoding secreted proteins that function inmore » fruit development and ripening, a yeast secretion trap (YST) screen was employed using pepper (Capsicum annuum) fruit cDNAs. The YST screen revealed 80 pepper fruit-related genes (CaPFRs) encoding secreted proteins including cell wall proteins, several of which have not been previously described. Transient GFP-fusion assay and an in planta secretion trap were used to validate the secretion of proteins encoded by selected YST clones. In addition, RNA gel blot analyses provided further insights into their expression and regulation during fruit development and ripening. Integrating our data, we conclude that the YST provides a valuable functional genomics tool for the identification of substantial numbers of novel secreted plant proteins that are associated with biological processes, including fruit development and ripening.« less

Development and initial validation of the Impression Motivation in Sport Questionnaire-Team.

PubMed

Payne, Simon Mark; Hudson, Joanne; Akehurst, Sally; Ntoumanis, Nikos

2013-06-01

Impression motivation is an important individual difference variable that has been under-researched in sport psychology, partly due to having no appropriate measure. This study was conducted to design a measure of impression motivation in team-sport athletes. Construct validity checks decreased the initial pool of items, factor analysis (n = 310) revealed the structure of the newly developed scale, and exploratory structural equation modeling procedures (n = 406) resulted in a modified scale that retained theoretical integrity and psychometric parsimony. This process produced a 15-item, 4-factor model; the Impression Motivation in Sport Questionnaire-Team (IMSQ-T) is forwarded as a valid measure of the respondent's dispositional strength of motivation to use self-presentation in striving for four distinct interpersonal objectives: self-development, social identity development, avoidance of negative outcomes, and avoidance of damaging impressions. The availability of this measure has contributed to theoretical development, will facilitate research, and offers a tool for use in applied settings.

Multi Sector Planning Tools for Trajectory-Based Operations

NASA Technical Reports Server (NTRS)

Prevot, Thomas; Mainini, Matthew; Brasil, Connie

2010-01-01

This paper discusses a suite of multi sector planning tools for trajectory-based operations that were developed and evaluated in the Airspace Operations Laboratory (AOL) at the NASA Ames Research Center. The toolset included tools for traffic load and complexity assessment as well as trajectory planning and coordination. The situation assessment tools included an integrated suite of interactive traffic displays, load tables, load graphs, and dynamic aircraft filters. The planning toolset allowed for single and multi aircraft trajectory planning and data communication-based coordination of trajectories between operators. Also newly introduced was a real-time computation of sector complexity into the toolset that operators could use in lieu of aircraft count to better estimate and manage sector workload, especially in situations with convective weather. The tools were used during a joint NASA/FAA multi sector planner simulation in the AOL in 2009 that had multiple objectives with the assessment of the effectiveness of the tools being one of them. Current air traffic control operators who were experienced as area supervisors and traffic management coordinators used the tools throughout the simulation and provided their usefulness and usability ratings in post simulation questionnaires. This paper presents these subjective assessments as well as the actual usage data that was collected during the simulation. The toolset was rated very useful and usable overall. Many elements received high scores by the operators and were used frequently and successfully. Other functions were not used at all, but various requests for new functions and capabilities were received that could be added to the toolset.

Field Performance of a Newly Developed Upflow Filtration Device

EPA Science Inventory

The objective of this research is to examine the removal capacities of a newly developed Upflow filtration device for treatment of stormwater. The device was developed by engineers at the University of Alabama through a Small Business Innovative Research (SBIR) grant from the U....

Robust detection, isolation and accommodation for sensor failures

NASA Technical Reports Server (NTRS)

Emami-Naeini, A.; Akhter, M. M.; Rock, S. M.

1986-01-01

The objective is to extend the recent advances in robust control system design of multivariable systems to sensor failure detection, isolation, and accommodation (DIA), and estimator design. This effort provides analysis tools to quantify the trade-off between performance robustness and DIA sensitivity, which are to be used to achieve higher levels of performance robustness for given levels of DIA sensitivity. An innovations-based DIA scheme is used. Estimators, which depend upon a model of the process and process inputs and outputs, are used to generate these innovations. Thresholds used to determine failure detection are computed based on bounds on modeling errors, noise properties, and the class of failures. The applicability of the newly developed tools are demonstrated on a multivariable aircraft turbojet engine example. A new concept call the threshold selector was developed. It represents a significant and innovative tool for the analysis and synthesis of DiA algorithms. The estimators were made robust by introduction of an internal model and by frequency shaping. The internal mode provides asymptotically unbiased filter estimates.The incorporation of frequency shaping of the Linear Quadratic Gaussian cost functional modifies the estimator design to make it suitable for sensor failure DIA. The results are compared with previous studies which used thresholds that were selcted empirically. Comparison of these two techniques on a nonlinear dynamic engine simulation shows improved performance of the new method compared to previous techniques

AmWeb: a novel interactive web tool for antimicrobial resistance surveillance, applicable to both community and hospital patients.

PubMed

Ironmonger, Dean; Edeghere, Obaghe; Gossain, Savita; Bains, Amardeep; Hawkey, Peter M

2013-10-01

Antimicrobial resistance (AMR) is recognized as one of the most significant threats to human health. Local and regional AMR surveillance enables the monitoring of temporal changes in susceptibility to antibiotics and can provide prescribing guidance to healthcare providers to improve patient management and help slow the spread of antibiotic resistance in the community. There is currently a paucity of routine community-level AMR surveillance information. The HPA in England sponsored the development of an AMR surveillance system (AmSurv) to collate local laboratory reports. In the West Midlands region of England, routine reporting of AMR data has been established via the AmSurv system from all diagnostic microbiology laboratories. The HPA Regional Epidemiology Unit developed a web-enabled database application (AmWeb) to provide microbiologists, pharmacists and other stakeholders with timely access to AMR data using user-configurable reporting tools. AmWeb was launched in the West Midlands in January 2012 and is used by microbiologists and pharmacists to monitor resistance profiles, perform local benchmarking and compile data for infection control reports. AmWeb is now being rolled out to all English regions. It is expected that AmWeb will become a valuable tool for monitoring the threat from newly emerging or currently circulating resistant organisms and helping antibiotic prescribers to select the best treatment options for their patients.

Development of a 3D ultrasound-guided system for thermal ablation of liver tumors

NASA Astrophysics Data System (ADS)

Neshat, Hamid R. S.; Cool, Derek W.; Barker, Kevin; Gardi, Lori; Kakani, Nirmal; Fenster, Aaron

2013-03-01

Two-dimensional ultrasound (2D US) imaging is commonly used for diagnostic and intraoperative guidance of interventional abdominal procedures including percutaneous thermal ablation of focal liver tumors with radiofrequency (RF) or microwave (MW) induced energy. However, in many situations 2D US may not provide enough anatomical detail and guidance information. Therefore, intra-procedural CT or MR imaging are used in many centers for guidance purposes. These modalities are costly and are mainly utilized to confirm tool placement rather than guiding the insertion. Three-dimensional ultrasound (3D US) has been introduced to address these issues. In this paper, we present our integrated solution to provide 3D US images using a newly developed mechanical transducer with a large field-ofview and without the need for external tracking devices to combine diagnostic and planning information of different modalities for intraoperative guidance. The system provides tools to segment the target(s), plan the treatment, and detect the ablation applicators during the procedure for guiding purposes. We present experimental results used to ensure that our system generates accurate measurements and our early clinical evaluation results. The results suggest that 3D US used for focal liver ablation can provide a more reliable planning and guidance tool compared to 2D US only, and in many cases offers comparable measurements to other alternatives at significantly lower cost, faster time and with no harmful radiation.

ISAAC - InterSpecies Analysing Application using Containers.

PubMed

Baier, Herbert; Schultz, Jörg

2014-01-15

Information about genes, transcripts and proteins is spread over a wide variety of databases. Different tools have been developed using these databases to identify biological signals in gene lists from large scale analysis. Mostly, they search for enrichments of specific features. But, these tools do not allow an explorative walk through different views and to change the gene lists according to newly upcoming stories. To fill this niche, we have developed ISAAC, the InterSpecies Analysing Application using Containers. The central idea of this web based tool is to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. Furthermore, one can easily switch back to previous states and perform new analyses. Currently, sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. As todays research usually is performed in larger teams and consortia, ISAAC provides group based functionalities. Here, sets as well as results of analyses can be exchanged between members of groups. ISAAC fills the gap between primary databases and tools for the analysis of large gene lists. With its highly modular, JavaEE based design, the implementation of new modules is straight forward. Furthermore, ISAAC comes with an extensive web-based administration interface including tools for the integration of third party data. Thus, a local installation is easily feasible. In summary, ISAAC is tailor made for highly explorative interactive analyses of gene, transcript and protein sets in a collaborative environment.

Enhanced terahertz imaging system performance analysis and design tool for concealed weapon identification

NASA Astrophysics Data System (ADS)

Murrill, Steven R.; Franck, Charmaine C.; Espinola, Richard L.; Petkie, Douglas T.; De Lucia, Frank C.; Jacobs, Eddie L.

2011-11-01

The U.S. Army Research Laboratory (ARL) and the U.S. Army Night Vision and Electronic Sensors Directorate (NVESD) have developed a terahertz-band imaging system performance model/tool for detection and identification of concealed weaponry. The details of the MATLAB-based model which accounts for the effects of all critical sensor and display components, and for the effects of atmospheric attenuation, concealment material attenuation, and active illumination, were reported on at the 2005 SPIE Europe Security & Defence Symposium (Brugge). An advanced version of the base model that accounts for both the dramatic impact that target and background orientation can have on target observability as related to specular and Lambertian reflections captured by an active-illumination-based imaging system, and for the impact of target and background thermal emission, was reported on at the 2007 SPIE Defense and Security Symposium (Orlando). This paper will provide a comprehensive review of an enhanced, user-friendly, Windows-executable, terahertz-band imaging system performance analysis and design tool that now includes additional features such as a MODTRAN-based atmospheric attenuation calculator and advanced system architecture configuration inputs that allow for straightforward performance analysis of active or passive systems based on scanning (single- or line-array detector element(s)) or staring (focal-plane-array detector elements) imaging architectures. This newly enhanced THz imaging system design tool is an extension of the advanced THz imaging system performance model that was developed under the Defense Advanced Research Project Agency's (DARPA) Terahertz Imaging Focal-Plane Technology (TIFT) program. This paper will also provide example system component (active-illumination source and detector) trade-study analyses using the new features of this user-friendly THz imaging system performance analysis and design tool.

Monitoring tools of COMPASS experiment at CERN

NASA Astrophysics Data System (ADS)

Bodlak, M.; Frolov, V.; Huber, S.; Jary, V.; Konorov, I.; Levit, D.; Novy, J.; Salac, R.; Tomsa, J.; Virius, M.

2015-12-01

This paper briefly introduces the data acquisition system of the COMPASS experiment and is mainly focused on the part that is responsible for the monitoring of the nodes in the whole newly developed data acquisition system of this experiment. The COMPASS is a high energy particle experiment with a fixed target located at the SPS of the CERN laboratory in Geneva, Switzerland. The hardware of the data acquisition system has been upgraded to use FPGA cards that are responsible for data multiplexing and event building. The software counterpart of the system includes several processes deployed in heterogenous network environment. There are two processes, namely Message Logger and Message Browser, taking care of monitoring. These tools handle messages generated by nodes in the system. While Message Logger collects and saves messages to the database, the Message Browser serves as a graphical interface over the database containing these messages. For better performance, certain database optimizations have been used. Lastly, results of performance tests are presented.

Forensic odontology as a victim identification tool in mass disasters: A feasibility study in the Indian scenario

PubMed Central

Sengupta, Shamindra; Sharma, Vandana; Gupta, Vineeta; Vij, Hitesh; Vij, Ruchieka; Prabhat, Kanika

2014-01-01

Aim: The aim of this study was to evaluate the awareness of practicing dentists about the subject of forensic odontology and to assess their willingness to maintain and share patient records. Materials and Methods: A blind questionnaire survey was carried out among 100 randomly selected practicing dentists in district Ghaziabad, Uttar Pradesh. Results: Most of the dentists interviewed were familiar with the subject of forensic odontology and its relation to dentistry, despite forensic dentistry having been newly introduced since 2007 into the undergraduate dental curriculum in India. However, dental records are maintained by only a few dentists, and only a very small percentage of them reported to have shared records, which may have helped in the identification of victims in a mass disaster. Conclusion: The result of our survey concluded that more awareness needs to be developed among practicing dentists regarding maintaining and sharing patient records for forensic odontology to succeed as a victim identification tool. PMID:24695834

Evaluation of MALDI-TOF mass spectrometry and Sepsityper Kit™ for the direct identification of organisms from sterile body fluids in a Canadian pediatric hospital.

PubMed

Tadros, Manal; Petrich, Astrid

2013-01-01

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) can be used to identify bacteria directly from positive blood and sterile fluid cultures. The authors evaluated a commercially available kit - the Sepsityper Kit (Bruker Daltonik, Germany) - and MALDI-TOF MS for the rapid identification of organisms from 80 flagged positive blood culture broths, of which 73 (91.2%) were blood culture specimens and seven (8.7%) were cerebrospinal fluid specimens, in comparison with conventional identification methods. Correct identification to the genus and species levels was obtained in 75 of 80 (93.8%) and 39 of 50 (78%) blood culture broths, respectively. Applying the blood culture analysis module, a newly developed software tool, improved the species identification of Gram-negative organisms from 94.7% to 100% and of Gram-positive organisms from 66.7% to 70%. MALDI-TOF MS is a promising tool for the direct identification of organisms cultured from sterile sites.

eap Gene as novel target for specific identification of Staphylococcus aureus.

PubMed

Hussain, Muzaffar; von Eiff, Christof; Sinha, Bhanu; Joost, Insa; Herrmann, Mathias; Peters, Georg; Becker, Karsten

2008-02-01

The cell surface-associated extracellular adherence protein (Eap) mediates adherence of Staphylococcus aureus to host extracellular matrix components and inhibits inflammation, wound healing, and angiogenesis. A well-characterized collection of S. aureus and non-S. aureus staphylococcal isolates (n = 813) was tested for the presence of the Eap-encoding gene (eap) by PCR to investigate the use of the eap gene as a specific diagnostic tool for identification of S. aureus. Whereas all 597 S. aureus isolates were eap positive, this gene was not detectable in 216 non-S. aureus staphylococcal isolates comprising 47 different species and subspecies of coagulase-negative staphylococci and non-S. aureus coagulase-positive or coagulase-variable staphylococci. Furthermore, non-S. aureus isolates did not express Eap homologs, as verified on the transcriptional and protein levels. Based on these data, the sensitivity and specificity of the newly developed PCR targeting the eap gene were both 100%. Thus, the unique occurrence of Eap in S. aureus offers a promising tool particularly suitable for molecular diagnostics of this pathogen.

On aerodynamic wake analysis and its relation to total aerodynamic drag in a wind tunnel environment

NASA Astrophysics Data System (ADS)

Guterres, Rui M.

The present work was developed with the goal of advancing the state of the art in the application of three-dimensional wake data analysis to the quantification of aerodynamic drag on a body in a low speed wind tunnel environment. Analysis of the existing tools, their strengths and limitations is presented. Improvements to the existing analysis approaches were made. Software tools were developed to integrate the analysis into a practical tool. A comprehensive derivation of the equations needed for drag computations based on three dimensional separated wake data is developed. A set of complete steps ranging from the basic mathematical concept to the applicable engineering equations is presented. An extensive experimental study was conducted. Three representative body types were studied in varying ground effect conditions. A detailed qualitative wake analysis using wake imaging and two and three dimensional flow visualization was performed. Several significant features of the flow were identified and their relation to the total aerodynamic drag established. A comprehensive wake study of this type is shown to be in itself a powerful tool for the analysis of the wake aerodynamics and its relation to body drag. Quantitative wake analysis techniques were developed. Significant post processing and data conditioning tools and precision analysis were developed. The quality of the data is shown to be in direct correlation with the accuracy of the computed aerodynamic drag. Steps are taken to identify the sources of uncertainty. These are quantified when possible and the accuracy of the computed results is seen to significantly improve. When post processing alone does not resolve issues related to precision and accuracy, solutions are proposed. The improved quantitative wake analysis is applied to the wake data obtained. Guidelines are established that will lead to more successful implementation of these tools in future research programs. Close attention is paid to implementation of issues that are of crucial importance for the accuracy of the results and that are not detailed in the literature. The impact of ground effect on the flows in hand is qualitatively and quantitatively studied. Its impact on the accuracy of the computations as well as the wall drag incompatibility with the theoretical model followed are discussed. The newly developed quantitative analysis provides significantly increased accuracy. The aerodynamic drag coefficient is computed within one percent of balance measured value for the best cases.

Three-dimensional variational assimilation of MODIS aerosol optical depth: Implementation and application to a dust storm over East Asia

NASA Astrophysics Data System (ADS)

Liu, Zhiquan; Liu, Quanhua; Lin, Hui-Chuan; Schwartz, Craig S.; Lee, Yen-Huei; Wang, Tijian

2011-12-01

Assimilation of the Moderate Resolution Imaging Spectroradiometer (MODIS) total aerosol optical depth (AOD) retrieval products (at 550 nm wavelength) from both Terra and Aqua satellites have been developed within the National Centers for Environmental Prediction (NCEP) Gridpoint Statistical Interpolation (GSI) three-dimensional variational (3DVAR) data assimilation system. This newly developed algorithm allows, in a one-step procedure, the analysis of 3-D mass concentration of 14 aerosol variables from the Goddard Chemistry Aerosol Radiation and Transport (GOCART) module. The Community Radiative Transfer Model (CRTM) was extended to calculate AOD using GOCART aerosol variables as input. Both the AOD forward model and corresponding Jacobian model were developed within the CRTM and used in the 3DVAR minimization algorithm to compute the AOD cost function and its gradient with respect to 3-D aerosol mass concentration. The impact of MODIS AOD data assimilation was demonstrated by application to a dust storm from 17 to 24 March 2010 over East Asia. The aerosol analyses initialized Weather Research and Forecasting/Chemistry (WRF/Chem) model forecasts. Results indicate that assimilating MODIS AOD substantially improves aerosol analyses and subsequent forecasts when compared to MODIS AOD, independent AOD observations from the Aerosol Robotic Network (AERONET) and Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) instrument, and surface PM10 (particulate matter with diameters less than 10 μm) observations. The newly developed AOD data assimilation system can serve as a tool to improve simulations of dust storms and general air quality analyses and forecasts.

Assessing College Students' Perceptions of a Case Teacher's Pedagogical Content Knowledge Using a Newly Developed Instrument

ERIC Educational Resources Information Center

Jang, Syh-Jong

2011-01-01

Ongoing professional development for college teachers has been much emphasized. However, previous research on learning environments has seldom addressed college students' perceptions of teachers' PCK. This study aimed to evaluate college students' perceptions of a physics teacher's PCK development using a newly developed instrument and workshop…

Preparing School Leaders: The Professional Development Needs of Newly Appointed Principals

ERIC Educational Resources Information Center

Ng, Shun-wing; Szeto, Sing-ying Elson

2016-01-01

In Hong Kong, there is an acute need to provide newly appointed principals with opportunities for continuous professional development so that they could face the impact of reforms and globalization on school development. The Education Bureau has commissioned the tertiary institutions to provide structured professional development courses to cater…

Soapy: an adaptive optics simulation written purely in Python for rapid concept development

NASA Astrophysics Data System (ADS)

Reeves, Andrew

2016-07-01

Soapy is a newly developed Adaptive Optics (AO) simulation which aims be a flexible and fast to use tool-kit for many applications in the field of AO. It is written purely in the Python language, adding to and taking advantage of the already rich ecosystem of scientific libraries and programs. The simulation has been designed to be extremely modular, such that each component can be used stand-alone for projects which do not require a full end-to-end simulation. Ease of use, modularity and code clarity have been prioritised at the expense of computational performance. Though this means the code is not yet suitable for large studies of Extremely Large Telescope AO systems, it is well suited to education, exploration of new AO concepts and investigations of current generation telescopes.

Structural response of existing spatial truss roof construction based on Cosserat rod theory

NASA Astrophysics Data System (ADS)

Miśkiewicz, Mikołaj

2018-04-01

Paper presents the application of the Cosserat rod theory and newly developed associated finite elements code as the tools that support in the expert-designing engineering practice. Mechanical principles of the 3D spatially curved rods, dynamics (statics) laws, principle of virtual work are discussed. Corresponding FEM approach with interpolation and accumulation techniques of state variables are shown that enable the formulation of the C0 Lagrangian rod elements with 6-degrees of freedom per node. Two test examples are shown proving the correctness and suitability of the proposed formulation. Next, the developed FEM code is applied to assess the structural response of the spatial truss roof of the "Olivia" Sports Arena Gdansk, Poland. The numerical results are compared with load test results. It is shown that the proposed FEM approach yields correct results.

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

PubMed Central

Yang, Wanneng; Guo, Zilong; Huang, Chenglong; Duan, Lingfeng; Chen, Guoxing; Jiang, Ni; Fang, Wei; Feng, Hui; Xie, Weibo; Lian, Xingming; Wang, Gongwei; Luo, Qingming; Zhang, Qifa; Liu, Qian; Xiong, Lizhong

2014-01-01

Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits. PMID:25295980

The Charm of Community Music

ERIC Educational Resources Information Center

Ruisen, Xu

2011-01-01

Music education in communities is a newly sprouted thing and is gradually catching people's attention. Music education seeks to promote community members' aesthetic senses. Music and the arts, the best tools for moving people's souls, link different hearts across various boundaries, affecting all aspects of social life. Music education can serve…

Virtual Reality: Visualization in Three Dimensions.

ERIC Educational Resources Information Center

McLellan, Hilary

Virtual reality is a newly emerging tool for scientific visualization that makes possible multisensory, three-dimensional modeling of scientific data. While the emphasis is on visualization, the other senses are added to enhance what the scientist can visualize. Researchers are working to extend the sensory range of what can be perceived in…

A conceptual framework to support exposure science research and complete the source-to-outcome continuum for risk assessment

EPA Science Inventory

While knowledge of exposure is fundamental to assessing and mitigating risks, exposure information has been costly and difficult to generate. Driven by major scientific advances in analytical methods, biomonitoring, computational tools, and a newly articulated vision for a great...

Florida City & County Government. A Condensed Reference Version.

ERIC Educational Resources Information Center

Massialas, Byron; Jenkins, Ann

Designed to serve as a reference tool on city and county government in Florida, this handbook consists of lessons that can be used by schools, community groups, newly elected officials, and libraries. These curriculum materials on Florida city and county governments specifically address the general purpose of local governments. Subject areas…

Degree-days as a tool for use in producing tilapia fry for sex inversion

USDA-ARS?s Scientific Manuscript database

Hormonal sex inversion of newly hatched tilapia fry continues to be an important method to produce monosex male tilapia fingerlings. Large numbers of tilapia fry suitable for sex inversion can be produced by periodic complete harvest of earthen reproduction ponds. Traditionally, harvest interval was...

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes.

PubMed

Ono, Hiromasa; Ogasawara, Osamu; Okubo, Kosaku; Bono, Hidemasa

2017-08-29

Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/.

Identification of GATC- and CCGG- recognizing Type II REases and their putative specificity-determining positions using Scan2S—a novel motif scan algorithm with optional secondary structure constraints

PubMed Central

Niv, Masha Y.; Skrabanek, Lucy; Roberts, Richard J.; Scheraga, Harold A.; Weinstein, Harel

2008-01-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering. PMID:17972284

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

PubMed Central

Ono, Hiromasa; Ogasawara, Osamu; Okubo, Kosaku; Bono, Hidemasa

2017-01-01

Gene expression data are exponentially accumulating; thus, the functional annotation of such sequence data from metadata is urgently required. However, life scientists have difficulty utilizing the available data due to its sheer magnitude and complicated access. We have developed a web tool for browsing reference gene expression pattern of mammalian tissues and cell lines measured using different methods, which should facilitate the reuse of the precious data archived in several public databases. The web tool is called Reference Expression dataset (RefEx), and RefEx allows users to search by the gene name, various types of IDs, chromosomal regions in genetic maps, gene family based on InterPro, gene expression patterns, or biological categories based on Gene Ontology. RefEx also provides information about genes with tissue-specific expression, and the relative gene expression values are shown as choropleth maps on 3D human body images from BodyParts3D. Combined with the newly incorporated Functional Annotation of Mammals (FANTOM) dataset, RefEx provides insight regarding the functional interpretation of unfamiliar genes. RefEx is publicly available at http://refex.dbcls.jp/. PMID:28850115

Identification of GATC- and CCGG-recognizing Type II REases and their putative specificity-determining positions using Scan2S--a novel motif scan algorithm with optional secondary structure constraints.

PubMed

Niv, Masha Y; Skrabanek, Lucy; Roberts, Richard J; Scheraga, Harold A; Weinstein, Harel

2008-05-01

Restriction endonucleases (REases) are DNA-cleaving enzymes that have become indispensable tools in molecular biology. Type II REases are highly divergent in sequence despite their common structural core, function and, in some cases, common specificities towards DNA sequences. This makes it difficult to identify and classify them functionally based on sequence, and has hampered the efforts of specificity-engineering. Here, we define novel REase sequence motifs, which extend beyond the PD-(D/E)XK hallmark, and incorporate secondary structure information. The automated search using these motifs is carried out with a newly developed fast regular expression matching algorithm that accommodates long patterns with optional secondary structure constraints. Using this new tool, named Scan2S, motifs derived from REases with specificity towards GATC- and CGGG-containing DNA sequences successfully identify REases of the same specificity. Notably, some of these sequences are not identified by standard sequence detection tools. The new motifs highlight potential specificity-determining positions that do not fully overlap for the GATC- and the CCGG-recognizing REases and are candidates for specificity re-engineering.

Solar Field Optical Characterization at Stillwater Geothermal/Solar Hybrid Plant

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

Zhu, Guangdong; Turchi, Craig

Concentrating solar power (CSP) can provide additional thermal energy to boost geothermal plant power generation. For a newly constructed solar field at a geothermal power plant site, it is critical to properly characterize its performance so that the prediction of thermal power generation can be derived to develop an optimum operating strategy for a hybrid system. In the past, laboratory characterization of a solar collector has often extended into the solar field performance model and has been used to predict the actual solar field performance, disregarding realistic impacting factors. In this work, an extensive measurement on mirror slope error andmore » receiver position error has been performed in the field by using the optical characterization tool called Distant Observer (DO). Combining a solar reflectance sampling procedure, a newly developed solar characterization program called FirstOPTIC and public software for annual performance modeling called System Advisor Model (SAM), a comprehensive solar field optical characterization has been conducted, thus allowing for an informed prediction of solar field annual performance. The paper illustrates this detailed solar field optical characterization procedure and demonstrates how the results help to quantify an appropriate tracking-correction strategy to improve solar field performance. In particular, it is found that an appropriate tracking-offset algorithm can improve the solar field performance by about 15%. The work here provides a valuable reference for the growing CSP industry.« less

Multidimensional Patient Impression of Change Following Interdisciplinary Pain Management.

PubMed

Gagnon, Christine M; Scholten, Paul; Atchison, James

2018-04-20

To assess patient impression of change following interdisciplinary pain management utilizing a newly developed Multidimensional Patient Impression of Change (MPIC) questionnaire. A heterogeneous group of chronic pain patients (N = 601) participated in an interdisciplinary treatment program. Programs included individual and group therapies (pain psychology, physical therapy, occupational therapy, relaxation training/biofeedback, aerobic conditioning, patient education and medical management). Patients completed measures of pain, mood, coping, physical functioning and pain acceptance both prior to and at completion of their treatment programs. The newly developed MPIC is an expansion to the Patient Global Impression of Change (PGIC) including seven additional domains (Pain, Mood, Sleep, Physical Functioning, Cope with Pain, Manage Pain Flare-ups, and Medication Effectiveness). The MPIC was administered to the patients post-treatment. There were statistically significant pre- to post-treatment improvements found on all outcome measures. The majority of these improvements were significantly correlated with all domains of the MPIC. The original PGIC item was significantly associated with all of the new MPIC domains and the domains were significantly associated with each other; but there were variations in the distribution of responses highlighting variation of perceived improvements among the domains. Our results support the use of the MPIC as a quick and easy post-treatment assessment screening tool. Future research is needed to examine relevant correlates to Medication Effectiveness. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Development and validation of a patient self-assessed questionnaire on satisfaction with communication of the multiple sclerosis diagnosis.

PubMed

Solari, A; Mattarozzi, K; Vignatelli, L; Giordano, A; Russo, P M; Uccelli, M Messmer; D'Alessandro, R

2010-10-01

We describe the development and clinical validation of a patient self-administered tool assessing the quality of multiple sclerosis diagnosis disclosure. A multiple sclerosis expert panel generated questionnaire items from the Doctor's Interpersonal Skills Questionnaire, literature review, and interviews with neurology inpatients. The resulting 19-item Comunicazione medico-paziente nella Sclerosi Multipla (COSM) was pilot tested/debriefed on seven patients with multiple sclerosis and administered to 80 patients newly diagnosed with multiple sclerosis. The resulting revised 20-item version (COSM-R) was debriefed on five patients with multiple sclerosis, field tested/debriefed on multiple sclerosis patients, and field tested on 105 patients newly diagnosed with multiple sclerosis participating in a clinical trial on an information aid. The hypothesized monofactorial structure of COSM-R section 2 was tested on the latter two groups. The questionnaire was well accepted. Scaling assumptions were satisfactory in terms of score distributions, item-total correlations and internal consistency. Factor analysis confirmed section 2's monofactorial structure, which was also test-retest reliable (intraclass correlation coefficient [ICC] 0.73; 95% CI 0.54-0.85). Section 1 had only fair test-retest reliability (ICC 0.45; 95% CI 0.12-0.69), and three items had 8-21% missed responses. COSM-R is a brief, easy-to-interpret MS-specific questionnaire for use as a health care indicator.

Estimates of abundance and diversity of Shewanella genus in natural and engineered aqueous environments with newly designed primers.

PubMed

Li, Bing-Bing; Cheng, Yuan-Yuan; Fan, Yang-Yang; Liu, Dong-Feng; Fang, Cai-Yun; Wu, Chao; Li, Wen-Wei; Yang, Zong-Chuang; Yu, Han-Qing

2018-05-12

Shewanella species have a diverse respiratory ability and wide distribution in environments and play an important role in bioremediation and the biogeochemical cycles of elements. Primers with more accuracy and broader coverage are required with consideration of the increasing number of Shewanella species and evaluation of their roles in various environments. In this work, a new primer set of 640F/815R was developed to quantify the abundance of Shewanella species in natural and engineered environments. In silico tools for primer evaluation, quantitative polymerase chain reaction (qPCR) and clone library results showed that 640F/815R had a higher specificity and coverage than the previous primers in quantitative analysis of Shewanella. Another newly developed primer pair of 211F/815cR was also adopted to analyze the Shewanella diversity and demonstrated to be the best candidate in terms of specificity and coverage. We detected more Shewanella-related species in freshwater environments and found them to be substantially different from those in marine environments. Abundance and diversity of Shewanella species in wastewater treatment plants were largely affected by the process and operating conditions. Overall, this study suggests that investigations of abundance and diversity of Shewanella in various environments are of great importance to evaluate their ecophysiology and potential ecological roles. Copyright © 2018 Elsevier B.V. All rights reserved.

Solar Field Optical Characterization at Stillwater Geothermal/Solar Hybrid Plant

DOE PAGES

Zhu, Guangdong; Turchi, Craig

2017-01-27

Concentrating solar power (CSP) can provide additional thermal energy to boost geothermal plant power generation. For a newly constructed solar field at a geothermal power plant site, it is critical to properly characterize its performance so that the prediction of thermal power generation can be derived to develop an optimum operating strategy for a hybrid system. In the past, laboratory characterization of a solar collector has often extended into the solar field performance model and has been used to predict the actual solar field performance, disregarding realistic impacting factors. In this work, an extensive measurement on mirror slope error andmore » receiver position error has been performed in the field by using the optical characterization tool called Distant Observer (DO). Combining a solar reflectance sampling procedure, a newly developed solar characterization program called FirstOPTIC and public software for annual performance modeling called System Advisor Model (SAM), a comprehensive solar field optical characterization has been conducted, thus allowing for an informed prediction of solar field annual performance. The paper illustrates this detailed solar field optical characterization procedure and demonstrates how the results help to quantify an appropriate tracking-correction strategy to improve solar field performance. In particular, it is found that an appropriate tracking-offset algorithm can improve the solar field performance by about 15%. The work here provides a valuable reference for the growing CSP industry.« less

Validity and reproducibility of a food frequency questionnaire (FFQ) for dietary assessment in Malay adolescents in Malaysia.

PubMed

Nurul-Fadhilah, Abdullah; Teo, Pey Sze; Foo, Leng Huat

2012-01-01

Food frequency questionnaire (FFQ) must be tailored to the target populations because dietary habits vary within the populations due to differences in cultural and lifestyles practices. Limited information is available to assess the validity of FFQ used among Malaysian adolescents. To construct the validity and reproducibility of a newly developed FFQ in assessing habitual nutrients intake over the past year of 170 Malay adolescent boys and girls in Kelantan, Malaysia. The FFQ that consisted of 124 food items was assessed, whereas three days of 24-hours dietary recalls (DR) was administered as the standard criteria method. Estimated mean intake for most nutrients assessed by the FFQ were higher as compared to the three DRs (p<0.05). Pearson correlation coefficients for energy-adjusted nutrients intake between both methods were ranged from 0.22 (zinc) to 0.68 (calcium) with a median r-value of 0.43. The cross classification of quartile analysis showed that most nutrients were classified into the same or adjacent quartiles (median=52.7%). For the reproducibility of FFQ, the correlation of nutrients ranged from 0.43 for carotene to 0.86 for total fat intake (median=0.67), after adjusting for total energy intake. The newly developed dietary FFQ is a relatively good and valid tool in assessing habitual nutrients intake for the past year among Malay adolescents in Malaysia.

PROGRESS REPORT ON THE DSSTOX DATABASE NETWORK: NEWLY LAUNCHED WEBSITE, APPLICATIONS, FUTURE PLANS

EPA Science Inventory

Progress Report on the DSSTox Database Network: Newly Launched Website, Applications, Future Plans

Progress will be reported on development of the Distributed Structure-Searchable Toxicity (DSSTox) Database Network and the newly launched public website that coordinates and...

Bioinformatics analysis and characteristics of VP23 encoded by the newly identified UL18 gene of duck enteritis virus

NASA Astrophysics Data System (ADS)

Chen, Xiwen; Cheng, Anchun; Wang, Mingshu; Xiang, Jun

2011-10-01

In this study, the predicted information about structures and functions of VP23 encoded by the newly identified DEV UL18 gene through bioinformatics softwares and tools. The DEV UL18 was predicted to encode a polypeptide with 322 amino acids, termed VP23, with a putative molecular mass of 35.250 kDa and a predicted isoelectric point (PI) of 8.37, no signal peptide and transmembrane domain in the polypeptide. The prediction of subcellular localization showed that the DEV-VP23 located at endoplasmic reticulum with 33.3%, mitochondrial with 22.2%, extracellular, including cell wall with 11.1%, vesicles of secretory system with 11.1%, Golgi with 11.1%, and plasma membrane with 11.1%. The acid sequence of analysis showed that the potential antigenic epitopes are situated in 45-47, 53-60, 102-105, 173-180, 185-189, 260-265, 267-271, and 292-299 amino acids. All the consequences inevitably provide some insights for further research about the DEV-VP23 and also provide a fundament for further study on the the new type clinical diagnosis of DEV and can be used for the development of new DEV vaccine.

Riems influenza a typing array (RITA): An RT-qPCR-based low density array for subtyping avian and mammalian influenza a viruses.

PubMed

Hoffmann, Bernd; Hoffmann, Donata; Henritzi, Dinah; Beer, Martin; Harder, Timm C

2016-06-03

Rapid and sensitive diagnostic approaches are of the utmost importance for the detection of humans and animals infected by specific influenza virus subtype(s). Cascade-like diagnostics starting with the use of pan-influenza assays and subsequent subtyping devices are normally used. Here, we demonstrated a novel low density array combining 32 TaqMan(®) real-time RT-PCR systems in parallel for the specific detection of the haemagglutinin (HA) and neuraminidase (NA) subtypes of avian and porcine hosts. The sensitivity of the newly developed system was compared with that of the pan-influenza assay, and the specificity of all RT-qPCRs was examined using a broad panel of 404 different influenza A virus isolates representing 45 different subtypes. Furthermore, we analysed the performance of the RT-qPCR assays with diagnostic samples obtained from wild birds and swine. Due to the open format of the array, adaptations to detect newly emerging influenza A virus strains can easily be integrated. The RITA array represents a competitive, fast and sensitive subtyping tool that requires neither new machinery nor additional training of staff in a lab where RT-qPCR is already established.

Explore GPM IMERG and Other Global Precipitation Products with GES DISC GIOVANNI

NASA Technical Reports Server (NTRS)

Liu, Zhong; Ostrenga, Dana M.; Vollmer, Bruce; MacRitchie, Kyle; Kempler, Steven

2015-01-01

New features and capabilities in the newly released GIOVANNI allow exploring GPM IMERG (Integrated Multi-satelliE Retrievals for GPM) Early, Late and Final Run global half-hourly and monthly precipitation products as well as other precipitation products distributed by the GES DISC such as TRMM Multi-Satellite Precipitation Analysis (TMPA), MERRA (Modern Era Retrospective-Analysis for Research and Applications), NLDAS (North American Land Data Assimilation Systems), GLDAS (Global Land Data Assimilation Systems), etc. GIOVANNI is a web-based tool developed by the GES DISC (Goddard Earth Sciences and Data Information Services Center) to visualize and analyze Earth science data without having to download data and software. The new interface in GIOVANNI allows searching and filtering precipitation products from different NASA missions and projects and expands the capabilities to inter-compare different precipitation products in one interface. Knowing differences in precipitation products is important to identify issues in retrieval algorithms, biases, uncertainties, etc. Due to different formats, data structures, units and so on, it is not easy to inter-compare precipitation products. Newly added features and capabilities (unit conversion, regridding, etc.) in GIOVANNI make inter-comparisons possible. In this presentation, we will describe these new features and capabilities along with examples.

Physiologically Based Pharmacokinetic Models: Integration of In Silico Approaches with Micro Cell Culture Analogues

PubMed Central

Chen, A.; Yarmush, M.L.; Maguire, T.

2014-01-01

There is a large emphasis within the pharmaceutical industry to provide tools that will allow early research and development groups to better predict dose ranges for and metabolic responses of candidate molecules in a high throughput manner, prior to entering clinical trials. These tools incorporate approaches ranging from PBPK, QSAR, and molecular dynamics simulations in the in silico realm, to micro cell culture analogue (CCAs)s in the in vitro realm. This paper will serve to review these areas of high throughput predictive research, and highlight hurdles and potential solutions. In particular we will focus on CCAs, as their incorporation with PBPK modeling has the potential to replace animal testing, with a more predictive assay that can combine multiple organ analogs on one microfluidic platform in physiologically correct volume ratios. While several advantages arise from the current embodiments of CCAS in a microfluidic format that can be exploited for realistic simulations of drug absorption, metabolism and action, we explore some of the concerns with these systems, and provide a potential path forward to realizing animal-free solutions. Furthermore we envision that, together with theoretical modeling, CCAs may produce reliable predictions of the efficacy of newly developed drugs. PMID:22571482

Identifying Novel Type ZBGs and Nonhydroxamate HDAC Inhibitors Through a SVM Based Virtual Screening Approach.

PubMed

Liu, X H; Song, H Y; Zhang, J X; Han, B C; Wei, X N; Ma, X H; Cui, W K; Chen, Y Z

2010-05-17

Histone deacetylase inhibitors (HDACi) have been successfully used for the treatment of cancers and other diseases. Search for novel type ZBGs and development of non-hydroxamate HDACi has become a focus in current research. To complement this, it is desirable to explore a virtual screening (VS) tool capable of identifying different types of potential inhibitors from large compound libraries with high yields and low false-hit rates similar to HTS. This work explored the use of support vector machines (SVM) combined with our newly developed putative non-inhibitor generation method as such a tool. SVM trained by 702 pre-2008 hydroxamate HDACi and 64334 putative non-HDACi showed good yields and low false-hit rates in cross-validation test and independent test using 220 diverse types of HDACi reported since 2008. The SVM hit rates in scanning 13.56 M PubChem and 168K MDDR compounds are comparable to HTS rates. Further structural analysis of SVM virtual hits suggests its potential for identification of non-hydroxamate HDACi. From this analysis, a series of novel ZBG and cap groups were proposed for HDACi design. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Affective and behavioral dysfunction under antiepileptic drugs in epilepsy: Development of a new drug-sensitive screening tool.

PubMed

Mertens, Lea Julia; Witt, Juri-Alexander; Helmstaedter, Christoph

2018-06-01

Behavioral problems and psychiatric symptoms are common in patients with epilepsy and have a multifactorial origin, including adverse effects of antiepileptic drugs (AEDs). In order to develop a screening tool for behavioral AED effects, the aim of this study was to identify behavioral problems and symptoms particularly sensitive to AED drug load and the presence/absence of AEDs with known negative psychotropic profiles. Four hundred ninety-four patients with epilepsy were evaluated who had been assessed with three self-report questionnaires on mood, personality, and behavior (Beck Depression Inventory, BDI; Neurological Disorders Depression Inventory for Epilepsy extended, NDDI-E; and Fragebogen zur Persönlichkeit bei zerebralen Erkrankungen, FPZ). Drug-sensitive items were determined via correlation analyses and entered into an exploratory factor analysis for scale construction. The resulting scales were then analyzed as a function of drug treatment. Analyses revealed 30 items, which could be allocated to six behavioral domains: Emotional Lability, Depression, Aggression/Irritability, Psychosis & Suicidality, Risk- & Sensation-seeking, and Somatization. Subsequent analysis showed significant effects of the number of AEDs on behavior, as in Emotional Lability (F=2.54, p=.029), Aggression/Irritability (F=2.29, p=.046), Psychosis & Suicidality (F=2.98, p=.012), and Somatization (F=2.39, p=.038). Affective and behavioral difficulties were more prominent in those patients taking AEDs with supposedly negative psychotropic profiles. These effects were largely domain-unspecific and primarily manifested in polytherapy. Drug-sensitive behavioral domains and items were identified which qualify for a self-report screening tool. The tool indicates impairments with a higher drug load and when administering AEDs with negative psychotropic profiles. The next steps require normalization in healthy subjects and the clinical validation of the newly developed screening tool PsyTrack along with antiepileptic drug treatment. Copyright © 2018 Elsevier Inc. All rights reserved.

Dupuytren Disease: Is There Enough Comprehensive Patient Information on the Internet?

PubMed Central

Raptis, Dimitri A; Fertsch, Sonia; Guggenheim, Merlin

2017-01-01

Background Dupuytren disease is a chronic nonmalign fibroproliferative disorder that causes finger contractures via proliferation of new tissue under the glabrous skin of the hand, resulting in multiple functional limitations for the patient. As many surgical therapy options exist, patients suffering from this condition actively search for information in their environment before consulting a health professional. Objective As little is known about the quality of Web-based patient information, the aim of this study was to conduct its systematic evaluation using a validated tool. Methods A total of 118 websites were included, and qualitative and quantitative assessment was performed using the modified Ensuring Quality Information for Patients (EQIP) tool. This standardized and reproducible tool consists of 36 items to assess available information in three categories: contents, identification, and structure data. Scientific data with restricted access, duplicates, and irrelevant websites were not included. Results Only 32 websites addressed more than 19 items, and the scores did not significantly differ among the website developers. The median number of items from the EQIP tool was 16, with the top websites addressing 28 out of 36 items. The quality of the newly developed websites did not increase with passing time. Conclusions This study revealed several shortcomings in the quality of Web-based information available for patients suffering from Dupuytren disease. In the world of continuously growing and instantly available Web-based information, it is the health providers’ negligence of the last two decades that there are very few good quality, informative, and educative websites that could be recommended to patients. PMID:28642214

LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons

PubMed Central

2012-01-01

Background Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets), making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. Results We have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. Conclusions LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining the output of software for predicting LTR retrotransposons up to the stage of preparing full-length reference sequence libraries. The LTRsift software is freely available at http://www.zbh.uni-hamburg.de/LTRsift under an open-source license. PMID:23131050

LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons.

PubMed

Steinbiss, Sascha; Kastens, Sascha; Kurtz, Stefan

2012-11-07

Long terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets), making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow. We have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort. LTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining the output of software for predicting LTR retrotransposons up to the stage of preparing full-length reference sequence libraries. The LTRsift software is freely available at http://www.zbh.uni-hamburg.de/LTRsift under an open-source license.

Mapping subsurface in proximity to newly-developed sinkhole along roadway.

DOT National Transportation Integrated Search

2013-02-01

MS&T acquired electrical resistivity tomography profiles in immediate proximity to a newly-developed sinkhole in Nixa Missouri : The sinkhole has closed a well-traveled municipal roadway and threatens proximal infrastructure. The intent of this inves...

Advancements in Large-Scale Data/Metadata Management for Scientific Data.

NASA Astrophysics Data System (ADS)

Guntupally, K.; Devarakonda, R.; Palanisamy, G.; Frame, M. T.

2017-12-01

Scientific data often comes with complex and diverse metadata which are critical for data discovery and users. The Online Metadata Editor (OME) tool, which was developed by an Oak Ridge National Laboratory team, effectively manages diverse scientific datasets across several federal data centers, such as DOE's Atmospheric Radiation Measurement (ARM) Data Center and USGS's Core Science Analytics, Synthesis, and Libraries (CSAS&L) project. This presentation will focus mainly on recent developments and future strategies for refining OME tool within these centers. The ARM OME is a standard based tool (https://www.archive.arm.gov/armome) that allows scientists to create and maintain metadata about their data products. The tool has been improved with new workflows that help metadata coordinators and submitting investigators to submit and review their data more efficiently. The ARM Data Center's newly upgraded Data Discovery Tool (http://www.archive.arm.gov/discovery) uses rich metadata generated by the OME to enable search and discovery of thousands of datasets, while also providing a citation generator and modern order-delivery techniques like Globus (using GridFTP), Dropbox and THREDDS. The Data Discovery Tool also supports incremental indexing, which allows users to find new data as and when they are added. The USGS CSAS&L search catalog employs a custom version of the OME (https://www1.usgs.gov/csas/ome), which has been upgraded with high-level Federal Geographic Data Committee (FGDC) validations and the ability to reserve and mint Digital Object Identifiers (DOIs). The USGS's Science Data Catalog (SDC) (https://data.usgs.gov/datacatalog) allows users to discover a myriad of science data holdings through a web portal. Recent major upgrades to the SDC and ARM Data Discovery Tool include improved harvesting performance and migration using new search software, such as Apache Solr 6.0 for serving up data/metadata to scientific communities. Our presentation will highlight the future enhancements of these tools which enable users to retrieve fast search results, along with parallelizing the retrieval process from online and High Performance Storage Systems. In addition, these improvements to the tools will support additional metadata formats like the Large-Eddy Simulation (LES) ARM Symbiotic and Observation (LASSO) bundle data.

Searching for new pharmacological targets for the treatment of Alzheimer's disease in Down syndrome.

PubMed

Caraci, Filippo; Iulita, M Florencia; Pentz, Rowan; Flores Aguilar, Lisi; Orciani, Chiara; Barone, Concetta; Romano, Corrado; Drago, Filippo; Cuello, A Claudio

2017-12-15

Individuals with Down syndrome are at increased risk of developing Alzheimer's disease due to increase gene dosage resulting from chromosome 21 triplication. Although virtually all adults with Down syndrome will exhibit the major neuropathological hallmarks that define Alzheimer's disease, not all of them will develop the clinical symptoms associated with this disorder (i.e. dementia). Therefore, a good understanding of the pathophysiology of Alzheimer's disease in Down syndrome will be crucial for the identification of novel pharmacological targets to develop disease-modifying therapies for the benefit of Down syndrome individuals and for Alzheimer's sufferers alike. The study of biomarkers will also be essential for the development of better screening tools to identify dementia at its incipient stages. This review discusses the best-validated pharmacological targets for the treatment of cognitive impairment and Alzheimer's disease in Down syndrome. We further examine the relevance of newly discovered biological markers for earlier dementia diagnosis in this population. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Assessing Competencies Needed to Engage With Digital Health Services: Development of the eHealth Literacy Assessment Toolkit.

PubMed

Karnoe, Astrid; Furstrand, Dorthe; Christensen, Karl Bang; Norgaard, Ole; Kayser, Lars

2018-05-10

To achieve full potential in user-oriented eHealth projects, we need to ensure a match between the eHealth technology and the user's eHealth literacy, described as knowledge and skills. However, there is a lack of multifaceted eHealth literacy assessment tools suitable for screening purposes. The objective of our study was to develop and validate an eHealth literacy assessment toolkit (eHLA) that assesses individuals' health literacy and digital literacy using a mix of existing and newly developed scales. From 2011 to 2015, scales were continuously tested and developed in an iterative process, which led to 7 tools being included in the validation study. The eHLA validation version consisted of 4 health-related tools (tool 1: "functional health literacy," tool 2: "health literacy self-assessment," tool 3: "familiarity with health and health care," and tool 4: "knowledge of health and disease") and 3 digitally-related tools (tool 5: "technology familiarity," tool 6: "technology confidence," and tool 7: "incentives for engaging with technology") that were tested in 475 respondents from a general population sample and an outpatient clinic. Statistical analyses examined floor and ceiling effects, interitem correlations, item-total correlations, and Cronbach coefficient alpha (CCA). Rasch models (RM) examined the fit of data. Tools were reduced in items to secure robust tools fit for screening purposes. Reductions were made based on psychometrics, face validity, and content validity. Tool 1 was not reduced in items; it consequently consists of 10 items. The overall fit to the RM was acceptable (Anderson conditional likelihood ratio, CLR=10.8; df=9; P=.29), and CCA was .67. Tool 2 was reduced from 20 to 9 items. The overall fit to a log-linear RM was acceptable (Anderson CLR=78.4, df=45, P=.002), and CCA was .85. Tool 3 was reduced from 23 to 5 items. The final version showed excellent fit to a log-linear RM (Anderson CLR=47.7, df=40, P=.19), and CCA was .90. Tool 4 was reduced from 12 to 6 items. The fit to a log-linear RM was acceptable (Anderson CLR=42.1, df=18, P=.001), and CCA was .59. Tool 5 was reduced from 20 to 6 items. The fit to the RM was acceptable (Anderson CLR=30.3, df=17, P=.02), and CCA was .94. Tool 6 was reduced from 5 to 4 items. The fit to a log-linear RM taking local dependency (LD) into account was acceptable (Anderson CLR=26.1, df=21, P=.20), and CCA was .91. Tool 7 was reduced from 6 to 4 items. The fit to a log-linear RM taking LD and differential item functioning into account was acceptable (Anderson CLR=23.0, df=29, P=.78), and CCA was .90. The eHLA consists of 7 short, robust scales that assess individual's knowledge and skills related to digital literacy and health literacy. ©Astrid Karnoe, Dorthe Furstrand, Karl Bang Christensen, Ole Norgaard, Lars Kayser. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 10.05.2018.

The development and psychometric testing of a Disaster Response Self-Efficacy Scale among undergraduate nursing students.

PubMed

Li, Hong-Yan; Bi, Rui-Xue; Zhong, Qing-Ling

2017-12-01

Disaster nurse education has received increasing importance in China. Knowing the abilities of disaster response in undergraduate nursing students is beneficial to promote teaching and learning. However, there are few valid and reliable tools that measure the abilities of disaster response in undergraduate nursing students. To develop a self-report scale of self-efficacy in disaster response for Chinese undergraduate nursing students and test its psychometric properties. Nursing students (N=318) from two medical colleges were chosen by purposive sampling. The Disaster Response Self-Efficacy Scale (DRSES) was developed and psychometrically tested. Reliability and content validity were studied. Construct validity was tested by exploratory and confirmatory factor analysis. Reliability was tested by internal consistency and test-retest reliability. The DRSES consisted of 3 factors and 19 items with a 5-point rating. The content validity was 0.91, Cronbach's alpha coefficient was 0.912, and the intraclass correlation coefficient for test-retest reliability was 0.953. The construct validity was good (χ 2 /df=2.440, RMSEA=0.068, NFI=0.907, CFI=0.942, IFI=0.430, p<0.001). The newly developed DRSES has proven good reliability and validity. It could therefore be used as an assessment tool to evaluate self-efficacy in disaster response for Chinese undergraduate nursing students. Copyright © 2017. Published by Elsevier Ltd.

Evaluation of new binders using newly developed fracture energy test.

DOT National Transportation Integrated Search

2013-07-01

This study evaluated a total of seven asphalt binders with various additives : using the newly developed binder fracture energy test. The researchers prepared and : tested PAV-aged and RTFO-plus-PAV-aged specimens. This study confirmed previous : res...

13 CFR 120.812 - Probationary period for newly certified CDCs.

Code of Federal Regulations, 2013 CFR

2013-01-01

... certified CDCs. 120.812 Section 120.812 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION BUSINESS LOANS Development Company Loan Program (504) Certification Procedures to Become A Cdc § 120.812 Probationary period for newly certified CDCs. (a) Newly certified CDCs will be on probation for a period of two...

13 CFR 120.812 - Probationary period for newly certified CDCs.

Code of Federal Regulations, 2014 CFR

2014-01-01

... certified CDCs. 120.812 Section 120.812 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION BUSINESS LOANS Development Company Loan Program (504) Certification Procedures to Become A Cdc § 120.812 Probationary period for newly certified CDCs. (a) Newly certified CDCs will be on probation for a period of two...

13 CFR 120.812 - Probationary period for newly certified CDCs.

Code of Federal Regulations, 2012 CFR

2012-01-01

... certified CDCs. 120.812 Section 120.812 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION BUSINESS LOANS Development Company Loan Program (504) Certification Procedures to Become A Cdc § 120.812 Probationary period for newly certified CDCs. (a) Newly certified CDCs will be on probation for a period of two...

13 CFR 120.812 - Probationary period for newly certified CDCs.

Code of Federal Regulations, 2011 CFR

2011-01-01

... certified CDCs. 120.812 Section 120.812 Business Credit and Assistance SMALL BUSINESS ADMINISTRATION BUSINESS LOANS Development Company Loan Program (504) Certification Procedures to Become A Cdc § 120.812 Probationary period for newly certified CDCs. (a) Newly certified CDCs will be on probation for a period of two...

Research Review: Attention Bias Modification (ABM)--A Novel Treatment for Anxiety Disorders

ERIC Educational Resources Information Center

Bar-Haim, Yair

2010-01-01

Attention bias modification (ABM) is a newly emerging therapy for anxiety disorders that is rooted in current cognitive models of anxiety and in established experimental data on threat-related attentional biases in anxiety. This review describes the evidence indicating that ABM has the potential to become an enhancing tool for current…

Generalized Data Management Systems--Some Perspectives.

ERIC Educational Resources Information Center

Minker, Jack

A Generalized Data Management System (GDMS) is a software environment provided as a tool for analysts, administrators, and programmers who are responsible for the maintenance, query and analysis of a data base to permit the manipulation of newly defined files and data with the existing programs and system. Because the GDMS technology is believed…

Social Network Analysis: A Simple but Powerful Tool for Identifying Teacher Leaders

ERIC Educational Resources Information Center

Smith, P. Sean; Trygstad, Peggy J.; Hayes, Meredith L.

2018-01-01

Instructional teacher leadership is central to a vision of distributed leadership. However, identifying instructional teacher leaders can be a daunting task, particularly for administrators who find themselves either newly appointed or faced with high staff turnover. This article describes the use of social network analysis (SNA), a simple but…

Leaf area and photosynthesis of newly emerged trifoliolate leaves are regulated by mature leaves in soybean.

PubMed

Wu, Yushan; Gong, Wanzhuo; Wang, Yangmei; Yong, Taiwen; Yang, Feng; Liu, Weigui; Wu, Xiaoling; Du, Junbo; Shu, Kai; Liu, Jiang; Liu, Chunyan; Yang, Wenyu

2018-03-29

Leaf anatomy and the stomatal development of developing leaves of plants have been shown to be regulated by the same light environment as that of mature leaves, but no report has yet been written on whether such a long-distance signal from mature leaves regulates the total leaf area of newly emerged leaves. To explore this question, we created an investigation in which we collected data on the leaf area, leaf mass per area (LMA), leaf anatomy, cell size, cell number, gas exchange and soluble sugar content of leaves from three soybean varieties grown under full sunlight (NS), shaded mature leaves (MS) or whole plants grown in shade (WS). Our results show that MS or WS cause a marked decline both in leaf area and LMA in newly developing leaves. Leaf anatomy also showed characteristics of shade leaves with decreased leaf thickness, palisade tissue thickness, sponge tissue thickness, cell size and cell numbers. In addition, in the MS and WS treatments, newly developed leaves exhibited lower net photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (E), but higher carbon dioxide (CO 2 ) concentration in the intercellular space (Ci) than plants grown in full sunlight. Moreover, soluble sugar content was significantly decreased in newly developed leaves in MS and WS treatments. These results clearly indicate that (1) leaf area, leaf anatomical structure, and photosynthetic function of newly developing leaves are regulated by a systemic irradiance signal from mature leaves; (2) decreased cell size and cell number are the major cause of smaller and thinner leaves in shade; and (3) sugars could possibly act as candidate signal substances to regulate leaf area systemically.

Validation and Development of a Modified Breast Graded Prognostic Assessment As a Tool for Survival in Patients With Breast Cancer and Brain Metastases.

PubMed

Subbiah, Ishwaria M; Lei, Xiudong; Weinberg, Jeffrey S; Sulman, Erik P; Chavez-MacGregor, Mariana; Tripathy, Debu; Gupta, Rohan; Varma, Ankur; Chouhan, Jay; Guevarra, Richard P; Valero, Vicente; Gilbert, Mark R; Gonzalez-Angulo, Ana M

2015-07-10

Several indices have been developed to predict overall survival (OS) in patients with breast cancer with brain metastases, including the breast graded prognostic assessment (breast-GPA), comprising age, tumor subtype, and Karnofsky performance score. However, number of brain metastases-a highly relevant clinical variable-is less often incorporated into the final model. We sought to validate the existing breast-GPA in an independent larger cohort and refine it integrating number of brain metastases. Data were retrospectively gathered from a prospectively maintained institutional database. Patients with newly diagnosed brain metastases from 1996 to 2013 were identified. After validating the breast-GPA, multivariable Cox regression and recursive partitioning analysis led to the development of the modified breast-GPA. The performances of the breast-GPA and modified breast-GPA were compared using the concordance index. In our cohort of 1,552 patients, the breast-GPA was validated as a prognostic tool for OS (P < .001). In multivariable analysis of the breast-GPA and number of brain metastases (> three v ≤ three), both were independent predictors of OS. We therefore developed the modified breast-GPA integrating a fourth clinical parameter. Recursive partitioning analysis reinforced the prognostic significance of these four factors. Concordance indices were 0.78 (95% CI, 0.77 to 0.80) and 0.84 (95% CI, 0.83 to 0.85) for the breast-GPA and modified breast-GPA, respectively (P < .001). The modified breast-GPA incorporates four simple clinical parameters of high prognostic significance. This index has an immediate role in the clinic as a formative part of the clinician's discussion of prognosis and direction of care and as a potential patient selection tool for clinical trials. © 2015 by American Society of Clinical Oncology.

Development of a field-friendly automated dietary assessment tool and nutrient database for India

PubMed Central

Daniel, Carrie R.; Kapur, Kavita; McAdams, Mary J.; Dixit-Joshi, Sujata; Devasenapathy, Niveditha; Shetty, Hemali; Hariharan, Sriram; George, Preethi S.; Mathew, Aleyamma; Sinha, Rashmi

2017-01-01

Studies of diet and disease risk in India and among other Asian-Indian populations are hindered by the need for a comprehensive dietary assessment tool to capture data on the wide variety of food and nutrient intakes across different regions and ethnic groups. The nutritional component of the India Health Study, a multicentre pilot cohort study, included 3908 men and women, aged 35–69 years, residing in three regions of India (New Delhi in the north, Mumbai in the west and Trivandrum in the south). We developed a computer-based, interviewer-administered dietary assessment software known as the ‘NINA-DISH (New Interactive Nutrition Assistant – Diet in India Study of Health)’, which consisted of four sections: (1) a diet history questionnaire with defined questions on frequency and portion size; (2) an open-ended section for each mealtime; (3) a food-preparer questionnaire; (4) a 24 h dietary recall. Using the preferred meal-based approach, frequency of intake and portion size were recorded and linked to a nutrient database that we developed and modified from a set of existing international databases containing data on Indian foods and recipes. The NINA-DISH software was designed to be easily adaptable and was well accepted by the interviewers and participants in the field. A predominant three-meal eating pattern emerged; however, patterns in the number of foods reported and the primary contributors to macro- and micronutrient intakes differed by region and demographic factors. The newly developed NINA-DISH software provides a much-needed tool for measuring diet and nutrient profiles across the diverse populations of India with the potential for application in other South Asian populations living throughout the world. PMID:23796477

Development of a field-friendly automated dietary assessment tool and nutrient database for India.

PubMed

Daniel, Carrie R; Kapur, Kavita; McAdams, Mary J; Dixit-Joshi, Sujata; Devasenapathy, Niveditha; Shetty, Hemali; Hariharan, Sriram; George, Preethi S; Mathew, Aleyamma; Sinha, Rashmi

2014-01-14

Studies of diet and disease risk in India and among other Asian-Indian populations are hindered by the need for a comprehensive dietary assessment tool to capture data on the wide variety of food and nutrient intakes across different regions and ethnic groups. The nutritional component of the India Health Study, a multicentre pilot cohort study, included 3908 men and women, aged 35-69 years, residing in three regions of India (New Delhi in the north, Mumbai in the west and Trivandrum in the south). We developed a computer-based, interviewer-administered dietary assessment software known as the 'NINA-DISH (New Interactive Nutrition Assistant - Diet in India Study of Health)', which consisted of four sections: (1) a diet history questionnaire with defined questions on frequency and portion size; (2) an open-ended section for each mealtime; (3) a food-preparer questionnaire; (4) a 24 h dietary recall. Using the preferred meal-based approach, frequency of intake and portion size were recorded and linked to a nutrient database that we developed and modified from a set of existing international databases containing data on Indian foods and recipes. The NINA-DISH software was designed to be easily adaptable and was well accepted by the interviewers and participants in the field. A predominant three-meal eating pattern emerged; however, patterns in the number of foods reported and the primary contributors to macro- and micronutrient intakes differed by region and demographic factors. The newly developed NINA-DISH software provides a much-needed tool for measuring diet and nutrient profiles across the diverse populations of India with the potential for application in other South Asian populations living throughout the world.

The Hubble Legacy Archive: Data Processing in the Era of AstroDrizzle

NASA Astrophysics Data System (ADS)

Strolger, Louis-Gregory; Hubble Legacy Archive Team, The Hubble Source Catalog Team

2015-01-01

The Hubble Legacy Archive (HLA) expands the utility of Hubble Space Telescope wide-field imaging data by providing high-level composite images and source lists, perusable and immediately available online. The latest HLA data release (DR8.0) marks a fundamental change in how these image combinations are produced, using DrizzlePac tools and Astrodrizzle to reduce geometric distortion and provide improved source catalogs for all publicly available data. We detail the HLA data processing and source list schemas, what products are newly updated and available for WFC3 and ACS, and how these data products are further utilized in the production of the Hubble Source Catalog. We also discuss plans for future development, including updates to WFPC2 products and field mosaics.

Variable stars around selected open clusters in the VVV area: Young Stellar Objects

NASA Astrophysics Data System (ADS)

Medina, Nicolas; Borissova, Jura; Bayo, Amelia; Kurtev, Radostin; Lucas, Philip

2017-09-01

Time-varying phenomena are one of the most substantial sources of astrophysical information, and led to many fundamental discoveries in modern astronomy. We have developed an automated tool to search and analyze variable sources in the near infrared Ks band, using the data from the Vista Variables in the Vía Láctea (VVV) ESO Public Survey ([5, 8]). One of our main goals is to investigate the Young Stellar Objects (YSOs) in the Galactic star forming regions, looking for: •Variability. •New pre-main sequence star clusters. Here we present the newly discovered YSOs within some selected stellar clusters in our Galaxy.

Comparison of PAM Systems for Acoustic Monitoring and Further Risk Mitigation Application.

PubMed

Ludwig, Stefan; Kreimeyer, Roman; Knoll, Michaela

2016-01-01

We present results of the SIRENA 2011 research cruises conducted by the NATO Undersea Research Centre (NURC) and joined by the Research Department for Underwater Acoustics and Geophysics (FWG), Bundeswehr Technical Centre (WTD 71) and the Universities of Kiel and Pavia. The cruises were carried out in the Ligurian Sea. The main aim of the FWG was to test and evaluate the newly developed towed hydrophone array as a passive acoustic monitoring (PAM) tool for risk mitigation applications. The system was compared with the PAM equipment used by the other participating institutions. Recorded sounds were used to improve an automatic acoustic classifier for marine mammals, and validated acoustic detections by observers were compared with the results of the classifier.

Wireless energy transfer platform for medical sensors and implantable devices.

PubMed

Zhang, Fei; Hackworth, Steven A; Liu, Xiaoyu; Chen, Haiyan; Sclabassi, Robert J; Sun, Mingui

2009-01-01

Witricity is a newly developed technique for wireless energy transfer. This paper presents a frequency adjustable witricity system to power medical sensors and implantable devices. New witricity resonators are designed for both energy transmission and reception. A prototype platform is described, including an RF power source, two resonators with new structures, and inductively coupled input and output stages. In vitro experiments, both in open air and using a human head phantom consisting of simulated tissues, are employed to verify the feasibility of this platform. An animal model is utilized to evaluate in vivo energy transfer within the body of a laboratory pig. Our experiments indicate that witricity is an effective new tool for providing a variety of medical sensors and devices with power.

Zirconium(IV)-Catalyzed Ring Opening of on-DNA Epoxides in Water.

PubMed

Fan, Lijun; Davie, Christopher P

2017-05-04

DNA-encoded library technology (ELT) has spurred wide interest in the pharmaceutical industry as a powerful tool for hit and lead generation. In recent years a number of "DNA-compatible" chemical modifications have been published and used to synthesize vastly diverse screening libraries. Herein we report a newly developed, zirconium tetrakis(dodecyl sulfate) [Zr(DS) 4 ] catalyzed ring-opening of on-DNA epoxides in water with amines, including anilines. Subsequent cyclization of the resulting on-DNA β-amino alcohols leads to a variety of biologically interesting, nonaromatic heterocycles. Under these conditions, a library of 137 million on-DNA β-amino alcohols and their cyclization products was assembled. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ranking of Business Process Simulation Software Tools with DEX/QQ Hierarchical Decision Model.

PubMed

Damij, Nadja; Boškoski, Pavle; Bohanec, Marko; Mileva Boshkoska, Biljana

2016-01-01

The omnipresent need for optimisation requires constant improvements of companies' business processes (BPs). Minimising the risk of inappropriate BP being implemented is usually performed by simulating the newly developed BP under various initial conditions and "what-if" scenarios. An effectual business process simulations software (BPSS) is a prerequisite for accurate analysis of an BP. Characterisation of an BPSS tool is a challenging task due to the complex selection criteria that includes quality of visual aspects, simulation capabilities, statistical facilities, quality reporting etc. Under such circumstances, making an optimal decision is challenging. Therefore, various decision support models are employed aiding the BPSS tool selection. The currently established decision support models are either proprietary or comprise only a limited subset of criteria, which affects their accuracy. Addressing this issue, this paper proposes a new hierarchical decision support model for ranking of BPSS based on their technical characteristics by employing DEX and qualitative to quantitative (QQ) methodology. Consequently, the decision expert feeds the required information in a systematic and user friendly manner. There are three significant contributions of the proposed approach. Firstly, the proposed hierarchical model is easily extendible for adding new criteria in the hierarchical structure. Secondly, a fully operational decision support system (DSS) tool that implements the proposed hierarchical model is presented. Finally, the effectiveness of the proposed hierarchical model is assessed by comparing the resulting rankings of BPSS with respect to currently available results.

Computer-facilitated rapid HIV testing in emergency care settings: provider and patient usability and acceptability.

PubMed

Spielberg, Freya; Kurth, Ann E; Severynen, Anneleen; Hsieh, Yu-Hsiang; Moring-Parris, Daniel; Mackenzie, Sara; Rothman, Richard

2011-06-01

Providers in emergency care settings (ECSs) often face barriers to expanded HIV testing. We undertook formative research to understand the potential utility of a computer tool, "CARE," to facilitate rapid HIV testing in ECSs. Computer tool usability and acceptability were assessed among 35 adult patients, and provider focus groups were held, in two ECSs in Washington State and Maryland. The computer tool was usable by patients of varying computer literacy. Patients appreciated the tool's privacy and lack of judgment and their ability to reflect on HIV risks and create risk reduction plans. Staff voiced concerns regarding ECS-based HIV testing generally, including resources for follow-up of newly diagnosed people. Computer-delivered HIV testing support was acceptable and usable among low-literacy populations in two ECSs. Such tools may help circumvent some practical barriers associated with routine HIV testing in busy settings though linkages to care will still be needed.

Nested PCR Assay for Eight Pathogens: A Rapid Tool for Diagnosis of Bacterial Meningitis.

PubMed

Bhagchandani, Sharda P; Kubade, Sushant; Nikhare, Priyanka P; Manke, Sonali; Chandak, Nitin H; Kabra, Dinesh; Baheti, Neeraj N; Agrawal, Vijay S; Sarda, Pankaj; Mahajan, Parikshit; Ganjre, Ashish; Purohit, Hemant J; Singh, Lokendra; Taori, Girdhar M; Daginawala, Hatim F; Kashyap, Rajpal S

2016-02-01

Bacterial meningitis is a dreadful infectious disease with a high mortality and morbidity if remained undiagnosed. Traditional diagnostic methods for bacterial meningitis pose a challenge in accurate identification of pathogen, making prognosis difficult. The present study is therefore aimed to design and evaluate a specific and sensitive nested 16S rDNA genus-based polymerase chain reaction (PCR) assay using clinical cerebrospinal fluid (CSF) for rapid diagnosis of eight pathogens causing the disease. The present work was dedicated to development of an in-house genus specific 16S rDNA nested PCR covering pathogens of eight genera responsible for causing bacterial meningitis using newly designed as well as literature based primers for respective genus. A total 150 suspected meningitis CSF obtained from the patients admitted to Central India Institute of Medical Sciences (CIIMS), India during the period from August 2011 to May 2014, were used to evaluate clinical sensitivity and clinical specificity of optimized PCR assays. The analytical sensitivity and specificity of our newly designed genus-specific 16S rDNA PCR were found to be ≥92%. With such a high sensitivity and specificity, our in-house nested PCR was able to give 100% sensitivity in clinically confirmed positive cases and 100% specificity in clinically confirmed negative cases indicating its applicability in clinical diagnosis. Our in-house nested PCR system therefore can diagnose the accurate pathogen causing bacterial meningitis and therefore be useful in selecting a specific treatment line to minimize morbidity. Results are obtained within 24 h and high sensitivity makes this nested PCR assay a rapid and accurate diagnostic tool compared to traditional culture-based methods.

The curiously suspicious: a role for Epstein-Barr virus in lupus.

PubMed

Harley, J B; Harley, I T W; Guthridge, J M; James, J A

2006-01-01

While the events initiating the development of autoantibodies in systemic lupus erythematosus (SLE) have not yet been convincingly established, newly developed tools for molecular investigation make such an undertaking increasingly practical. Applied to the earliest events in the sequence culminating in lupus autoimmunity, we present a critical potential role for Epstein-Barr virus (EBV) in the development and perhaps perpetuation of SLE. The expected properties for an environmental risk factor for SLE are found in this virus and the human host response against it. Existing data show the molecular progression to autoimmunity observed in SLE patient sera, the discovery of the first autoimmune epitopes in the Sm and Ro autoantigen systems, and the possible emergence of these autoantibodies from the heterologous antibodies against Epstein-Barr nuclear antigen-1 (EBNA-1). Further, existing data demonstrate association of SLE with EBV infection, even preceding the development of autoimmunity. Finally, the data are consistent with a proposed model of lupus pathogenesis that begins with antibodies to EBNA-1, predisposing to immune responses that develop crossreactive autoantibodies that culminate in the development of SLE autoimmunity.

[Chronic lymphocytic leukaemia: current management].

PubMed

Aurran-Schleinitz, T; Arnoulet, C; Ivanov, V; Coso, D; Rey, J; Schiano, J-M; Stoppa, A-M; Bouabdallah, R; Gastaut, J-A

2008-05-01

Chronic lymphocytic leukemia (CLL) is the most common leukaemia in the Western world. Recent advancement in the aetiology, pathophysiology and the development of new therapeutics tools have significantly modified the current management of CLL. The cellular origin of CLL is still unknown. The current main hypothesis will be first briefly described. This review will then focus on the newly defined prognostic factors and the development and use of new drugs for the treatment of CLL. To describe the modern and practical management of CLL, we will compare classical and new prognostic markers. Then, we will discuss the various therapeutic options including chemotherapy and immunotherapy (monoclonal antibodies, allogenic transplantation), and define their current respective indications. These new diagnostic and prognostic markers will allow the characterization of new prognostic subgroups of patients. This will lead to a targeted and individualized therapeutic approach. We will present the first results of clinical trials and the on-going studies conducted in this disease.

Enhanced CARES Software Enables Improved Ceramic Life Prediction

NASA Technical Reports Server (NTRS)

Janosik, Lesley A.

1997-01-01

The NASA Lewis Research Center has developed award-winning software that enables American industry to establish the reliability and life of brittle material (e.g., ceramic, intermetallic, graphite) structures in a wide variety of 21st century applications. The CARES (Ceramics Analysis and Reliability Evaluation of Structures) series of software is successfully used by numerous engineers in industrial, academic, and government organizations as an essential element of the structural design and material selection processes. The latest version of this software, CARES/Life, provides a general- purpose design tool that predicts the probability of failure of a ceramic component as a function of its time in service. CARES/Life was recently enhanced by adding new modules designed to improve functionality and user-friendliness. In addition, a beta version of the newly-developed CARES/Creep program (for determining the creep life of monolithic ceramic components) has just been released to selected organizations.

Advanced Aerodynamic Design of Passive Porosity Control Effectors

NASA Technical Reports Server (NTRS)

Hunter, Craig A.; Viken, Sally A.; Wood, Richard M.; Bauer, Steven X. S.

2001-01-01

This paper describes aerodynamic design work aimed at developing a passive porosity control effector system for a generic tailless fighter aircraft. As part of this work, a computational design tool was developed and used to layout passive porosity effector systems for longitudinal and lateral-directional control at a low-speed, high angle of attack condition. Aerodynamic analysis was conducted using the NASA Langley computational fluid dynamics code USM3D, in conjunction with a newly formulated surface boundary condition for passive porosity. Results indicate that passive porosity effectors can provide maneuver control increments that equal and exceed those of conventional aerodynamic effectors for low-speed, high-alpha flight, with control levels that are a linear function of porous area. This work demonstrates the tremendous potential of passive porosity to yield simple control effector systems that have no external moving parts and will preserve an aircraft's fixed outer mold line.

Second generation codon optimized minicircle (CoMiC) for nonviral reprogramming of human adult fibroblasts.

PubMed

Diecke, Sebastian; Lisowski, Leszek; Kooreman, Nigel G; Wu, Joseph C

2014-01-01

The ability to induce pluripotency in somatic cells is one of the most important scientific achievements in the fields of stem cell research and regenerative medicine. This technique allows researchers to obtain pluripotent stem cells without the controversial use of embryos, providing a novel and powerful tool for disease modeling and drug screening approaches. However, using viruses for the delivery of reprogramming genes and transcription factors may result in integration into the host genome and cause random mutations within the target cell, thus limiting the use of these cells for downstream applications. To overcome this limitation, various non-integrating techniques, including Sendai virus, mRNA, minicircle, and plasmid-based methods, have recently been developed. Utilizing a newly developed codon optimized 4-in-1 minicircle (CoMiC), we were able to reprogram human adult fibroblasts using chemically defined media and without the need for feeder cells.

Artificial Lipid Membranes: Past, Present, and Future

PubMed Central

Siontorou, Christina G.; Nikoleli, Georgia-Paraskevi; Nikolelis, Dimitrios P.

2017-01-01

The multifaceted role of biological membranes prompted early the development of artificial lipid-based models with a primary view of reconstituting the natural functions in vitro so as to study and exploit chemoreception for sensor engineering. Over the years, a fair amount of knowledge on the artificial lipid membranes, as both, suspended or supported lipid films and liposomes, has been disseminated and has helped to diversify and expand initial scopes. Artificial lipid membranes can be constructed by several methods, stabilized by various means, functionalized in a variety of ways, experimented upon intensively, and broadly utilized in sensor development, drug testing, drug discovery or as molecular tools and research probes for elucidating the mechanics and the mechanisms of biological membranes. This paper reviews the state-of-the-art, discusses the diversity of applications, and presents future perspectives. The newly-introduced field of artificial cells further broadens the applicability of artificial membranes in studying the evolution of life. PMID:28933723

Thermodynamic Analysis of Coherently Grown GaAsN/Ge: Effects of Different Gaseous Sources

NASA Astrophysics Data System (ADS)

Kawano, Jun; Kangawa, Yoshihiro; Yayama, Tomoe; Kakimoto, Koichi; Koukitu, Akinori

2013-04-01

Thermodynamic analysis of coherently grown GaAs1-xNx on Ge with low N content was performed to determine the relationship between solid composition and growth conditions. In this study, a new algorithm for the simulation code, which is applicable to wider combinations of gaseous sources than the traditional algorithm, was developed to determine the influence of different gaseous sources on N incorporation. Using this code, here we successfully compared two cases: one is a system using trimethylgallium (TMG), AsH3, and NH3, and the other uses dimethylhydrazine (DMHy) instead of NH3. It was found that the optimal N/As ratio of input gas in the system using DMHy was much lower than that using NH3. This shows that the newly developed algorithm could be a useful tool for analyzing the N incorporation during the vapor growth of GaAs1-xNx.

Organotypic cultures as tools for testing neuroactive drugs - link between in-vitro and in-vivo experiments.

PubMed

Drexler, B; Hentschke, H; Antkowiak, B; Grasshoff, C

2010-01-01

The development of neuroactive drugs is a time consuming procedure. Candidate drugs must be run through a battery of tests, including receptor studies and behavioural tests on animals. As a rule, numerous substances with promising properties as assessed in receptor studies must be eliminated from the development pipeline in advanced test phases because of unforeseen problems like intolerable side-effects or unsatisfactory performance in the whole organism. Clearly, test systems of intermediate complexity would alleviate this inefficiency. In this review, we propose cultured organotypic brain slices as model systems that could bridge the 'interpolation gap' between receptors and the brain, with a focus on the development of new general anaesthetics with lesser side effects. General anaesthesia is based on the modulation of neurotransmitter receptors and other conductances located on neurons in diverse brain regions, including cerebral cortex and spinal cord. It is well known that different components of general anaesthesia, e.g. hypnosis and immobility, are produced by the depression of neuronal activity in distinct brain regions. The ventral horn of the spinal cord is an important structure for the induction of immobility. Thus, the potentially immobilizing effects of a newly designed drug can be estimated from its depressant effect on neuronal network activity in cultured spinal slices. A drug's sedative and hypnotic potential can be examined in cortical cultures. Combined with genetically engineered mice, this approach can point to receptor subtypes most relevant to the drug's intended net effect and in return can help in the design of more selective drugs. In conclusion, the use of organotypic cultures permits predictions of neuroactive properties of newly designed drugs on an intermediate level, and should therefore open up avenues for a more creative and economic drug development process.

Development of radiometric assays for quantification of enzyme activities of the key enzymes of thyroid hormones metabolism.

PubMed

Pavelka, S

2014-01-01

We newly elaborated and adapted several radiometric enzyme assays for the determination of activities of the key enzymes engaged in the biosynthesis (thyroid peroxidase, TPO) and metabolic transformations (conjugating enzymes and iodothyronine deiodinases, IDs) of thyroid hormones (THs) in the thyroid gland and in peripheral tissues, especially in white adipose tissue (WAT). We also elaborated novel, reliable radiometric methods for extremely sensitive determination of enzyme activities of IDs of types 1, 2 and 3 in microsomal fractions of different rat and human tissues, as well as in homogenates of cultured mammalian cells. The use of optimized TLC separation of radioactive products from the unconsumed substrates and film-less autoradiography of radiochromatograms, taking advantage of storage phosphor screens, enabled us to determine IDs enzyme activities as low as 10(-18) katals. In studies of the interaction of fluoxetine (Fluox) with the metabolism of THs, we applied adapted radiometric enzyme assays for iodothyronine sulfotransferases (ST) and uridine 5'-diphospho-glucuronyltransferase (UDP-GT). Fluox is the most frequently used representative of a new group of non-tricyclic antidepressant drugs--selective serotonin re-uptake inhibitors. We used the elaborated assays for quantification the effects of Fluox and for the assessment of the degree of potential induction of rat liver ST and/or UDP-GT enzyme activities by Fluox alone or in combination with T(3). Furthermore, we studied possible changes in IDs activities in murine adipose tissue under the conditions that promoted either tissue hypertrophy (obesogenic treatment) or involution (caloric restriction), and in response to leptin, using our newly developed radiometric enzyme assays for IDs. Our results suggest that deiodinase D1 has a functional role in WAT, with D1 possibly being involved in the control of adipose tissue metabolism and/or accumulation of the tissue. Significant positive correlation between specific enzyme activity of D1 in WAT and plasma leptin levels was found. The newly developed and adapted radiometric enzyme assays proved to be very useful tools for studies of factors modulating THs metabolism, not only in model animals but also in clinical studies of human obesity.

Constructing Practical Knowledge of Teaching: Eleven Newly Qualified Language Teachers' Discursive Agency

ERIC Educational Resources Information Center

Ruohotie-Lyhty, Maria

2011-01-01

This paper explores the professional development of 11 newly qualified foreign language teachers. It draws on a qualitative longitudinal study conducted at the University of Jyvaskyla, Finland between 2002 and 2009. The paper concentrates on the personal side of teacher development by analysing participants' discourses concerning language…

Verification and Validation of the New Dynamic Mooring Modules Available in FAST v8: Preprint

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

Wendt, Fabian; Robertson, Amy; Jonkman, Jason

2016-08-01

The open-source aero-hydro-servo-elastic wind turbine simulation software, FAST v8, was recently coupled to two newly developed mooring dynamics modules: MoorDyn and FEAMooring. MoorDyn is a lumped-mass-based mooring dynamics module developed by the University of Maine, and FEAMooring is a finite-element-based mooring dynamics module developed by Texas A&M University. This paper summarizes the work performed to verify and validate these modules against other mooring models and measured test data to assess their reliability and accuracy. The quality of the fairlead load predictions by the open-source mooring modules MoorDyn and FEAMooring appear to be largely equivalent to what is predicted by themore » commercial tool OrcaFlex. Both mooring dynamic model predictions agree well with the experimental data, considering the given limitations in the accuracy of the platform hydrodynamic load calculation and the quality of the measurement data.« less

Verification and Validation of the New Dynamic Mooring Modules Available in FAST v8

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

Wendt, Fabian F.; Andersen, Morten T.; Robertson, Amy N.

2016-07-01

The open-source aero-hydro-servo-elastic wind turbine simulation software, FAST v8, was recently coupled to two newly developed mooring dynamics modules: MoorDyn and FEAMooring. MoorDyn is a lumped-mass-based mooring dynamics module developed by the University of Maine, and FEAMooring is a finite-element-based mooring dynamics module developed by Texas A&M University. This paper summarizes the work performed to verify and validate these modules against other mooring models and measured test data to assess their reliability and accuracy. The quality of the fairlead load predictions by the open-source mooring modules MoorDyn and FEAMooring appear to be largely equivalent to what is predicted by themore » commercial tool OrcaFlex. Both mooring dynamic model predictions agree well with the experimental data, considering the given limitations in the accuracy of the platform hydrodynamic load calculation and the quality of the measurement data.« less

Analysis of Lethality and Malformations During Zebrafish (Danio rerio) Development.

PubMed

Raghunath, Azhwar; Perumal, Ekambaram

2018-01-01

The versatility offered by zebrafish (Danio rerio) makes it a powerful and an attractive vertebrate model in developmental toxicity and teratogenicity assays. Apart from the newly introduced chemicals as drugs, xenobiotics also induce abnormal developmental abnormalities and congenital malformations in living organisms. Over the recent decades, zebrafish embryo/larva has emerged as a potential tool to test teratogenicity potential of these chemicals. Zebrafish responds to compounds as mammals do as they share similarities in their development, metabolism, physiology, and signaling pathways with that of mammals. The methodology used by the different scientists varies enormously in the zebrafish embryotoxicity test. In this chapter, we present methods to assess lethality and malformations during zebrafish development. We propose two major malformations scoring systems: binomial and relative morphological scoring systems to assess the malformations in zebrafish embryos/larvae. Based on the scoring of the malformations, the test compound can be classified as a teratogen or a nonteratogen and its teratogenic potential is evaluated.

A snapshot of patients' perceptions of oncology providers' cultural competence.

PubMed

Davey, Maureen P; Waite, Roberta; Nuñez, Ana; Niño, Alba; Kissil, Karni

2014-12-01

In this paper, we describe an anonymous cross-sectional survey with a sample of 100 racially diverse adult oncology patients using a newly developed patient-reported measure of providers' cultural competence, the Physicians' Cultural Competence for Patient Satisfaction Scale (PCCPS) [1, 2], which was developed using a US midwestern sample of primary care patients. Our primary aims were to examine the reliability of the PCCPS in a more racially diverse urban oncology clinical setting and to identify salient domains of oncology provider cultural competence based on patient-reported satisfaction with direct clinical encounters. Results suggest that patient-reported satisfaction was significantly associated with one of the four domains measured by the PCCPS, physician's patient-centered cultural competence (r = 0.40, p = 0.01), and female patients were more satisfied (t (91) = 5.23, p = 0.02). The PCCPS demonstrated good reliability in an urban diverse cancer patient population. Results help to inform the development of clinical tools that can improve oncology providers' cultural competency.

Detection of the reemerging agent Burkholderia mallei in a recent outbreak of glanders in the United Arab Emirates by a newly developed fliP-based polymerase chain reaction assay.

PubMed

Scholz, Holger C; Joseph, Marina; Tomaso, Herbert; Al Dahouk, Sascha; Witte, Angela; Kinne, Joerg; Hagen, Ralph M; Wernery, Renate; Wernery, Ulrich; Neubauer, Heinrich

2006-04-01

A polymerase chain reaction (PCR) assay targeting the flagellin P (fliP)-I S407A genomic region of Burkholderia mallei was developed for the specific detection of this organism in pure cultures and clinical samples from a recent outbreak of equine glanders. Primers deduced from the known fliP-IS407A sequence of B. mallei American Type Culture Collection (ATCC) 23344(T) allowed the specific amplification of a 989-bp fragment from each of the 20 B. mallei strains investigated, whereas other closely related organisms tested negative. The detection limit of the assay was 10 fg for purified DNA of B. mallei ATCC 23344(T). B. mallei DNA was also amplified from various tissues of horses with a generalized B. mallei infection. The developed PCR assay can be used as a simple and rapid tool for the specific and sensitive detection of B. mallei in clinical samples.

Rapid tests for diagnosis of leptospirosis: current tools and emerging technologies.

PubMed

Picardeau, Mathieu; Bertherat, Eric; Jancloes, Michel; Skouloudis, Andreas N; Durski, Kara; Hartskeerl, Rudy A

2014-01-01

Leptospirosis is an emerging zoonosis with a worldwide distribution but is more commonly found in impoverished populations in developing countries and tropical regions with frequent flooding. The rapid detection of leptospirosis is a critical step to effectively manage the disease and to control outbreaks in both human and animal populations. Therefore, there is a need for accurate and rapid diagnostic tests and appropriate surveillance and alert systems to identify outbreaks. This review describes current in-house methods and commercialized tests for the rapid diagnosis of acute leptospirosis. It focuses on diagnostic tests that can be performed with minimal training and limited equipment in less-developed and newly industrialized countries, particularly in resource-limited settings and with results in minutes to less than 4 hours. We also describe recent technological advances in the field of diagnostic tests that could allow for the development of innovative rapid tests in the near future. © 2013 Elsevier Inc. All rights reserved.

Assessment Methodology for Process Validation Lifecycle Stage 3A.

PubMed

Sayeed-Desta, Naheed; Pazhayattil, Ajay Babu; Collins, Jordan; Chen, Shu; Ingram, Marzena; Spes, Jana

2017-07-01

The paper introduces evaluation methodologies and associated statistical approaches for process validation lifecycle Stage 3A. The assessment tools proposed can be applied to newly developed and launched small molecule as well as bio-pharma products, where substantial process and product knowledge has been gathered. The following elements may be included in Stage 3A: number of 3A batch determination; evaluation of critical material attributes, critical process parameters, critical quality attributes; in vivo in vitro correlation; estimation of inherent process variability (IPV) and PaCS index; process capability and quality dashboard (PCQd); and enhanced control strategy. US FDA guidance on Process Validation: General Principles and Practices, January 2011 encourages applying previous credible experience with suitably similar products and processes. A complete Stage 3A evaluation is a valuable resource for product development and future risk mitigation of similar products and processes. Elements of 3A assessment were developed to address industry and regulatory guidance requirements. The conclusions made provide sufficient information to make a scientific and risk-based decision on product robustness.

Strengthening Interprofessional Requirements Engineering Through Action Sheets: A Pilot Study.

PubMed

Kunz, Aline; Pohlmann, Sabrina; Heinze, Oliver; Brandner, Antje; Reiß, Christina; Kamradt, Martina; Szecsenyi, Joachim; Ose, Dominik

2016-10-18

The importance of information and communication technology for healthcare is steadily growing. Newly developed tools are addressing different user groups: physicians, other health care professionals, social workers, patients, and family members. Since often many different actors with different expertise and perspectives are involved in the development process it can be a challenge to integrate the user-reported requirements of those heterogeneous user groups. Nevertheless, the understanding and consideration of user requirements is the prerequisite of building a feasible technical solution. In the course of the presented project it proved to be difficult to gain clear action steps and priorities for the development process out of the primary requirements compilation. Even if a regular exchange between involved teams took place there was a lack of a common language. The objective of this paper is to show how the already existing requirements catalog was subdivided into specific, prioritized, and coherent working packages and the cooperation of multiple interprofessional teams within one development project was reorganized at the same time. In the case presented, the manner of cooperation was reorganized and a new instrument called an Action Sheet was implemented. This paper introduces the newly developed methodology which was meant to smooth the development of a user-centered software product and to restructure interprofessional cooperation. There were 10 focus groups in which views of patients with colorectal cancer, physicians, and other health care professionals were collected in order to create a requirements catalog for developing a personal electronic health record. Data were audio- and videotaped, transcribed verbatim, and thematically analyzed. Afterwards, the requirements catalog was reorganized in the form of Action Sheets which supported the interprofessional cooperation referring to the development process of a personal electronic health record for the Rhine-Neckar region. In order to improve the interprofessional cooperation the idea arose to align the requirements arising from the implementation project with the method of software development applied by the technical development team. This was realized by restructuring the original requirements set in a standardized way and under continuous adjustment between both teams. As a result not only the way of displaying the user demands but also of interprofessional cooperation was steered in a new direction. User demands must be taken into account from the very beginning of the development process, but it is not always obvious how to bring them together with IT knowhow and knowledge of the contextual factors of the health care system. Action Sheets seem to be an effective tool for making the software development process more tangible and convertible for all connected disciplines. Furthermore, the working method turned out to support interprofessional ideas exchange.

Strengthening Interprofessional Requirements Engineering Through Action Sheets: A Pilot Study

PubMed Central

Pohlmann, Sabrina; Heinze, Oliver; Brandner, Antje; Reiß, Christina; Kamradt, Martina; Szecsenyi, Joachim; Ose, Dominik

2016-01-01

Background The importance of information and communication technology for healthcare is steadily growing. Newly developed tools are addressing different user groups: physicians, other health care professionals, social workers, patients, and family members. Since often many different actors with different expertise and perspectives are involved in the development process it can be a challenge to integrate the user-reported requirements of those heterogeneous user groups. Nevertheless, the understanding and consideration of user requirements is the prerequisite of building a feasible technical solution. In the course of the presented project it proved to be difficult to gain clear action steps and priorities for the development process out of the primary requirements compilation. Even if a regular exchange between involved teams took place there was a lack of a common language. Objective The objective of this paper is to show how the already existing requirements catalog was subdivided into specific, prioritized, and coherent working packages and the cooperation of multiple interprofessional teams within one development project was reorganized at the same time. In the case presented, the manner of cooperation was reorganized and a new instrument called an Action Sheet was implemented. This paper introduces the newly developed methodology which was meant to smooth the development of a user-centered software product and to restructure interprofessional cooperation. Methods There were 10 focus groups in which views of patients with colorectal cancer, physicians, and other health care professionals were collected in order to create a requirements catalog for developing a personal electronic health record. Data were audio- and videotaped, transcribed verbatim, and thematically analyzed. Afterwards, the requirements catalog was reorganized in the form of Action Sheets which supported the interprofessional cooperation referring to the development process of a personal electronic health record for the Rhine-Neckar region. Results In order to improve the interprofessional cooperation the idea arose to align the requirements arising from the implementation project with the method of software development applied by the technical development team. This was realized by restructuring the original requirements set in a standardized way and under continuous adjustment between both teams. As a result not only the way of displaying the user demands but also of interprofessional cooperation was steered in a new direction. Conclusions User demands must be taken into account from the very beginning of the development process, but it is not always obvious how to bring them together with IT knowhow and knowledge of the contextual factors of the health care system. Action Sheets seem to be an effective tool for making the software development process more tangible and convertible for all connected disciplines. Furthermore, the working method turned out to support interprofessional ideas exchange. PMID:27756716

Putting Connectivist Principles into Practice: A Case Study of an Online Tertiary Course

ERIC Educational Resources Information Center

Armatas, Christine; Spratt, Christine; Vincent, Andrew

2014-01-01

The Bachelor of Enterprise Learning is a newly accredited undergraduate degree where connectivist principles have been used to guide design of active, student-centered learning activities. A key feature of the curriculum is that it incorporates technology as both a source of information and a tool. Examples from this course are provided in this…

Enhancing Long-Term Retention of New Vocabulary Using Visual Images.

ERIC Educational Resources Information Center

Igelsrud, Karen

A practicum used a new learning tool to enhance long-term retention of new vocabulary. Sixteen seventh-graders in Language Arts, who had a long-term retention mean score of approximately 40% of newly learned vocabulary, increased their long-term retention of new vocabulary by 25% (a new mean of 65% of new vocabulary). Additional objectives…

Dynamic Re-Tasking: The JFACC and the Airborne Strike Package

DTIC Science & Technology

1999-04-01

Information Management ......................................................................... 23 The Future JAOC...complete the mission. It is assumed the re-tasked assets have no prior knowledge of their newly assigned target (i.e. that it is not a preplanned alternate...et al, The Fifth Discipline Fieldbook : Strategies and Tools for Building a Learning Organization, (New York: Doubleday, 1994), 530. 7 Chapter 2 JFACC

Determinants of health and disability in ageing population: the COURAGE in Europe Project (collaborative research on ageing in Europe).

PubMed

Leonardi, Matilde; Chatterji, Somnath; Koskinen, Seppo; Ayuso-Mateos, Jose Luis; Haro, Josep Maria; Frisoni, Giovanni; Frattura, Lucilla; Martinuzzi, Andrea; Tobiasz-Adamczyk, Beata; Gmurek, Michal; Serrano, Ramon; Finocchiaro, Carla

2014-01-01

COURAGE in Europe was a 3-year project involving 12 partners from four European countries and the World Health Organization. It was inspired by the pressing need to integrate international studies on disability and ageing in light of an innovative perspective based on a validated data-collection protocol. COURAGE in Europe Project collected data on the determinants of health and disability in an ageing population, with specific tools for the evaluation of the role of the built environment and social networks on health, disability, quality of life and well-being. The main survey was conducted by partners in Finland, Poland and Spain where the survey has been administered to a sample of 10,800 persons, which was completed in March 2012. The newly developed and validated COURAGE Protocol for Ageing Studies has proven to be a valid tool for collecting comparable data in ageing population, and the COURAGE in Europe Project has created valid and reliable scientific evidence, demonstrating cross-country comparability, for disability and ageing research and policy development. It is therefore recommended that future studies exploring determinants of health and disability in ageing use the COURAGE-derived methodology. COURAGE in Europe Project collected data on the determinants of health and disability in an ageing population, with specific tools for the evaluation of the role of built environment and social networks on health, disability quality of life and well-being. The COURAGE Protocol for Ageing Studies has proven to be a valid tool for collecting comparable data in the ageing population. The COURAGE in Europe Consortium recommends that future studies exploring determinants of health and disability in ageing use COURAGE-derived methodology. Copyright © 2013 John Wiley & Sons, Ltd.

Dupuytren Disease: Is There Enough Comprehensive Patient Information on the Internet?

PubMed

Zuk, Grzegorz; Reinisch, Katharina B; Raptis, Dimitri A; Fertsch, Sonia; Guggenheim, Merlin; Palma, Adrian F

2017-06-22

Dupuytren disease is a chronic nonmalign fibroproliferative disorder that causes finger contractures via proliferation of new tissue under the glabrous skin of the hand, resulting in multiple functional limitations for the patient. As many surgical therapy options exist, patients suffering from this condition actively search for information in their environment before consulting a health professional. As little is known about the quality of Web-based patient information, the aim of this study was to conduct its systematic evaluation using a validated tool. A total of 118 websites were included, and qualitative and quantitative assessment was performed using the modified Ensuring Quality Information for Patients (EQIP) tool. This standardized and reproducible tool consists of 36 items to assess available information in three categories: contents, identification, and structure data. Scientific data with restricted access, duplicates, and irrelevant websites were not included. Only 32 websites addressed more than 19 items, and the scores did not significantly differ among the website developers. The median number of items from the EQIP tool was 16, with the top websites addressing 28 out of 36 items. The quality of the newly developed websites did not increase with passing time. This study revealed several shortcomings in the quality of Web-based information available for patients suffering from Dupuytren disease. In the world of continuously growing and instantly available Web-based information, it is the health providers' negligence of the last two decades that there are very few good quality, informative, and educative websites that could be recommended to patients. ©Grzegorz Zuk, Katharina B Reinisch, Dimitri A Raptis, Sonia Fertsch, Merlin Guggenheim, Adrian F Palma. Originally published in the Interactive Journal of Medical Research (http://www.i-jmr.org/), 22.06.2017.

An enhanced MMW and SMMW/THz imaging system performance prediction and analysis tool for concealed weapon detection and pilotage obstacle avoidance

NASA Astrophysics Data System (ADS)

Murrill, Steven R.; Jacobs, Eddie L.; Franck, Charmaine C.; Petkie, Douglas T.; De Lucia, Frank C.

2015-10-01

The U.S. Army Research Laboratory (ARL) has continued to develop and enhance a millimeter-wave (MMW) and submillimeter- wave (SMMW)/terahertz (THz)-band imaging system performance prediction and analysis tool for both the detection and identification of concealed weaponry, and for pilotage obstacle avoidance. The details of the MATLAB-based model which accounts for the effects of all critical sensor and display components, for the effects of atmospheric attenuation, concealment material attenuation, and active illumination, were reported on at the 2005 SPIE Europe Security and Defence Symposium (Brugge). An advanced version of the base model that accounts for both the dramatic impact that target and background orientation can have on target observability as related to specular and Lambertian reflections captured by an active-illumination-based imaging system, and for the impact of target and background thermal emission, was reported on at the 2007 SPIE Defense and Security Symposium (Orlando). Further development of this tool that includes a MODTRAN-based atmospheric attenuation calculator and advanced system architecture configuration inputs that allow for straightforward performance analysis of active or passive systems based on scanning (single- or line-array detector element(s)) or staring (focal-plane-array detector elements) imaging architectures was reported on at the 2011 SPIE Europe Security and Defence Symposium (Prague). This paper provides a comprehensive review of a newly enhanced MMW and SMMW/THz imaging system analysis and design tool that now includes an improved noise sub-model for more accurate and reliable performance predictions, the capability to account for postcapture image contrast enhancement, and the capability to account for concealment material backscatter with active-illumination- based systems. Present plans for additional expansion of the model's predictive capabilities are also outlined.

Nonlinear inversion of resistivity sounding data for 1-D earth models using the Neighbourhood Algorithm

NASA Astrophysics Data System (ADS)

Ojo, A. O.; Xie, Jun; Olorunfemi, M. O.

2018-01-01

To reduce ambiguity related to nonlinearities in the resistivity model-data relationships, an efficient direct-search scheme employing the Neighbourhood Algorithm (NA) was implemented to solve the 1-D resistivity problem. In addition to finding a range of best-fit models which are more likely to be global minimums, this method investigates the entire multi-dimensional model space and provides additional information about the posterior model covariance matrix, marginal probability density function and an ensemble of acceptable models. This provides new insights into how well the model parameters are constrained and make assessing trade-offs between them possible, thus avoiding some common interpretation pitfalls. The efficacy of the newly developed program is tested by inverting both synthetic (noisy and noise-free) data and field data from other authors employing different inversion methods so as to provide a good base for comparative performance. In all cases, the inverted model parameters were in good agreement with the true and recovered model parameters from other methods and remarkably correlate with the available borehole litho-log and known geology for the field dataset. The NA method has proven to be useful whilst a good starting model is not available and the reduced number of unknowns in the 1-D resistivity inverse problem makes it an attractive alternative to the linearized methods. Hence, it is concluded that the newly developed program offers an excellent complementary tool for the global inversion of the layered resistivity structure.

A graphical simulation software for instruction in cardiovascular mechanics physiology.

PubMed

Wildhaber, Reto A; Verrey, François; Wenger, Roland H

2011-01-25

Computer supported, interactive e-learning systems are widely used in the teaching of physiology. However, the currently available complimentary software tools in the field of the physiology of cardiovascular mechanics have not yet been adapted to the latest systems software. Therefore, a simple-to-use replacement for undergraduate and graduate students' education was needed, including an up-to-date graphical software that is validated and field-tested. Software compatible to Windows, based on modified versions of existing mathematical algorithms, has been newly developed. Testing was performed during a full term of physiological lecturing to medical and biology students. The newly developed CLabUZH software models a reduced human cardiovascular loop containing all basic compartments: an isolated heart including an artificial electrical stimulator, main vessels and the peripheral resistive components. Students can alter several physiological parameters interactively. The resulting output variables are printed in x-y diagrams and in addition shown in an animated, graphical model. CLabUZH offers insight into the relations of volume, pressure and time dependency in the circulation and their correlation to the electrocardiogram (ECG). Established mechanisms such as the Frank-Starling Law or the Windkessel Effect are considered in this model. The CLabUZH software is self-contained with no extra installation required and runs on most of today's personal computer systems. CLabUZH is a user-friendly interactive computer programme that has proved to be useful in teaching the basic physiological principles of heart mechanics.

Online model evaluation of large-eddy simulations covering Germany with a horizontal resolution of 156 m

NASA Astrophysics Data System (ADS)

Hansen, Akio; Ament, Felix; Lammert, Andrea

2017-04-01

Large-eddy simulations have been performed since several decades, but due to computational limits most studies were restricted to small domains or idealised initial-/boundary conditions. Within the High definition clouds and precipitation for advancing climate prediction (HD(CP)2) project realistic weather forecasting like LES simulations were performed with the newly developed ICON LES model for several days. The domain covers central Europe with a horizontal resolution down to 156 m. The setup consists of more than 3 billion grid cells, by what one 3D dump requires roughly 500 GB. A newly developed online evaluation toolbox was created to check instantaneously for realistic model simulations. The toolbox automatically combines model results with observations and generates several quicklooks for various variables. So far temperature-/humidity profiles, cloud cover, integrated water vapour, precipitation and many more are included. All kind of observations like aircraft observations, soundings or precipitation radar networks are used. For each dataset, a specific module is created, which allows for an easy handling and enhancement of the toolbox. Most of the observations are automatically downloaded from the Standardized Atmospheric Measurement Database (SAMD). The evaluation tool should support scientists at monitoring computational costly model simulations as well as to give a first overview about model's performance. The structure of the toolbox as well as the SAMD database are presented. Furthermore, the toolbox was applied on an ICON LES sensitivity study, where example results are shown.

Optical imaging probes in oncology

PubMed Central

Martelli, Cristina; Dico, Alessia Lo; Diceglie, Cecilia; Lucignani, Giovanni; Ottobrini, Luisa

2016-01-01

Cancer is a complex disease, characterized by alteration of different physiological molecular processes and cellular features. Keeping this in mind, the possibility of early identification and detection of specific tumor biomarkers by non-invasive approaches could improve early diagnosis and patient management. Different molecular imaging procedures provide powerful tools for detection and non-invasive characterization of oncological lesions. Clinical studies are mainly based on the use of computed tomography, nuclear-based imaging techniques and magnetic resonance imaging. Preclinical imaging in small animal models entails the use of dedicated instruments, and beyond the already cited imaging techniques, it includes also optical imaging studies. Optical imaging strategies are based on the use of luminescent or fluorescent reporter genes or injectable fluorescent or luminescent probes that provide the possibility to study tumor features even by means of fluorescence and luminescence imaging. Currently, most of these probes are used only in animal models, but the possibility of applying some of them also in the clinics is under evaluation. The importance of tumor imaging, the ease of use of optical imaging instruments, the commercial availability of a wide range of probes as well as the continuous description of newly developed probes, demonstrate the significance of these applications. The aim of this review is providing a complete description of the possible optical imaging procedures available for the non-invasive assessment of tumor features in oncological murine models. In particular, the characteristics of both commercially available and newly developed probes will be outlined and discussed. PMID:27145373

Development and Assessment of Transgenic Rodent Parasites for the Preclinical Evaluation of Malaria Vaccines.

PubMed

Espinosa, Diego A; Radtke, Andrea J; Zavala, Fidel

2016-01-01

Rodent transgenic parasites are useful tools for the preclinical evaluation of malaria vaccines. Over the last decade, several studies have reported the development of transgenic rodent parasites expressing P. falciparum antigens for the assessment of vaccine-induced immune responses, which traditionally have been limited to in vitro assays. However, the genetic manipulation of rodent Plasmodium species can have detrimental effects on the parasite's infectivity and development. In this chapter, we present a few guidelines for designing transfection plasmids, which should improve transfection efficiency and facilitate the generation of functional transgenic parasite strains. In addition, we provide a transfection protocol for the development of transgenic P. berghei parasites as well as practical methods to assess the viability and infectivity of these newly generated strains throughout different stages of their life cycle. These techniques should allow researchers to develop novel rodent malaria parasites expressing antigens from human malaria species and to determine whether these transgenic strains are fully infectious and thus represent stringent platforms for the in vivo evaluation of malaria vaccine candidates.

Deska: Tool for Central Administration of a Grid Site

NASA Astrophysics Data System (ADS)

Kundrát, Jan; Krejčová, Martina; Hubík, Tomáš; Kerpl, Lukáš

2011-12-01

Running a typical Tier-2 site requires mastering quite a few tools for fabric management. Keeping an inventory of installed HW machines, their roles and detailed information, from IP addresses to rack locations, is typically done using various in-house applications ranging from simple spreadsheets to web applications. Such solutions, whose documentation usually leaves much to be desired, typically do not prevent a significant duplication of information, and therefore the data therein quickly become obsolete. After having deployed Cfengine as one of a few sites in the WLCG environment, the Prague Tier-2 site set forth to further automate the fabric management, developing the Deska project. The aim of the system is to provide a central place to perform changes, from adding new machines or moving them between racks to changing their assigned service roles and additional metadata. The database provides an authoritative source of information from which all other systems and services (like DHCP servers, Ethernet switches or the Cfengine system) pull their data, using newly developed configuration adaptors. An easy-to-use command line interface modelled after the Cisco IOS-based switches was developed, enabling the data center administrators to easily change any information in an intuitive way. We provide an overview of the current status of the implementation and describe our design choices aimed at further reducing the system engineers' workload.

Reliability and Normative Reference Values for the Vestibular/Ocular Motor Screening (VOMS) Tool in Youth Athletes.

PubMed

Moran, Ryan N; Covassin, Tracey; Elbin, R J; Gould, Dan; Nogle, Sally

2018-05-01

The Vestibular/Ocular Motor Screening (VOMS) measure is a newly developed vestibular and ocular motor symptom provocation screening tool for sport-related concussions. Baseline data, psychometric properties, and reliability of the VOMS are needed to further understand the applications of this tool, especially in the youth population, where research is scarce. To establish normative data and document the internal consistency and false-positive rate of the VOMS in a sample of nonconcussed youth athletes. Cross-sectional study; Level of evidence, 3. A total of 423 youth athletes (male = 278, female = 145) between the ages of 8 and 14 years completed baseline VOMS screening before the start of their respective sport seasons. Internal consistency was measured with Cronbach α and inter-item correlations. Approximately 60% of youth athletes reported no symptom provocation on baseline VOMS assessment, with 9% to 13% scoring over the cutoff levels (score of ≥2 for any individual VOMS symptom, near point convergence distance of ≥5 cm). The VOMS displayed a high internal consistency (Cronbach α = .97) at baseline among youth athletes. The current findings provide preliminary support for the implementation of VOMS baseline assessment into clinical practice, due to a high internal consistency, strong relationships between VOMS items, and a low false-positive rate at baseline in youth athletes.

A Quasi-Universal Nonword Repetition Task as a Diagnostic Tool for Bilingual Children Learning Dutch as a Second Language.

PubMed

Boerma, Tessel; Chiat, Shula; Leseman, Paul; Timmermeister, Mona; Wijnen, Frank; Blom, Elma

2015-12-01

This study evaluated a newly developed quasi-universal nonword repetition task (Q-U NWRT) as a diagnostic tool for bilingual children with language impairment (LI) who have Dutch as a 2nd language. The Q-U NWRT was designed to be minimally influenced by knowledge of 1 specific language in contrast to a language-specific NWRT with which it was compared. One hundred twenty monolingual and bilingual children with and without LI participated (30 per group). A mixed-design analysis of variance was used to investigate the effects of LI and bilingualism on the NWRTs. Receiver operating characteristic analyses were conducted to evaluate the instruments' diagnostic value. Large negative effects of LI were found on both NWRTs, whereas negative effects of bilingualism only occurred on the language-specific NWRT. Both instruments had high clinical accuracy in the monolingual group, but only the Q-U NWRT had high clinical accuracy in the bilingual group. This study indicates that the Q-U NWRT is a promising diagnostic tool to help identify LI in bilingual children learning Dutch as a 2nd language. The instrument was clinically accurate in both a monolingual and bilingual group of children and seems better able to disentangle LI from language disadvantage than more language-specific measures.

Wyoming greater sage-grouse habitat prioritization: A collection of multi-scale seasonal models and geographic information systems land management tools

USGS Publications Warehouse

O'Donnell, Michael S.; Aldridge, Cameron L.; Doherty, Kevin E.; Fedy, Bradley C.

2015-01-01

We deliver all products described herein as online geographic information system data for visualization and downloading. We outline the data properties for each model and their data inputs, describe the process of selecting appropriate data products for multifarious applications, describe all data products and software, provide newly derived model composites, and discuss how land managers may use the models to inform future sage-grouse studies and potentially refine conservation efforts. The models, software tools, and associated opportunities for novel applications of these products should provide a suite of additional, but not exclusive, tools for assessing Wyoming Greater Sage-grouse habitats, which land managers, conservationists, and scientists can apply to myriad applications.

Impact of peculiar features of construction of transport infrastructure on the choice of tools for reengineering of business processes

NASA Astrophysics Data System (ADS)

Khripko, Elena

2017-10-01

In the present article we study the issues of organizational resistance to reengineering of business processes in construction of transport infrastructure. Reengineering in a company of transport sector is, first and foremost, an innovative component of business strategy. We analyze the choice of forward and reverse reengineering tools and terms of their application in connection with organizational resistance. Reengineering is defined taking into account four aspects: fundamentality, radicality, abruptness, business process. We describe the stages of reengineering and analyze key requirements to newly created business processes.

Alternative Splicing as a Target for Cancer Treatment.

PubMed

Martinez-Montiel, Nancy; Rosas-Murrieta, Nora Hilda; Anaya Ruiz, Maricruz; Monjaraz-Guzman, Eduardo; Martinez-Contreras, Rebeca

2018-02-11

Alternative splicing is a key mechanism determinant for gene expression in metazoan. During alternative splicing, non-coding sequences are removed to generate different mature messenger RNAs due to a combination of sequence elements and cellular factors that contribute to splicing regulation. A different combination of splicing sites, exonic or intronic sequences, mutually exclusive exons or retained introns could be selected during alternative splicing to generate different mature mRNAs that could in turn produce distinct protein products. Alternative splicing is the main source of protein diversity responsible for 90% of human gene expression, and it has recently become a hallmark for cancer with a full potential as a prognostic and therapeutic tool. Currently, more than 15,000 alternative splicing events have been associated to different aspects of cancer biology, including cell proliferation and invasion, apoptosis resistance and susceptibility to different chemotherapeutic drugs. Here, we present well established and newly discovered splicing events that occur in different cancer-related genes, their modification by several approaches and the current status of key tools developed to target alternative splicing with diagnostic and therapeutic purposes.

File level metadata generation and use for diverse airborne and in situ data: Experiences with Operation IceBridge and SnowEx

NASA Astrophysics Data System (ADS)

Tanner, S.; Schwab, M.; Beam, K.; Skaug, M.

2017-12-01

Operation IceBridge has been flying campaigns in the Arctic and Antarctic for nearly 10 years and will soon be a decadal mission. During that time, the generation and use of file level metadata has evolved from nearly non-existent to robust spatio-temporal support. This evolution has been difficult at times, but the results speak for themselves in the form of production tools for search, discovery, access and analysis. The lessons learned from this experience are now being incorporated into SnowEx, a new mission to measure snow cover using airborne and ground-based measurements. This presentation will focus on techniques for generating metadata for such a diverse set of measurements as well as the resulting tools that utilize this information. This includes the development and deployment of MetGen, a semi-automated metadata generation capability that relies on collaboration between data producers and data archivers, the newly deployed IceBridge data portal which incorporates data browse capabilities and limited in-line analysis, and programmatic access to metadata and data for incorporation into larger automated workflows.

Climate Model Diagnostic Analyzer

NASA Technical Reports Server (NTRS)

Lee, Seungwon; Pan, Lei; Zhai, Chengxing; Tang, Benyang; Kubar, Terry; Zhang, Zia; Wang, Wei

2015-01-01

The comprehensive and innovative evaluation of climate models with newly available global observations is critically needed for the improvement of climate model current-state representation and future-state predictability. A climate model diagnostic evaluation process requires physics-based multi-variable analyses that typically involve large-volume and heterogeneous datasets, making them both computation- and data-intensive. With an exploratory nature of climate data analyses and an explosive growth of datasets and service tools, scientists are struggling to keep track of their datasets, tools, and execution/study history, let alone sharing them with others. In response, we have developed a cloud-enabled, provenance-supported, web-service system called Climate Model Diagnostic Analyzer (CMDA). CMDA enables the physics-based, multivariable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. At the same time, CMDA provides a crowd-sourcing space where scientists can organize their work efficiently and share their work with others. CMDA is empowered by many current state-of-the-art software packages in web service, provenance, and semantic search.

In Silico Prediction and Experimental Confirmation of HA Residues Conferring Enhanced Human Receptor Specificity of H5N1 Influenza A Viruses.

PubMed

Schmier, Sonja; Mostafa, Ahmed; Haarmann, Thomas; Bannert, Norbert; Ziebuhr, John; Veljkovic, Veljko; Dietrich, Ursula; Pleschka, Stephan

2015-06-19

Newly emerging influenza A viruses (IAV) pose a major threat to human health by causing seasonal epidemics and/or pandemics, the latter often facilitated by the lack of pre-existing immunity in the general population. Early recognition of candidate pandemic influenza viruses (CPIV) is of crucial importance for restricting virus transmission and developing appropriate therapeutic and prophylactic strategies including effective vaccines. Often, the pandemic potential of newly emerging IAV is only fully recognized once the virus starts to spread efficiently causing serious disease in humans. Here, we used a novel phylogenetic algorithm based on the informational spectrum method (ISM) to identify potential CPIV by predicting mutations in the viral hemagglutinin (HA) gene that are likely to (differentially) affect critical interactions between the HA protein and target cells from bird and human origin, respectively. Predictions were subsequently validated by generating pseudotyped retrovirus particles and genetically engineered IAV containing these mutations and characterizing potential effects on virus entry and replication in cells expressing human and avian IAV receptors, respectively. Our data suggest that the ISM-based algorithm is suitable to identify CPIV among IAV strains that are circulating in animal hosts and thus may be a new tool for assessing pandemic risks associated with specific strains.

In Silico Prediction and Experimental Confirmation of HA Residues Conferring Enhanced Human Receptor Specificity of H5N1 Influenza A Viruses

NASA Astrophysics Data System (ADS)

Schmier, Sonja; Mostafa, Ahmed; Haarmann, Thomas; Bannert, Norbert; Ziebuhr, John; Veljkovic, Veljko; Dietrich, Ursula; Pleschka, Stephan

2015-06-01

Newly emerging influenza A viruses (IAV) pose a major threat to human health by causing seasonal epidemics and/or pandemics, the latter often facilitated by the lack of pre-existing immunity in the general population. Early recognition of candidate pandemic influenza viruses (CPIV) is of crucial importance for restricting virus transmission and developing appropriate therapeutic and prophylactic strategies including effective vaccines. Often, the pandemic potential of newly emerging IAV is only fully recognized once the virus starts to spread efficiently causing serious disease in humans. Here, we used a novel phylogenetic algorithm based on the informational spectrum method (ISM) to identify potential CPIV by predicting mutations in the viral hemagglutinin (HA) gene that are likely to (differentially) affect critical interactions between the HA protein and target cells from bird and human origin, respectively. Predictions were subsequently validated by generating pseudotyped retrovirus particles and genetically engineered IAV containing these mutations and characterizing potential effects on virus entry and replication in cells expressing human and avian IAV receptors, respectively. Our data suggest that the ISM-based algorithm is suitable to identify CPIV among IAV strains that are circulating in animal hosts and thus may be a new tool for assessing pandemic risks associated with specific strains.

Tools for outcome prediction in patients with community acquired pneumonia.

PubMed

Khan, Faheem; Owens, Mark B; Restrepo, Marcos; Povoa, Pedro; Martin-Loeches, Ignacio

2017-02-01

Community-acquired pneumonia (CAP) is one of the most common causes of mortality world-wide. The mortality rate of patients with CAP is influenced by the severity of the disease, treatment failure and the requirement for hospitalization and/or intensive care unit (ICU) management, all of which may be predicted by biomarkers and clinical scoring systems. Areas covered: We review the recent literature examining the efficacy of established and newly-developed clinical scores, biological and inflammatory markers such as C-Reactive protein (CRP), procalcitonin (PCT) and Interleukin-6 (IL-6), whether used alone or in conjunction with clinical severity scores to assess the severity of CAP, predict treatment failure, guide acute in-hospital or ICU admission and predict mortality. Expert commentary: The early prediction of treatment failure using clinical scores and biomarkers plays a developing role in improving survival of patients with CAP by identifying high-risk patients requiring hospitalization or ICU admission; and may enable more efficient allocation of resources. However, it is likely that combinations of scoring systems and biomarkers will be of greater use than individual markers. Further larger studies are needed to corroborate the additive value of these markers to clinical prediction scores to provide a safer and more effective assessment tool for clinicians.

Use of an emergency medical pictorial communication book during simulated disaster conditions.

PubMed

Behar, Solomon; Benson Ii, Richard; Kurzweil, Ami; Azen, Colleen; Nager, Alan L

2013-10-01

During disasters, the needs of victims outstrip available resources. Rapid assessment of patients must be performed; however, language barriers can be an impediment to efficient patient assessment, especially if interpreter resources are limited. Dependency on interpretive services requiring technology such a telephones, cell phones, and video conferencing may be inefficient, as they may be unavailable during disaster conditions. A low-tech, portable tool that aids in communication with non-English speakers would be beneficial. The medical emergency communication (MEC) book, developed at Children's Hospital Los Angeles, has the potential to be a useful tool in this capacity. The goal of this pilot study was to compare the accuracy of a newly developed disaster-focused medical history obtained from Spanish-speaking patients or caregivers using the MEC book, compared to a control group with whom no book was used. Our hypothesis was that use of the MEC book improves accuracy of medical history taking between English-only speaking health care workers and Spanish-speaking patients better than a monolingual clinician trying to take a medical history without it. We anticipated a higher overall score in the group of subjects whose histories were taken using the MEC book than in the control group. Patient satisfaction with the MEC book also was measured.

Translating person-centered care into practice: A comparative analysis of motivational interviewing, illness-integration support, and guided self-determination.

PubMed

Zoffmann, Vibeke; Hörnsten, Åsa; Storbækken, Solveig; Graue, Marit; Rasmussen, Bodil; Wahl, Astrid; Kirkevold, Marit

2016-03-01

Person-centred care [PCC] can engage people in living well with a chronic condition. However, translating PCC into practice is challenging. We aimed to compare the translational potentials of three approaches: motivational interviewing [MI], illness integration support [IIS] and guided self-determination [GSD]. Comparative analysis included eight components: (1) philosophical origin; (2) development in original clinical setting; (3) theoretical underpinnings; (4) overarching goal and supportive processes; (5) general principles, strategies or tools for engaging peoples; (6) health care professionals' background and training; (7) fidelity assessment; (8) reported effects. Although all approaches promoted autonomous motivation, they differed in other ways. Their original settings explain why IIS and GSD strive for life-illness integration, whereas MI focuses on managing ambivalence. IIS and GSD were based on grounded theories, and MI was intuitively developed. All apply processes and strategies to advance professionals' communication skills and engagement; GSD includes context-specific reflection sheets. All offer training programs; MI and GSD include fidelity tools. Each approach has a primary application: MI, when ambivalence threatens positive change; IIS, when integrating newly diagnosed chronic conditions; and GSD, when problem solving is difficult, or deadlocked. Professionals must critically consider the context in their choice of approach. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A real-time PCR approach to detect predation on anchovy and sardine early life stages

NASA Astrophysics Data System (ADS)

Cuende, Elsa; Mendibil, Iñaki; Bachiller, Eneko; Álvarez, Paula; Cotano, Unai; Rodriguez-Ezpeleta, Naiara

2017-12-01

Recruitment of sardine (Sardina pilchardus Walbaum, 1792) and anchovy (Engraulis encrasicolus Linnaeus, 1758) is thought to be regulated by predation of their eggs and larvae. Predators of sardine and anchovy can be identified by visual taxonomic identification of stomach contents, but this method is time consuming, tedious and may underestimate predation, especially in small predators such as fish larvae. Alternatively, genetic tools may offer a more cost-effective and accurate alternative. Here, we have developed a multiplex real-time polymerase chain reaction (RT-PCR) assay based on TaqMan probes to simultaneously detect sardine and anchovy remains in gut contents of potential predators. The assay combines previously described and newly generated species-specific primers and probes for anchovy and sardine detection respectively, and allows the detection of 0,001 ng of target DNA (which corresponds to about one hundredth of the total DNA present in a single egg). We applied the method to candidate anchovy and sardine egg predators in the Bay of Biscay, Atlantic Mackerel (Scomber scombrus) larvae. Egg predation observed was limited primarily to those stations where sardine and/or anchovy eggs were present. Our developed assay offers a suitable tool to understand the effects of predation on the survival of anchovy and sardine early life stages.

Earthdata Developer Portal poster

NASA Astrophysics Data System (ADS)

Plofchan, P.

2016-12-01

A common theme at community conferences in the Earth science domain is the need for more integration with related services, clearer documentation for services available, and a general simplification of what it takes to leverage existing tools so that setup and administration time can be minimized and time spent researching can be maximized. NASA's Earthdata Developer Portal (EDP) is the newly-created central location for documentation related to interacting with services offered by the EOSDIS community. The EDP will provide technical documentation for APIs, process documentation that provides real-world examples of how to use existing APIs in the real world, release notes for applications and services so that the entire community can stay up to date on recent updates, and best practice suggestions to improve implementation of both front-end and back-end services. Application and service owners will own their documentation while the EDP will ingest the documentation, serve it up in an interface using both industry standard tools, such as Swagger, and custom "adapters". The content is then styled to ensure consistency with other documentation found throughout the site and will be made searchable from a single location. "Getting Started" paths will also provide those users new to the space a simple path to follow to perform common tasks such as "searching and getting data" or "hosting an application on the Earthdata platform."

Quantitative evaluation of DNA damage and mutation rate by atmospheric and room-temperature plasma (ARTP) and conventional mutagenesis.

PubMed

Zhang, Xue; Zhang, Chong; Zhou, Qian-Qian; Zhang, Xiao-Fei; Wang, Li-Yan; Chang, Hai-Bo; Li, He-Ping; Oda, Yoshimitsu; Xing, Xin-Hui

2015-07-01

DNA damage is the dominant source of mutation, which is the driving force of evolution. Therefore, it is important to quantitatively analyze the DNA damage caused by different mutagenesis methods, the subsequent mutation rates, and their relationship. Atmospheric and room temperature plasma (ARTP) mutagenesis has been used for the mutation breeding of more than 40 microorganisms. However, ARTP mutagenesis has not been quantitatively compared with conventional mutation methods. In this study, the umu test using a flow-cytometric analysis was developed to quantify the DNA damage in individual viable cells using Salmonella typhimurium NM2009 as the model strain and to determine the mutation rate. The newly developed method was used to evaluate four different mutagenesis systems: a new ARTP tool, ultraviolet radiation, 4-nitroquinoline-1-oxide (4-NQO), and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) mutagenesis. The mutation rate was proportional to the corresponding SOS response induced by DNA damage. ARTP caused greater DNA damage to individual living cells than the other conventional mutagenesis methods, and the mutation rate was also higher. By quantitatively comparing the DNA damage and consequent mutation rate after different types of mutagenesis, we have shown that ARTP is a potentially powerful mutagenesis tool with which to improve the characteristics of microbial cell factories.

76 FR 33419 - Nationally Recognized Statistical Rating Organizations

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-08

... documentation of the internal control structure) or should the factors focus on the design (i.e., establishment... related to implementing them. a. Controls reasonably designed to ensure that a newly developed methodology... U.S.C. 78o-7(r)(1)(A). b. Controls reasonably designed to ensure that a newly developed methodology...

The Spelling Project. Technical Report 1992-2.

ERIC Educational Resources Information Center

Green, Kathy E.; Schroeder, David H.

Results of an analysis of a newly developed spelling test and several related measures are reported. Information about the reliability of a newly developed spelling test; its distribution of scores; its relationship with the standard battery of aptitude tests of the Johnson O'Connor Research Foundation; and its relationships with sex, age,…

How Schools Can Promote Healthy Development for Newly Arrived Immigrant and Refugee Adolescents: Research Priorities

ERIC Educational Resources Information Center

McNeely, Clea A.; Morland, Lyn; Doty, S. Benjamin; Meschke, Laurie L.; Awad, Summer; Husain, Altaf; Nashwan, Ayat

2017-01-01

Background: The US education system must find creative and effective ways to foster the healthy development of the approximately 2 million newly arrived immigrant and refugee adolescents, many of whom contend with language barriers, limited prior education, trauma, and discrimination. We identify research priorities for promoting the school…

Development and application of a universal Hemoplasma screening assay based on the SYBR green PCR principle.

PubMed

Willi, Barbara; Meli, Marina L; Lüthy, Ruedi; Honegger, Hanspeter; Wengi, Nicole; Hoelzle, Ludwig E; Reusch, Claudia E; Lutz, Hans; Hofmann-Lehmann, Regina

2009-12-01

Hemotropic mycoplasmas (hemoplasmas) are the causative agents of infectious anemia in several mammalian species. Their zoonotic potential has recently been substantiated by the identification of a feline hemoplasma isolate in an immunocompromised human patient. Although species-specific diagnostic molecular methods have been developed, their application as screening tools is limited due to the species diversity of hemoplasmas. The goals of this study were to develop a universal hemoplasma screening assay with broad specificity based on the SYBR green PCR principle, to compare the assay with hemoplasma-specific TaqMan PCR, and to analyze potential tick vectors and human blood samples to address the zoonotic potential. The newly developed PCR assay based on the 16S rRNA gene amplified feline, canine, bovine, porcine, camelid, and murine hemoplasmas, as well as Mycoplasma penetrans and Mycoplasma pneumoniae. The lower detection limit for feline and canine hemoplasmas was 1 to 10 copies/PCR. The assay exhibited 98.2% diagnostic sensitivity and 92.1% diagnostic specificity for feline hemoplasmas. All 1,950 Ixodes ticks were PCR negative, suggesting that Ixodes ticks are not relevant vectors for the above-mentioned hemoplasma species in Switzerland. None of the 414 blood samples derived from anemic or immunocompromised human patients revealed a clear positive result. The SYBR green PCR assay described here is a suitable tool to screen for known and so-far-undiscovered hemoplasma species. Positive results should be confirmed by specific TaqMan PCR or sequencing.

PhOTO Zebrafish: A Transgenic Resource for In Vivo Lineage Tracing during Development and Regeneration

PubMed Central

Dempsey, William P.; Fraser, Scott E.; Pantazis, Periklis

2012-01-01

Background Elucidating the complex cell dynamics (divisions, movement, morphological changes, etc.) underlying embryonic development and adult tissue regeneration requires an efficient means to track cells with high fidelity in space and time. To satisfy this criterion, we developed a transgenic zebrafish line, called PhOTO, that allows photoconvertible optical tracking of nuclear and membrane dynamics in vivo. Methodology PhOTO zebrafish ubiquitously express targeted blue fluorescent protein (FP) Cerulean and photoconvertible FP Dendra2 fusions, allowing for instantaneous, precise targeting and tracking of any number of cells using Dendra2 photoconversion while simultaneously monitoring global cell behavior and morphology. Expression persists through adulthood, making the PhOTO zebrafish an excellent tool for studying tissue regeneration: after tail fin amputation and photoconversion of a ∼100µm stripe along the cut area, marked differences seen in how cells contribute to the new tissue give detailed insight into the dynamic process of regeneration. Photoconverted cells that contributed to the regenerate were separated into three distinct populations corresponding to the extent of cell division 7 days after amputation, and a subset of cells that divided the least were organized into an evenly spaced, linear orientation along the length of the newly regenerating fin. Conclusions/Significance PhOTO zebrafish have wide applicability for lineage tracing at the systems-level in the early embryo as well as in the adult, making them ideal candidate tools for future research in development, traumatic injury and regeneration, cancer progression, and stem cell behavior. PMID:22431986

Practices influenced by policy? An exploration of newly hired science teachers at sites in South Africa and the United States

NASA Astrophysics Data System (ADS)

Navy, S. L.; Luft, J. A.; Toerien, R.; Hewson, P. W.

2018-05-01

In many parts of the world, newly hired science teachers' practices are developing in a complex policy environment. However, little is known about how newly hired science teachers' practices are enacted throughout a cycle of instruction and how these practices can be influenced by macro-, meso-, and micro-policies. Knowing how policies impact practice can result in better policies or better support for certain policies in order to enhance the instruction of newly hired teachers. This comparative study investigated how 12 newly hired science teachers at sites in South Africa (SA) and the United States (US) progressed through an instructional cycle of planning, teaching, and reflection. The qualitative data were analysed through beginning teacher competency frameworks, the cycle of instruction, and institutional theory. Data analysis revealed prevailing areas of practice and connections to levels of policy within the instructional cycle phases. There were some differences between the SA and US teachers and among first-, second-, and third-year teachers. More importantly, this study indicates that newly hired teachers are susceptible to micro-policies and are progressively developing their practice. It also shows the importance of meso-level connectors. It suggests that teacher educators and policy makers must consider how to prepare and support newly hired science teachers to achieve the shared global visions of science teaching.

Performance characteristics of a brief Family History Questionnaire to screen for Lynch syndrome in women with newly diagnosed endometrial cancer.

PubMed

Eiriksson, Lua; Aronson, Melyssa; Clarke, Blaise; Mojtahedi, Golnessa; Massey, Christine; Oza, Amit M; Gallinger, Steven; Pollett, Aaron; Mackay, Helen; Bernardini, Marcus Q; Ferguson, Sarah E

2015-02-01

The brief Family History Questionnaire (bFHQ) was developed to identify endometrial cancer patients whose family histories suggest Lynch syndrome (LS). We compared the bFHQ, extended Family History Questionnaire (eFHQ) and dictated medical records (DMRs) to determine which family history screening strategy is superior in identifying LS in unselected women with newly diagnosed endometrial cancer that have undergone universal germline testing. Prospective cohort study recruited women with newly diagnosed endometrial cancer to evaluate screening strategies to identify LS. Participants completed bFHQ and eFHQ, had tumor assessed with immunohistochemistry (IHC) for mismatch repair proteins (MMR) and micro-satellite instability testing and underwent universal germline testing for LS. The sensitivity, specificity, positive and negative predictive values (PPV, NPV) were compared between the family history screening strategies as well as IHC. 118 of 182 eligible patients (65%) consented; 87 patients (74%) were evaluable with both family history and germline mutation status. Median age was 61years (range 26-91). All 7 patients with confirmed LS were correctly identified by bFHQ, compared to 5 and 4 by eFHQ and DMR, respectively. The sensitivity, specificity, PPV and NPV values of bFHQ were 100%, 76.5%, 25.9% and 100%, respectively, performing similar to IHC testing. While eFHQ was more specific than bFHQ (86.7% vs. 76.5%, P=0.007), 2 cases of LS were missed. The patient-administered bFHQ effectively identified women with confirmed LS and is a good screening tool to triage women with endometrial cancer for further genetic assessment. Copyright © 2014 Elsevier Inc. All rights reserved.

Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case.

PubMed

Amar, David; Frades, Itziar; Danek, Agnieszka; Goldberg, Tatyana; Sharma, Sanjeev K; Hedley, Pete E; Proux-Wera, Estelle; Andreasson, Erik; Shamir, Ron; Tzfadia, Oren; Alexandersson, Erik

2014-12-05

For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.

Multi-Hazard Advanced Seismic Probabilistic Risk Assessment Tools and Applications

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

Coleman, Justin L.; Bolisetti, Chandu; Veeraraghavan, Swetha

Design of nuclear power plant (NPP) facilities to resist natural hazards has been a part of the regulatory process from the beginning of the NPP industry in the United States (US), but has evolved substantially over time. The original set of approaches and methods was entirely deterministic in nature and focused on a traditional engineering margins-based approach. However, over time probabilistic and risk-informed approaches were also developed and implemented in US Nuclear Regulatory Commission (NRC) guidance and regulation. A defense-in-depth framework has also been incorporated into US regulatory guidance over time. As a result, today, the US regulatory framework incorporatesmore » deterministic and probabilistic approaches for a range of different applications and for a range of natural hazard considerations. This framework will continue to evolve as a result of improved knowledge and newly identified regulatory needs and objectives, most notably in response to the NRC activities developed in response to the 2011 Fukushima accident in Japan. Although the US regulatory framework has continued to evolve over time, the tools, methods and data available to the US nuclear industry to meet the changing requirements have not kept pace. Notably, there is significant room for improvement in the tools and methods available for external event probabilistic risk assessment (PRA), which is the principal assessment approach used in risk-informed regulations and risk-informed decision-making applied to natural hazard assessment and design. This is particularly true if PRA is applied to natural hazards other than seismic loading. Development of a new set of tools and methods that incorporate current knowledge, modern best practice, and state-of-the-art computational resources would lead to more reliable assessment of facility risk and risk insights (e.g., the SSCs and accident sequences that are most risk-significant), with less uncertainty and reduced conservatisms.« less

BioSpider: a web server for automating metabolome annotations.

PubMed

Knox, Craig; Shrivastava, Savita; Stothard, Paul; Eisner, Roman; Wishart, David S

2007-01-01

One of the growing challenges in life science research lies in finding useful, descriptive or quantitative data about newly reported biomolecules (genes, proteins, metabolites and drugs). An even greater challenge is finding information that connects these genes, proteins, drugs or metabolites to each other. Much of this information is scattered through hundreds of different databases, abstracts or books and almost none of it is particularly well integrated. While some efforts are being undertaken at the NCBI and EBI to integrate many different databases together, this still falls short of the goal of having some kind of human-readable synopsis that summarizes the state of knowledge about a given biomolecule - especially small molecules. To address this shortfall, we have developed BioSpider. BioSpider is essentially an automated report generator designed specifically to tabulate and summarize data on biomolecules - both large and small. Specifically, BioSpider allows users to type in almost any kind of biological or chemical identifier (protein/gene name, sequence, accession number, chemical name, brand name, SMILES string, InCHI string, CAS number, etc.) and it returns an in-depth synoptic report (approximately 3-30 pages in length) about that biomolecule and any other biomolecule it may target. This summary includes physico-chemical parameters, images, models, data files, descriptions and predictions concerning the query molecule. BioSpider uses a web-crawler to scan through dozens of public databases and employs a variety of specially developed text mining tools and locally developed prediction tools to find, extract and assemble data for its reports. Because of its breadth, depth and comprehensiveness, we believe BioSpider will prove to be a particularly valuable tool for researchers in metabolomics. BioSpider is available at: www.biospider.ca

Epidemiological surveillance methods for vector-borne diseases.

PubMed

Thompson, P N; Etter, E

2015-04-01

Compared with many other diseases, the ever-increasing threat of vector-borne diseases (VBDs) represents a great challenge to public and animal health managers. Complex life cycles, changing distribution ranges, a variety of potential vectors and hosts, and the possible role of reservoirs make surveillance for VBDs a grave concern in a changing environment with increasing economic constraints. Surveillance activities may have various specific objectives and may focus on clinical disease, pathogens, vectors, hosts and/or reservoirs, but ultimately such activities should improve our ability to predict, prevent and/or control the diseases concerned. This paper briefly reviews existing and newly developed tools for the surveillance of VBDs. A range of examples, by no means exhaustive, illustrates that VBD surveillance usually involves a combination of methods to achieve its aims, and is best accomplished when these techniques are adapted to the specific environment and constraints of the region. More so than any other diseases, VBDs respect no administrative boundaries; in addition, animal, human and commodity movements are increasing dramatically, with illegal or unknown movements difficult to quantify. Vector-borne disease surveillance therefore becomes a serious issue for local and national organisations and is being conducted more and more at the regional and international level through multidisciplinary networks. With economic and logistical constraints, tools for optimising and evaluating the performance of surveillance systems are essential and examples of recent developments in this area are included. The continuous development of mapping, analytical and modelling tools provides us with an enhanced ability to interpret, visualise and communicate surveillance results. This review also demonstrates the importance of the link between surveillance and research, with interactions and benefits in both directions.

Advancing Data Assimilation in Operational Hydrologic Forecasting: Progresses, Challenges, and Emerging Opportunities

NASA Technical Reports Server (NTRS)

Liu, Yuqiong; Weerts, A.; Clark, M.; Hendricks Franssen, H.-J; Kumar, S.; Moradkhani, H.; Seo, D.-J.; Schwanenberg, D.; Smith, P.; van Dijk, A. I. J. M.;

The Properties of Mortar Mixtures Blended with Natural, Crushed, and Recycled Fine Aggregates for Building Construction Materials

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

Yu, Myoung-Youl; Lee, Jae-Yong; Chung, Chul-Woo

2012-01-12

In this research, the possible applicability of fine aggregates blended with natural, crushed, and recycled fine aggregate are discussed. The fresh and hardened properties of mortar using blended fine aggregates are monitored depending on various blending ratio of fine aggregates. Newly developed ternary diagram was also utilized for better interpretation of the data. It was found that air content increased and unit weight decreased as recycled fine aggregate content increased. With moisture type processing of recycled fine aggregate, the mortar flow was not negatively affected by increase in the recycled fine aggregate content. The ternary diagram is found to bemore » an effective graphical presentation tool that can be used for the quality evaluation of mortar using blended fine aggregate.« less

Visualizing conserved gene location across microbe genomes

NASA Astrophysics Data System (ADS)

Shaw, Chris D.

2009-01-01

This paper introduces an analysis-based zoomable visualization technique for displaying the location of genes across many related species of microbes. The purpose of this visualizatiuon is to enable a biologist to examine the layout of genes in the organism of interest with respect to the gene organization of related organisms. During the genomic annotation process, the ability to observe gene organization in common with previously annotated genomes can help a biologist better confirm the structure and function of newly analyzed microbe DNA sequences. We have developed a visualization and analysis tool that enables the biologist to observe and examine gene organization among genomes, in the context of the primary sequence of interest. This paper describes the visualization and analysis steps, and presents a case study using a number of Rickettsia genomes.

Systems Level Engineering of Plant Cell Wall Biosynthesis to Improve Biofuel Feedstock Quality

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

Hazen, Samuel

2013-09-27

Our new regulatory model of cell wall biosynthesis proposes original network architecture with several newly incorporated components. The mapped set of protein-DNA interactions will serve as a foundation for 1) understanding the regulation of a complex and integral plant component and 2) the manipulation of crop species for biofuel and biotechnology purposes. This study revealed interesting and novel aspects of grass growth and development and further enforce the importance of a grass model system. By functionally characterizing a suite of genes, we have begun to improve the sparse model for transcription regulation of biomass accumulation in grasses. In the process,more » we have advanced methodology and brachy molecular genetic tools that will serve as valuable community resource.« less

Noninvasive in situ evaluation of osteogenic differentiation by time-resolved laser-induced fluorescence spectroscopy.

PubMed

Ashjian, Peter; Elbarbary, Amir; Zuk, Patricia; DeUgarte, Daniel A; Benhaim, Prosper; Marcu, Laura; Hedrick, Marc H

2004-01-01

The clinical implantation of bioengineered tissues requires an in situ nondestructive evaluation of the quality of tissue constructs developed in vitro before transplantation. Time-resolved laser-induced fluorescence spectroscopy (TR-LIFS) is demonstrated here to noninvasively monitor the formation of osteogenic extracellular matrix (ECM) produced by putative stem cells (PLA cells) derived from human adipose tissue. We show that this optical spectroscopy technique can assess the relative expression of collagens (types I, III, IV, and V) within newly forming osteogenic ECM. The results are consistent with those obtained by conventional histochemical techniques (immunofluorescence and Western blot) and demonstrate that TR-LIFS is a potential tool for monitoring the expression of distinct collagen types and the formation of collagen cross-links in intact tissue constructs.

Approaches for in silico finishing of microbial genome sequences

PubMed Central

Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

2017-01-01

Abstract The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as “drafts”, incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing. PMID:28898352

Increasing Diversity in Global Climate Change, Space Weather and Space Technology Research and Education

NASA Astrophysics Data System (ADS)

Johnson, L. P.; Austin, S. A.; Howard, A. M.; Boxe, C.; Jiang, M.; Tulsee, T.; Chow, Y. W.; Zavala-Gutierrez, R.; Barley, R.; Filin, B.; Brathwaite, K.

2015-12-01

This presentation describes projects at Medgar Evers College of the City University of New York that contribute to the preparation of a diverse workforce in the areas of ocean modeling, planetary atmospheres, space weather and space technology. Specific projects incorporating both undergraduate and high school students include Assessing Parameterizations of Energy Input to Internal Ocean Mixing, Reaction Rate Uncertainty on Mars Atmospheric Ozone, Remote Sensing of Solar Active Regions and Intelligent Software for Nano-satellites. These projects are accompanied by a newly developed Computational Earth and Space Science course to provide additional background on methodologies and tools for scientific data analysis. This program is supported by NSF award AGS-1359293 REU Site: CUNY/GISS Center for Global Climate Research and the NASA New York State Space Grant Consortium.

Geometry and design of origami bellows with tunable response

NASA Astrophysics Data System (ADS)

Reid, Austin; Lechenault, Frederic; Rica, Sergio; Adda-Bedia, Mokhtar

2017-01-01

Origami folded cylinders (origami bellows) have found increasingly sophisticated applications in space flight and medicine. In spite of this interest, a general understanding of the mechanics of an origami folded cylinder has been elusive. With a newly developed set of geometrical tools, we have found an analytic solution for all possible cylindrical rigid-face states of both Miura-ori and triangular tessellations. Although an idealized bellows in both of these families may have two allowed rigid-face configurations over a well-defined region, the corresponding physical device, limited by nonzero material thickness and forced to balance hinge and plate-bending energy, often cannot stably maintain a stowed configuration. We have identified the parameters that control this emergent bistability, and we have demonstrated the ability to design and fabricate bellows with tunable deployability.

Geometry and design of origami bellows with tunable response.

PubMed

Reid, Austin; Lechenault, Frederic; Rica, Sergio; Adda-Bedia, Mokhtar

2017-01-01

Origami folded cylinders (origami bellows) have found increasingly sophisticated applications in space flight and medicine. In spite of this interest, a general understanding of the mechanics of an origami folded cylinder has been elusive. With a newly developed set of geometrical tools, we have found an analytic solution for all possible cylindrical rigid-face states of both Miura-ori and triangular tessellations. Although an idealized bellows in both of these families may have two allowed rigid-face configurations over a well-defined region, the corresponding physical device, limited by nonzero material thickness and forced to balance hinge and plate-bending energy, often cannot stably maintain a stowed configuration. We have identified the parameters that control this emergent bistability, and we have demonstrated the ability to design and fabricate bellows with tunable deployability.

Approaches for in silico finishing of microbial genome sequences.

PubMed

Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva

The introduction of next-generation sequencing (NGS) had a significant effect on the availability of genomic information, leading to an increase in the number of sequenced genomes from a large spectrum of organisms. Unfortunately, due to the limitations implied by the short-read sequencing platforms, most of these newly sequenced genomes remained as "drafts", incomplete representations of the whole genetic content. The previous genome sequencing studies indicated that finishing a genome sequenced by NGS, even bacteria, may require additional sequencing to fill the gaps, making the entire process very expensive. As such, several in silico approaches have been developed to optimize the genome assemblies and facilitate the finishing process. The present review aims to explore some free (open source, in many cases) tools that are available to facilitate genome finishing.

Practices Influenced by Policy? An Exploration of Newly Hired Science Teachers at Sites in South Africa and the United States

ERIC Educational Resources Information Center

Navy, S. L.; Luft, J. A.; Toerien, R.; Hewson, P. W.

2018-01-01

In many parts of the world, newly hired science teachers' practices are developing in a complex policy environment. However, little is known about how newly hired science teachers' practices are enacted throughout a cycle of instruction and how these practices can be influenced by macro-, meso-, and micro-policies. Knowing how policies impact…

[Predicting the probability of development and progression of primary open angle glaucoma by regression modeling].

PubMed

Likhvantseva, V G; Sokolov, V A; Levanova, O N; Kovelenova, I V

2018-01-01

Prediction of the clinical course of primary open-angle glaucoma (POAG) is one of the main directions in solving the problem of vision loss prevention and stabilization of the pathological process. Simple statistical methods of correlation analysis show the extent of each risk factor's impact, but do not indicate the total impact of these factors in personalized combinations. The relationships between the risk factors is subject to correlation and regression analysis. The regression equation represents the dependence of the mathematical expectation of the resulting sign on the combination of factor signs. To develop a technique for predicting the probability of development and progression of primary open-angle glaucoma based on a personalized combination of risk factors by linear multivariate regression analysis. The study included 66 patients (23 female and 43 male; 132 eyes) with newly diagnosed primary open-angle glaucoma. The control group consisted of 14 patients (8 male and 6 female). Standard ophthalmic examination was supplemented with biochemical study of lacrimal fluid. Concentration of matrix metalloproteinase MMP-2 and MMP-9 in tear fluid in both eyes was determined using 'sandwich' enzyme-linked immunosorbent assay (ELISA) method. The study resulted in the development of regression equations and step-by-step multivariate logistic models that can help calculate the risk of development and progression of POAG. Those models are based on expert evaluation of clinical and instrumental indicators of hydrodynamic disturbances (coefficient of outflow ease - C, volume of intraocular fluid secretion - F, fluctuation of intraocular pressure), as well as personalized morphometric parameters of the retina (central retinal thickness in the macular area) and concentration of MMP-2 and MMP-9 in the tear film. The newly developed regression equations are highly informative and can be a reliable tool for studying of the influence vector and assessment of pathogenic potential of the independent risk factors in specific personalized combinations.

Developing an instrument for assessing students' concepts of the nature of technology

NASA Astrophysics Data System (ADS)

Liou, Pey-Yan

2015-05-01

Background:The nature of technology has been rarely discussed despite the fact that technology plays an essential role in modern society. It is important to discuss students' concepts of the nature of technology, and further to advance their technological literacy and adaptation to modern society. There is a need to assess high school students' concepts of the nature of technology. Purpose:This study aims to engage in discourse on students' concepts of the nature of technology based on a proposed theoretical framework. Moreover, another goal is to develop an instrument for measuring students' concepts of the nature of technology. Sample:Four hundred and fifty-five high school students' perceptions of technology were qualitatively analyzed. Furthermore, 530 students' responses to a newly developed questionnaire were quantitatively analyzed in the final test. Design and method:First, content analysis was utilized to discuss and categorize students' statements regarding technology and its related issues. The Student Concepts of the Nature of Technology Questionnaire was developed based on the proposed theoretical framework and was supported by the students' qualitative data. Finally, exploratory factor analysis and reliability analysis were applied to determine the structure of the items and the internal consistency of each scale. Results:Through a process of instrument development, the Student Concepts of the Nature of Technology Questionnaire was shown to be a valid and reliable tool for measuring students' concepts of the nature of technology. This newly developed questionnaire is composed of 29 items in six scales, namely 'technology as artifacts,' 'technology as an innovation change,' 'the current role of technology in society,' 'technology as a double-edged sword,' 'technology as a science-based form,' and 'history of technology.' Conclusions:The Student Concepts of the Nature of Technology Questionnaire has been confirmed as a reasonably valid and reliable instrument. This study provides a useful questionnaire for educational researchers and practitioners for measuring students' concepts of the nature of technology.

Creative Exercises (CEs) in the Biochemistry Domain: An Analysis of Students' Linking of Chemical and Biochemical Concepts

ERIC Educational Resources Information Center

Warfa, Abdi-Rizak M.; Odowa, N.

2015-01-01

Creative exercises (CEs), a specific form of open-ended assessment tools, have been shown to promote students' linking of prior and newly learned concepts within a course. In this study, we examined how often students in an upper-division undergraduate biochemistry course linked prior chemical concepts to biochemical ones in response to CE…

A newly discovered Bordetella species carries a transcriptionally active CRISPR-Cas with a small Cas9 endonuclease

USDA-ARS?s Scientific Manuscript database

The Cas9 endonuclease of the Type II-a clustered regularly interspersed short palindromic repeats (CRISPR), of Streptococcus pyogenes (SpCas9) has been adapted as a widely used tool for genome editing and genome engineering. Herein, we describe a gene encoding a novel Cas9 ortholog (BpsuCas9) and th...

The CEBAF Element Database and Related Operational Software

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

Larrieu, Theodore; Slominski, Christopher; Keesee, Marie

The newly commissioned 12GeV CEBAF accelerator relies on a flexible, scalable and comprehensive database to define the accelerator. This database delivers the configuration for CEBAF operational tools, including hardware checkout, the downloadable optics model, control screens, and much more. The presentation will describe the flexible design of the CEBAF Element Database (CED), its features and assorted use case examples.

Institutions of Higher Education as Public Diplomacy Tools: China-Based University Programs for the 21st Century

ERIC Educational Resources Information Center

Metzgar, Emily T.

2016-01-01

Two flagship Chinese universities are home to newly established English-language graduate programs intended to arm international cohorts of future leaders with the skills, knowledge, and insights necessary to thrive in a world in which China will play a leading role. Employing the literature of international education and public diplomacy, this…

Optimizing high performance computing workflow for protein functional annotation.

PubMed

Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

2014-09-10

Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

Optimizing high performance computing workflow for protein functional annotation

PubMed Central

Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

2014-01-01

Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data. PMID:25313296

The ASTRAL Compendium in 2004

DOE R&D Accomplishments Database

Chandonia, John-Marc; Hon, Gary; Walker, Nigel S.; Lo Conte, Loredana; Koehl, Patrice; Levitt, Michael; Brenner, Steven E.

2003-09-15

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. Partially derived from the SCOP database of protein structure domains, it includes sequences for each domain and other resources useful for studying these sequences and domain structures. The current release of ASTRAL contains 54,745 domains, more than three times as many as the initial release four years ago. ASTRAL has undergone major transformations in the past two years. In addition to several complete updates each year, ASTRAL is now updated on a weekly basis with preliminary classifications of domains from newly released PDB structures. These classifications are available as a stand-alone database, as well as available integrated into other ASTRAL databases such as representative subsets. To enhance the utility of ASTRAL to structural biologists, all SCOP domains are now made available as PDB-style coordinate files as well as sequences. In addition to sequences and representative subsets based on SCOP domains, sequences and subsets based on PDB chains are newly included in ASTRAL. Several search tools have been added to ASTRAL to facilitate retrieval of data by individual users and automated methods.

Vibrational imaging of newly synthesized proteins in live cells by stimulated Raman scattering microscopy

PubMed Central

Wei, Lu; Yu, Yong; Shen, Yihui; Wang, Meng C.; Min, Wei

2013-01-01

Synthesis of new proteins, a key step in the central dogma of molecular biology, has been a major biological process by which cells respond rapidly to environmental cues in both physiological and pathological conditions. However, the selective visualization of a newly synthesized proteome in living systems with subcellular resolution has proven to be rather challenging, despite the extensive efforts along the lines of fluorescence staining, autoradiography, and mass spectrometry. Herein, we report an imaging technique to visualize nascent proteins by harnessing the emerging stimulated Raman scattering (SRS) microscopy coupled with metabolic incorporation of deuterium-labeled amino acids. As a first demonstration, we imaged newly synthesized proteins in live mammalian cells with high spatial–temporal resolution without fixation or staining. Subcellular compartments with fast protein turnover in HeLa and HEK293T cells, and newly grown neurites in differentiating neuron-like N2A cells, are clearly identified via this imaging technique. Technically, incorporation of deuterium-labeled amino acids is minimally perturbative to live cells, whereas SRS imaging of exogenous carbon–deuterium bonds (C–D) in the cell-silent Raman region is highly sensitive, specific, and compatible with living systems. Moreover, coupled with label-free SRS imaging of the total proteome, our method can readily generate spatial maps of the quantitative ratio between new and total proteomes. Thus, this technique of nonlinear vibrational imaging of stable isotope incorporation will be a valuable tool to advance our understanding of the complex spatial and temporal dynamics of newly synthesized proteome in vivo. PMID:23798434

Genome Modification Technologies and Their Applications in Avian Species.

PubMed

Lee, Hong Jo; Kim, Young Min; Ono, Tamao; Han, Jae Yong

2017-10-26

The rapid development of genome modification technology has provided many great benefits in diverse areas of research and industry. Genome modification technologies have also been actively used in a variety of research areas and fields of industry in avian species. Transgenic technologies such as lentiviral systems and piggyBac transposition have been used to produce transgenic birds for diverse purposes. In recent years, newly developed programmable genome editing tools such as transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) have also been successfully adopted in avian systems with primordial germ cell (PGC)-mediated genome modification. These genome modification technologies are expected to be applied to practical uses beyond system development itself. The technologies could be used to enhance economic traits in poultry such as acquiring a disease resistance or producing functional proteins in eggs. Furthermore, novel avian models of human diseases or embryonic development could also be established for research purposes. In this review, we discuss diverse genome modification technologies used in avian species, and future applications of avian biotechnology.

In vivo cell biology in zebrafish - providing insights into vertebrate development and disease.

PubMed

Vacaru, Ana M; Unlu, Gokhan; Spitzner, Marie; Mione, Marina; Knapik, Ela W; Sadler, Kirsten C

2014-02-01

Over the past decades, studies using zebrafish have significantly advanced our understanding of the cellular basis for development and human diseases. Zebrafish have rapidly developing transparent embryos that allow comprehensive imaging of embryogenesis combined with powerful genetic approaches. However, forward genetic screens in zebrafish have generated unanticipated findings that are mirrored by human genetic studies: disruption of genes implicated in basic cellular processes, such as protein secretion or cytoskeletal dynamics, causes discrete developmental or disease phenotypes. This is surprising because many processes that were assumed to be fundamental to the function and survival of all cell types appear instead to be regulated by cell-specific mechanisms. Such discoveries are facilitated by experiments in whole animals, where zebrafish provides an ideal model for visualization and manipulation of organelles and cellular processes in a live vertebrate. Here, we review well-characterized mutants and newly developed tools that underscore this notion. We focus on the secretory pathway and microtubule-based trafficking as illustrative examples of how studying cell biology in vivo using zebrafish has broadened our understanding of the role fundamental cellular processes play in embryogenesis and disease.

Development of the implant surgical technique and assessment rating system

PubMed Central

Park, Jung-Chul; Hwang, Ji-Wan; Lee, Jung-Seok; Jung, Ui-Won; Choi, Seong-Ho; Cho, Kyoo-Sung; Chai, Jung-Kiu

2012-01-01

Purpose There has been no attempt to establish an objective implant surgical evaluation protocol to assess residents' surgical competence and improve their surgical outcomes. The present study presents a newly developed assessment and rating system and simulation model that can assist the teaching staffs to evaluate the surgical events and surgical skills of residents objectively. Methods Articles published in peer-reviewed English journals were selected using several scientific databases and subsequently reviewed regarding surgical competence and assessment tools. Particularly, medical journals reporting rating and evaluation protocols for various types of medical surgeries were thoroughly analyzed. Based on these studies, an implant surgical technique assessment and rating system (iSTAR) has been developed. Also, a specialized dental typodont was developed for the valid and reliable assessment of surgery. Results The iSTAR consists of two parts including surgical information and task-specific checklists. Specialized simulation model was subsequently produced and can be used in combination with iSTAR. Conclusions The assessment and rating system provided may serve as a reference guide for teaching staffs to evaluate the residents' implant surgical techniques. PMID:22413071

Simulink based behavioural modelling of a pulse oximeter for deployment in rapid development, prototyping and verification.

PubMed

Shokouhian, M; Morling, R C S; Kale, I

2012-01-01

The pulse oximeter is a well-known device for measuring the level of oxygen in blood. Since their invention, pulse oximeters have been under constant development in both aspects of hardware and software; however there are still unsolved problems that limit their performance [6], [7]. Many fresh algorithms and new design techniques are being suggested every year by industry and academic researchers which claim that they can improve accuracy of measurements [8], [9]. With the lack of an accurate computer-based behavioural model for pulse oximeters, the only way for evaluation of these newly developed systems and algorithms is through hardware implementation which can be both expensive and time consuming. This paper presents an accurate Simulink based behavioural model for a pulse oximeter that can be used by industry and academia alike working in this area, as an exploration as well as productivity enhancement tool during their research and development process. The aim of this paper is to introduce a new computer-based behavioural model which provides a simulation environment from which new ideas can be rapidly evaluated long before the real implementation.

Genome Modification Technologies and Their Applications in Avian Species

PubMed Central

Lee, Hong Jo; Kim, Young Min; Ono, Tamao

2017-01-01

The rapid development of genome modification technology has provided many great benefits in diverse areas of research and industry. Genome modification technologies have also been actively used in a variety of research areas and fields of industry in avian species. Transgenic technologies such as lentiviral systems and piggyBac transposition have been used to produce transgenic birds for diverse purposes. In recent years, newly developed programmable genome editing tools such as transcription activator-like effector nuclease (TALEN) and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) have also been successfully adopted in avian systems with primordial germ cell (PGC)-mediated genome modification. These genome modification technologies are expected to be applied to practical uses beyond system development itself. The technologies could be used to enhance economic traits in poultry such as acquiring a disease resistance or producing functional proteins in eggs. Furthermore, novel avian models of human diseases or embryonic development could also be established for research purposes. In this review, we discuss diverse genome modification technologies used in avian species, and future applications of avian biotechnology. PMID:29072628

Development and validation of a paediatric long-bone fracture classification. A prospective multicentre study in 13 European paediatric trauma centres

PubMed Central

2011-01-01

Background The aim of this study was to develop a child-specific classification system for long bone fractures and to examine its reliability and validity on the basis of a prospective multicentre study. Methods Using the sequentially developed classification system, three samples of between 30 and 185 paediatric limb fractures from a pool of 2308 fractures documented in two multicenter studies were analysed in a blinded fashion by eight orthopaedic surgeons, on a total of 5 occasions. Intra- and interobserver reliability and accuracy were calculated. Results The reliability improved with successive simplification of the classification. The final version resulted in an overall interobserver agreement of κ = 0.71 with no significant difference between experienced and less experienced raters. Conclusions In conclusion, the evaluation of the newly proposed classification system resulted in a reliable and routinely applicable system, for which training in its proper use may further improve the reliability. It can be recommended as a useful tool for clinical practice and offers the option for developing treatment recommendations and outcome predictions in the future. PMID:21548939

Helioviewer: A Web 2.0 Tool for Visualizing Heterogeneous Heliophysics Data

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Lynch, M. J.; Schmeidel, P.; Dimitoglou, G.; Müeller, D.; Fleck, B.

2008-12-01

Solar physics datasets are becoming larger, richer, more numerous and more distributed. Feature/event catalogs (describing objects of interest in the original data) are becoming important tools in navigating these data. In the wake of this increasing influx of data and catalogs there has been a growing need for highly sophisticated tools for accessing and visualizing this wealth of information. Helioviewer is a novel tool for integrating and visualizing disparate sources of solar and Heliophysics data. Taking advantage of the newly available power of modern web application frameworks, Helioviewer merges image and feature catalog data, and provides for Heliophysics data a familiar interface not unlike Google Maps or MapQuest. In addition to streamlining the process of combining heterogeneous Heliophysics datatypes such as full-disk images and coronagraphs, the inclusion of visual representations of automated and human-annotated features provides the user with an integrated and intuitive view of how different factors may be interacting on the Sun. Currently, Helioviewer offers images from The Extreme ultraviolet Imaging Telescope (EIT), The Large Angle and Spectrometric COronagraph experiment (LASCO) and the Michelson Doppler Imager (MDI) instruments onboard The Solar and Heliospheric Observatory (SOHO), as well as The Transition Region and Coronal Explorer (TRACE). Helioviewer also incorporates feature/event information from the LASCO CME List, NOAA Active Regions, CACTus CME and Type II Radio Bursts feature/event catalogs. The project is undergoing continuous development with many more data sources and additional functionality planned for the near future.

Ranking of Business Process Simulation Software Tools with DEX/QQ Hierarchical Decision Model

PubMed Central

2016-01-01

The omnipresent need for optimisation requires constant improvements of companies’ business processes (BPs). Minimising the risk of inappropriate BP being implemented is usually performed by simulating the newly developed BP under various initial conditions and “what-if” scenarios. An effectual business process simulations software (BPSS) is a prerequisite for accurate analysis of an BP. Characterisation of an BPSS tool is a challenging task due to the complex selection criteria that includes quality of visual aspects, simulation capabilities, statistical facilities, quality reporting etc. Under such circumstances, making an optimal decision is challenging. Therefore, various decision support models are employed aiding the BPSS tool selection. The currently established decision support models are either proprietary or comprise only a limited subset of criteria, which affects their accuracy. Addressing this issue, this paper proposes a new hierarchical decision support model for ranking of BPSS based on their technical characteristics by employing DEX and qualitative to quantitative (QQ) methodology. Consequently, the decision expert feeds the required information in a systematic and user friendly manner. There are three significant contributions of the proposed approach. Firstly, the proposed hierarchical model is easily extendible for adding new criteria in the hierarchical structure. Secondly, a fully operational decision support system (DSS) tool that implements the proposed hierarchical model is presented. Finally, the effectiveness of the proposed hierarchical model is assessed by comparing the resulting rankings of BPSS with respect to currently available results. PMID:26871694

Measurements, modeling, and simulation of semiconductor/gate dielectric defects using random telegraph signals

NASA Astrophysics Data System (ADS)

Nour, Mohamed

Constructing an effective statistical model and a simulation tool that can predict the phenomenon of random telegraph signals (RTS) is the objective of this work. The continuous scaling down of metal oxide -- semiconductor field effect transistors (MOSFETs) makes charging/discharging traps(s) located at the silicon/silicon dioxide interface or deep in the oxide bulk by mobile charge(s) a more pronounced problem for both analog and digital applications. The intent of this work is to develop an RTS statistical model and a simulation tool based on first principles and supported by extensive experimental data. The newly developed RTS statistical model and its simulation tool should be able to replicate and predict the RTS in time and frequency domains. First, room temperature RTS measurements are performed which provide limited information about the trap. They yield the extraction of some trap and RTS characteristics such as average capture and emission times associated with RTS traces, trap position in the oxide with respect to the Si/SiO 2 interface and along the channel with respect to the source, capture cross section, and trap energies in the Si and SiO2 band -- gaps. Variable temperature measurements, on the other hand, yield much more valuable information. Variable temperature RTS measurements from room temperature down to 80 K were performed, with the MOSFET biased from threshold voltage to strong inversion, in the linear and saturation regions. Variable temperature RTS measurements yield the extraction of trap characteristics such as capture cross -- section prefactor, capture and emission activation energies, change in entropy and enthalpy, and relaxation energy associated with a trap from which the nature and origin of a defect center can be identified. The newly developed Random Telegraph Signals Simulation (RTSSIM) is based on several physical principles and mechanisms e.g. (1) capturing and emitting a mobile charge from and to the channel is governed by phonon- assisted- tunneling, (2) traps only within a few kBT of the Fermi energy level are considered electrically active, (3) trap density is taken as U -- shaped in energy in the silicon band-gap, (4) device scalability is accounted for, (5) and temperature dependence of all parameters is considered. RTSSIM reconstructs the RTS traces in time domain from which the power spectral density (PSD) is evaluated. If there is 20 or more active traps, RTSSIM evaluates the PSD from the superposition of the RTS spectra. RTSSIM extracts RTS and trap characteristics from the simulated RTS data and outputs them to MS Excel files for further analyses and study. The novelty of this work is: (1) it is the first time quantum trap states have been accurately assigned to each switching level in a complex RTS corresponding to dependently and independently interacting traps, (2) new physics-based measurement-driven model and simulation tool has been developed for RTS phenomenon in a MOSFET, (3) and it is the first time a species in SiO2 responsible for RTS has been identified through time-domain measurements and extensive analysis using four trap characteristics at the same time.

Does the use of the revised psychosocial assessment tool (PATrev) result in improved quality of life and reduced psychosocial risk in Canadian families with a child newly diagnosed with cancer?

PubMed

Barrera, M; Hancock, K; Rokeach, A; Atenafu, E; Cataudella, D; Punnett, A; Johnston, D; Cassidy, M; Zelcer, S; Silva, M; Jansen, P; Bartels, U; Nathan, P C; Shama, W; Greenberg, C

2014-02-01

Early psychosocial screening may guide interventions and ameliorate the adverse psychosocial effects of childhood cancer. The revised psychosocial assessment tool provides risk information - Universal (typical distress), Targeted (additional specific distress), and Clinical (severe distress) - about the child with cancer and his or her family. This pilot study investigated the benefits of providing a summary of family psychosocial risk information to the medical team treating the newly diagnosed child (Experimental Group, EG). We conducted a pilot randomized control trial with a sample of 67 parents, comparing the EG to the control group (CG) on parental perception of family psychosocial difficulties (revised psychosocial assessment tool risk levels), child behavior (behavior assessment scale for children-2), pediatric quality of life (PedsQL), and parental anxiety (state-anxiety scale of the state-trait anxiety inventory ), 2-4 weeks after diagnosis (Time 1) and 6 months later (Time 2). Compared to the CG, participants in the EG had significantly reduced targeted and clinical risk (p < 0.001), and improved pain related PedsQL at Time 2 (p < 0.05). Scores for PedsQL total and nearly all subscales improved over time in both groups (p < 0.05 to p < 0.001). No changes in behavior scores were noted. Preliminary findings suggest that providing a summary of the Psychosocial Assessment Tool to the treating team shortly after diagnosis may help reduce family wide psychosocial risk 6 months later and improve quality of life related to pain for children who are undergoing treatment for cancer. Copyright © 2013 John Wiley & Sons, Ltd.

RCrane: semi-automated RNA model building.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2012-08-01

RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

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

Ameen, Raed Fawzi Mohammed, E-mail: MohammedAmeenRF@cardiff.ac.uk; Department of Civil Engineering, College of Engineering, University of Karbala; Mourshed, Monjur, E-mail: MourshedM@cardiff.ac.uk

Cities are responsible for the depletion of natural resources and agricultural lands, and 70% of global CO{sub 2} emissions. There are significant risks to cities from the impacts of climate change in addition to existing vulnerabilities, primarily because of rapid urbanization. Urban design and development are generally considered as the instrument to shape the future of the city and they determine the pattern of a city's resource usage and resilience to change, from climate or otherwise. Cities are inherently dynamic and require the participation and engagement of their diverse stakeholders for the effective management of change, which enables wider stakeholdermore » involvement and buy-in at various stages of the development process. Sustainability assessment of urban design and development is increasingly being seen as indispensable for informed decision-making. A sustainability assessment tool also acts as a driver for the uptake of sustainable pathways by recognizing excellence through their rating system and by creating a market demand for sustainable products and processes. This research reviews six widely used sustainability assessment tools for urban design and development: BREEAM Communities, LEED-ND, CASBEE-UD, SBTool{sup PT}–UP, Pearl Community Rating System (PCRS) and GSAS/QSAS, to identify, compare and contrast the aim, structure, assessment methodology, scoring, weighting and suitability for application in different geographical contexts. Strengths and weaknesses of each tool are critically discussed. The study highlights the disparity in local and international contexts for global sustainability assessment tools. Despite their similarities in aim on environmental aspects, differences exist in the relative importance and share of mandatory vs optional indicators in both environmental and social dimensions. PCRS and GSAS/QSAS are new incarnations, but have widely varying shares of mandatory indicators, at 45.4% and 11.36% respectively, compared to 30% in BREEAM Community. Considerations of economic and cultural aspects are only marginal in the reviewed sustainability assessment tools. However, the newly developed sustainability assessment tools such as GSAS/QSAS and PCRS diverge from their predecessors in their consideration of cultural aspects. - Highlights: • Reviews six urban sustainability assessment methods: LEED-ND, BREEAM Communities, CASBEE-UD, SBTool{sup PT}-UP, PCRS, GSAS/QSAS. • Reviewed methods are biased more towards the environmental, followed by social and economic dimensions of sustainability. • Water issues are highlighted in the Middle East but natural hazards are emphasized only in CASBEE and BREEAM Communities. • SBTool{sup PT}-UP, the most recent of the groups puts more weight (7.32%) on cultural aspects. • Share of mandatory indicators is highest (45.4%) in the Pearl Community Rating System (PCRS)« less

Measuring critical thinking in pre-registration midwifery students: A multi-method approach.

PubMed

Carter, Amanda G; Creedy, Debra K; Sidebotham, Mary

2018-02-01

Test the concurrent validity of three newly developed tools (student self-rating, preceptor rating, and reflective writing) that aim to measure critical thinking in midwifery practice. A descriptive matched cohort design was used. Australian research intensive university offering a three year Bachelor of Midwifery programme. Fifty-five undergraduate midwifery students. Students assessed their ability to apply critical thinking in midwifery practice using a 25-item tool and a 5-item subscale in Motivated Strategies for Learning Questionnaire. Clinical preceptors completed a 24-item tool assessing the students' application of critical thinking in practice. Reflective writing by students was assessed by midwifery academics using a 15-item tool. Internal reliability, and concurrent validity were assessed. Correlations, t-tests, multiple regression and confidence levels were calculated for the three scales and associations with student characteristics. The three scales achieved good internal reliability with a Cronbach's alpha coefficient between 0.93 and 0.97. Matched total scores for the three critical thinking scales were moderately correlated; student/preceptor (r=0.36, p<0.01); student/reflective writing (r=0.38, p<0.01); preceptor/reflective writing (r=0.30, p<0.05). All critical thinking mean scores were higher for students with a previous degree, but only significant for reflective writing (t (53)=-2.35, p=0.023). Preceptor ratings were predictive of GPA (beta=0.50, p<0.001, CI=0.10 to 0.30). Students' self-rating scores were predictive of year level (beta=0.32, p<0.05, CI=0.00 to 0.03). The student, preceptor, and reflective writing tools were found to be reliable and valid measures of critical thinking. The three tools can be used individually or in combination to provide students with various sources of feedback to improve their practice. The tools allow formative measurement of critical thinking over time. Further testing of the tools with larger, diverse samples is recommended. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Creating a school nutrition environment index and pilot testing it in elementary and middle schools in urban South Korea

PubMed Central

Kwon, Kwang-il; Kweon, Soon Ju; Wang, Youfa; Gittelsohn, Joel

2017-01-01

BACKGROUND/OBJECTIVES The role of a school's nutrition environment in explaining students' eating behaviors and weight status has not been examined in an Asian setting. The purpose of this study was to create a school nutrition environment index and to pilot test the index in elementary and middle schools in urban South Korea. SUBJECTS/METHODS This study used a mixed-methods approach. Environment assessment tools were developed based on formative research, which comprised literature reviews, in-depth interviews, and focus group discussions. Key elements from the formative research were included in the assessment tool, which consisted of a structured survey questionnaire for school dietitians. Fifteen school dietitians from 7 elementary and 8 middle schools in Seoul completed the questionnaire. RESULTS The formative research revealed four main sections that guided a summary index to assess a school's nutrition environment: resource availability, education and programs, dietitians' perceptions and characteristics, and school lunch menu. Based on the literature reviews and interviews, an index scoring system was developed. The total possible score from the combined four index sections was 40 points. From the 15 schools participating in the pilot survey, the mean school nutrition-environment index was 22.5 (standard deviation ± 3.2; range 17-28). The majority of the schools did not offer classroom-based nutrition education or nutrition counseling for students and parents. The popular modes of nutrition education were school websites, posters, and newsletters. CONCLUSIONS This paper illustrates the process used to develop an instrument to assess a school's nutrition environment. Moreover, it presents the steps used to develop a scoring system for creation of a school nutrition environment index. As pilot testing indicated the total index score has some variation across schools, we suggest applying this instrument in future studies involving a larger number of schools. Future studies with larger samples will allow investigation of the validity and reliability of this newly developed tool. PMID:28989577

Creating a school nutrition environment index and pilot testing it in elementary and middle schools in urban South Korea.

PubMed

Park, Sohyun; Kwon, Kwang-Il; Kweon, Soon Ju; Wang, Youfa; Gittelsohn, Joel

2017-10-01

The role of a school's nutrition environment in explaining students' eating behaviors and weight status has not been examined in an Asian setting. The purpose of this study was to create a school nutrition environment index and to pilot test the index in elementary and middle schools in urban South Korea. This study used a mixed-methods approach. Environment assessment tools were developed based on formative research, which comprised literature reviews, in-depth interviews, and focus group discussions. Key elements from the formative research were included in the assessment tool, which consisted of a structured survey questionnaire for school dietitians. Fifteen school dietitians from 7 elementary and 8 middle schools in Seoul completed the questionnaire. The formative research revealed four main sections that guided a summary index to assess a school's nutrition environment: resource availability, education and programs, dietitians' perceptions and characteristics, and school lunch menu. Based on the literature reviews and interviews, an index scoring system was developed. The total possible score from the combined four index sections was 40 points. From the 15 schools participating in the pilot survey, the mean school nutrition-environment index was 22.5 (standard deviation ± 3.2; range 17-28). The majority of the schools did not offer classroom-based nutrition education or nutrition counseling for students and parents. The popular modes of nutrition education were school websites, posters, and newsletters. This paper illustrates the process used to develop an instrument to assess a school's nutrition environment. Moreover, it presents the steps used to develop a scoring system for creation of a school nutrition environment index. As pilot testing indicated the total index score has some variation across schools, we suggest applying this instrument in future studies involving a larger number of schools. Future studies with larger samples will allow investigation of the validity and reliability of this newly developed tool.

Development of the Lupus Interactive Navigator as an Empowering Web-Based eHealth Tool to Facilitate Lupus Management: Users Perspectives on Usability and Acceptability.

PubMed

Neville, Carolyn; Da Costa, Deborah; Rochon, Murray; Peschken, Christine A; Pineau, Christian A; Bernatsky, Sasha; Keeling, Stephanie; Avina-Zubieta, Antonio; Lye, Elizabeth; Eng, Davy; Fortin, Paul R

2016-05-30

Systemic Lupus Erythematosus (SLE) is a serious, complex, and chronic illness. Similar to most other chronic illness states, there is great interest in helping persons with SLE engage in their disease management. The objectives of this study were to (1) develop the Lupus Interactive Navigator (LIN), a web-based self-management program for persons with SLE, and (2) test the LIN for usability and acceptability. The LIN development platform was based on the results of preliminary comprehensive needs assessments and adapted from the Oncology Interactive Navigator, a web-based tool developed for persons with cancer. Medical researchers, writers, designers, and programmers worked with clinical experts and persons with SLE to develop content for the LIN. Usability and acceptability of the LIN was tested on individuals with SLE meeting American College of Rheumatology criteria, who were recruited from five Canadian SLE clinics. Participants were provided with access to the LIN and were asked to use it over a two-week period. Following the testing period, participants were contacted for a 30-minute telephone interview to assess usability and acceptability. The content for the LIN was subdivided into six primary information topics with interview videos featuring rheumatologists, allied health professionals, and persons with SLE. Usability and acceptability of the LIN was tested on 43 females with SLE. Of these, 37 (86%) completed telephone interviews. The average age was 43.6 (SD 15.9) years and disease duration averaged 14.1 (SD 10.8) years. Median time spent on LIN was 16.3 (interquartile range [IQR]:13.7, 53.5) minutes and median number of sessions was 2 (IQR: 1, 3). Overall, Likert ratings (0=strongly disagree; 7=strongly agree) of website usability and content were very high, with 75% scoring >6 out of 7 on all items. All participants agreed that LIN was easy to use, would recommend it to others with SLE, and would refer to it for future questions about SLE. Very high ratings were also given to relevancy, credibility, and usefulness of the information provided. Overall, 73% of the participants rated all topics helpful to very helpful. Participants who reported more prior knowledge about SLE rated items regarding improvement in knowledge and helpfulness relatively lower than persons with less prior knowledge. Most participants commented that the LIN would be very useful to those newly diagnosed with SLE. Minor revisions were recommended. This study furthers the understanding of the needs in the SLE community and delivers a unique eHealth tool to promote self-management in persons with SLE. The LIN was found to be highly acceptable in content and usability. The information provided on LIN may be most helpful for individuals with less experience with the disease, such as those newly diagnosed, indicating the need to tailor the content for persons with more SLE experience.

REM sleep selectively prunes and maintains new synapses in development and learning.

PubMed

Li, Wei; Ma, Lei; Yang, Guang; Gan, Wen-Biao

2017-03-01

The functions and underlying mechanisms of rapid eye movement (REM) sleep remain unclear. Here we show that REM sleep prunes newly formed postsynaptic dendritic spines of layer 5 pyramidal neurons in the mouse motor cortex during development and motor learning. This REM sleep-dependent elimination of new spines facilitates subsequent spine formation during development and when a new motor task is learned, indicating a role for REM sleep in pruning to balance the number of new spines formed over time. Moreover, REM sleep also strengthens and maintains newly formed spines, which are critical for neuronal circuit development and behavioral improvement after learning. We further show that dendritic calcium spikes arising during REM sleep are important for pruning and strengthening new spines. Together, these findings indicate that REM sleep has multifaceted functions in brain development, learning and memory consolidation by selectively eliminating and maintaining newly formed synapses via dendritic calcium spike-dependent mechanisms.

Adaptive evolution of the Hox gene family for development in bats and dolphins.

PubMed

Liang, Lu; Shen, Yong-Yi; Pan, Xiao-Wei; Zhou, Tai-Cheng; Yang, Chao; Irwin, David M; Zhang, Ya-Ping

2013-01-01

Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation.

Adaptive Evolution of the Hox Gene Family for Development in Bats and Dolphins

PubMed Central

Pan, Xiao-Wei; Zhou, Tai-Cheng; Yang, Chao; Irwin, David M.; Zhang, Ya-Ping

2013-01-01

Bats and cetaceans (i.e., whales, dolphins, porpoises) are two kinds of mammals with unique locomotive styles and occupy novel niches. Bats are the only mammals capable of sustained flight in the sky, while cetaceans have returned to the aquatic environment and are specialized for swimming. Associated with these novel adaptations to their environment, various development changes have occurred to their body plans and associated structures. Given the importance of Hox genes in many aspects of embryonic development, we conducted an analysis of the coding regions of all Hox gene family members from bats (represented by Pteropus vampyrus, Pteropus alecto, Myotis lucifugus and Myotis davidii) and cetaceans (represented by Tursiops truncatus) for adaptive evolution using the available draft genome sequences. Differences in the selective pressures acting on many Hox genes in bats and cetaceans were found compared to other mammals. Positive selection, however, was not found to act on any of the Hox genes in the common ancestor of bats and only upon Hoxb9 in cetaceans. PCR amplification data from additional bat and cetacean species, and application of the branch-site test 2, showed that the Hoxb2 gene within bats had significant evidence of positive selection. Thus, our study, with genomic and newly sequenced Hox genes, identifies two candidate Hox genes that may be closely linked with developmental changes in bats and cetaceans, such as those associated with the pancreatic, neuronal, thymus shape and forelimb. In addition, the difference in our results from the genome-wide scan and newly sequenced data reveals that great care must be taken in interpreting results from draft genome data from a limited number of species, and deep genetic sampling of a particular clade is a powerful tool for generating complementary data to address this limitation. PMID:23825528

Evaluation of inapparent nosocomial severe acute respiratory syndrome coronavirus infection in Vietnam by use of highly specific recombinant truncated nucleocapsid protein-based enzyme-linked immunosorbent assay.

PubMed

Yu, Fuxun; Le, Mai Quynh; Inoue, Shingo; Thai, Hong Thi Cam; Hasebe, Futoshi; Del Carmen Parquet, Maria; Morita, Kouichi

2005-07-01

Severe acute respiratory syndrome (SARS) is a recently emerged human disease associated with pneumonia. Inapparent infection with SARS coronavirus (CoV) is not well characterized. To develop a safe, simple, and reliable screening method for SARS diagnosis and epidemiological study, two recombinant SARS-CoV nucleocapsid proteins (N' protein and (N)Delta(121) protein) were expressed in Escherichia coli, purified by affinity chromatography, and used as antigens for indirect, immunoglobulin G enzyme-linked immunosorbent assays (ELISA). Serum samples collected from healthy volunteers and SARS patients in Vietnam were used to evaluate the newly developed methods. The N' protein-based ELISA showed a highly nonspecific reaction. The (N)Delta(121) protein-based ELISA, with a nonspecific reaction drastically reduced compared to that of the nearly-whole-length N' protein-based ELISA, resulted in higher rates of positive reactions, higher titers, and earlier detection than the SARS-CoV-infected cell lysate-based ELISA. These results indicate that our newly developed SARS-CoV (N)Delta(121) protein-based ELISA is not only safe but also a more specific and more sensitive method to diagnose SARS-CoV infection and hence a useful tool for large-scale epidemiological studies. To identify inapparent SARS-CoV infections, serum samples collected from health care workers (HCWs) in Vietnam were screened by the (N)Delta(121) protein-based ELISA, and positive samples were confirmed by a virus neutralization test. Four out of 149 HCWs were identified to have inapparent SARS-CoV infection in Vietnam, indicating that subclinical SARS-CoV infection in Vietnam is rare but does exist.

Evaluation of Inapparent Nosocomial Severe Acute Respiratory Syndrome Coronavirus Infection in Vietnam by Use of Highly Specific Recombinant Truncated Nucleocapsid Protein-Based Enzyme-Linked Immunosorbent Assay

PubMed Central

Yu, Fuxun; Le, Mai Quynh; Inoue, Shingo; Thai, Hong Thi Cam; Hasebe, Futoshi; del Carmen Parquet, Maria; Morita, Kouichi

2005-01-01

Severe acute respiratory syndrome (SARS) is a recently emerged human disease associated with pneumonia. Inapparent infection with SARS coronavirus (CoV) is not well characterized. To develop a safe, simple, and reliable screening method for SARS diagnosis and epidemiological study, two recombinant SARS-CoV nucleocapsid proteins (N′ protein and NΔ121 protein) were expressed in Escherichia coli, purified by affinity chromatography, and used as antigens for indirect, immunoglobulin G enzyme-linked immunosorbent assays (ELISA). Serum samples collected from healthy volunteers and SARS patients in Vietnam were used to evaluate the newly developed methods. The N′ protein-based ELISA showed a highly nonspecific reaction. The NΔ121 protein-based ELISA, with a nonspecific reaction drastically reduced compared to that of the nearly-whole-length N′ protein-based ELISA, resulted in higher rates of positive reactions, higher titers, and earlier detection than the SARS-CoV-infected cell lysate-based ELISA. These results indicate that our newly developed SARS-CoV NΔ121 protein-based ELISA is not only safe but also a more specific and more sensitive method to diagnose SARS-CoV infection and hence a useful tool for large-scale epidemiological studies. To identify inapparent SARS-CoV infections, serum samples collected from health care workers (HCWs) in Vietnam were screened by the NΔ121 protein-based ELISA, and positive samples were confirmed by a virus neutralization test. Four out of 149 HCWs were identified to have inapparent SARS-CoV infection in Vietnam, indicating that subclinical SARS-CoV infection in Vietnam is rare but does exist. PMID:16002634

Application of newly developed Fluoro-QC software for image quality evaluation in cardiac X-ray systems.

PubMed

Oliveira, M; Lopez, G; Geambastiani, P; Ubeda, C

2018-05-01

A quality assurance (QA) program is a valuable tool for the continuous production of optimal quality images. The aim of this paper is to assess a newly developed automatic computer software for image quality (IR) evaluation in fluoroscopy X-ray systems. Test object images were acquired using one fluoroscopy system, Siemens Axiom Artis model (Siemens AG, Medical Solutions Erlangen, Germany). The software was developed as an ImageJ plugin. Two image quality parameters were assessed: high-contrast spatial resolution (HCSR) and signal-to-noise ratio (SNR). The time between manual and automatic image quality assessment procedures were compared. The paired t-test was used to assess the data. p Values of less than 0.05 were considered significant. The Fluoro-QC software generated faster IQ evaluation results (mean = 0.31 ± 0.08 min) than manual procedure (mean = 4.68 ± 0.09 min). The mean difference between techniques was 4.36 min. Discrepancies were identified in the region of interest (ROI) areas drawn manually with evidence of user dependence. The new software presented the results of two tests (HCSR = 3.06, SNR = 5.17) and also collected information from the DICOM header. Significant differences were not identified between manual and automatic measures of SNR (p value = 0.22) and HCRS (p value = 0.46). The Fluoro-QC software is a feasible, fast and free to use method for evaluating imaging quality parameters on fluoroscopy systems. Copyright © 2017 The College of Radiographers. Published by Elsevier Ltd. All rights reserved.

A New Flow-Diverter (the FloWise): In-Vivo Evaluation in an Elastase-Induced Rabbit Aneurysm Model.

PubMed

Kim, Byung Moon; Kim, Dong Joon; Kim, Dong Ik

2016-01-01

We aimed to evaluate the efficacy and safety of a newly developed, partially retrievable flow-diverter (the FloWise) in an elastase-induced rabbit aneurysm model. We developed a partially retrievable flow diverter composed of 48 strands of Nitinol and platinum wire. The FloWise is compatible with any microcatheter of 0.027-inch inner diameter, and is retrievable up to 70% deployment. The efficacy and safety of the FloWise were evaluated in the elastase-induced rabbit aneurysm model. The rate of technical success (full coverage of aneurysm neck) and assessment of aneurysm occlusion and stent patency was conducted by angiograms and histologic examinations at the 1-month, 3-month, and 6-month follow-up. The patency of small arterial branches (intercostal or lumbar arteries) covered by the FloWise were also assessed in the 5 subjects. We attempted FloWise insertion in a total of 32 aneurysm models. FloWise placement was successful in 31 subjects (96.9%). Two stents (6.2%) were occluded at the 3-month follow-up, but there was no evidence of in-stent stenosis in other subjects. All stented aneurysms showed progressive occlusion: grade I (complete aneurysm occlusion) in 44.4% and grade II (aneurysm occlusion > 90%) in 55.6% at 1 month; grade I in 90% and II in 10% at 3 months; and grade I in 90% and II in 10% at 6 months. All small arterial branches covered by the FloWise remained patent. A newly developed, partially retrievable flow-diverter seems to be a safe and effective tool of aneurysm occlusion, as evaluated in the rabbit aneurysm model.

The Distress Thermometer for screening for severe fatigue in newly diagnosed breast and colorectal cancer patients.

PubMed

Abrahams, H J G; Gielissen, M F M; de Lugt, M; Kleijer, E F W; de Roos, W K; Balk, E; Verhagen, C A H H V M; Knoop, H

2017-05-01

Internationally, the Distress Thermometer and associated Problem List are increasingly used in oncology as screening tools for psychological distress. Cancer-related fatigue is common but often overlooked in clinical practice. We examined if severe fatigue in cancer patients can be identified with the fatigue item of the Problem List. Newly diagnosed breast (N = 334) and colorectal (N = 179) cancer patients were screened for severe fatigue, which was defined as having a positive score on the fatigue item of the Problem List. The Fatigue Severity subscale of the Checklist Individual Strength was used as gold standard measure for severe fatigue. In total, 78% of breast cancer patients and 81% of colorectal cancer patients were correctly identified with the fatigue item. The sensitivity was 89% in breast cancer patients and 91% in colorectal cancer patients. The specificity was 75% in breast cancer patients and 77% in colorectal cancer patients. The positive predictive value was 53% in breast cancer patients and 64% in colorectal cancer patients, whereas the negative predictive value was 95% in both tumor types. The fatigue item of the Problem List performs satisfactorily as a quick screening tool for severe fatigue. However, a positive screen should be followed up with a more thorough assessment of fatigue, ie, a questionnaire with a validated cutoff point. Given time pressure of clinicians, this already implemented and brief screening tool may prevent severe fatigue from going undetected in clinical practice. Copyright © 2016 John Wiley & Sons, Ltd.

Enhanced development of a catalyst chamber for the decomposition of up to 1.0 kg/s hydrogen peroxide

NASA Astrophysics Data System (ADS)

Božić, Ognjan; Porrmann, Dennis; Lancelle, Daniel; May, Stefan

2016-06-01

A new innovative hybrid rocket engine concept is developed within the AHRES program of the German Aerospace Center (DLR). This rocket engine based on hydroxyl-terminated polybutadiene (HTPB) with metallic additives as solid fuel and high test peroxide (HTP) as liquid oxidizer. Instead of a conventional ignition system, a catalyst chamber with a silver mesh catalyst is designed to decompose the HTP. The newly modified catalyst chamber is able to decompose up to 1.0 kg/s of 87.5 wt% HTP. Used as a monopropellant thruster, this equals an average thrust of 1600 N. The catalyst chamber is designed using the self-developed software tool SHAKIRA. The applied kinetic law, which determines catalytic decomposition of HTP within the catalyst chamber, is given and commented. Several calculations are carried out to determine the appropriate geometry for complete decomposition with a minimum of catalyst material. A number of tests under steady state conditions are carried out, using 87.5 wt% HTP with different flow rates and a constant amount of catalyst material. To verify the decomposition, the temperature is measured and compared with the theoretical prediction. The experimental results show good agreement with the results generated by the design tool. The developed catalyst chamber provides a simple, reliable ignition system for hybrid rocket propulsion systems based on hydrogen peroxide as oxidizer. This system is capable for multiple reignition. The developed hardware and software can be used to design full scale monopropellant thrusters based on HTP and catalyst chambers for hybrid rocket engines.

The Earthquake Source Inversion Validation (SIV) - Project: Summary, Status, Outlook

NASA Astrophysics Data System (ADS)

Mai, P. M.

2017-12-01

Finite-fault earthquake source inversions infer the (time-dependent) displacement on the rupture surface from geophysical data. The resulting earthquake source models document the complexity of the rupture process. However, this kinematic source inversion is ill-posed and returns non-unique solutions, as seen for instance in multiple source models for the same earthquake, obtained by different research teams, that often exhibit remarkable dissimilarities. To address the uncertainties in earthquake-source inversions and to understand strengths and weaknesses of various methods, the Source Inversion Validation (SIV) project developed a set of forward-modeling exercises and inversion benchmarks. Several research teams then use these validation exercises to test their codes and methods, but also to develop and benchmark new approaches. In this presentation I will summarize the SIV strategy, the existing benchmark exercises and corresponding results. Using various waveform-misfit criteria and newly developed statistical comparison tools to quantify source-model (dis)similarities, the SIV platforms is able to rank solutions and identify particularly promising source inversion approaches. Existing SIV exercises (with related data and descriptions) and all computational tools remain available via the open online collaboration platform; additional exercises and benchmark tests will be uploaded once they are fully developed. I encourage source modelers to use the SIV benchmarks for developing and testing new methods. The SIV efforts have already led to several promising new techniques for tackling the earthquake-source imaging problem. I expect that future SIV benchmarks will provide further innovations and insights into earthquake source kinematics that will ultimately help to better understand the dynamics of the rupture process.

PTMscape: an open source tool to predict generic post-translational modifications and map modification crosstalk in protein domains and biological processes.

PubMed

Li, Ginny X H; Vogel, Christine; Choi, Hyungwon

2018-06-07

While tandem mass spectrometry can detect post-translational modifications (PTM) at the proteome scale, reported PTM sites are often incomplete and include false positives. Computational approaches can complement these datasets by additional predictions, but most available tools use prediction models pre-trained for single PTM type by the developers and it remains a difficult task to perform large-scale batch prediction for multiple PTMs with flexible user control, including the choice of training data. We developed an R package called PTMscape which predicts PTM sites across the proteome based on a unified and comprehensive set of descriptors of the physico-chemical microenvironment of modified sites, with additional downstream analysis modules to test enrichment of individual or pairs of PTMs in protein domains. PTMscape is flexible in the ability to process any major modifications, such as phosphorylation and ubiquitination, while achieving the sensitivity and specificity comparable to single-PTM methods and outperforming other multi-PTM tools. Applying this framework, we expanded proteome-wide coverage of five major PTMs affecting different residues by prediction, especially for lysine and arginine modifications. Using a combination of experimentally acquired sites (PSP) and newly predicted sites, we discovered that the crosstalk among multiple PTMs occur more frequently than by random chance in key protein domains such as histone, protein kinase, and RNA recognition motifs, spanning various biological processes such as RNA processing, DNA damage response, signal transduction, and regulation of cell cycle. These results provide a proteome-scale analysis of crosstalk among major PTMs and can be easily extended to other types of PTM.

Identifying key components for an effective case report poster: an observational study.

PubMed

Willett, Lisa L; Paranjape, Anuradha; Estrada, Carlos

2009-03-01

Residents demonstrate scholarly activity by presenting posters at academic meetings. Although recommendations from national organizations are available, evidence identifying which components are most important is not. To develop and test an evaluation tool to measure the quality of case report posters and identify the specific components most in need of improvement. Faculty evaluators reviewed case report posters and provided on-site feedback to presenters at poster sessions of four annual academic general internal medicine meetings. A newly developed ten-item evaluation form measured poster quality for specific components of content, discussion, and format (5-point Likert scale, 1 = lowest, 5 = highest). Evaluation tool performance, including Cronbach alpha and inter-rater reliability, overall poster scores, differences across meetings and evaluators and specific components of the posters most in need of improvement. Forty-five evaluators from 20 medical institutions reviewed 347 posters. Cronbach's alpha of the evaluation form was 0.84 and inter-rater reliability, Spearman's rho 0.49 (p < 0.001). The median score was 4.1 (Q1 -Q3, 3.7-4.6)(Q1 = 25th, Q3 = 75th percentile). The national meeting median score was higher than the regional meetings (4.4 vs, 4.0, P < 0.001). We found no difference in faculty scores. The following areas were identified as most needing improvement: clearly state learning objectives, tie conclusions to learning objectives, and use appropriate amount of words. Our evaluation tool provides empirical data to guide trainees as they prepare posters for presentation which may improve poster quality and enhance their scholarly productivity.

MVIAeval: a web tool for comprehensively evaluating the performance of a new missing value imputation algorithm.

PubMed

Wu, Wei-Sheng; Jhou, Meng-Jhun

2017-01-13

Missing value imputation is important for microarray data analyses because microarray data with missing values would significantly degrade the performance of the downstream analyses. Although many microarray missing value imputation algorithms have been developed, an objective and comprehensive performance comparison framework is still lacking. To solve this problem, we previously proposed a framework which can perform a comprehensive performance comparison of different existing algorithms. Also the performance of a new algorithm can be evaluated by our performance comparison framework. However, constructing our framework is not an easy task for the interested researchers. To save researchers' time and efforts, here we present an easy-to-use web tool named MVIAeval (Missing Value Imputation Algorithm evaluator) which implements our performance comparison framework. MVIAeval provides a user-friendly interface allowing users to upload the R code of their new algorithm and select (i) the test datasets among 20 benchmark microarray (time series and non-time series) datasets, (ii) the compared algorithms among 12 existing algorithms, (iii) the performance indices from three existing ones, (iv) the comprehensive performance scores from two possible choices, and (v) the number of simulation runs. The comprehensive performance comparison results are then generated and shown as both figures and tables. MVIAeval is a useful tool for researchers to easily conduct a comprehensive and objective performance evaluation of their newly developed missing value imputation algorithm for microarray data or any data which can be represented as a matrix form (e.g. NGS data or proteomics data). Thus, MVIAeval will greatly expedite the progress in the research of missing value imputation algorithms.

Soft, flexible micromanipulators comprising polypyrrole trilayer microactuators

NASA Astrophysics Data System (ADS)

Khaldi, Alexandre; Maziz, Ali; Alici, Gursel; Spinks, Geoffrey M.; Jager, Edwin W. H.

2015-04-01

Within the areas of cell biology, biomedicine and minimal invasive surgery, there is a need for soft, flexible and dextrous biocompatible manipulators for handling biological objects, such as single cells and tissues. Present day technologies are based on simple suction using micropipettes for grasping objects. The micropipettes lack the possibility of accurate force control, nor are they soft and compliant and may thus cause damage to the cells or tissue. Other micromanipulators use conventional electric motors however the further miniaturization of electrical motors and their associated gear boxes and/or push/pull wires has reached its limits. Therefore there is an urgent need for new technologies for micromanipulation of soft biological matter. We are developing soft, flexible micromanipulators such as micro- tweezers for the handling and manipulation of biological species including cells and surgical tools for minimal invasive surgery. Our aim is to produce tools with minimal dimensions of 100 μm to 1 mm in size, which is 1-2 orders of magnitude smaller than existing technology. We present newly developed patterning and microfabrication methods for polymer microactuators as well as the latest results to integrate these microactuators into easy to use manipulation tools. The outcomes of this study contribute to the realisation of low-foot print devices articulated with electroactive polymer actuators for which the physical interface with the power source has been a significant challenge limiting their application. Here, we present a new bottom-up microfabrication process. We show for the first time that such a bottom-up fabricated actuator performs a movement in air. This is a significant step towards widening the application areas of the soft microactuators.

Microgrid Utilities for Rural Electrification in East Africa: Challenges and Opportunities

NASA Astrophysics Data System (ADS)

Williams, Nathaniel J.

Expanding access to electricity is central to development in East Africa but massive increases in investment are required to achieve universal access. Private sector participation in electrification is essential to meeting electricity access targets. Policy makers have acknowledged that grid extension in many remote rural areas is not as cost effective as decentralized alternatives such as microgrids. Microgrid companies have been unable to scale beyond pilot projects due in part to challenges in raising capital for a business model that is perceived to be risky. This thesis aims to identify and quantify the primary sources of investment risk in microgrid utilities and study ways to mitigate these risks to make these businesses more viable. Two modeling tools have been developed to this end. The Stochastic Techno-Economic Microgrid Model (STEMM) models the technical and financial performance of microgrid utilities using uncertain and dynamic inputs to permit explicit modeling of financial risk. This model is applied in an investment risk assessment and case study in Rwanda. Key findings suggest that the most important drivers of risk are fuel prices, foreign exchange rates, demand for electricity, and price elasticity of demand for electricity. The relative importance of these factors is technology dependent with demand uncertainty figuring stronger for solar and high solar penetration hybrid systems and fuel prices driving risk in diesel power and low solar penetration hybrid systems. Considering uncertainty in system sizing presents a tradeoff whereby a decrease in expected equity return decreases downside risk. High solar penetration systems are also found to be more attractive to lenders. The second modeling tool leverages electricity consumption and demographic data from four microgrids in Tanzania to forecast demand for electricity in newly electrified communities. Using statistical learning techniques, improvements in prediction performance was achieved over the historical mean baseline. I have also identified important predictors in estimating electricity consumption of newly connected customers. These include tariff structures and prices, pre- connection sources of electricity and lighting, levels of spending on electricity services and airtime, and pre-connection appliance ownership. Prior exposure to electricity, disposable income, and price are dominant factors in estimating demand.

6 CFR 7.26 - Derivative classification.

Code of Federal Regulations, 2011 CFR

2011-01-01

... already classified, and marking the newly developed material consistent with the classification markings... classification decisions and carry forward to any newly created documents the pertinent classification markings. (d) Information classified derivatively from other classified information shall be classified and...

The experience of learning to speak up: a narrative inquiry on newly graduated registered nurses.

PubMed

Law, Bernice Yee-Shui; Chan, Engle Angela

2015-07-01

To explore the process of learning to speak up in practice among newly graduated registered nurses. Speaking up is an important aspect of communication to ensure patient safety within a healthcare team. However, nurses have reported being hesitant about speaking up or being unable to be heard, despite adopting various safety tools. A power differential could be a factor in their hesitation to speak up. While a large number of new graduates are employed in the lower rungs of the hospital hierarchy to resolve local and global nursing shortages, the process of their learning to speak up remains under-explored. The narrative concept of experience is addressed through the three-dimensional space of a narrative inquiry. Eighteen new graduates were recruited. Stories of experiences of speaking up emerged naturally during repeated unstructured interviews and ongoing email conversations with three participants. The complex process of learning to speak up is schematically represented. Three interrelated narrative threads were identified: (1) learning to speak up requires more than one-off training and safety tools, (2) mentoring speaking up in the midst of educative and miseducative experiences and (3) making public spaces safe for telling secret stories. Speaking up requires ongoing mentoring to see new possibilities for sustaining professional identities in the midst of miseducative experiences under the potential shaping of the Chinese culture and generational differences. Appreciative inquiry might be a new approach that can be used to promote positive cultural changes to encourage newly graduated registered nurses to learn to speak up to ensure patient safety. Cultivating a safe and open culture of communication and mentoring new graduates to speak up will benefit patient safety now and in the future by helping to retain committed patient advocates who could mentor future generations. © 2015 John Wiley & Sons Ltd.

Estimation of basal metabolic rate in Chinese: are the current prediction equations applicable?

PubMed

Camps, Stefan G; Wang, Nan Xin; Tan, Wei Shuan Kimberly; Henry, C Jeyakumar

2016-08-31

Measurement of basal metabolic rate (BMR) is suggested as a tool to estimate energy requirements. Therefore, BMR prediction equations have been developed in multiple populations because indirect calorimetry is not always feasible. However, there is a paucity of data on BMR measured in overweight and obese adults living in Asia and equations developed for this group of interest. The aim of this study was to develop a new BMR prediction equation for Chinese adults applicable for a large BMI range and compare it with commonly used prediction equations. Subjects were 121 men and 111 women (age: 21-67 years, BMI: 16-41 kg/m(2)). Height, weight, and BMR were measured. Continuous open-circuit indirect calorimetry using a ventilated hood system for 30 min was used to measure BMR. A regression equation was derived using stepwise regression and accuracy was compared to 6 existing equations (Harris-Benedict, Henry, Liu, Yang, Owen and Mifflin). Additionally, the newly derived equation was cross-validated in a separate group of 70 Chinese subjects (26 men and 44 women, age: 21-69 years, BMI: 17-39 kg/m(2)). The equation developed from our data was: BMR (kJ/d) = 52.6 x weight (kg) + 828 x gender + 1960 (women = 0, men = 1; R(2) = 0.81). The accuracy rate (within 10 % accurate) was 78 % which compared well to Owen (70 %), Henry (67 %), Mifflin (67 %), Liu (58 %), Harris-Benedict (45 %) and Yang (37 %) for the whole range of BMI. For a BMI greater than 23, the Singapore equation reached an accuracy rate of 76 %. Cross-validation proved an accuracy rate of 80 %. To date, the newly developed Singapore equation is the most accurate BMR prediction equation in Chinese and is applicable for use in a large BMI range including those overweight and obese.

'Doing the writing' and 'working in parallel': how 'distal nursing' affects delegation and supervision in the emerging role of the newly qualified nurse.

PubMed

Johnson, Martin; Magnusson, Carin; Allan, Helen; Evans, Karen; Ball, Elaine; Horton, Khim; Curtis, Kathy; Westwood, Sue

2015-02-01

The role of the acute hospital nurse has moved away from the direct delivery of patient care and more towards the management of the delivery of bedside care by healthcare assistants. How newly qualified nurses delegate to and supervise healthcare assistants is important as failures can lead to care being missed, duplicated and/or incorrectly performed. The data described here form part of a wider study which explored how newly qualified nurses recontextualise knowledge into practice, and develop and apply effective delegation and supervision skills. This article analyses team working between newly qualified nurses and healthcare assistants, and nurses' balancing of administrative tasks with bedside care. Ethnographic case studies were undertaken in three hospital sites in England, using a mixed methods approach involving: participant observations; interviews with 33 newly qualified nurses, 10 healthcare assistants and 12 ward managers. Data were analysed using thematic analysis, aided by the qualitative software NVivo. Multiple demands upon the newly qualified nurses' time, particularly the pressures to maintain records, can influence how effectively they delegate to, and supervise, healthcare assistants. While some nurses and healthcare assistants work successfully together, others work 'in parallel' rather than as an efficient team. While some ward cultures and individual working styles promote effective team working, others lead to less efficient collaboration between newly qualified nurses and healthcare assistants. In particular the need for qualified nurses to maintain records can create a gap between them, and between nurses and patients. Newly qualified nurses require more assistance in managing their own time and developing successful working relationships with healthcare assistants. Copyright © 2014 Elsevier Ltd. All rights reserved.

Virtual Reality: An Emerging Tool to Treat Pain

DTIC Science & Technology

2010-04-01

burn patients, physical therapy stretching of the newly healing skin helps to counteract the healing skin’s natural contraction as it scars...room, and substitute more calming music and sound effects. The patient interacts with the virtual world, throwing snowballs at objects in the virtual...care (Hoffman, Patterson et al, 2008) and physical therapy (Hoffman, Patterson, Carrougher, 2000; Hoffman, Patterson, Carrougher, Sharar, 2001; Sharar

Self-Perception of Readiness to Learn and Self-Efficacy among Nursing Students in an Online Baccalaureate (BSN) Program

ERIC Educational Resources Information Center

Cadet, Myriam Jean

2016-01-01

This study investigated the relationship between readiness to learn and self-efficacy among newly enrolled BSN students in an online program. A sample of 27 students completed the 45-item Test of Online Learning Success (ToOLS) and 10-item General Self Efficacy (GSE) scales via Survey Monkey. Knowles' (1980) adult learning theory and Bandura's…

Social Support to Empower Parents (STEP): an intervention for parents of young children newly diagnosed with type 1 diabetes.

PubMed

Sullivan-Bolyai, Susan; Bova, Carol; Leung, Katherine; Trudeau, Allison; Lee, Mary; Gruppuso, Philip

2010-01-01

The purpose of this study was to test the efficacy of a social support intervention with parents of children <13 years old newly diagnosed with type 1 diabetes mellitus (T1DM). For this randomized, controlled clinical trial, 10 parent mentors of children diagnosed with T1DM >or=1 year and 60 parent participants were recruited from 2 pediatric diabetes centers. Mentors were trained to provide social support (home visits and phone calls) for 12 months to families in the experimental arm (32 mothers). Control group parents (28 mothers) received the phone number of an experienced parent (not trained to give social support) to call as needed. Findings Mothers in the experimental and control arms differed at baseline only in birth order of the child with T1DM. The 2 groups did not differ significantly at 3, 6, or 12 months in parent concern, confidence, worry, impact on the family, or perceived social support. Mothers in the experimental arm identified the parent mentor as someone they would seek for advice and issues regarding growth and development, sleep, eating habits, and identification of community agencies. Parent mentors consistently referred mothers to health care providers for advice on medications and treatments but helped them incorporate this advice into day-to-day management. Mothers in the experimental arm valued the mentors' help in adjusting to the diagnosis, but this value was not measured by the study instruments. Focus group research is under way to clarify the concept of parent mentor social support and to develop a social support measurement tool.

SANDPUMA: ensemble predictions of nonribosomal peptide chemistry reveal biosynthetic diversity across Actinobacteria.

PubMed

Chevrette, Marc G; Aicheler, Fabian; Kohlbacher, Oliver; Currie, Cameron R; Medema, Marnix H

2017-10-15

Nonribosomally synthesized peptides (NRPs) are natural products with widespread applications in medicine and biotechnology. Many algorithms have been developed to predict the substrate specificities of nonribosomal peptide synthetase adenylation (A) domains from DNA sequences, which enables prioritization and dereplication, and integration with other data types in discovery efforts. However, insufficient training data and a lack of clarity regarding prediction quality have impeded optimal use. Here, we introduce prediCAT, a new phylogenetics-inspired algorithm, which quantitatively estimates the degree of predictability of each A-domain. We then systematically benchmarked all algorithms on a newly gathered, independent test set of 434 A-domain sequences, showing that active-site-motif-based algorithms outperform whole-domain-based methods. Subsequently, we developed SANDPUMA, a powerful ensemble algorithm, based on newly trained versions of all high-performing algorithms, which significantly outperforms individual methods. Finally, we deployed SANDPUMA in a systematic investigation of 7635 Actinobacteria genomes, suggesting that NRP chemical diversity is much higher than previously estimated. SANDPUMA has been integrated into the widely used antiSMASH biosynthetic gene cluster analysis pipeline and is also available as an open-source, standalone tool. SANDPUMA is freely available at https://bitbucket.org/chevrm/sandpuma and as a docker image at https://hub.docker.com/r/chevrm/sandpuma/ under the GNU Public License 3 (GPL3). chevrette@wisc.edu or marnix.medema@wur.nl. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Specific Features of Dumping Syndrome after Various Types of Gastrectomy as Assessed by a Newly Developed Integrated Questionnaire, the PGSAS-45.

PubMed

Tanizawa, Yutaka; Tanabe, Kazuaki; Kawahira, Hiroshi; Fujita, Junya; Takiguchi, Nobuhiro; Takahashi, Masazumi; Ito, Yuichi; Mitsumori, Norio; Namikawa, Tsutomu; Oshio, Atsushi; Nakada, Koji

2016-01-01

Dumping syndrome is a well-known adverse outcome after gastrectomy, but the precise clinical features have not been described. The aim of this study was to examine global aspects of dumping syndrome and to explore factors affecting the intensity of dumping syndrome in a large cohort using a newly developed integrated questionnaire, the Post-Gastrectomy Syndrome Assessment Scale (PGSAS)-45. Eligible questionnaires retrieved from 2,368 patients after 6 types of gastrectomy were analyzed. The incidence, intensity and number of symptoms of early general, early abdominal and late dumping syndrome were examined across various types of gastrectomy, and clinical factors affecting the intensity of each category of dumping syndrome were identified by multiple regression analysis. Dumping syndromes occurred most frequently and strongly in patients who underwent total gastrectomy with Roux-en-Y (TGRY), followed by proximal gastrectomy (PG), distal gastrectomy with Billroth-I, distal gastrectomy with Roux-en-Y, pylorus-preserving gastrectomy (PPG) and local resection (LR), in that order. Significant positive correlations among different categories of dumping syndromes were observed. TGRY, female sex, younger age, division of the celiac branch of the vagus nerve, PG and shorter postoperative period were independently related to worse dumping syndrome. Dumping syndromes were most common after TGRY and least common after PPG and LR among the various gastrectomy procedures. Type of gastrectomy and several clinical factors were related to the intensity of dumping syndrome. PGSAS-45 could offer a useful tool for evaluating dumping syndrome after gastrectomy. © 2015 S. Karger AG, Basel.

Integrative Analysis of Omics Big Data.

PubMed

Yu, Xiang-Tian; Zeng, Tao

2018-01-01

The diversity and huge omics data take biology and biomedicine research and application into a big data era, just like that popular in human society a decade ago. They are opening a new challenge from horizontal data ensemble (e.g., the similar types of data collected from different labs or companies) to vertical data ensemble (e.g., the different types of data collected for a group of person with match information), which requires the integrative analysis in biology and biomedicine and also asks for emergent development of data integration to address the great changes from previous population-guided to newly individual-guided investigations.Data integration is an effective concept to solve the complex problem or understand the complicate system. Several benchmark studies have revealed the heterogeneity and trade-off that existed in the analysis of omics data. Integrative analysis can combine and investigate many datasets in a cost-effective reproducible way. Current integration approaches on biological data have two modes: one is "bottom-up integration" mode with follow-up manual integration, and the other one is "top-down integration" mode with follow-up in silico integration.This paper will firstly summarize the combinatory analysis approaches to give candidate protocol on biological experiment design for effectively integrative study on genomics and then survey the data fusion approaches to give helpful instruction on computational model development for biological significance detection, which have also provided newly data resources and analysis tools to support the precision medicine dependent on the big biomedical data. Finally, the problems and future directions are highlighted for integrative analysis of omics big data.

Evaluation of treatment related fear using a newly developed fear scale for children: "Fear assessment picture scale" and its association with physiological response.

PubMed

Tiwari, Nishidha; Tiwari, Shilpi; Thakur, Ruchi; Agrawal, Nikita; Shashikiran, N D; Singla, Shilpy

2015-01-01

Dental treatment is usually a poignant phenomenon for children. Projective scales are preferred over psychometric scales to recognize it, and to obtain the self-report from children. The aims were to evaluate treatment related fear using a newly developed fear scale for children, fear assessment picture scale (FAPS), and anxiety with colored version of modified facial affective scale (MFAS) - three faces along with physiologic responses (pulse rate and oxygen saturation) obtained by pulse oximeter before and during pulpectomy procedure. Total, 60 children of age 6-8 years who were visiting the dental hospital for the first time and needed pulpectomy treatment were selected. Children selected were of sound physical, physiological, and mental condition. Two projective scales were used; one to assess fear - FAPS and to assess anxiety - colored version of MFAS - three faces. These were co-related with the physiological responses (oxygen saturation and pulse rate) of children obtained by pulse oximeter before and during the pulpectomy procedure. Shapiro-Wilk test, McNemar's test, Wilcoxon signed ranks test, Kruskal-Wallis test, Mann-Whitney test were applied in the study. The physiological responses showed association with FAPS and MFAS though not significant. However, oxygen saturation with MFAS showed a significant change between "no anxiety" and "some anxiety" as quantified by Kruskal-Wallis test value 6.287, P = 0.043 (<0.05) before pulpectomy procedure. The FAPS can prove to be a pragmatic tool in spotting the fear among young children. This test is easy and fast to apply on children and reduces the chair-side time.

An electronic clinical decision support tool to assist primary care providers in cardiovascular disease risk management: development and mixed methods evaluation.

PubMed

Peiris, David P; Joshi, Rohina; Webster, Ruth J; Groenestein, Patrick; Usherwood, Tim P; Heeley, Emma; Turnbull, Fiona M; Lipman, Alexandra; Patel, Anushka A

2009-12-17

Challenges remain in translating the well-established evidence for management of cardiovascular disease (CVD) risk into clinical practice. Although electronic clinical decision support (CDS) systems are known to improve practitioner performance, their development in Australian primary health care settings is limited. Study aims were to (1) develop a valid CDS tool that assists Australian general practitioners (GPs) in global CVD risk management, and (2) preliminarily evaluate its acceptability to GPs as a point-of-care resource for both general and underserved populations. CVD risk estimation (based on Framingham algorithms) and risk-based management advice (using recommendations from six Australian guidelines) were programmed into a software package. Tool validation: Data from 137 patients attending a physician's clinic were analyzed to compare the tool's risk scores with those obtained from an independently programmed algorithm in a separate statistics package. The tool's management advice was compared with a physician's recommendations based on a manual review of the guidelines. Field test: The tool was then tested with 21 GPs from eight general practices and three Aboriginal Medical Services. Customized CDS-based recommendations were generated for 200 routinely attending patients (33% Aboriginal) using information extracted from the health record by a research assistant. GPs reviewed these recommendations during each consultation. Changes in CVD risk factor measurement and management were recorded. In-depth interviews with GPs were conducted. Validation testing: the tool's risk assessment algorithm correlated very highly with the independently programmed version in the separate statistics package (intraclass correlation coefficient 0.999). For management advice, there were only two cases of disagreement between the tool and the physician. Field test: GPs found 77% (153/200) of patient outputs easy to understand and agreed with screening and prescribing recommendations in 72% and 64% of outputs, respectively; 26% of patients had their CVD risk factor history updated; 73% had at least one CVD risk factor measured or tests ordered. For people assessed at high CVD risk (n = 82), 10% and 9%, respectively, had lipid-lowering and BP-lowering medications commenced or dose adjustments made, while 7% newly commenced anti-platelet medications. Three key qualitative findings emerged: (1) GPs found the tool enabled a systematic approach to care; (2) the tool greatly influenced CVD risk communication; (3) successful implementation into routine care would require integration with practice software, minimal data entry, regular revision with updated guidelines, and a self-auditing feature. There were no substantive differences in study findings for Aboriginal Medical Services GPs, and the tool was generally considered appropriate for use with Aboriginal patients. A fully-integrated, self-populating, and potentially Internet-based CDS tool could contribute to improved global CVD risk management in Australian primary health care. The findings from this study will inform a large-scale trial intervention.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-05-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-01-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Universality of Schmidt decomposition and particle identity

NASA Astrophysics Data System (ADS)

Sciara, Stefania; Lo Franco, Rosario; Compagno, Giuseppe

2017-03-01

Schmidt decomposition is a widely employed tool of quantum theory which plays a key role for distinguishable particles in scenarios such as entanglement characterization, theory of measurement and state purification. Yet, its formulation for identical particles remains controversial, jeopardizing its application to analyze general many-body quantum systems. Here we prove, using a newly developed approach, a universal Schmidt decomposition which allows faithful quantification of the physical entanglement due to the identity of particles. We find that it is affected by single-particle measurement localization and state overlap. We study paradigmatic two-particle systems where identical qubits and qutrits are located in the same place or in separated places. For the case of two qutrits in the same place, we show that their entanglement behavior, whose physical interpretation is given, differs from that obtained before by different methods. Our results are generalizable to multiparticle systems and open the way for further developments in quantum information processing exploiting particle identity as a resource.

Universality of Schmidt decomposition and particle identity

PubMed Central

Sciara, Stefania; Lo Franco, Rosario; Compagno, Giuseppe

2017-01-01

Schmidt decomposition is a widely employed tool of quantum theory which plays a key role for distinguishable particles in scenarios such as entanglement characterization, theory of measurement and state purification. Yet, its formulation for identical particles remains controversial, jeopardizing its application to analyze general many-body quantum systems. Here we prove, using a newly developed approach, a universal Schmidt decomposition which allows faithful quantification of the physical entanglement due to the identity of particles. We find that it is affected by single-particle measurement localization and state overlap. We study paradigmatic two-particle systems where identical qubits and qutrits are located in the same place or in separated places. For the case of two qutrits in the same place, we show that their entanglement behavior, whose physical interpretation is given, differs from that obtained before by different methods. Our results are generalizable to multiparticle systems and open the way for further developments in quantum information processing exploiting particle identity as a resource. PMID:28333163

Recent Advances in Neural Electrode-Tissue Interfaces.

PubMed

Woeppel, Kevin; Yang, Qianru; Cui, Xinyan Tracy

2017-12-01

Neurotechnology is facing an exponential growth in the recent decades. Neural electrode-tissue interface research has been well recognized as an instrumental component of neurotechnology development. While satisfactory long-term performance was demonstrated in some applications, such as cochlear implants and deep brain stimulators, more advanced neural electrode devices requiring higher resolution for single unit recording or microstimulation still face significant challenges in reliability and longevity. In this article, we review the most recent findings that contribute to our current understanding of the sources of poor reliability and longevity in neural recording or stimulation, including the material failure, biological tissue response and the interplay between the two. The newly developed characterization tools are introduced from electrophysiology models, molecular and biochemical analysis, material characterization to live imaging. The effective strategies that have been applied to improve the interface are also highlighted. Finally, we discuss the challenges and opportunities in improving the interface and achieving seamless integration between the implanted electrodes and neural tissue both anatomically and functionally.

[Innovations in vaccinology: challenge and opportunities for Africa].

PubMed

Diop, Doudou; Sanicas, Melvin

2017-01-01

Immunization is undoubtedly one of the most effective and most cost-effective health interventions. Vaccines continue to revolutionize our ability to prevent diseases and improve health. With all the technological advances, we are able to extend the benefits of vaccines to more people and to provide better protection from life-threatening infectious diseases. Nevertheless, thanks to the unceasing implementation of novel microbial strains on a worldwide basis, research in vaccinology must innovate continuously. African countries have made great progress in increasing routine immunization coverage rates and in introducing newly developed vaccines. New types of vaccines associated with vectorization, administration and specific licensing tools as well as with adjuvants designed to finely modulate immune responses are expected to be achieved in the near future. African countries need to work to develop a regional approach to respond effectively to the many challenges. Providing better information, implementing healthcare personnel vaccinology training programs and well targeted research projects are the keys to future achievements in the field.

Universality of Schmidt decomposition and particle identity.

PubMed

Sciara, Stefania; Lo Franco, Rosario; Compagno, Giuseppe

2017-03-23

Schmidt decomposition is a widely employed tool of quantum theory which plays a key role for distinguishable particles in scenarios such as entanglement characterization, theory of measurement and state purification. Yet, its formulation for identical particles remains controversial, jeopardizing its application to analyze general many-body quantum systems. Here we prove, using a newly developed approach, a universal Schmidt decomposition which allows faithful quantification of the physical entanglement due to the identity of particles. We find that it is affected by single-particle measurement localization and state overlap. We study paradigmatic two-particle systems where identical qubits and qutrits are located in the same place or in separated places. For the case of two qutrits in the same place, we show that their entanglement behavior, whose physical interpretation is given, differs from that obtained before by different methods. Our results are generalizable to multiparticle systems and open the way for further developments in quantum information processing exploiting particle identity as a resource.

Transformative occupational therapy: We are wired to be transformers.

PubMed

Dubouloz, Claire-Jehanne

2014-10-01

Transformative learning involves critical self-reflection as the motor for transforming values, beliefs, knowledge, and feelings and discovering the new meaning of daily life following a catastrophic injury or illness. Transformation has been conceptualized in various disciplines as a transcendent experience, rebirth process, and meaning-making process and within occupational therapy as a meaning perspective process. This Muriel Driver lecture explores the concept of transformation and presents the newly developed Meaning Perspectives Transformation model, constructed from research conducted with several different rehabilitation client groups. The model is characterized by three phases: trigger, changing, and outcomes. A client's critical self-reflection acts as a catalyst for moving between the phases and is represented in the model as a moment of readiness for change leading to the development of alternative ways of performing. The Meaning Perspectives Transformation model provides a tool for being an effective occupational therapist, encouraging therapists to listen closely to their clients to identify their weakening and emerging meaning perspectives and enable their occupational evolution and transformation.

Integrative sensing and prediction of urban water for sustainable cities (iSPUW)

NASA Astrophysics Data System (ADS)

Seo, D. J.; Fang, N. Z.; Yu, X.; Zink, M.; Gao, J.; Kerkez, B.

2014-12-01

We describe a newly launched project in the Dallas-Fort Worth Metroplex (DFW) area to develop a cyber-physical prototype system that integrates advanced sensing, modeling and prediction of urban water, to support its early adoption by a spectrum of users and stakeholders, and to educate a new generation of future sustainability scientists and engineers. The project utilizes the very high-resolution precipitation and other sensing capabilities uniquely available in DFW as well as crowdsourcing and cloud computing to advance understanding of the urban water cycle and to improve urban sustainability from transient shocks of heavy-to-extreme precipitation under climate change and urbanization. All available water information from observations and models will be fused objectively via advanced data assimilation to produce the best estimate of the state of the uncertain system. Modeling, prediction and decision support tools will be developed in the ensemble framework to increase the information content of the analysis and prediction and to support risk-based decision making.

Web-Based Quality Assurance Process Drives Improvements in Obstetric Ultrasound in 5 Low- and Middle-Income Countries

PubMed Central

Swanson, Jonathan O; Plotner, David; Franklin, Holly L; Swanson, David L; Lokomba Bolamba, Victor; Lokangaka, Adrien; Sayury Pineda, Irma; Figueroa, Lester; Garces, Ana; Muyodi, David; Esamai, Fabian; Kanaiza, Nancy; Mirza, Waseem; Naqvi, Farnaz; Saleem, Sarah; Mwenechanya, Musaku; Chiwila, Melody; Hamsumonde, Dorothy; McClure, Elizabeth M; Goldenberg, Robert L; Nathan, Robert O

2016-01-01

ABSTRACT High quality is important in medical imaging, yet in many geographic areas, highly skilled sonographers are in short supply. Advances in Internet capacity along with the development of reliable portable ultrasounds have created an opportunity to provide centralized remote quality assurance (QA) for ultrasound exams performed at rural sites worldwide. We sought to harness these advances by developing a web-based tool to facilitate QA activities for newly trained sonographers who were taking part in a cluster randomized trial investigating the role of limited obstetric ultrasound to improve pregnancy outcomes in 5 low- and middle-income countries. We were challenged by connectivity issues, by country-specific needs for website usability, and by the overall need for a high-throughput system. After systematically addressing these needs, the resulting QA website helped drive ultrasound quality improvement across all 5 countries. It now offers the potential for adoption by future ultrasound- or imaging-based global health initiatives. PMID:28031304

MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go.

PubMed

Muth, Thilo; Kohrs, Fabian; Heyer, Robert; Benndorf, Dirk; Rapp, Erdmann; Reichl, Udo; Martens, Lennart; Renard, Bernhard Y

2018-01-02

Metaproteomics, the mass spectrometry-based analysis of proteins from multispecies samples faces severe challenges concerning data analysis and results interpretation. To overcome these shortcomings, we here introduce the MetaProteomeAnalyzer (MPA) Portable software. In contrast to the original server-based MPA application, this newly developed tool no longer requires computational expertise for installation and is now independent of any relational database system. In addition, MPA Portable now supports state-of-the-art database search engines and a convenient command line interface for high-performance data processing tasks. While search engine results can easily be combined to increase the protein identification yield, an additional two-step workflow is implemented to provide sufficient analysis resolution for further postprocessing steps, such as protein grouping as well as taxonomic and functional annotation. Our new application has been developed with a focus on intuitive usability, adherence to data standards, and adaptation to Web-based workflow platforms. The open source software package can be found at https://github.com/compomics/meta-proteome-analyzer .

Development of a functional thyroid model based on an organoid culture system.

PubMed

Saito, Yoshiyuki; Onishi, Nobuyuki; Takami, Hiroshi; Seishima, Ryo; Inoue, Hiroyoshi; Hirata, Yuki; Kameyama, Kaori; Tsuchihashi, Kenji; Sugihara, Eiji; Uchino, Shinya; Ito, Koichi; Kawakubo, Hirofumi; Takeuchi, Hiroya; Kitagawa, Yuko; Saya, Hideyuki; Nagano, Osamu

2018-03-04

The low turnover rate of thyroid follicular cells and the lack of a long-term thyroid cell culture system have hampered studies of thyroid carcinogenesis. We have now established a thyroid organoid culture system that supports thyroid cell proliferation in vitro. The established mouse thyroid organoids performed thyroid functions including thyroglobulin synthesis, iodide uptake, and the production and release of thyroid hormone. Furthermore, transplantation of the organoids into recipient mice resulted in the formation of normal thyroid-like tissue capable of iodide uptake and thyroglobulin production in vivo. Finally, forced expression of oncogenic NRAS (NRAS Q61R ) in thyroid organoids established from p53 knockout mice and transplantation of the manipulated organoids into mouse recipients generated a model of poorly differentiated thyroid cancer. Our findings suggest that this newly developed thyroid organoid culture system is a potential research tool for the study of thyroid physiology and pathology including thyroid cancer. Copyright © 2018 Elsevier Inc. All rights reserved.

ADAPTING A PARENT-COMPLETED, SOCIOEMOTIONAL QUESTIONNAIRE IN CHINA: THE AGES & STAGES QUESTIONNAIRES: SOCIAL-EMOTIONAL.

PubMed

Bian, Xiaoyan; Xie, Huichao; Squires, Jane; Chen, Chieh-Yu

2017-03-01

The Ages & Stages Questionnaire: Social-Emotional (ASQ:SE; Squires, Bricker, & Twombly, 2002a), developed in the United States, was translated and adapted for use in China. Lack of valid and reliable instruments for identifying social and emotional delays in young children is a worldwide issue. Professionals in China have recently focused efforts on developing methods for early identification of social, emotional, and behavioral issues in the birth-to-5 population. Following the guidelines of the International Test Commission, the ASQ:SE was translated into Simplified Chinese (ASQ:SE-C) to collect a normative sample of 2,528 children across China. Data were analyzed to evaluate the psychometric properties of the ASQ:SE-C, using both classical test theory and item response theory, including generating cutoff points appropriate for the Chinese sample. A panel of Chinese experts was surveyed to assess face validity and estimated utility of the newly adapted tool. Discussions of research findings and implications for future studies are provided. © 2017 Michigan Association for Infant Mental Health.

Failure Study of Composite Materials by the Yeh-Stratton Criterion

NASA Technical Reports Server (NTRS)

Yeh, Hsien-Yang; Richards, W. Lance

1997-01-01

The newly developed Yeh-Stratton (Y-S) Strength Criterion was used to study the failure of composite materials with central holes and normal cracks. To evaluate the interaction parameters for the Y-S failure theory, it is necessary to perform several biaxial loading tests. However, it is indisputable that the inhomogeneous and anisotropic nature of composite materials have made their own contribution to the complication of the biaxial testing problem. To avoid the difficulties of performing many biaxial tests and still consider the effects of the interaction term in the Y-S Criterion, a simple modification of the Y-S Criterion was developed. The preliminary predictions by the modified Y-S Criterion were relatively conservative compared to the testing data. Thus, the modified Y-S Criterion could be used as a design tool. To further understand the composite failure problem, an investigation of the damage zone in front of the crack tip coupled with the Y-S Criterion is imperative.

Deducing chemical structure from crystallographically determined atomic coordinates

PubMed Central

Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

2011-01-01

An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

XML-based data model and architecture for a knowledge-based grid-enabled problem-solving environment for high-throughput biological imaging.

PubMed

Ahmed, Wamiq M; Lenz, Dominik; Liu, Jia; Paul Robinson, J; Ghafoor, Arif

2008-03-01

High-throughput biological imaging uses automated imaging devices to collect a large number of microscopic images for analysis of biological systems and validation of scientific hypotheses. Efficient manipulation of these datasets for knowledge discovery requires high-performance computational resources, efficient storage, and automated tools for extracting and sharing such knowledge among different research sites. Newly emerging grid technologies provide powerful means for exploiting the full potential of these imaging techniques. Efficient utilization of grid resources requires the development of knowledge-based tools and services that combine domain knowledge with analysis algorithms. In this paper, we first investigate how grid infrastructure can facilitate high-throughput biological imaging research, and present an architecture for providing knowledge-based grid services for this field. We identify two levels of knowledge-based services. The first level provides tools for extracting spatiotemporal knowledge from image sets and the second level provides high-level knowledge management and reasoning services. We then present cellular imaging markup language, an extensible markup language-based language for modeling of biological images and representation of spatiotemporal knowledge. This scheme can be used for spatiotemporal event composition, matching, and automated knowledge extraction and representation for large biological imaging datasets. We demonstrate the expressive power of this formalism by means of different examples and extensive experimental results.

AE Monitoring of Diamond Turned Rapidly Soldified Aluminium 443

NASA Astrophysics Data System (ADS)

Onwuka, G.; Abou-El-Hossein, K.; Mkoko, Z.

2017-05-01

The fast replacement of conventional aluminium with rapidly solidified aluminium alloys has become a noticeable trend in the current manufacturing industries involved in the production of optics and optical molding inserts. This is as a result of the improved performance and durability of rapidly solidified aluminium alloys when compared to conventional aluminium. Melt spinning process is vital for manufacturing rapidly solidified aluminium alloys like RSA 905, RSA 6061 and RSA 443 which are common in the industries today. RSA 443 is a newly developed alloy with few research findings and huge research potential. There is no available literature focused on monitoring the machining of RSA 443 alloys. In this research, Acoustic Emission sensing technique was applied to monitor the single point diamond turning of RSA 443 on an ultrahigh precision lathe machine. The machining process was carried out after careful selection of feed, speed and depths of cut. The monitoring process was achieved with a high sampling data acquisition system using different tools while concurrent measurement of the surface roughness and tool wear were initiated after covering a total feed distance of 13km. An increasing trend of raw AE spikes and peak to peak signal were observed with an increase in the surface roughness and tool wear values. Hence, acoustic emission sensing technique proves to be an effective monitoring method for the machining of RSA 443 alloy.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

PubMed

Vermaas, Josh V; Hardy, David J; Stone, John E; Tajkhorshid, Emad; Kohlmeyer, Axel

2016-06-27

Molecular dynamics (MD) simulation engines use a variety of different approaches for modeling molecular systems with force fields that govern their dynamics and describe their topology. These different approaches introduce incompatibilities between engines, and previously published software bridges the gaps between many popular MD packages, such as between CHARMM and AMBER or GROMACS and LAMMPS. While there are many structure building tools available that generate topologies and structures in CHARMM format, only recently have mechanisms been developed to convert their results into GROMACS input. We present an approach to convert CHARMM-formatted topology and parameters into a format suitable for simulation with GROMACS by expanding the functionality of TopoTools, a plugin integrated within the widely used molecular visualization and analysis software VMD. The conversion process was diligently tested on a comprehensive set of biological molecules in vacuo. The resulting comparison between energy terms shows that the translation performed was lossless as the energies were unchanged for identical starting configurations. By applying the conversion process to conventional benchmark systems that mimic typical modestly sized MD systems, we explore the effect of the implementation choices made in CHARMM, NAMD, and GROMACS. The newly available automatic conversion capability breaks down barriers between simulation tools and user communities and allows users to easily compare simulation programs and leverage their unique features without the tedium of constructing a topology twice.

Pending studies at hospital discharge: a pre-post analysis of an electronic medical record tool to improve communication at hospital discharge.

PubMed

Kantor, Molly A; Evans, Kambria H; Shieh, Lisa

2015-03-01

Achieving safe transitions of care at hospital discharge requires accurate and timely communication. Both the presence of and follow-up plan for diagnostic studies that are pending at hospital discharge are expected to be accurately conveyed during these transitions, but this remains a challenge. To determine the prevalence, characteristics, and communication of studies pending at hospital discharge before and after the implementation of an electronic medical record (EMR) tool that automatically generates a list of pending studies. Pre-post analysis. 260 consecutive patients discharged from inpatient general medicine services from July to August 2013. Development of an EMR-based tool that automatically generates a list of studies pending at discharge. The main outcomes were prevalence and characteristics of pending studies and communication of studies pending at hospital discharge. We also surveyed internal medicine house staff on their attitudes about communication of pending studies. Pre-intervention, 70% of patients had at least one pending study at discharge, but only 18% of these were communicated in the discharge summary. Most studies were microbiology cultures (68%), laboratory studies (16%), or microbiology serologies (10%). The majority of study results were ultimately normal (83%), but 9% were newly abnormal. Post-intervention, communication of studies pending increased to 43% (p < 0.001). Most patients are discharged from the hospital with pending studies, but in usual practice, the presence of these studies has rarely been communicated to outpatient providers in the discharge summary. Communication significantly increased with the implementation of an EMR-based tool that automatically generated a list of pending studies from the EMR and allowed users to import this list into the discharge summary. This is the first study to our knowledge to introduce an automated EMR-based tool to communicate pending studies.

Design, construction, and technical implementation of a web-based interdisciplinary symptom evaluation (WISE) - a heuristic proposal for orofacial pain and temporomandibular disorders.

PubMed

Ettlin, Dominik A; Sommer, Isabelle; Brönnimann, Ben; Maffioletti, Sergio; Scheidt, Jörg; Hou, Mei-Yin; Lukic, Nenad; Steiger, Beat

2016-12-01

Medical symptoms independent of body location burden individuals to varying degrees and may require care by more than one expert. Various paper and computer-based tools exist that aim to comprehensively capture data for optimal clinical management and research. A web-based interdisciplinary symptom evaluation (WISE) was newly designed, constructed, and technically implemented. For worldwide applicability and to avoid copyright infringements, open source software tools and free validated questionnaires available in multiple languages were used. Highly secure data storage limits access strictly to those who use the tool for collecting, storing, and evaluating their data. Concept and implementation is illustrated by a WISE sample tailored for the requirements of a single center in Switzerland providing interdisciplinary care to orofacial pain and temporomandibular disorder patients. By combining a symptom- burden checklist with in-depth questionnaires serving as case-finding instruments, an algorithm was developed that assists in clarifying case complexity and need for targeted expert evaluation. This novel modular approach provides a personalized, response-tailored instrument for the time- and cost-effective collection of symptom-burden focused quantitative data. The tool includes body drawing options and instructional videos. It is applicable for biopsychosocial evaluation in a variety of clinical settings and offers direct feedback by a case report summary. In clinical practice, the new instrument assists in clarifying case complexity and referral need, based on symptom burden and response -tailored case finding. It provides single-case summary reports from a biopsychosocial perspective and includes graphical symptom maps. Secure, centrally stored data collection of anonymous data is possible. The tool enables personalized medicine, facilitates interprofessional education and collaboration, and allows for multicenter patient-reported outcomes research.

Application of the CO2-PENS risk analysis tool to the Rock Springs Uplift, Wyoming

USGS Publications Warehouse

Stauffer, P.H.; Pawar, R.J.; Surdam, R.C.; Jiao, Z.; Deng, H.; Lettelier, B.C.; Viswanathan, H.S.; Sanzo, D.L.; Keating, G.N.

2011-01-01

We describe preliminary application of the CO2-PENS performance and risk analysis tool to a planned geologic CO2 sequestration demonstration project in the Rock Springs Uplift (RSU), located in south western Wyoming. We use data from the RSU to populate CO2-PENS, an evolving system-level modeling tool developed at Los Alamos National Laboratory. This tool has been designed to generate performance and risk assessment calculations for the geologic sequestration of carbon dioxide. Our approach follows Systems Analysis logic and includes estimates of uncertainty in model parameters and Monte-Carlo simulations that lead to probabilistic results. Probabilistic results provide decision makers with a range in the likelihood of different outcomes. Herein we present results from a newly implemented approach in CO 2-PENS that captures site-specific spatially coherent details such as topography on the reservoir/cap-rock interface, changes in saturation and pressure during injection, and dip on overlying aquifers that may be impacted by leakage upward through wellbores and faults. We present simulations of CO 2 injection under different uncertainty distributions for hypothetical leaking wells and faults. Although results are preliminary and to be used only for demonstration of the approach, future results of the risk analysis will form the basis for a discussion on methods to reduce uncertainty in the risk calculations. Additionally, we present ideas on using the model to help locate monitoring equipment to detect potential leaks. By maintaining site-specific details in the CO2-PENS analysis we provide a tool that allows more logical presentations to stakeholders in the region. ?? 2011 Published by Elsevier Ltd.

Development of an Online Toolkit for Measuring Performance in Health Emergency Response Exercises.

PubMed

Agboola, Foluso; Bernard, Dorothy; Savoia, Elena; Biddinger, Paul D

2015-10-01

Exercises that simulate emergency scenarios are accepted widely as an essential component of a robust Emergency Preparedness program. Unfortunately, the variability in the quality of the exercises conducted, and the lack of standardized processes to measure performance, has limited the value of exercises in measuring preparedness. In order to help health organizations improve the quality and standardization of the performance data they collect during simulated emergencies, a model online exercise evaluation toolkit was developed using performance measures tested in over 60 Emergency Preparedness exercises. The exercise evaluation toolkit contains three major components: (1) a database of measures that can be used to assess performance during an emergency response exercise; (2) a standardized data collection tool (form); and (3) a program that populates the data collection tool with the measures that have been selected by the user from the database. The evaluation toolkit was pilot tested from January through September 2014 in collaboration with 14 partnering organizations representing 10 public health agencies and four health care agencies from eight states across the US. Exercise planners from the partnering organizations were asked to use the toolkit for their exercise evaluation process and were interviewed to provide feedback on the use of the toolkit, the generated evaluation tool, and the usefulness of the data being gathered for the development of the exercise after-action report. Ninety-three percent (93%) of exercise planners reported that they found the online database of performance measures appropriate for the creation of exercise evaluation forms, and they stated that they would use it again for future exercises. Seventy-two percent (72%) liked the exercise evaluation form that was generated from the toolkit, and 93% reported that the data collected by the use of the evaluation form were useful in gauging their organization's performance during the exercise. Seventy-nine percent (79%) of exercise planners preferred the evaluation form generated by the toolkit to other forms of evaluations. Results of this project show that users found the newly developed toolkit to be user friendly and more relevant to measurement of specific public health and health care capabilities than other tools currently available. The developed toolkit may contribute to the further advancement of developing a valid approach to exercise performance measurement.

Evaluation of an animation tool developed to supplement dental student study of the cranial nerves.

PubMed

Lone, M; McKenna, J P; Cryan, J F; Vagg, T; Toulouse, A; Downer, E J

2017-12-30

The structure/function of the cranial nerves is a core topic for dental students. However, due to the perceived complexity of the subject, it is often difficult for students to develop a comprehensive understanding of key concepts using textbooks and models. It is accepted that the acquisition of anatomical knowledge can be facilitated by visualisation of structures. This study aimed to develop and assess a novel cranial nerve animation as a supplemental learning aid for dental students. A multidisciplinary team of anatomists, neuroscientists and a computer scientist developed a novel animation depicting the cranial nerves. The animation was viewed by newly enrolled first-year dental students, graduate entry dental students (year 1) and dental hygiene students (year 1). A simple life scenario employing the use of the cranial nerves was developed using a cartoon-type animation with a viewing time of 3.58 minutes. The animation was developed with emphasis on a life scenario. The animation was placed online for 2 weeks with open access or viewed once in a controlled laboratory setting. Questionnaires were designed to assess the participants' attitude towards the animation and their knowledge of the cranial nerves before and after visualisation. This study was performed before the delivery of core lectures on the cranial nerves. Our findings indicate that the use of the animation can act as a supplemental tool to improve student knowledge of the cranial nerves. Indeed, data indicate that a single viewing of the animation, in addition to 2-week access to the animation, can act as a supplemental learning tool to assist student understanding of the structure and function of cranial nerves. The animation significantly enhanced the student's opinion that their cranial nerve knowledge had improved. From a qualitative point of view, the students described the animation as an enjoyable and useful supplement to reading material/lectures and indicated that the animation was a useful tool in understanding the cranial nerves. Overall, these findings indicate that an animation demonstrating the cranial nerves in a simple, everyday functional scenario may act as a learning aid in the study of cranial nerves. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Chromium-Containing Traditional Chinese Medicine, Tianmai Xiaoke Tablet, for Newly Diagnosed Type 2 Diabetes Mellitus: A Meta-Analysis and Systematic Review of Randomized Clinical Trials.

PubMed

Gu, Yuming; Xu, Xuemin; Wang, Zhe; Xu, Yunsheng; Liu, Xiuzhi; Cao, Lejun; Wang, Xueyang; Li, Zhengxin; Feng, Bo

2018-01-01

Chromium-containing traditional Chinese medicine Tianmai Xiaoke tablet (TMXKT) is approved for treating newly diagnosed type 2 diabetes mellitus (T2DM) in China. This review aimed to compile the evidence from randomized clinical trials (RCTs) and quantify the effects of TMXKT on newly diagnosed T2DM. Seven online databases were investigated up to March 20, 2017. The meta-analysis included RCTs investigating the treatment of newly diagnosed T2DM, in which TMXKT combined with conventional therapy was compared with placebo or conventional therapy. The risk of bias was evaluated using the Cochrane Collaboration tool. The estimated mean difference (MD) and the standardized mean difference were within 95% confidence intervals (CI) with respect to the interstudy heterogeneity. The outcomes were measured using fasting blood glucose (FBG), 2-h postprandial blood glucose (2hPG), glycosylated hemoglobin A1c (HbA1c), and body mass index (BMI) levels. TMXKT combined with conventional therapy lowered FBG level (MD = -0.68, 95% CI -0.90 to -0.45, P < 0.00001), 2hPG (MD = -1.33, 95% CI -1.86 to -0.79, P < 0.00001), HbA1c (MD = -0.46, 95% CI -0.57 to -0.36, P < 0.00001), and BMI (MD = -0.77, 95% CI -1.12 to -0.41, P < 0.00001). TMXKT combined with conventional therapy is beneficial for patients with newly diagnosed T2DM. However, the effectiveness and safety of TMXKT are uncertain because of the limited number of trials and low methodological quality. Therefore, practitioners should be cautious when applying TMXKT in daily practice. Also, well-designed clinical trials are needed in the future.

Evaluation of MARC for the analysis of rotating composite blades

NASA Technical Reports Server (NTRS)

Bartos, Karen F.; Ernst, Michael A.

1993-01-01

The suitability of the MARC code for the analysis of rotating composite blades was evaluated using a four-task process. A nonlinear displacement analysis and subsequent eigenvalue analysis were performed on a rotating spring mass system to ensure that displacement-dependent centrifugal forces were accounted for in the eigenvalue analysis. Normal modes analyses were conducted on isotropic plates with various degrees of twist to evaluate MARC's ability to handle blade twist. Normal modes analyses were conducted on flat composite plates to validate the newly developed coupled COBSTRAN-MARC methodology. Finally, normal modes analyses were conducted on four composite propfan blades that were designed, analyzed, and fabricated at NASA Lewis Research Center. Results were compared with experimental data. The research documented herein presents MARC as a viable tool for the analysis of rotating composite blades.

Evaluation of MARC for the analysis of rotating composite blades

NASA Astrophysics Data System (ADS)

Bartos, Karen F.; Ernst, Michael A.

1993-03-01

The suitability of the MARC code for the analysis of rotating composite blades was evaluated using a four-task process. A nonlinear displacement analysis and subsequent eigenvalue analysis were performed on a rotating spring mass system to ensure that displacement-dependent centrifugal forces were accounted for in the eigenvalue analysis. Normal modes analyses were conducted on isotropic plates with various degrees of twist to evaluate MARC's ability to handle blade twist. Normal modes analyses were conducted on flat composite plates to validate the newly developed coupled COBSTRAN-MARC methodology. Finally, normal modes analyses were conducted on four composite propfan blades that were designed, analyzed, and fabricated at NASA Lewis Research Center. Results were compared with experimental data. The research documented herein presents MARC as a viable tool for the analysis of rotating composite blades.

World Wide Web-based system for the calculation of substituent parameters and substituent similarity searches.

PubMed

Ertl, P

1998-02-01

Easy to use, interactive, and platform-independent WWW-based tools are ideal for development of chemical applications. By using the newly emerging Web technologies such as Java applets and sophisticated scripting, it is possible to deliver powerful molecular processing capabilities directly to the desk of synthetic organic chemists. In Novartis Crop Protection in Basel, a Web-based molecular modelling system has been in use since 1995. In this article two new modules of this system are presented: a program for interactive calculation of important hydrophobic, electronic, and steric properties of organic substituents, and a module for substituent similarity searches enabling the identification of bioisosteric functional groups. Various possible applications of calculated substituent parameters are also discussed, including automatic design of molecules with the desired properties and creation of targeted virtual combinatorial libraries.

Hybrid microneedles devices for diagnostic and therapeutic applications: fabrication and preliminary results

NASA Astrophysics Data System (ADS)

Dardano, P.; Caliò, A.; Politi, J.; Di Palma, V.; Bevilacqua, M. F.; Rea, I.; Casalino, M.; Di Matteo, A.; Rendina, I.; De Stefano, L.

2015-06-01

Microneedles are newly developed biomedical devices, whose advantages are mainly in the non-invasiveness, discretion and versatility of use both as diagnostics and as therapeutics tool. In fact, they can be used both for drugs delivery in the interstitial fluids and for the analysis of the interstitial fluid. In this work we present the preliminary results for two devices based on micro needles in PolyEthylene (Glycol). The first for the drugs delivery includes a membrane whose optical reflected wavelength is related to the concentration of drug. Here, we present our preliminary result in diffusion of drugs between the membrane and the microneedles. The second device is gold coated and it works as electrode for the electrochemical detection of species in the interstitial fluid. A preliminary result in detection of glucose will be shown.

Implantable self-reset CMOS image sensor and its application to hemodynamic response detection in living mouse brain

NASA Astrophysics Data System (ADS)

Yamaguchi, Takahiro; Takehara, Hiroaki; Sunaga, Yoshinori; Haruta, Makito; Motoyama, Mayumi; Ohta, Yasumi; Noda, Toshihiko; Sasagawa, Kiyotaka; Tokuda, Takashi; Ohta, Jun

2016-04-01

A self-reset pixel of 15 × 15 µm2 with high signal-to-noise ratio (effective peak SNR ≃64 dB) for an implantable image sensor has been developed for intrinsic signal detection arising from hemodynamic responses in a living mouse brain. For detecting local conversion between oxyhemoglobin (HbO) and deoxyhemoglobin (HbR) in brain tissues, an implantable imaging device was fabricated with our newly designed self-reset image sensor and orange light-emitting diodes (LEDs; λ = 605 nm). We demonstrated imaging of hemodynamic responses in the sensory cortical area accompanied by forelimb stimulation of a living mouse. The implantable imaging device for intrinsic signal detection is expected to be a powerful tool to measure brain activities in living animals used in behavioral analysis.

Breed-Predispositions to Cancer in Pedigree Dogs

PubMed Central

Dobson, Jane M.

2013-01-01

Cancer is a common problem in dogs and although all breeds of dog and crossbred dogs may be affected, it is notable that some breeds of pedigree dogs appear to be at increased risk of certain types of cancer suggesting underlying genetic predisposition to cancer susceptibility. Although the aetiology of most cancers is likely to be multifactorial, the limited genetic diversity seen in purebred dogs facilitates genetic linkage or association studies on relatively small populations as compared to humans, and by using newly developed resources, genome-wide association studies in dog breeds are proving to be a powerful tool for unravelling complex disorders. This paper will review the literature on canine breed susceptibility to histiocytic sarcoma, osteosarcoma, haemangiosarcoma, mast cell tumours, lymphoma, melanoma, and mammary tumours including the recent advances in knowledge through molecular genetic, cytogenetic, and genome wide association studies. PMID:23738139

Autonomous cloud based site monitoring through hydro geophysical data assimilation, processing and result delivery

NASA Astrophysics Data System (ADS)

Versteeg, R.; Johnson, D. V.; Rodzianko, A.; Zhou, H.; Dafflon, B.; Leger, E.; de Kleine, M.

2017-12-01

Understanding of processes in the shallow subsurface requires that geophysical, biogeochemical, hydrological and remote sensing datasets are assimilated, processed and interpreted. Multiple enabling software capabilities for process understanding have been developed by the science community. These include information models (ODM2), reactive transport modeling (PFLOTRAN, Modflow, CLM, Landlab), geophysical inversion (E4D, BERT), parameter estimation (PEST, DAKOTA), visualization (ViSiT, Paraview, D3, QGIS) as well as numerous tools written in python and R for petrophysical mapping, stochastic modeling, data analysis and so on. These capabilities use data collected using sensors and analytical tools developed by multiple manufacturers which produce many different measurements. While scientists obviously leverage tools, capabilities and lessons learned from one site at other sites, the current approach to site characterization and monitoring is very labor intensive and does not scale well. Our objective is to be able to monitor many (hundreds - thousands) of sites. This requires that monitoring can be done in a near time, affordable, auditable and essentially autonomous manner. For this we have developed a modular vertically integrated cloud based software framework which was designed from the ground up for effective site and process monitoring. This software framework (PAF - Predictive Assimilation Framework) is multitenant software and provides automation of data ingestion, processing and visualization of hydrological, geochemical and geophysical (ERT/DTS) data. The core organizational element of PAF is a project/user one in which capabilities available to users are controlled by a combination of available data and access permissions. All PAF capabilities are exposed through APIs, making it easy to quickly add new components. PAF is fully integrated with newly developed autonomous electrical geophysical hardware and thus allows for automation of electrical geophysical ingestion and processing and the ability for co analysis and visualization of the raw and processed data with other data of interest (e.g. soil temperature, soil moisture, precipitation). We will demonstrate current PAF capabilities and discuss future efforts.

A Comprehensive High Performance Predictive Tool for Fusion Liquid Metal Hydromagnetics

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

Huang, Peter; Chhabra, Rupanshi; Munipalli, Ramakanth

In Phase I SBIR project, HyPerComp and Texcel initiated the development of two induction-based MHD codes as a predictive tool for fusion hydro-magnetics. The newly-developed codes overcome the deficiency of other MHD codes based on the quasi static approximation by defining a more general mathematical model that utilizes the induced magnetic field rather than the electric potential as the main electromagnetic variable. The UCLA code is a finite-difference staggered-mesh code that serves as a supplementary tool to the massively-parallel finite-volume code developed by HyPerComp. As there is no suitable experimental data under blanket-relevant conditions for code validation, code-to-code comparisons andmore » comparisons against analytical solutions were successfully performed for three selected test cases: (1) lid-driven MHD flow, (2) flow in a rectangular duct in a transverse magnetic field, and (3) unsteady finite magnetic Reynolds number flow in a rectangular enclosure. The performed tests suggest that the developed codes are accurate and robust. Further work will focus on enhancing the code capabilities towards higher flow parameters and faster computations. At the conclusion of the current Phase-II Project we have completed the preliminary validation efforts in performing unsteady mixed-convection MHD flows (against limited data that is currently available in literature), and demonstrated flow behavior in large 3D channels including important geometrical features. Code enhancements such as periodic boundary conditions, unmatched mesh structures are also ready. As proposed, we have built upon these strengths and explored a much increased range of Grashof numbers and Hartmann numbers under various flow conditions, ranging from flows in a rectangular duct to prototypic blanket modules and liquid metal PFC. Parametric studies, numerical and physical model improvements to expand the scope of simulations, code demonstration, and continued validation activities have also been completed.« less

Microvesicating effects of sulfur mustard on an in vitro human skin model.

PubMed

Hayden, Patrick J; Petrali, John P; Stolper, Gina; Hamilton, Tracey A; Jackson, George R; Wertz, Philip W; Ito, Susumu; Smith, William J; Klausner, Mitchell

2009-10-01

Bis-(beta-chloroethyl) sulfide (SM) is a potent skin vesicant previously used for chemical warfare. Progress in determination of the mechanistic basis of SM pathology, and development of prophylactic and/or therapeutic countermeasures to SM exposure has been hampered by lack of physiologically relevant models of human skin. The current work evaluated a newly developed tissue engineered full-thickness human skin model in a completely in vitro approach to investigation of SM-induced dermal pathology. The model was first characterized with regard to overall morphology, lipid composition, basement membrane (BM) composition and ultrastructural features that are important targets of SM pathologic activity. Well-developed BM ultrastructural features were observed at the dermal-epidermal junction (DEJ), thus demonstrating successful resolution of a primary deficiency of models previously evaluated for SM studies. Studies were then conducted to evaluate histopathological effects of SM on the model. Good replication of in vivo effects was observed, including apoptosis of basal keratinocytes (KC) and microblister formation at the DEJ. Tissue engineered skin models with well-developed basement membrane structures thus appear to be useful tools for in vitro mechanistic studies of SM vesicant activity and development of preventive/therapeutic approaches for SM pathology.

Initial lessons from public-private partnerships in drug and vaccine development.

PubMed Central

Wheeler, C.; Berkley, S.

2001-01-01

In recent years, venture capital approaches have delivered impressive results in identifying and funding promising health discoveries and bringing them to market. This success has inspired public sector experiments with "social venture capital" approaches to address the dearth of affordable treatment and prevention for diseases of the developing world. Employing the same focus on well-defined and measurable objectives, and the same type of connections to pool and deploy resources as their for-profit counterparts, social venture capitalists seek to use the tools and incentives of capitalism to solve one of its biggest failures: the lack of drugs and vaccines for diseases endemic to low-income populations. As part of a larger trend of partnerships emerging in health product donation and distribution, public-private partnerships for pharmaceutical development have led research and development (R&D) efforts to generate more accessible and efficacious products for diseases such as malaria, tuberculosis, and AIDS. In this article, three R&D-focused partnerships are explored: the International AIDS Vaccine Initiative; the Medicines for Malaria Venture; and the newly formed Global Alliance for TB Drug Development. The article highlights key elements essential to the success of these ventures. PMID:11545329

A Feminine Care Clinical Research Program Transforms Women's Lives.

PubMed

Tzeghai, Ghebre E; Ajayi, Funmilayo O; Miller, Kenneth W; Imbescheid, Frank; Sobel, Jack D; Farage, Miranda A

2012-12-17

Feminine hygiene products and menstruation education have transformed the lives of women throughout the world. The P&G Feminine Care Clinical Innovation Research Program has played a key role by expanding scientific knowledge as well as developing technical insights and tools for the development of feminine hygiene products. The aim has been to meet the needs of women throughout their life stages, advancing their urogenital health beyond just menstruation, as well as helping to understand the role of sex hormones in various important health issues that women face. This review article highlights key contributions and research findings in female hygiene products, urogenital health research, and method development. The clinical research team focused on utilizing the results of clinical safety studies to advance the acceptance of feminine hygiene products world-wide. Key findings include that perception of skin sensitivity is not limited to the facial area, but is also relevant to the body and the genital area. Also, they shed light on the role of estrogen in autoimmune diseases as well as premenstrual syndrome. Efforts in the method development area focused on innovative tools that are reliable, predictive of clinical trial results and capable of measuring wear comfort, genital skin health, and the impact of product use on the consumer's quality of life. A novel method, behind-the-knee (BTK) test, developed to model irritation under normal wear conditions, was the first to account for both chemical and mechanical sources of irritation. The method has been accepted by the FDA as a substitute in clinical trials in some cases, and by American Society for Testing and Materials as a global standard test method. Additional proprietary methods were developed to enhance visual grading of irritation using cross-polarized light, to measure the amount of lotion transferred from sanitary pads, and to evaluate the skin mildness. Finally, the Farage Quality of Life tool was created to measure consumer's well-being. Based on the results of this extensive clinical research and the newly developed testing methods, the changing needs of women throughout their life stages are better met.

A Feminine Care Clinical Research Program Transforms Women’s Lives

PubMed Central

Tzeghai, Ghebre E.; Ajayi, Funmilayo O.; Miller, Kenneth W.; Imbescheid, Frank; Sobel, Jack D.; Farage, Miranda A.

2015-01-01

Feminine hygiene products and menstruation education have transformed the lives of women throughout the world. The P&G Feminine Care Clinical Innovation Research Program has played a key role by expanding scientific knowledge as well as developing technical insights and tools for the development of feminine hygiene products. The aim has been to meet the needs of women throughout their life stages, advancing their urogenital health beyond just menstruation, as well as helping to understand the role of sex hormones in various important health issues that women face. This review article highlights key contributions and research findings in female hygiene products, urogenital health research, and method development. The clinical research team focused on utilizing the results of clinical safety studies to advance the acceptance of feminine hygiene products world-wide. Key findings include that perception of skin sensitivity is not limited to the facial area, but is also relevant to the body and the genital area. Also, they shed light on the role of estrogen in autoimmune diseases as well as premenstrual syndrome. Efforts in the method development area focused on innovative tools that are reliable, predictive of clinical trial results and capable of measuring wear comfort, genital skin health, and the impact of product use on the consumer’s quality of life. A novel method, behind-the-knee (BTK) test, developed to model irritation under normal wear conditions, was the first to account for both chemical and mechanical sources of irritation. The method has been accepted by the FDA as a substitute in clinical trials in some cases, and by American Society for Testing and Materials as a global standard test method. Additional proprietary methods were developed to enhance visual grading of irritation using cross-polarized light, to measure the amount of lotion transferred from sanitary pads, and to evaluate the skin mildness. Finally, the Farage Quality of Life tool was created to measure consumer’s well-being. Based on the results of this extensive clinical research and the newly developed testing methods, the changing needs of women throughout their life stages are better met. PMID:25946910

Fluorescent Probes for Single-Step Detection and Proteomic Profiling of Histone Deacetylases.

PubMed

Xie, Yusheng; Ge, Jingyan; Lei, Haipeng; Peng, Bo; Zhang, Huatang; Wang, Danyang; Pan, Sijun; Chen, Ganchao; Chen, Lanfang; Wang, Yi; Hao, Quan; Yao, Shao Q; Sun, Hongyan

2016-12-07

Histone deacetylases (HDACs) play important roles in regulating various physiological and pathological processes. Developing fluorescent probes capable of detecting HDAC activity can help further elucidate the roles of HDACs in biology. In this study, we first developed a set of activity-based fluorescent probes by incorporating the Kac residue and the O-NBD group. Upon enzymatic removal of the acetyl group in the Kac residue, the released free amine reacted intramolecularly with the O-NBD moiety, resulting in turn-on fluorescence. These designed probes are capable of detecting HDAC activity in a continuous fashion, thereby eliminating the extra step of fluorescence development. Remarkably, the amount of turn-on fluorescence can be as high as 50-fold, which is superior to the existing one-step HDAC fluorescent probes. Inhibition experiments further proved that the probes can serve as useful tools for screening HDAC inhibitors. Building on these results, we moved on and designed a dual-purpose fluorescent probe by introducing a diazirine photo-cross-linker into the probe. The resulting probe was not only capable of reporting enzymatic activity but also able to directly identify and capture the protein targets from the complex cellular environment. By combining a fluorometric method and in-gel fluorescence scanning technique, we found that epigenetic readers and erasers can be readily identified and differentiated using a single probe. This is not achievable with traditional photoaffinity probes. In light of the prominent properties and the diverse functions of this newly developed probe, we envision that it can provide a robust tool for functional analysis of HDACs and facilitate future drug discovery in epigenetics.

Development of a downhole tool measuring real-time concentration of ionic tracers and pH in geothermal reservoirs

NASA Astrophysics Data System (ADS)

Hess, Ryan F.; Boyle, Timothy J.; Limmer, Steven; Yelton, William G.; Bingham, Samuel; Stillman, Greg; Lindblom, Scott; Cieslewski, Grzegorz

2014-06-01

For enhanced or Engineered Geothermal Systems (EGS) geothermal brine is pumped to the surface via the production wells, the heat extracted to turn a turbine to generate electricity, and the spent brine re-injected via injection wells back underground. If designed properly, the subsurface rock formations will lead this water back to the extraction well as heated brine. Proper monitoring of these geothermal reservoirs is essential for developing and maintaining the necessary level of productivity of the field. Chemical tracers are commonly used to characterize the fracture network and determine the connectivity between the injection and production wells. Currently, most tracer experiments involve injecting the tracer at the injection well, manually collecting liquid samples at the wellhead of the production well, and sending the samples off for laboratory analysis. While this method provides accurate tracer concentration data at very low levels of detection, it does not provide information regarding the location of the fractures which were conducting the tracer between wellbores. Sandia is developing a high-temperature electrochemical sensor capable of measuring tracer concentrations and pH downhole on a wireline tool. The goal of this effort is to collect real-time pH and ionic tracer concentration data at temperatures up to 225 °C and pressures up to 3000 psi. In this paper, a prototype electrochemical sensor and the initial data obtained will be presented detailing the measurement of iodide tracer concentrations at high temperature and pressure in a newly developed laboratory scale autoclave.