Chamomile decoction extract inhibits human neutrophils ROS production and attenuates alcohol-induced haematological parameters changes and erythrocytes oxidative stress in rat.

PubMed

Jabri, Mohamed-Amine; Sani, Mamane; Rtibi, Kais; Marzouki, Lamjed; El-Benna, Jamel; Sakly, Mohsen; Sebai, Hichem

2016-03-31

The aim of this study was to evaluate the protective effects of subacute pre-treatment with chamomile (Matricaria recutita L.) decoction extract (CDE) against stimulated neutrophils ROS production as well as ethanol (EtOH)-induced haematological changes and erythrocytes oxidative stress in rat. Neutrophils were isolated and ROS generation was measured by luminol-amplified chemiluminescence. Superoxide anion generation was detected by the cytochrome c reduction assay. Adult male wistar rats were used and divided into six groups of ten each: control, EtOH, EtOH + various doses of CDE (25, 50, and 100 mg/kg, b.w.), and EtOH+ ascorbic acid (AA). Animals were pre-treated with CDE extract during 10 days. We found that CDE inhibited (P ≤ 0.0003) luminol-amplified chemiluminescence of resting neutrophils and N-formyl methionylleucyl-phenylalanine (fMLF) or phorbolmyristate acetate (PMA) stimulated neutrophils, in a dose-dependent manner. CDE had no effect on superoxide anion, but it inhibited (P ≤ 0.0004) H2O2 production in cell free system. In vivo, CDE counteracted (P ≤ 0.0034) the effect of single EtOH administration which induced (P < 0.0001) an increase of white blood cells (WBC) and platelets (PLT) counts. Our results also demonstrated that alcohol administration significantly (P < 0.0001) induced erythrocytes lipoperoxidation increase and depletion of sulfhydryl groups (-SH) content as well as antioxidant enzyme activities as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx). More importantly, we found that acute alcohol administration increased (P < 0.0001) erythrocytes and plasma hydrogen peroxide (H2O2), free iron, and calcium levels while the CDE pre-treatment reversed increased (P ≤ 0.0051) all these intracellular disturbances. These findings suggest that CDE inhibits neutrophil ROS production and protects against EtOH-induced haematologiacal parameters changes and erythrocytes oxidative stress. The haematoprotection offered by chamomile might involve in part its antioxidant properties as well as its opposite effect on some intracellular mediators such as H2O2, free iron, and calcium.

Pentoxifylline does not alter the response to inhaled grain dust.

PubMed

Jagielo, P J; Watt, J L; Quinn, T J; Knapp, H R; Schwartz, D A

1997-05-01

Pentoxifylline (PTX) has been shown to reduce sepsis-induced neutrophil sequestration in the lung and inhibit endotoxin-mediated release of tumor necrosis factor-alpha (TNF-alpha). Previously, we have shown that endotoxin appears to be the principal agent in grain dust causing airway inflammation and airflow obstruction following grain dust inhalation. To determine whether PTX affects the physiologic and inflammatory events following acute grain dust inhalation, 10 healthy, nonsmoking subjects with normal airway reactivity were treated with PTX or placebo (PL) followed by corn dust extract (CDE) inhalation (0.08 mL/kg), using a single-blinded, crossover design. Subjects received PTX (1,200 mg/d) or PL for 4 days prior to CDE inhalation and 400 mg PTX or PL on the exposure day. Both respiratory symptoms and declines in FEV1 and FVC occurred following CDE exposure in both groups, but there were no significant differences in the frequency of symptoms or percent declines from baseline in the FEV1 and FVC at any of the time points measured in the study. Elevations in peripheral blood leukocyte and neutrophil concentrations and BAL total cell, neutrophil, TNF-alpha, and interleukin-8 concentrations were measured 4 h following exposure to CDE in both the PTX- and PL-treated subjects, but no significant differences were found between treatment groups. These results suggest that pretreatment with PTX prior to inhalation of CDE, in the doses used in this study, does not alter the acute physiologic or inflammatory events following exposure to inhaled CDE.

Human reductive halothane metabolism in vitro is catalyzed by cytochrome P450 2A6 and 3A4.

PubMed

Spracklin, D K; Thummel, K E; Kharasch, E D

1996-09-01

The anesthetic halothane undergoes extensive oxidative and reductive biotransformation, resulting in metabolites that cause hepatotoxicity. Halothane is reduced anaerobically by cytochrome P450 (P450) to the volatile metabolites 2-chloro-1,1-difluoroethene (CDE) and 2-chloro-1,1,1-trifluoroethane (CTE). The purpose of this investigation was to identify the human P450 isoform(s) responsible for reductive halothane metabolism. CDE and CTE formation from halothane metabolism by human liver microsomes was determined by GC/MS analysis. Halothane metabolism to CDE and CTE under reductive conditions was completely inhibited by carbon monoxide, which implicates exclusively P450 in this reaction. Eadie-Hofstee plots of both CDE and CTE formation were nonlinear, suggesting multiple P450 isoform involvement. Microsomal CDE and CTE formation were each inhibited 40-50% by P450 2A6-selective inhibitors (coumarin and 8-methoxypsoralen) and 55-60% by P450 3A4-selective inhibitors (ketoconazole and troleandomycin). P450 1A-, 2B6-, 2C9/10-, and 2D6-selective inhibitors (7,8-benzoflavone, furafylline, orphenadrine, sulfaphenazole, and quinidine) had no significant effect on reductive halothane metabolism. Measurement of product formation catalyzed by a panel of cDNA-expressed P450 isoforms revealed that maximal rates of CDE formation occurred with P450 2A6, followed by P450 3A4. P450 3A4 was the most effective catalyst of CTE formation. Among a panel of 11 different human livers, there were significant linear correlations between the rate of CDE formation and both 2A6 activity (r = 0.64, p < 0.04) and 3A4 activity (r = 0.64, p < 0.03). Similarly, there were significant linear correlations between CTE formation and both 2A6 activity (r = 0.55, p < 0.08) and 3A4 activity (r = 0.77, p < 0.005). The P450 2E1 inhibitors 4-methylpyrazole and diethyldithiocarbamate inhibited CDE and CTE formation by 20-45% and 40-50%, respectively; however, cDNA-expressed P450 2E1 did not catalyze significant amounts of CDE or CTE production, and microsomal metabolite formation was not correlated with P450 2E1 activity. This investigation demonstrated that human liver microsomal reductive halothane metabolism is catalyzed predominantly by P450 2A6 and 3A4. This isoform selectivity for anaerobic halothane metabolism contrasts with that for oxidative human halothane metabolism, which is catalyzed predominantly by P450 2E1.

Impairment of NADH dehydrogenase and regulation of anaerobic metabolism by the small RNA RyhB and NadE for improved biohydrogen production in Enterobacter aerogenes.

PubMed

Wu, Yan; Hao, Yaqiao; Wei, Xuan; Shen, Qi; Ding, Xuanwei; Wang, Liyan; Zhao, Hongxin; Lu, Yuan

2017-01-01

Enterobacter aerogenes is a facultative anaerobe and is one of the most widely studied bacterial strains because of its ability to use a variety of substrates, to produce hydrogen at a high rate, and its high growth rate during dark fermentation. However, the rate of hydrogen production has not been optimized. In this present study, three strategies to improve hydrogen production in E. aerogenes , namely the disruption of nuoCDE , overexpression of the small RNA RyhB and of NadE to regulate global anaerobic metabolism, and the redistribution of metabolic flux. The goal of this study was to clarify the effect of nuoCDE , RyhB, and NadE on hydrogen production and how the perturbation of NADH influences the yield of hydrogen gas from E. aerogenes . NADH dehydrogenase activity was impaired by knocking out nuoCD or nuoCDE in E. aerogenes IAM1183 using the CRISPR-Cas9 system to explore the consequent effect on hydrogen production. The hydrogen yields from IAM1183-CD( ∆nuoC / ∆nuoD ) and IAM1183-CDE ( ∆nuoC / ∆nuoD / ∆nuoE ) increased, respectively, by 24.5 and 45.6% in batch culture (100 mL serum bottles). The hydrogen produced via the NADH pathway increased significantly in IAM1183-CDE, suggesting that nuoE plays an important role in regulating NADH concentration in E. aerogenes . Batch-cultivating experiments showed that by the overexpression of NadE (N), the hydrogen yields of IAM1183/N, IAM1183-CD/N, and IAM1183-CDE/N increased 1.06-, 1.35-, and 1.55-folds, respectively, compared with IAM1183. Particularly worth mentioning is that the strain IAM118-CDE/N reached 2.28 mol in H 2 yield, per mole of glucose consumed. IAN1183/R, IAM1183-CD/R, and IAM1183-CDE/R showed increasing H 2 yields in batch culture. Metabolic flux analysis indicated that increased expression of RyhB led to a significant shift in metabolic patterns. We further investigated IAM1183-CDE/N, which had the best hydrogen-producing traits, as a potential candidate for industry applications using a 5-L fermenter; hydrogen production reached up to 1.95 times greater than that measured for IAM1183. Knockout of nuoCD or nuoCDE and the overexpression of nadE in E. aerogenes resulted in a redistribution of metabolic flux and improved the hydrogen yield. Overexpression of RyhB had an significant change on the hydrogen production via NADH pathway. A combination of strategies would be a novel approach for developing a more economic and efficient bioprocess for hydrogen production in E. aerogenes . Finally, the latest CRISPR-Cas9 technology was successful for editing genes in E. aerogenes to develop our engineered strain for hydrogen production.

[Contribution of medical technologists in team medical care of diabetics].

PubMed

Sato, Itsuko; Jikimoto, Takumi; Ooyabu, Chinami; Kusuki, Mari; Okano, Yosie; Mukai, Masahiko; Kawano, Seiji; Kumagai, Shunichi

2006-08-01

For the effective treatment of diabetic mellitus (DM), patients are encouraged to self-manage their disease according to the doctor's instructions and advice from certified diabetes educators (CDE) and other comedical staff. Therefore, the cooperation of medical staff consisting of a doctor, CDE, nurse, pharmacist, dietitian, and medical technologist is important for DM education. Medical technologists licensed for CDE (MT-CDE) have been participating in the DM education team in Kobe University Hospital since 2000. MT-CDE are in charge of classes for medical tests, guidance for self-monitoring of blood glucose and teaching how to read the fluctuation graph of the blood glucose level in the education program for hospitalized DM patients. MT-CDEs teach at the bedside how to read the results of medical tests during the first few days of hospitalization using pamphlets for medical tests. The pamphlets are made comprehensible for patients by using graphics and photographs as much as possible. It is important to create a friendly atmosphere and answer frank questions from patients, since they often feel stress when having medical tests at the early stage of hospitalization. This process of questions and answers promotes their understanding of medical tests, and seems to reduce their anxiety about having tests. We repeatedly evaluate their level of understanding during hospitalization. By showing them the fluctuation graph of the glucose level, patients can easily understand the status of their DM. When prescriptions are written on the graph, their therapeutic effects are more comprehensible for the patients. The items written on the graph are chosen to meet the level of understanding of each patient to promote their motivation. In summary, the introduction of MT-CDE has been successful in the education program for DM patients in our hospital. We plan to utilize the skills and knowledge of MT-CDE more in our program so that our DM education program will help patients cope with life with DM.

[Reliability for detection of developmental problems using the semaphore from the Child Development Evaluation test: Is a yellow result different from a red result?

PubMed

Rizzoli-Córdoba, Antonio; Ortega-Ríosvelasco, Fernando; Villasís-Keever, Miguel Ángel; Pizarro-Castellanos, Mariel; Buenrostro-Márquez, Guillermo; Aceves-Villagrán, Daniel; O'Shea-Cuevas, Gabriel; Muñoz-Hernández, Onofre

The Child Development Evaluation (CDE) is a screening tool designed and validated in Mexico for detecting developmental problems. The result is expressed through a semaphore. In the CDE test, both yellow and red results are considered positive, although a different intervention is proposed for each. The aim of this work was to evaluate the reliability of the CDE test to discriminate between children with yellow/red result based on the developmental domain quotient (DDQ) obtained through the Battelle Development Inventory, 2nd edition (in Spanish) (BDI-2). The information was obtained for the study from the validation. Children with a normal (green) result in the CDE were excluded. Two different cut-off points of the DDQ were used (BDI-2): <90 to include low average, and developmental delay was considered with a cut-off<80 per domain. Results were analyzed based on the correlation of the CDE test and each domain from the BDI-2 and by subgroups of age. With a cut-off DDQ<90, 86.8% of tests with yellow result (CDE) indicated at least one domain affected and 50% 3 or more compared with 93.8% and 78.8% for red result, respectively. There were differences in every domain (P<0.001) for the percent of children with DDQ<80 between yellow and red result (CDE): cognitive 36.1% vs. 61.9%; communication: 27.8% vs. 50.4%, motor: 18.1% vs. 39.9%; personal-social: 20.1% vs. 28.9%; and adaptive: 6.9% vs. 20.4%. The semaphore result yellow/red allows identifying different magnitudes of delay in developmental domains or subdomains, supporting the recommendation of different interventions for each one. Copyright © 2014 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

There is no A in CD&E, Neither for Analysis nor for Anarchy - Ensuring Scientific Rigour and Analytical Structure while maintaining Military Relevance and Artistic Freedom

DTIC Science & Technology

2010-04-01

Journal of Supply Chain Management , Vol. 4, No. 4. pp. 7-27. [21] Ellram, L. M. (1996): The use of the case study method in logistics research. Journal ...logistics. European Journal of Operational Research, No. 144, pp. 321-332. There is no ´A´ in CD&E, neither for Analysis nor for Anarchy – Ensuring...analytical support as quality assurance. For managers of CD&E, it is necessary to be able to state that scarce resources are being used to develop the

75 FR 60169 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-29

... October 29, 2010 to be assured of consideration. Community Development Financial Institutions (CDFI) Fund...: CDFI/CDE Fund Project Profile Web Form. Form: CDFI 0030. Description: The voluntary collection of narrative descriptions of projects financed by CDFI Fund awardees and allocates via the CDFI/CDE Project...

Assessment of online continuing dental education in North Carolina.

PubMed

Francis, B; Mauriello, S M; Phillips, C; Englebardt, S; Grayden, S K

2000-01-01

Dental professionals are discovering the unique advantages of asynchronous lifelong learning through continuing dental education (CDE) opportunities offered online. The purpose of this study was to evaluate both the process and outcomes of online CDE in North Carolina. The assessment was designed to provide a better understanding of practicing dental professionals experiences with online CDE and to determine the effectiveness of this learning strategy. Dental professionals from four North Carolina Area Health Education Centers regions evaluated two pilot online CDE modules in 1998. Thirty-one participants were recruited and subsequently enrolled with 23 completing at least one module. Each module included objectives, a multiple-choice pretest, interactive core material, and a post-test. Participants completed three online surveys measuring individual demographics and computer skill level, module design, and use and overall reaction to online learning. Most participants agreed that the modules were comprehensive, were pleasing in appearance, provided clear instructions, provided adequate feedback, and were easy to navigate. Most participants agreed that knowledge of the material increased. This was validated by a significant increase in mean pre- to post-test scores (p = .0001). Participants agreed that convenience was a definite advantage, and they would choose online courses again to meet their CDE needs. The least-liked aspects included technical and formatting issues. Participants were enthusiastic about online learning and learned effectively with this teaching strategy, but desired much more interactivity than existed in the current design.

76 FR 17660 - National Institute of Mental Health; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-30

... Health, Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Open...: National Institutes of Health, Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E..., NIH, Neuroscience Center, 6001 Executive Blvd., Room 6154, MSC 9609, Bethesda, MD 20892-9609, 301-443...

Ontology-based reusable clinical document template production system.

PubMed

Nam, Sejin; Lee, Sungin; Kim, James G Boram; Kim, Hong-Gee

2012-01-01

Clinical documents embody professional clinical knowledge. This paper shows an effective clinical document template (CDT) production system that uses a clinical description entity (CDE) model, a CDE ontology, and a knowledge management system called STEP that manages ontology-based clinical description entities. The ontology represents CDEs and their inter-relations, and the STEP system stores and manages CDE ontology-based information regarding CDTs. The system also provides Web Services interfaces for search and reasoning over clinical entities. The system was populated with entities and relations extracted from 35 CDTs that were used in admission, discharge, and progress reports, as well as those used in nursing and operation functions. A clinical document template editor is shown that uses STEP.

An Observational Analysis of Coaching Behaviors for Career Development Event Teams: A Mixed Methods Study

ERIC Educational Resources Information Center

Ball, Anna L.; Bowling, Amanda M.; Sharpless, Justin D.

2016-01-01

School Based Agricultural Education (SBAE) teachers can use coaching behaviors, along with their agricultural content knowledge to help their Career Development Event (CDE) teams succeed. This mixed methods, collective case study observed three SBAE teachers preparing multiple CDEs throughout the CDE season. The teachers observed had a previous…

Colorado Department of Education Abbreviated Information Management Annual Plan (CDE IMAP).

ERIC Educational Resources Information Center

Laughlin, Richard

The Colorado Department of Education (CDE), including Access Colorado Library and Information Network (ACLIN) and the Colorado School for the Deaf and the Blind, provides state- level guidance and resources for Colorado's local school districts, local and regional libraries, and special populations. Technology is the enabler that offers basic,…

Ready, Set, Algebra?

ERIC Educational Resources Information Center

Levy, Alissa Beth

2012-01-01

The California Department of Education (CDE) has long asserted that success Algebra I by Grade 8 is the goal for all California public school students. In fact, the state's accountability system penalizes schools that do not require all of their students to take the Algebra I end-of-course examination by Grade 8 (CDE, 2009). In this dissertation,…

77 FR 24972 - National Institute of Mental Health Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-26

..., Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Closed: 1:15 p.m. to..., Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Contact Person: Jane... Health, NIH, Neuroscience Center, 6001 Executive Blvd., Room 6154, MSC 9609, Bethesda, MD 20892-9609, 301...

76 FR 51379 - National Institute of Mental Health Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-18

..., Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Closed: 1:30 p.m. to..., Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Contact Person: Jane..., NIH, Neuroscience Center, 6001 Executive Blvd., Room 6154, MSC 9609, Bethesda, MD 20892-9609, 301-443...

78 FR 52551 - National Institute of Mental Health; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-23

...), Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Closed: 2:30 p.m. to..., Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Contact Person: Jane... Health, NIH, Neuroscience Center, 6001 Executive Blvd., Room 6154, MSC 9609, Bethesda, MD 20892-9609, 301...

77 FR 48998 - National Institute of Mental Health; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-15

... Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Closed: 2:30 p.m. to... Neuroscience Center, 6001 Executive Boulevard, Conference Room C/D/E, Rockville, MD 20852. Contact Person: Jane... Health, NIH, Neuroscience Center, 6001 Executive Blvd., Room 6154, MSC 9609, Bethesda, MD 20892-9609, 301...

A Collaborative Decision Environment for UAV Operations

NASA Technical Reports Server (NTRS)

D'Ortenzio, Matthew V.; Enomoto, Francis Y.; Johan, Sandra L.

2005-01-01

NASA is developing Intelligent Mission Management (IMM) technology for science missions employing long endurance unmanned aerial vehicles (UAV's). The IMM groundbased component is the Collaborative Decision Environment (CDE), a ground system that provides the Mission/Science team with situational awareness, collaboration, and decisionmaking tools. The CDE is used for pre-flight planning, mission monitoring, and visualization of acquired data. It integrates external data products used for planning and executing a mission, such as weather, satellite data products, and topographic maps by leveraging established and emerging Open Geospatial Consortium (OGC) standards to acquire external data products via the Internet, and an industry standard geographic information system (GIs) toolkit for visualization As a Science/Mission team may be geographically dispersed, the CDE is capable of providing access to remote users across wide area networks using Web Services technology. A prototype CDE is being developed for an instrument checkout flight on a manned aircraft in the fall of 2005, in preparation for a full deployment in support of the US Forest Service and NASA Ames Western States Fire Mission in 2006.

Common Data Elements for Muscle Biopsy Reporting

PubMed Central

Dastgir, Jahannaz; Rutkowski, Anne; Alvarez, Rachel; Cossette, Stacy A.; Yan, Ke; Hoffmann, Raymond G.; Sewry, Caroline; Hayashi, Yukiko K.; Goebel, Hans-Hilmar; Bonnemann, Carsten; Lawlor, Michael W.

2016-01-01

Context There is no current standard among myopathologists for reporting muscle biopsy findings. The National Institute of Neurological Disorders and Stroke has recently launched a common data element (CDE) project to standardize neuromuscular data collected in clinical reports and to facilitate their use in research. Objective To develop a more-uniform, prospective reporting tool for muscle biopsies, incorporating the elements identified by the CDE project, in an effort to improve reporting and educational resources. Design The variation in current biopsy reporting practice was evaluated through a study of 51 muscle biopsy reports from self-reported diagnoses of genetically confirmed or undiagnosed muscle disease from the Congenital Muscle Disease International Registry. Two reviewers independently extracted data from deidentified reports and entered them into the revised CDE format to identify what was missing and whether or not information provided on the revised CDE report (complete/incomplete) could be successfully interpreted by a neuropathologist. Results Analysis of the data highlighted showed (1) inconsistent reporting of key clinical features from referring physicians, and (2) considerable variability in the reporting of pertinent positive and negative histologic findings by pathologists. Conclusions We propose a format for muscle-biopsy reporting that includes the elements in the CDE checklist and a brief narrative comment that interprets the data in support of a final interpretation. Such a format standardizes cataloging of pathologic findings across the spectrum of muscle diseases and serves emerging clinical care and research needs with the expansion of genetic-testing therapeutic trials. PMID:26132600

Role of bone marrow cells in the development of pancreatic fibrosis in a rat model of pancreatitis induced by a choline-deficient/ethionine-supplemented diet

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

Akita, Shingo; Kubota, Koji; Kobayashi, Akira, E-mail: kbys@shinshu-u.ac.jp

Highlights: Black-Right-Pointing-Pointer BMC-derived PSCs play a role in a rat CDE diet-induced pancreatitis model. Black-Right-Pointing-Pointer BMC-derived PSCs contribute mainly to the early stage of pancreatic fibrosis. Black-Right-Pointing-Pointer BMC-derived activated PSCs can produce PDGF and TGF {beta}1. -- Abstract: Bone marrow cell (BMC)-derived myofibroblast-like cells have been reported in various organs, including the pancreas. However, the contribution of these cells to pancreatic fibrosis has not been fully discussed. The present study examined the possible involvement of pancreatic stellate cells (PSCs) originating from BMCs in the development of pancreatic fibrosis in a clinically relevant rat model of acute pancreatitis induced by amore » choline-deficient/ethionine-supplemented (CDE) diet. BMCs from female transgenic mice ubiquitously expressing green fluorescent protein (GFP) were transplanted into lethally irradiated male rats. Once chimerism was established, acute pancreatitis was induced by a CDE diet. Chronological changes in the number of PSCs originating from the donor BMCs were examined using double immunofluorescence for GFP and markers for PSCs, such as desmin and alpha smooth muscle actin ({alpha}SMA), 1, 3 and 8 weeks after the initiation of CDE feeding. We also used immunohistochemical staining to evaluate whether the PSCs from the BMCs produce growth factors, such as platelet-derived growth factor (PDGF) and transforming growth factor (TGF) {beta}1. The percentage of BMC-derived activated PSCs increased significantly, peaking after 1 week of CDE treatment (accounting for 23.3 {+-} 0.9% of the total population of activated PSCs) and then decreasing. These cells produced both PDGF and TGF{beta}1 during the early stage of pancreatic fibrosis. Our results suggest that PSCs originating from BMCs contribute mainly to the early stage of pancreatic injury, at least in part, by producing growth factors in a rat CDE diet-induced pancreatitis model.« less

Contaminant transport in soil with depth-dependent reaction coefficients and time-dependent boundary conditions.

PubMed

Gao, Guangyao; Fu, Bojie; Zhan, Hongbin; Ma, Ying

2013-05-01

Predicting the fate and movement of contaminant in soils and groundwater is essential to assess and reduce the risk of soil contamination and groundwater pollution. Reaction processes of contaminant often decreased monotonously with depth. Time-dependent input sources usually occurred at the inlet of natural or human-made system such as radioactive waste disposal site. This study presented a one-dimensional convection-dispersion equation (CDE) for contaminant transport in soils with depth-dependent reaction coefficients and time-dependent inlet boundary conditions, and derived its analytical solution. The adsorption coefficient and degradation rate were represented as sigmoidal functions of soil depth. Solute breakthrough curves (BTCs) and concentration profiles obtained from CDE with depth-dependent and constant reaction coefficients were compared, and a constant effective reaction coefficient, which was calculated by arithmetically averaging the depth-dependent reaction coefficient, was proposed to reflect the lumped depth-dependent reaction effect. With the effective adsorption coefficient and degradation rate, CDE could produce similar BTCs and concentration profiles as those from CDE with depth-dependent reactions in soils with moderate chemical heterogeneity. In contrast, the predicted concentrations of CDE with fitted reaction coefficients at a certain depth departed significantly from those of CDE with depth-dependent reactions. Parametric analysis was performed to illustrate the effects of sinusoidally and exponentially decaying input functions on solute BTCs. The BTCs and concentration profiles obtained from the solutions for finite and semi-infinite domain were compared to investigate the effects of effluent boundary condition. The finite solution produced higher concentrations at the increasing limb of the BTCs and possessed a higher peak concentration than the semi-infinite solution which had a slightly long tail. Furthermore, the finite solution gave a higher concentration in the immediate vicinity of the exit boundary than the semi-infinite solution. The applicability of the proposed model was tested with a field herbicide and tracer leaching experiment in an agricultural area of northeastern Greece. The simulation results indicated that the proposed CDE with depth-dependent reaction coefficients was able to capture the evolution of metolachlor concentration at the upper soil depths. However, the simulation results at deep depths were not satisfactory as the proposed model did not account for preferential flow observed in the field. Copyright © 2013 Elsevier Ltd. All rights reserved.

Online Learning Policy and Practice Survey: A Survey of the States

ERIC Educational Resources Information Center

Center for Digital Education, 2008

2008-01-01

In 2008, the Center for Digital Education (CDE) conducted a review of state policy and programs to determine the status of online learning policy and practice across the United States. CDE interviewed state education officials across the nation to evaluate the overall landscape of online learning. The rankings reflect the vision, policies,…

Sharing behavioral data through a grid infrastructure using data standards

PubMed Central

Min, Hua; Ohira, Riki; Collins, Michael A; Bondy, Jessica; Avis, Nancy E; Tchuvatkina, Olga; Courtney, Paul K; Moser, Richard P; Shaikh, Abdul R; Hesse, Bradford W; Cooper, Mary; Reeves, Dianne; Lanese, Bob; Helba, Cindy; Miller, Suzanne M; Ross, Eric A

2014-01-01

Objective In an effort to standardize behavioral measures and their data representation, the present study develops a methodology for incorporating measures found in the National Cancer Institute's (NCI) grid-enabled measures (GEM) portal, a repository for behavioral and social measures, into the cancer data standards registry and repository (caDSR). Methods The methodology consists of four parts for curating GEM measures into the caDSR: (1) develop unified modeling language (UML) models for behavioral measures; (2) create common data elements (CDE) for UML components; (3) bind CDE with concepts from the NCI thesaurus; and (4) register CDE in the caDSR. Results UML models have been developed for four GEM measures, which have been registered in the caDSR as CDE. New behavioral concepts related to these measures have been created and incorporated into the NCI thesaurus. Best practices for representing measures using UML models have been utilized in the practice (eg, caDSR). One dataset based on a GEM-curated measure is available for use by other systems and users connected to the grid. Conclusions Behavioral and population science data can be standardized by using and extending current standards. A new branch of CDE for behavioral science was developed for the caDSR. It expands the caDSR domain coverage beyond the clinical and biological areas. In addition, missing terms and concepts specific to the behavioral measures addressed in this paper were added to the NCI thesaurus. A methodology was developed and refined for curation of behavioral and population science data. PMID:24076749

[Design of a supervision model for administration of the Child Development Evaluation Test at primary care facilities in Mexico].

PubMed

Villasís-Keever, Miguel Ángel; Rizzoli-Córdoba, Antonio; Delgado-Ginebra, Ismael; Mares-Serratos, Blanca Berenice; Martell-Valdez, Liliana; Sánchez-Velázquez, Olivia; Reyes-Morales, Hortensia; O'Shea-Cuevas, Gabriel; Aceves-Villagrán, Daniel; Carrasco-Mendoza, Joaquín; Antillón-Ocampo, Fátima Adriana; Villagrán-Muñoz, Víctor Manuel; Halley-Castillo, Elizabeth; Baqueiro-Hernández, César Iván; Pizarro-Castellanos, Mariel; Martain-Pérez, Itzamara Jacqueline; Palma-Tavera, Josuha Alexander; Vargas-López, Guillermo; Muñoz-Hernández, Onofre

The Child Development Evaluation (CDE) test designed and validated in Mexico has been used as a screening tool for developmental problems in primary care facilities across Mexico. Heterogeneous results were found among those states where these were applied, despite using the same standardized training model for application. The objective was to evaluate a supervision model for quality of application of the CDE test at primary care facilities. A study was carried out in primary care facilities from three Mexican states to evaluate concordance of the results between supervisor and primary care personnel who administered the test using two different methods: direct observation (shadow study) or reapplication of the CDE test (consistency study). There were 380 shadow studies applied to 51 psychologists. General concordance of the shadow study was 86.1% according to the supervisor: green 94.5%, yellow 73.2% and red 80.0%. There were 302 re-test evaluations with a concordance of 88.1% (n=266): green 96.8%, yellow 71.7% and red 81.8%. There were no differences between CDE test subgroups by age. Both shadow and re-test study were adequate for the evaluation of the quality of the administration of the CDE Test and may be useful as a model of supervision in primary care facilities. The decision of which test to use relies on the availability of supervisors. Copyright © 2015 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

A Case Study of Learning, Motivation, and Performance Strategies for Teaching and Coaching CDE Teams

ERIC Educational Resources Information Center

Ball, Anna; Bowling, Amanda; Bird, Will

2016-01-01

This intrinsic case study examined the case of students on CDE (Career Development Event) teams preparing for state competitive events and the teacher preparing them in a school with a previous exemplary track record of winning multiple state and national career development events. The students were interviewed multiple times during the 16-week…

A time fractional convection-diffusion equation to model gas transport through heterogeneous soil and gas reservoirs

NASA Astrophysics Data System (ADS)

Chang, Ailian; Sun, HongGuang; Zheng, Chunmiao; Lu, Bingqing; Lu, Chengpeng; Ma, Rui; Zhang, Yong

2018-07-01

Fractional-derivative models have been developed recently to interpret various hydrologic dynamics, such as dissolved contaminant transport in groundwater. However, they have not been applied to quantify other fluid dynamics, such as gas transport through complex geological media. This study reviewed previous gas transport experiments conducted in laboratory columns and real-world oil-gas reservoirs and found that gas dynamics exhibit typical sub-diffusive behavior characterized by heavy late-time tailing in the gas breakthrough curves (BTCs), which cannot be effectively captured by classical transport models. Numerical tests and field applications of the time fractional convection-diffusion equation (fCDE) have shown that the fCDE model can capture the observed gas BTCs including their apparent positive skewness. Sensitivity analysis further revealed that the three parameters used in the fCDE model, including the time index, the convection velocity, and the diffusion coefficient, play different roles in interpreting the delayed gas transport dynamics. In addition, the model comparison and analysis showed that the time fCDE model is efficient in application. Therefore, the time fractional-derivative models can be conveniently extended to quantify gas transport through natural geological media such as complex oil-gas reservoirs.

Grain dust-induced lung inflammation is reduced by Rhodobacter sphaeroides diphosphoryl lipid A.

PubMed

Jagielo, P J; Quinn, T J; Qureshi, N; Schwartz, D A

1998-01-01

To further determine the importance of endotoxin in grain dust-induced inflammation of the lower respiratory tract, we evaluated the efficacy of pentaacylated diphosphoryl lipid A derived from the lipopolysaccharide of Rhodobacter sphaeroides (RsDPLA) as a partial agonist of grain dust-induced airway inflammation. RsDPLA is a relatively inactive compound compared with lipid A derived from Escherichia coli (LPS) and has been demonstrated to act as a partial agonist of LPS-induced inflammation. To assess the potential stimulatory effect of RsDPLA in relation to LPS, we incubated THP-1 cells with RsDPLA (0.001-100 micrograms/ml), LPS (0.02 microgram endotoxin activity/ml), or corn dust extract (CDE; 0.02 microgram endotoxin activity/ml). Incubation with RsDPLA revealed a tumor necrosis factor (TNF)-alpha stimulatory effect at 100 micrograms/ml. In contrast, incubation with LPS or CDE resulted in TNF-alpha release at 0.02 microgram/ml. Pretreatment of THP-1 cells with varying concentrations of RsDPLA before incubation with LPS or CDE (0.02 microgram endotoxin activity/ml) resulted in a dose-dependent reduction in the LPS- or CDE-induced release of TNF-alpha with concentrations of RsDPLA of up to 10 micrograms/ml but not at 100 micrograms/ml. To further understand the role of endotoxin in grain dust-induced airway inflammation, we utilized the unique LPS inhibitory property of RsDPLA to determine the inflammatory response to inhaled CDE in mice in the presence of RsDPLA. Ten micrograms of RsDPLA intratracheally did not cause a significant inflammatory response compared with intratracheal saline. However, pretreatment of mice with 10 micrograms of RsDPLA intratracheally before exposure to CDE (5.4 and 0.2 micrograms/m3) or LPS (7.2 and 0.28 micrograms/m3) resulted in significant reductions in the lung lavage concentrations of total cells, neutrophils, and specific proinflammatory cytokines compared with mice pretreated with sterile saline. These results confirm the LPS-inhibitory effect of RsDPLA and support the role of endotoxin as the principal agent in grain dust causing airway inflammation.

Effects of cadmium, estradiol-17beta and their interaction on gonadal condition and metamorphosis of male and female African clawed frog, Xenopus laevis

USGS Publications Warehouse

Sharma, Bibek; Patino, Reynaldo

2010-01-01

To assess interaction effects between cadmium (Cd, a putative xenoestrogen) and estradiol-17beta (E(2)) on sex differentiation and metamorphosis, Xenopus laevis were exposed to solvent-control (0.005% ethanol), Cd (10microgL(-1)), E(2) (1microgL(-1)), or Cd and E(2) (Cd+E(2)) in FETAX medium from fertilization to 75d postfertilization. Each treatment was applied to four aquaria, each with 30 fertilized eggs. Mortality was recorded and animals were sampled as they completed metamorphosis (Nieuwkoop and Faber stage 66). Gonadal sex of individuals (including >or= tadpoles NF stage 55 at day 75) was determined gross-morphologically and used to compute sex ratios. Time course and percent completion of metamorphosis, snout-vent length (SVL), hindlimb length (HLL) and weight were analyzed for each gender separately. Survival rates did not differ among treatments. The E(2) and Cd+E(2) treatments significantly skewed sex ratios towards females; however, no sex-ratio differences were observed between the control and Cd treatments or between the E(2) and Cd+E(2) treatments. Time course of metamorphosis was generally delayed and percent completion of metamorphosis was generally reduced in males and females exposed to Cd, E(2) or their combination compared to control animals. In males, but not females, the effect of Cd+E(2) was greater than that of individual chemicals. Weight at completion of metamorphosis was reduced only in females and only by the Cd+E(2) treatment. In conclusion, although Cd at an environmentally relevant concentration did not exhibit direct or indirect feminizing effects in Xenopus tadpoles, the metal and E(2) both had similar inhibitory effects on metamorphosis that were of greater magnitude in males than females.

Sharing behavioral data through a grid infrastructure using data standards.

PubMed

Min, Hua; Ohira, Riki; Collins, Michael A; Bondy, Jessica; Avis, Nancy E; Tchuvatkina, Olga; Courtney, Paul K; Moser, Richard P; Shaikh, Abdul R; Hesse, Bradford W; Cooper, Mary; Reeves, Dianne; Lanese, Bob; Helba, Cindy; Miller, Suzanne M; Ross, Eric A

2014-01-01

In an effort to standardize behavioral measures and their data representation, the present study develops a methodology for incorporating measures found in the National Cancer Institute's (NCI) grid-enabled measures (GEM) portal, a repository for behavioral and social measures, into the cancer data standards registry and repository (caDSR). The methodology consists of four parts for curating GEM measures into the caDSR: (1) develop unified modeling language (UML) models for behavioral measures; (2) create common data elements (CDE) for UML components; (3) bind CDE with concepts from the NCI thesaurus; and (4) register CDE in the caDSR. UML models have been developed for four GEM measures, which have been registered in the caDSR as CDE. New behavioral concepts related to these measures have been created and incorporated into the NCI thesaurus. Best practices for representing measures using UML models have been utilized in the practice (eg, caDSR). One dataset based on a GEM-curated measure is available for use by other systems and users connected to the grid. Behavioral and population science data can be standardized by using and extending current standards. A new branch of CDE for behavioral science was developed for the caDSR. It expands the caDSR domain coverage beyond the clinical and biological areas. In addition, missing terms and concepts specific to the behavioral measures addressed in this paper were added to the NCI thesaurus. A methodology was developed and refined for curation of behavioral and population science data. 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.

Targeted Pressure Management During CO 2 Sequestration: Optimization of Well Placement and Brine Extraction

DOE PAGES

Cihan, Abdullah; Birkholzer, Jens; Bianchi, Marco

2014-12-31

Large-scale pressure increases resulting from carbon dioxide (CO 2) injection in the subsurface can potentially impact caprock integrity, induce reactivation of critically stressed faults, and drive CO 2 or brine through conductive features into shallow groundwater. Pressure management involving the extraction of native fluids from storage formations can be used to minimize pressure increases while maximizing CO2 storage. However, brine extraction requires pumping, transportation, possibly treatment, and disposal of substantial volumes of extracted brackish or saline water, all of which can be technically challenging and expensive. This paper describes a constrained differential evolution (CDE) algorithm for optimal well placement andmore » injection/ extraction control with the goal of minimizing brine extraction while achieving predefined pressure contraints. The CDE methodology was tested for a simple optimization problem whose solution can be partially obtained with a gradient-based optimization methodology. The CDE successfully estimated the true global optimum for both extraction well location and extraction rate, needed for the test problem. A more complex example application of the developed strategy was also presented for a hypothetical CO 2 storage scenario in a heterogeneous reservoir consisting of a critically stressed fault nearby an injection zone. Through the CDE optimization algorithm coupled to a numerical vertically-averaged reservoir model, we successfully estimated optimal rates and locations for CO 2 injection and brine extraction wells while simultaneously satisfying multiple pressure buildup constraints to avoid fault activation and caprock fracturing. The study shows that the CDE methodology is a very promising tool to solve also other optimization problems related to GCS, such as reducing ‘Area of Review’, monitoring design, reducing risk of leakage and increasing storage capacity and trapping.« less

Correlation transfer and diffusion of ultrasound-modulated multiply scattered light.

PubMed

Sakadzić, Sava; Wang, Lihong V

2006-04-28

We develop a temporal correlation transfer equation (CTE) and a temporal correlation diffusion equation (CDE) for ultrasound-modulated multiply scattered light. These equations can be applied to an optically scattering medium with embedded optically scattering and absorbing objects to calculate the power spectrum of light modulated by a nonuniform ultrasound field. We present an analytical solution based on the CDE and Monte Carlo simulation results for light modulated by a cylinder of ultrasound in an optically scattering slab. We further validate with experimental measurements the numerical calculations for an actual ultrasound field. The CTE and CDE are valid for moderate ultrasound pressures and on a length scale comparable with the optical transport mean-free path. These equations should be applicable to a wide spectrum of conditions for ultrasound-modulated optical tomography of soft biological tissues.

Unraveling a molecular determinant for clathrin-independent internalization of the M2 muscarinic acetylcholine receptor

PubMed Central

Wan, Min; Zhang, Wenhua; Tian, Yangli; Xu, Chanjuan; Xu, Tao; Liu, Jianfeng; Zhang, Rongying

2015-01-01

Endocytosis and postendocytic sorting of G-protein-coupled receptors (GPCRs) is important for the regulation of both their cell surface density and signaling profile. Unlike the mechanisms of clathrin-dependent endocytosis (CDE), the mechanisms underlying the control of GPCR signaling by clathrin-independent endocytosis (CIE) remain largely unknown. Among the muscarinic acetylcholine receptors (mAChRs), the M4 mAChR undergoes CDE and recycling, whereas the M2 mAChR is internalized through CIE and targeted to lysosomes. Here we investigated the endocytosis and postendocytic trafficking of M2 mAChR based on a comparative analysis of the third cytoplasmic domain in M2 and M4 mAChRs. For the first time, we identified that the sequence 374KKKPPPS380 servers as a sorting signal for the clathrin-independent internalization of M2 mAChR. Switching 374KKKPPPS380 to the i3 loop of the M4 mAChR shifted the receptor into lysosomes through the CIE pathway; and therefore away from CDE and recycling. We also found another previously unidentified sequence that guides CDE of the M2 mAChR, 361VARKIVKMTKQPA373, which is normally masked in the presence of the downstream sequence 374KKKPPPS380. Taken together, our data indicate that endocytosis and postendocytic sorting of GPCRs that undergo CIE could be sequence-dependent. PMID:26094760

(Non-)symbolic magnitude processing in children with mathematical difficulties: A meta-analysis.

PubMed

Schwenk, Christin; Sasanguie, Delphine; Kuhn, Jörg-Tobias; Kempe, Sophia; Doebler, Philipp; Holling, Heinz

2017-05-01

Symbolic and non-symbolic magnitude representations, measured by digit or dot comparison tasks, are assumed to underlie the development of arithmetic skills. The comparison distance effect (CDE) has been suggested as a hallmark of the preciseness of mental magnitude representations. It implies that two magnitudes are harder to discriminate when the numerical distance between them is small, and may therefore differ in children with mathematical difficulties (MD), i.e. low mathematical achievement or dyscalculia. However, empirical findings on the CDE in children with MD are heterogeneous, and only few studies assess both symbolic and non-symbolic skills. This meta-analysis therefore integrates 44 symbolic and 48 non-symbolic response time (RT) outcomes reported in nineteen studies (N=1630 subjects, aged 6-14 years). Independent of age, children with MD show significantly longer mean RTs than typically achieving controls, particularly on symbolic (Hedges' g=0.75; 95% CI [0.51; 0.99]), but to a significantly lower extent also on non-symbolic (g=0.24; 95% CI [0.13; 0.36]) tasks. However, no group differences were found for the CDE. Extending recent work, these meta-analytical findings on children with MD corroborate the diagnostic importance of magnitude comparison speed in symbolic tasks. By contrast, the validity of CDE measures in assessing MD is questioned. Copyright © 2017 Elsevier Ltd. All rights reserved.

Long-range dynamic polarization potentials for 11Be projectiles on 64Zn

NASA Astrophysics Data System (ADS)

So, W. Y.; Kim, K. S.; Choi, K. S.; Cheoun, Myung-Ki

2015-07-01

We investigate the effects of the long-range dynamic polarization (LRDP) potential, which consists of the Coulomb dipole excitation (CDE) potential and the long-range nuclear (LRN) potential, for the 11Be projectile on 64Zn. To study these effects, we perform a χ2 analysis of an optical model including the LRDP potential as well as a conventional short-range nuclear (SRN) potential. To take these effects into account, we argue that both the CDE and LRN potentials are essential to explaining the experimental values of PE, which is the ratio of the elastic scattering cross section to the Rutherford cross section. The Coulomb and nuclear parts of the LRDP potential are found to contribute to a strong absorption effect. Strong absorption occurs because the real part of the CDE and LRN potentials lowers the barrier, and the imaginary part of the CDE and LRN potentials removes the flux from the elastic channel in the 11Be+64Zn system. Finally, we extract the total reaction cross section σR including the inelastic, breakup, and fusion cross sections. The contribution of the inelastic scattering by the first excited state at ɛx1 st=0.32 MeV (1 /2-) is found to be relatively large and cannot be ignored. In addition, our results are shown to agree quite well with the experimental breakup reaction cross section by using a fairly large radius parameter.

Transcriptional regulation of Saccharomyces cerevisiaeCYS3 encoding cystathionine γ-lyase

PubMed Central

Hiraishi, Hiroyuki; Miyake, Tsuyoshi

2008-01-01

In studying the regulation of GSH11, the structural gene of the high-affinity glutathione transporter (GSH-P1) in Saccharomyces cerevisiae, a cis-acting cysteine responsive element, CCGCCACAC (CCG motif), was detected. Like GSH-P1, the cystathionine γ-lyase encoded by CYS3 is induced by sulfur starvation and repressed by addition of cysteine to the growth medium. We detected a CCG motif (−311 to −303) and a CGC motif (CGCCACAC; −193 to −186), which is one base shorter than the CCG motif, in the 5′-upstream region of CYS3. One copy of the centromere determining element 1, CDE1 (TCACGTGA; −217 to −210), being responsible for regulation of the sulfate assimilation pathway genes, was also detected. We tested the roles of these three elements in the regulation of CYS3. Using a lacZ-reporter assay system, we found that the CCG/CGC motif is required for activation of CYS3, as well as for its repression by cysteine. In contrast, the CDE1 motif was responsible for only activation of CYS3. We also found that two transcription factors, Met4 and VDE, are responsible for activation of CYS3 through the CCG/CGC and CDE1 motifs. These observations suggest a dual regulation of CYS3 by factors that interact with the CDE1 motif and the CCG/CGC motifs. PMID:18317767

Thermal stress imposed by prototype bilayer and current ground crew chemical defense ensembles: a limited laboratory comparison. Final report, 30 June 1986-1 January 1987

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

Krock, L.P.; Navalta, R.; Myhre, L.G.

An open bilayer ground-crew chemical defense ensemble (CDE) was proposed to reduce the thermal burden during vapor-only exposure periods. This study compared the thermal-stress profile of the proposed ensemble to that produced by the currently employed closed CDE. Four subjects, alternating ensembles on separate days, walked on a treadmill in an environmental chamber at 5.3 km/h (3.3 mph) and 2% grade (an energy expenditure of 350 kcal/h) for alternating work/rest to achieve significant recovery. Mean total sweat production was lower (1.38 vs. 2.50 liters) and percent sweat evaporation greater (65.7% vs. 30.0%) in the prototype ensemble than in the CDE.more » The prototype ensemble provided greater heat dissipation and allowed more-efficient sweat evaporation which had the double benefit of reducing heat storage and limiting dehydration.« less

Control of head lice with a coconut-derived emulsion shampoo.

PubMed

Connolly, M; Stafford, K A; Coles, G C; Kennedy, C T C; Downs, A M R

2009-01-01

To evaluate a novel coconut-derived emulsion (CDE) shampoo against head lice infestation in children. A school trial in which pupils were treated on days 0 and 7 and checked on days 8 and 15 and a family trial where product was applied by parents three times in 2 weeks or used as a cosmetic shampoo and checked on days 14 and days 70. UK schools in Bristol and Western-super-Mare and families in Northern Somerset. Numbers of children free from infestation after treatment. In the school trial, percentage cures at day 8 were 14% (permethrin, n=7) and 61% (CDE, n=37). In the family trial where all family members were treated, cure rate was 96% (n=28), and if the shampoo was subsequently used as a cosmetic shampoo, only 1 of 12 children became re-infested after 10 weeks. CDE shampoo is a novel effective method of controlling head lice and used after treatment as a cosmetic shampoo can aid in the reduction of re-infestation.

Common data elements for clinical research in mitochondrial disease: a National Institute for Neurological Disorders and Stroke project.

PubMed

Karaa, Amel; Rahman, Shamima; Lombès, Anne; Yu-Wai-Man, Patrick; Sheikh, Muniza K; Alai-Hansen, Sherita; Cohen, Bruce H; Dimmock, David; Emrick, Lisa; Falk, Marni J; McCormack, Shana; Mirsky, David; Moore, Tony; Parikh, Sumit; Shoffner, John; Taivassalo, Tanja; Tarnopolsky, Mark; Tein, Ingrid; Odenkirchen, Joanne C; Goldstein, Amy

2017-05-01

The common data elements (CDE) project was developed by the National Institute of Neurological Disorders and Stroke (NINDS) to provide clinical researchers with tools to improve data quality and allow for harmonization of data collected in different research studies. CDEs have been created for several neurological diseases; the aim of this project was to develop CDEs specifically curated for mitochondrial disease (Mito) to enhance clinical research. Nine working groups (WGs), composed of international mitochondrial disease experts, provided recommendations for Mito clinical research. They initially reviewed existing NINDS CDEs and instruments, and developed new data elements or instruments when needed. Recommendations were organized, internally reviewed by the Mito WGs, and posted online for external public comment for a period of eight weeks. The final version was again reviewed by all WGs and the NINDS CDE team prior to posting for public use. The NINDS Mito CDEs and supporting documents are publicly available on the NINDS CDE website ( https://commondataelements.ninds.nih.gov/ ), organized into domain categories such as Participant/Subject Characteristics, Assessments, and Examinations. We developed a comprehensive set of CDE recommendations, data definitions, case report forms (CRFs), and guidelines for use in Mito clinical research. The widespread use of CDEs is intended to enhance Mito clinical research endeavors, including natural history studies, clinical trial design, and data sharing. Ongoing international collaboration will facilitate regular review, updates and online publication of Mito CDEs, and support improved consistency of data collection and reporting.

Prospective study of Centurion® versus Infiniti® phacoemulsification systems: surgical and visual outcomes.

PubMed

Oh, Lawrence J; Nguyen, Chu Luan; Wong, Eugene; Wang, Samuel S Y; Francis, Ian C

2017-01-01

To evaluate surgical outcomes (SOs) and visual outcomes (VOs) in cataract surgery comparing the Centurion ® phacoemulsification system (CPS) with the Infiniti ® phacoemulsification system (IPS). Prospective, consecutive study in a single-site private practice. Totally 412 patients undergoing cataract surgery with either the CPS using the 30-degree balanced ® tip ( n =207) or the IPS using the 30-degree Kelman ® tip ( n =205). Intraoperative and postoperative outcomes were documented prospectively up to one month follow-up. Nuclear sclerosis (NS) grade, cumulated dissipated energy (CDE), preoperative corrected distance visual acuity (CDVA), and CDVA at one month were recorded. CDE was 13.50% less in the whole CPS compared with the whole IPS subcohort. In eyes with NS grade III or greater, CDE was 28.87% less with CPS ( n =70) compared with IPS ( n =44) ( P =0.010). Surgical complications were not statistically different between the two subcohorts ( P =0.083), but in the one case of vitreous loss using the CPS, CDVA of 6/4 was achieved at one month. The mean CDVAs (VOs) at one month for NS grade III and above cataracts were -0.17 logMAR (6/4.5) in the CPS and -0.15 logMAR (6/4.5) in the IPS subcohort respectively ( P =0.033). CDE is 28.87% less, and VOs are significantly improved, in denser cataracts in the CPS compared with the IPS. The authors recommend the CPS for cases with denser nuclei.

Macular edema after uncomplicated cataract surgery: a role for phacoemulsification energy and vitreoretinal interface status?

PubMed

Anastasilakis, Konstantinos; Mourgela, Anna; Symeonidis, Chrysanthos; Dimitrakos, Stavros A; Ekonomidis, Panayiotis; Tsinopoulos, Ioannis

2015-01-01

To study postoperative macular thickness fluctuations measured by spectral-domain optical coherence tomography (SD-OCT) and to investigate a potential correlation among macular edema (ME) incidence, cumulative dissipated energy (CDE) released during phacoemulsification, and vitreoretinal interface status. This is a prospective, cross-sectional study of 106 cataract patients with no macular disorder who underwent phacoemulsification. Best-corrected visual acuity measurement, slit-lamp examination, OCT scans were performed preoperatively and 30 and 90 days postoperatively. The intraoperative parameters measured were CDE and total phacoemulsification time. The SD-OCT parameters assessed were central subfield thickness (CST), cube average thickness (CAT), cube macular volume, vitreoretinal interface status, and presence of cystoid or diffuse ME. Four patients (3.8%) developed subclinical ME. Regarding ME, there was no significant difference between patients with presence or absence of posterior vitreous detachment (chi-square, p = 0.57), although 75% of ME cases were observed in patients with attached posterior vitreous. With regard to comparison between eyes with and without subclinical CME incidence, CDE (p = 0.05), phacoemulsification time (p = 0.001), CST at month 1 (p = 0.002), cube macular volume at month 1 (p = 0.039), and CAT at month 1 (p = 0.050) were significantly higher in the subclinical CME group. This study provides evidence that OCT macular thickness parameters increase significantly at first and third month postoperatively and that the incidence of pseudophakic ME can be affected by CDE.

Radiographic outcomes among South African coal miners.

PubMed

Naidoo, Rajen N; Robins, Thomas G; Solomon, A; White, Neil; Franzblau, Alfred

2004-10-01

This study, the first to document the prevalence of pneumoconiosis among a living South African coal mining cohort, describes dose-response relationships between coal workers' pneumoconiosis and respirable dust exposure, and relationships between pneumoconiosis and both lung function deterioration and respiratory symptoms. A total of 684 current miners and 188 ex-miners from three bituminous-coal mines in Mpumalanga, South Africa, was studied. Chest radiographs were read according to the International Labour Organization (ILO) classification by two experienced readers, one an accredited National Institute for Occupational Safety and Health (NIOSH) "B" reader. Interviews were conducted to assess symptoms, work histories (also obtained from company records), smoking, and other risk factors. Spirometry was performed by trained technicians. Cumulative respirable dust exposure (CDE) estimates were constructed from historical company-collected sampling and researcher-collected personal dust measurements. kappa-Statistics compared the radiographic outcomes predicted by the two readers. An average profusion score was used in the analysis for the outcomes of interest. Because of possible confounding by employment status, most analyses were stratified on current and ex-miner status. The overall prevalence of pneumoconiosis was low (2%-4%). The degree of agreement between the two readers for profusion was moderate to high (kappa=0.58). A significant association (P<0.001) and trend (P<0.001) was seen for pneumoconiosis with increasing categories of CDE among current miners only. A significant (P<0.0001) additional 58 mg-years/m3 CDE was seen among those with pneumoconiosis compared to those without. CDE contributed to a statistically significant 0.19% and 0.11% greater decline in the percent predicted 1-second forced expiration volume (FEV1) and forced vital capacity (FVC), respectively, among current miners with pneumoconiosis than among those without. Logistic regression models showed no significant relationships between pneumoconiosis and symptoms. The overall prevalence of pneumoconiosis, although significantly associated with CDE, was low. The presence of pneumoconiosis is associated with meaningful health effects, including deterioration in lung function. Intervention measures that control exposure are indicated, to reduce these functional effects.

Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups

PubMed Central

Solbrig, Harold R; Chute, Christopher G

2012-01-01

Objective The objective of this study is to develop an approach to evaluate the quality of terminological annotations on the value set (ie, enumerated value domain) components of the common data elements (CDEs) in the context of clinical research using both unified medical language system (UMLS) semantic types and groups. Materials and methods The CDEs of the National Cancer Institute (NCI) Cancer Data Standards Repository, the NCI Thesaurus (NCIt) concepts and the UMLS semantic network were integrated using a semantic web-based framework for a SPARQL-enabled evaluation. First, the set of CDE-permissible values with corresponding meanings in external controlled terminologies were isolated. The corresponding value meanings were then evaluated against their NCI- or UMLS-generated semantic network mapping to determine whether all of the meanings fell within the same semantic group. Results Of the enumerated CDEs in the Cancer Data Standards Repository, 3093 (26.2%) had elements drawn from more than one UMLS semantic group. A random sample (n=100) of this set of elements indicated that 17% of them were likely to have been misclassified. Discussion The use of existing semantic web tools can support a high-throughput mechanism for evaluating the quality of large CDE collections. This study demonstrates that the involvement of multiple semantic groups in an enumerated value domain of a CDE is an effective anchor to trigger an auditing point for quality evaluation activities. Conclusion This approach produces a useful quality assurance mechanism for a clinical study CDE repository. PMID:22511016

Prospective study of Centurion® versus Infiniti® phacoemulsification systems: surgical and visual outcomes

PubMed Central

Oh, Lawrence J.; Nguyen, Chu Luan; Wong, Eugene; Wang, Samuel S.Y.; Francis, Ian C.

2017-01-01

AIM To evaluate surgical outcomes (SOs) and visual outcomes (VOs) in cataract surgery comparing the Centurion® phacoemulsification system (CPS) with the Infiniti® phacoemulsification system (IPS). METHODS Prospective, consecutive study in a single-site private practice. Totally 412 patients undergoing cataract surgery with either the CPS using the 30-degree balanced® tip (n=207) or the IPS using the 30-degree Kelman® tip (n=205). Intraoperative and postoperative outcomes were documented prospectively up to one month follow-up. Nuclear sclerosis (NS) grade, cumulated dissipated energy (CDE), preoperative corrected distance visual acuity (CDVA), and CDVA at one month were recorded. RESULTS CDE was 13.50% less in the whole CPS compared with the whole IPS subcohort. In eyes with NS grade III or greater, CDE was 28.87% less with CPS (n=70) compared with IPS (n=44) (P=0.010). Surgical complications were not statistically different between the two subcohorts (P=0.083), but in the one case of vitreous loss using the CPS, CDVA of 6/4 was achieved at one month. The mean CDVAs (VOs) at one month for NS grade III and above cataracts were -0.17 logMAR (6/4.5) in the CPS and -0.15 logMAR (6/4.5) in the IPS subcohort respectively (P=0.033). CONCLUSION CDE is 28.87% less, and VOs are significantly improved, in denser cataracts in the CPS compared with the IPS. The authors recommend the CPS for cases with denser nuclei. PMID:29181313

Outcomes of torsional microcoaxial phacoemulsification performed by 12-degree and 22-degree bent tips.

PubMed

Helvacioglu, Firat; Yeter, Celal; Tunc, Zeki; Sencan, Sadik

2013-08-01

To compare the safety and efficacy of Ozil Intelligent Phaco torsional microcoaxial phacoemulsification surgeries performed with 12-degree and 22-degree bent tips using the Infiniti Vision System. Maltepe University School of Medicine Department of Ophthalmology, Istanbul, Turkey. Comparative case series. Eyes were assigned to 2.2 mm microcoaxial phacoemulsification using the torsional mode with a 22-degree bent tip (Group 1) or a 12-degree bent tip (Group 2). The primary outcome measures were ultrasound time (UST), cumulative dissipated energy (CDE), longitudinal and torsional ultrasound (US) amplitudes, mean surgical time, mean volume of balanced salt solution used, and surgical complications. Both groups included 45 eyes. The mean UST, CDE, longitudinal US amplitude, and torsional US amplitude were 65 seconds ± 27.23 (SD), 11.53 ± 6.99, 0.22 ± 0.26, and 42.86 ± 15.64, respectively, in Group 1 and 84 ± 45.04 seconds, 16.68 ± 10.66, 0.48 ± 0.68, and 46.27 ± 14.74, respectively, in Group 2. The mean UST, CDE, and longitudinal amplitudes were significantly lower in Group 1 (P=.003, P=.008, and P=.022, respectively). The mean volume of balanced salt solution was 73.33 ± 28.58 cc in Group 1 and 82.08 ± 26.21 cc in Group 2 (P=.134). Torsional phacoemulsification performed with 22-degree bent tips provided more effective lens removal than 12-degree bent tips, with a lower UST and CDE. Copyright © 2013 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

An evaluation of intraoperative and postoperative outcomes of torsional mode versus longitudinal ultrasound mode phacoemulsification: a Meta-analysis.

PubMed

Leon, Pia; Umari, Ingrid; Mangogna, Alessandro; Zanei, Andrea; Tognetto, Daniele

2016-01-01

To evaluate and compare the intraoperative parameters and postoperative outcomes of torsional mode and longitudinal mode of phacoemulsification. Pertinent studies were identified by a computerized MEDLINE search from January 2002 to September 2013. The Meta-analysis is composed of two parts. In the first part the intraoperative parameters were considered: ultrasound time (UST) and cumulative dissipated energy (CDE). The intraoperative values were also distinctly considered for two categories (moderate and hard cataract group) depending on the nuclear opacity grade. In the second part of the study the postoperative outcomes as the best corrected visual acuity (BCVA) and the endothelial cell loss (ECL) were taken in consideration. The UST and CDE values proved statistically significant in support of torsional mode for both moderate and hard cataract group. The analysis of BCVA did not present statistically significant difference between the two surgical modalities. The ECL count was statistically significant in support of torsional mode (P<0.001). The Meta-analysis shows the superiority of the torsional mode for intraoperative parameters (UST, CDE) and postoperative ECL outcomes.

An evaluation of intraoperative and postoperative outcomes of torsional mode versus longitudinal ultrasound mode phacoemulsification: a Meta-analysis

PubMed Central

Leon, Pia; Umari, Ingrid; Mangogna, Alessandro; Zanei, Andrea; Tognetto, Daniele

2016-01-01

AIM To evaluate and compare the intraoperative parameters and postoperative outcomes of torsional mode and longitudinal mode of phacoemulsification. METHODS Pertinent studies were identified by a computerized MEDLINE search from January 2002 to September 2013. The Meta-analysis is composed of two parts. In the first part the intraoperative parameters were considered: ultrasound time (UST) and cumulative dissipated energy (CDE). The intraoperative values were also distinctly considered for two categories (moderate and hard cataract group) depending on the nuclear opacity grade. In the second part of the study the postoperative outcomes as the best corrected visual acuity (BCVA) and the endothelial cell loss (ECL) were taken in consideration. RESULTS The UST and CDE values proved statistically significant in support of torsional mode for both moderate and hard cataract group. The analysis of BCVA did not present statistically significant difference between the two surgical modalities. The ECL count was statistically significant in support of torsional mode (P<0.001). CONCLUSION The Meta-analysis shows the superiority of the torsional mode for intraoperative parameters (UST, CDE) and postoperative ECL outcomes. PMID:27366694

Initial Flight Tests of the NASA F-15B Propulsion Flight Test Fixture

NASA Technical Reports Server (NTRS)

Palumbo, Nathan; Moes, Timothy R.; Vachon, M. Jake

2002-01-01

Flights of the F-15B/Propulsion Flight Test Fixture (PFTF) with a Cone Drag Experiment (CDE) attached have been accomplished at NASA Dryden Flight Research Center. Mounted underneath the fuselage of an F-15B airplane, the PFTF provides volume for experiment systems and attachment points for propulsion experiments. A unique feature of the PFTF is the incorporation of a six-degree-of-freedom force balance. The force balance mounts between the PFTF and experiment and measures three forces and moments. The CDE has been attached to the force balance for envelope expansion flights. This experiment spatially and inertially simulates a large propulsion test article. This report briefly describes the F-15B airplane, the PFTF, and the force balance. A detailed description of the CDE is provided. Force-balance ground testing and stiffness modifications are described. Flight profiles and selected flight data from the envelope expansion flights are provided and discussed, including force-balance data, the internal PFTF thermal and vibration environment, a handling qualities assessment, and performance capabilities of the F-15B airplane with the PFTF installed.

Disentangling interacting dark energy cosmologies with the three-point correlation function

NASA Astrophysics Data System (ADS)

Moresco, Michele; Marulli, Federico; Baldi, Marco; Moscardini, Lauro; Cimatti, Andrea

2014-10-01

We investigate the possibility of constraining coupled dark energy (cDE) cosmologies using the three-point correlation function (3PCF). Making use of the CODECS N-body simulations, we study the statistical properties of cold dark matter (CDM) haloes for a variety of models, including a fiducial ΛCDM scenario and five models in which dark energy (DE) and CDM mutually interact. We measure both the halo 3PCF, ζ(θ), and the reduced 3PCF, Q(θ), at different scales (2 < r [h-1 Mpc ] < 40) and redshifts (0 ≤ z ≤ 2). In all cDE models considered in this work, Q(θ) appears flat at small scales (for all redshifts) and at low redshifts (for all scales), while it builds up the characteristic V-shape anisotropy at increasing redshifts and scales. With respect to the ΛCDM predictions, cDE models show lower (higher) values of the halo 3PCF for perpendicular (elongated) configurations. The effect is also scale-dependent, with differences between ΛCDM and cDE models that increase at large scales. We made use of these measurements to estimate the halo bias, that results in fair agreement with the one computed from the two-point correlation function (2PCF). The main advantage of using both the 2PCF and 3PCF is to break the bias-σ8 degeneracy. Moreover, we find that our bias estimates are approximately independent of the assumed strength of DE coupling. This study demonstrates the power of a higher order clustering analysis in discriminating between alternative cosmological scenarios, for both present and forthcoming galaxy surveys, such as e.g. Baryon Oscillation Spectroscopic Survey and Euclid.

Comparison of cumulative dissipated energy delivered by active-fluidic pressure control phacoemulsification system versus gravity-fluidics.

PubMed

Gonzalez-Salinas, Roberto; Garza-Leon, Manuel; Saenz-de-Viteri, Manuel; Solis-S, Juan C; Gulias-Cañizo, Rosario; Quiroz-Mercado, Hugo

2017-08-22

To compare the cumulative dissipated energy (CDE), aspiration time and estimated aspiration fluid utilized during phacoemulsification cataract surgery using two phacoemulsification systems . A total of 164 consecutive eyes of 164 patients undergoing cataract surgery, 82 in the active-fluidics group and 82 in the gravity-fluidics group were enrolled in this study. Cataracts graded NII to NIII using LOCS II were included. Each subject was randomly assigned to one of the two platforms with a specific configuration: the active-fluidics Centurion ® phacoemulsification system or the gravity-fluidics Infiniti ® Vision System. CDE, aspiration time (AT) and the mean estimated aspiration fluid (EAF) were registered and compared. A mean age of 68.3 ± 9.8 years was found (range 57-92 years), and no significant difference was evident between both groups. A positive correlation between the CDE values obtained by both platforms was verified (r = 0.271, R 2  = 0.073, P = 0.013). Similarly, a significant correlation was evidenced for the EAF (r = 0.334, R 2  = 0.112, P = 0.046) and AT values (r = 0.156, R 2  = 0.024, P = 0.161). A statistically significantly lower CDE count, aspiration time and estimated fluid were obtained using the active-fluidics configuration when compared to the gravity-fluidics configuration by 19.29, 12.10 and 9.29%, respectively (P = 0.001, P < 0.0001 and P = 0.001). The active-fluidics Centurion ® phacoemulsification system achieved higher surgical efficiency than the gravity-fluidics Infiniti ® IP system for NII and NIII cataracts.

[Impact of a training model for the Child Development Evaluation Test in primary care].

PubMed

Rizzoli-Córdoba, Antonio; Delgado-Ginebra, Ismael; Cruz-Ortiz, Leopoldo Alfonso; Baqueiro-Hernández, César Iván; Martain-Pérez, Itzamara Jacqueline; Palma-Tavera, Josuha Alexander; Villasís-Keever, Miguel Ángel; Reyes-Morales, Hortensia; O'Shea-Cuevas, Gabriel; Aceves-Villagrán, Daniel; Carrasco-Mendoza, Joaquín; Antillón-Ocampo, Fátima Adriana; Villagrán-Muñoz, Víctor Manuel; Halley-Castillo, Elizabeth; Vargas-López, Guillermo; Muñoz-Hernández, Onofre

The Child Development Evaluation (CDE) Test is a screening tool designed and validated in Mexico for the early detection of child developmental problems. For professionals who will be administering the test in primary care facilities, previous acquisition of knowledge about the test is required in order to generate reliable results. The aim of this work was to evaluate the impact of a training model for primary care workers from different professions through the comparison of knowledge acquired during the training course. The study design was a before/after type considering the participation in a training course for the CDE test as the intervention. The course took place in six different Mexican states from October to December 2013. The same questions were used before and after. There were 394 participants included. Distribution according to professional profile was as follows: general physicians 73.4%, nursing 7.7%, psychology 7.1%, nutrition 6.1% and other professions 5.6%. The questions with the lowest correct answer rates were associated with the scoring of the CDE test. In the initial evaluation, 64.9% obtained a grade lower than 20 compared with 1.8% in the final evaluation. In the initial evaluation only 1.8% passed compared with 75.15% in the final evaluation. The proposed model allows the participants to acquire general knowledge about the CDE Test. To improve the general results in future training courses, it is required to reinforce during training the scoring and interpretation of the test together with the previous lecture of the material by the participants. Copyright © 2015 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

Role of Tellurite Resistance Operon in Filamentous Growth of Yersinia pestis in Macrophages.

PubMed

Ponnusamy, Duraisamy; Clinkenbeard, Kenneth D

2015-01-01

Yersinia pestis initiates infection by parasitism of host macrophages. In response to macrophage infections, intracellular Y. pestis can assume a filamentous cellular morphology which may mediate resistance to host cell innate immune responses. We previously observed the expression of Y. pestis tellurite resistance proteins TerD and TerE from the terZABCDE operon during macrophage infections. Others have observed a filamentous response associated with expression of tellurite resistance operon in Escherichia coli exposed to tellurite. Therefore, in this study we examine the potential role of Y. pestis tellurite resistance operon in filamentous cellular morphology during macrophage infections. In vitro treatment of Y. pestis culture with sodium tellurite (Na2TeO3) caused the bacterial cells to assume a filamentous phenotype similar to the filamentous phenotype observed during macrophage infections. A deletion mutant for genes terZAB abolished the filamentous morphologic response to tellurite exposure or intracellular parasitism, but without affecting tellurite resistance. However, a terZABCDE deletion mutant abolished both filamentous morphologic response and tellurite resistance. Complementation of the terZABCDE deletion mutant with terCDE, but not terZAB, partially restored tellurite resistance. When the terZABCDE deletion mutant was complemented with terZAB or terCDE, Y. pestis exhibited filamentous morphology during macrophage infections as well as while these complemented genes were being expressed under an in vitro condition. Further in E. coli, expression of Y. pestis terZAB, but not terCDE, conferred a filamentous phenotype. These findings support the role of Y. pestis terZAB mediation of the filamentous response phenotype; whereas, terCDE confers tellurite resistance. Although the beneficial role of filamentous morphological responses by Y. pestis during macrophage infections is yet to be fully defined, it may be a bacterial adaptive strategy to macrophage associated stresses.

Designing, Implementing, and Evaluating Secure Web Browsers

ERIC Educational Resources Information Center

Grier, Christopher L.

2009-01-01

Web browsers are plagued with vulnerabilities, providing hackers with easy access to computer systems using browser-based attacks. Efforts that retrofit existing browsers have had limited success since modern browsers are not designed to withstand attack. To enable more secure web browsing, we design and implement new web browsers from the ground…

A brief introduction to web-based genome browsers.

PubMed

Wang, Jun; Kong, Lei; Gao, Ge; Luo, Jingchu

2013-03-01

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome browsers. In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization. To give a brief introduction to the multiple-species genome browser, we describe the user interface and main functions of the Ensembl and UCSC genome browsers using the human alpha-globin gene cluster as an example. We further use the MSU and the Rice-Map genome browsers to show some special features of species-specific genome browser, taking a rice transcription factor gene OsSPL14 as an example.

Computational analysis in support of the SSTO flowpath test

NASA Astrophysics Data System (ADS)

Duncan, Beverly S.; Trefny, Charles J.

1994-10-01

A synergistic approach of combining computational methods and experimental measurements is used in the analysis of a hypersonic inlet. There are four major focal points within this study which examine the boundary layer growth on a compression ramp upstream of the cowl lip of a scramjet inlet. Initially, the boundary layer growth on the NASP Concept Demonstrator Engine (CDE) is examined. The follow-up study determines the optimum diverter height required by the SSTO Flowpath test to best duplicate the CDE results. These flow field computations are then compared to the experimental measurements and the mass average Mach number is determined for this inlet.

Computational Analysis in Support of the SSTO Flowpath Test

NASA Technical Reports Server (NTRS)

Duncan, Beverly S.; Trefny, Charles J.

1994-01-01

A synergistic approach of combining computational methods and experimental measurements is used in the analysis of a hypersonic inlet. There are four major focal points within this study which examine the boundary layer growth on a compression ramp upstream of the cowl lip of a scramjet inlet. Initially, the boundary layer growth on the NASP Concept Demonstrator Engine (CDE) is examined. The follow-up study determines the optimum diverter height required by the SSTO Flowpath test to best duplicate the CDE results. These flow field computations are then compared to the experimental measurements and the mass average Mach number is determined for this inlet.

Fundamental Understanding of Crack Growth in Structural Components of Generation IV Supercritical Light Water Reactors

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

Iouri I. Balachov; Takao Kobayashi; Francis Tanzella

2004-11-17

This work contributes to the design of safe and economical Generation-IV Super-Critical Water Reactors (SCWRs) by providing a basis for selecting structural materials to ensure the functionality of in-vessel components during the entire service life. During the second year of the project, we completed electrochemical characterization of the oxide film properties and investigation of crack initiation and propagation for candidate structural materials steels under supercritical conditions. We ranked candidate alloys against their susceptibility to environmentally assisted degradation based on the in situ data measure with an SRI-designed controlled distance electrochemistry (CDE) arrangement. A correlation between measurable oxide film properties andmore » susceptibility of austenitic steels to environmentally assisted degradation was observed experimentally. One of the major practical results of the present work is the experimentally proven ability of the economical CDE technique to supply in situ data for ranking candidate structural materials for Generation-IV SCRs. A potential use of the CDE arrangement developed ar SRI for building in situ sensors monitoring water chemistry in the heat transport circuit of Generation-IV SCWRs was evaluated and proved to be feasible.« less

Chlorella vulgaris triggers apoptosis in hepatocarcinogenesis-induced rats*

PubMed Central

Mohd Azamai, Emey Suhana; Sulaiman, Suhaniza; Mohd Habib, Shafina Hanim; Looi, Mee Lee; Das, Srijit; Abdul Hamid, Nor Aini; Wan Ngah, Wan Zurinah; Mohd Yusof, Yasmin Anum

2009-01-01

Chlorella vulgaris (CV) has been reported to have antioxidant and anticancer properties. We evaluated the effect of CV on apoptotic regulator protein expression in liver cancer-induced rats. Male Wistar rats (200~250 g) were divided into eight groups: control group (normal diet), CDE group (choline deficient diet supplemented with ethionine in drinking water to induce hepatocarcinogenesis), CV groups with three different doses of CV (50, 150, and 300 mg/kg body weight), and CDE groups treated with different doses of CV (50, 150, and 300 mg/kg body weight). Rats were sacrificed at various weeks and liver tissues were embedded in paraffin blocks for immunohistochemistry studies. CV, at increasing doses, decreased the expression of anti-apoptotic protein, Bcl-2, but increased the expression of pro-apoptotic protein, caspase 8, in CDE rats, which was correlated with decreased hepatoctyes proliferation and increased apoptosis as determined by bromodeoxy-uridine (BrdU) labeling and terminal deoxynucleotidyl transferase mediated dUTP nick-end labeling (TUNEL) assay, respectively. Our study shows that CV has definite chemopreventive effect by inducing apoptosis via decreasing the expression of Bcl-2 and increasing the expression of caspase 8 in hepatocarcinogenesis-induced rats. PMID:19198018

Overview of several applications of chemical downstream etching (CDE) for IC manufacturing: advantages and drawbacks versus WET processes

NASA Astrophysics Data System (ADS)

de Buttet, Côme; Prevost, Emilie; Campo, Alain; Garnier, Philippe; Zoll, Stephane; Vallier, Laurent; Cunge, Gilles; Maury, Patrick; Massin, Thomas; Chhun, Sonarith

2017-03-01

Today the IC manufacturing faces lots of problematics linked to the continuous down scaling of printed structures. Some of those issues are related to wet processing, which are often used in the IC manufacturing flow for wafer cleaning, material etching and surface preparation. In the current work we summarize the limitations for the next nodes of wet processing such as metallic contaminations, wafer charging, corrosion and pattern collapse. As a replacement, we promoted the isotropic chemical dry etching (CDE) which is supposed to fix all the above drawbacks. Etching steps of SI3N4 layers were evaluated in order to prove the interest of such technique.

Dry Eye Following Phacoemulsification Surgery and its Relation to Associated Intraoperative Risk Factors.

PubMed

Sahu, P K; Das, G K; Malik, Aman; Biakthangi, Laura

2015-01-01

The purpose was to study dry eye following phacoemulsification surgery and analyze its relation to associated intra-operative risk factors. A prospective observational study was carried out on 100 eyes of 100 patients without preoperative dry eye. Schirmer's Test I, tear meniscus height, tear break-up time, and lissamine green staining of cornea and conjunctiva were performed preoperatively and at 5 days, 10 days, 1-month, and 2 months after phacoemulsification surgery, along with the assessment of subjective symptoms, using the dry eye questionnaire. The correlations between these values and the operating microscope light exposure time along with the cumulative dissipated energy (CDE) were investigated. There was a significant deterioration of all dry eye test values following phacoemulsification surgery along with an increase in subjective symptoms. These values started improving after 1-month postoperatively, but preoperative levels were not achieved till 2 months after surgery. Correlations of dry eye test values were noted with the operating microscope light exposure time and CDE, but they were not significant. Phacoemulsification surgery is capable of inducing dry eye, and patients should be informed accordingly prior to surgery. The clinician should also be cognizant that increased CDE can induce dry eyes even in eyes that were healthy preoperatively. In addition, intraoperative exposure to the microscopic light should be minimized.

Non-dispersive carrier transport in molecularly doped polymers and the convection-diffusion equation

NASA Astrophysics Data System (ADS)

Tyutnev, A. P.; Parris, P. E.; Saenko, V. S.

2015-08-01

We reinvestigate the applicability of the concept of trap-free carrier transport in molecularly doped polymers and the possibility of realistically describing time-of-flight (TOF) current transients in these materials using the classical convection-diffusion equation (CDE). The problem is treated as rigorously as possible using boundary conditions appropriate to conventional time of flight experiments. Two types of pulsed carrier generation are considered. In addition to the traditional case of surface excitation, we also consider the case where carrier generation is spatially uniform. In our analysis, the front electrode is treated as a reflecting boundary, while the counter electrode is assumed to act either as a neutral contact (not disturbing the current flow) or as an absorbing boundary at which the carrier concentration vanishes. As expected, at low fields transient currents exhibit unusual behavior, as diffusion currents overwhelm drift currents to such an extent that it becomes impossible to determine transit times (and hence, carrier mobilities). At high fields, computed transients are more like those typically observed, with well-defined plateaus and sharp transit times. Careful analysis, however, reveals that the non-dispersive picture, and predictions of the CDE contradict both experiment and existing disorder-based theories in important ways, and that the CDE should be applied rather cautiously, and even then only for engineering purposes.

Regulation of the Min Cell Division Inhibition Complex by the Rcs Phosphorelay in Proteus mirabilis.

PubMed

Howery, Kristen E; Clemmer, Katy M; Şimşek, Emrah; Kim, Minsu; Rather, Philip N

2015-08-01

A key regulator of swarming in Proteus mirabilis is the Rcs phosphorelay, which represses flhDC, encoding the master flagellar regulator FlhD4C2. Mutants in rcsB, the response regulator in the Rcs phosphorelay, hyperswarm on solid agar and differentiate into swarmer cells in liquid, demonstrating that this system also influences the expression of genes central to differentiation. To gain a further understanding of RcsB-regulated genes involved in swarmer cell differentiation, transcriptome sequencing (RNA-Seq) was used to examine the RcsB regulon. Among the 133 genes identified, minC and minD, encoding cell division inhibitors, were identified as RcsB-activated genes. A third gene, minE, was shown to be part of an operon with minCD. To examine minCDE regulation, the min promoter was identified by 5' rapid amplification of cDNA ends (5'-RACE), and both transcriptional lacZ fusions and quantitative real-time reverse transcriptase (qRT) PCR were used to confirm that the minCDE operon was RcsB activated. Purified RcsB was capable of directly binding the minC promoter region. To determine the role of RcsB-mediated activation of minCDE in swarmer cell differentiation, a polar minC mutation was constructed. This mutant formed minicells during growth in liquid, produced shortened swarmer cells during differentiation, and exhibited decreased swarming motility. This work describes the regulation and role of the MinCDE cell division system in P. mirabilis swarming and swarmer cell elongation. Prior to this study, the mechanisms that inhibit cell division and allow swarmer cell elongation were unknown. In addition, this work outlines for the first time the RcsB regulon in P. mirabilis. Taken together, the data presented in this study begin to address how P. mirabilis elongates upon contact with a solid surface. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

[Diagnostic evaluation of the developmental level in children identified at risk of delay through the Child Development Evaluation Test].

PubMed

Rizzoli-Córdoba, Antonio; Campos-Maldonado, Martha Carmen; Vélez-Andrade, Víctor Hugo; Delgado-Ginebra, Ismael; Baqueiro-Hernández, César Iván; Villasís-Keever, Miguel Ángel; Reyes-Morales, Hortensia; Ojeda-Lara, Lucía; Davis-Martínez, Erika Berenice; O'Shea-Cuevas, Gabriel; Aceves-Villagrán, Daniel; Carrasco-Mendoza, Joaquín; Villagrán-Muñoz, Víctor Manuel; Halley-Castillo, Elizabeth; Sidonio-Aguayo, Beatriz; Palma-Tavera, Josuha Alexander; Muñoz-Hernández, Onofre

The Child Development Evaluation (or CDE Test) was developed in Mexico as a screening tool for child developmental problems. It yields three possible results: normal, slow development or risk of delay. The modified version was elaborated using the information obtained during the validation study but its properties according to the base population are not known. The objective of this work was to establish diagnostic confirmation of developmental delay in children 16- to 59-months of age previously identified as having risk of delay through the CDE Test in primary care facilities. A population-based cross-sectional study was conducted in one Mexican state. CDE test was administered to 11,455 children 16- to 59-months of age from December/2013 to March/2014. The eligible population represented the 6.2% of the children (n=714) who were identified at risk of delay through the CDE Test. For inclusion in the study, a block randomization stratified by sex and age group was performed. Each participant included in the study had a diagnostic evaluation using the Battelle Development Inventory, 2 nd edition. From the 355 participants included with risk of delay, 65.9% were male and 80.2% were from rural areas; 6.5% were false positives (Total Development Quotient ˃90) and 6.8% did not have any domain with delay (Domain Developmental Quotient <80). The proportion of delay for each domain was as follows: communication 82.5%; cognitive 80.8%; social-personal 33.8%; motor 55.5%; and adaptive 41.7%. There were significant differences in the percentages of delay both by age and by domain/subdomain evaluated. In 93.2% of the participants, developmental delay was corroborated in at least one domain evaluated. Copyright © 2015 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

Enabling interspecies epigenomic comparison with CEpBrowser.

PubMed

Cao, Xiaoyi; Zhong, Sheng

2013-05-01

We developed the Comparative Epigenome Browser (CEpBrowser) to allow the public to perform multi-species epigenomic analysis. The web-based CEpBrowser integrates, manages and visualizes sequencing-based epigenomic datasets. Five key features were developed to maximize the efficiency of interspecies epigenomic comparisons. CEpBrowser is a web application implemented with PHP, MySQL, C and Apache. URL: http://www.cepbrowser.org/.

Recommendations for the National Institute for Neurologic Disorders and Stroke spinal cord injury common data elements for children and youth with SCI.

PubMed

Mulcahey, M J; Vogel, L C; Sheikh, M; Arango-Lasprilla, J C; Augutis, M; Garner, E; Hagen, E M; Jakeman, L B; Kelly, E; Martin, R; Odenkirchen, J; Scheel-Sailer, A; Schottler, J; Taylor, H; Thielen, C C; Zebracki, K

2017-04-01

In 2014, the adult spinal cord injury (SCI) common data element (CDE) recommendations were made available. This project was a review of the adult SCI CDE for relevance to children and youth with SCI. The objective of this study was to review the National Institute of Neurologic Disorders and Stroke (NINDS) adult SCI CDEs for relevance to children and youth with SCI. International. The pediatric working group consisted of international members with varied fields of expertise related to pediatric SCI. The group convened biweekly meetings for 6 months in 2015. All of the adult SCI CDEs were reviewed, evaluated and modified/created for four age groups: 0-5 years, 6-12 years, 13-15 years and 16-18 years. Whenever possible, results of published research studies were used to guide recommendations. In the absence of empirical support, grey literature and international content expert consensus were garnered. Existing pediatric NINDS CDEs and new CDEs were developed in areas where adult recommendations were not appropriate. After internal working group review of domain recommendations, these pediatric CDEs were vetted during a public review from November through December 2015. Version 1.0 of the pediatric SCI CDEs was posted in February 2016. The pediatric SCI CDEs are incorporated directly into the NINDS SCI CDE sets and can be found at https://commondataelements.ninds.nih.gov.

A pivotal role of BEX1 in liver progenitor cell expansion in mice.

PubMed

Gu, Yuting; Wei, Weiting; Cheng, Yiji; Wan, Bing; Ding, Xinyuan; Wang, Hui; Zhang, Yanyun; Jin, Min

2018-06-15

The activation and expansion of bipotent liver progenitor cells (LPCs) are indispensable for liver regeneration after severe or chronic liver injury. However, the underlying molecular mechanisms regulating LPCs and LPC-mediated liver regeneration remain elusive. Hepatic brain-expressed X-linked 1 (BEX1) expression was evaluated using microarray screening, real-time polymerase chain reaction, immunoblotting and immunofluorescence. LPC activation and liver injury were studied following a choline-deficient, ethionine-supplemented (CDE) diet in wild-type (WT) and Bex1 -/- mice. Proliferation, apoptosis, colony formation and hepatic differentiation were examined in LPCs from WT and Bex1 -/- mice. Peroxisome proliferator-activated receptor gamma was detected in Bex1-deficient LPCs and mouse livers, and was silenced to analyse the expansion of LPCs from WT and Bex1 -/- mice. Hepatic BEX1 expression was increased during CDE diet-induced liver injury and was highly elevated primarily in LPCs. Bex1 -/- mice fed a CDE diet displayed impaired LPC expansion and liver regeneration. Bex1 deficiency inhibited LPC proliferation and enhanced LPC apoptosis in vitro. Additionally, Bex1 deficiency inhibited the colony formation of LPCs but had no effect on their hepatic differentiation. Mechanistically, BEX1 inhibited peroxisome proliferator-activated receptor gamma to promote LPC expansion. Our findings indicate that BEX1 plays a pivotal role in LPC activation and expansion during liver regeneration, potentially providing novel targets for liver regeneration and chronic liver disease therapies.

A Policy Based Approach for the Management of Web Browser Resources to Prevent Anonymity Attacks in Tor

NASA Astrophysics Data System (ADS)

Navarro-Arribas, Guillermo; Garcia-Alfaro, Joaquin

Web browsers are becoming the universal interface to reach applications and services related with these systems. Different browsing contexts may be required in order to reach them, e.g., use of VPN tunnels, corporate proxies, anonymisers, etc. By browsing context we mean how the user browsers the Web, including mainly the concrete configuration of its browser. When the context of the browser changes, its security requirements also change. In this work, we present the use of authorisation policies to automatise the process of controlling the resources of a Web browser when its context changes. The objective of our proposal is oriented towards easing the adaptation to the security requirements of the new context and enforce them in the browser without the need for user intervention. We present a concrete application of our work as a plug-in for the adaption of security requirements in Mozilla/Firefox browser when a context of anonymous navigation through the Tor network is enabled.

Choosing a genome browser for a Model Organism Database: surveying the Maize community

PubMed Central

Sen, Taner Z.; Harper, Lisa C.; Schaeffer, Mary L.; Andorf, Carson M.; Seigfried, Trent E.; Campbell, Darwin A.; Lawrence, Carolyn J.

2010-01-01

As the B73 maize genome sequencing project neared completion, MaizeGDB began to integrate a graphical genome browser with its existing web interface and database. To ensure that maize researchers would optimally benefit from the potential addition of a genome browser to the existing MaizeGDB resource, personnel at MaizeGDB surveyed researchers’ needs. Collected data indicate that existing genome browsers for maize were inadequate and suggest implementation of a browser with quick interface and intuitive tools would meet most researchers’ needs. Here, we document the survey’s outcomes, review functionalities of available genome browser software platforms and offer our rationale for choosing the GBrowse software suite for MaizeGDB. Because the genome as represented within the MaizeGDB Genome Browser is tied to detailed phenotypic data, molecular marker information, available stocks, etc., the MaizeGDB Genome Browser represents a novel mechanism by which the researchers can leverage maize sequence information toward crop improvement directly. Database URL: http://gbrowse.maizegdb.org/ PMID:20627860

Chlorite dismutases, DyPs, and EfeB: 3 microbial heme enzyme families comprise the CDE structural superfamily

PubMed Central

Goblirsch, Brandon; Kurker, Richard C.; Streit, Bennett R.; Wilmot, Carrie M.; DuBois, Jennifer L.

2011-01-01

Heme proteins are extremely diverse, widespread, and versatile biocatalysts, sensors, and molecular transporters. The chlorite dismutase family of hemoproteins received its name due to the ability of the first-isolated members to detoxify anthropogenic ClO2−, a function believed to have evolved only in the last few decades. Family members have since been found in fifteen bacterial and archaeal genera, suggesting ancient roots. A structure- and sequence-based examination of the family is presented, in which key sequence and structural motifs are identified and possible functions for family proteins are proposed. Newly identified structural homologies moreover demonstrate clear connections to two other large, ancient, and functionally mysterious protein families. We propose calling them collectively the CDE superfamily of heme proteins. PMID:21354424

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

Exploring the enjoyment of playing browser games.

PubMed

Klimmt, Christoph; Schmid, Hannah; Orthmann, Julia

2009-04-01

Browser games--mostly persistent game worlds that can be used without client software and monetary cost with a Web browser--belong to the understudied digital game types, although they attract large player communities and motivate sustained play. The present work reports findings from an online survey of 8,203 players of a German strategy browser game ("Travian"). Results suggest that multiplayer browser games are enjoyed primarily because of the social relationships involved in game play and the specific time and flexibility characteristics ("easy-in, easy-out"). Competition, in contrast, seems to be less important for browser gamers than for users of other game types. Findings are discussed in terms of video game enjoyment and game addiction.

Reduction of chemotherapy-induced febrile leucopenia by prophylactic use of ciprofloxacin and roxithromycin in small-cell lung cancer patients: an EORTC double-blind placebo-controlled phase III study.

PubMed

Tjan-Heijnen, V C; Postmus, P E; Ardizzoni, A; Manegold, C H; Burghouts, J; van Meerbeeck, J; Gans, S; Mollers, M; Buchholz, E; Biesma, B; Legrand, C; Debruyne, C; Giaccone, G

2001-10-01

CDE (cyclophosphamide, doxorubicin, etoposide) is one of the standard chemotherapy regimens in the treatment of small-cell lung cancer (SCLC), with myelosuppression as dose-limiting toxicity. In this trial the impact of prophylactic antibiotics on incidence of febrile leucopenia (FL) during chemotherapy for SCLC was evaluated. Patients with chemo-naïve SCLC were randomized to standard-dose CDE (C 1,000 mg/m2 day 1, D 45 mg/m2 day 1, E 100 mg/m2 days 1-3. i.v., q 3 weeks, x5) or to intensified CDE chemotherapy (125% dose, q 2 weeks, x4, with filgrastim 5 microg/kg/day days 4-13) to assess the impact on survival (n = 240 patients). Patients were also randomized to prophylactic antibiotics (ciprofloxacin 750 mg plus roxithromycin 150 mg, bid. days 4-13) or to placebo in a 2 x 2 factorial design (first 163 patients). This manuscript focuses on the antibiotics question. The incidence of FL during the first cycle was 25% of patients in the placebo and 11% in the antibiotics arm (P = 0.010; 1-sided), with an overall incidence through all cycles of 43% vs. 24% respectively (P = 0.007; 1-sided). There were less Gram-positive (12 vs. 4), Gram-negative (20 vs. 5) and clinically documented (38 vs. 15) infections in the antibiotics arm. The use of therapeutic antibiotics was reduced (P = 0.013; 1-sided), with less hospitalizations due to FL (31 vs. 17 patients, P = 0.013: 1-sided). However, the overall number of days of hospitalization was not reduced (P = 0.05; 1-sided). The number of infectious deaths was nil in the antibiotics vs. five (6%) in the placebo arm (P = 0.022; 2-sided). Prophylactic ciprofloxacin plus roxithromycin during CDE chemotherapy reduced the incidence of FL, the number of infections, the use of therapeutic antibiotics and hospitalizations due to FL by approximately 50%, with reduced number of infectious deaths. For patients with similar risk for FL, the prophylactic use of antibiotics should be considered.

Clinical study using a new phacoemulsification system with surgical intraocular pressure control.

PubMed

Solomon, Kerry D; Lorente, Ramón; Fanney, Doug; Cionni, Robert J

2016-04-01

To compare cumulative dissipated energy (CDE), aspiration fluid used, and aspiration time during phacoemulsification cataract extraction using 2 surgical configurations. Two clinical sites in the United States and 1 in Spain. Prospective randomized clinical case series. For each patient, the first eye having surgery was randomized to the active-fluidics configuration (Centurion Vision System with Active Fluidics, 0.9 mm 45-degree Intrepid Balanced tip, and 0.9 mm Intrepid Ultra infusion sleeve) or the gravity-fluidics configuration (Infiniti Vision System with gravity fluidics, 0.9 mm 45-degree Mini-Flared Kelman tip, and 0.9 mm Ultra infusion sleeve). Second-eye surgery was completed within 14 days after first-eye surgery using the alternate configuration. The CDE, aspiration fluid used, and aspiration time were compared between configurations, and adverse events were summarized. Patient demographics and cataract characteristics were similar between configurations (100 per group). The CDE was significantly lower with the active-fluidics configuration than with the gravity-fluidics configuration (mean ± standard error, 4.32 ± 0.28 percent-seconds) (P < .001). The active-fluidics configuration used significantly less aspiration fluid than the gravity-fluidics configuration (mean 46.56 ± 1.39 mL versus 52.68 ± 1.40 mL) (P < .001) and required significantly shorter aspiration time (mean 151.9 ± 4.1 seconds versus 167.6 ± 4.1 seconds) (P < .001). No serious ocular adverse events related to the study devices or device deficiencies were observed. Significantly less CDE, aspiration fluid used, and aspiration time were observed with the active-fluidics configuration than with the gravity-fluidics configuration, showing improved surgical efficiency. Drs. Solomon and Cionni are consultants to Alcon Research, Ltd., and received compensation for conduct of the study. Dr. Lorente received compensation for clinical work in the study. Mr. Fanney is an employee of Alcon Research, Ltd. Copyright © 2016 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Inverse agonist abolishes desensitization of a constitutively active mutant of thyrotropin-releasing hormone receptor: role of cellular calcium and protein kinase C

PubMed Central

Grimberg, Hagit; Zaltsman, Ilona; Lupu-Meiri, Monica; Gershengorn, Marvin C; Oron, Yoram

1999-01-01

C335Stop is a constitutively active mutant of the TRH receptor (TRH-R). To investigate the mechanism of the decreased responsiveness of C335Stop TRH-R, we studied cellular Ca2+ concentrations ([Ca2+]i) in AtT20 cells stably transfected with C335Stop TRH-R cDNA, or Ca2+-activated chloride currents in Xenopus laevis oocytes expressing this mutant receptor after injection of cRNA. The competitive TRH-R binding antagonist, chlorodiazepoxide (CDE), was used as an inverse agonist to study the contribution of constitutive activity to desensitization. Acute treatment with CDE resulted in a rapid (within minutes) decrease in [Ca2+]i and an increase in the response amplitude to TRH with no measurable change in receptor density. Conversely, removal of chronically administered CDE caused a rapid increase in [Ca2+]i and a decrease in TRH response amplitude. CDE abolished heterologous desensitization induced by C335Stop TRH-R on muscarinic m1-receptor (m1-R) co-expressed in Xenopus oocytes. Chelation of extracellular calcium with EGTA caused a rapid decrease in [Ca2+]i and a concomitant increase in the response to TRH in AtT20 cells expressing C335Stop TRH-Rs. Chelerythrine, a specific inhibitor of protein kinase C (PKC), reversed the heterologous desensitization of the response to acetylcholine (ACh). The phosphoserine/phosphothreonine phosphatase inhibitor, okadaic acid, abolished the effect of chelerythrine. Down-regulation of PKC by chronic exposure to phorbol 12-myristate 13-acetate (PMA) or acute inhibition with chelerythrine caused a partial resensitization of the response to TRH. Western analysis indicated that the α subtype of protein kinase C was down-regulated in cells expressing C335Stop TRH-Rs. Following a 5 min exposure to PMA, the residual αPKC translocated to the particular fraction. We propose that cells expressing the constitutively active mutant TRH-R rapidly desensitize their response, utilizing a mechanism mediated by an increase in [Ca2+]i and PKC. PMID:10204996

National Institute of Neurological Disorders and Stroke Common Data Element Project - approach and methods.

PubMed

Grinnon, Stacie T; Miller, Kristy; Marler, John R; Lu, Yun; Stout, Alexandra; Odenkirchen, Joanne; Kunitz, Selma

2012-06-01

In neuroscience clinical research studies, much time and effort are devoted to deciding what data to collect and developing data collection forms and data management systems to capture the data. Many investigators receiving funding from National Institute of Neurological Disorders and Stroke (NINDS), the National Institutes of Health (NIH), are required to share their data once their studies are complete, but the multitude of data definitions and formats make it extremely difficult to aggregate data or perform meta-analyses across studies. In an effort to assist investigators and accelerate data sharing in neuroscience clinical research, the NINDS has embarked upon the Common Data Element (CDE) Project. The data standards developed through the NINDS CDE Project enable clinical investigators to systematically collect data and should facilitate study start-up and data aggregation across the research community. The NINDS CDE Team has taken a systematic, iterative approach to develop the critical core and the disease-specific CDEs. The CDE development process provides a mechanism for community involvement and buy-in, offers a structure for decision making, and includes a technical support team. Upon conclusion of the development process, the CDEs and accompanying tools are available on the Project Web site - http://www.commondataelements.ninds.nih.gov/. The Web site currently includes the critical core (aka general) CDEs that are applicable to all clinical research studies regardless of therapeutic area as well as several disease-specific CDEs. Additional disease-specific CDEs will be added to the Web site once they are developed and vetted over the next 12 months. The CDEs will continue to evolve and will improve only if clinical researchers use and offer feedback about their experience with them. Thus, the NINDS program staff strongly encourages its clinical research grantees to use the CDEs and is expanding its efforts to educate the neuroscience research community about the CDEs and to train research teams to incorporate them into their studies. Version 1.0 of a set of CDEs has been published, but publication is not the end of the development process. All CDEs will be evaluated and revised at least annually to ensure that they reflect current clinical research practices in neuroscience.

West facade of clubhouse. Showing first and second floor loggais ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

West facade of clubhouse. Showing first and second floor loggais - Clubhouse Verandah and citation statue in foreground: CD-E. - Hialeah Park Race Track, East Fourth Avenue, Hialeah, Miami-Dade County, FL

Chemotherapy drug extravasation in totally implantable venous access port systems: how effective is early surgical lavage?

PubMed

Azaïs, Henri; Bresson, Lucie; Bassil, Alfred; Katdare, Ninad; Merlot, Benjamin; Houpeau, Jean-Louis; El Bedoui, Sophie; Meurant, Jean-Pierre; Tresch, Emmanuelle; Narducci, Fabrice

2015-01-01

Totally implantable venous access port systems (TIVAPS) are a widely used and an essential tool in the efficient delivery of chemotherapy. Chemotherapy drug extravasation (CDE) can have dire consequences and will delay treatment. The purpose of this study is to both clarify the management of CDE and show the effectiveness of early surgical lavage (ESL). Patients who had presented to the Cancer Center of Lille (France) with TIVAPS inserted between January 2004 and April 2013 and CDE had their medical records reviewed retrospectively. Thirty patients and 33 events were analyzed. Implicated agents were vesicants (51.5%), irritants (45.5%) and non-vesicants (3%). Huber needle malpositionning was involved in 27 cases. Surgery was performed in 97% of cases, 87.5% of which were for ESL with 53.1% of the latter requiring TIVAPS extraction. Six patients required a second intervention due to adverse outcomes (severe cases). Vesicants were found to be implicated in four out of six severe cases and oxaliplatin in two others. Extravasated volume was above 50 ml in 80% of cases. Only one patient required a skin graft. CDEs should be managed in specialized centers. ESL allows for limited tissue contact of the chemotherapy drug whilst using a simple, widely accessible technique. The two main factors that correlate with adverse outcome seem to be the nature of the implicated agent (vesicants) and the extravasated volume (above 50 ml) leading to worse outcomes. Oxaliplatin should be considered as a vesicant.

Interleukins-17 and 27 promote liver regeneration by sequentially inducing progenitor cell expansion and differentiation.

PubMed

Guillot, Adrien; Gasmi, Imène; Brouillet, Arthur; Ait-Ahmed, Yeni; Calderaro, Julien; Ruiz, Isaac; Gao, Bin; Lotersztajn, Sophie; Pawlotsky, Jean-Michel; Lafdil, Fouad

2018-03-01

Liver progenitor cells (LPCs)/ductular reactions (DRs) are associated with inflammation and implicated in the pathogenesis of chronic liver diseases. However, how inflammation regulates LPCs/DRs remains largely unknown. Identification of inflammatory processes that involve LPC activation and expansion represent a key step in understanding the pathogenesis of liver diseases. In the current study, we found that diverse types of chronic liver diseases are associated with elevation of infiltrated interleukin (IL)-17-positive (+) cells and cytokeratin 19 (CK19) + LPCs, and both cell types colocalized and their numbers positively correlated with each other. The role of IL-17 in the induction of LPCs was examined in a mouse model fed a choline-deficient and ethionine-supplemented (CDE) diet. Feeding of wild-type mice with the CDE diet markedly elevated CK19 + Ki67 + proliferating LPCs and hepatic inflammation. Disruption of the IL-17 gene or IL-27 receptor, alpha subunit (WSX-1) gene abolished CDE diet-induced LPC expansion and inflammation. In vitro treatment with IL-17 promoted proliferation of bipotential murine oval liver cells (a liver progenitor cell line) and markedly up-regulated IL-27 expression in macrophages. Treatment with IL-27 favored the differentiation of bipotential murine oval liver cells and freshly isolated LPCs into hepatocytes. Conclusion : The current data provide evidence for a collaborative role between IL-17 and IL-27 in promoting LPC expansion and differentiation, respectively, thereby contributing to liver regeneration. ( Hepatology Communications 2018;2:329-343).

Common Data Elements for Spinal Cord Injury Clinical Research: A National Institute for Neurological Disorders and Stroke Project

PubMed Central

Biering-Sørensen, Fin; Alai, Sherita; Anderson, Kim; Charlifue, Susan; Chen, Yuying; DeVivo, Michael; Flanders, Adam E.; Jones, Linda; Kleitman, Naomi; Lans, Aria; Noonan, Vanessa K.; Odenkirchen, Joanne; Steeves, John; Tansey, Keith; Widerström-Noga, Eva; Jakeman, Lyn B.

2015-01-01

Objective To develop a comprehensive set of common data elements (CDEs), data definitions, case report forms and guidelines for use in spinal cord injury (SCI) clinical research, as part of the CDE project at the National Institute of Neurological Disorders and Stroke (NINDS) of the USA National Institutes of Health. Setting International Working Groups Methods Nine working groups composed of international experts reviewed existing CDEs and instruments, created new elements when needed, and provided recommendations for SCI clinical research. The project was carried out in collaboration with and cross-referenced to development of the International Spinal Cord Society (ISCoS) International SCI Data Sets. The recommendations were compiled, subjected to internal review, and posted online for external public comment. The final version was reviewed by all working groups and the NINDS CDE team prior to release. Results The NINDS SCI CDEs and supporting documents are publically available on the NINDS CDE website and the ISCoS website. The CDEs span the continuum of SCI care and the full range of domains of the International Classification of Functioning, Disability and Health. Conclusions Widespread use of common data elements can facilitate SCI clinical research and trial design, data sharing, and retrospective analyses. Continued international collaboration will enable consistent data collection and reporting, and will help ensure that the data elements are updated, reviewed and broadcast as additional evidence is obtained. PMID:25665542

Design and implementation of a P300-based brain-computer interface for controlling an internet browser.

PubMed

Mugler, Emily M; Ruf, Carolin A; Halder, Sebastian; Bensch, Michael; Kubler, Andrea

2010-12-01

An electroencephalographic (EEG) brain-computer interface (BCI) internet browser was designed and evaluated with 10 healthy volunteers and three individuals with advanced amyotrophic lateral sclerosis (ALS), all of whom were given tasks to execute on the internet using the browser. Participants with ALS achieved an average accuracy of 73% and a subsequent information transfer rate (ITR) of 8.6 bits/min and healthy participants with no prior BCI experience over 90% accuracy and an ITR of 14.4 bits/min. We define additional criteria for unrestricted internet access for evaluation of the presented and future internet browsers, and we provide a review of the existing browsers in the literature. The P300-based browser provides unrestricted access and enables free web surfing for individuals with paralysis.

77 FR 59705 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-28

... to investors in the form of a tax credit, which is expected to stimulate investment in new private capital in low income communities. Applicants must be a CDE to apply for allocation. Affected Public...

BrainBrowser: distributed, web-based neurological data visualization.

PubMed

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C

2014-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible.

BrainBrowser: distributed, web-based neurological data visualization

PubMed Central

Sherif, Tarek; Kassis, Nicolas; Rousseau, Marc-Étienne; Adalat, Reza; Evans, Alan C.

2015-01-01

Recent years have seen massive, distributed datasets become the norm in neuroimaging research, and the methodologies used to analyze them have, in response, become more collaborative and exploratory. Tools and infrastructure are continuously being developed and deployed to facilitate research in this context: grid computation platforms to process the data, distributed data stores to house and share them, high-speed networks to move them around and collaborative, often web-based, platforms to provide access to and sometimes manage the entire system. BrainBrowser is a lightweight, high-performance JavaScript visualization library built to provide easy-to-use, powerful, on-demand visualization of remote datasets in this new research environment. BrainBrowser leverages modern web technologies, such as WebGL, HTML5 and Web Workers, to visualize 3D surface and volumetric neuroimaging data in any modern web browser without requiring any browser plugins. It is thus trivial to integrate BrainBrowser into any web-based platform. BrainBrowser is simple enough to produce a basic web-based visualization in a few lines of code, while at the same time being robust enough to create full-featured visualization applications. BrainBrowser can dynamically load the data required for a given visualization, so no network bandwidth needs to be waisted on data that will not be used. BrainBrowser's integration into the standardized web platform also allows users to consider using 3D data visualization in novel ways, such as for data distribution, data sharing and dynamic online publications. BrainBrowser is already being used in two major online platforms, CBRAIN and LORIS, and has been used to make the 1TB MACACC dataset openly accessible. PMID:25628562

Firefox add-ons for medical reference.

PubMed

Hoy, Matthew B

2010-07-01

Firefox is a Web browser created by the Mozilla project, an open-source software group. Features of the browser include automated updates, advanced security and standards compliance, and the ability to add functionality through add-ons and extensions. First introduced in 2004, Firefox now accounts for roughly 30% of the browser market. This article will focus primarily on add-ons and extensions available for the browser that are useful to medical researchers.

Web Browser Trends and Technologies.

ERIC Educational Resources Information Center

Goodwin-Jones, Bob

2000-01-01

Discusses Web browsers and how their capabilities have been expanded, support for Web browsing on different devices (cell phones, palmtop computers, TV sets), and browser support for the next-generation Web authoring language, XML ("extensible markup language"). (Author/VWL)

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

PubMed

Barrios, David; Prieto, Carlos

2017-05-01

Genome browsers are useful not only for showing final results but also for improving analysis protocols, testing data quality, and generating result drafts. Its integration in analysis pipelines allows the optimization of parameters, which leads to better results. New developments that facilitate the creation and utilization of genome browsers could contribute to improving analysis results and supporting the quick visualization of genomic data. D3 Genome Browser is an interactive genome browser that can be easily integrated in analysis protocols and shared on the Web. It is distributed as an R package, a Python module, and a WordPress plugin to facilitate its integration in pipelines and the utilization of platform capabilities. It is compatible with popular data formats such as GenBank, GFF, BED, FASTA, and VCF, and enables the exploration of genomic data with a Web browser.

Eco-Health Relationship Browser

EPA Science Inventory

The Eco-Health Relationship Browser (Browser) is a web tool designed to portray, in an engaging and intuitive way, the linkages between ecosystems, their services, and potential health outcomes that have been associated with those services in the literature. It functions an inte...

The EPIRARE proposal of a set of indicators and common data elements for the European platform for rare disease registration.

PubMed

Taruscio, Domenica; Mollo, Emanuela; Gainotti, Sabina; Posada de la Paz, Manuel; Bianchi, Fabrizio; Vittozzi, Luciano

2014-01-01

The European Union acknowledges the relevance of registries as key instruments for developing rare disease (RD) clinical research, improving patient care and health service (HS) planning and funded the EPIRARE project to improve standardization and data comparability among patient registries and to support new registries and data collections. A reference list of patient registry-based indicators has been prepared building on the work of previous EU projects and on the platform stakeholders' information needs resulting from the EPIRARE surveys and consultations. The variables necessary to compute these indicators have been analysed for their scope and use and then organized in data domains. The reference indicators span from disease surveillance, to socio-economic burden, HS monitoring, research and product development, policy equity and effectiveness. The variables necessary to compute these reference indicators have been selected and, with the exception of more sophisticated indicators for research and clinical care quality, they can be collected as data elements common (CDE) to all rare diseases. They have been organized in data domains characterized by their contents and main goal and a limited set of mandatory data elements has been defined, which allows case notification independently of the physician or the health service. The definition of a set of CDE for the European platform for RD patient registration is the first step in the promotion of the use of common tools for the collection of comparable data. The proposed organization of the CDE contributes to the completeness of case ascertainment, with the possible involvement of patients and patient associations in the registration process.

Cloning, Sequencing, and Characterization of the SdeAB Multidrug Efflux Pump of Serratia marcescens

PubMed Central

Kumar, Ayush; Worobec, Elizabeth A.

2005-01-01

Serratia marcescens is an important nosocomial agent known for causing various infections in immunocompromised individuals. Resistance of this organism to a broad spectrum of antibiotics makes the treatment of infections very difficult. This study was undertaken to identify multidrug resistance efflux pumps in S. marcescens. Three mutant strains of S. marcescens were isolated in vitro by the serial passaging of a wild-type strain in culture medium supplemented with ciprofloxacin, norfloxacin, or ofloxacin. Fluoroquinolone accumulation assays were performed to detect the presence of a proton gradient-dependent efflux mechanism. Two of the mutant strains were found to be effluxing norfloxacin, ciprofloxacin, and ofloxacin, while the third was found to efflux only ofloxacin. A genomic library of S. marcescens wild-type strain UOC-67 was constructed and screened for RND pump-encoding genes by using DNA probes for two putative RND pump-encoding genes. Two different loci were identified: sdeAB, encoding an MFP and an RND pump, and sdeCDE, encoding an MFP and two different RND pumps. Northern blot analysis revealed overexpression of sdeB in two mutant strains effluxing fluoroquinolones. Analysis of the sdeAB and sdeCDE loci in Escherichia coli strain AG102MB, deficient in the RND pump (AcrB), revealed that gene products of sdeAB are responsible for the efflux of a diverse range of substrates that includes ciprofloxacin, norfloxacin, ofloxacin, chloramphenicol, sodium dodecyl sulfate, ethidium bromide, and n-hexane, while those of sdeCDE did not result in any change in susceptibilities to any of these agents. PMID:15793131

Cloning, sequencing, and characterization of the SdeAB multidrug efflux pump of Serratia marcescens.

PubMed

Kumar, Ayush; Worobec, Elizabeth A

2005-04-01

Serratia marcescens is an important nosocomial agent known for causing various infections in immunocompromised individuals. Resistance of this organism to a broad spectrum of antibiotics makes the treatment of infections very difficult. This study was undertaken to identify multidrug resistance efflux pumps in S. marcescens. Three mutant strains of S. marcescens were isolated in vitro by the serial passaging of a wild-type strain in culture medium supplemented with ciprofloxacin, norfloxacin, or ofloxacin. Fluoroquinolone accumulation assays were performed to detect the presence of a proton gradient-dependent efflux mechanism. Two of the mutant strains were found to be effluxing norfloxacin, ciprofloxacin, and ofloxacin, while the third was found to efflux only ofloxacin. A genomic library of S. marcescens wild-type strain UOC-67 was constructed and screened for RND pump-encoding genes by using DNA probes for two putative RND pump-encoding genes. Two different loci were identified: sdeAB, encoding an MFP and an RND pump, and sdeCDE, encoding an MFP and two different RND pumps. Northern blot analysis revealed overexpression of sdeB in two mutant strains effluxing fluoroquinolones. Analysis of the sdeAB and sdeCDE loci in Escherichia coli strain AG102MB, deficient in the RND pump (AcrB), revealed that gene products of sdeAB are responsible for the efflux of a diverse range of substrates that includes ciprofloxacin, norfloxacin, ofloxacin, chloramphenicol, sodium dodecyl sulfate, ethidium bromide, and n-hexane, while those of sdeCDE did not result in any change in susceptibilities to any of these agents.

Survey of Michigan dentists and radiation oncologists on oral care of patients undergoing head and neck radiation therapy.

PubMed

Patel, Yoshita; Bahlhorn, Hannah; Zafar, Saniya; Zwetchkenbaum, Samuel; Eisbruch, Avraham; Murdoch-Kinch, Carol Anne

2012-07-01

Oral complications of radiation therapy for head and neck cancer (HNC) are associated with a significant decline in oral health-related quality of life (OHQOL). The dentist, working with the radiation oncologist and the rest of the health care team, plays an important role in the prevention and management of these complications, but patients do not always receive care consistent with current guidelines. This study investigated barriers to recommended care. There is variability in knowledge and practice among dentists and radiation oncologists regarding the dental management of patients treated with head and neck radiotherapy (HNRT), and inadequate communication and collaboration between members of the patient's health care team contribute to inconsistencies in application of clinical care guidelines. There is on interest and need for continuing dental (CDE) and medical education (CME) on this topic. A questionnaire was developed to assess dentists' knowledge and practice of dental management of HNC patients and their interest in CDE on this topic. All members of the Michigan Dental Association (MDA) with email addresses were asked to complete the survey online, and a random sample of MDA members without email addresses was invited to complete a paper version of the same survey. All Michigan members of the American Society for Radiation Oncology (ASTRO) were invited to complete an online version of the survey modified for radiation oncologists. The response rate for dentists was 47.9% and radiation oncologists was 22.3%. Of the dentists who responded, 81% reported that a major barrier to providing dental treatment before radiotherapy was a lack of time between initial dental consultation and the start of radiation; inadequate communication between health care providers was blamed most frequently for this. Ten percent of the dentists and 25% of the radiation oncologists reported that they did not treat HNC patients because they lacked adequate training, and 55% of dental respondents said that they did not feel adequately trained in dental school to treat patients who have had head and neck radiation therapy. Most respondents (radiation oncologists 67%; dentists 72%) were interested in CDE and CME on this topic. These results suggest a need for CDE and CME for Michigan dentists and radiation oncologists on the oral management of HNC patients. Improved training and communication between health professionals could improve patient outcomes and more consistent application of clinical care guidelines.

CERESVis: A QC Tool for CERES that Leverages Browser Technology for Data Validation

NASA Astrophysics Data System (ADS)

Chu, C.; Sun-Mack, S.; Heckert, E.; Chen, Y.; Doelling, D.

2015-12-01

In this poster, we are going to present three user interfaces that CERES team uses to validate pixel-level data. Besides our home grown tools, we will aslo present the browser technology that we use to provide interactive interfaces, such as jquery, HighCharts and Google Earth. We pass data to the users' browsers and use the browsers to do some simple computations. The three user interfaces are: Thumbnails -- it displays hundrends images to allow users to browse 24-hour data files in few seconds. Multiple-synchronized cursors -- it allows users to compare multiple images side by side. Bounding Boxes and Histograms -- it allows users to draw multiple bounding boxes on an image and the browser computes/display the histograms.

Navigating protected genomics data with UCSC Genome Browser in a Box.

PubMed

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James

2015-03-01

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). © The Author 2014. Published by Oxford University Press.

47 CFR 14.61 - Obligations with respect to internet browsers built into mobile phones.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 1 2014-10-01 2014-10-01 false Obligations with respect to internet browsers... GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Internet... internet browsers built into mobile phones. (a) Accessibility. If on or after October 8, 2013 a...

47 CFR 14.61 - Obligations with respect to internet browsers built into mobile phones.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 1 2013-10-01 2013-10-01 false Obligations with respect to internet browsers... GENERAL ACCESS TO ADVANCED COMMUNICATIONS SERVICES AND EQUIPMENT BY PEOPLE WITH DISABILITIES Internet... internet browsers built into mobile phones. (a) Accessibility. If on or after October 8, 2013 a...

Ajax and Firefox: New Web Applications and Browsers

ERIC Educational Resources Information Center

Godwin-Jones, Bob

2005-01-01

Alternative browsers are gaining significant market share, and both Apple and Microsoft are releasing OS upgrades which portend some interesting changes in Web development. Of particular interest for language learning professionals may be new developments in the area of Web browser based applications, particularly using an approach dubbed "Ajax."…

ABO, Rhesus, and Kell Antigens, Alleles, and Haplotypes in West Bengal, India

PubMed Central

Basu, Debapriya; Datta, Suvro Sankha; Montemayor, Celina; Bhattacharya, Prasun; Mukherjee, Krishnendu; Flegel, Willy A.

2018-01-01

Background Few studies have documented the blood group antigens in the population of eastern India. Frequencies of some common alleles and haplotypes were unknown. We describe phenotype, allele, and haplotype frequencies in the state of West Bengal, India. Methods We tested 1,528 blood donors at the Medical College Hospital, Kolkata. The common antigens of the ABO, Rhesus, and Kell blood group systems were determined by standard serologic methods in tubes. Allele and haplotype frequencies were calculated with an iterative method that yielded maximum-likelihood estimates under the assumption of a Hardy-Weinberg equilibrium. Results The prevalence of ABO antigens were B (34%), O (32%), A (25%), and AB (9%) with ABO allele frequencies for O = 0.567, A = 0.189, and B = 0.244. The D antigen (RH1) was observed in 96.6% of the blood donors with RH haplotype frequencies, such as for CDe = 0.688809, cde = 0.16983 and CdE = 0.000654. The K antigen (K1) was observed in 12 donors (0.79%) with KEL allele frequencies for K = 0.004 and k = 0.996. Conclusions: For the Bengali population living in the south of West Bengal, we established the frequencies of the major clinically relevant antigens in the ABO, Rhesus, and Kell blood group systems and derived estimates for the underlying ABO and KEL alleles and RH haplotypes. Such blood donor screening will improve the availability of compatible red cell units for transfusion. Our approach using widely available routine methods can readily be applied in other regions, where the sufficient supply of blood typed for the Rh and K antigens is lacking. PMID:29593462

Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology.

PubMed

Lin, Xiaoxi B; Gänzle, Michael G

2014-09-01

This study determined the effects of specific metabolic traits of Lactobacillus reuteri on its competitiveness in sourdoughs. The competitiveness of lactobacilli in sourdough generally depends on their growth rate; acid resistance additionally contributes to competitiveness in sourdoughs with long fermentation times. Glycerol metabolism via glycerol dehydratase (gupCDE) accelerates growth by the regeneration of reduced cofactors; glutamate metabolism via glutamate decarboxylase (gadB) increases acid resistance by generating a proton motive force. Glycerol and glutamate metabolisms are lineage-specific traits in L. reuteri; therefore, this study employed glycerol dehydratase-positive sourdough isolates of human-adapted L. reuteri lineage I, glutamate decarboxylase-positive strains of rodent-adapted L. reuteri lineage II, as well as mutants with deletions in gadB or gupCDE. The competitivenesses of the strains were quantified by inoculation of wheat and sorghum sourdoughs with defined strains, followed by propagation of doughs with a 10% inoculum and 12-h or 72-h fermentation cycles. Lineage I L. reuteri strains dominated sourdoughs propagated with 12-h fermentation cycles; lineage II L. reuteri strains dominated sourdoughs propagated with 72-h fermentation cycles. L. reuteri 100-23ΔgadB was outcompeted by its wild-type strain in sourdoughs fermented with 72-h fermentation cycles; L. reuteri FUA3400ΔgupCDE was outcompeted by its wild-type strain in sourdoughs fermented with both 12-h and 72-h fermentation cycles. Competition experiments with isogenic pairs of strains resulted in a constant rate of strain displacement of the less competitive mutant strain. In conclusion, lineage-specific traits of L. reuteri determine the competitiveness of this species in sourdough fermentations. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

[Population-based study of child developmental screening in Mexican PROSPERA beneficiaries younger than 5 years old].

PubMed

Rizzoli-Córdoba, Antonio; Martell-Valdez, Liliana; Delgado-Ginebra, Ismael; Villasís-Keever, Miguel Ángel; Reyes-Morales, Hortensia; O'Shea-Cuevas, Gabriel; Aceves-Villagrán, Daniel; Carrasco-Mendoza, Joaquín; Villagrán-Muñoz, Víctor Manuel; Halley-Castillo, Elizabeth; Vargas-López, Guillermo; Muñoz-Hernández, Onofre

Evaluación del Desarrollo Infantil or Child Development Evaluation (CDE) test, a screening tool designed and validated in Mexico, classifies child development as normal (green) or abnormal (developmental lag or yellow and risk of delay or red). Population-based results of child development level with this tool are not known. The objective of this work was to evaluate the developmental level of children aged 1-59 months living in poverty (PROSPERA program beneficiaries) through application of the CDE test. CDE tests were applied by specifically trained and standardized personnel to children <5 years old who attended primary care facilities for a scheduled appointment for nutrition, growth and development evaluation from November 2013 to May 2014. There were 5,527 children aged 1-59 months who were evaluated; 83.8% (n=4,632) were classified with normal development (green) and 16.2% (n=895) as abnormal: 11.9% (n=655) as yellow and 4.3% (n=240) as red. The proportion of abnormal results was 9.9% in children <1 year of age compared with 20.8% at 4 years old. The most affected areas according to age were language at 2 years (9.35%) and knowledge at 4 years old (11.1%). Gross motor and social areas were more affected in children from rural areas; fine motor skills, language and knowledge were more affected in males. The proportion of children with abnormal results is similar to other population-based studies. The highest rate in older children reinforces the need for an early-based intervention. The different pattern of areas affected between urban and rural areas suggests the need for a differentiated intervention. Copyright © 2015 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

PACS on mobile devices

NASA Astrophysics Data System (ADS)

Parikh, Ashesh; Mehta, Nihal

2015-03-01

Recent advances in internet browser technologies makes it possible to incorporate advanced functionality of a traditional PACS for viewing DICOM medical images on standard web browsers without the need to pre-install any plug-ins, apps or software. We demonstrate some of the capabilities of standard web browsers setting the stage for a cloud-based PACS.

YADBrowser: A Browser for Web-Based Educational Applications

ERIC Educational Resources Information Center

Zaldivar, Vicente Arturo Romero; Arandia, Jon Ander Elorriaga; Brito, Mateo Lezcano

2005-01-01

In this article, the main characteristics of the educational browser YADBrowser are described. One of the main objectives of this project is to define new languages and object models which facilitate the creation of educational applications for the Internet. The fundamental characteristics of the object model of the browser are also described.…

Report on the CDE Examination

ERIC Educational Resources Information Center

Haga, Enoch J.

1971-01-01

The Certificate in Data Education (Basic) examination is designed to certify that successful candidates are academically proficient in those principles and concepts of automation, computing, and data processing (including social and user implications) which are usually taught in basic introductory courses at the college or university level. (CK)

Quantum Dynamics Scattering Study of AB+CDE Reactions: A Seven Dimensional Treatment for the H2+C2H Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou

2003-01-01

A time-dependent wave-packet approach is presented for the quantum dynamics study of the AB+CDE reaction system for zero total angular momentum. A seven-degree-of-freedom calculation is employed to study the chemical reaction of H2+C2H yields H + C2H2 by treating C2H as a linear molecule. Initial state selected reaction probabilities are presented for various initial ro-vibrational states. This study shows that vibrational excitation of H2 enhances the reaction probability, whereas the excitation of C2H has only a small effect on the reactivity. An integral cross section is also reported for the initial ground states of H2 and C2H. The theoretical and experimental results agree with each other very well when the calculated seven dimensional results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculations.

Update on Thales flexure bearing coolers and drive electronics

NASA Astrophysics Data System (ADS)

Willems, D.; Benschop, T.; v. d. Groep, W.; Mullié, J.; v. d. Weijden, H.; Tops, M.

2009-05-01

Thales Cryogenics has a long background in delivering cryogenic coolers with an MTTF far above 20.000 hrs for military, civil and space programs. Developments in these markets required continuous update of the flexure bearing cooler portfolio for new and emerging applications. The cooling requirements of new application have not only their influence on the size of the compressor, cold finger and cooling technology used but also on the integration and control of the cooler in the application. Thales Cryogenics developed a compact Cooler Drive Electronics based on DSP technology that could be used for driving linear flexure bearing coolers with extreme temperature stability and with additional diagnostics inside the CDE. This CDE has a wide application and can be modified to specific customer requirements. During the presentation the latest developments in flexure bearing cooler technology will be presented both for Stirling and Pulse Tube coolers. Also the relation between the most important recent detector requirements and possible available solutions on cryocooler level will be presented.

Information-Flow-Based Access Control for Web Browsers

NASA Astrophysics Data System (ADS)

Yoshihama, Sachiko; Tateishi, Takaaki; Tabuchi, Naoshi; Matsumoto, Tsutomu

The emergence of Web 2.0 technologies such as Ajax and Mashup has revealed the weakness of the same-origin policy[1], the current de facto standard for the Web browser security model. We propose a new browser security model to allow fine-grained access control in the client-side Web applications for secure mashup and user-generated contents. We propose a browser security model that is based on information-flow-based access control (IBAC) to overcome the dynamic nature of the client-side Web applications and to accurately determine the privilege of scripts in the event-driven programming model.

An Asynchronous P300-Based Brain-Computer Interface Web Browser for Severely Disabled People.

PubMed

Martinez-Cagigal, Victor; Gomez-Pilar, Javier; Alvarez, Daniel; Hornero, Roberto

2017-08-01

This paper presents an electroencephalographic (EEG) P300-based brain-computer interface (BCI) Internet browser. The system uses the "odd-ball" row-col paradigm for generating the P300 evoked potentials on the scalp of the user, which are immediately processed and translated into web browser commands. There were previous approaches for controlling a BCI web browser. However, to the best of our knowledge, none of them was focused on an assistive context, failing to test their applications with a suitable number of end users. In addition, all of them were synchronous applications, where it was necessary to introduce a "read-mode" command in order to avoid a continuous command selection. Thus, the aim of this study is twofold: 1) to test our web browser with a population of multiple sclerosis (MS) patients in order to assess the usefulness of our proposal to meet their daily communication needs; and 2) to overcome the aforementioned limitation by adding a threshold that discerns between control and non-control states, allowing the user to calmly read the web page without undesirable selections. The browser was tested with sixteen MS patients and five healthy volunteers. Both quantitative and qualitative metrics were obtained. MS participants reached an average accuracy of 84.14%, whereas 95.75% was achieved by control subjects. Results show that MS patients can successfully control the BCI web browser, improving their personal autonomy.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

PubMed

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation. The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

75 FR 11993 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-12

... before April 12, 2010 to be assured of consideration. Community Development Financial Institutions (CDFI... related to Community Development Entity (CDE)/New Markets Tax Credit material events, as well as Community Development Financial Institutions (CDFI) material events in a single form. The form will provide a more...

HotJava: Sun's Animated Interactive World Wide Web Browser for the Internet.

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Examines HotJava and Java, World Wide Web technology for use on the Internet. HotJava, an interactive, animated Web browser, based on the object-oriented Java programming language, is different from HTML-based browsers such as Netscape. Its client/server design does not understand Internet protocols but can dynamically find what it needs to know.…

Lexicon Sextant: Modeling a Mnemonic System for Customizable Browser Information Organization and Management

ERIC Educational Resources Information Center

Shen, Siu-Tsen

2016-01-01

This paper presents an ongoing study of the development of a customizable web browser information organization and management system, which the author has named Lexicon Sextant (LS). LS is a user friendly, graphical web based add-on to the latest generation of web browsers, such as Google Chrome, making it easier and more intuitive to store and…

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes.

PubMed

Hallin, Peter F; Stærfeldt, Hans-Henrik; Rotenberg, Eva; Binnewies, Tim T; Benham, Craig J; Ussery, David W

2009-09-25

We present an interactive web application for visualizing genomic data of prokaryotic chromosomes. The tool (GeneWiz browser) allows users to carry out various analyses such as mapping alignments of homologous genes to other genomes, mapping of short sequencing reads to a reference chromosome, and calculating DNA properties such as curvature or stacking energy along the chromosome. The GeneWiz browser produces an interactive graphic that enables zooming from a global scale down to single nucleotides, without changing the size of the plot. Its ability to disproportionally zoom provides optimal readability and increased functionality compared to other browsers. The tool allows the user to select the display of various genomic features, color setting and data ranges. Custom numerical data can be added to the plot allowing, for example, visualization of gene expression and regulation data. Further, standard atlases are pre-generated for all prokaryotic genomes available in GenBank, providing a fast overview of all available genomes, including recently deposited genome sequences. The tool is available online from http://www.cbs.dtu.dk/services/gwBrowser. Supplemental material including interactive atlases is available online at http://www.cbs.dtu.dk/services/gwBrowser/suppl/.

Natural Language Processing in aid of FlyBase curators

PubMed Central

Karamanis, Nikiforos; Seal, Ruth; Lewin, Ian; McQuilton, Peter; Vlachos, Andreas; Gasperin, Caroline; Drysdale, Rachel; Briscoe, Ted

2008-01-01

Background Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. Results PaperBrowser is the first NLP-powered interface that was developed under a user-centered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we appraise PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. Conclusion We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully. PMID:18410678

Sealife: a semantic grid browser for the life sciences applied to the study of infectious diseases.

PubMed

Schroeder, Michael; Burger, Albert; Kostkova, Patty; Stevens, Robert; Habermann, Bianca; Dieng-Kuntz, Rose

2006-01-01

The objective of Sealife is the conception and realisation of a semantic Grid browser for the life sciences, which will link the existing Web to the currently emerging eScience infrastructure. The SeaLife Browser will allow users to automatically link a host of Web servers and Web/Grid services to the Web content he/she is visiting. This will be accomplished using eScience's growing number of Web/Grid Services and its XML-based standards and ontologies. The browser will identify terms in the pages being browsed through the background knowledge held in ontologies. Through the use of Semantic Hyperlinks, which link identified ontology terms to servers and services, the SeaLife Browser will offer a new dimension of context-based information integration. In this paper, we give an overview over the different components of the browser and their interplay. This SeaLife Browser will be demonstrated within three application scenarios in evidence-based medicine, literature & patent mining, and molecular biology, all relating to the study of infectious diseases. The three applications vertically integrate the molecule/cell, the tissue/organ and the patient/population level by covering the analysis of high-throughput screening data for endocytosis (the molecular entry pathway into the cell), the expression of proteins in the spatial context of tissue and organs, and a high-level library on infectious diseases designed for clinicians and their patients. For more information see http://www.biote.ctu-dresden.de/sealife.

78 FR 32302 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-29

... burden estimate, or any other aspect of the information collection, including suggestion for reducing the... capture information related to Community Development Entity (CDE)/New Markets Tax Credit material events... indicate, through a series of specific questions, whether or not the event will have an impact on areas of...

Electricity Data Browser

EIA Publications

The Electricity Data Browser shows generation, consumption, fossil fuel receipts, stockpiles, retail sales, and electricity prices. The data appear on an interactive web page and are updated each month. The Electricity Data Browser includes all the datasets collected and published in EIA's Electric Power Monthly and allows users to perform dynamic charting of data sets as well as map the data by state. The data browser includes a series of reports that appear in the Electric Power Monthly and allows readers to drill down to plant level statistics, where available. All images and datasets are available for download. Users can also link to the data series in EIA's Application Programming Interface (API). An API makes our data machine-readable and more accessible to users.

Plugin free remote visualization in the browser

NASA Astrophysics Data System (ADS)

Tamm, Georg; Slusallek, Philipp

2015-01-01

Today, users access information and rich media from anywhere using the web browser on their desktop computers, tablets or smartphones. But the web evolves beyond media delivery. Interactive graphics applications like visualization or gaming become feasible as browsers advance in the functionality they provide. However, to deliver large-scale visualization to thin clients like mobile devices, a dedicated server component is necessary. Ideally, the client runs directly within the browser the user is accustomed to, requiring no installation of a plugin or native application. In this paper, we present the state-of-the-art of technologies which enable plugin free remote rendering in the browser. Further, we describe a remote visualization system unifying these technologies. The system transfers rendering results to the client as images or as a video stream. We utilize the upcoming World Wide Web Consortium (W3C) conform Web Real-Time Communication (WebRTC) standard, and the Native Client (NaCl) technology built into Chrome, to deliver video with low latency.

A Java viewer to publish Digital Imaging and Communications in Medicine (DICOM) radiologic images on the World Wide Web.

PubMed

Setti, E; Musumeci, R

2001-06-01

The world wide web is an exciting service that allows one to publish electronic documents made of text and images on the internet. Client software called a web browser can access these documents, and display and print them. The most popular browsers are currently Microsoft Internet Explorer (Microsoft, Redmond, WA) and Netscape Communicator (Netscape Communications, Mountain View, CA). These browsers can display text in hypertext markup language (HTML) format and images in Joint Photographic Expert Group (JPEG) and Graphic Interchange Format (GIF). Currently, neither browser can display radiologic images in native Digital Imaging and Communications in Medicine (DICOM) format. With the aim to publish radiologic images on the internet, we wrote a dedicated Java applet. Our software can display radiologic and histologic images in DICOM, JPEG, and GIF formats, and provides a a number of functions like windowing and magnification lens. The applet is compatible with some web browsers, even the older versions. The software is free and available from the author.

UCSC genome browser: deep support for molecular biomedical research.

PubMed

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

2008-01-01

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

Reliability of SNOMED-CT Coding by Three Physicians using Two Terminology Browsers

PubMed Central

Chiang, Michael F.; Hwang, John C.; Yu, Alexander C.; Casper, Daniel S.; Cimino, James J.; Starren, Justin

2006-01-01

SNOMED-CT has been promoted as a reference terminology for electronic health record (EHR) systems. Many important EHR functions are based on the assumption that medical concepts will be coded consistently by different users. This study is designed to measure agreement among three physicians using two SNOMED-CT terminology browsers to encode 242 concepts from five ophthalmology case presentations in a publicly-available clinical journal. Inter-coder reliability, based on exact coding match by each physician, was 44% using one browser and 53% using the other. Intra-coder reliability testing revealed that a different SNOMED-CT code was obtained up to 55% of the time when the two browsers were used by one user to encode the same concept. These results suggest that the reliability of SNOMED-CT coding is imperfect, and may be a function of browsing methodology. A combination of physician training, terminology refinement, and browser improvement may help increase the reproducibility of SNOMED-CT coding. PMID:17238317

WebVR: an interactive web browser for virtual environments

NASA Astrophysics Data System (ADS)

Barsoum, Emad; Kuester, Falko

2005-03-01

The pervasive nature of web-based content has lead to the development of applications and user interfaces that port between a broad range of operating systems and databases, while providing intuitive access to static and time-varying information. However, the integration of this vast resource into virtual environments has remained elusive. In this paper we present an implementation of a 3D Web Browser (WebVR) that enables the user to search the internet for arbitrary information and to seamlessly augment this information into virtual environments. WebVR provides access to the standard data input and query mechanisms offered by conventional web browsers, with the difference that it generates active texture-skins of the web contents that can be mapped onto arbitrary surfaces within the environment. Once mapped, the corresponding texture functions as a fully integrated web-browser that will respond to traditional events such as the selection of links or text input. As a result, any surface within the environment can be turned into a web-enabled resource that provides access to user-definable data. In order to leverage from the continuous advancement of browser technology and to support both static as well as streamed content, WebVR uses ActiveX controls to extract the desired texture skin from industry strength browsers, providing a unique mechanism for data fusion and extensibility.

Exploratory Visual Analytics of a Dynamically Built Network of Nodes in a WebGL-Enabled Browser

DTIC Science & Technology

2014-01-01

dimensionality reduction, feature extraction, high-dimensional data, t-distributed stochastic neighbor embedding, neighbor retrieval visualizer, visual...WebGL-enabled rendering is supported natively by browsers such as the latest Mozilla Firefox , Google Chrome, and Microsoft Internet Explorer 11. At the...appropriate names. The resultant 26-node network is displayed in a Mozilla Firefox browser in figure 2 (also see appendix B). 3 Figure 1. The

The MycoBrowser portal: a comprehensive and manually annotated resource for mycobacterial genomes.

PubMed

Kapopoulou, Adamandia; Lew, Jocelyne M; Cole, Stewart T

2011-01-01

In this paper, we present the MycoBrowser portal (http://mycobrowser.epfl.ch/), a resource that provides both in silico generated and manually reviewed information within databases dedicated to the complete genomes of Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum and Mycobacterium smegmatis. A central component of MycoBrowser is TubercuList (http://tuberculist.epfl.ch), which has recently benefited from a new data management system and web interface. These improvements were extended to all MycoBrowser databases. We provide an overview of the functionalities available and the different ways of interrogating the data then discuss how both the new information and the latest features are helping the mycobacterial research communities. Copyright © 2010 Elsevier Ltd. All rights reserved.

Effects of Agricultural Sales CDE Modules on Content Knowledge and Argumentation Skill

ERIC Educational Resources Information Center

Sapp, Sarah B.; Thoron, Andrew C.

2014-01-01

The purpose of this study was to determine the effects of the type of training module on argumentation skill, student content knowledge achievement, and performance in an agricultural sales practicum completed by secondary school agriculture students. Current research has concluded that most students do not possess the academic or transferable…

Residence and Race: 1619 to 2019. CDE Working Paper 88-19.

ERIC Educational Resources Information Center

Taeuber, Karl E.

In the United states, late in the twentieth century, racial separation prevails in family life, playgrounds, churches, and local community activities. Segregation of housing is a key mechanism for maintaining the subordinate status of blacks. Housing policies and practices have been a leading cause of the nation's decaying central cities and…

Leadership Curriculum and Materials Used by High School Agricultural Science Teachers: A National Study of the Pre-"LifeKnowledge" Days

ERIC Educational Resources Information Center

Morgan, A. Christian; Fuhrman, Nicholas E.; King, Diana L.; Flanders, Frank B.; Rudd, Rick D.

2013-01-01

Agricultural science programs have provided many opportunities for leadership education through classroom, supervised agricultural experience (SAE), and FFA Organization activities. Past studies have focused on leadership developed through activities such as career development events (CDE), SAE activities, FFA Organization conventions, and other…

Teacher Educators: Addressing the Needs of All Learners

ERIC Educational Resources Information Center

Cook, Ellen

2017-01-01

This qualitative dissertation examines how teacher preparation programs take up policy messages from two state agencies. These questions guided the study: (1) What are the messages about RTI and MTSS from the California Department of Education [CDE] and the California Commission on Teacher Credentialing [CCTC]; and (2) How are RtI and MTSS taken…

Division site selection in Escherichia coli involves dynamic redistribution of Min proteins within coiled structures that extend between the two cell poles

NASA Astrophysics Data System (ADS)

Shih, Yu-Ling; Le, Trung; Rothfield, Lawrence

2003-06-01

The MinCDE proteins of Escherichia coli are required for proper placement of the division septum at midcell. The site selection process requires the rapid oscillatory redistribution of the proteins from pole to pole. We report that the three Min proteins are organized into extended membrane-associated coiled structures that wind around the cell between the two poles. The pole-to-pole oscillation of the proteins reflects oscillatory changes in their distribution within the coiled structure. We also report that the E. coli MreB protein, which is required for maintaining the rod shape of the cell, also forms extended coiled structures, which are similar to the MreB structures that have previously been reported in Bacillus subtilis. The MreB and MinCDE coiled arrays do not appear identical. The results suggest that at least two functionally distinct cytoskeletal-like elements are present in E. coli and that structures of this type can undergo dynamic changes that play important roles in division site placement and possibly other aspects of the life of the cell.

Conditioned inhibition in the spatial domain.

PubMed

Sansa, J; Rodrigo, T; Santamaría, J J; Manteiga, R D; Chamizo, V D

2009-10-01

Using a variation on the standard procedure of conditioned inhibition (Trials A+ and AX-), rats (Rattus norvegicus) in a circular pool were trained to find a hidden platform that was located in a specific spatial position in relation to 2 individual landmarks (Trials A --> platform and B --> platform; Experiments 1a and 1b) and to 2 configurations of landmarks (Trials ABC --> platform and FGH --> platform; Experiment 2a). The rats also underwent inhibitory trials (Experiment 1: Trials AZ --> no platform; Experiment 2a: Trials CDE --> no platform) interspersed with these excitatory trials. In both experiments, subsequent test trials without the platform showed both a summation effect and retardation of excitatory conditioning, and in Experiment 2a rats learned to avoid the CDE quadrant over the course of the experiment. Two further experiments established that these results could not be attributed to any difference in salience between the conditioned inhibitors and the control stimuli. All these results contribute to the growing body of evidence consistent with the idea that there is a general mechanism of learning that is associative in nature. PsycINFO Database Record (c) 2009 APA, all rights reserved.

[Computer-assisted phacoemulsification for hard cataracts].

PubMed

Zemba, M; Papadatu, Adriana-Camelia; Sîrbu, Laura-Nicoleta; Avram, Corina

2012-01-01

to evaluate the efficiency of new torsional phacoemulsification software (Ozil IP system) in hard nucleus cataract extraction. 45 eyes with hard senile cataract (degree III and IV) underwent phacoemulsification performed by the same surgeon, using the same technique (stop and chop). Infiniti (Alcon) platform was used, with Ozil IP software and Kelman phaco tip miniflared, 45 degrees. The nucleus was split into two and after that the first half was phacoemulsificated with IP-on (group 1) and the second half with IP-off (group 2). For every group we measured: cumulative dissipated energy (CDE), numbers of tip closure that needed manual desobstruction the amount of BSS used. The mean CDE was the same in group 1 and in group 2 (between 6.2 and 14.9). The incidence of occlusion that needed manual desobstruction was lower in group 1 (5 times) than in group 2 (13 times). Group 2 used more BSS compared to group 1. The new torsional software (IP system) significantly decreased occlusion time and balanced salt solution use over standard torsional software, particularly with denser cataracts.

Effects of thermal blooming on systems comprised of tiled subapertures

NASA Astrophysics Data System (ADS)

Leakeas, Charles L.; Bartell, Richard J.; Krizo, Matthew J.; Fiorino, Steven T.; Cusumano, Salvatore J.; Whiteley, Matthew R.

2010-04-01

Laser weapon systems comprise of tiled subapertures are rapidly emerging in the directed energy community. The Air Force Institute of Technology Center for Directed Energy (AFIT/CDE), under sponsorship of the HEL Joint Technology Office has developed performance models of such laser weapon system configurations consisting of tiled arrays of both slab and fiber subapertures. These performance models are based on results of detailed waveoptics analyses conducted using WaveTrain. Previous performance model versions developed in this effort represent system characteristics such as subaperture shape, aperture fill factor, subaperture intensity profile, subaperture placement in the primary aperture, subaperture mutual coherence (piston), subaperture differential jitter (tilt), and beam quality wave-front error associated with each subaperture. The current work is a prerequisite for the development of robust performance models for turbulence and thermal blooming effects for tiled systems. Emphasis is placed on low altitude tactical scenarios. The enhanced performance model developed will be added to AFIT/CDE's HELEEOS parametric one-on-one engagement level model via the Scaling for High Energy Laser and Relay Engagement (SHaRE) toolbox.

The Streptococcus sanguinis competence regulon is not required for infective endocarditis virulence in a rabbit model.

PubMed

Callahan, Jill E; Munro, Cindy L; Kitten, Todd

2011-01-01

Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility in S. sanguinis. Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction with a variety of virulence assays, we determined that both mutants possessed infectivity equivalent to that of a virulent control strain, and that measures of disease were similar in rabbits infected with each strain. These results suggest that the com regulon is not required for S. sanguinis infective endocarditis virulence in this model. We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species.

Identification of the DNA-Binding Domains of Human Replication Protein A That Recognize G-Quadruplex DNA

PubMed Central

Prakash, Aishwarya; Natarajan, Amarnath; Marky, Luis A.; Ouellette, Michel M.; Borgstahl, Gloria E. O.

2011-01-01

Replication protein A (RPA), a key player in DNA metabolism, has 6 single-stranded DNA-(ssDNA-) binding domains (DBDs) A-F. SELEX experiments with the DBDs-C, -D, and -E retrieve a 20-nt G-quadruplex forming sequence. Binding studies show that RPA-DE binds preferentially to the G-quadruplex DNA, a unique preference not observed with other RPA constructs. Circular dichroism experiments show that RPA-CDE-core can unfold the G-quadruplex while RPA-DE stabilizes it. Binding studies show that RPA-C binds pyrimidine- and purine-rich sequences similarly. This difference between RPA-C and RPA-DE binding was also indicated by the inability of RPA-CDE-core to unfold an oligonucleotide containing a TC-region 5′ to the G-quadruplex. Molecular modeling studies of RPA-DE and telomere-binding proteins Pot1 and Stn1 reveal structural similarities between the proteins and illuminate potential DNA-binding sites for RPA-DE and Stn1. These data indicate that DBDs of RPA have different ssDNA recognition properties. PMID:21772997

Mortality from non‐malignant respiratory diseases among people with silicosis in Hong Kong: exposure–response analyses for exposure to silica dust

PubMed Central

Tse, L A; Yu, I T S; Leung, C C; Tam, W; Wong, T W

2007-01-01

Objectives To examine the exposure–response relationships between various indices of exposure to silica dust and the mortality from non‐malignant respiratory diseases (NMRDs) or chronic obstructive pulmonary diseases (COPDs) among a cohort of workers with silicosis in Hong Kong. Methods The concentrations of respirable silica dust were assigned to each industry and job task according to historical industrial hygiene measurements documented previously in Hong Kong. Exposure indices included cumulative dust exposure (CDE) and mean dust concentration (MDC). Penalised smoothing spline models were used as a preliminary step to detect outliers and guide further analyses. Multiple Cox's proportional hazard models were used to estimate the dust effects on the risk of mortality from NMRDs or COPDs after truncating the highest exposures. Results 371 of the 853 (43.49%) deaths occurring among 2789 workers with silicosis during 1981–99 were from NMRDs, and 101 (27.22%) NMRDs were COPDs. Multiple Cox's proportional hazard models showed that CDE (p = 0.009) and MDC (p<0.001) were significantly associated only with NMRD mortality. Subgroup analysis showed that deaths from NMRDs (p<0.01) and COPDs (p<0.05) were significantly associated with both CDE and MDC among underground caisson workers and among those ever employed in other occupations with high exposure to silica dust. No exposure–response relationship was observed for surface construction workers with low exposures. A clear upward trend for both NMRDs and COPDs mortality was found with increasing severity of radiological silicosis. Conclusion This study documented an exposure–response relationship between exposure to silica dust and the risk of death from NMRDs or COPDs among workers with silicosis, except for surface construction workers with low exposures. The risk of mortality from NMRDs increased significantly with the progression of International Labor Organization categories, independent of dust effects. PMID:16973737

The National Institute of Neurological Disorders and Stroke and Department of Defense Sport-Related Concussion Common Data Elements Version 1.0 Recommendations.

PubMed

Broglio, Steven P; Kontos, Anthony P; Levin, Harvey; Schneider, Kathryn; Wilde, Elisabeth A; Cantu, Robert C; Feddermann-Demont, Nina; Fuller, Gordon; Gagnon, Isabelle; Gioia, Gerry; Giza, Christopher C; Griesbach, Grace Sophia; Leddy, John J; Lipton, Michael L; Mayer, Andrew; McAllister, Thomas; McCrea, Michael; McKenzie, Lara; Putukian, Margot; Signoretti, Stefano; Suskauer, Stacy J; Tamburro, Robert; Turner, Michael; Yeates, Keith Owen; Zemek, Roger; Ala'i, Sherita; Esterlitz, Joy; Gay, Katelyn; Bellgowan, Patrick S F; Joseph, Kristen

2018-05-02

Through a partnership with the National Institute of Neurological Disorders and Stroke (NINDS), National Institutes of Health (NIH), and Department of Defense (DoD), the development of Sport-Related Concussion (SRC) Common Data Elements (CDEs) was initiated. The aim of this collaboration was to increase the efficiency and effectiveness of clinical research studies and clinical treatment outcomes, increase data quality, facilitate data sharing across studies, reduce study start-up time, more effectively aggregate information into metadata results, and educate new clinical investigators. The SRC CDE Working Group consisted of 34 worldwide experts in concussion from varied fields of related expertise, divided into three Subgroups: Acute (<72 hours post-concussion), Subacute (3 days-3 months post-concussion) and Persistent/Chronic (>3 months post-concussion). To develop CDEs, the Subgroups reviewed various domains, and then selected from, refined, and added to existing CDEs, case report forms and field-tested data elements from national registries and funded research studies. Recommendations were posted to the NINDS CDE Website for Public Review from February 2017 to April 2017. Following an internal Working Group review of recommendations, along with consideration of comments received from the Public Review period, the first iteration (Version 1.0) of the NINDS SRC CDEs was completed in June 2017. The recommendations include Core and Supplemental - Highly Recommended CDEs for cognitive data elements and symptom checklists, as well as other outcomes and endpoints (e.g., vestibular, oculomotor, balance, anxiety, depression) and sample case report forms (e.g., injury reporting, demographics, concussion history) for domains typically included in clinical research studies. The NINDS SRC CDEs and supporting documents are publicly available on the NINDS CDE website https://www.commondataelements.ninds.nih.gov/. Widespread use of CDEs by researchers and clinicians will facilitate consistent SRC clinical research and trial design, data sharing, and metadata retrospective analysis.

Staphylococcal enterotoxin A-activated regulatory T cells promote allergen-specific TH2 response to intratracheal allergen inoculation.

PubMed

Zeng, Wei-Ping; McFarland, Margaret M; Zhou, Baohua; Holtfreter, Silva; Flesher, Susan; Cheung, Ambrose; Mallick, Avishek

2017-02-01

T H 2 responses are implicated in asthma pathobiology. Epidemiologic studies have found a positive association between asthma and exposure to staphylococcal enterotoxins. We used a mouse model of asthma to determine whether staphylococcal enterotoxins promote T H 2 differentiation of allergen-specific CD4 conventional T (Tcon) cells and asthma by activating allergen-nonspecific regulatory T (Treg) cells to create a T H 2-polarizing cytokine milieu. Ovalbumin (OVA)-specific, staphylococcal enterotoxin A (SEA)-nonreactive naive CD4 Tcon cells were cocultured with SEA-reactive allergen-nonspecific Treg or CD4 Tcon cells in the presence of OVA and SEA. The OVA-specific CD4 T cells were then analyzed for IL-13 and IFN-γ expression. SEA-activated Treg cells were analyzed for the expression of the T H 2-polarizing cytokine IL-4 and the T-cell activation markers CD69 and CD62L. For asthma induction, mice were intratracheally sensitized with OVA or cat dander extract (CDE) alone or together with SEA and then challenged with OVA or CDE. Mice were also subject to transient Treg cell depletion before sensitization with OVA plus SEA. Asthma features and T H 2 differentiation in these mice were analyzed. SEA-activated Treg cells induced IL-13 but suppressed IFN-γ expression in OVA-specific CD4 Tcon cells. SEA-activated Treg cells expressed IL-4, upregulated CD69, and downregulated CD62L. Sensitization with OVA plus SEA but not OVA alone induced asthma, and SEA exacerbated asthma induced by CDE. Depletion of Treg cells abolished these effects of SEA and IL-13 expression in OVA-specific T cells. SEA promoted T H 2 responses of allergen-specific T cells and asthma pathogenesis by activating Treg cells. Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Clusterin and Pycr1 alterations associate with strain and model differences in susceptibility to experimental pancreatitis.

PubMed

Iyer, Sapna; Park, Min-Jung; Moons, David; Kwan, Raymond; Liao, Jian; Liu, Li; Omary, M Bishr

2017-01-22

Acute pancreatitis has several underlying etiologies, and results in consequences ranging from mild to complex multi-organ failure. The wide range of pathology suggests a genetic predisposition for progression. We compared the susceptibility to acute pancreatitis in BALB/c and FVB/N mice, coupled with proteomic analysis, in order to identify potential protein associations with pancreatitis progression. Pancreatitis was induced in BALB/c and FVB/N mice by administration of cerulein or feeding a choline-deficient, ethionine-supplemented (CDE) diet. Histology and changes in serum amylase were examined. Proteome profiling in cerulein-treated mice was performed using 2-dimensional differential in gel electrophoresis (2D-DIGE) followed by mass spectrometry analysis and biochemical validation. Male and female FVB/N mice manifested more severe cerulein-induced pancreatitis as compared with BALB/c mice, but both strains were similarly susceptible to CDE-induced pancreatitis. Few of the 2D-DIGE alterations were validated by immunoblotting. Clusterin was markedly up-regulated after cerulein-induced pancreatitis in FVB/N but less-so in BALB/c mice. Pyrroline-5-carboxylate reductase (Pycr1), an enzyme involved in proline biosynthesis, had higher basal levels in FVB/N male and female mouse pancreata compared with BALB/c pancreata, and was relatively more resistant to degradation in FVB/N pancreata. However, serum and pancreas tissue proline levels were similar in the two strains. FVB/N is more susceptible than BALB/c mice to cerulein-induced but not CDE-induced pancreatitis. Most of the 2D-DIGE alterations in the two strains likely relate to posttranslational modifications rather than protein level differences. Clusterin levels increase dramatically in association with pancreatitis severity, while Pycr1 is higher in FVB/N versus BALB/c pancreata basally and after induction of pancreatitis. Changes in proline metabolism may represent a novel potential genetic modifier in the context of pancreatitis. Published by Elsevier Inc.

[Preliminary evaluation of the femtosecond laser-assisted cataract surgery in 300 cases].

PubMed

Wang, Yong; Bao, Xianyi; Zhou, Yanli; Xu, Rong; Peng, Tingting; Sun, Ming; Cao, Danmin; He, Ling

2015-09-01

To evaluate the clinical outcome of the femtosecond laser-assisted cataract surgery (FLACS) in our first 300 cases. In this retrospective study, the study group comprised 300 cases (300 eyes) in which FLACS was done. The control group comprised 300 cases (300 eyes) in which phacoemulsification was performed. The steps of the FLACS included capsulotomy, lens fragmentation, corneal incisions, and creation of incisions within the peripheral cornea to aid the correction of pre-existing astigmatism. After the FLACS, 2.2-mm coaxial micro-incision phacoemulsification and implantation of an intraocular lens were operated. The preoperative best corrected visual acuity (BCVA) and postoperative uncorrected visual acuity (UCVA), the cumulative dissipated energy (CDE) of the phacoemulsification, and the parameters of the FLACS, including the docking time, the suction time and the laser time, were recorded. The complications of the FLACS were analyzed. The FLACS was successfully completed in 99.33% of the cases. The docking time was (24.6 ± 16.8) sec, the suction time was (101.27 ± 20.09) sec, and the laser time was (23.3 ± 5.5) sec. The most common complications of the FLACS included suction break (7/300, 2.33%), subconjunctival hemorrhage (58/300, 19.33%), pupillary constriction (47/300, 15.67%), incision at a wrong site (13/300, 4.33%), anterior capsular tag (17/300, 5.67%), decentration of the capsulorhexis (11/300, 3.67%), failure to split the lens nucleus (5/300, 1.67%), and posterior capsular ruptures (1/300, 0.33%). The CDE was 5.52 ± 5.18 in the FLACS group and 8.37 ± 7.91 in the traditional phaco group (P < 0.05). The UCVA was 0.12 ± 0.08 and 0.13 ± 0.11 at 1 month after the FLACS and traditional phaco, respectively (P > 0.05). Compared with the conventional phacoemulsification surgery, the FLACS can achieve less CDE and better early postoperative visual acuity. Long-term effects remain to be investigated.

Torsional ultrasound mode versus combined torsional and conventional ultrasound mode phacoemulsification for eyes with hard cataract.

PubMed

Fakhry, Mohamed A; El Shazly, Malak I

2011-01-01

To compare torsional versus combined torsional and conventional ultrasound modes in hard cataract surgery regarding ultrasound energy and time and effect on corneal endothelium. Kasr El Aini hospital, Cairo University, and International Eye Hospital, Cairo, Egypt. Ninety-eight eyes of 63 patients were enrolled in this prospective comparative randomized masked clinical study. All eyes had nuclear cataracts of grades III and IV using the Lens Opacities Classification System III (LOCS III). Two groups were included, each having an equal number of eyes (49). The treatment for group A was combined torsional and conventional US mode phacoemulsification, and for group B torsional US mode phacoemulsification only. Pre- and post-operative assessments included best corrected visual acuity (BCVA), intraocular pressure (IOP), slit-lamp evaluation, and fundoscopic evaluation. Endothelial cell density (ECD) and central corneal thickness (CCT) were measured preoperatively, 1 day, 7 days, and 1 month postoperatively. All eyes were operated on using the Alcon Infiniti System (Alcon, Fort Worth, TX) with the quick chop technique. All eyes were implanted with AcrySof SA60AT (Alcon) intraocular lens (IOL). The main phaco outcome parameters included the mean ultrasound time (UST), the mean cumulative dissipated energy (CDE), and the percent of average torsional amplitude in position 3 (%TUSiP3). Improvement in BCVA was statistically significant in both groups (P < 0.001). Comparing UST and CDE for both groups revealed results favoring the pure torsional group (P = 0.002 and P < 0.001 for UST; P = 0.058 and P = 0.009 for CDE). As for %TUSiP3, readings were higher for the pure torsional group (P = 0.03 and P = 0.01). All changes of CCT, and ECD over time were found statistically significant using one-way ANOVA testing (P < 0.001). Both modes are safe in hard cataract surgery, however the pure torsional mode showed less US energy used.

Torsional ultrasound mode versus combined torsional and conventional ultrasound mode phacoemulsification for eyes with hard cataract

PubMed Central

Fakhry, Mohamed A; Shazly, Malak I El

2011-01-01

Purpose To compare torsional versus combined torsional and conventional ultrasound modes in hard cataract surgery regarding ultrasound energy and time and effect on corneal endothelium. Settings Kasr El Aini hospital, Cairo University, and International Eye Hospital, Cairo, Egypt. Methodology Ninety-eight eyes of 63 patients were enrolled in this prospective comparative randomized masked clinical study. All eyes had nuclear cataracts of grades III and IV using the Lens Opacities Classification System III (LOCS III). Two groups were included, each having an equal number of eyes (49). The treatment for group A was combined torsional and conventional US mode phacoemulsification, and for group B torsional US mode phacoemulsification only. Pre- and post-operative assessments included best corrected visual acuity (BCVA), intraocular pressure (IOP), slit-lamp evaluation, and fundoscopic evaluation. Endothelial cell density (ECD) and central corneal thickness (CCT) were measured preoperatively, 1 day, 7 days, and 1 month postoperatively. All eyes were operated on using the Alcon Infiniti System (Alcon, Fort Worth, TX) with the quick chop technique. All eyes were implanted with AcrySof SA60AT (Alcon) intraocular lens (IOL). The main phaco outcome parameters included the mean ultrasound time (UST), the mean cumulative dissipated energy (CDE), and the percent of average torsional amplitude in position 3 (%TUSiP3). Results Improvement in BCVA was statistically significant in both groups (P < 0.001). Comparing UST and CDE for both groups revealed results favoring the pure torsional group (P = 0.002 and P < 0.001 for UST; P = 0.058 and P = 0.009 for CDE). As for %TUSiP3, readings were higher for the pure torsional group (P = 0.03 and P = 0.01). All changes of CCT, and ECD over time were found statistically significant using one-way ANOVA testing (P < 0.001). Conclusion Both modes are safe in hard cataract surgery, however the pure torsional mode showed less US energy used. PMID:21792288

Human exposure to PCDDs and their precursors from heron and tern eggs in the Yangtze River Delta indicate PCP origin.

PubMed

Zhou, Yihui; Yin, Ge; Asplund, Lillemor; Stewart, Kathryn; Rantakokko, Panu; Bignert, Anders; Ruokojärvi, Päivi; Kiviranta, Hannu; Qiu, Yanling; Ma, Zhijun; Bergman, Åke

2017-06-01

Polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are highly toxic to humans and wildlife. In the present study, PCDD/Fs were analyzed in the eggs of whiskered terns (Chlidonias hybrida), and genetically identified eggs from black-crowned night herons (Nycticorax nycticorax) sampled from two lakes in the Yangtze River Delta area, China. The median toxic equivalent (TEQ) of PCDD/Fs were 280 (range: 95-1500) and 400 (range: 220-1100) pg TEQ g -1 lw (WHO, 1998 for birds) in the eggs of black-crowned night heron and whiskered tern, respectively. Compared to known sources, concentrations of PCDDs relative to the sum of PCDD/Fs in bird eggs, demonstrated high abundance of octachlorodibenzo-p-dioxin (OCDD), 1,2,3,4,6,7,8-heptaCDD and 1,2,3,6,7,8-hexaCDD indicating pentachlorophenol (PCP), and/or sodium pentachlorophenolate (Na-PCP) as significant sources of the PCDD/Fs. The presence of polychlorinated diphenyl ethers (PCDEs), hydroxylated and methoxylated polychlorinated diphenyl ethers (OH- and MeO-PCDEs, known impurities in PCP products), corroborates this hypothesis. Further, significant correlations were found between the predominant congener CDE-206, 3'-OH-CDE-207, 2'-MeO-CDE-206 and OCDD, indicating a common origin. Eggs from the two lakes are sometimes used for human consumption. The WHO health-based tolerable intake of PCDD/Fs is exceeded if eggs from the two lakes are consumed regularly on a weekly basis, particularly for children. The TEQs extensively exceed maximum levels for PCDD/Fs in hen eggs and egg products according to EU legislation (2.5 pg TEQ g -1 lw). The results suggest immediate action should be taken to manage the contamination, and further studies evaluating the impacts of egg consumption from wild birds in China. Likewise, studies on dioxins and other POPs in common eggs need to be initiated around China. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Polychlorinated diphenyl ethers (PCDEs) in surface sediments, suspended particulate matter (SPM) and surface water of Chaohu Lake, China.

PubMed

Zhang, Xuesheng; Wang, Tantan; Gao, Lei; Feng, Mingbao; Qin, Li; Shi, Jiaqi; Cheng, Danru

2018-05-31

Polychlorinated diphenyl ethers (PCDEs) are typical halogenated aromatic pollutants that have shown various toxicological effects on organisms. However, the contamination status of PCDEs in the fresh water lakes of China remains poorly researched. In this study, the levels of 15 congeners of PCDEs in the sediments, suspended particulate matter (SPM) and water of Chaohu Lake were determined. The results showed that the ranges of concentrations of total PCDEs (ΣPCDEs) in the sediment, SPM and water were 0.279 ng g -1 dry weight (d.w.)-2.474 ng g -1 d.w., 0.331 ng g -1 d.w.-2.013 ng g -1 d.w. and 0.351 ng L -1 -2.021 ng L -1 , respectively. The most abundant congeners found in sediments, SPM and water were 3,3',4,4'-tetra-CDE, deca-CDE and 2,4,6-tri-CDE, with average contributive ratios of 17.36%, 15.48% and 20.63%, respectively. The medium and higher chlorinated PCDEs (e.g., penta- and deca-CDEs) were the dominant congeners in sediments and SPM. The percentages of lower chlorinated PCDEs (e.g., tri-CDEs) in the water were higher than those in the sediments. The combined input of ΣPCDEs from the eight main tributaries to Chaohu Lake was estimated at 6.94 kg y -1 . Strong linear correlations between the concentrations of ΣPCDEs and organic carbon (OC) contents in three type samples from Chaohu Lake suggested OC could influence the distribution of PCDEs in Chaohu Lake substantially. In addition, the calculated average organic carbon normalized partition coefficients (logK oc ) of 15 PCDEs between water and SPM were in the range of 4.55-5.45 mL g -1 . This study confirmed that Chaohu Lake is contaminated by PCDEs. Copyright © 2018 Elsevier Ltd. All rights reserved.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML

NASA Astrophysics Data System (ADS)

Naito, O.

A browser-based tool for conversion between Fortran NAMELIST and XML/HTML is presented. It runs on an HTML5 compliant browser and generates reusable XML files to aid interoperability. It also provides a graphical interface for editing and annotating variables in NAMELIST, hence serves as a primitive code documentation environment. Although the tool is not comprehensive, it could be viewed as a test bed for integrating legacy codes into modern systems.

A user-centred evaluation framework for the Sealife semantic web browsers

PubMed Central

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-01-01

Background Semantically-enriched browsing has enhanced the browsing experience by providing contextualised dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. Methods This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. Results It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Conclusion Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues. PMID:19796398

A user-centred evaluation framework for the Sealife semantic web browsers.

PubMed

Oliver, Helen; Diallo, Gayo; de Quincey, Ed; Alexopoulou, Dimitra; Habermann, Bianca; Kostkova, Patty; Schroeder, Michael; Jupp, Simon; Khelif, Khaled; Stevens, Robert; Jawaheer, Gawesh; Madle, Gemma

2009-10-01

Semantically-enriched browsing has enhanced the browsing experience by providing contextualized dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic Web technologies is limited and user perception from the non-IT domain sceptical. Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback. The Sealife project investigates semantic browsing and its application to the life science domain. Sealife's main objective is to develop the notion of context-based information integration by extending three existing Semantic Web browsers (SWBs) to link the existing Web to the eScience infrastructure. This paper describes a user-centred evaluation framework that was developed to evaluate the Sealife SWBs that elicited feedback on users' perceptions on ease of use and information findability. Three sources of data: i) web server logs; ii) user questionnaires; and iii) semi-structured interviews were analysed and comparisons made between each browser and a control system. It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and polished interface was rated higher for usability, and semantic links were used by the users of all three browsers. Confirmation or contradiction of our original hypotheses with relation to SWBs is detailed along with observations of implementation issues.

A browser-based event display for the CMS experiment at the LHC

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

Hategan, M.; McCauley, T.; Nguyen, P.

2012-01-01

The line between native and web applications is becoming increasingly blurred as modern web browsers are becoming powerful platforms on which applications can be run. Such applications are trivial to install and are readily extensible and easy to use. In an educational setting, web applications permit a way to deploy deploy tools in a highly-restrictive computing environment. The I2U2 collaboration has developed a browser-based event display for viewing events in data collected and released to the public by the CMS experiment at the LHC. The application itself reads a JSON event format and uses the JavaScript 3D rendering engine pre3d.more » The only requirement is a modern browser using HTML5 canvas. The event display has been used by thousands of high school students in the context of programs organized by I2U2, QuarkNet, and IPPOG. This browser-based approach to display of events can have broader usage and impact for experts and public alike.« less

Evaluating Web accessibility at different processing phases

NASA Astrophysics Data System (ADS)

Fernandes, N.; Lopes, R.; Carriço, L.

2012-09-01

Modern Web sites use several techniques (e.g. DOM manipulation) that allow for the injection of new content into their Web pages (e.g. AJAX), as well as manipulation of the HTML DOM tree. This has the consequence that the Web pages that are presented to users (i.e. after browser processing) are different from the original structure and content that is transmitted through HTTP communication (i.e. after browser processing). This poses a series of challenges for Web accessibility evaluation, especially on automated evaluation software. This article details an experimental study designed to understand the differences posed by accessibility evaluation after Web browser processing. We implemented a Javascript-based evaluator, QualWeb, that can perform WCAG 2.0 based accessibility evaluations in the two phases of browser processing. Our study shows that, in fact, there are considerable differences between the HTML DOM trees in both phases, which have the consequence of having distinct evaluation results. We discuss the impact of these results in the light of the potential problems that these differences can pose to designers and developers that use accessibility evaluators that function before browser processing.

Single Mothers, the Underclass, and Social Policy. CDE Working Paper 88-30.

ERIC Educational Resources Information Center

McLanahan, Sara; Garfinkel, Irv

Although the vast majority of single mothers do not fit the description of an underclass, there is a small group of predominantly black single mothers concentrated in northern urban ghettos that is persistently weakly attached to the labor force, socially isolated, and reproducing itself. Although welfare programs are necessary for those who are…

Twenty-Five Years after "Larry P.": The California Response to Overrepresentation of African Americans in Special Education

ERIC Educational Resources Information Center

Powers, Kristin M.; Hagans-Murillo, Kristi S.; Restori, Alberto F.

2004-01-01

In this article, major laws, regulations, court cases, policies and practices related to intelligence testing of African American students in California are reviewed. A California Department of Education (CDE) ban on intelligence testing of African American students for the purpose of determining special education eligibility is in effect and…

Children Designing & Engineering: Contextual Learning Units in Primary Design and Technology

ERIC Educational Resources Information Center

Hutchinson, Patricia

2002-01-01

The Children Designing & Engineering (CD&E) Project at the College of New Jersey is a collaborative effort of the College's Center for Design and Technology and the New Jersey Chamber of Commerce. The Project, funded by the National Science Foundation (NSF), has been charged to develop instructional materials for grades K-5. The twelve…

Guidebook for the California Healthy Kids Survey. Part I: Administration. 2004-2005 Edition

ERIC Educational Resources Information Center

Austin, G.; Duerr, M.

2004-01-01

The California Healthy Kids Survey (CHKS) is a comprehensive youth health risk and resilience data collection service for local education agencies (LEAs) sponsored by the California Department of Education (CDE). It is an easily customized, comprehensive self-report youth survey for grades 5-12. It assesses all major areas of health-related risk…

47 CFR 14.60 - Applicability.

Code of Federal Regulations, 2013 CFR

2013-10-01

... BY PEOPLE WITH DISABILITIES Internet Browsers Built Into Telephones Used With Public Mobile Services... mobile services (as such term is defined in 47 U.S.C. 710(b)(4)(B)) that includes an Internet browser in...

47 CFR 14.60 - Applicability.

Code of Federal Regulations, 2014 CFR

2014-10-01

... BY PEOPLE WITH DISABILITIES Internet Browsers Built Into Telephones Used With Public Mobile Services... mobile services (as such term is defined in 47 U.S.C. 710(b)(4)(B)) that includes an Internet browser in...

Setting Up the JBrowse Genome Browser

PubMed Central

Skinner, Mitchell E; Holmes, Ian H

2010-01-01

JBrowse is a web-based tool for visualizing genomic data. Unlike most other web-based genome browsers, JBrowse exploits the capabilities of the user's web browser to make scrolling and zooming fast and smooth. It supports the browsers used by almost all internet users, and is relatively simple to install. JBrowse can utilize multiple types of data in a variety of common genomic data formats, including genomic feature data in bioperl databases, GFF files, and BED files, and quantitative data in wiggle files. This unit describes how to obtain the JBrowse software, set it up on a Linux or Mac OS X computer running as a web server and incorporate genome annotation data from multiple sources into JBrowse. After completing the protocols described in this unit, the reader will have a web site that other users can visit to browse the genomic data. PMID:21154710

Controlling EPICS from a web browser.

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

Evans, K., Jr.

1999-04-13

An alternative to using a large graphical display manager like MEDM [1,2] to interface to a control system, is to use individual control objects, such as text boxes, meters, etc., running in a browser. This paper presents three implementations of this concept, one using ActiveX controls, one with Java applets, and another with Microsoft Agent. The ActiveX controls have performance nearing that of MEDM, but they only work on Windows platforms. The Java applets require a server to get around Web security restrictions and are not as fast, but they have the advantage of working on most platforms and withmore » both of the leading Web browsers. The agent works on Windows platforms with and without a browser and allows voice recognition and speech synthesis, making it somewhat more innovative than MEDM.« less

Genome Maps, a new generation genome browser.

PubMed

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Genome Maps, a new generation genome browser

PubMed Central

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-01-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

Comparing Commercial WWW Browsers.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

Four commercial World Wide Web browsers are evaluated for features such as handling of WWW protocols and different URLs: FTP, Telnet, Gopher and WAIS, and e-mail and news; bookmark capabilities; navigation features; file management; and security support. (JKP)

US NDC Modernization Iteration E2 Prototyping Report: User Interface Framework

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

Lewis, Jennifer E.; Palmer, Melanie A.; Vickers, James Wallace

2014-12-01

During the second iteration of the US NDC Modernization Elaboration phase (E2), the SNL US NDC Modernization project team completed follow-on Rich Client Platform (RCP) exploratory prototyping related to the User Interface Framework (UIF). The team also developed a survey of browser-based User Interface solutions and completed exploratory prototyping for selected solutions. This report presents the results of the browser-based UI survey, summarizes the E2 browser-based UI and RCP prototyping work, and outlines a path forward for the third iteration of the Elaboration phase (E3).

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data.

PubMed

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-09-18

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A low-latency, big database system and browser for storage, querying and visualization of 3D genomic data

PubMed Central

Butyaev, Alexander; Mavlyutov, Ruslan; Blanchette, Mathieu; Cudré-Mauroux, Philippe; Waldispühl, Jérôme

2015-01-01

Recent releases of genome three-dimensional (3D) structures have the potential to transform our understanding of genomes. Nonetheless, the storage technology and visualization tools need to evolve to offer to the scientific community fast and convenient access to these data. We introduce simultaneously a database system to store and query 3D genomic data (3DBG), and a 3D genome browser to visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against state-of-the-art systems and demonstrate that it is faster than previous solutions, and importantly gracefully scales with the size of data. We also illustrate the usefulness of our 3D genome Web browser to explore human genome structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. PMID:25990738

Children's Representation of Symbolic and Nonsymbolic Magnitude Examined with the Priming Paradigm

ERIC Educational Resources Information Center

Defever, Emmy; Sasanguie, Delphine; Gebuis, Titia; Reynvoet, Bert

2011-01-01

How people process and represent magnitude has often been studied using number comparison tasks. From the results of these tasks, a comparison distance effect (CDE) is generated, showing that it is easier to discriminate two numbers that are numerically further apart (e.g., 2 and 8) compared with numerically closer numbers (e.g., 6 and 8).…

Analytical Concept: Development of a Multinational Information Strategy

DTIC Science & Technology

2008-10-31

16 1.4.3 Training and Mentoring/ Coaching ............................................................. 16 1.5 Analysis Requirements...America. These priority focus areas will become subject to experimentation in a number of consecutive phases of the 2008 Major Integrating Event ( MIE ...factor in general, in the MNE 5 CD&E program, focused on supporting concept validation in the 2008 MIE . The Analytical Concept outlines processes and

CAP4K Teacher Tour: Aligning State-Level Support with Classroom-Level Needs

ERIC Educational Resources Information Center

Colorado Department of Education, 2009

2009-01-01

In January 2009, the Colorado Department of Education (CDE) and the Colorado Education Association (CEA) initiated a 13-city teacher tour to engage teachers in a statewide discussion about CAP4K, its relevance to practice, its impact on teaching and learning and the kind of help that teachers would find useful for classroom implementation. Between…

One-loop matching and running with covariant derivative expansion

DOE PAGES

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

2018-01-24

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these “mixed” one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-knownmore » matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of “integrating out” heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.« less

Quorum Sensing Regulation of Competence and Bacteriocins in Streptococcus pneumoniae and mutans

PubMed Central

Shanker, Erin; Federle, Michael J.

2017-01-01

The human pathogens Streptococcus pneumoniae and Streptococcus mutans have both evolved complex quorum sensing (QS) systems that regulate the production of bacteriocins and the entry into the competent state, a requirement for natural transformation. Natural transformation provides bacteria with a mechanism to repair damaged genes or as a source of new advantageous traits. In S. pneumoniae, the competence pathway is controlled by the two-component signal transduction pathway ComCDE, which directly regulates SigX, the alternative sigma factor required for the initiation into competence. Over the past two decades, effectors of cellular killing (i.e., fratricides) have been recognized as important targets of the pneumococcal competence QS pathway. Recently, direct interactions between the ComCDE and the paralogous BlpRH pathway, regulating bacteriocin production, were identified, further strengthening the interconnections between these two QS systems. Interestingly, a similar theme is being revealed in S. mutans, the primary etiological agent of dental caries. This review compares the relationship between the bacteriocin and the competence QS pathways in both S. pneumoniae and S. mutans, and hopes to provide clues to regulatory pathways across the genus Streptococcus as a potential tool to efficiently investigate putative competence pathways in nontransformable streptococci. PMID:28067778

One-loop matching and running with covariant derivative expansion

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

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these “mixed” one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-knownmore » matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of “integrating out” heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.« less

The Streptococcus sanguinis Competence Regulon Is Not Required for Infective Endocarditis Virulence in a Rabbit Model

PubMed Central

Callahan, Jill E.; Munro, Cindy L.; Kitten, Todd

2011-01-01

Streptococcus sanguinis is an important component of dental plaque and a leading cause of infective endocarditis. Genetic competence in S. sanguinis requires a quorum sensing system encoded by the early comCDE genes, as well as late genes controlled by the alternative sigma factor, ComX. Previous studies of Streptococcus pneumoniae and Streptococcus mutans have identified functions for the >100-gene com regulon in addition to DNA uptake, including virulence. We investigated this possibility in S. sanguinis. Strains deleted for the comCDE or comX master regulatory genes were created. Using a rabbit endocarditis model in conjunction with a variety of virulence assays, we determined that both mutants possessed infectivity equivalent to that of a virulent control strain, and that measures of disease were similar in rabbits infected with each strain. These results suggest that the com regulon is not required for S. sanguinis infective endocarditis virulence in this model. We propose that the different roles of the S. sanguinis, S. pneumoniae, and S. mutans com regulons in virulence can be understood in relation to the pathogenic mechanisms employed by each species. PMID:22039480

One-loop matching and running with covariant derivative expansion

NASA Astrophysics Data System (ADS)

Henning, Brian; Lu, Xiaochuan; Murayama, Hitoshi

2018-01-01

We develop tools for performing effective field theory (EFT) calculations in a manifestly gauge-covariant fashion. We clarify how functional methods account for one-loop diagrams resulting from the exchange of both heavy and light fields, as some confusion has recently arisen in the literature. To efficiently evaluate functional traces containing these "mixed" one-loop terms, we develop a new covariant derivative expansion (CDE) technique that is capable of evaluating a much wider class of traces than previous methods. The technique is detailed in an appendix, so that it can be read independently from the rest of this work. We review the well-known matching procedure to one-loop order with functional methods. What we add to this story is showing how to isolate one-loop terms coming from diagrams involving only heavy propagators from diagrams with mixed heavy and light propagators. This is done using a non-local effective action, which physically connects to the notion of "integrating out" heavy fields. Lastly, we show how to use a CDE to do running analyses in EFTs, i.e. to obtain the anomalous dimension matrix. We demonstrate the methodologies by several explicit example calculations.

A Comparison of Three Different Thick Epinucleus Removal Techniques in Cataract Surgery.

PubMed

Hwang, Ho Sik; Lim, Byung-Su; Kim, Man Soo; Kim, Eun Chul

2017-01-01

To compare the outcomes of cataract surgery performed with three different types of the epinucleus removal techniques (safe boat, infusion/aspiration (I/A) cannulas, and phacoemulsification tip). Ninety eyes with thick adhesive epinuclei were randomly subdivided into three groups according to epinucleus removal technique: epinucleus floating (safe boat) technique, 30 patients; I/A tip, 30 patients; and phaco tip, 30 patients. Intraoperative measurements included ultrasound time (UST), mean cumulative dissipated ultrasound energy (CDE), and balanced salt solution (BSS) use. Clinical measurements were made preoperatively, and at one day, one month and two months postoperatively, including the best corrected visual acuity (BCVA), the central corneal thickness (CCT), and the endothelial cell count (ECC). Intraoperative measurements showed significantly less UST, CDE, and BSS use in the safe boat group than in the phaco tip groups (p < 0.05). The percentage of endothelial cell loss in the safe boat group was significantly lower than that in the phaco tip groups at two months post-cataract surgery (p < 0.05). The safe boat technique is a safer and more effective epinucleus removal technique than phaco tip techniques in cases with thick epinucleus.

a Kml-Based Approach for Distributed Collaborative Interpretation of Remote Sensing Images in the Geo-Browser

NASA Astrophysics Data System (ADS)

Huang, L.; Zhu, X.; Guo, W.; Xiang, L.; Chen, X.; Mei, Y.

2012-07-01

Existing implementations of collaborative image interpretation have many limitations for very large satellite imageries, such as inefficient browsing, slow transmission, etc. This article presents a KML-based approach to support distributed, real-time, synchronous collaborative interpretation for remote sensing images in the geo-browser. As an OGC standard, KML (Keyhole Markup Language) has the advantage of organizing various types of geospatial data (including image, annotation, geometry, etc.) in the geo-browser. Existing KML elements can be used to describe simple interpretation results indicated by vector symbols. To enlarge its application, this article expands KML elements to describe some complex image processing operations, including band combination, grey transformation, geometric correction, etc. Improved KML is employed to describe and share interpretation operations and results among interpreters. Further, this article develops some collaboration related services that are collaboration launch service, perceiving service and communication service. The launch service creates a collaborative interpretation task and provides a unified interface for all participants. The perceiving service supports interpreters to share collaboration awareness. Communication service provides interpreters with written words communication. Finally, the GeoGlobe geo-browser (an extensible and flexible geospatial platform developed in LIESMARS) is selected to perform experiments of collaborative image interpretation. The geo-browser, which manage and visualize massive geospatial information, can provide distributed users with quick browsing and transmission. Meanwhile in the geo-browser, GIS data (for example DEM, DTM, thematic map and etc.) can be integrated to assist in improving accuracy of interpretation. Results show that the proposed method is available to support distributed collaborative interpretation of remote sensing image

ToxMystery

MedlinePlus

Accessibility - This is a link to an external javascript file that searchs for a flash browser plug-in and what version of the browser is being used. The javascript is functional ToxMystery uses Adobe Flash Player. If you cannot install Flash Player, please use ...

THE NEVADA GEOSPATIAL DATA BROWSER

EPA Science Inventory

The Nevada Geospatial Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) with the assistance and collaboration of the University of Idaho (Moscow, ID) and Lockheed-Martin Environmental Services (Las Vegas, NV).

NEVADA GEOSPATICAL DATA BROWSER

EPA Science Inventory

The Nevada Geospatial Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) with the assistance and collaboration of the University of Idaho (Moscow, ID) and Lockheed-Martin Environmental Services Office (Las Vegas,...

South Platte Data Browser

EPA Science Inventory

The common goal among the developers of the South Platte River Basin Data Browser is to improve decision-making relative to environmental management through the development of applied research. The focus of the research has been to design an integrated system of landscape metri...

THE NEVADA GEOSPATIAL DATA BROWSER

EPA Science Inventory

The Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV) has developed the Nevada Geospatial Data Browser, a spatial data archive to centralize and distribute the geospatial data used to create the land cover, vertebrate habitat models, and land o...

SAN PEDRO GEODATA BROWSER

EPA Science Inventory

The San Pedro Data Browser was developed by the Landscape Ecology Branch of the U.S. Environmental Protection Agency (Las Vegas, NV). The goal of the Landscape Sciences Program is to improve decision-making relative to natural and human resource management through the development...

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video.

PubMed

Harper, Lisa C; Schaeffer, Mary L; Thistle, Jordan; Gardiner, Jack M; Andorf, Carson M; Campbell, Darwin A; Cannon, Ethalinda K S; Braun, Bremen L; Birkett, Scott M; Lawrence, Carolyn J; Sen, Taner Z

2011-01-01

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is 'Using the MaizeGDB Genome Browser', which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser. Database

The UCSC genome browser: what every molecular biologist should know.

PubMed

Mangan, Mary E; Williams, Jennifer M; Kuhn, Robert M; Lathe, Warren C

2009-10-01

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one's understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser.

Comparative analysis and visualization of multiple collinear genomes

PubMed Central

2012-01-01

Background Genome browsers are a common tool used by biologists to visualize genomic features including genes, polymorphisms, and many others. However, existing genome browsers and visualization tools are not well-suited to perform meaningful comparative analysis among a large number of genomes. With the increasing quantity and availability of genomic data, there is an increased burden to provide useful visualization and analysis tools for comparison of multiple collinear genomes such as the large panels of model organisms which are the basis for much of the current genetic research. Results We have developed a novel web-based tool for visualizing and analyzing multiple collinear genomes. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. Conclusions Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse laboratory strains. PMID:22536897

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes

PubMed Central

Lee, Moon Young; Park, Chanjae; Berent, Robyn M.; Park, Paul J.; Fuchs, Robert; Syn, Hannah; Chin, Albert; Townsend, Jared; Benson, Craig C.; Redelman, Doug; Shen, Tsai-wei; Park, Jong Kun; Miano, Joseph M.; Sanders, Kenton M.; Ro, Seungil

2015-01-01

Genome-scale expression data on the absolute numbers of gene isoforms offers essential clues in cellular functions and biological processes. Smooth muscle cells (SMCs) perform a unique contractile function through expression of specific genes controlled by serum response factor (SRF), a transcription factor that binds to DNA sites known as the CArG boxes. To identify SRF-regulated genes specifically expressed in SMCs, we isolated SMC populations from mouse small intestine and colon, obtained their transcriptomes, and constructed an interactive SMC genome and CArGome browser. To our knowledge, this is the first online resource that provides a comprehensive library of all genetic transcripts expressed in primary SMCs. The browser also serves as the first genome-wide map of SRF binding sites. The browser analysis revealed novel SMC-specific transcriptional variants and SRF target genes, which provided new and unique insights into the cellular and biological functions of the cells in gastrointestinal (GI) physiology. The SRF target genes in SMCs, which were discovered in silico, were confirmed by proteomic analysis of SMC-specific Srf knockout mice. Our genome browser offers a new perspective into the alternative expression of genes in the context of SRF binding sites in SMCs and provides a valuable reference for future functional studies. PMID:26241044

Low functional redundancy among mammalian browsers in regulating an encroaching shrub (Solanum campylacanthum) in African savannah

PubMed Central

Pringle, Robert M.; Goheen, Jacob R.; Palmer, Todd M.; Charles, Grace K.; DeFranco, Elyse; Hohbein, Rhianna; Ford, Adam T.; Tarnita, Corina E.

2014-01-01

Large herbivorous mammals play an important role in structuring African savannahs and are undergoing widespread population declines and local extinctions, with the largest species being the most vulnerable. The impact of these declines on key ecological processes hinges on the degree of functional redundancy within large-herbivore assemblages, a subject that has received little study. We experimentally quantified the effects of three browser species (elephant, impala and dik-dik) on individual- and population-level attributes of Solanum campylacanthum (Solanum incanum sensu lato), an encroaching woody shrub, using semi-permeable exclosures that selectively removed different-sized herbivores. After nearly 5 years, shrub abundance was lowest where all browser species were present and increased with each successive species deletion. Different browsers ate the same plant species in different ways, thereby exerting distinct suites of direct and indirect effects on plant performance and density. Not all of these effects were negative: elephants and impala also dispersed viable seeds and indirectly reduced seed predation by rodents and insects. We integrated these diffuse positive effects with the direct negative effects of folivory using a simple population model, which reinforced the conclusion that different browsers have complementary net effects on plant populations, and further suggested that under some conditions, these net effects may even differ in direction. PMID:24789900

Reaction time effects in lab- versus Web-based research: Experimental evidence.

PubMed

Hilbig, Benjamin E

2016-12-01

Although Web-based research is now commonplace, it continues to spur skepticism from reviewers and editors, especially whenever reaction times are of primary interest. Such persistent preconceptions are based on arguments referring to increased variation, the limits of certain software and technologies, and a noteworthy lack of comparisons (between Web and lab) in fully randomized experiments. To provide a critical test, participants were randomly assigned to complete a lexical decision task either (a) in the lab using standard experimental software (E-Prime), (b) in the lab using a browser-based version (written in HTML and JavaScript), or (c) via the Web using the same browser-based version. The classical word frequency effect was typical in size and corresponded to a very large effect in all three conditions. There was no indication that the Web- or browser-based data collection was in any way inferior. In fact, if anything, a larger effect was obtained in the browser-based conditions than in the condition relying on standard experimental software. No differences between Web and lab (within the browser-based conditions) could be observed, thus disconfirming any substantial influence of increased technical or situational variation. In summary, the present experiment contradicts the still common preconception that reaction time effects of only a few hundred milliseconds cannot be detected in Web experiments.

HEP Computing

Science.gov Websites

Argonne National Laboratory High Energy Physics Division Windows Desktops Problem Report Service Request Password Help New Users Back to HEP Computing Email on ANL Exchange: See Windows Clients section (Outlook or Thunderbird recommended) Web Browsers: Web Browsers for Windows Desktops Software: Available

Development of a Global Marine Environmental Library

DTIC Science & Technology

2010-06-01

Gulf. Marine Geology , 129, 237- 269. [4] Lerner, S., & Maffei, A. (2001). 4DGeoBrowser: A Web-based data browser and server for accessing and...Digital Library as a Catalyst for Collaboration: Voyages across Disciplinary and Institutional Boundaries with SIO Explorer; Digital Scholarship

South Platte River Basin Data Browser Report

EPA Science Inventory

The purpose of this data browser is to provide a spatial toolkit that delivers primary data that can be used for primary input information for assessments related to environmental endpoints, e.g. surface water hydrology and habitat mapping, related to ecosystem services. A neces...

Indicators of Family and Household Structure of Racial and Ethnic Minorities in the U.S. CDE Working Paper 77-29.

ERIC Educational Resources Information Center

Sweet, James A.

This paper reviews some of the issues and concerns that have prompted the growth of interest in the demography of the family. It also examines a number of aspects of the family and the household structure of racial and ethnic minorities. The five racial minorities discussed are blacks, Chinese, Japanese, Filipinos and American Indians. The…

Guidebook for the California Healthy Kids Survey. Part III: School Climate Survey for Teachers and Other Staff. 2005-2006 Edition

ERIC Educational Resources Information Center

Austin, G.; Duerr, M.

2005-01-01

No Child Left Behind (NCLB) mandates that schools receiving federal Safe and Drug-Free Schools and Community (SDFSC) funds conduct an anonymous teacher survey of the incidence of, prevalence of, and attitudes related to drug use and violence. To meet this NCLB mandate, the California Department of Education (CDE) funded the development of the…

Building Accountability in California: A Review of State Standards and Requirements for K-12 Public School Facility Planning and Design

ERIC Educational Resources Information Center

Vincent, Jeffrey M.

2016-01-01

This study aims to inform the California Department of Education (CDE) in ensuring the standards contained in Title 5 appropriately promote the planning and design of healthy, safe and educationally suitable K-12 school facilities. The study gathers and analyzes K-12 facility standards in ten case study states across the country to understand…

Poverty, School Size and Charter Designation as Predictors of Student Achievement on a Statewide High-Stakes Testing Program

ERIC Educational Resources Information Center

Chamberlin, James L.

2007-01-01

Over the past five years the Colorado Department of Education (CDE) has used the results of the Colorado Student Assessment Program (CSAP) to rate public school performance on the School Accountability Report (SAR). The public often considers the school ratings as indicative of the school's quality. There appears to be a lack of quantitative…

Household Composition Change and Economic Welfare Inequality: 1960 to 1980. CDE Working Paper 88-18.

ERIC Educational Resources Information Center

Wojtkiewicz, Roger A.

This paper considers the following dimensions of the change in household composition of the United States population between 1960 and 1980: (1) a decrease in the number of households headed by a couple; and (2) a decrease in the number of children per household. Examination of census figures from 1960, 1970, and 1980 reveals that blacks and whites…

JPRS Report, Arms Control

DTIC Science & Technology

1989-03-22

to remove the armour which straitjacketed collaboration, under - standing and detente on this continent. JPRS-TAC-89-012 22 March 1989 31 EAST...USSR-Polish-GDR Military Exercise Announced Under CDE Accord [East Berlin ADN 8 Mar] 2 BULGARIA Foreign Minister Mladenov Speaks at CFE/CSBM...Warsaw TV 3 Mar] 23 Two Tank Regiments Dissolved, Ceremonies Held [PAP 4 Mar] 23 General Staff Academy To Undergo Restructuring Under New Defensive

Building Accountability: A Review of State Standards and Requirements for K-12 Public School Facility Planning and Design. Appendices

ERIC Educational Resources Information Center

Vincent, Jeffrey M.

2016-01-01

The purpose of this study was to inform the California Department of Education (CDE) in ensuring the standards contained in Title 5 appropriately promote the planning and design of healthy, safe and educationally suitable K-12 school facilities. The study gathers and analyzes K-12 facility standards in other states across the country to understand…

Lymphotoxin-beta receptor signaling regulates hepatic stellate cell function and wound healing in a murine model of chronic liver injury.

PubMed

Ruddell, Richard G; Knight, Belinda; Tirnitz-Parker, Janina E E; Akhurst, Barbara; Summerville, Lesa; Subramaniam, V Nathan; Olynyk, John K; Ramm, Grant A

2009-01-01

Lymphotoxin-beta (LTbeta) is a proinflammatory cytokine and a member of the tumor necrosis factor (TNF) superfamily known for its role in mediating lymph node development and homeostasis. Our recent studies suggest a role for LTbeta in mediating the pathogenesis of human chronic liver disease. We hypothesize that LTbeta co-ordinates the wound healing response in liver injury via direct effects on hepatic stellate cells. This study used the choline-deficient, ethionine-supplemented (CDE) dietary model of chronic liver injury, which induces inflammation, liver progenitor cell proliferation, and portal fibrosis, to assess (1) the cellular expression of LTbeta, and (2) the role of LTbeta receptor (LTbetaR) in mediating wound healing, in LTbetaR(-/-) versus wild-type mice. In addition, primary isolates of hepatic stellate cells were treated with LTbetaR-ligands LTbeta and LTbeta-related inducible ligand competing for glycoprotein D binding to herpesvirus entry mediator on T cells (LIGHT), and mediators of hepatic stellate cell function and fibrogenesis were assessed. LTbeta was localized to progenitor cells immediately adjacent to activated hepatic stellate cells in the periportal region of the liver in wild-type mice fed the CDE diet. LTbetaR(-/-) mice fed the CDE diet showed significantly reduced fibrosis and a dysregulated immune response. LTbetaR was demonstrated on isolated hepatic stellate cells, which when stimulated by LTbeta and LIGHT, activated the nuclear factor kappa B (NF-kappaB) signaling pathway. Neither LTbeta nor LIGHT had any effect on alpha-smooth muscle actin, tissue inhibitor of metalloproteinase 1, transforming growth factor beta, or procollagen alpha(1)(I) expression; however, leukocyte recruitment-associated factors intercellular adhesion molecule 1 and regulated upon activation T cells expressed and secreted (RANTES) were markedly up-regulated. RANTES caused the chemotaxis of a liver progenitor cell line expressing CCR5. This study suggests that LTbetaR on hepatic stellate cells may be involved in paracrine signaling with nearby LTbeta-expressing liver progenitor cells mediating recruitment of progenitor cells, hepatic stellate cells, and leukocytes required for wound healing and regeneration during chronic liver injury.

78 FR 30226 - Accessibility Requirements for Internet Browsers

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-22

... products and services with peripheral devices or specialized customer premise equipment commonly used by... the telephone or services that such manufacturer or provider offers is accessible to and usable by... requires certain Internet browsers used for advanced communications services to be accessible to people...

Network Security Risks of Online Social Networking in the Workplace

DTIC Science & Technology

2013-11-01

Facebook explains pornographic shock spam, hints at browser vulnera- bility, nakedsecurity. URL – http://nakedsecurity.sophos.com/2011/11/16/ facebook...explains- pornographic -shock-spam-hints-at-browser-vul nerability/. 22 UNCLASSIFIED UNCLASSIFIED DSTO–GD–0772 44. Blatz, J. (2011) CSRF: attack and

Emissions & Generation Resource Integrated Database (eGRID), eGRID2002 (with years 1996 - 2000 data)

EPA Pesticide Factsheets

The Emissions & Generation Resource Integrated Database (eGRID) is a comprehensive source of data on the environmental characteristics of almost all electric power generated in the United States. These environmental characteristics include air emissions for nitrogen oxides, sulfur dioxide, carbon dioxide, methane, nitrous oxide, and mercury; emissions rates; net generation; resource mix; and many other attributes. eGRID2002 (years 1996 through 2000 data) contains 16 Excel spreadsheets and the Technical Support Document, as well as the eGRID Data Browser, User's Manual, and Readme file. Archived eGRID data can be viewed as spreadsheets or by using the eGRID Data Browser. The eGRID spreadsheets can be manipulated by data users and enables users to view all the data underlying eGRID. The eGRID Data Browser enables users to view key data using powerful search features. Note that the eGRID Data Browser will not run on a Mac-based machine without Windows emulation.

WEBSLIDE: A "Virtual" Slide Projector Based on World Wide Web

NASA Astrophysics Data System (ADS)

Barra, Maria; Ferrandino, Salvatore; Scarano, Vittorio

1999-03-01

We present here the design key concepts of WEBSLIDE, a software project whose objective is to provide a simple, cheap and efficient solution for showing slides during lessons in computer labs. In fact, WEBSLIDE allows the video monitors of several client machines (the "STUDENTS") to be synchronously updated by the actions of a particular client machine, called the "INSTRUCTOR." The system is based on the World Wide Web and the software components of WEBSLIDE mainly consists in a WWW server, browsers and small Cgi-Bill scripts. What makes WEBSLIDE particularly appealing for small educational institutions is that WEBSLIDE is built with "off the shelf" products: it does not involve using a specifically designed program but any Netscape browser, one of the most popular browsers available on the market, is sufficient. Another possible use is to use our system to implement "guided automatic tours" through several pages or Intranets internal news bulletins: the company Web server can broadcast to all employees relevant information on their browser.

Nessi: An EEG-Controlled Web Browser for Severely Paralyzed Patients

PubMed Central

Bensch, Michael; Karim, Ahmed A.; Mellinger, Jürgen; Hinterberger, Thilo; Tangermann, Michael; Bogdan, Martin; Rosenstiel, Wolfgang; Birbaumer, Niels

2007-01-01

We have previously demonstrated that an EEG-controlled web browser based on self-regulation of slow cortical potentials (SCPs) enables severely paralyzed patients to browse the internet independently of any voluntary muscle control. However, this system had several shortcomings, among them that patients could only browse within a limited number of web pages and had to select links from an alphabetical list, causing problems if the link names were identical or if they were unknown to the user (as in graphical links). Here we describe a new EEG-controlled web browser, called Nessi, which overcomes these shortcomings. In Nessi, the open source browser, Mozilla, was extended by graphical in-place markers, whereby different brain responses correspond to different frame colors placed around selectable items, enabling the user to select any link on a web page. Besides links, other interactive elements are accessible to the user, such as e-mail and virtual keyboards, opening up a wide range of hypertext-based applications. PMID:18350132

The UCSC Genome Browser: What Every Molecular Biologist Should Know

PubMed Central

Mangan, Mary E.; Williams, Jennifer M.; Kuhn, Robert M.; Lathe, Warren C.

2016-01-01

Electronic data resources can enable molecular biologists to query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one’s understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. PMID:19816931

[Design of the image browser for PACS image workstation].

PubMed

Li, Feng; Zhou, He-Qin

2006-09-01

The design of PACS image workstation based on DICOM3.0 is introduced in the paper, then the designing method of the PACS image browser based on the control system theory is presented,focusing on two main units:DICOM analyzer and the information mapping transformer.

NATIONAL LANDSCAPE METRICS BROWSER (V1.0)

EPA Science Inventory

This metric browser website describes and displays wall-to-wall landscape metrics that have been calculated for the entire conterminous U.S. The intent is to provide the user with an overview of the nature and utility of this landscape metric data set. The land cover and pattern ...

International Portal

EIA Publications

The International Energy Portal includes a powerful data browser that provides country-level energy data; many countries have at least 30 years of historical data. The data browser provides users the ability to view and download complete datasets for consumption, production, trade, reserves, and carbon dioxide emissions for different fuels and energy sources.

Introduction to the fathead minnow genome browser and opportunities for collaborative development

EPA Science Inventory

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minno...

Toward Exposing Timing-Based Probing Attacks in Web Applications †

PubMed Central

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-01-01

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users’ browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach. PMID:28245610

Toward Exposing Timing-Based Probing Attacks in Web Applications.

PubMed

Mao, Jian; Chen, Yue; Shi, Futian; Jia, Yaoqi; Liang, Zhenkai

2017-02-25

Web applications have become the foundation of many types of systems, ranging from cloud services to Internet of Things (IoT) systems. Due to the large amount of sensitive data processed by web applications, user privacy emerges as a major concern in web security. Existing protection mechanisms in modern browsers, e.g., the same origin policy, prevent the users' browsing information on one website from being directly accessed by another website. However, web applications executed in the same browser share the same runtime environment. Such shared states provide side channels for malicious websites to indirectly figure out the information of other origins. Timing is a classic side channel and the root cause of many recent attacks, which rely on the variations in the time taken by the systems to process different inputs. In this paper, we propose an approach to expose the timing-based probing attacks in web applications. It monitors the browser behaviors and identifies anomalous timing behaviors to detect browser probing attacks. We have prototyped our system in the Google Chrome browser and evaluated the effectiveness of our approach by using known probing techniques. We have applied our approach on a large number of top Alexa sites and reported the suspicious behavior patterns with corresponding analysis results. Our theoretical analysis illustrates that the effectiveness of the timing-based probing attacks is dramatically limited by our approach.

JSXGraph--Dynamic Mathematics with JavaScript

ERIC Educational Resources Information Center

Gerhauser, Michael; Valentin, Bianca; Wassermann, Alfred

2010-01-01

Since Java applets seem to be on the retreat in web application, other approaches for displaying interactive mathematics in the web browser are needed. One such alternative could be our open-source project JSXGraph. It is a cross-browser library for displaying interactive geometry, function plotting, graphs, and data visualization in a web…

Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Cancer Genomics Browser | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The Cancer Analysis Virtual Machine (CAVM) project will leverage cloud technology, the UCSC Cancer Genomics Browser, and the Galaxy analysis workflow system to provide investigators with a flexible, scalable platform for hosting, visualizing and analyzing their own genomic data.

Vulnerability Assessment of Open Source Wireshark and Chrome Browser

DTIC Science & Technology

2013-08-01

UNLIMITED 5 We spent much of the initial time learning about the logical model that modern HTML5 web browsers support, including how users interact with...are supposed to protect users of that site against cross-site scripting) and the new powerful an all-encompassing HTML5 standard. This vulnerability

Airborne Hazards and Open Burn Pit Registry

MedlinePlus

... Burn Pit Registry requires a common web browser technology to guide you through the registry questionnaire. You may try a different browser, or you may try from a different computer. You may also see this problem if you are in a high security environment where this is disabled by a network policy. ...

JPRS Report, East Europe

DTIC Science & Technology

1990-07-30

disposable syringes and needles which the Bul- garian government will set up in the country in conjunc- tion with Medical Stores. Speaking in his...Kam Limited—Plovdiv, a medical stores company in Bulgaria and Cde Vladimir Zlatrov, chairman of the Electroimpex that setting up of the project...discussing the problem of direct supplies that would eliminate middlemen.— ZANA . CZECHOSLOVAKIA CPCZ’s Election Program 90CH0095A Prague RUDE PRA

JPRS Report Africa (Sub-Sahara)

DTIC Science & Technology

1987-09-16

farmers, civilians, South African Police and medical services (see diagram). The system represents a breakthrough in communications for the province as...In an interview with Zana after he toured a number of remote areas in the district, Cde Musoko- twane said the Party and its Government was...trucks with 3,400 bags of mealie meal had arrived from National Milling Company. — Zana . /13046 CSO: 3400/154 112 REACTION TO RURAL

Management of Biomedical Waste: An Exploratory Study.

PubMed

Abhishek, K N; Suryavanshi, Harshal N; Sam, George; Chaithanya, K H; Punde, Prashant; Singh, S Swetha

2015-09-01

Dental operatories pose a threat due to the high chances of infection transmission both to the clinician and the patients. Hence, management of dental waste becomes utmost importance not only for the health benefit of the dentist himself, but also people who can come into contact with these wastes directly or indirectly. The present study was conducted to find out the management of biomedical waste in private dental practice among 3 districts of Karnataka. The study population included 186 private practitioners in 3 districts of Karnataka (Coorg, Mysore, Hassan), South India. A pre-tested self-administered questionnaire was distributed to assess the knowledge and practices regarding dental waste management. Descriptive statistics was used to summarize the results. Out of 186 study subjects, 71 (38%) were females and 115 (62%) were males. The maximum number of participants belonged to the age group of 28-33 years (29%). Undergraduate qualification was more (70%). 90 (48%) participants had an experience of 0-5 years. Chi-square analysis showed a highly significant association between participant who attended continuing dental education (CDE) program and their practice of dental waste management. Education with regards to waste management will help in enhancing practices regarding the same. In order to fill this vacuum CDE programs have to be conducted in pursuance to maintain health of the community.

An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division

PubMed Central

Xiong, Liping; Lan, Ganhui

2015-01-01

Sustained molecular oscillations are ubiquitous in biology. The obtained oscillatory patterns provide vital functions as timekeepers, pacemakers and spacemarkers. Models based on control theory have been introduced to explain how specific oscillatory behaviors stem from protein interaction feedbacks, whereas the energy dissipation through the oscillating processes and its role in the regulatory function remain unexplored. Here we developed a general framework to assess an oscillator’s regulation performance at different dissipation levels. Using the Escherichia coli MinCDE oscillator as a model system, we showed that a sufficient amount of energy dissipation is needed to switch on the oscillation, which is tightly coupled to the system’s regulatory performance. Once the dissipation level is beyond this threshold, unlike stationary regulators’ monotonic performance-to-cost relation, excess dissipation at certain steps in the oscillating process damages the oscillator’s regulatory performance. We further discovered that the chemical free energy from ATP hydrolysis has to be strategically assigned to the MinE-aided MinD release and the MinD immobilization steps for optimal performance, and a higher energy budget improves the robustness of the oscillator. These results unfold a novel mode by which living systems trade energy for regulatory function. PMID:26317492

Information-Seeking Behaviors of Dental Practitioners in Three Practice-Based Research Networks

PubMed Central

Botello-Harbaum, Maria T.; Demko, Catherine A.; Curro, Frederick A.; Rindal, D. Brad; Collie, Damon; Gilbert, Gregg H.; Hilton, Thomas J.; Craig, Ronald G.; Wu, Juliann; Funkhouser, Ellen; Lehman, Maryann; McBride, Ruth; Thompson, Van; Lindblad, Anne

2013-01-01

Research on the information-seeking behaviors of dental practitioners is scarce. Knowledge of dentists’ information-seeking behaviors should advance the translational gap between clinical dental research and dental practice. A cross-sectional survey was conducted to examine the self-reported information-seeking behaviors of dentists in three dental practice-based research networks (PBRNs). A total of 950 dentists (65 percent response rate) completed the survey. Dental journals and continuing dental education (CDE) sources used and their influence on practice guidance were assessed. PBRN participation level and years since dental degree were measured. Full-participant dentists reported reading the Journal of the American Dental Association and General Dentistry more frequently than did their reference counterparts. Printed journals were preferred by most dentists. A lower proportion of full participants obtained their CDE credits at dental meetings compared to partial participants. Experienced dentists read other dental information sources more frequently than did less experienced dentists. Practitioners involved in a PBRN differed in their approaches to accessing information sources. Peer-reviewed sources were more frequently used by full participants and dentists with fifteen years of experience or more. Dental PBRNs potentially play a significant role in the dissemination of evidence-based information. This study found that specific educational sources might increase and disseminate knowledge among dentists. PMID:23382524

A benchmark of co-flow and cyclic deposition/etch approaches for the selective epitaxial growth of tensile-strained Si:P

NASA Astrophysics Data System (ADS)

Hartmann, J. M.; Veillerot, M.; Prévitali, B.

2017-10-01

We have compared co-flow and cyclic deposition/etch processes for the selective epitaxial growth of Si:P layers. High growth rates, relatively low resistivities and significant amounts of tensile strain (up to 10 nm min-1, 0.55 mOhm cm and a strain equivalent to 1.06% of substitutional C in Si:C layers) were obtained at 700 °C, 760 Torr with a co-flow approach and a SiH2Cl2 + PH3 + HCl chemistry. This approach was successfully used to thicken the sources and drains regions of n-type fin-shaped Field Effect Transistors. Meanwhile, the (Si2H6 + PH3/HCl + GeH4) CDE process evaluated yielded at 600 °C, 80 Torr even lower resistivities (0.4 mOhm cm, typically), at the cost however of the tensile strain which was lost due to (i) the incorporation of Ge atoms (1.5%, typically) into the lattice during the selective etch steps and (ii) a reduction by a factor of two of the P atomic concentration in CDE layers compared to that in layers grown in a single step (5 × 1020 cm-3 compared to 1021 cm-3).

Natural Attenuation of Nonionic Surfactants Used in Hydraulic Fracturing Fluids: Degradation Rates, Pathways, and Mechanisms.

PubMed

Heyob, Katie M; Blotevogel, Jens; Brooker, Michael; Evans, Morgan V; Lenhart, John J; Wright, Justin; Lamendella, Regina; Borch, Thomas; Mouser, Paula J

2017-12-05

Hydraulic fracturing fluids are injected into shales to extend fracture networks that enhance oil and natural gas production from unconventional reservoirs. Here we evaluated the biodegradability of three widely used nonionic polyglycol ether surfactants (alkyl ethoxylates (AEOs), nonylphenol ethoxylates (NPEOs), and polypropylene glycols (PPGs)) that function as weatherizers, emulsifiers, wetting agents, and corrosion inhibitors in injected fluids. Under anaerobic conditions, we observed complete removal of AEOs and NPEOs from solution within 3 weeks regardless of whether surfactants were part of a chemical mixture or amended as individual additives. Microbial enzymatic chain shortening was responsible for a shift in ethoxymer molecular weight distributions and the accumulation of the metabolite acetate. PPGs bioattenuated the slowest, producing sizable concentrations of acetone, an isomer of propionaldehyde. Surfactant chain shortening was coupled to an increased abundance of the diol dehydratase gene cluster (pduCDE) in Firmicutes metagenomes predicted from the 16S rRNA gene. The pduCDE enzymes are responsible for cleaving ethoxylate chain units into aldehydes before their fermentation into alcohols and carboxylic acids. These data provide new mechanistic insight into the environmental fate of hydraulic fracturing surfactants after accidental release through chain shortening and biotransformation, emphasizing the importance of compound structure disclosure for predicting biodegradation products.

76 FR 10628 - Self-Regulatory Organizations; the Depository Trust Company; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-25

... Change Regarding Providing Participants With a New Optional Settlement Web Interface February 22, 2011... Rule Change The proposed rule change will establish a new browser-based interface, the ``Settlement Web... Browser System (``PBS'').\\4\\ Based on request from its Participants, DTC has created a more user-friendly...

On the Nets. Comparing Web Browsers: Mosaic, Cello, Netscape, WinWeb and InternetWorks Life.

ERIC Educational Resources Information Center

Notess, Greg R.

1995-01-01

World Wide Web browsers are compared by speed, setup, hypertext transport protocol (HTTP) handling, management of file transfer protocol (FTP), telnet, gopher, and wide area information server (WAIS); bookmark options; and communication functions. Netscape has the most features, the fastest retrieval, sophisticated bookmark capabilities. (JMV)

Baby Steps: Starting Out on the World Wide Web.

ERIC Educational Resources Information Center

Simpson, Carol; McElmeel, Sharron L.

1997-01-01

While the Internet is the physical medium used to transport data, the World Wide Web is the collection of protocols and standards used to access the information. This article provides a basic explanation of what the Web is and describes common browser commands. Discusses graphic Web browsers; universal resource locators (URLs); file, message,…

The ranking algorithm of the Coach browser for the UMLS metathesaurus.

PubMed Central

Harbourt, A. M.; Syed, E. J.; Hole, W. T.; Kingsland, L. C.

1993-01-01

This paper presents the novel ranking algorithm of the Coach Metathesaurus browser which is a major module of the Coach expert search refinement program. An example shows how the ranking algorithm can assist in creating a list of candidate terms useful in augmenting a suboptimal Grateful Med search of MEDLINE. PMID:8130570

World-Wide Web: Adding Multimedia to Cyberspace.

ERIC Educational Resources Information Center

Descy, Don E.

1994-01-01

Describes the World-Wide Web (WWW), a network information resource based on hypertext. How to access WWW browsers through remote login (telnet) or though free browser software, such as Mosaic, is provided. Eight information sources that can be accessed through the WWW are listed. The address of a listserv reporting on Internet developments is…

Visits, Hits, Caching and Counting on the World Wide Web: Old Wine in New Bottles?

ERIC Educational Resources Information Center

Berthon, Pierre; Pitt, Leyland; Prendergast, Gerard

1997-01-01

Although web browser caching speeds up retrieval, reduces network traffic, and decreases the load on servers and browser's computers, an unintended consequence for marketing research is that Web servers undercount hits. This article explores counting problems, caching, proxy servers, trawler software and presents a series of correction factors…

Decoding Technology: Web Browsers

ERIC Educational Resources Information Center

Walker, Tim; Donohue, Chip

2007-01-01

More than ever, early childhood administrators are relying on the Internet for information. A key to becoming an exceptional Web "surfer" is getting to know the ins and outs of the Web browser being used. There are several options available, and almost all can be downloaded for free. However, many of the functions and features they offer are very…

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software

PubMed Central

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong

2017-01-01

Abstract Background: Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. Results: We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. Conclusions: As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. PMID:28327936

STAR: an integrated solution to management and visualization of sequencing data.

PubMed

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W; Ecker, Joseph R; Millar, A Harvey; Ren, Bing; Wang, Wei

2013-12-15

Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser.

plas.io: Open Source, Browser-based WebGL Point Cloud Visualization

NASA Astrophysics Data System (ADS)

Butler, H.; Finnegan, D. C.; Gadomski, P. J.; Verma, U. K.

2014-12-01

Point cloud data, in the form of Light Detection and Ranging (LiDAR), RADAR, or semi-global matching (SGM) image processing, are rapidly becoming a foundational data type to quantify and characterize geospatial processes. Visualization of these data, due to overall volume and irregular arrangement, is often difficult. Technological advancement in web browsers, in the form of WebGL and HTML5, have made interactivity and visualization capabilities ubiquitously available which once only existed in desktop software. plas.io is an open source JavaScript application that provides point cloud visualization, exploitation, and compression features in a web-browser platform, reducing the reliance for client-based desktop applications. The wide reach of WebGL and browser-based technologies mean plas.io's capabilities can be delivered to a diverse list of devices -- from phones and tablets to high-end workstations -- with very little custom software development. These properties make plas.io an ideal open platform for researchers and software developers to communicate visualizations of complex and rich point cloud data to devices to which everyone has easy access.

GWIPS-viz: development of a ribo-seq genome browser

PubMed Central

Michel, Audrey M.; Fox, Gearoid; M. Kiran, Anmol; De Bo, Christof; O’Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V.

2014-01-01

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing. PMID:24185699

Multi-Sector Sustainability Browser (MSSB) User Manual: A ...

EPA Pesticide Factsheets

EPA’s Sustainable and Healthy Communities (SHC) Research Program is developing methodologies, resources, and tools to assist community members and local decision makers in implementing policy choices that facilitate sustainable approaches in managing their resources affecting the built environment, natural environment, and human health. In order to assist communities and decision makers in implementing sustainable practices, EPA is developing computer-based systems including models, databases, web tools, and web browsers to help communities decide upon approaches that support their desired outcomes. Communities need access to resources that will allow them to achieve their sustainability objectives through intelligent decisions in four key sustainability areas: • Land Use • Buildings and Infrastructure • Transportation • Materials Management (i.e., Municipal Solid Waste [MSW] processing and disposal) The Multi-Sector Sustainability Browser (MSSB) is designed to support sustainable decision-making for communities, local and regional planners, and policy and decision makers. Document is an EPA Technical Report, which is the user manual for the Multi-Sector Sustainability Browser (MSSB) tool. The purpose of the document is to provide basic guidance on use of the tool for users

Quantifying the web browser ecosystem

PubMed Central

Ferdman, Sela; Minkov, Einat; Gefen, David

2017-01-01

Contrary to the assumption that web browsers are designed to support the user, an examination of a 900,000 distinct PCs shows that web browsers comprise a complex ecosystem with millions of addons collaborating and competing with each other. It is possible for addons to “sneak in” through third party installations or to get “kicked out” by their competitors without user involvement. This study examines that ecosystem quantitatively by constructing a large-scale graph with nodes corresponding to users, addons, and words (terms) that describe addon functionality. Analyzing addon interactions at user level using the Personalized PageRank (PPR) random walk measure shows that the graph demonstrates ecological resilience. Adapting the PPR model to analyzing the browser ecosystem at the level of addon manufacturer, the study shows that some addon companies are in symbiosis and others clash with each other as shown by analyzing the behavior of 18 prominent addon manufacturers. Results may herald insight on how other evolving internet ecosystems may behave, and suggest a methodology for measuring this behavior. Specifically, applying such a methodology could transform the addon market. PMID:28644833

Winning by a neck: tall giraffes avoid competing with shorter browsers.

PubMed

Cameron, Elissa Z; du Toit, Johan T

2007-01-01

With their vertically elongated body form, giraffes generally feed above the level of other browsers within the savanna browsing guild, despite having access to foliage at lower levels. They ingest more leaf mass per bite when foraging high in the tree, perhaps because smaller, more selective browsers deplete shoots at lower levels or because trees differentially allocate resources to promote shoot growth in the upper canopy. We erected exclosures around individual Acacia nigrescens trees in the greater Kruger ecosystem, South Africa. After a complete growing season, we found no differences in leaf biomass per shoot across height zones in excluded trees but significant differences in control trees. We conclude that giraffes preferentially browse at high levels in the canopy to avoid competition with smaller browsers. Our findings are analogous with those from studies of grazing guilds and demonstrate that resource partitioning can be driven by competition when smaller foragers displace larger foragers from shared resources. This provides the first experimental support for the classic evolutionary hypothesis that vertical elongation of the giraffe body is an outcome of competition within the browsing ungulate guild.

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2002-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth s radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth s Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

Using a Web Browser for Environmental and Climate Change Studies

NASA Technical Reports Server (NTRS)

Bess, T. Dale; Stackhouse, Paul; Mangosing, Daniel; Smith, G. Louis

2005-01-01

A new web browser for viewing and manipulating meteorological data sets is located on a web server at NASA, Langley Research Center. The browser uses a live access server (LAS) developed by the Thermal Modeling and Analysis Project at NOAA's Pacific Marine Environmental Laboratory. LAS allows researchers to interact directly with the data to view, select, and subset the data in terms of location (latitude, longitude) and time such as day, month, or year. In addition, LAS can compare two data sets and can perform averages and variances, LAS is used here to show how it functions as an internet/web browser for use by the scientific and educational community. In particular its versatility in displaying and manipulating data sets of atmospheric measurements in the earth's radiation budget (ERB) or energy balance, which includes measurements of absorbed solar radiation, reflected shortwave radiation (RSW), thermal outgoing longwave radiation (OLR), and net radiation is demonstrated. These measurements are from the Clouds and the Earth's Radiant Energy System (CERES) experiment and the surface radiation budget (SRB) experiment.

The UCSC Genome Browser database: extensions and updates 2013.

PubMed

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Raney, Brian J; Pohl, Andy; Malladi, Venkat S; Li, Chin H; Lee, Brian T; Learned, Katrina; Kirkup, Vanessa; Hsu, Fan; Heitner, Steve; Harte, Rachel A; Haeussler, Maximilian; Guruvadoo, Luvina; Goldman, Mary; Giardine, Belinda M; Fujita, Pauline A; Dreszer, Timothy R; Diekhans, Mark; Cline, Melissa S; Clawson, Hiram; Barber, Galt P; Haussler, David; Kent, W James

2013-01-01

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software.

PubMed

Mittal, Varun; Hung, Ling-Hong; Keswani, Jayant; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2017-04-01

Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line-based tool, and many bioinformatics pipelines consist of components that require a graphical user interface. We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud. As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead. © The Authors 2017. Published by Oxford University Press.

Does partner selection mediate the relationship between school attendance and HIV/HSV-2 among adolescent girls and young women in South Africa: An analysis of HPTN 068 data.

PubMed

Stoner, Marie Cd; Edwards, Jessie K; Miller, William C; Aiello, Allison E; Halpern, Carolyn T; Julien, Aimée; Rucinski, Katherine B; Selin, Amanda; Twine, Rhian; Hughes, James P; Wang, Jing; Agyei, Yaw; Gómez-Olivé, F Xavier; Wagner, Ryan G; Laeyendecker, Oliver; Macphail, Catherine; Kahn, Kathleen; Pettifor, Audrey

2018-05-22

Similar prior publications by the first author using the same data source include: Stoner M.C.D, Edwards J, Miller W, Aiello A, Halpern C, Selin A, Hughes J, Wang J, Laeyendecker O, Agyei Y, McPhail C, Kahn K, Pettifor A.(2017) The effect of schooling on incident HIV and HSV-2 infection in young South African women enrolled in HPTN 068. AIDS. 24;31(15):2127-213. PMC5599334. Stoner M.C.D, Edwards J, Miller W, Aiello A, Halpern C, Julien Suarez, Selin A, Hughes J, Wang J, McPhail C, Kahn K, Pettifor A. (2017) The effect of schooling on age-disparate relationships and number of sexual partners among young women in rural South Africa enrolled in HPTN 068. J Acquir Immune Defic Syndr. 76 (5):e107-e114. PMC56801112This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial License 4.0 (CCBY-NC), where it is permissible to download, share, remix, transform, and buildup the work provided it is properly cited. The work cannot be used commercially without permission from the journal.Abstract OBJECTIVE:: School attendance prevents HIV and HSV-2 in adolescent girls and young women (AGYW) but the mechanisms to explain this relationship remain unclear. Our study assesses the extent to which characteristics of sex partners, partner age and number, mediate the relationship between attendance and risk of infection in AGYW in South Africa. We use longitudinal data from the HPTN 068 randomized controlled trial in rural South Africa where girls were enrolled in early adolescence and followed in the main trial for over three years. We examined older partners and number of partners as possible mediators. We use the parametric g-formula to estimate 4-year risk differences for the effect of school attendance on cumulative incidence of HIV/HSV-2 overall and the controlled direct effect (CDE) for mediation. We examined mediation separately and jointly for the mediators of interest. We found that young women with high attendance in school had a lower cumulative incidence of HIV compared to those with low attendance (risk difference=-1.6%). Partner age difference (CDE=-1.2%) and number of partners (CDE=-0.4%) mediated a large portion of this effect. In fact, when we accounted for the mediators jointly, the effect of schooling on HIV was almost removed showing full mediation (CDE= -0.3%). The same patterns were observed for the relationship between school attendance and cumulative incidence of HSV-2 infection. Increasing school attendance reduces risk of acquiring HIV and HSV-2. Our results indicate the importance of school attendance in reducing partner number and partner age difference in this relationship.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial License 4.0 (CCBY-NC), where it is permissible to download, share, remix, transform, and buildup the work provided it is properly cited. The work cannot be used commercially without permission from the journal.

A browser-based event display for the CMS Experiment at the LHC using WebGL

NASA Astrophysics Data System (ADS)

McCauley, T.

2017-10-01

Modern web browsers are powerful and sophisticated applications that support an ever-wider range of uses. One such use is rendering high-quality, GPU-accelerated, interactive 2D and 3D graphics in an HTML canvas. This can be done via WebGL, a JavaScript API based on OpenGL ES. Applications delivered via the browser have several distinct benefits for the developer and user. For example, they can be implemented using well-known and well-developed technologies, while distribution and use via a browser allows for rapid prototyping and deployment and ease of installation. In addition, delivery of applications via the browser allows for easy use on mobile, touch-enabled devices such as phones and tablets. iSpy WebGL is an application for visualization of events detected and reconstructed by the CMS Experiment at the Large Hadron Collider at CERN. The first event display developed for an LHC experiment to use WebGL, iSpy WebGL is a client-side application written in JavaScript, HTML, and CSS and uses the WebGL API three.js. iSpy WebGL is used for monitoring of CMS detector performance, for production of images and animations of CMS collisions events for the public, as a virtual reality application using Google Cardboard, and asa tool available for public education and outreach such as in the CERN Open Data Portal and the CMS masterclasses. We describe here its design, development, and usage as well as future plans.

SU-E-J-114: Web-Browser Medical Physics Applications Using HTML5 and Javascript.

PubMed

Bakhtiari, M

2012-06-01

Since 2010, there has been a great attention about HTML5. Application developers and browser makers fully embrace and support the web of the future. Consumers have started to embrace HTML5, especially as more users understand the benefits and potential that HTML5 can mean for the future.Modern browsers such as Firefox, Google Chrome, and Safari are offering better and more robust support for HTML5, CSS3, and JavaScript. The idea is to introduce the HTML5 to medical physics community for open source software developments. The benefit of using HTML5 is developing portable software systems. The HTML5, CSS, and JavaScript programming languages were used to develop several applications for Quality Assurance in radiation therapy. The canvas element of HTML5 was used for handling and displaying the images, and JavaScript was used to manipulate the data. Sample application were developed to: 1. analyze the flatness and symmetry of the radiotherapy fields in a web browser, 2.analyze the Dynalog files from Varian machines, 3. visualize the animated Dynamic MLC files, 4. Simulation via Monte Carlo, and 5. interactive image manipulation. The programs showed great performance and speed in uploading the data and displaying the results. The flatness and symmetry program and Dynalog file analyzer ran in a fraction of second. The reason behind this performance is using JavaScript language which is a lower level programming language in comparison to the most of the scientific programming packages such as Matlab. The second reason is that JavaScript runs locally on client side computers not on the web-servers. HTML5 and JavaScript can be used to develop useful applications that can be run online or offline on different modern web-browsers. The programming platform can be also one of the modern web-browsers which are mostly open source (such as Firefox). © 2012 American Association of Physicists in Medicine.

Sub-Saharan Africa Report.

DTIC Science & Technology

1987-01-29

Economic Upturn ^ (SAPA, 15 Dec 86) . • • • * *’ Heavy Rains Raise Hope of Record 1987 Maize Crop (Mick Collins; BUSINESS DAY, 17 Dec 86) New...been successful to the extent that the resi- dents had more than six months’ supply of vegetables to addition to growing green maize and wheat. Cde...displaced per- sons suggested that one immediate need, was that of vegetables. - The displaced persona were then train» ed In irrigation canal

USAF Aircraft Maintenance Officer Knowledge, Skills and Abilities and Commonalities among the Logistics Officer Corps

DTIC Science & Technology

2013-02-01

distribution managemen t operations to include managing cargo distribution functions such as receiving, inspecting, tracing, tracking, packaging, and...Production Management DE CDE ABCDEFG Scheduling DE ADEF ABCDEF T ie r 2 Flightline Operations E BDE Systems Engineering D ABDEG Table 19: 21R...logistics units/ elements and as members of general or executive s t affs in t he operating forces, supporting establishment, and joint staffs . They

Mount St. Helens Long-Term Sediment Management Plan for Flood Risk Reduction

DTIC Science & Technology

2010-06-01

one dredge would direct pump to the Wasser Winters disposal site, located along the southern bank of the Cowlitz River mouth. The average annual...dredge would pipeline pump either upstream to disposal site 20cde or downstream to the Wasser Winters site. Pumping distances would not exceed 6.0...estimates referenced the Wasser Winters upland preparation estimates and were based on the relationship between acreage and effort. Total site

Substructural Logical Specifications

DTIC Science & Technology

2012-11-14

and independently in the context of CLF by Schack-Nielsen [SN07] and by Cruz and Hou [CH12]; Schack-Nielsen proves the equivalence of the two specifi...cations, whereas Cruz and Hou used the connection informally. The contribution of this section is to describe a general transformation (of which...Functional Programming (LFP’86), pages 13–27. ACM, 1986. 5.1 [CDE+11] Manuel Clavel, Francisco Durán, Steven Eker, Patrick Lincoln, Narciso Martı́- 290 Oliet

Web 2.0 and You

ERIC Educational Resources Information Center

Baumbach, Donna J.

2009-01-01

The World Wide Web has come a long way in a very short time. A little more than a decade ago, with the invention of Mosaic, the first browser to display images inline with text instead of displaying images in a separate window, and Netscape, the first graphical user interface (browser), people began to experience a rapid expansion of information.…

BROWSER: An Automatic Indexing On-Line Text Retrieval System. Annual Progress Report.

ERIC Educational Resources Information Center

Williams, J. H., Jr.

The development and testing of the Browsing On-line With Selective Retrieval (BROWSER) text retrieval system allowing a natural language query statement and providing on-line browsing capabilities through an IBM 2260 display terminal is described. The prototype system contains data bases of 25,000 German language patent abstracts, 9,000 English…

Visual Links in the World-Wide Web: The Uses and Limitations of Image Maps.

ERIC Educational Resources Information Center

Cochenour, John J.; And Others

As information delivery systems on the Internet increasingly evolve into World Wide Web browsers, understanding key graphical elements of the browser interface is critical to the design of effective information display and access tools. Image maps are one such element, and this document describes a pilot study that collected, reviewed, and…

USDA Plant Hardiness Zone Map

Science.gov Websites

those with slower Internet access. Users may also simply type in a ZIP Code and find the hardiness zone : Find Javascript is not enabled in this Internet Browser For a better experience throughout this web site, please enable Javascript in your Internet Browser What is a Captcha and why am I seeing one (on

Formats and Network Protocols for Browser Access to 2D Raster Data

NASA Astrophysics Data System (ADS)

Plesea, L.

2015-12-01

Tiled web maps in browsers are a major success story, forming the foundation of many current web applications. Enabling tiled data access is the next logical step, and is likely to meet with similar success. Many ad-hoc approaches have already started to appear, and something similar is explored within the Open Geospatial Consortium. One of the main obstacles in making browser data access a reality is the lack of a well-known data format. This obstacle also represents an opportunity to analyze the requirements and possible candidates, applying lessons learned from web tiled image services and protocols. Similar to the image counterpart, a web tile raster data format needs to have good intrinsic compression and be able to handle high byte count data types including floating point. An overview of a possible solution to the format problem, a 2D data raster compression algorithm called Limited Error Raster Compression (LERC) will be presented. In addition to the format, best practices for high request rate HTTP services also need to be followed. In particular, content delivery network (CDN) caching suitability needs to be part of any design, not an after-thought. Last but not least, HTML 5 browsers will certainly be part of any solution since they provide improved access to binary data, as well as more powerful ways to view and interact with the data in the browser. In a simple but relevant application, digital elevation model (DEM) raster data is served as LERC compressed data tiles which are used to generate terrain by a HTML5 scene viewer.

[RadLex - German version: a radiological lexicon for indexing image and report information].

PubMed

Marwede, D; Daumke, P; Marko, K; Lobsien, D; Schulz, S; Kahn, T

2009-01-01

Since 2003 the Radiological Society of North America (RSNA) has been developing a lexicon of standardized radiological terms (RadLex) intended to support the structured reporting of imaging observations and the indexing of teaching cases. The aim of this study was to translate the first version of the lexicon (1 - 2007) into German and to implement a language-independent online term browser. RadLex version 1 - 2007 contains 6303 terms in nine main categories. Two radiologists independently translated the lexicon using medical dictionaries. Terms translated differently were revised and translated by consensus. For the development of an online term browser, a text processing algorithm called morphosemantic indexing was used which splits up words into small semantic units and compares those units to language-specific subword thesauri. In total 6240 of 6303 terms (99 %) were translated. Of those terms 3965 were German, 1893 were Latin, 359 were multilingual, and 23 were English terms that are also used in German and were therefore maintained. The online term browser supports a language-independent term search in RadLex (German/English) and other common medical terminology (e. g., ICD 10). The term browser displays term hierarchies and translations in different frames and the complexity of the result lists can be adapted by the user. RadLex version 1 - 2007 developed by the RSNA is now available in German and can be accessed online through a term browser with an efficient search function. This is an important precondition for the future comparison of national and international indexed radiological examination results and the interoperability between digital teaching resources.

Addressing an I/O Bottleneck in a Web-Based CERES QC Tool

NASA Astrophysics Data System (ADS)

Heckert, E.; Sun-Mack, S.; Chen, Y.; Chu, C.; Smith, R. A.

2016-12-01

In this poster, we explore the technologies we have used to overcome the problem of transmitting and analyzing large datasets in our web-based CERES Quality Control tool and consider four technologies to potentially adopt for future performance improvements. The CERES team uses this tool to validate pixel-level data from Terra, Aqua, SNPP, MSG, MTSAT, and many geostationary GOES satellites, as well as to develop cloud retrieval algorithms. The tool includes a histogram feature that allows the user to aggregate data from many different timestamps and different scenes globally or locally selected by the user by drawing bounding boxes. In order to provide a better user experience, the tool passes a large amount of data to the user's browser. The browser then processes the data in order to present it to users in various formats, for example as a histogram. In addition to using multiple servers to subset data and pass a smaller set of data to the browser, the tool also makes use of a compression technology, Gzip, to reduce the size of the data. However, sometimes the application in the browser is still slow when dealing with these large sets of data due to the delay in the browser receiving the server's response. To address this I/O bottleneck, we will investigate four alternatives and present the results in this poster: 1) sending uncompressed data, 2) ESRI's Limited Error Raster Compression (LERC), 3) Gzip, and 4) WebSocket protocol. These approaches are compared to each other and to the uncompressed control to determine the optimal solution.

Effect of IOP based infusion system with and without balanced phaco tip on cumulative dissipated energy and estimated fluid usage in comparison to gravity fed infusion in torsional phacoemulsification.

PubMed

Malik, Praveen K; Dewan, Taru; Patidar, Arun Kr; Sain, Ekta

2017-01-01

To evaluate the effect of three different combinations of tip designs and infusion systems in torsional phacoemulsification (INFINITI and CENTURION) in patients with cataract. According to the manufacturer, two unique improvements in the Centurion are: active fluid dynamic management system and use of an intrepid balanced tip. The study specifically aimed to evaluate the beneficial effects, if any, of change in tip design and infusion system individually and in combination on both per-operative parameters as well as endothelial health over 6 months. One hundred and twenty six consenting patients of grade 4.0-6.9 senile cataract were randomized into three groups for phacoemulsification: Group A ( n  = 42): Gravity fed infusion system and 45 0 Kelman miniflared ABS phaco tip; Group B ( n  = 42): intraocular pressure (IOP) based infusion system and 45 0 Kelman miniflared ABS phaco tip; Group C ( n  = 42): IOP based infusion system and 45 0 Intrepid balanced phaco tip. The cumulative dissipated energy (CDE), estimated fluid usage (EFU) and total aspiration time (TAT) were compared peroperatively. The endothelial parameters were followed up postoperatively for six months. The three arms were matched for age ( p  = 0.525), gender ( p  = 0.96) and grade of cataract ( p  = 0.177). Group C was associated with significant reductions in CDE ( p  = 0.001), EFU ( p  < 0.0005) as well as TAT ( p  = 0.001) in comparison to the other groups. All three groups had comparable baseline endothelial cell density ( p  = 0.876) and central corneal thickness ( p  = 0.561). On post-operative evaluation, although all groups were comparable till 3 months, by 6 months, the percentage losses in endothelial cell density were significantly lower in group C as compared to the other groups. Use of an IOP based phacoemulsification system in association with use of the Intrepid balanced tip reduces the CDE, EFU and TAT in comparison to a gravity fed system with a mini flared tip or IOP based system with a mini flared tip while also providing better endothelial preservation thus favouring the use of an IOP fed system with a balanced tip. Trial registration No.: CTRI/2016/06/007022.

The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation

PubMed Central

Engels, Christina; Ruscheweyh, Hans-Joachim; Beerenwinkel, Niko; Lacroix, Christophe; Schwab, Clarissa

2016-01-01

Eubacterium hallii is considered an important microbe in regard to intestinal metabolic balance due to its ability to utilize glucose and the fermentation intermediates acetate and lactate, to form butyrate and hydrogen. Recently, we observed that E. hallii is capable of metabolizing glycerol to 3-hydroxypropionaldehyde (3-HPA, reuterin) with reported antimicrobial properties. The key enzyme for glycerol to 3-HPA conversion is the cobalamin-dependent glycerol/diol dehydratase PduCDE which also utilizes 1,2-propanediol (1,2-PD) to form propionate. Therefore our primary goal was to investigate glycerol to 3-HPA metabolism and 1,2-PD utilization by E. hallii along with its ability to produce cobalamin. We also investigated the relative abundance of E. hallii in stool of adults using 16S rRNA and pduCDE based gene screening to determine the contribution of E. hallii to intestinal propionate formation. We found that E. hallii utilizes glycerol to produce up to 9 mM 3-HPA but did not further metabolize 3-HPA to 1,3-propanediol. Utilization of 1,2-PD in the presence and absence of glucose led to the formation of propanal, propanol and propionate. E. hallii formed cobalamin and was detected in stool of 74% of adults using 16S rRNA gene as marker gene (n = 325). Relative abundance of the E. hallii 16S rRNA gene ranged from 0 to 0.59% with a mean relative abundance of 0.044%. E. hallii PduCDE was detected in 63 to 81% of the metagenomes depending on which subunit was investigated beside other taxons such as Ruminococcus obeum, R. gnavus, Flavonifractor plautii, Intestinimonas butyriciproducens, and Veillonella spp. In conclusion, we identified E. hallii as a common gut microbe with the ability to convert glycerol to 3-HPA, a step that requires the production of cobalamin, and to utilize 1,2-PD to form propionate. Our results along with its ability to use a broad range of substrates point at E. hallii as a key species within the intestinal trophic chain with the potential to highly impact the metabolic balance as well as the gut microbiota/host homeostasis by the formation of different short chain fatty acids. PMID:27242734

The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation.

PubMed

Engels, Christina; Ruscheweyh, Hans-Joachim; Beerenwinkel, Niko; Lacroix, Christophe; Schwab, Clarissa

2016-01-01

Eubacterium hallii is considered an important microbe in regard to intestinal metabolic balance due to its ability to utilize glucose and the fermentation intermediates acetate and lactate, to form butyrate and hydrogen. Recently, we observed that E. hallii is capable of metabolizing glycerol to 3-hydroxypropionaldehyde (3-HPA, reuterin) with reported antimicrobial properties. The key enzyme for glycerol to 3-HPA conversion is the cobalamin-dependent glycerol/diol dehydratase PduCDE which also utilizes 1,2-propanediol (1,2-PD) to form propionate. Therefore our primary goal was to investigate glycerol to 3-HPA metabolism and 1,2-PD utilization by E. hallii along with its ability to produce cobalamin. We also investigated the relative abundance of E. hallii in stool of adults using 16S rRNA and pduCDE based gene screening to determine the contribution of E. hallii to intestinal propionate formation. We found that E. hallii utilizes glycerol to produce up to 9 mM 3-HPA but did not further metabolize 3-HPA to 1,3-propanediol. Utilization of 1,2-PD in the presence and absence of glucose led to the formation of propanal, propanol and propionate. E. hallii formed cobalamin and was detected in stool of 74% of adults using 16S rRNA gene as marker gene (n = 325). Relative abundance of the E. hallii 16S rRNA gene ranged from 0 to 0.59% with a mean relative abundance of 0.044%. E. hallii PduCDE was detected in 63 to 81% of the metagenomes depending on which subunit was investigated beside other taxons such as Ruminococcus obeum, R. gnavus, Flavonifractor plautii, Intestinimonas butyriciproducens, and Veillonella spp. In conclusion, we identified E. hallii as a common gut microbe with the ability to convert glycerol to 3-HPA, a step that requires the production of cobalamin, and to utilize 1,2-PD to form propionate. Our results along with its ability to use a broad range of substrates point at E. hallii as a key species within the intestinal trophic chain with the potential to highly impact the metabolic balance as well as the gut microbiota/host homeostasis by the formation of different short chain fatty acids.

New Perspectives on Popular Culture, Science and Technology: Web Browsers and the New Illiteracy

ERIC Educational Resources Information Center

Charters, Elizabeth

2004-01-01

Analysts predict that the knowledge economy of the near future will require people to be both computer literate and print literate. However, some of the reading and thinking habits of current college students suggest that electronic media such as web browsers may be limiting the new generation's ability to absorb and process what they read. Their…

A Freely-Available Authoring System for Browser-Based CALL with Speech Recognition

ERIC Educational Resources Information Center

O'Brien, Myles

2017-01-01

A system for authoring browser-based CALL material incorporating Google speech recognition has been developed and made freely available for download. The system provides a teacher with a simple way to set up CALL material, including an optional image, sound or video, which will elicit spoken (and/or typed) answers from the user and check them…

Browser-Based Online Applications: Something for Everyone!

ERIC Educational Resources Information Center

Descy, Don E.

2007-01-01

Just as many people log onto a Web mail site (Gmail, Yahoo, MSN, etc.) to read, write and store their email, there are Web sites out there with word processing, database, and a myriad of other software applications that are not downloadable but used on the site through a Web browser. The user does not have to download the applications to a…

Enabling Efficient Intelligence Analysis in Degraded Environments

DTIC Science & Technology

2013-06-01

Magnets Grid widget for multidimensional information exploration ; and a record browser of Visual Summary Cards widget for fast visual identification of...evolution analysis; a Magnets Grid widget for multi- dimensional information exploration ; and a record browser of Visual Summary Cards widget for fast...attention and inattentional blindness. It also explores and develops various techniques to represent information in a salient way and provide efficient

STAR: an integrated solution to management and visualization of sequencing data

PubMed Central

Wang, Tao; Liu, Jie; Shen, Li; Tonti-Filippini, Julian; Zhu, Yun; Jia, Haiyang; Lister, Ryan; Whitaker, John W.; Ecker, Joseph R.; Millar, A. Harvey; Ren, Bing; Wang, Wei

2013-01-01

Motivation: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data. We developed STAR, an integrated web application that enables online management, visualization and track-based analysis of NGS data. Results: STAR is a multilayer web service system. On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools that range from providing simple track configuration controls to sophisticated feature detection within datasets. On the server side, STAR supports private session state retention via an account management system and provides data management modules that enable collection, visualization and analysis of third-party sequencing data from the public domain with over thousands of tracks hosted to date. Overall, STAR represents a next-generation data exploration solution to match the requirements of NGS data, enabling both intuitive visualization and dynamic analysis of data. Availability and implementation: STAR browser system is freely available on the web at http://wanglab.ucsd.edu/star/browser and https://github.com/angell1117/STAR-genome-browser. Contact: wei-wang@ucsd.edu PMID:24078702

Brain-controlled applications using dynamic P300 speller matrices.

PubMed

Halder, Sebastian; Pinegger, Andreas; Käthner, Ivo; Wriessnegger, Selina C; Faller, Josef; Pires Antunes, João B; Müller-Putz, Gernot R; Kübler, Andrea

2015-01-01

Access to the world wide web and multimedia content is an important aspect of life. We present a web browser and a multimedia user interface adapted for control with a brain-computer interface (BCI) which can be used by severely motor impaired persons. The web browser dynamically determines the most efficient P300 BCI matrix size to select the links on the current website. This enables control of the web browser with fewer commands and smaller matrices. The multimedia player was based on an existing software. Both applications were evaluated with a sample of ten healthy participants and three end-users. All participants used a visual P300 BCI with face-stimuli for control. The healthy participants completed the multimedia player task with 90% accuracy and the web browsing task with 85% accuracy. The end-users completed the tasks with 62% and 58% accuracy. All healthy participants and two out of three end-users reported that they felt to be in control of the system. In this study we presented a multimedia application and an efficient web browser implemented for control with a BCI. Both applications provide access to important areas of modern information retrieval and entertainment. Copyright © 2014 Elsevier B.V. All rights reserved.

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

NASA Astrophysics Data System (ADS)

Buszko, Marian L.; Buszko, Dominik; Wang, Daniel C.

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance.

The Causal Mediation Formula - A Guide to the Assessment of Pathways and Mechanisms

DTIC Science & Technology

2011-10-01

for estimating CDE(z) in observational studies (in the presence of unobserved confounders) can be derived using do- calculus (Pearl, 2009, pp. 85–88...2011; Albert and Nelson , 2011). 7In the presence of measured and unmeasured confounders, the general conditions under which NDE is estimable from...achieve this independence (see footnote 7), that Z may represent a vector of variables, and that integrals should replace summations when dealing with

Comparison of torsional and longitudinal modes using phacoemulsification parameters.

PubMed

Rekas, Marek; Montés-Micó, Robert; Krix-Jachym, Karolina; Kluś, Adam; Stankiewicz, Andrzej; Ferrer-Blasco, Teresa

2009-10-01

To compare phacoemulsification parameters of torsional and longitudinal ultrasound modes. Ophthalmology Department, Military Health Service Institute, Warsaw, Poland. This prospective study evaluated eyes 1, 7, and 30 days after phacoemulsification with an Infiniti Vision System using the torsional or longitudinal ultrasound (US) mode. Cataract classification was according to the Lens Opacities Classification System II. Nucleus fragmentation was by the phaco-chop and quick-chop methods. Primary outcome measures were phaco time, mean phaco power, mean torsional amplitude, and aspiration time. Total energy, defined as cumulative dissipated energy (CDE) x aspiration time, and the effective coefficient, defined as aspiration time/phaco time, were also calculated. Four hundred eyes were evaluated. The CDE was statistically significantly lower in the torsional mode for nucleus grades I, II, and III (P<.001) but not for grade IV (P>.05). Aspiration time was statistically significantly shorter in the torsional mode than in the longitudinal mode for nucleus grades III and IV (P<.05). Total energy was significantly lower in the torsional mode for all nucleus densities (P<.05). The effective coefficient was significantly lower in the longitudinal mode except for nucleus grade I (P<.05). Torsional phacoemulsification was more effective than longitudinal phacoemulsification in the amount of applied fluid and the quantity of US energy expended. With the torsional method, it was possible to maintain a constant ratio of amount of fluid flow to quantity of US energy used, regardless of nucleus density.

Use of Online Sources of Information by Dental Practitioners: Findings from The Dental Practice-Based Research Network

PubMed Central

Funkhouser, Ellen; Agee, Bonita S.; Gordan, Valeria V.; Rindal, D. Brad; Fellows, Jeffrey L.; Qvist, Vibeke; McClelland, Jocelyn; Gilbert, Gregg H.

2013-01-01

Objectives Estimate the proportion of dental practitioners who use online sources of information for practice guidance. Methods From a survey of 657 dental practitioners in The Dental Practice Based Research Network, four indicators of online use for practice guidance were calculated: read journals online, obtained continuing education (CDE) through online sources, rated an online source as most influential, and reported frequently using an online source for guidance. Demographics, journals read, and use of various sources of information for practice guidance in terms of frequency and influence were ascertained for each. Results Overall, 21% (n=138) were classified into one of the four indicators of online use: 14% (n=89) rated an online source as most influential and 13% (n=87) reported frequently using an online source for guidance; few practitioners (5%, n=34) read journals online, fewer (3%, n=17) obtained CDE through online sources. Use of online information sources varied considerably by region and practice characteristics. In general, the 4 indicators represented practitioners with as many differences as similarities to each other and to offline users. Conclusion A relatively small proportion of dental practitioners use information from online sources for practice guidance. Variation exists regarding practitioners’ use of online source resources and how they rate the value of offline information sources for practice guidance. PMID:22994848

Transcriptional Regulator LsrB of Sinorhizobium meliloti Positively Regulates the Expression of Genes Involved in Lipopolysaccharide Biosynthesis

PubMed Central

Tang, Guirong; Wang, Ying

2014-01-01

Rhizobia induce nitrogen-fixing nodules on host legumes, which is important in agriculture and ecology. Lipopolysaccharide (LPS) produced by rhizobia is required for infection or bacteroid survival in host cells. Genes required for LPS biosynthesis have been identified in several Rhizobium species. However, the regulation of their expression is not well understood. Here, Sinorhizobium meliloti LsrB, a member of the LysR family of transcriptional regulators, was found to be involved in LPS biosynthesis by positively regulating the expression of the lrp3-lpsCDE operon. An lsrB in-frame deletion mutant displayed growth deficiency, sensitivity to the detergent sodium dodecyl sulfate, and acidic pH compared to the parent strain. This mutant produced slightly less LPS due to lower expression of the lrp3 operon. Analysis of the transcriptional start sites of the lrp3 and lpsCDE gene suggested that they constitute one operon. The expression of lsrB was positively autoregulated. The promoter region of lrp3 was specifically precipitated by anti-LsrB antibodies in vivo. The promoter DNA fragment containing TN11A motifs was bound by the purified LsrB protein in vitro. These new findings suggest that S. meliloti LsrB is associated with LPS biosynthesis, which is required for symbiotic nitrogen fixation on some ecotypes of alfalfa plants. PMID:24951786

Development of a browser application to foster research on linking climate and health datasets: Challenges and opportunities.

PubMed

Hajat, Shakoor; Whitmore, Ceri; Sarran, Christophe; Haines, Andy; Golding, Brian; Gordon-Brown, Harriet; Kessel, Anthony; Fleming, Lora E

2017-01-01

Improved data linkages between diverse environment and health datasets have the potential to provide new insights into the health impacts of environmental exposures, including complex climate change processes. Initiatives that link and explore big data in the environment and health arenas are now being established. To encourage advances in this nascent field, this article documents the development of a web browser application to facilitate such future research, the challenges encountered to date, and how they were addressed. A 'storyboard approach' was used to aid the initial design and development of the application. The application followed a 3-tier architecture: a spatial database server for storing and querying data, server-side code for processing and running models, and client-side browser code for user interaction and for displaying data and results. The browser was validated by reproducing previously published results from a regression analysis of time-series datasets of daily mortality, air pollution and temperature in London. Data visualisation and analysis options of the application are presented. The main factors that shaped the development of the browser were: accessibility, open-source software, flexibility, efficiency, user-friendliness, licensing restrictions and data confidentiality, visualisation limitations, cost-effectiveness, and sustainability. Creating dedicated data and analysis resources, such as the one described here, will become an increasingly vital step in improving understanding of the complex interconnections between the environment and human health and wellbeing, whilst still ensuring appropriate confidentiality safeguards. The issues raised in this paper can inform the future development of similar tools by other researchers working in this field. Copyright © 2016 Elsevier B.V. All rights reserved.

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

PubMed Central

Almeida, Jonas S.; Iriabho, Egiebade E.; Gorrepati, Vijaya L.; Wilkinson, Sean R.; Grüneberg, Alexander; Robbins, David E.; Hackney, James R.

2012-01-01

Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results: Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. Conclusions: The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local “download and installation”. PMID:22934238

The UCSC genome browser and associated tools

PubMed Central

Haussler, David; Kent, W. James

2013-01-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting. PMID:22908213

The UCSC genome browser and associated tools.

PubMed

Kuhn, Robert M; Haussler, David; Kent, W James

2013-03-01

The UCSC Genome Browser (http://genome.ucsc.edu) is a graphical viewer for genomic data now in its 13th year. Since the early days of the Human Genome Project, it has presented an integrated view of genomic data of many kinds. Now home to assemblies for 58 organisms, the Browser presents visualization of annotations mapped to genomic coordinates. The ability to juxtapose annotations of many types facilitates inquiry-driven data mining. Gene predictions, mRNA alignments, epigenomic data from the ENCODE project, conservation scores from vertebrate whole-genome alignments and variation data may be viewed at any scale from a single base to an entire chromosome. The Browser also includes many other widely used tools, including BLAT, which is useful for alignments from high-throughput sequencing experiments. Private data uploaded as Custom Tracks and Data Hubs in many formats may be displayed alongside the rich compendium of precomputed data in the UCSC database. The Table Browser is a full-featured graphical interface, which allows querying, filtering and intersection of data tables. The Saved Session feature allows users to store and share customized views, enhancing the utility of the system for organizing multiple trains of thought. Binary Alignment/Map (BAM), Variant Call Format and the Personal Genome Single Nucleotide Polymorphisms (SNPs) data formats are useful for visualizing a large sequencing experiment (whole-genome or whole-exome), where the differences between the data set and the reference assembly may be displayed graphically. Support for high-throughput sequencing extends to compact, indexed data formats, such as BAM, bigBed and bigWig, allowing rapid visualization of large datasets from RNA-seq and ChIP-seq experiments via local hosting.

An optimized web-based approach for collaborative stereoscopic medical visualization

PubMed Central

Kaspar, Mathias; Parsad, Nigel M; Silverstein, Jonathan C

2013-01-01

Objective Medical visualization tools have traditionally been constrained to tethered imaging workstations or proprietary client viewers, typically part of hospital radiology systems. To improve accessibility to real-time, remote, interactive, stereoscopic visualization and to enable collaboration among multiple viewing locations, we developed an open source approach requiring only a standard web browser with no added client-side software. Materials and Methods Our collaborative, web-based, stereoscopic, visualization system, CoWebViz, has been used successfully for the past 2 years at the University of Chicago to teach immersive virtual anatomy classes. It is a server application that streams server-side visualization applications to client front-ends, comprised solely of a standard web browser with no added software. Results We describe optimization considerations, usability, and performance results, which make CoWebViz practical for broad clinical use. We clarify technical advances including: enhanced threaded architecture, optimized visualization distribution algorithms, a wide range of supported stereoscopic presentation technologies, and the salient theoretical and empirical network parameters that affect our web-based visualization approach. Discussion The implementations demonstrate usability and performance benefits of a simple web-based approach for complex clinical visualization scenarios. Using this approach overcomes technical challenges that require third-party web browser plug-ins, resulting in the most lightweight client. Conclusions Compared to special software and hardware deployments, unmodified web browsers enhance remote user accessibility to interactive medical visualization. Whereas local hardware and software deployments may provide better interactivity than remote applications, our implementation demonstrates that a simplified, stable, client approach using standard web browsers is sufficient for high quality three-dimensional, stereoscopic, collaborative and interactive visualization. PMID:23048008

Integration and visualization of systems biology data in context of the genome

PubMed Central

2010-01-01

Background High-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment. Results The Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data. A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome. Conclusions Genomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment. PMID:20642854

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

PubMed

Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

2012-01-01

Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design.

PubMed

Yuan, Shuguang; Chan, H C Stephen; Hu, Zhenquan

2017-06-01

Web browsers have long been recognized as potential platforms for remote macromolecule visualization. However, the difficulty in transferring large-scale data to clients and the lack of native support for hardware-accelerated applications in the local browser undermine the feasibility of such utilities. With the introduction of WebGL and HTML5 technologies in recent years, it is now possible to exploit the power of a graphics-processing unit (GPU) from a browser without any third-party plugin. Many new tools have been developed for biological molecule visualization and modern drug discovery. In contrast to traditional offline tools, real-time computing, interactive data analysis, and cross-platform analyses feature WebGL- and HTML5-based tools, facilitating biological research in a more efficient and user-friendly way. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Genomic HyperBrowser: an analysis web server for genome-scale data

PubMed Central

Sandve, Geir K.; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K.; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalaš, Matúš; Lien, Tonje; Rye, Morten B.; Frigessi, Arnoldo; Hovig, Eivind

2013-01-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome. PMID:23632163

Internet Technology in Magnetic Resonance: A Common Gateway Interface Program for the World-Wide Web NMR Spectrometer

PubMed

Buszko; Buszko; Wang

1998-04-01

A custom-written Common Gateway Interface (CGI) program for remote control of an NMR spectrometer using a World Wide Web browser has been described. The program, running on a UNIX workstation, uses multiple processes to handle concurrent tasks of interacting with the user and with the spectrometer. The program's parent process communicates with the browser and sends out commands to the spectrometer; the child process is mainly responsible for data acquisition. Communication between the processes is via the shared memory mechanism. The WWW pages that have been developed for the system make use of the frames feature of web browsers. The CGI program provides an intuitive user interface to the NMR spectrometer, making, in effect, a complex system an easy-to-use Web appliance. Copyright 1998 Academic Press.

The Genomic HyperBrowser: an analysis web server for genome-scale data.

PubMed

Sandve, Geir K; Gundersen, Sveinung; Johansen, Morten; Glad, Ingrid K; Gunathasan, Krishanthi; Holden, Lars; Holden, Marit; Liestøl, Knut; Nygård, Ståle; Nygaard, Vegard; Paulsen, Jonas; Rydbeck, Halfdan; Trengereid, Kai; Clancy, Trevor; Drabløs, Finn; Ferkingstad, Egil; Kalas, Matús; Lien, Tonje; Rye, Morten B; Frigessi, Arnoldo; Hovig, Eivind

2013-07-01

The immense increase in availability of genomic scale datasets, such as those provided by the ENCODE and Roadmap Epigenomics projects, presents unprecedented opportunities for individual researchers to pose novel falsifiable biological questions. With this opportunity, however, researchers are faced with the challenge of how to best analyze and interpret their genome-scale datasets. A powerful way of representing genome-scale data is as feature-specific coordinates relative to reference genome assemblies, i.e. as genomic tracks. The Genomic HyperBrowser (http://hyperbrowser.uio.no) is an open-ended web server for the analysis of genomic track data. Through the provision of several highly customizable components for processing and statistical analysis of genomic tracks, the HyperBrowser opens for a range of genomic investigations, related to, e.g., gene regulation, disease association or epigenetic modifications of the genome.

Contingency Table Browser - prediction of early stage protein structure.

PubMed

Kalinowska, Barbara; Krzykalski, Artur; Roterman, Irena

2015-01-01

The Early Stage (ES) intermediate represents the starting structure in protein folding simulations based on the Fuzzy Oil Drop (FOD) model. The accuracy of FOD predictions is greatly dependent on the accuracy of the chosen intermediate. A suitable intermediate can be constructed using the sequence-structure relationship information contained in the so-called contingency table - this table expresses the likelihood of encountering various structural motifs for each tetrapeptide fragment in the amino acid sequence. The limited accuracy with which such structures could previously be predicted provided the motivation for a more indepth study of the contingency table itself. The Contingency Table Browser is a tool which can visualize, search and analyze the table. Our work presents possible applications of Contingency Table Browser, among them - analysis of specific protein sequences from the point of view of their structural ambiguity.

An Excellent Pilot Model for the Korean Air Force.

DTIC Science & Technology

1988-12-01

Address i cirv, state, and ZIP c^-de 10 Source of Funding Numbers Proeram Element No Protect No Task No Work Inn Accession N i Title...undergraduate pilots in the Korean Air Force. ui ^t Accession Fcr • - • - ORAJcI i; U": it : • in .’ H J . m _ . ; . • fr A...Squares (OLS) method. Table 22. RESULTS OF THE REGRESSION MODEL Variables Coefficient Prob>|t| Beta Coefficient Intercept 516. SS7 (56.2S6) APT

A Novel Mechanism of High-Level, Broad-Spectrum Antibiotic Resistance Caused by a Single Base Pair Change in Neisseria gonorrhoeae

DTIC Science & Technology

2011-09-20

significantly alter the regulation of the mtrCDE operon and result in increased resistance to anti- microbials. IMPORTANCE Gonorrhea is the second most...causative agent of the sexually trans-mitted infection gonorrhea , is a Gram-negative diplococcus and is strictly a human pathogen. Clinical isolates of N...produced in response to experimental human gonorrhea . J. Infect. Dis. 172:186 –191. 34. Schmidt KA, et al. 2001. Experimental gonococcal urethritis and

Bubble Memory Module.

DTIC Science & Technology

1980-12-01

I AD-A093 642 ROCKWELL INTERNATIONAL ANAHEIM CA AUOEISSTAE-T F/S V/2 I BU13LE MEMORY MODULE. (U) DEC 80 0 0 BOHNING. F J BECKER NASI -14174...Cde under Contract NASI -14174 Dist’m/o National Aeronautics and Space Administration Scientific and Technical Information BranchA 1980 J Approvod ior...9/ BUBBLE M MORY MODULE.(U) DEC 80 0 BHNING, F J BECKER NASI -14174 NCLASSIFIED CB-569/201 NASA-CR-3380 ML22-fllfllf ll l ff mmlmmmmm.l®fmmM EEmmEI

Challenges in the Development and Evolution of Secure Open Architecture Command and Control Systems (Briefing Charts)

DTIC Science & Technology

2013-06-01

widgets for an OA system Design-time architecture: Browser, email, widget, DB, OS Go ogle Instance architecture: Chrome, Gmail, Google...provides functionally similar components or applications compatible with an OA system design Firefox Browser, WP, calendar Opera Instance...architecture: Firefox , AbiWord, Evolution, Fedora GPL Ab1Word Google Docs Instance ardlitecture: Fire fox, OR Google cal., Google Docs, Fedora

Local-Rapid Evaluation of Atmospheric Conditions (L-REAC)

DTIC Science & Technology

2009-01-15

installation available 24/7 to all forms of browser-based access such as mobile blackberry browser. In 2006, the ARL presented data at an International...Oceanic and Atmospheric Administration (NOAA)/Environmental Protection Agency (EPA) Wind Tunnel study with tens-of-meter-scaled measurements sampled around...urban flow in wind tunnels , as well as articles from professional urban meteorological journals. The need to maintain a visual sensor for persons who

Defense AT and L. Volume 44, Number 3

DTIC Science & Technology

2015-06-01

CommunityBrowser.aspx?id=527436 Product Support Key References https://acc.dau.mil/productsupport CLL 011 Performance-Based Life Cycle Product Support (PBL...http://icatalog.dau.mil/onlinecatalog/courses.aspx?crs_id=269 CLL 031 PBL Contracting Strategies http://icatalog.dau.mil/onlinecatalog/courses.aspx...CommunityBrowser.aspx?id=527436 Product Support Key References https://acc.dau.mil/productsupport CLL 011 Performance-Based Life Cycle Product Support (PBL) http

CPTAC Proteomics Data on UCSC Genome Browser | Office of Cancer Clinical Proteomics Research

Cancer.gov

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium scientists are working together with the University of California, Santa Cruz (UCSC) Genomics Institute to provide public access to cancer proteomics data via the UCSC Genome Browser. This effort extends accessibility of the CPTAC data to more researchers and provides an additional level of analysis to assist the cancer biology community.

Aladin Lite: Lightweight sky atlas for browsers

NASA Astrophysics Data System (ADS)

Boch, Thomas

2014-02-01

Aladin Lite is a lightweight version of the Aladin tool, running in the browser and geared towards simple visualization of a sky region. It allows visualization of image surveys (JPEG multi-resolution HEALPix all-sky surveys) and permits superimposing tabular (VOTable) and footprints (STC-S) data. Aladin Lite is powered by HTML5 canvas technology and is easily embeddable on any web page and can also be controlled through a Javacript API.

Optimization of knowledge sharing through multi-forum using cloud computing architecture

NASA Astrophysics Data System (ADS)

Madapusi Vasudevan, Sriram; Sankaran, Srivatsan; Muthuswamy, Shanmugasundaram; Ram, N. Sankar

2011-12-01

Knowledge sharing is done through various knowledge sharing forums which requires multiple logins through multiple browser instances. Here a single Multi-Forum knowledge sharing concept is introduced which requires only one login session which makes user to connect multiple forums and display the data in a single browser window. Also few optimization techniques are introduced here to speed up the access time using cloud computing architecture.

A Connection Model between the Positioning Mechanism and Ultrasonic Measurement System via a Web Browser to Assess Acoustic Target Strength

NASA Astrophysics Data System (ADS)

Ishii, Ken; Imaizumi, Tomohito; Abe, Koki; Takao, Yoshimi; Tamura, Shuko

This paper details a network-controlled measurement system for use in fisheries engineering. The target strength (TS) of fish is important in order to convert acoustic integration values obtained during acoustic surveys into estimates of fish abundance. The target strength pattern is measured with the combination of the rotation system for the aspect of the sample and the echo data acquisition system using the underwater supersonic wave. The user interface of the network architecture is designed for collaborative use with researchers in other organizations. The flexible network architecture is based on the web direct-access model for the rotation mechanism. The user interface is available for monitoring and controlling via a web browser that is installed in any terminal PC (personal computer). Previously the combination of two applications was performed not by a web browser but by the exclusive interface program. So a connection model is proposed between two applications by indirect communication via the DCOM (Distributed Component Object Model) server and added in the web direct-access model. A prompt report system in the TS measurement system and a positioning and measurement system using an electric flatcar via a web browser are developed. By a secure network architecture, DCOM communications via both Intranet and LAN are successfully certificated.

New Interfaces to Web Documents and Services

NASA Technical Reports Server (NTRS)

Carlisle, W. H.

1996-01-01

This paper reports on investigations into how to extend capabilities of the Virtual Research Center (VRC) for NASA's Advanced Concepts Office. The work was performed as part of NASA's 1996 Summer Faculty Fellowship program, and involved research into and prototype development of software components that provide documents and services for the World Wide Web (WWW). The WWW has become a de-facto standard for sharing resources over the internet, primarily because web browsers are freely available for the most common hardware platforms and their operating systems. As a consequence of the popularity of the internet, tools, and techniques associated with web browsers are changing rapidly. New capabilities are offered by companies that support web browsers in order to achieve or remain a dominant participant in internet services. Because a goal of the VRC is to build an environment for NASA centers, universities, and industrial partners to share information associated with Advanced Concepts Office activities, the VRC tracks new techniques and services associated with the web in order to determine the their usefulness for distributed and collaborative engineering research activities. Most recently, Java has emerged as a new tool for providing internet services. Because the major web browser providers have decided to include Java in their software, investigations into Java were conducted this summer.

SMC Message Browser Projects

NASA Technical Reports Server (NTRS)

Wichmann, Benjamin C.

2013-01-01

I work directly with the System Monitoring and Control (SMC) software engineers who develop, test and release custom and commercial software in support of the Kennedy Space Center Spaceport Command and Control System. (SCCS). SMC uses Commercial Off-The-Shelf (COTS) Enterprise Management Systems (EMS) software which provides a centralized subsystem for configuring, monitoring, and controlling SCCS hardware and software used in the Control Rooms. There are multiple projects being worked on using the COTS EMS software. I am currently working with the HP Operations Manager for UNIX (OMU) software which allows Master Console Operators (MCO) to access, view and interpret messages regarding the status of the SCCS hardware and software. The OMU message browser gets cluttered with messages which can make it difficult for the MCO to manage. My main project involves determining ways to reduce the number of messages being displayed in the OMU message browser. I plan to accomplish this task in two different ways: (1) by correlating multiple messages into one single message being displayed and (2) to create policies that will determine the significance of each message and whether or not it needs to be displayed to the MCO. The core idea is to lessen the number of messages being sent to the OMU message browser so the MCO can more effectively use it.

Web-based visualization of gridded dataset usings OceanBrowser

NASA Astrophysics Data System (ADS)

Barth, Alexander; Watelet, Sylvain; Troupin, Charles; Beckers, Jean-Marie

2015-04-01

OceanBrowser is a web-based visualization tool for gridded oceanographic data sets. Those data sets are typically four-dimensional (longitude, latitude, depth and time). OceanBrowser allows one to visualize horizontal sections at a given depth and time to examine the horizontal distribution of a given variable. It also offers the possibility to display the results on an arbitrary vertical section. To study the evolution of the variable in time, the horizontal and vertical sections can also be animated. Vertical section can be generated by using a fixed distance from coast or fixed ocean depth. The user can customize the plot by changing the color-map, the range of the color-bar, the type of the plot (linearly interpolated color, simple contours, filled contours) and download the current view as a simple image or as Keyhole Markup Language (KML) file for visualization in applications such as Google Earth. The data products can also be accessed as NetCDF files and through OPeNDAP. Third-party layers from a web map service can also be integrated. OceanBrowser is used in the frame of the SeaDataNet project (http://gher-diva.phys.ulg.ac.be/web-vis/) and EMODNET Chemistry (http://oceanbrowser.net/emodnet/) to distribute gridded data sets interpolated from in situ observation using DIVA (Data-Interpolating Variational Analysis).

Network Analysis of Reconnaissance and Intrusion of an Industrial Control System

DTIC Science & Technology

2016-09-01

simulated a plant engineer using the engineering workstation web browser to authenticate to the vegetable cooker HMI. While the engineer established the...observed the vegetable cooker HMI web display, the attacker stopped capturing network traffic. Acting as the attacker, we searched the attacker’s pcap...manually controlled by human activity. In this testbed network, only web browser traffic (HTTP) is created by an operator to view an HMI status

Coal Data Browser

EIA Publications

The Coal Data Browser gives users easy access to coal information from EIA's electricity and coal surveys as well as data from the Mine Safety and Health Administration and trade information from the U.S. Census Bureau. Users can also see the shipment data from individual mines that deliver coal to the U.S. electric power fleet, have the ability to track supplies delivered to a given power plant, and to see which mines serve each particular plant.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Semantic Body Browser: graphical exploration of an organism and spatially resolved expression data visualization.

PubMed

Lekschas, Fritz; Stachelscheid, Harald; Seltmann, Stefanie; Kurtz, Andreas

2015-03-01

Advancing technologies generate large amounts of molecular and phenotypic data on cells, tissues and organisms, leading to an ever-growing detail and complexity while information retrieval and analysis becomes increasingly time-consuming. The Semantic Body Browser is a web application for intuitively exploring the body of an organism from the organ to the subcellular level and visualising expression profiles by means of semantically annotated anatomical illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users. The Semantic Body Browser is a JavaScript web application that is freely available at http://sbb.cellfinder.org. The source code is provided on https://github.com/flekschas/sbb. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Self-study program on HTML browser--application to Clinical Nursing General Remarks Course.

PubMed

Ochiai, N; Sota, Y; Ezumi, H

1997-01-01

We created a self-study program using HTML browser on the Clinical Nursing General Remarks Course, Eighty-three students each selected a published book on a personal history (written personal reflections from individuals who had undergone medical treatment and hospitalization), read it and submitted reports of their impressions of the histories. Their reports were arranged from a nursing perspective and entered on the home page of our college using HTML browser. We intended that the students would become more interested in reading of the personal histories, and that they would acquire new self-study skills and increase their interest in Internet through use of our program. In addition, we hoped that this program would encourage positive communication and mutual sharing of information. The students were able to easily refer to a personal history according to their interest from a nursing perspective. Therefore this program realized the mutual learning among students and other users.

Use of mobile devices to answer online surveys: implications for research.

PubMed

Cunningham, John A; Neighbors, Clayton; Bertholet, Nicolas; Hendershot, Christian S

2013-07-08

There is a growing use of mobile devices to access the Internet. We examined whether participants who used a mobile device to access a brief online survey were quicker to respond to the survey but also, less likely to complete it than participants using a traditional web browser. Using data from a recently completed online intervention trial, we found that participants using mobile devices were quicker to access the survey but less likely to complete it compared to participants using a traditional web browser. More concerning, mobile device users were also less likely to respond to a request to complete a six week follow-up survey compared to those using traditional web browsers. With roughly a third of participants using mobile devices to answer an online survey in this study, the impact of mobile device usage on survey completion rates is a concern. ClinicalTrials.gov: NCT01521078.

Interactive Web Graphs with Fewer Restrictions

NASA Technical Reports Server (NTRS)

Fiedler, James

2012-01-01

There is growing popularity for interactive, statistical web graphs and programs to generate them. However, it seems that these programs tend to be somewhat restricted in which web browsers and statistical software are supported. For example, the software might use SVG (e.g., Protovis, gridSVG) or HTML canvas, both of which exclude most versions of Internet Explorer, or the software might be made specifically for R (gridSVG, CRanvas), thus excluding users of other stats software. There are more general tools (d3, Rapha lJS) which are compatible with most browsers, but using one of these to make statistical graphs requires more coding than is probably desired, and requires learning a new tool. This talk will present a method for making interactive web graphs, which, by design, attempts to support as many browsers and as many statistical programs as possible, while also aiming to be relatively easy to use and relatively easy to extend.

[A solution for display and processing of DICOM images in web PACS].

PubMed

Xue, Wei-jing; Lu, Wen; Wang, Hai-yang; Meng, Jian

2009-03-01

Use the technique of Java Applet to realize the supporting of DICOM image in ordinary Web browser, thereby to expand the processing function of medical image. First analyze the format of DICOM file and design a class which can acquire the pixels, then design two Applet classes, of which one is used to disposal the DICOM image, the other is used to display DICOM image that have been disposaled in the first Applet. They all embedded in the View page, and they communicate by Applet Context object. The method designed in this paper can make users display and process DICOM images directly by using ordinary Web browser, which makes Web PACS not only have the advantages of B/S model, but also have the advantages of the C/S model. Java Applet is the key for expanding the Web browser's function in Web PACS, which provides a guideline to sharing of medical images.

JavaScript Access to DICOM Network and Objects in Web Browser.

PubMed

Drnasin, Ivan; Grgić, Mislav; Gogić, Goran

2017-10-01

Digital imaging and communications in medicine (DICOM) 3.0 standard provides the baseline for the picture archiving and communication systems (PACS). The development of Internet and various communication media initiated demand for non-DICOM access to PACS systems. Ever-increasing utilization of the web browsers, laptops and handheld devices, as opposed to desktop applications and static organizational computers, lead to development of different web technologies. The DICOM standard officials accepted those subsequently as tools of alternative access. This paper provides an overview of the current state of development of the web access technology to the DICOM repositories. It presents a different approach of using HTML5 features of the web browsers through the JavaScript language and the WebSocket protocol by enabling real-time communication with DICOM repositories. JavaScript DICOM network library, DICOM to WebSocket proxy and a proof-of-concept web application that qualifies as a DICOM 3.0 device were developed.

jsPsych: a JavaScript library for creating behavioral experiments in a Web browser.

PubMed

de Leeuw, Joshua R

2015-03-01

Online experiments are growing in popularity, and the increasing sophistication of Web technology has made it possible to run complex behavioral experiments online using only a Web browser. Unlike with offline laboratory experiments, however, few tools exist to aid in the development of browser-based experiments. This makes the process of creating an experiment slow and challenging, particularly for researchers who lack a Web development background. This article introduces jsPsych, a JavaScript library for the development of Web-based experiments. jsPsych formalizes a way of describing experiments that is much simpler than writing the entire experiment from scratch. jsPsych then executes these descriptions automatically, handling the flow from one task to another. The jsPsych library is open-source and designed to be expanded by the research community. The project is available online at www.jspsych.org .

A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains.

PubMed

Sinaci, A Anil; Laleci Erturkmen, Gokce B

2013-10-01

In order to enable secondary use of Electronic Health Records (EHRs) by bridging the interoperability gap between clinical care and research domains, in this paper, a unified methodology and the supporting framework is introduced which brings together the power of metadata registries (MDR) and semantic web technologies. We introduce a federated semantic metadata registry framework by extending the ISO/IEC 11179 standard, and enable integration of data element registries through Linked Open Data (LOD) principles where each Common Data Element (CDE) can be uniquely referenced, queried and processed to enable the syntactic and semantic interoperability. Each CDE and their components are maintained as LOD resources enabling semantic links with other CDEs, terminology systems and with implementation dependent content models; hence facilitating semantic search, much effective reuse and semantic interoperability across different application domains. There are several important efforts addressing the semantic interoperability in healthcare domain such as IHE DEX profile proposal, CDISC SHARE and CDISC2RDF. Our architecture complements these by providing a framework to interlink existing data element registries and repositories for multiplying their potential for semantic interoperability to a greater extent. Open source implementation of the federated semantic MDR framework presented in this paper is the core of the semantic interoperability layer of the SALUS project which enables the execution of the post marketing safety analysis studies on top of existing EHR systems. Copyright © 2013 Elsevier Inc. All rights reserved.

Results of endocapsular phacofracture debulking of hard cataracts.

PubMed

Davison, James A

2015-01-01

To present a phacoemulsification technique for hard cataracts and compare postoperative results using two different ultrasonic tip motions during quadrant removal. A phacoemulsification technique which employs in situ fracture and endocapsular debulking for hard cataracts is presented. The prospective study included 56 consecutive cases of hard cataract (LOCS III NC [Lens Opacification Classification System III, nuclear color], average 4.26), which were operated using the Infiniti machine and the Partial Kelman tip. Longitudinal tip movement was used for sculpting for all cases which were randomized to receive longitudinal or torsional/interjected longitudinal (Intelligent Phaco [IP]) strategies for quadrant removal. Measurements included cumulative dissipated energy (CDE), 3 months postoperative surgically induced astigmatism (SIA), and corneal endothelial cell density (ECD) losses. No complications were recorded in any of the cases. Respective overall and longitudinal vs IP means were as follows: CDE, 51.6±15.6 and 55.7±15.5 vs 48.6±15.1; SIA, 0.36±0.2 D and 0.4±0.2 D vs 0.3±0.2 D; and mean ECD loss, 4.1%±10.8% and 5.9%±13.4% vs 2.7%±7.8%. The differences between longitudinal and IP were not significant for any of the three categories. The endocapsular phacofracture debulking technique is safe and effective for phacoemulsification of hard cataracts using longitudinal or torsional IP strategies for quadrant removal with the Infiniti machine and Partial Kelman tip.

Effects of Pisha sandstone content on solute transport in a sandy soil.

PubMed

Zhen, Qing; Zheng, Jiyong; He, Honghua; Han, Fengpeng; Zhang, Xingchang

2016-02-01

In sandy soil, water, nutrients and even pollutants are easily leaching to deeper layers. The objective of this study was to assess the effects of Pisha sandstone on soil solute transport in a sandy soil. The miscible displacement technique was used to obtain breakthrough curves (BTCs) of Br(-) as an inert non-adsorbed tracer and Na(+) as an adsorbed tracer. The incorporation of Pisha sandstone into sandy soil was able to prevent the early breakthrough of both tracers by decreasing the saturated hydraulic conductivity compared to the controlled sandy soil column, and the impeding effects increased with Pisha sandstone content. The BTCs of Br(-) were accurately described by both the convection-dispersion equation (CDE) and the two-region model (T-R), and the T-R model fitted the experimental data slightly better than the CDE. The two-site nonequilibrium model (T-S) accurately fit the Na(+) transport data. Pisha sandstone impeded the breakthrough of Na(+) not only by decreasing the saturated hydraulic conductivity but also by increasing the adsorption capacity of the soil. The measured CEC values of Pisha sandstone were up to 11 times larger than those of the sandy soil. The retardation factors (R) determined by the T-S model increased with increasing Pisha sandstone content, and the partition coefficient (K(d)) showed a similar trend to R. According to the results of this study, Pisha sandstone can successfully impede solute transport in a sandy soil column. Copyright © 2015 Elsevier Ltd. All rights reserved.

[Design and validation of a questionnaire for psychosocial nursing diagnosis in Primary Care].

PubMed

Brito-Brito, Pedro Ruymán; Rodríguez-Álvarez, Cristobalina; Sierra-López, Antonio; Rodríguez-Gómez, José Ángel; Aguirre-Jaime, Armando

2012-01-01

To develop a valid, reliable and easy-to-use questionnaire for a psychosocial nursing diagnosis. The study was performed in two phases: first phase, questionnaire design and construction; second phase, validity and reliability tests. A bank of items was constructed using the NANDA classification as a theoretical framework. Each item was assigned a Likert scale or dichotomous response. The combination of responses to the items constituted the diagnostic rules to assign up to 28 labels. A group of experts carried out the validity test for content. Other validated scales were used as reference standards for the criterion validity tests. Forty-five nurses provided the questionnaire to the patients on three separate occasions over a period of three weeks, and the other validated scales only once to 188 randomly selected patients in Primary Care centres in Tenerife (Spain). Validity tests for construct confirmed the six dimensions of the questionnaire with 91% of total variance explained. Validity tests for criterion showed a specificity of 66%-100%, and showed high correlations with the reference scales when the questionnaire was assigning nursing diagnoses. Reliability tests showed agreement of 56%-91% (P<.001), and a 93% internal consistency. The Questionnaire for Psychosocial Nursing Diagnosis was called CdePS, and included 61 items. The CdePS is a valid, reliable and easy-to-use tool in Primary Care centres to improve the assigning of a psychosocial nursing diagnosis. Copyright © 2011 Elsevier España, S.L. All rights reserved.

An Image Understanding Environment for DARPA Supported Research and Applications, Second Annual Report

DTIC Science & Technology

1992-05-01

relatively independent of the 29 30 Basic Objects Support Objects GUI Access Objects Displays Display Mapping Menues Pixel Snapshot Gizmos /Widgets...a user interactively or set from some gizmo /widget, or that a particular browser field is to be updated when some state occurs or a process completes...also want to distinguish tree graph browsers.] 4.3.2 Simplified access to GUI objects "* Gizmos and Widgets: The IUE should provide simplified

The rendering context for stereoscopic 3D web

NASA Astrophysics Data System (ADS)

Chen, Qinshui; Wang, Wenmin; Wang, Ronggang

2014-03-01

3D technologies on the Web has been studied for many years, but they are basically monoscopic 3D. With the stereoscopic technology gradually maturing, we are researching to integrate the binocular 3D technology into the Web, creating a stereoscopic 3D browser that will provide users with a brand new experience of human-computer interaction. In this paper, we propose a novel approach to apply stereoscopy technologies to the CSS3 3D Transforms. Under our model, each element can create or participate in a stereoscopic 3D rendering context, in which 3D Transforms such as scaling, translation and rotation, can be applied and be perceived in a truly 3D space. We first discuss the underlying principles of stereoscopy. After that we discuss how these principles can be applied to the Web. A stereoscopic 3D browser with backward compatibility is also created for demonstration purposes. We take advantage of the open-source WebKit project, integrating the 3D display ability into the rendering engine of the web browser. For each 3D web page, our 3D browser will create two slightly different images, each representing the left-eye view and right-eye view, both to be combined on the 3D display to generate the illusion of depth. And as the result turns out, elements can be manipulated in a truly 3D space.

jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web.

PubMed

Smits, Samuel A; Ouverney, Cleber C

2010-08-18

Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees. We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is designed to work across all major browsers and renders an alternative format for those browsers that do not support SVG. The library provides tools for building rectangular and circular phylograms with integrated charting. Interactive features may be integrated and made to respond to events such as clicks on any element of the tree, including labels. jsPhyloSVG is an open-source solution for rendering dynamic phylogenetic trees. It is capable of generating complex and interactive phylogenetic trees across all major browsers without the need for plugins. It is novel in supporting the ability to interpret the tree inference formats directly, exposing the underlying markup to data-mining services. The library source code, extensive documentation and live examples are freely accessible at www.jsphylosvg.com.

A web implementation: the good and the not-so-good.

PubMed

Bergsneider, C; Piraino, D; Fuerst, M

2001-06-01

E-commerce, e-mail, e-greeting, e-this, and e-that everywhere you turn there is a new "e" word for an internet or Web application. We, at the Cleveland Clinic Foundation, have been "e-nlightened" and will discuss in this report the implementation of a web-based radiology information system (RIS) in our radiology division or "e-radiology" division. The application, IDXRad Version 10.0 from IDX Corp, Burlington, VT, is in use at the Cleveland Clinic Foundation and has both intranet (for use in Radiology) and internet (referring physician viewing) modules. We will concentrate on the features of using a web browser for the application's front-end, including easy prototyping for screen review, easier mock-ups of demonstrations by vendors and developers, and easier training as more people become web-addicted. Project communication can be facilitated with an internal project web page, and use of the web browser can accommodate quicker turnaround of software upgrades as the software code is centrally located. Compared with other technologies, including client/server, there is a smaller roll out cost when using a standard web browser. However, the new technology requires a change and changes are never implemented without challenges. A seasoned technologist using a legacy system can enter data quicker using function keys than using a graphical user interface and pointing and clicking through a series of pop-up windows. Also, effective use of a web browser depends on intuitive design for it to be easily implemented and accepted by the user. Some software packages will not work on both of the popular web browsers and then are tailored to specific release levels. As computer-based patient records become a standard, patient confidentiality must be enforced. The technical design and application security features that support the web-based software package will be discussed. Also web technologies have their own implementation issues.

Pervasive interactions between ungulate browsers and disturbance regimes promote temperate forest herbaceous diversity.

PubMed

Royo, Alejandro A; Collins, Rachel; Adams, Mary Beth; Kirschbaum, Chad; Carson, Walter P

2010-01-01

Disruptions to historic disturbance and herbivory regimes have altered plant assemblages in forests worldwide. An emerging consensus suggests that these disruptions often result in impoverished forest biotas. This is particularly true for eastern U.S. deciduous forests where large gaps and understory fires were once relatively common and browsers were far less abundant. Although much research has focused on how disturbance and browsers affect tree diversity, far less attention has been devoted to forest understories where the vast majority (>75%) of the vascular species reside. Here we test the hypothesis that the reintroduction of disturbances resembling historic disturbance regimes and moderate levels of ungulate browsing enhance plant diversity. We explore whether once-common disturbances and their interaction with the top-down influence of browsers can create conditions favorable for the maintenance of a rich herbaceous layer in a region recognized as a temperate biodiversity hotspot in West Virginia, U.S.A. We tested this hypothesis via a factorial experiment whereby we manipulated canopy gaps (presence/absence) of a size typically found in old-growth stands, low-intensity understory fire (burned/unburned), and deer browsing (fenced/unfenced). We tracked the abundance and diversity of more than 140 herb species for six years. Interactions among our treatments were pervasive. The combination of canopy gaps and understory fire increased herbaceous layer richness, cover, and diversity well beyond either disturbance alone. Furthermore, we documented evidence that deer at moderate levels of abundance promote herbaceous richness and abundance by preferentially browsing fast-growing pioneer species that thrive following co-occurring disturbances (i.e., fire and gaps). This finding sharply contrasts with the negative impact browsers have when their populations reach levels well beyond those that occurred for centuries. Although speculative, our results suggest that interactions among fire, canopy gaps, and browsing provided a variable set of habitats and conditions across the landscape that was potentially capable of maintaining much of the plant diversity found in temperate forests.

A Voice Enabled Procedure Browser for the International Space Station

NASA Technical Reports Server (NTRS)

Rayner, Manny; Chatzichrisafis, Nikos; Hockey, Beth Ann; Farrell, Kim; Renders, Jean-Michel

2005-01-01

Clarissa, an experimental voice enabled procedure browser that has recently been deployed on the International Space Station (ISS), is to the best of our knowledge the first spoken dialog system in space. This paper gives background on the system and the ISS procedures, then discusses the research developed to address three key problems: grammar-based speech recognition using the Regulus toolkit; SVM based methods for open microphone speech recognition; and robust side-effect free dialogue management for handling undos, corrections and confirmations.

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

1999-02-01

We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

Surfing for Data: A Gathering Trend in Data Storage Is the Use of Web-Based Applications that Make It Easy for Authorized Users to Access Hosted Server Content with Just a Computing Device and Browser

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

In recent years, the widespread availability of networks and the flexibility of Web browsers have shifted the industry from a client-server model to a Web-based one. In the client-server model of computing, clients run applications locally, with the servers managing storage, printing functions, and network traffic. Because every client is…

Few-body model approach to the bound states of helium-like exotic three-body systems

NASA Astrophysics Data System (ADS)

Khan, Md A.

2016-10-01

In this paper, calculated energies of the lowest bound S-state of Coulomb three-body systems containing an electron (e —), a negatively charged muon (μ—) and a nucleus (NZ+) of charge number Z are reported. The 3-body relative wave function in the resulting Schrödinger equation is expanded in the complete set of hyperspherical harmonics (HH). Use of the orthonormality of HH leads to an infinite set of coupled differential equations (CDE) which are solved numerically to get the energy E.

Semiconductor/Insulator Films for Corrosion Protection.

DTIC Science & Technology

1985-10-01

8217%, V -ED C~ SAVE AS RPP El Z)TC IjSERS I Unclassified V :.%- ES~YSB-D DA.22b TELEPH-ONE (Include 4rea Cde 2c JFFCE S’iMBOL V.Agarwaa DD FORM 1473, 4 VAP ...starting solution is aspirated through the injector nozzle using a high pressure nitrogen gas stream. The resultant mist is sprayed into the reactor where...approxi- mately 390-430 0C. The starting solution is aspirated with nitrogen and sprayed directly on the aluminum substrate. The height and angle of the

Chemical Stockpile Disposal Program. Risk Analysis of the Disposal of Chemical Munitions at Regional or National Sites.

DTIC Science & Technology

1987-08-01

THE DISPOSAL OF CNEM.. CU) GA TECHNOLOGIES INC SRN DIEGO CA A H SARSELL ET AL. RUG 97 GA-C- i @563 UNLRSS FIED S APEO-CDE-IS- 9 ?SIGDRAA±5-85-D-822...F/ 15/.3 NL I ihhhhhhhhhhhhlm I fflfflffllfllfllfllf smhhhhhhhhhhh ~1.02 U.,5 A I *Pig- FiLE copy CHEMICAL STOCKPILE DISPOSAL PROGRAM RISK ANALYSIS...vr~. ’ . - a ’ a’ ’- . ,I1 - .V [ N- VW; W UU V. , U .U : , r ,,, - . ..... . SECURITY CLASSIFICATION OF THIS PAGE IM : I omApproved

The Effects of an Acute Bout of Strenuous Aerobic Exercise on Plasma, Erythrocyte, Urinary and Dietary Values for Selected Trace Minerals

DTIC Science & Technology

1996-12-09

some serum copper parameters in trained professional soccer players and control subjects. J. Sports Med. Phys. Fitness. 31:4123-416, 1991. 110. Ruz, M...WOMAN’S UNIVERSITY DEPARTMENT OF NUTRITION AND FOOD SCIENCES COLLEGE OF HEALTH SCIENCES BY KIMBERLY K. EDGREN, RD, BS, CDE DENTON, TEXAS DECEMBER 1996...of the requirements for the degree of Master of Science, with a major in Nutrition . Bett,/B. Alfor ,Ph.D., Major Professor We have read this thesis and

Worldwide Research, Worldwide Participation: Web-Based Test Logger

NASA Technical Reports Server (NTRS)

Clark, David A.

1998-01-01

Thanks to the World Wide Web, a new paradigm has been born. ESCORT (steady state data system) facilities can now be configured to use a Web-based test logger, enabling worldwide participation in tests. NASA Lewis Research Center's new Web-based test logger for ESCORT automatically writes selected test and facility parameters to a browser and allows researchers to insert comments. All data can be viewed in real time via Internet connections, so anyone with a Web browser and the correct URL (universal resource locator, or Web address) can interactively participate. As the test proceeds and ESCORT data are taken, Web browsers connected to the logger are updated automatically. The use of this logger has demonstrated several benefits. First, researchers are free from manual data entry and are able to focus more on the tests. Second, research logs can be printed in report format immediately after (or during) a test. And finally, all test information is readily available to an international public.

Automatically assisting human memory: a SenseCam browser.

PubMed

Doherty, Aiden R; Moulin, Chris J A; Smeaton, Alan F

2011-10-01

SenseCams have many potential applications as tools for lifelogging, including the possibility of use as a memory rehabilitation tool. Given that a SenseCam can log hundreds of thousands of images per year, it is critical that these be presented to the viewer in a manner that supports the aims of memory rehabilitation. In this article we report a software browser constructed with the aim of using the characteristics of memory to organise SenseCam images into a form that makes the wealth of information stored on SenseCam more accessible. To enable a large amount of visual information to be easily and quickly assimilated by a user, we apply a series of automatic content analysis techniques to structure the images into "events", suggest their relative importance, and select representative images for each. This minimises effort when browsing and searching. We provide anecdotes on use of such a system and emphasise the need for SenseCam images to be meaningfully sorted using such a browser.

BigWig and BigBed: enabling browsing of large distributed datasets.

PubMed

Kent, W J; Zweig, A S; Barber, G; Hinrichs, A S; Karolchik, D

2010-09-01

BigWig and BigBed files are compressed binary indexed files containing data at several resolutions that allow the high-performance display of next-generation sequencing experiment results in the UCSC Genome Browser. The visualization is implemented using a multi-layered software approach that takes advantage of specific capabilities of web-based protocols and Linux and UNIX operating systems files, R trees and various indexing and compression tricks. As a result, only the data needed to support the current browser view is transmitted rather than the entire file, enabling fast remote access to large distributed data sets. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/. Source code for the creation and visualization software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. The UCSC Genome Browser is available at http://genome.ucsc.edu.

Adobe acrobat: an alternative electronic teaching file construction methodology independent of HTML restrictions.

PubMed

Katzman, G L

2001-03-01

The goal of the project was to create a method by which an in-house digital teaching file could be constructed that was simple, inexpensive, independent of hypertext markup language (HTML) restrictions, and appears identical on multiple platforms. To accomplish this, Microsoft PowerPoint and Adobe Acrobat were used in succession to assemble digital teaching files in the Acrobat portable document file format. They were then verified to appear identically on computers running Windows, Macintosh Operating Systems (OS), and the Silicon Graphics Unix-based OS as either a free-standing file using Acrobat Reader software or from within a browser window using the Acrobat browser plug-in. This latter display method yields a file viewed through a browser window, yet remains independent of underlying HTML restrictions, which may confer an advantage over simple HTML teaching file construction. Thus, a hybrid of HTML-distributed Adobe Acrobat generated WWW documents may be a viable alternative for digital teaching file construction and distribution.

A Browser-Based Multi-User Working Environment for Physicists

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, R.; Glaser, C.; Klingebiel, D.; Komm, M.; Müller, G.; Rieger, M.; Steggemann, J.; Urban, M.; Winchen, T.

2014-06-01

Many programs in experimental particle physics do not yet have a graphical interface, or demand strong platform and software requirements. With the most recent development of the VISPA project, we provide graphical interfaces to existing software programs and access to multiple computing clusters through standard web browsers. The scalable clientserver system allows analyses to be performed in sizable teams, and disburdens the individual physicist from installing and maintaining a software environment. The VISPA graphical interfaces are implemented in HTML, JavaScript and extensions to the Python webserver. The webserver uses SSH and RPC to access user data, code and processes on remote sites. As example applications we present graphical interfaces for steering the reconstruction framework OFFLINE of the Pierre-Auger experiment, and the analysis development toolkit PXL. The browser based VISPA system was field-tested in biweekly homework of a third year physics course by more than 100 students. We discuss the system deployment and the evaluation by the students.

EntrezAJAX: direct web browser access to the Entrez Programming Utilities.

PubMed

Loman, Nicholas J; Pallen, Mark J

2010-06-21

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/

Launch Control System Master Console Event Message Reduction

NASA Technical Reports Server (NTRS)

Nguyen, Uyen

2014-01-01

System monitoring and control (SMC) message browsers receive so many messages daily that operators do not need to see. Important messages are often mixed up among the less important ones. My job is to reduce the messages displayed in the message browser so that warning and emergency messages can be seen easily and therefore, responded promptly. There are multiple methods to achieve this. Firstly, duplicate messages should not appear many times in the message browser. Instead, the message should appear only once but with a number that counts the times that it appears. This method is called duplicate message suppression. Secondly, messages that update the most recent state (e.g. up/down) of a component should replace the old-state messages. This method is called state based message correlation. Thirdly, messages that display "normal" alarm level should be suppressed unless it's a response to an operator action. In addition to message reduction, I also work on correcting the severity level and text formats on messages.

Using Mobile Devices to Display, Overlay, and Animate Geophysical Data and Imagery

NASA Astrophysics Data System (ADS)

Batzli, S.; Parker, D.

2011-12-01

A major challenge in mobile-device map application development is to offer rich content and features with simple and intuitive controls and fast performance. Our goal is to bring visualization, animation, and notifications of near real-time weather and earth observation information derived from satellite and sensor data to mobile devices. Our robust back-end processing infrastructure can deliver content in the form of images, shapes, standard descriptive formats (eg. KML, JSON) or raw data to a variety of desktop software, browsers, and mobile devices on demand. We have developed custom interfaces for low-bandwidth browsers (including mobile phones) and high-feature browsers (including smartphones), as well as native applications for Android and iOS devices. Mobile devices offer time- and location-awareness and persistent data connections, allowing us to tailor timely notifications and displays to the user's geographic and time context. This presentation includes a live demo of how our mobile apps deliver animation of standard and custom data products in an interactive map interface.

The UCSC Genome Browser: What Every Molecular Biologist Should Know

PubMed Central

Mangan, Mary E.; Williams, Jennifer M.; Kuhn, Robert M.; Lathe, Warren C.

2014-01-01

Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data make benchwork much more efficient and drive new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. PMID:24984850

SVGMap: configurable image browser for experimental data.

PubMed

Rafael-Palou, Xavier; Schroeder, Michael P; Lopez-Bigas, Nuria

2012-01-01

Spatial data visualization is very useful to represent biological data and quickly interpret the results. For instance, to show the expression pattern of a gene in different tissues of a fly, an intuitive approach is to draw the fly with the corresponding tissues and color the expression of the gene in each of them. However, the creation of these visual representations may be a burdensome task. Here we present SVGMap, a java application that automatizes the generation of high-quality graphics for singular data items (e.g. genes) and biological conditions. SVGMap contains a browser that allows the user to navigate the different images created and can be used as a web-based results publishing tool. SVGMap is freely available as precompiled java package as well as source code at http://bg.upf.edu/svgmap. It requires Java 6 and any recent web browser with JavaScript enabled. The software can be run on Linux, Mac OS X and Windows systems. nuria.lopez@upf.edu

MDB: the Metalloprotein Database and Browser at The Scripps Research Institute

PubMed Central

Castagnetto, Jesus M.; Hennessy, Sean W.; Roberts, Victoria A.; Getzoff, Elizabeth D.; Tainer, John A.; Pique, Michael E.

2002-01-01

The Metalloprotein Database and Browser (MDB; http://metallo.scripps.edu) at The Scripps Research Institute is a web-accessible resource for metalloprotein research. It offers the scientific community quantitative information on geometrical parameters of metal-binding sites in protein structures available from the Protein Data Bank (PDB). The MDB also offers analytical tools for the examination of trends or patterns in the indexed metal-binding sites. A user can perform interactive searches, metal-site structure visualization (via a Java applet), and analysis of the quantitative data by accessing the MDB through a web browser without requiring an external application or platform-dependent plugin. The MDB also has a non-interactive interface with which other web sites and network-aware applications can seamlessly incorporate data or statistical analysis results from metal-binding sites. The information contained in the MDB is periodically updated with automated algorithms that find and index metal sites from new protein structures released by the PDB. PMID:11752342

Context-Dependent Diversity-Effects of Seaweed Consumption on Coral Reefs in Kenya

PubMed Central

Humphries, Austin T.; McQuaid, Christopher D.; McClanahan, Tim R.

2015-01-01

Consumers and prey diversity, their interactions, and subsequent effects on ecosystem function are important for ecological processes but not well understood in high diversity ecosystems such as coral reefs. Consequently, we tested the potential for diversity-effects with a series of surveys and experiments evaluating the influence of browsing herbivores on macroalgae in Kenya’s fringing reef ecosystem. We surveyed sites and undertook experiments in reefs subject to three levels of human fishing influence: open access fished reefs, small and recently established community-managed marine reserves, and larger, older government-managed marine reserves. Older marine reserves had a greater overall diversity of herbivores and browsers but this was not clearly associated with reduced macroalgal diversity or abundance. Experiments studying succession on hard substrata also found no effects of consumer diversity. Instead, overall browser abundance of either sea urchins or fishes was correlated with declines in macroalgal cover. An exception was that the absence of a key fish browser genus, Naso, which was correlated with the persistence of Sargassum in a marine reserve. Algal selectivity assays showed that macroalgae were consumed at variable rates, a product of strong species-specific feeding and low overlap in the selectivity of browsing fishes. We conclude that the effects of browser and herbivore diversity are less than the influences of key species, whose impacts emerge in different contexts that are influenced by fisheries management. Consequently, identifying key herbivore species and managing to protect them may assist protecting reef functions. PMID:26673609

QMachine: commodity supercomputing in web browsers.

PubMed

Wilkinson, Sean R; Almeida, Jonas S

2014-06-09

Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics' "Big Data" from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running "download and install" software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments.

Making the PACS workstation a browser of image processing software: a feasibility study using inter-process communication techniques.

PubMed

Wang, Chunliang; Ritter, Felix; Smedby, Orjan

2010-07-01

To enhance the functional expandability of a picture archiving and communication systems (PACS) workstation and to facilitate the integration of third-part image-processing modules, we propose a browser-server style method. In the proposed solution, the PACS workstation shows the front-end user interface defined in an XML file while the image processing software is running in the background as a server. Inter-process communication (IPC) techniques allow an efficient exchange of image data, parameters, and user input between the PACS workstation and stand-alone image-processing software. Using a predefined communication protocol, the PACS workstation developer or image processing software developer does not need detailed information about the other system, but will still be able to achieve seamless integration between the two systems and the IPC procedure is totally transparent to the final user. A browser-server style solution was built between OsiriX (PACS workstation software) and MeVisLab (Image-Processing Software). Ten example image-processing modules were easily added to OsiriX by converting existing MeVisLab image processing networks. Image data transfer using shared memory added <10ms of processing time while the other IPC methods cost 1-5 s in our experiments. The browser-server style communication based on IPC techniques is an appealing method that allows PACS workstation developers and image processing software developers to cooperate while focusing on different interests.

Experiments in MPEG-4 content authoring, browsing, and streaming

NASA Astrophysics Data System (ADS)

Puri, Atul; Schmidt, Robert L.; Basso, Andrea; Civanlar, Mehmet R.

2000-12-01

In this paper, within the context of the MPEG-4 standard we report on preliminary experiments in three areas -- authoring of MPEG-4 content, a player/browser for MPEG-4 content, and streaming of MPEG-4 content. MPEG-4 is a new standard for coding of audiovisual objects; the core of MPEG-4 standard is complete while amendments are in various stages of completion. MPEG-4 addresses compression of audio and visual objects, their integration by scene description, and interactivity of users with such objects. MPEG-4 scene description is based on VRML like language for 3D scenes, extended to 2D scenes, and supports integration of 2D and 3D scenes. This scene description language is called BIFS. First, we introduce the basic concepts behind BIFS and then show with an example, textual authoring of different components needed to describe an audiovisual scene in BIFS; the textual BIFS is then saved as compressed binary file/s for storage or transmission. Then, we discuss a high level design of an MPEG-4 player/browser that uses the main components from authoring such as encoded BIFS stream, media files it refers to, and multiplexed object descriptor stream to play an MPEG-4 scene. We also discuss our extensions to such a player/browser. Finally, we present our work in streaming of MPEG-4 -- the payload format, modification to client MPEG-4 player/browser, server-side infrastructure and example content used in our MPEG-4 streaming experiments.

Science Plan Visualisation for Rosetta

NASA Astrophysics Data System (ADS)

Schmidt, A.; Grieger, B.; Völk, S.

2013-12-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in mid-2014. The trajectories and their corresponding operations are flexible and particularly complex. To make informed decisions among the many free parameters novel ways to communicate operations to the community have been explored. To support science planning by communicating operational ideas and disseminating operational scenarios, the science ground segment makes use of Web-based visualisation technologies. To keep the threshold to analysing operations proposals as low as possible, various implementation techniques have been investigated. An important goal was to use the Web to make the content as accessible as possible. By adopting the recent standard WebGL and generating static pages of time-dependent three-dimensional views of the spacecraft as well as the corresponding field-of-views of instruments, directly from the operational and for-study files, users are given the opportunity to explore interactively in their Web browsers what is being proposed in addition to using the traditional file products and analysing them in detail. The scenes and animations can be viewed in any modern Web browser and be combined with other analyses. This is to facilitate verification and cross-validation of complex products, often done by comparing different independent analyses and studies. By providing different timesteps in animations, it is possible to focus on long-term planning or short-term planning without distracting the user from the essentials. This is particularly important since the information that can be displayed in a Web browser is somewhat related to data volume that can be transferred across the wire. In Web browsers, it is more challenging to do numerical calculations on demand. Since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. The volume of data that can be kept in a browser environment is limited and might have to be transferred over often slow network links. Thus, careful design and reduction of data is required. Regarding user interaction, Web browsers are often limited to a mouse and keyboards. In terms of benefits, the threshold and turn-around times for discussing operational ideas by using the visualisation techniques described here are lowered. An additional benefit of the approach was the cooperative use of products by distributed users which resulted in higher-quality software and data by incorporating more feedback than what would usually have been available.

Communication of Science Plans in the Rosetta Mission

NASA Astrophysics Data System (ADS)

Schmidt, Albrecht; Grieger, Björn; Völk, Stefan

2014-05-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in mid-2014. The trajectories and their corresponding operations are both flexible and particularly complex. To make informed decisions among the many free parameters, novel ways to communicate operations to the community have been explored. To support science planning by communicating operational ideas and disseminating operational scenarios, the science ground segment makes use of Web-based visualisation technologies. To keep the threshold to analysing operations proposals as low as possible, various implementation techniques have been investigated. An important goal was to use the Web to make the content as accessible as possible. By adopting the recent standard WebGL and generating static pages of time-dependent three-dimensional views of the spacecraft as well as the corresponding field-of-views of instruments, directly from the operational and for-study files, users are given the opportunity to explore interactively in their Web browsers what is being proposed in addition to using the traditional file products and analysing them in detail. The scenes and animations can be viewed in any modern Web browser and be combined with other analyses. This is to facilitate verification and cross-validation of complex products, often done by comparing different independent analyses and studies. By providing different timesteps in animations, it is possible to focus on long-term planning or short-term planning without distracting the user from the essentials. This is particularly important since the information that can be displayed in a Web browser is somewhat related to data volume that can be transferred across the wire. In Web browsers, it is more challenging to do numerical calculations on demand. Since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. The volume of data that can be kept in a browser environment is limited and might have to be transferred over often slow network links. Thus, careful design and reduction of data is required. Regarding user interaction, Web browsers are often limited to a mouse and keyboards. In terms of benefits, the threshold and turn-around times for discussing operational ideas by using the visualisation techniques described here are lowered. An additional benefit of the approach was the cooperative use of products by distributed users which resulted in higher-quality software and data by incorporating more feedback than what would usually have been available.

STANDARDIZING THE STRUCTURE OF STROKE CLINICAL AND EPIDEMIOLOGIC RESEARCH DATA: THE NINDS STROKE COMMON DATA ELEMENT (CDE) PROJECT

PubMed Central

Saver, Jeffrey L.; Warach, Steven; Janis, Scott; Odenkirchen, Joanne; Becker, Kyra; Benavente, Oscar; Broderick, Joseph; Dromerick, Alexander W.; Duncan, Pamela; Elkind, Mitchell S. V.; Johnston, Karen; Kidwell, Chelsea S.; Meschia, James F.; Schwamm, Lee

2012-01-01

Background and Purpose The National Institute of Neurological Disorders and Stroke initiated development of stroke-specific Common Data Elements (CDEs) as part of a project to develop data standards for funded clinical research in all fields of neuroscience. Standardizing data elements in translational, clinical and population research in cerebrovascular disease could decrease study start-up time, facilitate data sharing, and promote well-informed clinical practice guidelines. Methods A Working Group of diverse experts in cerebrovascular clinical trials, epidemiology, and biostatistics met regularly to develop a set of Stroke CDEs, selecting among, refining, and adding to existing, field-tested data elements from national registries and funded trials and studies. Candidate elements were revised based on comments from leading national and international neurovascular research organizations and the public. Results The first iteration of the NINDS stroke-specific CDEs comprises 980 data elements spanning nine content areas: 1) Biospecimens and Biomarkers; 2) Hospital Course and Acute Therapies; 3) Imaging; 4) Laboratory Tests and Vital Signs; 5) Long Term Therapies; 6) Medical History and Prior Health Status; 7) Outcomes and Endpoints; 8) Stroke Presentation; 9) Stroke Types and Subtypes. A CDE website provides uniform names and structures for each element, a data dictionary, and template case report forms (CRFs) using the CDEs. Conclusion Stroke-specific CDEs are now available as standardized, scientifically-vetted variable structures to facilitate data collection and data sharing in cerebrovascular patient-oriented research. The CDEs are an evolving resource that will be iteratively improved based on investigator use, new technologies, and emerging concepts and research findings. PMID:22308239

The diabetes nutrition education study randomized controlled trial: A comparative effectiveness study of approaches to nutrition in diabetes self-management education.

PubMed

Bowen, Michael E; Cavanaugh, Kerri L; Wolff, Kathleen; Davis, Dianne; Gregory, Rebecca P; Shintani, Ayumi; Eden, Svetlana; Wallston, Ken; Elasy, Tom; Rothman, Russell L

2016-08-01

To compare the effectiveness of different approaches to nutrition education in diabetes self-management education and support (DSME/S). We randomized 150 adults with type 2 diabetes to either certified diabetes educator (CDE)-delivered DSME/S with carbohydrate gram counting or the modified plate method versus general health education. The primary outcome was change in HbA1C over 6 months. At 6 months, HbA1C improved within the plate method [-0.83% (-1.29, -0.33), P<0.001] and carbohydrate counting [-0.63% (-1.03, -0.18), P=0.04] groups but not the control group [P=0.34]. Change in HbA1C from baseline between the control and intervention groups was not significant at 6 months (carbohydrate counting, P=0.36; modified plate method, P=0.08). In a pre-specified subgroup analysis of patients with a baseline HbA1C 7-10%, change in HbA1C from baseline improved in the carbohydrate counting [-0.86% (-1.47, -0.26), P=0.006] and plate method groups [-0.76% (-1.33, -0.19), P=0.01] compared to controls. CDE-delivered DSME/S focused on carbohydrate counting or the modified plate method improved glycemic control in patients with an initial HbA1C between 7 and 10%. Both carbohydrate counting and the modified plate method improve glycemic control as part of DSME/S. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Training community health promoters to implement diabetes self-management support programs for urban minority adults.

PubMed

Comellas, Mariceli; Walker, Elizabeth A; Movsas, Sharon; Merkin, Sheryl; Zonszein, Joel; Strelnick, Hal

2010-01-01

To develop, implement, and evaluate a peer-led diabetes self-management support program in English and Spanish for a diverse, urban, low-income population. The program goals and objectives were to improve diabetes self-management behaviors, especially becoming more physically active, healthier eating, medication adherence, problem solving, and goal setting. After a new training program for peers led by a certified diabetes educator (CDE) was implemented with 5 individuals, this pilot evaluation study was conducted in 2 community settings in the East and South Bronx. Seventeen adults with diabetes participated in the new peer-led 5-session program. Survey data were collected pre- and postintervention on diabetes self-care activities, quality of well-being, and number of steps using a pedometer. This pilot study established the acceptance and feasibility of both the peer training program and the community-based, peer-led program for underserved, minority adults with diabetes. Significant improvements were found in several physical activity and nutrition activities, with a modest improvement in well-being. Feedback from both peer facilitators and participants indicated that a longer program, but with the same educational materials, was desirable. To reduce health disparities in urban communities, it is essential to continue program evaluation of the critical elements of peer-led programs for multiethnic adults with diabetes to promote self-management support in a cost-effective and culturally appropriate manner. Practice Implications A diabetes self-management support program can be successfully implemented in the community by peers, within a model including remote supervision by a CDE.

The Comparison between Torsional and Conventional Mode Phacoemulsification in Moderate and Hard Cataracts

PubMed Central

Kim, Dong-Hyun; Wee, Won-Ryang; Lee, Jin-Hak

2010-01-01

Purpose To compare the intraoperative performances and postoperative outcomes of cataract surgery performed with longitudinal phacoemulsification and torsional phacoemulsification in moderate and hard cataracts. Methods Of 85 patients who had senile cataracts, 102 eyes were operated on using the Infiniti Vision System. Preoperative examinations (slit lamp examination, mean central corneal thickness, and central endothelial cell counts) were performed for each patient. Cataracts were subdivided into moderate and hard, according to the Lens Opacities Classification System III grading of nucleus opalescence (NO). Eyes in each cataract group were randomly assigned to conventional and torsional phaco-mode. Intraoperative parameters, including ultrasound time (UST), cumulative dissipated energy (CDE), and the balanced salt solution plus (BSSP) volume utilized were evaluated. Best corrected visual acuity (BCVA) was checked on postoperative day 30; mean central corneal thickness and central endothelial cell counts were investigated on postoperative days 7 and 30. Results Preoperative BCVA and mean grading of NO showed no difference in both groups. Preoperative endothelial cell count and central corneal thickness also showed no significant difference in both groups. In the moderate cataract group, the CDE, UST, and BSSP volume were significantly lower in the torsional mode than the longitudinal mode, but they did not show any difference in the hard cataract group. Torsional group showed less endothelial cell loss and central corneal thickening at postoperative day seven in moderate cataracts but showed no significant differences, as compared with the longitudinal group, by postoperative day 30. Conclusions Torsional phacoemulsification showed superior efficiency for moderate cataracts, as compared with longitudinal phacoemulsification, in the early postoperative stage. PMID:21165231

The comparison between torsional and conventional mode phacoemulsification in moderate and hard cataracts.

PubMed

Kim, Dong-Hyun; Wee, Won-Ryang; Lee, Jin-Hak; Kim, Mee-Kum

2010-12-01

To compare the intraoperative performances and postoperative outcomes of cataract surgery performed with longitudinal phacoemulsification and torsional phacoemulsification in moderate and hard cataracts. Of 85 patients who had senile cataracts, 102 eyes were operated on using the Infiniti Vision System. Preoperative examinations (slit lamp examination, mean central corneal thickness, and central endothelial cell counts) were performed for each patient. Cataracts were subdivided into moderate and hard, according to the Lens Opacities Classification System III grading of nucleus opalescence (NO). Eyes in each cataract group were randomly assigned to conventional and torsional phaco-mode. Intraoperative parameters, including ultrasound time (UST), cumulative dissipated energy (CDE), and the balanced salt solution plus (BSSP) volume utilized were evaluated. Best corrected visual acuity (BCVA) was checked on postoperative day 30; mean central corneal thickness and central endothelial cell counts were investigated on postoperative days 7 and 30. Preoperative BCVA and mean grading of NO showed no difference in both groups. Preoperative endothelial cell count and central corneal thickness also showed no significant difference in both groups. In the moderate cataract group, the CDE, UST, and BSSP volume were significantly lower in the torsional mode than the longitudinal mode, but they did not show any difference in the hard cataract group. Torsional group showed less endothelial cell loss and central corneal thickening at postoperative day seven in moderate cataracts but showed no significant differences, as compared with the longitudinal group, by postoperative day 30. Torsional phacoemulsification showed superior efficiency for moderate cataracts, as compared with longitudinal phacoemulsification, in the early postoperative stage.

Comparison of endothelial changes and power settings between torsional and longitudinal phacoemulsification.

PubMed

Reuschel, Anna; Bogatsch, Holger; Barth, Thomas; Wiedemann, Renate

2010-11-01

To compare the intraoperative and postoperative outcomes of conventional longitudinal phacoemulsification and torsional phacoemulsification. Department of Ophthalmology, University of Leipzig, Germany. Randomized single-center clinical trial. Eyes with senile cataract were randomized to have phacoemulsification using the Infiniti Vision System and the torsional mode (OZil) or conventional longitudinal mode. Primary outcomes were corrected distance visual acuity (CDVA) and central endothelial cell density (ECD), calculated according to the Conference on Harmonisation-E9 Guidelines in which missing values were substituted by the median in each group (primary analysis) and the loss was then calculated using actual data (secondary analysis). Secondary outcomes were ultrasound (US) time, cumulative dissipated energy (CDE), and percentage total equivalent power in position 3. Postoperative follow-up was at 3 months. The mean preoperative CDVA was 0.41 logMAR in the torsional group and 0.38 logMAR in the longitudinal group, improving to 0.07 logMAR postoperatively in both groups. The mean ECD loss was 7.2% ± 4.6% in the torsional group (72 patients) and 7.1% ± 4.4% in the longitudinal group (76 patients), with no statistically significant differences in the primary analysis (P = .342) or secondary analysis (P = .906). The mean US time, CDE, and percentage total equivalent power in position 3 were statistically significantly lower in the torsional group (98 patients) than in the longitudinal group (94 patients) (P<.001). The torsional mode was as safe as the longitudinal mode in phacoemulsification for age-related cataract. Copyright © 2010 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Microcoaxial cataract surgery outcomes: comparison of 1.8 mm system and 2.2 mm system.

PubMed

Lee, Kyung-Min; Kwon, Hyung-Goo; Joo, Choun-Ki

2009-05-01

To compare clinical outcomes of a 1.8 mm and a 2.2 mm microcoaxial cataract surgery system. Department of Ophthalmology and Visual Science, Kangnam St. Mary's Hospital, College of Medicine, Catholic University of Korea, Seoul, Korea. In a prospective study, eyes were randomly selected to have phacoemulsification using a Stellaris system or an Intrepid Infiniti system. The initial incision size was 1.8 mm and 2.2 mm, respectively. Measured intraoperative parameters included phacoemulsification time, mean cumulative dissipated ultrasound energy (CDE), change in incision size at each step of surgery, and total volume of balanced salt solution (BSS) used. The best corrected visual acuity (BCVA), corneal astigmatism, corneal thickness, and endothelial cell count were evaluated preoperatively and postoperatively. The study evaluated 86 eyes of 78 patients (43 eyes in each group). There were no significant differences in postoperative BCVA, surgically induced astigmatism, or amount of BSS used between the 2 systems (P >.05). However, for high-density cataracts, the 1.8 mm group had a greater change between the initial incision size and the incision size after phacoemulsification (P = .019, nuclear opalescence [NO] NO3; P = .001, NO4), a longer phacoemulsification time (P = .013, NO3), greater mean CDE (P = .005, NO3; P = .001, NO4), and greater corneal endothelial cell loss (P = .003, NO4). Both systems were safe and effective in microcoaxial phacoemulsification. The 1.8 mm system performed better with cortical-type cataract and the 2.2 mm system, with high-density nuclear-type cataract.

Results of endocapsular phacofracture debulking of hard cataracts

PubMed Central

Davison, James A

2015-01-01

Purpose/aim of the study To present a phacoemulsification technique for hard cataracts and compare postoperative results using two different ultrasonic tip motions during quadrant removal. Materials and methods A phacoemulsification technique which employs in situ fracture and endocapsular debulking for hard cataracts is presented. The prospective study included 56 consecutive cases of hard cataract (LOCS III NC [Lens Opacification Classification System III, nuclear color], average 4.26), which were operated using the Infiniti machine and the Partial Kelman tip. Longitudinal tip movement was used for sculpting for all cases which were randomized to receive longitudinal or torsional/interjected longitudinal (Intelligent Phaco [IP]) strategies for quadrant removal. Measurements included cumulative dissipated energy (CDE), 3 months postoperative surgically induced astigmatism (SIA), and corneal endothelial cell density (ECD) losses. Results No complications were recorded in any of the cases. Respective overall and longitudinal vs IP means were as follows: CDE, 51.6±15.6 and 55.7±15.5 vs 48.6±15.1; SIA, 0.36±0.2 D and 0.4±0.2 D vs 0.3±0.2 D; and mean ECD loss, 4.1%±10.8% and 5.9%±13.4% vs 2.7%±7.8%. The differences between longitudinal and IP were not significant for any of the three categories. Conclusion The endocapsular phacofracture debulking technique is safe and effective for phacoemulsification of hard cataracts using longitudinal or torsional IP strategies for quadrant removal with the Infiniti machine and Partial Kelman tip. PMID:26203213

Ozil IP torsional mode versus combined torsional/longitudinal microcoaxial phacoemulsification.

PubMed

Helvacioglu, Firat; Tunc, Zeki; Yeter, Celal; Oguzhan, Hasan; Sencan, Sadik

2012-01-01

To compare the safety and efficacy of microcoaxial phacoemulsification surgeries performed with the Ozil Intelligent Phaco (IP) torsional mode and combined torsional/longitudinal ultrasound (US) mode using the Infiniti Vision System (Alcon Laboratories). In this prospective randomized comparative study, 60 eyes were assigned to 2.2-mm microcoaxial phacoemulsification using the Ozil IP torsional mode (group 1) or combined torsional/longitudinal US mode (group 2). The primary outcome measures were US time (UST), cumulative dissipated energy (CDE), longitudinal and torsional ultrasound amplitudes, mean operation time, mean volume of balanced salt solution (BSS) used, and surgical complications. Both groups included 30 eyes. Mean UST, CDE, and longitudinal and torsional ultrasound amplitudes in group 1 were 1 minute 15±34.33 seconds, 8.74±5.64, 0.43±0.74, and 25.56±8.56, respectively, and these parameters in group 2 were 1 minute 40±51.44 seconds, 9.28±5.99, 3.64±1.55, and 3.71±1.34, respectively. UST and longitudinal amplitudes were found to be significantly low in group 1 (p<0.001, p<0.001), whereas torsional amplitude was found to be significantly high in this group (p=0.001). Mean volumes of BSS used in groups 1 and 2 were 63.30±18.00 cc and 84.50±28.65 cc, respectively (p=0.001). The Ozil IP torsional mode may provide more effective lens removal than the combined torsional/longitudinal US mode with a lower UST and volume of BSS used.

High-energy laser tactical decision aid (HELTDA) for mission planning and predictive avoidance

NASA Astrophysics Data System (ADS)

Burley, Jarred L.; Fiorino, Steven T.; Randall, Robb M.; Bartell, Richard J.; Cusumano, Salvatore J.

2012-06-01

This study demonstrates the development of a high energy laser tactical decision aid (HELTDA) by the AFIT/CDE for mission planning High Energy Laser (HEL) weapon system engagements as well as centralized, decentralized, or hybrid predictive avoidance (CPA/DPA/HPA) assessments. Analyses of example HEL mission engagements are described as well as how mission planners are expected to employ the software. Example HEL engagement simulations are based on geographic location and recent/current atmospheric weather conditions. The atmospheric effects are defined through the AFIT/CDE Laser Environmental Effects Definition and Reference (LEEDR) model or the High Energy Laser End-to-End Operational Simulation (HELEEOS) model upon which the HELTDA is based. These models enable the creation of vertical profiles of temperature, pressure, water vapor content, optical turbulence, and atmospheric particulates and hydrometeors as they relate to line-by-line layer extinction coefficient magnitude at wavelengths from the UV to the RF. Seasonal and boundary layer variations (summer/winter) and time of day variations for a range of relative humidity percentile conditions are considered to determine optimum efficiency in a specific environment. Each atmospheric particulate/hydrometeor is evaluated based on its wavelength-dependent forward and off-axis scattering characteristics and absorption effects on the propagating environment to and beyond the target. In addition to realistic vertical profiles of molecular and aerosol absorption and scattering, correlated optical turbulence profiles in probabilistic (percentile) format are included. Numerical weather model forecasts are incorporated in the model to develop comprehensive understanding of HEL weapon system performance.

Validating Multidimensional Outcome Assessment Using the TBI Common Data Elements: An Analysis of the TRACK-TBI Pilot Sample.

PubMed

Nelson, Lindsay D; Ranson, Jana; Ferguson, Adam R; Giacino, Joseph; Okonkwo, David O; Valadka, Alex; Manley, Geoffrey; McCrea, Michael

2017-06-08

The Glasgow Outcome Scale-Extended (GOSE) is often the primary outcome measure in clinical trials for traumatic brain injury (TBI). Although the GOSE's capture of global function outcome has several strengths, concerns have been raised about its limited ability to identify mild disability and failure to capture the full scope of problems patients exhibit after TBI. This analysis examined the convergence of disability ratings across a multidimensional set of outcome domains in the Transforming Research and Clinical Knowledge in Traumatic Brain Injury (TRACK-TBI) Pilot study. The study collected measures recommended by the TBI Common Data Elements (CDE) Workgroup. Patients presenting to 3 emergency departments with a TBI of any severity enrolled in TRACK-TBI prospectively after injury; outcome measures were collected at 3 and six months postinjury. Analyses examined frequency of impairment and overlap between impairment status across the CDE outcome domains of Global Level of Functioning (GOSE), Neuropsychological (cognitive) Impairment, Psychological Status, TBI Symptoms, and Quality of Life. GOSE score correlated in the expected direction with other outcomes (M Spearman's rho = .21 and .49 with neurocognitive and self-report outcomes, respectively). The subsample in the Upper Good Recovery (GOSE 8) category appeared quite healthy across most other outcomes, although 19.0% had impaired executive functioning (Trail Making Test Part B). A significant minority of participants in the Lower Good Recovery subgroup (GOSE 7) met criteria for impairment across numerous other outcome measures. The findings highlight the multidimensional nature of TBI recovery and the limitations of applying only a single outcome measure.

Using a mentoring approach to implement an inpatient glycemic control program in United States hospitals.

PubMed

Rushakoff, Robert J; Sullivan, Mary M; Seley, Jane Jeffrie; Sadhu, Archana; O'Malley, Cheryl W; Manchester, Carol; Peterson, Eric; Rogers, Kendall M

2014-09-01

establishing an inpatient glycemic control program is challenging, requires years of work, significant education and coordination of medical, nursing, dietary, and pharmacy staff, and support from administration and Performance Improvement departments. We undertook a 2 year quality improvement project assisting 10 medical centers (academic and community) across the US to implement inpatient glycemic control programs. the project was comprised of 3 interventions. (1) One day site visit with a faculty team (MD and CDE) to meet with key personnel, identify deficiencies and barriers to change, set site specific goals and develop strategies and timelines for performance improvement. (2) Three webinar follow-up sessions. (3) Web site for educational resources. Updates, challenges, and accomplishments for each site were reviewed at the time of each webinar and progress measured at the completion of the project with an evaluation questionnaire. as a result of our intervention, institutions revised and simplified formularies and insulin order sets (with CHO counting options); implemented glucometrics and CDE monitoring of inpatient glucoses (assisting providers with orders); added new protocols for DKA and perinatal treatment; and implemented nursing, physician and patient education initiatives. Changes were institution specific, fitting the local needs and cultures. As to the extent to which Institution׳s goals were satisfied: 2 reported "completely", 4 "mostly," 3 "partially," and 1 "marginally". Institutions continue to move toward fulfilling their goals. an individualized, structured, performance improvement approach with expert faculty mentors can help facilitate change in an institution dedicated to implementing an inpatient glycemic control program. Copyright © 2014 Elsevier Inc. All rights reserved.

Comparison of the cellular transport mechanism of cationic, star-shaped polymers and liposomes in HaCat cells.

PubMed

Luo, Heng-Cong; Li, Na; Yan, Li; Mai, Kai-Jin; Sun, Kan; Wang, Wei; Lao, Guo-Juan; Yang, Chuan; Zhang, Li-Ming; Ren, Meng

2017-01-01

Several biological barriers must be overcome to achieve efficient nonviral gene delivery. These barriers include target cell uptake, lysosomal degradation, and dissociation from the carrier. In this study, we compared the differences in the uptake mechanism of cationic, star-shaped polymer/MMP-9siRNA complexes (β-CD-(D3)7/MMP-9siRNA complexes: polyplexes) and commercial liposome/MMP-9siRNA complexes (Lipofectamine ® 2000/MMP-9siRNA complexes: liposomes). The uptake pathway and transfection efficiency of the polyplexes and liposomes were determined by fluorescence microscopy, flow cytometry, and reverse transcriptase-polymerase chain reaction. The occurrence of intracellular processing was assessed by confocal laser scanning microscopy. Endosomal acidification inhibitors were used to explore the endosomal escape mechanisms of the polyplexes and lysosomes. We concluded that the polyplexes were internalized by non-caveolae- and non-clathrin-mediated pathways, with no lysosomal trafficking, thereby inducing successful transfection, while the majority of liposomes were internalized by clathrin-dependent endocytosis (CDE), caveolae-mediated endocytosis, and macropinocytosis, and only CDE induced successful transfection. Liposomes might escape more quickly than polyplexes, and the digestion effect of acidic organelles on liposomes was faint compared to the polyplexes, although both complexes escaped from endolysosomes via the proton sponge mechanism. This may be the key aspect that leads to the lower transfection efficiency of the β-CD-(D3)7/MMP-9siRNA complexes. The present study may offer some insights for the rational design of novel delivery systems with increased transfection efficiency but decreased toxicity.

The PPARγ2 A/B-Domain Plays a Gene-Specific Role in Transactivation and Cofactor Recruitment

PubMed Central

Bugge, Anne; Grøntved, Lars; Aagaard, Mads M.; Borup, Rehannah; Mandrup, Susanne

2009-01-01

We have previously shown that adenoviral expression of peroxisome proliferator-activated receptors (PPARs) leads to rapid establishment of transcriptionally active complexes and activation of target gene expression within 5–8 h after transduction. Here we have used the adenoviral delivery system combined with expression array analysis to identify novel putative PPARγ target genes in murine fibroblasts and to determine the role of the A/B-domain in PPARγ-mediated transactivation of genomic target genes. Of the 257 genes found to be induced by PPARγ2 expression, only 25 displayed A/B-domain dependency, i.e. significantly reduced induction in the cells expressing the truncated PPARγ lacking the A/B-domain (PPARγCDE). Nine of the 25 A/B-domain-dependent genes were involved in lipid storage, and in line with this, triglyceride accumulation was considerably decreased in the cells expressing PPARγCDE compared with cells expressing full-length PPARγ2. Using chromatin immunoprecipitation, we demonstrate that PPARγ binding to genomic target sites and recruitment of the mediator component TRAP220/MED1/PBP/DRIP205 is not affected by the deletion of the A/B-domain. By contrast, the PPARγ-mediated cAMP response element-binding protein (CREB)-binding protein (CBP) and p300 recruitment to A/B-domain-dependent target genes is compromised by deletion of the A/B-domain. These results indicate that the A/B-domain of PPARγ2 is specifically involved in the recruitment or stabilization of CBP- and p300-containing cofactor complexes to a subset of target genes. PMID:19282365

Arachne—A web-based event viewer for MINERνA

NASA Astrophysics Data System (ADS)

Tagg, N.; Brangham, J.; Chvojka, J.; Clairemont, M.; Day, M.; Eberly, B.; Felix, J.; Fields, L.; Gago, A. M.; Gran, R.; Harris, D. A.; Kordosky, M.; Lee, H.; Maggi, G.; Maher, E.; Mann, W. A.; Marshall, C. M.; McFarland, K. S.; McGowan, A. M.; Mislivec, A.; Mousseau, J.; Osmanov, B.; Osta, J.; Paolone, V.; Perdue, G.; Ransome, R. D.; Ray, H.; Schellman, H.; Schmitz, D. W.; Simon, C.; Solano Salinas, C. J.; Tice, B. G.; Walding, J.; Walton, T.; Wolcott, J.; Zhang, D.; Ziemer, B. P.; MinerνA Collaboration

2012-06-01

Neutrino interaction events in the MINERνA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERνA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

Arachne - A web-based event viewer for MINERvA

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

Tagg, N.; /Otterbein Coll.; Brangham, J.

2011-11-01

Neutrino interaction events in the MINERvA detector are visually represented with a web-based tool called Arachne. Data are retrieved from a central server via AJAX, and client-side JavaScript draws images into the user's browser window using the draft HTML 5 standard. These technologies allow neutrino interactions to be viewed by anyone with a web browser, allowing for easy hand-scanning of particle interactions. Arachne has been used in MINERvA to evaluate neutrino data in a prototype detector, to tune reconstruction algorithms, and for public outreach and education.

mod_bio: Apache modules for Next-Generation sequencing data.

PubMed

Lindenbaum, Pierre; Redon, Richard

2015-01-01

We describe mod_bio, a set of modules for the Apache HTTP server that allows the users to access and query fastq, tabix, fasta and bam files through a Web browser. Those data are made available in plain text, HTML, XML, JSON and JSON-P. A javascript-based genome browser using the JSON-P communication technique is provided as an example of cross-domain Web service. https://github.com/lindenb/mod_bio. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data.

PubMed

Vanderkam, Dan; Aksoy, B Arman; Hodes, Isaac; Perrone, Jaclyn; Hammerbacher, Jeff

2016-08-01

P: ileup.js is a new browser-based genome viewer. It is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library. The code and documentation for pileup.js is publicly available at https://github.com/hammerlab/pileup.js under the Apache 2.0 license. correspondence@hammerlab.org. © The Author 2016. Published by Oxford University Press.

CliniSpace: a multiperson 3D online immersive training environment accessible through a browser.

PubMed

Dev, Parvati; Heinrichs, W LeRoy; Youngblood, Patricia

2011-01-01

Immersive online medical environments, with dynamic virtual patients, have been shown to be effective for scenario-based learning (1). However, ease of use and ease of access have been barriers to their use. We used feedback from prior evaluation of these projects to design and develop CliniSpace. To improve usability, we retained the richness of prior virtual environments but modified the user interface. To improve access, we used a Software-as-a-Service (SaaS) approach to present a richly immersive 3D environment within a web browser.

Mid Miocene Terrestrial Ecosystems: Information from Mammalian Herbivore Communities.

NASA Astrophysics Data System (ADS)

Janis, C. M.; Damuth, J.; Theodor, J. M.

2001-05-01

In present day ecosystems the numbers and proportions of different kinds of ecologically distinct ungulates (hoofed mammals) provide an indicator of the nature of the vegetation in the habitat. Different vegetation types (such as forest, savanna, or grassland) are characteristically associated with different arrays of ungulates, with species exhibiting differences in diet, body size, and type of digestive fermentation system. These biological attributes can also be inferred for fossil ungulate species, the first two from quantitative assessment of skull and dental anatomy, and the last from phylogenetic affinity. Thus fossil ungulate communities may be used as indicators of the vegetation types of the habitats in which they lived. Vegetation types, in turn, are determined largely by a number of physical environmental factors. Typical ungulate communities of the late early to early middle Miocene (17 - 15 Ma) from the Great Plains of North America contained a diversity of browsing (leaf-eating) and grazing (grass-eating) species, with proportions of dietary types and a diversity of body sizes indicative of a woodland savanna habitat. Paleobotanical evidence also indicates a woodland savanna type of vegetation. However, these communities included a much larger number of ungulate species than can be found in any present-day community. The "excess" ungulate species were primarily browsers. Throughout the rest of the middle Miocene both species numbers and the proportion of browsers in ungulate communities appear to have declined steadily. During this decline in browser species the numbers of grazer species remained relatively constant. Within-community species numbers comparable to the present day were attained by the late Miocene. We suggest that the early Miocene browser-rich communities, and their subsequent decline, carry an important paleoenvironmental signal. In particular, communities "over rich" in browsers may reflect higher levels of primary productivity in mid Miocene vegetation types in comparison with corresponding, structurally equivalent present-day vegetation types. The observed decline in species numbers may represent a gradual decline in terrestrial primary productivity, which would be consistent with one current hypothesis of a mid-Miocene decrease in atmospheric carbon dioxide concentrations from higher mid-Cenozoic values.

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks.

PubMed

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-02-01

Hybrid mobile applications (apps) combine the features of Web applications and "native" mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources-file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies "bridges" that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources-the ability to read and write contacts list, local files, etc.-to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model.

GenColors: annotation and comparative genomics of prokaryotes made easy.

PubMed

Romualdi, Alessandro; Felder, Marius; Rose, Dominic; Gausmann, Ulrike; Schilhabel, Markus; Glöckner, Gernot; Platzer, Matthias; Sühnel, Jürgen

2007-01-01

GenColors (gencolors.fli-leibniz.de) is a new web-based software/database system aimed at an improved and accelerated annotation of prokaryotic genomes considering information on related genomes and making extensive use of genome comparison. It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. A variety of export/import filters manages an effective data flow from sequence assembly and manipulation programs (e.g., GAP4) to GenColors and back as well as to standard GenBank file(s). The genome comparison tools include best bidirectional hits, gene conservation, syntenies, and gene core sets. Precomputed UniProt matches allow annotation and analysis in an effective manner. In addition to these analysis options, base-specific quality data (coverage and confidence) can also be handled if available. The GenColors system can be used both for annotation purposes in ongoing genome projects and as an analysis tool for finished genomes. GenColors comes in two types, as dedicated genome browsers and as the Jena Prokaryotic Genome Viewer (JPGV). Dedicated genome browsers contain genomic information on a set of related genomes and offer a large number of options for genome comparison. The system has been efficiently used in the genomic sequencing of Borrelia garinii and is currently applied to various ongoing genome projects on Borrelia, Legionella, Escherichia, and Pseudomonas genomes. One of these dedicated browsers, the Spirochetes Genome Browser (sgb.fli-leibniz.de) with Borrelia, Leptospira, and Treponema genomes, is freely accessible. The others will be released after finalization of the corresponding genome projects. JPGV (jpgv.fli-leibniz.de) offers information on almost all finished bacterial genomes, as compared to the dedicated browsers with reduced genome comparison functionality, however. As of January 2006, this viewer includes 632 genomic elements (e.g., chromosomes and plasmids) of 293 species. The system provides versatile quick and advanced search options for all currently known prokaryotic genomes and generates circular and linear genome plots. Gene information sheets contain basic gene information, database search options, and links to external databases. GenColors is also available on request for local installation.

Genomes as geography: using GIS technology to build interactive genome feature maps

PubMed Central

Dolan, Mary E; Holden, Constance C; Beard, M Kate; Bult, Carol J

2006-01-01

Background Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. Results We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. Conclusion Mapping tools developed specifically for geographic data can be exploited to display, explore and interact with genome data. The approach we describe here is organism independent and is equally useful for linear and circular chromosomes. One of the unique capabilities of GenoSIS compared to existing genome browsers is the capacity to generate genome feature maps dynamically in response to complex attribute and spatial queries. PMID:16984652

Concertina browsers: a formative evaluation of user preference.

PubMed

Harper, Simon; Christophorou, Nicola

2008-09-01

Evidence suggests that concertina browsers - browsers with the facility to expand and contract sections of information - are important in providing the reader with an enhanced cognition of small to medium amounts of information. These systems have been shown to be useful for visually disabled users surfing the World Wide Web (Web), and with the development of the Mobile Web, there has been renewed interest in their use. This is due to the similarities of reduced or constrained vision found to exist between visually impaired users and the users of mobile devices. The cognition of information fragments is key to the user experience and the reduction of 'information overload'; as such we are concerned with assisting designers of concertina browsers in providing an enhanced user experience by ascertaining user preference through a formative evaluation of concertina summaries. This aspect of browsing is important because in all concertina systems there is a distinct cognition speed/depth trade-off. Here we investigate a number of these concertina summarization techniques against each other. We describe a formative evaluation which concludes that users prefer concertina summarization of Web documents starting from 6.25% slices of both the top and bottom and expanding from the top in 2% steps to a target maximum of 18.50% (being 12.25% from the top and 6.25% from the bottom). These preferences were found to be representative of documents of less than 600 words of content, and included the preference to not fragment an individual sentence even if that meant slightly increasing the target: Starting, maximum, and step percentage slices.

QMachine: commodity supercomputing in web browsers

PubMed Central

2014-01-01

Background Ongoing advancements in cloud computing provide novel opportunities in scientific computing, especially for distributed workflows. Modern web browsers can now be used as high-performance workstations for querying, processing, and visualizing genomics’ “Big Data” from sources like The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) without local software installation or configuration. The design of QMachine (QM) was driven by the opportunity to use this pervasive computing model in the context of the Web of Linked Data in Biomedicine. Results QM is an open-sourced, publicly available web service that acts as a messaging system for posting tasks and retrieving results over HTTP. The illustrative application described here distributes the analyses of 20 Streptococcus pneumoniae genomes for shared suffixes. Because all analytical and data retrieval tasks are executed by volunteer machines, few server resources are required. Any modern web browser can submit those tasks and/or volunteer to execute them without installing any extra plugins or programs. A client library provides high-level distribution templates including MapReduce. This stark departure from the current reliance on expensive server hardware running “download and install” software has already gathered substantial community interest, as QM received more than 2.2 million API calls from 87 countries in 12 months. Conclusions QM was found adequate to deliver the sort of scalable bioinformatics solutions that computation- and data-intensive workflows require. Paradoxically, the sandboxed execution of code by web browsers was also found to enable them, as compute nodes, to address critical privacy concerns that characterize biomedical environments. PMID:24913605

Isotropic plasma etching of Ge Si and SiN x films

DOE PAGES

Henry, Michael David; Douglas, Erica Ann

2016-08-31

This study reports on selective isotropic dry etching of chemically vapor deposited (CVD) Ge thin film, release layers using a Shibaura chemical downstream etcher (CDE) with NF 3 and Ar based plasma chemistry. Relative etch rates between Ge, Si and SiN x are described with etch rate reductions achieved by adjusting plasma chemistry with O 2. Formation of oxides reducing etch rates were measured for both Ge and Si, but nitrides or oxy-nitrides created using direct injection of NO into the process chamber were measured to increase Si and SiN x etch rates while retarding Ge etching.

svviz: a read viewer for validating structural variants.

PubMed

Spies, Noah; Zook, Justin M; Salit, Marc; Sidow, Arend

2015-12-15

Visualizing read alignments is the most effective way to validate candidate structural variants (SVs) with existing data. We present svviz, a sequencing read visualizer for SVs that sorts and displays only reads relevant to a candidate SV. svviz works by searching input bam(s) for potentially relevant reads, realigning them against the inferred sequence of the putative variant allele as well as the reference allele and identifying reads that match one allele better than the other. Separate views of the two alleles are then displayed in a scrollable web browser view, enabling a more intuitive visualization of each allele, compared with the single reference genome-based view common to most current read browsers. The browser view facilitates examining the evidence for or against a putative variant, estimating zygosity, visualizing affected genomic annotations and manual refinement of breakpoints. svviz supports data from most modern sequencing platforms. svviz is implemented in python and freely available from http://svviz.github.io/. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

PubMed

Gattiker, Alexandre; Niederhauser-Wiederkehr, Christa; Moore, James; Hermida, Leandro; Primig, Michael

2007-01-01

We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at http://www.germonline.org/.

ASCIIGenome: a command line genome browser for console terminals.

PubMed

Beraldi, Dario

2017-05-15

Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data. ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers. Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io . Dario.beraldi@cruk.cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Seed Dispersers, Seed Predators, and Browsers Act Synergistically as Biotic Filters in a Mosaic Landscape

PubMed Central

Zamora, Regino; Matías, Luis

2014-01-01

In this study, we analize the functional influence of animals on the plants they interact with in a mediterranean mountain. We hypothesise that seed dispersers, seed predators, and browsers can act as biotic filters for plant communities. We analyse the combined effects of mutualistic (seed dispersal) and antagonistic (seed predation, herbivory) animal interactions in a mosaic landscape of Mediterranean mountains, basing our results on observational and experimental field. Most of the dispersed seeds came from tree species, whereas the population of saplings was composed predominantly of zoochorous shrub species. Seed predators preferentially consumed seeds from tree species, whereas seeds from the dominant fleshy-fruited shrubs had a higher probability of escaping these predators. The same pattern was repeated among the different landscape units by browsers, since they browsed selectively and far more intensely on tree-species saplings than on the surrounding shrubs. In synthesis, our work identifies the major biotic processes that appear to be favoring a community dominated by shrubs versus trees because seed dispersers, predators, and herbivores together favored shrub dispersal and establishment versus trees. PMID:25233342

EntrezAJAX: direct web browser access to the Entrez Programming Utilities

PubMed Central

2010-01-01

Web applications for biology and medicine often need to integrate data from Entrez services provided by the National Center for Biotechnology Information. However, direct access to Entrez from a web browser is not possible due to 'same-origin' security restrictions. The use of "Asynchronous JavaScript and XML" (AJAX) to create rich, interactive web applications is now commonplace. The ability to access Entrez via AJAX would be advantageous in the creation of integrated biomedical web resources. We describe EntrezAJAX, which provides access to Entrez eUtils and is able to circumvent same-origin browser restrictions. EntrezAJAX is easily implemented by JavaScript developers and provides identical functionality as Entrez eUtils as well as enhanced functionality to ease development. We provide easy-to-understand developer examples written in JavaScript to illustrate potential uses of this service. For the purposes of speed, reliability and scalability, EntrezAJAX has been deployed on Google App Engine, a freely available cloud service. The EntrezAJAX webpage is located at http://entrezajax.appspot.com/ PMID:20565938

Natural bounds on herbivorous coral reef fishes

PubMed Central

Hoey, Andrew S.; Williams, Gareth J.; Williams, Ivor D.

2016-01-01

Humans are an increasingly dominant driver of Earth's biological communities, but differentiating human impacts from natural drivers of ecosystem state is crucial. Herbivorous fish play a key role in maintaining coral dominance on coral reefs, and are widely affected by human activities, principally fishing. We assess the relative importance of human and biophysical (habitat and oceanographic) drivers on the biomass of five herbivorous functional groups among 33 islands in the central and western Pacific Ocean. Human impacts were clear for some, but not all, herbivore groups. Biomass of browsers, large excavators, and of all herbivores combined declined rapidly with increasing human population density, whereas grazers, scrapers, and detritivores displayed no relationship. Sea-surface temperature had significant but opposing effects on the biomass of detritivores (positive) and browsers (negative). Similarly, the biomass of scrapers, grazers, and detritivores correlated with habitat structural complexity; however, relationships were group specific. Finally, the biomass of browsers and large excavators was related to island geomorphology, both peaking on low-lying islands and atolls. The substantial variability in herbivore populations explained by natural biophysical drivers highlights the need for locally appropriate management targets on coral reefs. PMID:27881745

The UCSC Genome Browser: What Every Molecular Biologist Should Know.

PubMed

Mangan, Mary E; Williams, Jennifer M; Kuhn, Robert M; Lathe, Warren C

2014-07-01

Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data makes benchwork much more efficient and drives new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser. Copyright © 2014 John Wiley & Sons, Inc.

Software for Displaying Data from Planetary Rovers

NASA Technical Reports Server (NTRS)

Powell, Mark; Backers, Paul; Norris, Jeffrey; Vona, Marsette; Steinke, Robert

2003-01-01

Science Activity Planner (SAP) DownlinkBrowser is a computer program that assists in the visualization of processed telemetric data [principally images, image cubes (that is, multispectral images), and spectra] that have been transmitted to Earth from exploratory robotic vehicles (rovers) on remote planets. It is undergoing adaptation to (1) the Field Integrated Design and Operations (FIDO) rover (a prototype Mars-exploration rover operated on Earth as a test bed) and (2) the Mars Exploration Rover (MER) mission. This program has evolved from its predecessor - the Web Interface for Telescience (WITS) software - and surpasses WITS in the processing, organization, and plotting of data. SAP DownlinkBrowser creates Extensible Markup Language (XML) files that organize data files, on the basis of content, into a sortable, searchable product database, without the overhead of a relational database. The data-display components of SAP DownlinkBrowser (descriptively named ImageView, 3DView, OrbitalView, PanoramaView, ImageCubeView, and SpectrumView) are designed to run in a memory footprint of at least 256MB on computers that utilize the Windows, Linux, and Solaris operating systems.

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

PubMed

Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

2012-07-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

Savant Genome Browser 2: visualization and analysis for population-scale genomics

PubMed Central

Smith, Eric J. M.; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M.; Robinson, Mark D.; Wodak, Shoshana J.; Brudno, Michael

2012-01-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com. PMID:22638571

Web Extensible Display Manager

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

Slominski, Ryan; Larrieu, Theodore L.

Jefferson Lab's Web Extensible Display Manager (WEDM) allows staff to access EDM control system screens from a web browser in remote offices and from mobile devices. Native browser technologies are leveraged to avoid installing and managing software on remote clients such as browser plugins, tunnel applications, or an EDM environment. Since standard network ports are used firewall exceptions are minimized. To avoid security concerns from remote users modifying a control system, WEDM exposes read-only access and basic web authentication can be used to further restrict access. Updates of monitored EPICS channels are delivered via a Web Socket using a webmore » gateway. The software translates EDM description files (denoted with the edl suffix) to HTML with Scalable Vector Graphics (SVG) following the EDM's edl file vector drawing rules to create faithful screen renderings. The WEDM server parses edl files and creates the HTML equivalent in real-time allowing existing screens to work without modification. Alternatively, the familiar drag and drop EDM screen creation tool can be used to create optimized screens sized specifically for smart phones and then rendered by WEDM.« less

SoyFN: a knowledge database of soybean functional networks.

PubMed

Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

2014-01-01

Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure.

PubMed

Milreu, Paulo Vieira; Klein, Cecilia Coimbra; Cottret, Ludovic; Acuña, Vicente; Birmelé, Etienne; Borassi, Michele; Junot, Christophe; Marchetti-Spaccamela, Alberto; Marino, Andrea; Stougie, Leen; Jourdan, Fabien; Crescenzi, Pierluigi; Lacroix, Vincent; Sagot, Marie-France

2014-01-01

The increasing availability of metabolomics data enables to better understand the metabolic processes involved in the immediate response of an organism to environmental changes and stress. The data usually come in the form of a list of metabolites whose concentrations significantly changed under some conditions, and are thus not easy to interpret without being able to precisely visualize how such metabolites are interconnected. We present a method that enables to organize the data from any metabolomics experiment into metabolic stories. Each story corresponds to a possible scenario explaining the flow of matter between the metabolites of interest. These scenarios may then be ranked in different ways depending on which interpretation one wishes to emphasize for the causal link between two affected metabolites: enzyme activation, enzyme inhibition or domino effect on the concentration changes of substrates and products. Equally probable stories under any selected ranking scheme can be further grouped into a single anthology that summarizes, in a unique subnetwork, all equivalently plausible alternative stories. An anthology is simply a union of such stories. We detail an application of the method to the response of yeast to cadmium exposure. We use this system as a proof of concept for our method, and we show that we are able to find a story that reproduces very well the current knowledge about the yeast response to cadmium. We further show that this response is mostly based on enzyme activation. We also provide a framework for exploring the alternative pathways or side effects this local response is expected to have in the rest of the network. We discuss several interpretations for the changes we see, and we suggest hypotheses that could in principle be experimentally tested. Noticeably, our method requires simple input data and could be used in a wide variety of applications. The code for the method presented in this article is available at http://gobbolino.gforge.inria.fr.

Avatar Web-Based Self-Report Survey System Technology for Public Health Research: Technical Outcome Results and Lessons Learned.

PubMed

Savel, Craig; Mierzwa, Stan; Gorbach, Pamina M; Souidi, Samir; Lally, Michelle; Zimet, Gregory; Interventions, Aids

2016-01-01

This paper reports on a specific Web-based self-report data collection system that was developed for a public health research study in the United States. Our focus is on technical outcome results and lessons learned that may be useful to other projects requiring such a solution. The system was accessible from any device that had a browser that supported HTML5. Report findings include: which hardware devices, Web browsers, and operating systems were used; the rate of survey completion; and key considerations for employing Web-based surveys in a clinical trial setting.

PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

PubMed

Tsai, Richard Tzong-Han; Dai, Hong-Jie; Lai, Po-Ting; Huang, Chi-Hsin

2009-11-15

PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

Standardizing the structure of stroke clinical and epidemiologic research data: the National Institute of Neurological Disorders and Stroke (NINDS) Stroke Common Data Element (CDE) project.

PubMed

Saver, Jeffrey L; Warach, Steven; Janis, Scott; Odenkirchen, Joanne; Becker, Kyra; Benavente, Oscar; Broderick, Joseph; Dromerick, Alexander W; Duncan, Pamela; Elkind, Mitchell S V; Johnston, Karen; Kidwell, Chelsea S; Meschia, James F; Schwamm, Lee

2012-04-01

The National Institute of Neurological Disorders and Stroke initiated development of stroke-specific Common Data Elements (CDEs) as part of a project to develop data standards for funded clinical research in all fields of neuroscience. Standardizing data elements in translational, clinical, and population research in cerebrovascular disease could decrease study start-up time, facilitate data sharing, and promote well-informed clinical practice guidelines. A working group of diverse experts in cerebrovascular clinical trials, epidemiology, and biostatistics met regularly to develop a set of stroke CDEs, selecting among, refining, and adding to existing, field-tested data elements from national registries and funded trials and studies. Candidate elements were revised on the basis of comments from leading national and international neurovascular research organizations and the public. The first iteration of the National Institute of Neurological Disorders and Stroke (NINDS) stroke-specific CDEs comprises 980 data elements spanning 9 content areas: (1) biospecimens and biomarkers; (2) hospital course and acute therapies; (3) imaging; (4) laboratory tests and vital signs; (5) long-term therapies; (6) medical history and prior health status; (7) outcomes and end points; (8) stroke presentation; and (9) stroke types and subtypes. A CDE website provides uniform names and structures for each element, a data dictionary, and template case report forms, using the CDEs. Stroke-specific CDEs are now available as standardized, scientifically vetted, variable structures to facilitate data collection and data sharing in cerebrovascular patient-oriented research. The CDEs are an evolving resource that will be iteratively improved based on investigator use, new technologies, and emerging concepts and research findings.

Effect of pore water velocities and solute input methods on chloride transport in the undisturbed soil columns of Loess Plateau

NASA Astrophysics Data System (ADS)

Zhou, BeiBei; Wang, QuanJiu

2017-09-01

Studies on solute transport under different pore water velocity and solute input methods in undisturbed soil could play instructive roles for crop production. Based on the experiments in the laboratory, the effect of solute input methods with small pulse input and large pulse input, as well as four pore water velocities, on chloride transport in the undisturbed soil columns obtained from the Loess Plateau under controlled condition was studied. Chloride breakthrough curves (BTCs) were generated using the miscible displacement method under water-saturated, steady flow conditions. Using the 0.15 mol L-1 CaCl2 solution as a tracer, a small pulse (0.1 pore volumes) was first induced, and then, after all the solution was wash off, a large pulse (0.5 pore volumes) was conducted. The convection-dispersion equation (CDE) and the two-region model (T-R) were used to describe the BTCs, and their prediction accuracies and fitted parameters were compared as well. All the BTCs obtained for the different input methods and the four pore water velocities were all smooth. However, the shapes of the BTCs varied greatly; small pulse inputs resulted in more rapid attainment of peak values that appeared earlier with increases in pore water velocity, whereas large pulse inputs resulted in an opposite trend. Both models could fit the experimental data well, but the prediction accuracy of the T-R was better. The values of the dispersivity, λ, calculated from the dispersion coefficient obtained from the CDE were about one order of magnitude larger than those calculated from the dispersion coefficient given by the T-R, but the calculated Peclet number, Pe, was lower. The mobile-immobile partition coefficient, β, decreased, while the mass exchange coefficient increased with increases in pore water velocity.

Bromodomain and extraterminal (BET) proteins regulate biliary-driven liver regeneration.

PubMed

Ko, Sungjin; Choi, Tae-Young; Russell, Jacquelyn O; So, Juhoon; Monga, Satdarshan P S; Shin, Donghun

2016-02-01

During liver regeneration, hepatocytes are derived from pre-existing hepatocytes. However, if hepatocyte proliferation is compromised, biliary epithelial cells (BECs) become the source of new hepatocytes. We recently reported on a zebrafish liver regeneration model in which BECs extensively contribute to hepatocytes. Using this model, we performed a targeted chemical screen to identify important factors that regulate BEC-driven liver regeneration, the mechanisms of which remain largely unknown. Using Tg(fabp10a:CFP-NTR) zebrafish, we examined the effects of 44 selected compounds on BEC-driven liver regeneration. Liver size was assessed by fabp10a:DsRed expression; liver marker expression was analyzed by immunostaining, in situ hybridization and quantitative PCR. Proliferation and apoptosis were also examined. Moreover, we used a mouse liver injury model, choline-deficient, ethionine-supplemented (CDE) diet. We identified 10 compounds that affected regenerating liver size. Among them, only bromodomain and extraterminal domain (BET) inhibitors, JQ1 and iBET151, blocked both Prox1 and Hnf4a induction in BECs. BET inhibition during hepatocyte ablation blocked BEC dedifferentiation into hepatoblast-like cells (HB-LCs). Intriguingly, after JQ1 washout, liver regeneration resumed, indicating temporal, but not permanent, perturbation of liver regeneration by BET inhibition. BET inhibition after hepatocyte ablation suppressed the proliferation of newly generated hepatocytes and delayed hepatocyte maturation. Importantly, Myca overexpression, in part, rescued the proliferation defect. Furthermore, oval cell numbers in mice fed CDE diet were greatly reduced upon JQ1 administration, supporting the zebrafish findings. BET proteins regulate BEC-driven liver regeneration at multiple steps: BEC dedifferentiation, HB-LC proliferation, the proliferation of newly generated hepatocytes, and hepatocyte maturation. Copyright © 2015 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

Preclinical evaluation of transcriptional targeting strategy for human hepatocellular carcinoma in an orthotopic xenograft mouse model.

PubMed

Sia, Kian Chuan; Huynh, Hung; Chung, Alexander Yaw Fui; Ooi, London Lucien Peng Jin; Lim, Kiat Hon; Hui, Kam Man; Lam, Paula Yeng Po

2013-08-01

Gene regulation of many key cell-cycle players in S-, G(2) phase, and mitosis results from transcriptional repression in their respective promoter regions during the G(0) and G(1) phases of cell cycle. Within these promoter regions are phylogenetically conserved sequences known as the cell-cycle-dependent element (CDE) and cell-cycle genes homology regions (CHR) sites. Thus, we hypothesize that transcriptional regulation of cell-cycle regulation via the CDE/CHR region together with liver-specific apolipoprotein E (apoE)-hAAT promoter could bring about a selective transgene expression in proliferating human hepatocellular carcinoma. We show that the newly generated vector AH-6CC-L2C could mediate hepatocyte-targeted luciferase gene expression in tumor cells and freshly isolated short-term hepatocellular carcinoma cultures from patient biopsy. In contrast, normal murine and human hepatocytes infected with AH-6CC-L2C expressed minimal or low luciferase activities. In the presence of prodrug 5-fluorocytosine (5-FC), AH-6CC-L2C effectively suppressed the growth of orthotopic hepatocellular carcinoma patient-derived xenograft mouse model via the expression of yeast cytosine deaminase (yCD) that converts 5-FC to anticancer metabolite 5-fluoruracil. More importantly, we show that combination treatment of AH-6CC-L2C with an EZH2 inhibitor, DZNep, that targets EpCAM-positive hepatocellular carcinoma, can bring about a greater therapeutic efficacy compared with a single treatment of virus or inhibitor. Our study showed that targeting proliferating human hepatocellular carcinoma cells through the transcriptional control of therapeutic gene could represent a feasible approach against hepatocellular carcinoma.

Numerical analysis of field-scale transport of bromacil

NASA Astrophysics Data System (ADS)

Russo, David; Tauber-Yasur, Inbar; Laufer, Asher; Yaron, Bruno

Field-scale transport of bromacil (5-bromo-3- sec-butyl-6-methyluracil) was analyzed using two different model processes for local description of the transport. The first was the classical, one-region convection dispersion equation (CDE) model while the second was the two-region, mobile-immobile (MIM) model. The analyses were performed by means of detailed three-dimensional, numerical simulations of the flow and the transport [Russo, D., Zaidel, J. and Laufer, A., Numerical analysis of flow and transport in a three-dimensional partially saturated heterogeneous soil. Water Resour. Res., 1998, in press], employing local soil hydraulic properties parameters from field measurements and local adsorption/desorption coefficients and the first-order degradation rate coefficient from laboratory measurements. Results of the analyses suggest that for a given flow regime, mass exchange between the mobile and the immobile regions retards the bromacil degradation, considerably affects the distribution of the bromacil resident concentration, c, at relatively large travel times, slightly affects the spatial moments of the distribution of c, and increases the skewing of the bromacil breakthrough and the uncertainty in its prediction, compared with the case in which the soil contained only a single (mobile) region. Mean and standard deviation of the simulated concentration profiles at various elapsed times were compared with measurements from a field-scale transport experiment [Tauber-Yasur, I., Hadas, A., Russo, D. and Yaron, B., Leaching of terbuthylazine and bromacil through field soils. Water, Air Soil Poln., 1998, in press] conducted at the Bet Dagan site. Given the limitations of the present study (e.g. the lack of detailed field data on the spatial variability of the soil chemical properties) the main conclusion of the present study is that the field-scale transport of bromacil at the Bet Dagan site is better quantified with the MIM model than the CDE model.

Microinterventional endocapsular nucleus disassembly: novel technique and results of first-in-human randomised controlled study.

PubMed

Ianchulev, Tsontcho; Chang, David F; Koo, Edward; MacDonald, Susan; Calvo, Ernesto; Tyson, Farrell Toby; Vasquez, Andrea; Ahmed, Iqbal Ike K

2018-04-18

To assess the safety and efficacy of microinterventional endocapsular nuclear fragmentation in moderate to severe cataracts. This was a prospective single-masked multisurgeon interventional randomised controlled trial (ClinicalTrials.gov NCT02843594) where 101 eyes of 101 subjects with grade 3-4+ nuclear cataracts were randomised to torsional phacoemulsification alone (controls) or torsional phacoemulsification with adjunctive endocapsular nuclear fragmentation using a manual microinterventional nitinol filament loop device (miLOOP group). Outcome measures were phacoemulsification efficiency as measured by ultrasound energy (cumulative dispersed energy (CDE) units) and fluidics requirements (total irrigation fluid used) as well as incidence of intraoperative and postoperative complications. Only high-grade advanced cataracts were enrolled with more than 85% of eyes with baseline best corrected visual acuity (BCVA) of 20/200 or worse in either group. Mean CDE was 53% higher in controls (32.8±24.9 vs 21.4±13.1 with miLOOP assistance) (p=0.004). Endothelial cell loss after surgery was low and similar between groups (7-8%, p=0.561) One-month BCVA averaged 20/27 Snellen in miLOOP eyes and 20/24 in controls. No direct complications were caused by the miLOOP. In two cases, capsular tears occurred during IOL implantation and in all remaining cases during phacoemulsification, with none occurring during the miLOOP nucleus disassembly part of the procedure. Microinterventional endocapsular fragmentation with the manual, disposable miLOOP device achieved consistent, ultrasound-free, full-thickness nucleus disassembly and significantly improved overall phaco efficiency in advanced cataracts. NCT02843594. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

ABrowse--a customizable next-generation genome browser framework.

PubMed

Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2012-01-05

With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

Relationships between oral morphology and feeding style in the Ungulata: a phylogenetically controlled evaluation.

PubMed

Pérez-Barbería, F J; Gordon, I J

2001-05-22

In ungulates it is argued that specialization in the consumption of a particular type of food (feeding style) is reflected in morphological adaptations of the organs involved in the selection, processing and digestion of food. We analysed the differences in size and morphology of some oral traits that have been functionally related to food-selection ability (muzzle width, incisor-arcade shape, incisor shape), prehension of food (incisor protrusion), food comminution (molar occlusal surface area, hypsodonty (high-crowned molars)) and intake rate (incisor breadth) between ungulate species with different feeding styles (browser, mixed feeder, grazer). Grazers were characterized by large-body-size species. After controlling only for body mass, we found that grazers had wider muzzles and incisors, more-protruding incisors and more-bulky and higher-crowned molars than did mixed feeders and browsers. When the analyses took into account both body mass and phylogeny, only body mass and two out of the three hypsodonty indexes used remained significantly different between feeding styles. Browsers were smaller, on average, than mixed feeders and grazers, whilst grazers and mixed feeders did not differ in size. Also, browsers had shorter and less-bulky molars than did mixed feeders and grazers; the latter two feeding styles did not differ from each other in any of the hypsodonty indexes. We conclude that the adaptation to different dietary types in most of the oral traits studied is subsumed by the effects of body mass and the sharing of common ancestors. We hypothesize that differences in the ability to exploit different food resources primarily result from differences in body mass between species, and also discuss why hypsodonty characterizes feeding styles.

Relationships between oral morphology and feeding style in the Ungulata: a phylogenetically controlled evaluation.

PubMed Central

Pérez-Barbería, F. J.; Gordon, I. J.

2001-01-01

In ungulates it is argued that specialization in the consumption of a particular type of food (feeding style) is reflected in morphological adaptations of the organs involved in the selection, processing and digestion of food. We analysed the differences in size and morphology of some oral traits that have been functionally related to food-selection ability (muzzle width, incisor-arcade shape, incisor shape), prehension of food (incisor protrusion), food comminution (molar occlusal surface area, hypsodonty (high-crowned molars)) and intake rate (incisor breadth) between ungulate species with different feeding styles (browser, mixed feeder, grazer). Grazers were characterized by large-body-size species. After controlling only for body mass, we found that grazers had wider muzzles and incisors, more-protruding incisors and more-bulky and higher-crowned molars than did mixed feeders and browsers. When the analyses took into account both body mass and phylogeny, only body mass and two out of the three hypsodonty indexes used remained significantly different between feeding styles. Browsers were smaller, on average, than mixed feeders and grazers, whilst grazers and mixed feeders did not differ in size. Also, browsers had shorter and less-bulky molars than did mixed feeders and grazers; the latter two feeding styles did not differ from each other in any of the hypsodonty indexes. We conclude that the adaptation to different dietary types in most of the oral traits studied is subsumed by the effects of body mass and the sharing of common ancestors. We hypothesize that differences in the ability to exploit different food resources primarily result from differences in body mass between species, and also discuss why hypsodonty characterizes feeding styles. PMID:11375086

DEB: A Diagnostic Experience Browser using similarity networks

NASA Technical Reports Server (NTRS)

Casadaban, Cyprian E.

1990-01-01

Diagnostic Experience Browser (DEB): a fusion of knowledge base and data base that allows users to examine only the data which is most useful to them is described. The system combines a data base of historical cases of diagnostic trouble-shooting experience with similarity networks. A menu-driven natural language interface receives input about the user's current problem. Similarity networks provide the user with references to past cases that are most similar or most related to those they now face. The user can then choose the case that is most pertinent and browse its full textual description which, in turn, may include references to other related cases.

Avatar Web-Based Self-Report Survey System Technology for Public Health Research: Technical Outcome Results and Lessons Learned

PubMed Central

Savel, Craig; Mierzwa, Stan; Gorbach, Pamina M.; Souidi, Samir; Lally, Michelle; Zimet, Gregory; Interventions, AIDS

2016-01-01

This paper reports on a specific Web-based self-report data collection system that was developed for a public health research study in the United States. Our focus is on technical outcome results and lessons learned that may be useful to other projects requiring such a solution. The system was accessible from any device that had a browser that supported HTML5. Report findings include: which hardware devices, Web browsers, and operating systems were used; the rate of survey completion; and key considerations for employing Web-based surveys in a clinical trial setting. PMID:28149445

Figure summarizer browser extensions for PubMed Central

PubMed Central

Agarwal, Shashank; Yu, Hong

2011-01-01

Summary: Figures in biomedical articles present visual evidence for research facts and help readers understand the article better. However, when figures are taken out of context, it is difficult to understand their content. We developed a summarization algorithm to summarize the content of figures and used it in our figure search engine (http://figuresearch.askhermes.org/). In this article, we report on the development of web browser extensions for Mozilla Firefox, Google Chrome and Apple Safari to display summaries for figures in PubMed Central and NCBI Images. Availability: The extensions can be downloaded from http://figuresearch.askhermes.org/articlesearch/extensions.php. Contact: agarwal@uwm.edu PMID:21493658

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

PubMed Central

Harper, Lisa C.; Schaeffer, Mary L.; Thistle, Jordan; Gardiner, Jack M.; Andorf, Carson M.; Campbell, Darwin A.; Cannon, Ethalinda K.S.; Braun, Bremen L.; Birkett, Scott M.; Lawrence, Carolyn J.; Sen, Taner Z.

2011-01-01

Video tutorials are an effective way for researchers to quickly learn how to use online tools offered by biological databases. At MaizeGDB, we have developed a number of video tutorials that demonstrate how to use various tools and explicitly outline the caveats researchers should know to interpret the information available to them. One such popular video currently available is ‘Using the MaizeGDB Genome Browser’, which describes how the maize genome was sequenced and assembled as well as how the sequence can be visualized and interacted with via the MaizeGDB Genome Browser. Database URL: http://www.maizegdb.org/ PMID:21565781

Performance evaluation of a distance learning program.

PubMed

Dailey, D J; Eno, K R; Brinkley, J F

1994-01-01

This paper presents a performance metric which uses a single number to characterize the response time for a non-deterministic client-server application operating over the Internet. When applied to a Macintosh-based distance learning application called the Digital Anatomist Browser, the metric allowed us to observe that "A typical student doing a typical mix of Browser commands on a typical data set will experience the same delay if they use a slow Macintosh on a local network or a fast Macintosh on the other side of the country accessing the data over the Internet." The methodology presented is applicable to other client-server applications that are rapidly appearing on the Internet.

Using GBrowse 2.0 to visualize and share next-generation sequence data

PubMed Central

2013-01-01

GBrowse is a mature web-based genome browser that is suitable for deployment on both public and private web sites. It supports most of genome browser features, including qualitative and quantitative (wiggle) tracks, track uploading, track sharing, interactive track configuration, semantic zooming and limited smooth track panning. As of version 2.0, GBrowse supports next-generation sequencing (NGS) data by providing for the direct display of SAM and BAM sequence alignment files. SAM/BAM tracks provide semantic zooming and support both local and remote data sources. This article provides step-by-step instructions for configuring GBrowse to display NGS data. PMID:23376193

Fulfillment of HTTP Authentication Based on Alcatel OmniSwitch 9700

NASA Astrophysics Data System (ADS)

Liu, Hefu

This paper provides a way of HTTP authentication On Alcatel OmniSwitch 9700. Authenticated VLANs control user access to network resources based on VLAN assignment and user authentication. The user can be authenticated through the switch via any standard Web browser software. Web browser client displays the username and password prompts. Then a way for HTML forms can be given to pass HTTP authentication data when it's submitted. A radius server will provide a database of user information that the switch checks whenever it tries to authenticate through the switch. Before or after authentication, the client can get an address from a Dhcp server.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context

PubMed Central

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-01-01

Background Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. Results lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. Conclusion lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired. PMID:17877794

Bringing Control System User Interfaces to the Web

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

Chen, Xihui; Kasemir, Kay

With the evolution of web based technologies, especially HTML5 [1], it becomes possible to create web-based control system user interfaces (UI) that are cross-browser and cross-device compatible. This article describes two technologies that facilitate this goal. The first one is the WebOPI [2], which can seamlessly display CSS BOY [3] Operator Interfaces (OPI) in web browsers without modification to the original OPI file. The WebOPI leverages the powerful graphical editing capabilities of BOY and provides the convenience of re-using existing OPI files. On the other hand, it uses generic JavaScript and a generic communication mechanism between the web browser andmore » web server. It is not optimized for a control system, which results in unnecessary network traffic and resource usage. Our second technology is the WebSocket-based Process Data Access (WebPDA) [4]. It is a protocol that provides efficient control system data communication using WebSocket [5], so that users can create web-based control system UIs using standard web page technologies such as HTML, CSS and JavaScript. WebPDA is control system independent, potentially supporting any type of control system.« less

Ajax Architecture Implementation Techniques

NASA Astrophysics Data System (ADS)

Hussaini, Syed Asadullah; Tabassum, S. Nasira; Baig, Tabassum, M. Khader

2012-03-01

Today's rich Web applications use a mix of Java Script and asynchronous communication with the application server. This mechanism is also known as Ajax: Asynchronous JavaScript and XML. The intent of Ajax is to exchange small pieces of data between the browser and the application server, and in doing so, use partial page refresh instead of reloading the entire Web page. AJAX (Asynchronous JavaScript and XML) is a powerful Web development model for browser-based Web applications. Technologies that form the AJAX model, such as XML, JavaScript, HTTP, and XHTML, are individually widely used and well known. However, AJAX combines these technologies to let Web pages retrieve small amounts of data from the server without having to reload the entire page. This capability makes Web pages more interactive and lets them behave like local applications. Web 2.0 enabled by the Ajax architecture has given rise to a new level of user interactivity through web browsers. Many new and extremely popular Web applications have been introduced such as Google Maps, Google Docs, Flickr, and so on. Ajax Toolkits such as Dojo allow web developers to build Web 2.0 applications quickly and with little effort.

GBshape: a genome browser database for DNA shape annotations

PubMed Central

Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley J.; Parker, Stephen C.J.; Nuzhdin, Sergey V.; Tullius, Thomas D.; Rohs, Remo

2015-01-01

Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species. PMID:25326329

Web Program for Development of GUIs for Cluster Computers

NASA Technical Reports Server (NTRS)

Czikmantory, Akos; Cwik, Thomas; Klimeck, Gerhard; Hua, Hook; Oyafuso, Fabiano; Vinyard, Edward

2003-01-01

WIGLAF (a Web Interface Generator and Legacy Application Facade) is a computer program that provides a Web-based, distributed, graphical-user-interface (GUI) framework that can be adapted to any of a broad range of application programs, written in any programming language, that are executed remotely on any cluster computer system. WIGLAF enables the rapid development of a GUI for controlling and monitoring a specific application program running on the cluster and for transferring data to and from the application program. The only prerequisite for the execution of WIGLAF is a Web-browser program on a user's personal computer connected with the cluster via the Internet. WIGLAF has a client/server architecture: The server component is executed on the cluster system, where it controls the application program and serves data to the client component. The client component is an applet that runs in the Web browser. WIGLAF utilizes the Extensible Markup Language to hold all data associated with the application software, Java to enable platform-independent execution on the cluster system and the display of a GUI generator through the browser, and the Java Remote Method Invocation software package to provide simple, effective client/server networking.

Implications for Late Pleistocene Mastodon Diet from Opal Phytoliths in Tooth Calculus

NASA Astrophysics Data System (ADS)

Gobetz, Katrina E.; Bozarth, Steven R.

2001-03-01

Calculus removed from the molar teeth of four American mastodons (Mammut americanum) contained opal phytoliths which reflect major dietary components. Three samples contained abundant grass phytoliths (ca. 86% of total), with long cells and trapezoidal pooid short cells dominant (ca. 25 and 31%, respectively). Dicot phytoliths from hackberry (Celtis sp.) seeds and indeterminate deciduous trees were rare (1-3%), though well preserved, whereas phytoliths from conifer trees were not recognizable in any of the samples. Comparative analysis of calculus from modern and fossil browsers and mixed feeders implies that dicots and conifers are nearly invisible in the phytolith record. This scarcity may result from poor preservation, low silica production in woody taxa, and/or animals' selection of young, silica-poor leaves and shoots. However, abundant grass phytoliths in the mixed feeders suggest that presence versus absence of grass phytoliths may distinguish mixed feeders and grazers from browsers. Mastodons are traditionally considered browsers, but grass phytolith assemblages in three individual mastodons contained similarly high concentrations of pooids, suggesting that these grasses were a significant part of the diet. Abundant pooid phytoliths, in addition to diatoms, indicate that these mastodons grazed in a cool, moist late Pleistocene environment, possibly near water.

Multimedia consultation session recording and playback using Java-based browser in global PACS

NASA Astrophysics Data System (ADS)

Martinez, Ralph; Shah, Pinkesh J.; Yu, Yuan-Pin

1998-07-01

The current version of the Global PACS software system uses a Java-based implementation of the Remote Consultation and Diagnosis (RCD) system. The Java RCD includes a multimedia consultation session between physicians that includes text, static image, image annotation, and audio data. The JAVA RCD allows 2-4 physicians to collaborate on a patient case. It allows physicians to join the session via WWW Java-enabled browsers or stand alone RCD application. The RCD system includes a distributed database archive system for archiving and retrieving patient and session data. The RCD system can be used for store and forward scenarios, case reviews, and interactive RCD multimedia sessions. The RCD system operates over the Internet, telephone lines, or in a private Intranet. A multimedia consultation session can be recorded, and then played back at a later time for review, comments, and education. A session can be played back using Java-enabled WWW browsers on any operating system platform. The JAVA RCD system shows that a case diagnosis can be captured digitally and played back with the original real-time temporal relationships between data streams. In this paper, we describe design and implementation of the RCD session playback.

e-Stars Template Builder

NASA Technical Reports Server (NTRS)

Cox, Brian

2003-01-01

e-Stars Template Builder is a computer program that implements a concept of enabling users to rapidly gain access to information on projects of NASA's Jet Propulsion Laboratory. The information about a given project is not stored in a data base, but rather, in a network that follows the project as it develops. e-Stars Template Builder resides on a server computer, using Practical Extraction and Reporting Language (PERL) scripts to create what are called "e-STARS node templates," which are software constructs that allow for project-specific configurations. The software resides on the server and does not require specific software on the user machine except for an Internet browser. A user's computer need not be equipped with special software (other than an Internet-browser program). e-Stars Template Builder is compatible with Windows, Macintosh, and UNIX operating systems. A user invokes e-Stars Template Builder from a browser window. Operations that can be performed by the user include the creation of child processes and the addition of links and descriptions of documentation to existing pages or nodes. By means of this addition of "child processes" of nodes, a network that reflects the development of a project is generated.

Microprocessor-controlled, wide-range streak camera

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

Amy E. Lewis, Craig Hollabaugh

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storagemore » using flash-based storage media. The camera’s user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.« less

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

PubMed

Faith, Jeremiah J; Olson, Andrew J; Gardner, Timothy S; Sachidanandam, Ravi

2007-09-18

Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standard flat-file formats and bypassing the database needs of most visualization tools. Visualization as an aide to discovery requires display of novel data in conjunction with static annotations in their chromosomal context. With database-based systems, displaying dynamic results requires temporary tables that need to be tracked for removal. lwgv simplifies the visualization of user-generated results on a local computer. The dynamic results of these analyses are written to transient files, which can import static content from a more permanent file. lwgv is currently used in many different applications, from whole genome browsers to single-gene RNAi design visualization, demonstrating its applicability in a large variety of contexts and scales. lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses in their chromosomal context. It is particularly suited for applications ranging from short sequences to medium-sized genomes when the creation and maintenance of a large software and database infrastructure is not necessary or desired.

Natural bounds on herbivorous coral reef fishes.

PubMed

Heenan, Adel; Hoey, Andrew S; Williams, Gareth J; Williams, Ivor D

2016-11-30

Humans are an increasingly dominant driver of Earth's biological communities, but differentiating human impacts from natural drivers of ecosystem state is crucial. Herbivorous fish play a key role in maintaining coral dominance on coral reefs, and are widely affected by human activities, principally fishing. We assess the relative importance of human and biophysical (habitat and oceanographic) drivers on the biomass of five herbivorous functional groups among 33 islands in the central and western Pacific Ocean. Human impacts were clear for some, but not all, herbivore groups. Biomass of browsers, large excavators, and of all herbivores combined declined rapidly with increasing human population density, whereas grazers, scrapers, and detritivores displayed no relationship. Sea-surface temperature had significant but opposing effects on the biomass of detritivores (positive) and browsers (negative). Similarly, the biomass of scrapers, grazers, and detritivores correlated with habitat structural complexity; however, relationships were group specific. Finally, the biomass of browsers and large excavators was related to island geomorphology, both peaking on low-lying islands and atolls. The substantial variability in herbivore populations explained by natural biophysical drivers highlights the need for locally appropriate management targets on coral reefs. © 2016 The Authors.

Microprocessor-controlled wide-range streak camera

NASA Astrophysics Data System (ADS)

Lewis, Amy E.; Hollabaugh, Craig

2006-08-01

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storage using flash-based storage media. The camera's user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.

Breaking and Fixing Origin-Based Access Control in Hybrid Web/Mobile Application Frameworks

PubMed Central

Georgiev, Martin; Jana, Suman; Shmatikov, Vitaly

2014-01-01

Hybrid mobile applications (apps) combine the features of Web applications and “native” mobile apps. Like Web applications, they are implemented in portable, platform-independent languages such as HTML and JavaScript. Like native apps, they have direct access to local device resources—file system, location, camera, contacts, etc. Hybrid apps are typically developed using hybrid application frameworks such as PhoneGap. The purpose of the framework is twofold. First, it provides an embedded Web browser (for example, WebView on Android) that executes the app's Web code. Second, it supplies “bridges” that allow Web code to escape the browser and access local resources on the device. We analyze the software stack created by hybrid frameworks and demonstrate that it does not properly compose the access-control policies governing Web code and local code, respectively. Web code is governed by the same origin policy, whereas local code is governed by the access-control policy of the operating system (for example, user-granted permissions in Android). The bridges added by the framework to the browser have the same local access rights as the entire application, but are not correctly protected by the same origin policy. This opens the door to fracking attacks, which allow foreign-origin Web content included into a hybrid app (e.g., ads confined in iframes) to drill through the layers and directly access device resources. Fracking vulnerabilities are generic: they affect all hybrid frameworks, all embedded Web browsers, all bridge mechanisms, and all platforms on which these frameworks are deployed. We study the prevalence of fracking vulnerabilities in free Android apps based on the PhoneGap framework. Each vulnerability exposes sensitive local resources—the ability to read and write contacts list, local files, etc.—to dozens of potentially malicious Web domains. We also analyze the defenses deployed by hybrid frameworks to prevent resource access by foreign-origin Web content and explain why they are ineffectual. We then present NoFrak, a capability-based defense against fracking attacks. NoFrak is platform-independent, compatible with any framework and embedded browser, requires no changes to the code of the existing hybrid apps, and does not break their advertising-supported business model. PMID:25485311

Vcs.js - Visualization Control System for the Web

NASA Astrophysics Data System (ADS)

Chaudhary, A.; Lipsa, D.; Doutriaux, C.; Beezley, J. D.; Williams, D. N.; Fries, S.; Harris, M. B.

2016-12-01

VCS is a general purpose visualization library, optimized for climate data, which is part of the UV-CDAT system. It provides a Python API for drawing 2D plots such as lineplots, scatter plots, Taylor diagrams, data colored by scalar values, vector glyphs, isocontours and map projections. VCS is based on the VTK library. Vcs.js is the corresponding JavaScript API, designed to be as close as possible to the original VCS Python API and to provide similar functionality for the Web. Vcs.js includes additional functionality when compared with VCS. This additional API is used to introspect data files available on the server and variables available in a data file. Vcs.js can display plots in the browser window. It always works with a server that reads a data file, extracts variables from the file and subsets the data. From this point, two alternate paths are possible. First the system can render the data on the server using VCS producing an image which is send to the browser to be displayed. This path works for for all plot types and produces a reference image identical with the images produced by VCS. This path uses the VTK-Web library. As an optimization, usable in certain conditions, a second path is possible. Data is packed, and sent to the browser which uses a JavaScript plotting library, such as plotly, to display the data. Plots that work well in the browser are line-plots, scatter-plots for any data and many other plot types for small data and supported grid types. As web technology matures, more plots could be supported for rendering in the browser. Rendering can be done either on the client or on the server and we expect that the best place to render will change depending on the available web technology, data transfer costs, server management costs and value provided to users. We intend to provide a flexible solution that allows for both client and server side rendering and a meaningful way to choose between the two. We provide a web-based user interface called vCdat which uses Vcs.js as its visualization library. Our paper will discuss the principles guiding our design choices for Vcs.js, present our design in detail and show a sample usage of the library.

Experience of Soviet Medicine in a Great Patriotic War 1941-1945. Part 3 (Opyt Sovetskoy Meditsimy v Velikoy Otechestvennoy Voyne 1941-1945),

DTIC Science & Technology

1981-04-15

development of suppurative flcws was always the indicator of the march/passage of process into the teavier form. Based on materials of the onion ...on the average the oparability of those wounded the shin composed 84.lc/o. on all DMP of cDe of the armies in ccbat fcr the great onions (November...Bits Depewoua (13) t𔃺(51 ( Uepos *TOpOI tpeTHA UTsepTuan OCKUAbqaTb . . 48,7 45,5 40.7 i 39. I (tPaapo6nenH.fi 19,9 22,7 2". Kay: (1). Porn /species of

The 2017 Diabetes Educator and the Diabetes Self-Management Education National Practice Survey.

PubMed

Rinker, Joanne; Dickinson, Jane K; Litchman, Michelle L; Williams, Ann S; Kolb, Leslie E; Cox, Carla; Lipman, Ruth D

2018-06-01

Purpose The American Association of Diabetes Educators conducts the National Practice Survey (NPS) biennially to document current practice in diabetes education in the United States. The purpose of the study is to obtain insight about factors influencing the work of the diabetes educator. Method The 2017 NPS was comprised of 100 questions covering diabetes educator demographics, profile populations of people with diabetes, practice information, program accreditation, program curriculum, staffing, education delivery methods, data collection, and reporting. The basic survey consisted of 22 questions using branch logic, from which respondents were then directed to questions tailored to their particular practice setting, enabling them to answer only a relevant subset of the remaining questions. The web-based survey was sent to approximately 32 000 individuals who were either members of the American Association of Diabetes Educators (AADE) or Certified Diabetes Educators (CDE) with the National Certification Board for Diabetes Educators (NCBDE) but not AADE members. Weekly reminder e-mails were sent to recipients who had not yet responded. The outreach efforts resulted in the survey being completed by 4696 individuals, a 17% response rate yielding 95% confidence that these responses are within ±5% accuracy. Results Diabetes Self-Management Education and Support (DSMES) continues to be a field dominated by women (95%). Diabetes educators represent a diverse health care profession, with educators indicating most commonly that their primary discipline is nursing (48%), nutrition (38%), and pharmacy (7%). When asked about credentials, 82.6% indicated that they held a CDE, 3.8% held the Board Certified-Advanced Diabetes Management (BC-ADM) credential, and 16.5% held neither the CDE nor the BC-ADM. Nearly 75% characterized their role as a diabetes educator as providing direct patient care. DSMES continued to be provided in a varied array of settings to educationally, socioeconomically, and racially diverse patient populations. DSMES was delivered using a number of different educational strategies. Diabetes educators have direct influence in care and services that people with diabetes receive. Conclusions The results of the 2017 NPS demonstrate that diabetes educators are meeting the needs of varied populations in various practice settings. They are working with individuals with type 1 and type 2 diabetes, those at risk for diabetes, and women with gestational diabetes and are involved in recommending, implementing, and providing key referrals and recommendations for diabetes care, including insulin initiation, titration, medication adjustments, recommendations on devices, and technology. Identified areas for improvement include needs for increased racial and ethnic diversity in the workforce, recruiting young professionals, drawing practice approaches from related disciplines (eg, mental health and disability rehabilitation), and encouraging tracking of more areas of outcomes data. Diabetes educators are playing an increasingly central role within multidisciplinary care teams with people at risk for diabetes, those who have diabetes, and those with other chronic conditions.

Exploring JavaScript and ROOT technologies to create Web-based ATLAS analysis and monitoring tools

NASA Astrophysics Data System (ADS)

Sánchez Pineda, A.

2015-12-01

We explore the potential of current web applications to create online interfaces that allow the visualization, interaction and real cut-based physics analysis and monitoring of processes through a web browser. The project consists in the initial development of web- based and cloud computing services to allow students and researchers to perform fast and very useful cut-based analysis on a browser, reading and using real data and official Monte- Carlo simulations stored in ATLAS computing facilities. Several tools are considered: ROOT, JavaScript and HTML. Our study case is the current cut-based H → ZZ → llqq analysis of the ATLAS experiment. Preliminary but satisfactory results have been obtained online.

Web-Accessible Scientific Workflow System for Performance Monitoring

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

Roelof Versteeg; Roelof Versteeg; Trevor Rowe

2006-03-01

We describe the design and implementation of a web accessible scientific workflow system for environmental monitoring. This workflow environment integrates distributed, automated data acquisition with server side data management and information visualization through flexible browser based data access tools. Component technologies include a rich browser-based client (using dynamic Javascript and HTML/CSS) for data selection, a back-end server which uses PHP for data processing, user management, and result delivery, and third party applications which are invoked by the back-end using webservices. This environment allows for reproducible, transparent result generation by a diverse user base. It has been implemented for several monitoringmore » systems with different degrees of complexity.« less

Web-based segmentation and display of three-dimensional radiologic image data.

PubMed

Silverstein, J; Rubenstein, J; Millman, A; Panko, W

1998-01-01

In many clinical circumstances, viewing sequential radiological image data as three-dimensional models is proving beneficial. However, designing customized computer-generated radiological models is beyond the scope of most physicians, due to specialized hardware and software requirements. We have created a simple method for Internet users to remotely construct and locally display three-dimensional radiological models using only a standard web browser. Rapid model construction is achieved by distributing the hardware intensive steps to a remote server. Once created, the model is automatically displayed on the requesting browser and is accessible to multiple geographically distributed users. Implementation of our server software on large scale systems could be of great service to the worldwide medical community.

An innovative browser-based data exploration tool with simultaneous scrolling in time and wavelength domains

NASA Astrophysics Data System (ADS)

Slater, Gregory L.; Schiff, David; De Pontieu, Bart; Tarbell, Theodore D.; Freeland, Samuel L.

2017-08-01

We present Cruiser, a new web tool for the precision interactive blending of image series across time and wavelength domains. Scrolling in two dimensions enables discovery and investigation of similarities and differences in structure and evolution across multiple wavelengths. Cruiser works in the latest versions of standards compliant browsers on both desktop and IOS platforms. Co-aligned data cubes have been generated for AIA, IRIS, and Hinode SOT FG, and image data from additional instruments, both space-based and ground-based, can be data sources. The tool has several movie playing and image adjustment controls which will be described in the poster and demonstrated on a MacOS notebook and iPad.

Modelling Safe Interface Interactions in Web Applications

NASA Astrophysics Data System (ADS)

Brambilla, Marco; Cabot, Jordi; Grossniklaus, Michael

Current Web applications embed sophisticated user interfaces and business logic. The original interaction paradigm of the Web based on static content pages that are browsed by hyperlinks is, therefore, not valid anymore. In this paper, we advocate a paradigm shift for browsers and Web applications, that improves the management of user interaction and browsing history. Pages are replaced by States as basic navigation nodes, and Back/Forward navigation along the browsing history is replaced by a full-fledged interactive application paradigm, supporting transactions at the interface level and featuring Undo/Redo capabilities. This new paradigm offers a safer and more precise interaction model, protecting the user from unexpected behaviours of the applications and the browser.

A web access script language to support clinical application development.

PubMed

O'Kane, K C; McColligan, E E

1998-02-01

This paper describes the development of a script language to support the implementation of decentralized, clinical information applications on the World Wide Web (Web). The goal of this work is to facilitate construction of low overhead, fully functional clinical information systems that can be accessed anywhere by low cost Web browsers to search, retrieve and analyze stored patient data. The Web provides a model of network access to data bases on a global scale. Although it was originally conceived as a means to exchange scientific documents, Web browsers and servers currently support access to a wide variety of audio, video, graphical and text based data to a rapidly growing community. Access to these services is via inexpensive client software browsers that connect to servers by means of the open architecture of the Internet. In this paper, the design and implementation of a script language that supports the development of low cost, Web-based, distributed clinical information systems for both Inter- and Intra-Net use is presented. The language is based on the Mumps language and, consequently, supports many legacy applications with few modifications. Several enhancements, however, have been made to support modern programming practices and the Web interface. The interpreter for the language also supports standalone program execution on Unix, MS-Windows, OS/2 and other operating systems.

GBshape: a genome browser database for DNA shape annotations.

PubMed

Chiu, Tsu-Pei; Yang, Lin; Zhou, Tianyin; Main, Bradley J; Parker, Stephen C J; Nuzhdin, Sergey V; Tullius, Thomas D; Rohs, Remo

2015-01-01

Many regulatory mechanisms require a high degree of specificity in protein-DNA binding. Nucleotide sequence does not provide an answer to the question of why a protein binds only to a small subset of the many putative binding sites in the genome that share the same core motif. Whereas higher-order effects, such as chromatin accessibility, cooperativity and cofactors, have been described, DNA shape recently gained attention as another feature that fine-tunes the DNA binding specificities of some transcription factor families. Our Genome Browser for DNA shape annotations (GBshape; freely available at http://rohslab.cmb.usc.edu/GBshape/) provides minor groove width, propeller twist, roll, helix twist and hydroxyl radical cleavage predictions for the entire genomes of 94 organisms. Additional genomes can easily be added using the GBshape framework. GBshape can be used to visualize DNA shape annotations qualitatively in a genome browser track format, and to download quantitative values of DNA shape features as a function of genomic position at nucleotide resolution. As biological applications, we illustrate the periodicity of DNA shape features that are present in nucleosome-occupied sequences from human, fly and worm, and we demonstrate structural similarities between transcription start sites in the genomes of four Drosophila species. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Aladin Lite: Embed your Sky in the Browser

NASA Astrophysics Data System (ADS)

Boch, T.; Fernique, P.

2014-05-01

I will introduce and describe Aladin Lite1, a lightweight interactive sky viewer running natively in the browser. The past five years have seen the emergence of powerful and complex web applications, thanks to major improvements in JavaScript engines and the advent of HTML5. At the same time, browser plugins Java applets, Flash, Silverlight) that were commonly used to run rich Internet applications are declining and are not well suited for mobile devices. The Aladin team took this opportunity to develop Aladin Lite, a lightweight version of Aladin geared towards simple visualization of a sky region. Relying on the widely supported HTML5 canvas element, it provides an intuitive user interface running on desktops and tablets. This first version allows one to interactively visualize multi-resolution HEALPix image and superimpose tabular data and footprints. Aladin Lite is easily embeddable on any web page and may be of interest for data providers which will be able to use it as an interactive previewer for their own image surveys, previously pre-processed as explained in details in the poster "Create & publish your Hierarchical Progressive Survey". I will present the main features of Aladin Lite as well as the JavaScript API which gives the building blocks to create rich interactions between a web page and Aladin Lite.

A topological framework for interactive queries on 3D models in the Web.

PubMed

Figueiredo, Mauro; Rodrigues, José I; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications.

A Topological Framework for Interactive Queries on 3D Models in the Web

PubMed Central

Figueiredo, Mauro; Rodrigues, José I.; Silvestre, Ivo; Veiga-Pires, Cristina

2014-01-01

Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications. PMID:24977236

Alignment-Annotator web server: rendering and annotating sequence alignments.

PubMed

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-07-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Alignment-Annotator web server: rendering and annotating sequence alignments

PubMed Central

Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

2014-01-01

Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

Display gamma is an important factor in Web image viewing

NASA Astrophysics Data System (ADS)

Zhang, Xuemei; Lavin, Yingmei; Silverstein, D. Amnon

2001-06-01

We conducted a perceptual image preference experiment over the web to find our (1) if typical computer users have significant variations in their display gamma settings, and (2) if so, do the gamma settings have significant perceptual effect on the appearance of images in their web browsers. The digital image renderings used were found to have preferred tone characteristics from a previous lab- controlled experiment. They were rendered with 4 different gamma settings. The subjects were asked to view the images over the web, with their own computer equipment and web browsers. The subjects werewe asked to view the images over the web, with their own computer equipment and web browsers. The subjects made pair-wise subjective preference judgements on which rendering they liked bets for each image. Each subject's display gamma setting was estimated using a 'gamma estimator' tool, implemented as a Java applet. The results indicated that (1) the user's gamma settings, as estimated in the experiment, span a wide range from about 1.8 to about 3.0; (2) the subjects preferred images that werewe rendered with a 'correct' gamma value matching their display setting. Subjects disliked images rendered with a gamma value not matching their displays'. This indicates that display gamma estimation is a perceptually significant factor in web image optimization.

vMon-mobile provides wireless connection to the electronic patient record

NASA Astrophysics Data System (ADS)

Oliveira, Pedro P., Jr.; Rebelo, Marina; Pilon, Paulo E.; Gutierrez, Marco A.; Tachinardi, Umberto

2002-05-01

This work presents the development of a set of tools to help doctors to continuously monitor critical patients. Real-time monitoring signals are displayed via a Web Based Electronic Patient Record (Web-EPR) developed at the Heart Institute. Any computer on the Hospital's Intranet can access the Web-EPR that will open a browser plug-in called vMon. Recently vMon was adapted to wireless mobile devices providing the same real-time visualization of vital signals of its desktop counterpart. The monitoring network communicates with the hospital network through a gateway using HL7 messages and has the ability to export waveforms in real time using the multicast protocol through an API library. A dedicated ActiveX component was built that establishes the streaming of the biomedical signals under monitoring and displays them on an Internet Explorer 5.x browser. The mobile version - called vMon-mobile - will parse the browser window and deliver it to a PDA device connected to a local area network. The result is a virtual monitor presenting real-time data on a mobile device. All parameters and signals acquired from the moment the patient is connected to the monitors are stored for a few days. The most clinically relevant information is added to patient's EPR.

On-demand server-side image processing for web-based DICOM image display

NASA Astrophysics Data System (ADS)

Sakusabe, Takaya; Kimura, Michio; Onogi, Yuzo

2000-04-01

Low cost image delivery is needed in modern networked hospitals. If a hospital has hundreds of clients, cost of client systems is a big problem. Naturally, a Web-based system is the most effective solution. But a Web browser could not display medical images with certain image processing such as a lookup table transformation. We developed a Web-based medical image display system using Web browser and on-demand server-side image processing. All images displayed on a Web page are generated from DICOM files on a server, delivered on-demand. User interaction on the Web page is handled by a client-side scripting technology such as JavaScript. This combination makes a look-and-feel of an imaging workstation not only for its functionality but also for its speed. Real time update of images with tracing mouse motion is achieved on Web browser without any client-side image processing which may be done by client-side plug-in technology such as Java Applets or ActiveX. We tested performance of the system in three cases. Single client, small number of clients in a fast speed network, and large number of clients in a normal speed network. The result shows that there are very slight overhead for communication and very scalable in number of clients.

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications

PubMed Central

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-01-01

Background Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. Results The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. Conclusion The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools. PMID:18021453

GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.

PubMed

Gundersen, Gregory W; Jones, Matthew R; Rouillard, Andrew D; Kou, Yan; Monteiro, Caroline D; Feldmann, Axel S; Hu, Kevin S; Ma'ayan, Avi

2015-09-15

Identification of differentially expressed genes is an important step in extracting knowledge from gene expression profiling studies. The raw expression data from microarray and other high-throughput technologies is deposited into the Gene Expression Omnibus (GEO) and served as Simple Omnibus Format in Text (SOFT) files. However, to extract and analyze differentially expressed genes from GEO requires significant computational skills. Here we introduce GEO2Enrichr, a browser extension for extracting differentially expressed gene sets from GEO and analyzing those sets with Enrichr, an independent gene set enrichment analysis tool containing over 70 000 annotated gene sets organized into 75 gene-set libraries. GEO2Enrichr adds JavaScript code to GEO web-pages; this code scrapes user selected accession numbers and metadata, and then, with one click, users can submit this information to a web-server application that downloads the SOFT files, parses, cleans and normalizes the data, identifies the differentially expressed genes, and then pipes the resulting gene lists to Enrichr for downstream functional analysis. GEO2Enrichr opens a new avenue for adding functionality to major bioinformatics resources such GEO by integrating tools and resources without the need for a plug-in architecture. Importantly, GEO2Enrichr helps researchers to quickly explore hypotheses with little technical overhead, lowering the barrier of entry for biologists by automating data processing steps needed for knowledge extraction from the major repository GEO. GEO2Enrichr is an open source tool, freely available for installation as browser extensions at the Chrome Web Store and FireFox Add-ons. Documentation and a browser independent web application can be found at http://amp.pharm.mssm.edu/g2e/. avi.maayan@mssm.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications.

PubMed

Bare, J Christopher; Shannon, Paul T; Schmid, Amy K; Baliga, Nitin S

2007-11-19

Information resources on the World Wide Web play an indispensable role in modern biology. But integrating data from multiple sources is often encumbered by the need to reformat data files, convert between naming systems, or perform ongoing maintenance of local copies of public databases. Opportunities for new ways of combining and re-using data are arising as a result of the increasing use of web protocols to transmit structured data. The Firegoose, an extension to the Mozilla Firefox web browser, enables data transfer between web sites and desktop tools. As a component of the Gaggle integration framework, Firegoose can also exchange data with Cytoscape, the R statistical package, Multiexperiment Viewer (MeV), and several other popular desktop software tools. Firegoose adds the capability to easily use local data to query KEGG, EMBL STRING, DAVID, and other widely-used bioinformatics web sites. Query results from these web sites can be transferred to desktop tools for further analysis with a few clicks. Firegoose acquires data from the web by screen scraping, microformats, embedded XML, or web services. We define a microformat, which allows structured information compatible with the Gaggle to be embedded in HTML documents. We demonstrate the capabilities of this software by performing an analysis of the genes activated in the microbe Halobacterium salinarum NRC-1 in response to anaerobic environments. Starting with microarray data, we explore functions of differentially expressed genes by combining data from several public web resources and construct an integrated view of the cellular processes involved. The Firegoose incorporates Mozilla Firefox into the Gaggle environment and enables interactive sharing of data between diverse web resources and desktop software tools without maintaining local copies. Additional web sites can be incorporated easily into the framework using the scripting platform of the Firefox browser. Performing data integration in the browser allows the excellent search and navigation capabilities of the browser to be used in combination with powerful desktop tools.

IBM techexplorer and MathML: Interactive Multimodal Scientific Documents

NASA Astrophysics Data System (ADS)

Diaz, Angel

2001-06-01

The World Wide Web provides a standard publishing platform for disseminating scientific and technical articles, books, journals, courseware, or even homework on the internet; however, the transition from paper to web-based interactive content has brought new opportunities for creating interactive content. Students, scientists, and engineers are now faced with the task of rendering the 2D presentational structure of mathematics, harnessing the wealth of scientific and technical software, and creating truly accessible scientific portals across international boundaries and markets. The recent emergence of World Wide Web Consortium (W3C) standards such as the Mathematical Markup Language (MathML), Language (XSL), and Aural CSS (ACSS) provide a foundation whereby mathematics can be displayed, enlivened, computed, and audio formatted. With interoperability ensured by standards, software applications can be easily brought together to create extensible and interactive scientific content. In this presentation we will provide an overview of the IBM techexplorer Hypermedia Browser, a web browser plug-in and ActiveX control aimed at bringing interactive mathematics to the masses across platforms and applications. We will demonstrate "live" mathematics where documents that contain MathML expressions can be edited and computed right inside your favorite web browser. This demonstration will be generalized as we show how MathML can be used to enliven even PowerPoint presentations. Finally, we will close the loop by demonstrating a novel approach to spoken mathematics based on MathML, DOM, XSL, ACSS, techexplorer, and IBM ViaVoice. By making use of techexplorer as the glue that binds the rendered content to the web browser, the back-end computation software, the Java applets that augment the exposition, and voice-rendering systems such as ViaVoice, authors can indeed create truly extensible and interactive scientific content. For more information see: [http://www.software.ibm.com/techexplorer] [http://www.alphaworks.ibm.com] [http://www.w3.org

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

WebGL for Rosetta Science Planning

NASA Astrophysics Data System (ADS)

Schmidt, Albrecht; Völk, Stefan; Grieger, Björn

2013-04-01

Rosetta is a mission of the European Space Agency (ESA) to rendez-vous with comet Churyumov-Gerasimenko in 2014. The trajectory and operations of the mission are particularly complex, have many free parameters and are novel to the community. To support science planning, communicate operational ideas and disseminate operational scenarios to the scientific community, the science ground segment makes use of Web-based visualisation technologies. Using the recent standard WebGL, static pages of time-dependent three-dimensional views of the spacecraft and the field-of-views of the instruments are generated, directly from the operational files. These can then be viewed in modern Web browsers for understanding or verification, be analysed and correlated with other studies. Variable timesteps make it possible to provide both overviews and detailed animated scenes. The technical challenges that are particular to Web-based environments include: (1) In traditional OpenGL, is much easier to compute needed data on demand since the visualisation runs natively on a usually quite powerful computer. In WebGL application, since requests for additional data have to be passed through a Web server, they are more complex and also require a more complex infrastructure. (2) The volume of data that can be kept in a browser environment is limited and has to be transferred over often slow network links. Thus, careful design and reduction of data is required. (3) Although browser support for WebGL has improved since the authors started using it, it is often not well supported on mobile and small devices. (4) Web browsers often only support limited end user interactions with a mouse or keyboards. While some of the challenges can be expected to become less important as technological progress continues, others seem to be more inherent to the approach. On the positive side, the authors' experiences include: (1) low threshold in the community to using the visualisations, (2), thus, cooperative use of the products, and (3) good and still improving tool and library support.

Taking advantage of HTML5 browsers to realize the concepts of session state and workflow sharing in web-tool applications

NASA Astrophysics Data System (ADS)

Suftin, I.; Read, J. S.; Walker, J.

2013-12-01

Scientists prefer not having to be tied down to a specific machine or operating system in order to analyze local and remote data sets or publish work. Increasingly, analysis has been migrating to decentralized web services and data sets, using web clients to provide the analysis interface. While simplifying workflow access, analysis, and publishing of data, the move does bring with it its own unique set of issues. Web clients used for analysis typically offer workflows geared towards a single user, with steps and results that are often difficult to recreate and share with others. Furthermore, workflow results often may not be easily used as input for further analysis. Older browsers further complicate things by having no way to maintain larger chunks of information, often offloading the job of storage to the back-end server or trying to squeeze it into a cookie. It has been difficult to provide a concept of "session storage" or "workflow sharing" without a complex orchestration of the back-end for storage depending on either a centralized file system or database. With the advent of HTML5, browsers gained the ability to store more information through the use of the Web Storage API (a browser-cookie holds a maximum of 4 kilobytes). Web Storage gives us the ability to store megabytes of arbitrary data in-browser either with an expiration date or just for a session. This allows scientists to create, update, persist and share their workflow without depending on the backend to store session information, providing the flexibility for new web-based workflows to emerge. In the DSASWeb portal ( http://cida.usgs.gov/DSASweb/ ), using these techniques, the representation of every step in the analyst's workflow is stored as plain-text serialized JSON, which we can generate as a text file and provide to the analyst as an upload. This file may then be shared with others and loaded back into the application, restoring the application to the state it was in when the session file was generated. A user may then view results produced during that session or go back and alter input parameters, creating new results and producing new, unique sessions which they can then again share. This technique not only provides independence for the user to manage their session as they like, but also allows much greater freedom for the application provider to scale out without having to worry about carrying over user information or maintaining it in a central location.

Adam: a Unix Desktop Application Manager

NASA Astrophysics Data System (ADS)

LiÉBana, M.; Marquina, M.; Ramos, R.

ADAM stands for Affordable Desktop Application Manager. It is a GUI developed at CERN with the aim to ease access to applications. The motivation to develop ADAM came from the unavailability of environments like COSE/CDE and their heavy resource consumption. ADAM has proven to be user friendly: new users are able to customize it to their needs in few minutes. Groups of users may share through ADAM a common application environment. ADAM also integrates the Unix and the PC world. PC users can access Unix applications in the same way as their usual Windows applications. This paper describes all the ADAM features, how they are used at CERN Public Services, and the future plans for ADAM.

Eyes on the Earth 3D

NASA Technical Reports Server (NTRS)

Kulikov, anton I.; Doronila, Paul R.; Nguyen, Viet T.; Jackson, Randal K.; Greene, William M.; Hussey, Kevin J.; Garcia, Christopher M.; Lopez, Christian A.

2013-01-01

Eyes on the Earth 3D software gives scientists, and the general public, a realtime, 3D interactive means of accurately viewing the real-time locations, speed, and values of recently collected data from several of NASA's Earth Observing Satellites using a standard Web browser (climate.nasa.gov/eyes). Anyone with Web access can use this software to see where the NASA fleet of these satellites is now, or where they will be up to a year in the future. The software also displays several Earth Science Data sets that have been collected on a daily basis. This application uses a third-party, 3D, realtime, interactive game engine called Unity 3D to visualize the satellites and is accessible from a Web browser.

Web-phreeq: a WWW instructional tool for modeling the distribution of chemical species in water

NASA Astrophysics Data System (ADS)

Saini-Eidukat, Bernhardt; Yahin, Andrew

1999-05-01

A WWW-based tool, WEB-PHREEQ, was developed for classroom teaching and for routine calculation of low temperature aqueous speciation. Accessible with any computer that has an internet-connected forms-capable WWW-browser, WEB-PHREEQ provides user interface and other support for modeling, creates a properly formatted input file, passes it to the public domain program PHREEQC and returns the output to the WWW browser. Users can calculate the equilibrium speciation of a solution over a range of temperatures or can react solid minerals or gases with a particular water and examine the resulting chemistry. WEB-PHREEQ is one of a number of interactive distributed-computing programs available on the WWW that are of interest to geoscientists.

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

Write, read and answer emails with a dry 'n' wireless brain-computer interface system.

PubMed

Pinegger, Andreas; Deckert, Lisa; Halder, Sebastian; Barry, Norbert; Faller, Josef; Käthner, Ivo; Hintermüller, Christoph; Wriessnegger, Selina C; Kübler, Andrea; Müller-Putz, Gernot R

2014-01-01

Brain-computer interface (BCI) users can control very complex applications such as multimedia players or even web browsers. Therefore, different biosignal acquisition systems are available to noninvasively measure the electrical activity of the brain, the electroencephalogram (EEG). To make BCIs more practical, hardware and software are nowadays designed more user centered and user friendly. In this paper we evaluated one of the latest innovations in the area of BCI: A wireless EEG amplifier with dry electrode technology combined with a web browser which enables BCI users to use standard webmail. With this system ten volunteers performed a daily life task: Write, read and answer an email. Experimental results of this study demonstrate the power of the introduced BCI system.

Virtual Earth System Laboratory (VESL): A Virtual Research Environment for The Visualization of Earth System Data and Process Simulations

NASA Astrophysics Data System (ADS)

Cheng, D. L. C.; Quinn, J. D.; Larour, E. Y.; Halkides, D. J.

2017-12-01

The Virtual Earth System Laboratory (VESL) is a Web application, under continued development at the Jet Propulsion Laboratory and UC Irvine, for the visualization of Earth System data and process simulations. As with any project of its size, we have encountered both successes and challenges during the course of development. Our principal point of success is the fact that VESL users can interact seamlessly with our earth science simulations within their own Web browser. Some of the challenges we have faced include retrofitting the VESL Web application to respond to touch gestures, reducing page load time (especially as the application has grown), and accounting for the differences between the various Web browsers and computing platforms.

nodeGame: Real-time, synchronous, online experiments in the browser.

PubMed

Balietti, Stefano

2017-10-01

nodeGame is a free, open-source JavaScript/ HTML5 framework for conducting synchronous experiments online and in the lab directly in the browser window. It is specifically designed to support behavioral research along three dimensions: (i) larger group sizes, (ii) real-time (but also discrete time) experiments, and (iii) batches of simultaneous experiments. nodeGame has a modular source code, and defines an API (application programming interface) through which experimenters can create new strategic environments and configure the platform. With zero-install, nodeGame can run on a great variety of devices, from desktop computers to laptops, smartphones, and tablets. The current version of the software is 3.0, and extensive documentation is available on the wiki pages at http://nodegame.org .

Engineering the ATLAS TAG Browser

NASA Astrophysics Data System (ADS)

Zhang, Qizhi; ATLAS Collaboration

2011-12-01

ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services are discussed. We also describe strategies for dealing with data that may vary over time, such as run-dependent trigger decision decoding. Along with examples, we illustrate how programming techniques in multiple languages (PHP, JAVASCRIPT, XML, AJAX, and PL/SQL) have been blended to achieve the required results. Finally, we evaluate features of the ELSSI service in terms of functionality, scalability, and performance.

Towards Artificial Speech Therapy: A Neural System for Impaired Speech Segmentation.

PubMed

Iliya, Sunday; Neri, Ferrante

2016-09-01

This paper presents a neural system-based technique for segmenting short impaired speech utterances into silent, unvoiced, and voiced sections. Moreover, the proposed technique identifies those points of the (voiced) speech where the spectrum becomes steady. The resulting technique thus aims at detecting that limited section of the speech which contains the information about the potential impairment of the speech. This section is of interest to the speech therapist as it corresponds to the possibly incorrect movements of speech organs (lower lip and tongue with respect to the vocal tract). Two segmentation models to detect and identify the various sections of the disordered (impaired) speech signals have been developed and compared. The first makes use of a combination of four artificial neural networks. The second is based on a support vector machine (SVM). The SVM has been trained by means of an ad hoc nested algorithm whose outer layer is a metaheuristic while the inner layer is a convex optimization algorithm. Several metaheuristics have been tested and compared leading to the conclusion that some variants of the compact differential evolution (CDE) algorithm appears to be well-suited to address this problem. Numerical results show that the SVM model with a radial basis function is capable of effective detection of the portion of speech that is of interest to a therapist. The best performance has been achieved when the system is trained by the nested algorithm whose outer layer is hybrid-population-based/CDE. A population-based approach displays the best performance for the isolation of silence/noise sections, and the detection of unvoiced sections. On the other hand, a compact approach appears to be clearly well-suited to detect the beginning of the steady state of the voiced signal. Both the proposed segmentation models display outperformed two modern segmentation techniques based on Gaussian mixture model and deep learning.

SELF BLOOD GLUCOSE MONITORING UNDERESTIMATES HYPERGLYCEMIA AND HYPOGLYCEMIA AS COMPARED TO CONTINUOUS GLUCOSE MONITORING IN TYPE 1 AND TYPE 2 DIABETES.

PubMed

Mangrola, Devna; Cox, Christine; Furman, Arianne S; Krishnan, Sridevi; Karakas, Sidika E

2018-01-01

When glucose records from self blood glucose monitoring (SBGM) do not reflect estimated average glucose from glycosylated hemoglobin (HgBA1) or when patients' clinical symptoms are not explained by their SBGM records, clinical management of diabetes becomes a challenge. Our objective was to determine the magnitude of differences in glucose values reported by SBGM versus those documented by continuous glucose monitoring (CGM). The CGM was conducted by a clinical diabetes educator (CDE)/registered nurse by the clinic protocol, using the Medtronic iPRO2 ™ system. Patients continued SBGM and managed their diabetes without any change. Data from 4 full days were obtained, and relevant clinical information was recorded. De-identified data sets were provided to the investigators. Data from 61 patients, 27 with type 1 diabetes (T1DM) and 34 with T2DM were analyzed. The lowest, highest, and average glucose recorded by SBGM were compared to the corresponding values from CGM. The lowest glucose values reported by SBGM were approximately 25 mg/dL higher in both T1DM ( P = .0232) and T2DM ( P = .0003). The highest glucose values by SBGM were approximately 30 mg/dL lower in T1DM ( P = .0005) and 55 mg/dL lower in T2DM ( P<.0001). HgBA1c correlated with the highest and average glucose by SBGM and CGM. The lowest glucose values were seen most frequently during sleep and before breakfast; the highest were seen during the evening and postprandially. SBGM accurately estimates the average glucose but underestimates glucose excursions. CGM uncovers glucose patterns that common SBGM patterns cannot. CDE = certified diabetes educator; CGM = continuous glucose monitoring; HgBA1c = glycosylated hemoglobin; MAD = mean absolute difference; SBGM = self blood glucose monitoring; T1DM = type 1 diabetes; T2DM = type 2 diabetes.

The Sinorhizobium fredii HH103 Lipopolysaccharide Is Not Only Relevant at Early Soybean Nodulation Stages but Also for Symbiosome Stability in Mature Nodules

PubMed Central

Margaret, Isabel; Lucas, M. Mercedes; Acosta-Jurado, Sebastián; Buendía-Clavería, Ana M.; Fedorova, Elena; Hidalgo, Ángeles; Rodríguez-Carvajal, Miguel A.; Rodriguez-Navarro, Dulce N.; Ruiz-Sainz, José E.; Vinardell, José M.

2013-01-01

In this work we have characterised the Sinorhizobium fredii HH103 greA lpsB lpsCDE genetic region and analysed for the first time the symbiotic performance of Sinorhizobium fredii lps mutants on soybean. The organization of the S. fredii HH103 greA, lpsB, and lpsCDE genes was equal to that of Sinorhizobium meliloti 1021. S. fredii HH103 greA, lpsB, and lpsE mutant derivatives produced altered LPS profiles that were characteristic of the gene mutated. In addition, S. fredii HH103 greA mutants showed a reduction in bacterial mobility and an increase of auto-agglutination in liquid cultures. RT-PCR and qPCR experiments demonstrated that the HH103 greA gene has a positive effect on the transcription of lpsB. Soybean plants inoculated with HH103 greA, lpsB or lpsE mutants formed numerous ineffective pseudonodules and showed severe symptoms of nitrogen starvation. However, HH103 greA and lps mutants were also able to induce the formation of a reduced number of soybean nodules of normal external morphology, allowing the possibility of studying the importance of bacterial LPS in later stages of the S. fredii HH103-soybean symbiosis. The infected cells of these nodules showed signs of early termination of symbiosis and lytical clearance of bacteroids. These cells also had very thick walls and accumulation of phenolic-like compounds, pointing to induced defense reactions. Our results show the importance of bacterial LPS in later stages of the S. fredii HH103-soybean symbiosis and their role in preventing host cell defense reactions. S. fredii HH103 lpsB mutants also showed reduced nodulation with Vigna unguiculata, although the symbiotic impairment was less pronounced than in soybean. PMID:24098345

Intraoperative performance and postoperative outcomes of microcoaxial phacoemulsification. Observational study.

PubMed

Vasavada, Viraj; Vasavada, Vaishali; Raj, Shetal M; Vasavada, Abhay R

2007-06-01

To evaluate the intraoperative performance and postoperative outcomes after microcoaxial phacoemulsification. Iladevi Cataract & IOL Research Centre, Ahmedabad, India. A prospective observational case series comprised 84 eyes with age-related uncomplicated cataract having microcoaxial phacoemulsification through a 2.2 mm clear corneal incision by a standard surgical technique. Phacoemulsification parameters (Infiniti Vision System, Alcon) were microburst width, 30 ms; preset power, 50%; vacuum, 650 mm Hg; aspiration flow rate, 25 cc/minute. A single-piece Alcon AcrySof intraocular lens was implanted with the C cartridge (Alcon) cartridge. The incision was measured at the end of surgery. Observations included surgical time (from commencement of sculpting to end of epinucleus removal), cumulative dissipated energy (CDE), wound burns, intraoperative complications, postoperative increase in mean central corneal thickness (CCT) at 1 day and 1 month, mean % decrease in endothelial cell density (ECD), absolute mean change in coefficient of variation (cv) 3 months, and uncorrected visual acuity (UCVA) at 1 day. Data were analyzed using a 1-sample t test with 95% confidence intervals (CIs). The mean follow up was 3 months +/- 0.3 (SD). The mean incision size at the end of surgery was 2.3 +/- .09 mm; mean surgical time, 4.5 +/- 1.5 minutes; and mean CDE, 2.3 +/- 2.2 seconds. No wound burns or other intraoperative complications occurred. The postoperative CCT increased by a mean of 16 microm at 1 day (95% CI, 8-25; P = .66;) and by a mean of 3.14 microm at 1 month (95% CI, 2.26-4.05; P = .92). The ECD decreased by a mean of 5.8% (95% CI, 6.8-3.5; P = .82) and the mean coefficient of variation, by 3.3 (95% CI, 4.5-2.0; P = .65). At 1 day, the UCVA was 20/20 in 29% of cases, 20/20 to 20/40 in 58%, and 20/40 to 20/50 in 12%. Microcoaxial phacoemulsification was safely and effectively performed, achieving consistent and satisfactory postoperative outcomes.

Pore-scale dynamics of salt transport and distribution in drying porous media

NASA Astrophysics Data System (ADS)

Shokri, Nima

2014-01-01

Understanding the physics of water evaporation from saline porous media is important in many natural and engineering applications such as durability of building materials and preservation of monuments, water quality, and mineral-fluid interactions. We applied synchrotron x-ray micro-tomography to investigate the pore-scale dynamics of dissolved salt distribution in a three dimensional drying saline porous media using a cylindrical plastic column (15 mm in height and 8 mm in diameter) packed with sand particles saturated with CaI2 solution (5% concentration by mass) with a spatial and temporal resolution of 12 μm and 30 min, respectively. Every time the drying sand column was set to be imaged, two different images were recorded using distinct synchrotron x-rays energies immediately above and below the K-edge value of Iodine. Taking the difference between pixel gray values enabled us to delineate the spatial and temporal distribution of CaI2 concentration at pore scale. Results indicate that during early stages of evaporation, air preferentially invades large pores at the surface while finer pores remain saturated and connected to the wet zone at bottom via capillary-induced liquid flow acting as evaporating spots. Consequently, the salt concentration increases preferentially in finer pores where evaporation occurs. Higher salt concentration was observed close to the evaporating surface indicating a convection-driven process. The obtained salt profiles were used to evaluate the numerical solution of the convection-diffusion equation (CDE). Results show that the macro-scale CDE could capture the overall trend of the measured salt profiles but fail to produce the exact slope of the profiles. Our results shed new insight on the physics of salt transport and its complex dynamics in drying porous media and establish synchrotron x-ray tomography as an effective tool to investigate the dynamics of salt transport in porous media at high spatial and temporal resolution.

Striving for the impossible dream: a community-based multi-practice collaborative model of diabetes management.

PubMed

Distiller, L A; Brown, M A; Joffe, B I; Kramer, B D

2010-02-01

In 1994 the Centre for Diabetes and Endocrinology (CDE) based in Johannesburg, South Africa established a novel community-based capitation and risk-sharing model for diabetes management. We here describe the model and present a recent survey of the performance/outcomes of this unique diabetes care programme. Data on 17 043 patients managed by the CDE Diabetes Management Programme at its Centre and its 262 affiliated Centres were analysed from its national database. From this total cohort, 1520 Type 1 and 8026 Type 2 diabetes patients have been in the Programme for > 5 years. The 5-year outcome data on hospital admission rates, glycaemic control (HbA(1c)), and microvascular complication rates were assessed in this subgroup of patients. Major reductions in hospital admission rates for both acute metabolic emergencies and all causes (40% overall) were achieved in patients enrolled onto the Diabetes Management Programme. The mean HBA(1c) on enrolment was 9.2% for subjects with Type 1 and 8.8% for those with Type 2 diabetes. After 1 year, mean HbA(1c) fell to 7.6% and 7.3% for the Type 1 and Type 2 subjects, respectively. At 5 years the HbA(1c) remained similar at 7.7% for the Type 1 subjects and 7.4% for the Type 2 subjects, demonstrating sustained improvement. Progression of microvascular complications appears to have been delayed. This managed care model of diabetes care in the context of the South African Private Health Care System achieved long-term improvement in glycaemic control and all-cause hospital admission rates. This may be due to the cost-containment being in the hands of the treating doctor, supported by an annual training programme. This programme is based on an individualized and holistic approach encompassing intensive patient education to facilitate self-empowerment and including prompting for the management of risk factors.

Pore-scale dynamics of salt transport and distribution in drying porous media

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

Shokri, Nima, E-mail: nima.shokri@manchester.ac.uk

2014-01-15

Understanding the physics of water evaporation from saline porous media is important in many natural and engineering applications such as durability of building materials and preservation of monuments, water quality, and mineral-fluid interactions. We applied synchrotron x-ray micro-tomography to investigate the pore-scale dynamics of dissolved salt distribution in a three dimensional drying saline porous media using a cylindrical plastic column (15 mm in height and 8 mm in diameter) packed with sand particles saturated with CaI{sub 2} solution (5% concentration by mass) with a spatial and temporal resolution of 12 μm and 30 min, respectively. Every time the drying sandmore » column was set to be imaged, two different images were recorded using distinct synchrotron x-rays energies immediately above and below the K-edge value of Iodine. Taking the difference between pixel gray values enabled us to delineate the spatial and temporal distribution of CaI{sub 2} concentration at pore scale. Results indicate that during early stages of evaporation, air preferentially invades large pores at the surface while finer pores remain saturated and connected to the wet zone at bottom via capillary-induced liquid flow acting as evaporating spots. Consequently, the salt concentration increases preferentially in finer pores where evaporation occurs. Higher salt concentration was observed close to the evaporating surface indicating a convection-driven process. The obtained salt profiles were used to evaluate the numerical solution of the convection-diffusion equation (CDE). Results show that the macro-scale CDE could capture the overall trend of the measured salt profiles but fail to produce the exact slope of the profiles. Our results shed new insight on the physics of salt transport and its complex dynamics in drying porous media and establish synchrotron x-ray tomography as an effective tool to investigate the dynamics of salt transport in porous media at high spatial and temporal resolution.« less

Unexpected suppression of anti-Fya and prevention of hemolytic disease of the fetus and newborn after administration of Rh immune globulin.

PubMed

Branch, Donald R; Scofield, Terry L; Moulds, John J; Swanson, Jane L

2011-04-01

Rh immune globulin (RhIG) has been used successfully for many years for the antenatal suppression of anti-D in D- mothers carrying D+ babies to prevent hemolytic disease of the fetus and newborn. Although the mechanism of RhIG-induced immunosuppression remains unknown, a recent report (TRANSFUSION 2006;46:1316-22) has shown that women receiving RhIG produce elevated levels of transforming growth factor (TGF)β-1, a powerful immunosuppressant cytokine. It was suggested that induction of TGFβ-1 and immunosuppression may be independent of cognate antigen recognition by RhIG. Herein, we present a description of a mother and baby that supports this hypothesis. Red blood cells and serum were analyzed using saline-tube indirect antiglobulin test methods. RhIG (RhoGAM) was administered after each amniocentesis performed at 28, 31, and 36 weeks' gestation. A group A, D-(cde), K+, Fy(a-b+), MNs, Jk(a+b+) mother with no detectable anti-D had an anti-Fy(a) titer of 4096 before RhIG but only 256 after RhIG. Mother gave birth to a group O, D-(cde), Fy(a+b+) healthy baby boy having a weak-positive direct antiglobulin test with anti-Fy(a) eluted from his cells and the titer in the cord serum was 4. This case demonstrates the potential immunosuppressive properties of RhIG for down regulation of a possible clinically significant alloantibody, not anti-D, where no D+ antigen is in the circulation of the mother. The case illustrates the potential utility for using RhIG to modulate antibody levels in situations other than for classical suppression of anti-D production. Although the mechanism in this case is unknown, TGFβ-1-mediated or antibody-mediated immunosuppression to soluble nonparticulate antigens are possible mechanisms. © 2010 American Association of Blood Banks.

Principle of Parsimony, Fake Science, and Scales

NASA Astrophysics Data System (ADS)

Yeh, T. C. J.; Wan, L.; Wang, X. S.

2017-12-01

Considering difficulties in predicting exact motions of water molecules, and the scale of our interests (bulk behaviors of many molecules), Fick's law (diffusion concept) has been created to predict solute diffusion process in space and time. G.I. Taylor (1921) demonstrated that random motion of the molecules reach the Fickian regime in less a second if our sampling scale is large enough to reach ergodic condition. Fick's law is widely accepted for describing molecular diffusion as such. This fits the definition of the parsimony principle at the scale of our concern. Similarly, advection-dispersion or convection-dispersion equation (ADE or CDE) has been found quite satisfactory for analysis of concentration breakthroughs of solute transport in uniformly packed soil columns. This is attributed to the solute is often released over the entire cross-section of the column, which has sampled many pore-scale heterogeneities and met the ergodicity assumption. Further, the uniformly packed column contains a large number of stationary pore-size heterogeneity. The solute thus reaches the Fickian regime after traveling a short distance along the column. Moreover, breakthrough curves are concentrations integrated over the column cross-section (the scale of our interest), and they meet the ergodicity assumption embedded in the ADE and CDE. To the contrary, scales of heterogeneity in most groundwater pollution problems evolve as contaminants travel. They are much larger than the scale of our observations and our interests so that the ergodic and the Fickian conditions are difficult. Upscaling the Fick's law for solution dispersion, and deriving universal rules of the dispersion to the field- or basin-scale pollution migrations are merely misuse of the parsimony principle and lead to a fake science ( i.e., the development of theories for predicting processes that can not be observed.) The appropriate principle of parsimony for these situations dictates mapping of large-scale heterogeneities as detailed as possible and adapting the Fick's law for effects of small-scale heterogeneity resulting from our inability to characterize them in detail.

HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants.

PubMed

Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming

2016-03-11

Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are located in the non-protein coding regions, and therefore it is challenging to hypothesize the functions of these non-coding GWAS variants. Recent large efforts such as the ENCODE and Roadmap Epigenomics projects have predicted a large number of regulatory elements. However, the target genes of these regulatory elements remain largely unknown. Chromatin conformation capture based technologies such as Hi-C can directly measure the chromatin interactions and have generated an increasingly comprehensive catalog of the interactome between the distal regulatory elements and their potential target genes. Leveraging such information revealed by Hi-C holds the promise of elucidating the functions of genetic variants in human diseases. In this work, we present HiView, the first integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. HiView is able to display Hi-C data and statistical evidence for chromatin interactions in genomic regions surrounding any given GWAS variant, enabling straightforward visualization and interpretation. We believe that as the first GWAS variants-centered Hi-C genome browser, HiView is a useful tool guiding post-GWAS functional genomics studies. HiView is freely accessible at: http://www.unc.edu/~yunmli/HiView .

LightWAVE: Waveform and Annotation Viewing and Editing in a Web Browser.

PubMed

Moody, George B

2013-09-01

This paper describes LightWAVE, recently-developed open-source software for viewing ECGs and other physiologic waveforms and associated annotations (event markers). It supports efficient interactive creation and modification of annotations, capabilities that are essential for building new collections of physiologic signals and time series for research. LightWAVE is constructed of components that interact in simple ways, making it straightforward to enhance or replace any of them. The back end (server) is a common gateway interface (CGI) application written in C for speed and efficiency. It retrieves data from its data repository (PhysioNet's open-access PhysioBank archives by default, or any set of files or web pages structured as in PhysioBank) and delivers them in response to requests generated by the front end. The front end (client) is a web application written in JavaScript. It runs within any modern web browser and does not require installation on the user's computer, tablet, or phone. Finally, LightWAVE's scribe is a tiny CGI application written in Perl, which records the user's edits in annotation files. LightWAVE's data repository, back end, and front end can be located on the same computer or on separate computers. The data repository may be split across multiple computers. For compatibility with the standard browser security model, the front end and the scribe must be loaded from the same domain.

Introduction to the fathead minnow genome browser and ...

EPA Pesticide Factsheets

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minnow genomic sequence. This work is meant to extend the utility of fathead minnow genome as a resource and enable the continued development of this species as a model organism. The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporti

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

ChemBrowser: a flexible framework for mining chemical documents.

PubMed

Wu, Xian; Zhang, Li; Chen, Ying; Rhodes, James; Griffin, Thomas D; Boyer, Stephen K; Alba, Alfredo; Cai, Keke

2010-01-01

The ability to extract chemical and biological entities and relations from text documents automatically has great value to biochemical research and development activities. The growing maturity of text mining and artificial intelligence technologies shows promise in enabling such automatic chemical entity extraction capabilities (called "Chemical Annotation" in this paper). Many techniques have been reported in the literature, ranging from dictionary and rule-based techniques to machine learning approaches. In practice, we found that no single technique works well in all cases. A combinatorial approach that allows one to quickly compose different annotation techniques together for a given situation is most effective. In this paper, we describe the key challenges we face in real-world chemical annotation scenarios. We then present a solution called ChemBrowser which has a flexible framework for chemical annotation. ChemBrowser includes a suite of customizable processing units that might be utilized in a chemical annotator, a high-level language that describes the composition of various processing units that would form a chemical annotator, and an execution engine that translates the composition language to an actual annotator that can generate annotation results for a given set of documents. We demonstrate the impact of this approach by tailoring an annotator for extracting chemical names from patent documents and show how this annotator can be easily modified with simple configuration alone.

Long-Term Exposure to Silica Dust and Risk of Total and Cause-Specific Mortality in Chinese Workers: A Cohort Study

PubMed Central

Chen, Weihong; Liu, Yuewei; Wang, Haijiao; Hnizdo, Eva; Sun, Yi; Su, Liangping; Zhang, Xiaokang; Weng, Shaofan; Bochmann, Frank; Hearl, Frank J.; Chen, Jingqiong; Wu, Tangchun

2012-01-01

Background Human exposure to silica dust is very common in both working and living environments. However, the potential long-term health effects have not been well established across different exposure situations. Methods and Findings We studied 74,040 workers who worked at 29 metal mines and pottery factories in China for 1 y or more between January 1, 1960, and December 31, 1974, with follow-up until December 31, 2003 (median follow-up of 33 y). We estimated the cumulative silica dust exposure (CDE) for each worker by linking work history to a job–exposure matrix. We calculated standardized mortality ratios for underlying causes of death based on Chinese national mortality rates. Hazard ratios (HRs) for selected causes of death associated with CDE were estimated using the Cox proportional hazards model. The population attributable risks were estimated based on the prevalence of workers with silica dust exposure and HRs. The number of deaths attributable to silica dust exposure among Chinese workers was then calculated using the population attributable risk and the national mortality rate. We observed 19,516 deaths during 2,306,428 person-years of follow-up. Mortality from all causes was higher among workers exposed to silica dust than among non-exposed workers (993 versus 551 per 100,000 person-years). We observed significant positive exposure–response relationships between CDE (measured in milligrams/cubic meter–years, i.e., the sum of silica dust concentrations multiplied by the years of silica exposure) and mortality from all causes (HR 1.026, 95% confidence interval 1.023–1.029), respiratory diseases (1.069, 1.064–1.074), respiratory tuberculosis (1.065, 1.059–1.071), and cardiovascular disease (1.031, 1.025–1.036). Significantly elevated standardized mortality ratios were observed for all causes (1.06, 95% confidence interval 1.01–1.11), ischemic heart disease (1.65, 1.35–1.99), and pneumoconiosis (11.01, 7.67–14.95) among workers exposed to respirable silica concentrations equal to or lower than 0.1 mg/m3. After adjustment for potential confounders, including smoking, silica dust exposure accounted for 15.2% of all deaths in this study. We estimated that 4.2% of deaths (231,104 cases) among Chinese workers were attributable to silica dust exposure. The limitations of this study included a lack of data on dietary patterns and leisure time physical activity, possible underestimation of silica dust exposure for individuals who worked at the mines/factories before 1950, and a small number of deaths (4.3%) where the cause of death was based on oral reports from relatives. Conclusions Long-term silica dust exposure was associated with substantially increased mortality among Chinese workers. The increased risk was observed not only for deaths due to respiratory diseases and lung cancer, but also for deaths due to cardiovascular disease. Please see later in the article for the Editors' Summary PMID:22529751

[Condition of neurohumoral regulation of bronchial tone and gallbladder in patients with chronic cholecystitis and chronic obstructive pulmonary disease].

PubMed

Dudka, T V; Khukhlina, O S; Dudka, I V

2014-01-01

SUMMARY The paper presents data from a study of the neuroendocrine regulation of nonstriated muscles, bronchial tree and the gallbladder tones by means of an assessment of the adrenergic and cholinergic systems state in patients, suffering from chronic obstructive pulmonary disease and chronic acalculous cholecystitis. Adrenergic and cholinergic activities as well as cortisol secretion have significantly changed. To study the features of adrenergic and cholinergic regulations of bronchial tone and that of the gallbladder in patients with combined course of chronic acalculous cholecystitis and chronic obstructive pulmonary disease. 92 patients were involved in the study: 30 patients with COPD (1st group), 30 patients with COPD of comorbid CAC in the acute phase (2nd group), 32 patients with CAC in the acute phase (3rd group) and a control group--30 practically healthy individuals (PHI) of the respective age. All the patients with COPD and COPD combined with CAC had a marked predominance of the parasympathetic nervous system, as evidenced by the established significant decrease of CDE (Table) in patients with isolated COPD is 1.4 times (p < 0.05), in patients with COPD combined with CAC--there was more intense inhibition of enzyme activity--in 1.8 times (p < 0.05) and in patients with CAC of the 3rd group there were identical changes--a decreased activity of CDE in 1.6 times (p < 0.05) with significant intergroup differences between the groups (p < 0.05). An analysis of the studies showed significant changes in the CDE of the surveyed individuals. For instance, the CDA in the individuals of groups 1 and 2 was lower by 1.6 and 2.4 times respectively (p < 0.001) than in the group of PHI; in the patients of the 3rd group--the changes were minor--a decline of 14.6% (p < 0.05) compared with practically healthy individuals (Table). Participation of sympathoadrenal system in the pathogenesis of COPD occurrence has been proved, however, in patients with COPD and CAC, the ability to deposit CA, when combined with CAC has significantly dropped. The study of cortisol density in the blood serum of the patients under examination showed its significant drop in all groups observed. For instance, the first group patients' blood contained 2.7 times (p < 0.05) less cortisol than that of PHI; in the patients of the second group the inhibition of the functional state of the adrenal cortex was even more intense--cortisol was lower than its index in the control group by 3.7 times (p < 0.05); the 3d group patients had the maximum drop in cortisol secretion by 1.7 times (p < 0.05) with reliable intergroup difference. The base of regulatory neuroendocrine and paracrine mecganisms imbalance, contributing to a development of COPD, is the cholinergic imbalance (reduction in blood acetylcholinesterase activity, hypertensive sphincter of Oddi dysfunction), adrenergic imbalance, reduction in catecholamine-depositing erythrocytes function, hypokinetic gallbladder dysfunction, adrenal dysfunction (decreased cortisol levels) that contribute to the development and progression of chronic cholecystitis against a background of hypokinetic gallbladder dysfunction.

Brisement

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Subtalar Arthroscopy

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Peroneal Tendinosis

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Ankle Cheilectomy

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Disobedient Child

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Turn ... some disobedient children, you may need to obtain professional mental health treatment. Here are some situations where ...

Distraction Arthroplasty

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Pediatric Specialists

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Turn ... for Referral to Pediatric Surgical Specialists Sports Medicine Professionals What is a Child Abuse Pediatrician? What is ...

Virginia Natural Heritage Program

Science.gov Websites

Heritage About Natural Heritage Overview, Mission Natural Heritage Inventory Community Ecology Program ) | Strategic Plan (PDF) | Executive Progress Report (PDF) | Code of Ethics (PDF) Your browser does not support

The Cadmio XML healthcare record.

PubMed

Barbera, Francesco; Ferri, Fernando; Ricci, Fabrizio L; Sottile, Pier Angelo

2002-01-01

The management of clinical data is a complex task. Patient related information reported in patient folders is a set of heterogeneous and structured data accessed by different users having different goals (in local or geographical networks). XML language provides a mechanism for describing, manipulating, and visualising structured data in web-based applications. XML ensures that the structured data is managed in a uniform and transparent manner independently from the applications and their providers guaranteeing some interoperability. Extracting data from the healthcare record and structuring them according to XML makes the data available through browsers. The MIC/MIE model (Medical Information Category/Medical Information Elements), which allows the definition and management of healthcare records and used in CADMIO, a HISA based project, is described in this paper, using XML for allowing the data to be visualised through web browsers.

VisPort: Web-Based Access to Community-Specific Visualization Functionality [Shedding New Light on Exploding Stars: Visualization for TeraScale Simulation of Neutrino-Driven Supernovae (Final Technical Report)

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

Baker, M Pauline

2007-06-30

The VisPort visualization portal is an experiment in providing Web-based access to visualization functionality from any place and at any time. VisPort adopts a service-oriented architecture to encapsulate visualization functionality and to support remote access. Users employ browser-based client applications to choose data and services, set parameters, and launch visualization jobs. Visualization products typically images or movies are viewed in the user's standard Web browser. VisPort emphasizes visualization solutions customized for specific application communities. Finally, VisPort relies heavily on XML, and introduces the notion of visualization informatics - the formalization and specialization of information related to the process and productsmore » of visualization.« less

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

PubMed Central

Milreu, Paulo Vieira; Klein, Cecilia Coimbra; Cottret, Ludovic; Acuña, Vicente; Birmelé, Etienne; Borassi, Michele; Junot, Christophe; Marchetti-Spaccamela, Alberto; Marino, Andrea; Stougie, Leen; Jourdan, Fabien; Crescenzi, Pierluigi; Lacroix, Vincent; Sagot, Marie-France

2014-01-01

Motivation: The increasing availability of metabolomics data enables to better understand the metabolic processes involved in the immediate response of an organism to environmental changes and stress. The data usually come in the form of a list of metabolites whose concentrations significantly changed under some conditions, and are thus not easy to interpret without being able to precisely visualize how such metabolites are interconnected. Results: We present a method that enables to organize the data from any metabolomics experiment into metabolic stories. Each story corresponds to a possible scenario explaining the flow of matter between the metabolites of interest. These scenarios may then be ranked in different ways depending on which interpretation one wishes to emphasize for the causal link between two affected metabolites: enzyme activation, enzyme inhibition or domino effect on the concentration changes of substrates and products. Equally probable stories under any selected ranking scheme can be further grouped into a single anthology that summarizes, in a unique subnetwork, all equivalently plausible alternative stories. An anthology is simply a union of such stories. We detail an application of the method to the response of yeast to cadmium exposure. We use this system as a proof of concept for our method, and we show that we are able to find a story that reproduces very well the current knowledge about the yeast response to cadmium. We further show that this response is mostly based on enzyme activation. We also provide a framework for exploring the alternative pathways or side effects this local response is expected to have in the rest of the network. We discuss several interpretations for the changes we see, and we suggest hypotheses that could in principle be experimentally tested. Noticeably, our method requires simple input data and could be used in a wide variety of applications. Availability and implementation: The code for the method presented in this article is available at http://gobbolino.gforge.inria.fr. Contact: pvmilreu@gmail.com; vincent.lacroix@univ-lyon1.fr; marie-france.sagot@inria.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24167155

Utilizing multisource remotely sensed data to dynamically monitor drought in China

NASA Astrophysics Data System (ADS)

Liu, Sanchao; Li, Wenbo

2011-12-01

Drought is one of major nature disaster in the world and China. China has a vast territory and very different spatio-temporal distribution weather condition. Therefore, drought disasters occur frequently throughout China, which may affect large areas and cause great economic loss every year. In this paper, geostationary meteorological remote sensing data, FY-2C/D/E VISSR and three quantitative remotely sensed models including Cloud Parameters Method (CPM), Vegetation Supply Water Index (VSWI), and Temperature Vegetation Dryness Index (TVDI) have been used to dynamically monitor severe drought in southwest China from 2009 to 2010. The results have effectively revealed the occurrence, development and disappearance of this drought event. The monitoring results can be used for the relevant disaster management departments' decision-making works.

Finite Element Program for Calculating Flows in Turbomachines with Results for NASA Task-1 Compressor.

DTIC Science & Technology

1982-10-01

CR !PT Jr,4 CF THE FUPEP ELiAEN5 + f ,, 4, S**444444**44*4*4*444++ 44 4.+414++++++4++ + +++4+++44 f 44*4* ++ +444. + 172 FILE: IdES!’ GEN FC4TRAN Al...CLCC-(-"II e(1) 21...X’) STE’T ST’ICT *SSICT 179 FILE: PESI- GEN FCRTPAN Al NAVNL POSTGRAOLATE SCHO󈧣 70C CCITTNJUE P~lUPN C *****+*+*+4*+ *.4+..*4.4...PEtC IN fCCiNFC7Iv1TY IPATP:X, Lr..%L NdCDE NLVhJ3E S STAPT AT ELVEPTIS i.;PIi iR!G~e r~ fANC LC,.% IND) TAV -QSi Mih. C REIC IN 11-E FLEPOENT TypE

Early Direct Imaging and Spectral Characterization of Extrasolar Planets with the SCExAO/CHARIS

NASA Astrophysics Data System (ADS)

Currie, Thayne; Guyon, Olivier; Kasdin, Jeremy; Brandt, Timothy; Groff, Tyler; Jovanovic, Nemanja; Lozi, Julien; Chilcote, Jeffrey K.; Uyama, Taichi; Ascensio-Torres, Ruben; Tamura, Motohide; Norris, Barnaby

2018-01-01

We present selected direct imaging/spectroscopy results from Subaru’s extreme adaptive optics system, SCExAO, coupled with the CHARIS integral field spectrograph obtained from the first full year of CHARIS’s operation. SCExAO/CHARIS yields high signal-to-noise detections and 1.1—2.4 micron spectra of benchmark directly-imaged companions like HR 8799 cde and kappa And b that clarify their atmospheric properties. We describe these results and multi-epoch, multi-wavelength imaging of LkCa 15 to assess the (non-)existence of protoplanetary companions, and briefly describe upgrades to SCExAO that will allow it to image and characterize even fainter self-luminous extrasolar planets and eventually mature planets in reflected light.

The Trouble with Color.

ERIC Educational Resources Information Center

Merchant, David

1999-01-01

Discusses problems with color quality in Web sites. Topics include differences in monitor settings, including contrast; amount of video RAM; user preference settings; browser-safe colors; cross-platform readability; and gamma values. (LRW)

NOAA Photo Library - HOME

Science.gov Websites

gold line COLLECTIONS * America's Coastlines * Art of the Photo Library * Beginnings/Endings * C&GS of the Day ~ This application requires that your browser be Javascript enabled. gold line Publication

Cavus Foot Surgery

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Bunionette Deformity Correction

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Shyness in Children

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Turn ... then an evaluation by a child mental-health professional would be helpful. Time to adjust Most shy ...

Percutaneous Achilles Tendon Lengthening

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Where to Donate Blood

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Find ... Correspondence Regulatory and Public Meetings Stop the Bleed Professional Development Education Annual Meeting International Cord Blood Symposium ...

Detecting Heap-Spraying Code Injection Attacks in Malicious Web Pages Using Runtime Execution

NASA Astrophysics Data System (ADS)

Choi, Younghan; Kim, Hyoungchun; Lee, Donghoon

The growing use of web services is increasing web browser attacks exponentially. Most attacks use a technique called heap spraying because of its high success rate. Heap spraying executes a malicious code without indicating the exact address of the code by copying it into many heap objects. For this reason, the attack has a high potential to succeed if only the vulnerability is exploited. Thus, attackers have recently begun using this technique because it is easy to use JavaScript to allocate the heap memory area. This paper proposes a novel technique that detects heap spraying attacks by executing a heap object in a real environment, irrespective of the version and patch status of the web browser. This runtime execution is used to detect various forms of heap spraying attacks, such as encoding and polymorphism. Heap objects are executed after being filtered on the basis of patterns of heap spraying attacks in order to reduce the overhead of the runtime execution. Patterns of heap spraying attacks are based on analysis of how an web browser accesses benign web sites. The heap objects are executed forcibly by changing the instruction register into the address of them after being loaded into memory. Thus, we can execute the malicious code without having to consider the version and patch status of the browser. An object is considered to contain a malicious code if the execution reaches a call instruction and then the instruction accesses the API of system libraries, such as kernel32.dll and ws_32.dll. To change registers and monitor execution flow, we used a debugger engine. A prototype, named HERAD(HEap spRAying Detector), is implemented and evaluated. In experiments, HERAD detects various forms of exploit code that an emulation cannot detect, and some heap spraying attacks that NOZZLE cannot detect. Although it has an execution overhead, HERAD produces a low number of false alarms. The processing time of several minutes is negligible because our research focuses on detecting heap spraying. This research can be applied to existing systems that collect malicious codes, such as Honeypot.

DASMiner: discovering and integrating data from DAS sources

PubMed Central

2009-01-01

Background DAS is a widely adopted protocol for providing syntactic interoperability among biological databases. The popularity of DAS is due to a simplified and elegant mechanism for data exchange that consists of sources exposing their RESTful interfaces for data access. As a growing number of DAS services are available for molecular biology resources, there is an incentive to explore this protocol in order to advance data discovery and integration among these resources. Results We developed DASMiner, a Matlab toolkit for querying DAS data sources that enables creation of integrated biological models using the information available in DAS-compliant repositories. DASMiner is composed by a browser application and an API that work together to facilitate gathering of data from different DAS sources, which can be used for creating enriched datasets from multiple sources. The browser is used to formulate queries and navigate data contained in DAS sources. Users can execute queries against these sources in an intuitive fashion, without the need of knowing the specific DAS syntax for the particular source. Using the source's metadata provided by the DAS Registry, the browser's layout adapts to expose only the set of commands and coordinate systems supported by the specific source. For this reason, the browser can interrogate any DAS source, independently of the type of data being served. The API component of DASMiner may be used for programmatic access of DAS sources by programs in Matlab. Once the desired data is found during navigation, the query is exported in the format of an API call to be used within any Matlab application. We illustrate the use of DASMiner by creating integrative models of histone modification maps and protein-protein interaction networks. These enriched datasets were built by retrieving and integrating distributed genomic and proteomic DAS sources using the API. Conclusion The support of the DAS protocol allows that hundreds of molecular biology databases to be treated as a federated, online collection of resources. DASMiner enables full exploration of these resources, and can be used to deploy applications and create integrated views of biological systems using the information deposited in DAS repositories. PMID:19919683

Shoes and Orthotics for Diabetics

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... By working with a physician and a footwear professional, such as a certified pedorthist, many patients can ...

How to Tape an Ankle

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Emotional Development: 2 Year Olds

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Turn ... probably refer your child to a mental health professional for a consultation. Last Updated 8/1/2009 ...

How to "Read" Your Footprint

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Plantar Fibroma and Plantar Fibromatosis

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Home ... The content is not intended to substitute for professional medical advice, diagnoses or treatments. If you need ...

Muscle Cramp - A Common Pain

MedlinePlus

... this site from a secured browser on the server. Please enable scripts and reload this page. Physicians ... Media Center The DO JAOA AOA Health Watch Professional Development AOA Board Certification Continuing Medical Education Research ...

Medicare: Physician Compare

MedlinePlus

... application currently does not support browsers with "JavaScript" disabled. Please enable JavaScript and refresh the page to ... not support or have Cascading Style Sheets (CSS) disabled. For a more optimal experience viewing this application, ...