SEER Cancer Query Systems (CanQues)

Cancer.gov

These applications provide access to cancer statistics including incidence, mortality, survival, prevalence, and probability of developing or dying from cancer. Users can display reports of the statistics or extract them for additional analyses.

The utility of atmospheric analyses for the mitigation of artifacts in InSAR

USGS Publications Warehouse

Foster, James; Kealy, John; Cherubini, Tiziana; Businger, S.; Lu, Zhong; Murphy, Michael

2013-01-01

The numerical weather models (NWMs) developed by the meteorological community are able to provide accurate analyses of the current state of the atmosphere in addition to the predictions of the future state. To date, most attempts to apply the NWMs to estimate the refractivity of the atmosphere at the time of satellite synthetic aperture radar (SAR) data acquisitions have relied on predictive models. We test the hypothesis that performing a final assimilative routine, ingesting all available meteorological observations for the times of SAR acquisitions, and generating customized analyses of the atmosphere at those times will better mitigate atmospheric artifacts in differential interferograms. We find that, for our study area around Mount St. Helens (Amboy, Washington, USA), this approach is unable to model the refractive changes and provides no mean benefit for interferogram analysis. The performance is improved slightly by ingesting atmospheric delay estimates derived from the limited local GPS network; however, the addition of water vapor products from the GOES satellites reduces the quality of the corrections. We interpret our results to indicate that, even with this advanced approach, NWMs are not a reliable mitigation technique for regions such as Mount St. Helens with highly variable moisture fields and complex topography and atmospheric dynamics. It is possible, however, that the addition of more spatially dense meteorological data to constrain the analyses might significantly improve the performance of weather modeling of atmospheric artifacts in satellite radar interferograms.

Personality and job performance: the Big Five revisited.

PubMed

Hurtz, G M; Donovan, J J

2000-12-01

Prior meta-analyses investigating the relation between the Big 5 personality dimensions and job performance have all contained a threat to construct validity, in that much of the data included within these analyses was not derived from actual Big 5 measures. In addition, these reviews did not address the relations between the Big 5 and contextual performance. Therefore, the present study sought to provide a meta-analytic estimate of the criterion-related validity of explicit Big 5 measures for predicting job performance and contextual performance. The results for job performance closely paralleled 2 of the previous meta-analyses, whereas analyses with contextual performance showed more complex relations among the Big 5 and performance. A more critical interpretation of the Big 5-performance relationship is presented, and suggestions for future research aimed at enhancing the validity of personality predictors are provided.

mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray

PubMed Central

Bodrossy, Levente; Stralis-Pavese, Nancy; Konrad-Köszler, Marianne; Weilharter, Alexandra; Reichenauer, Thomas G.; Schöfer, David; Sessitsch, Angela

2006-01-01

A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities. PMID:16461725

First- and Second-Line Bevacizumab in Addition to Chemotherapy for Metastatic Colorectal Cancer: A United States–Based Cost-Effectiveness Analysis

PubMed Central

Goldstein, Daniel A.; Chen, Qiushi; Ayer, Turgay; Howard, David H.; Lipscomb, Joseph; El-Rayes, Bassel F.; Flowers, Christopher R.

2015-01-01

Purpose The addition of bevacizumab to fluorouracil-based chemotherapy is a standard of care for previously untreated metastatic colorectal cancer. Continuation of bevacizumab beyond progression is an accepted standard of care based on a 1.4-month increase in median overall survival observed in a randomized trial. No United States–based cost-effectiveness modeling analyses are currently available addressing the use of bevacizumab in metastatic colorectal cancer. Our objective was to determine the cost effectiveness of bevacizumab in the first-line setting and when continued beyond progression from the perspective of US payers. Methods We developed two Markov models to compare the cost and effectiveness of fluorouracil, leucovorin, and oxaliplatin with or without bevacizumab in the first-line treatment and subsequent fluorouracil, leucovorin, and irinotecan with or without bevacizumab in the second-line treatment of metastatic colorectal cancer. Model robustness was addressed by univariable and probabilistic sensitivity analyses. Health outcomes were measured in life-years and quality-adjusted life-years (QALYs). Results Using bevacizumab in first-line therapy provided an additional 0.10 QALYs (0.14 life-years) at a cost of $59,361. The incremental cost-effectiveness ratio was $571,240 per QALY. Continuing bevacizumab beyond progression provided an additional 0.11 QALYs (0.16 life-years) at a cost of $39,209. The incremental cost-effectiveness ratio was $364,083 per QALY. In univariable sensitivity analyses, the variables with the greatest influence on the incremental cost-effectiveness ratio were bevacizumab cost, overall survival, and utility. Conclusion Bevacizumab provides minimal incremental benefit at high incremental cost per QALY in both the first- and second-line settings of metastatic colorectal cancer treatment. PMID:25691669

iTOUGH2 v7.1

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

FINSTERLE, STEFAN; JUNG, YOOJIN; KOWALSKY, MICHAEL

2016-09-15

iTOUGH2 (inverse TOUGH2) provides inverse modeling capabilities for TOUGH2, a simulator for multi-dimensional, multi-phase, multi-component, non-isothermal flow and transport in fractured porous media. iTOUGH2 performs sensitivity analyses, data-worth analyses, parameter estimation, and uncertainty propagation analyses in geosciences and reservoir engineering and other application areas. iTOUGH2 supports a number of different combinations of fluids and components (equation-of-state (EOS) modules). In addition, the optimization routines implemented in iTOUGH2 can also be used for sensitivity analysis, automatic model calibration, and uncertainty quantification of any external code that uses text-based input and output files using the PEST protocol. iTOUGH2 solves the inverse problem bymore » minimizing a non-linear objective function of the weighted differences between model output and the corresponding observations. Multiple minimization algorithms (derivative-free, gradient-based, and second-order; local and global) are available. iTOUGH2 also performs Latin Hypercube Monte Carlo simulations for uncertainty propagation analyses. A detailed residual and error analysis is provided. This upgrade includes (a) global sensitivity analysis methods, (b) dynamic memory allocation (c) additional input features and output analyses, (d) increased forward simulation capabilities, (e) parallel execution on multicore PCs and Linux clusters, and (f) bug fixes. More details can be found at http://esd.lbl.gov/iTOUGH2.« less

Adding thin-ideal internalization and impulsiveness to the cognitive-behavioral model of bulimic symptoms.

PubMed

Schnitzler, Caroline E; von Ranson, Kristin M; Wallace, Laurel M

2012-08-01

This study evaluated the cognitive-behavioral (CB) model of bulimia nervosa and an extension that included two additional maintaining factors - thin-ideal internalization and impulsiveness - in 327 undergraduate women. Participants completed measures of demographics, self-esteem, concern about shape and weight, dieting, bulimic symptoms, thin-ideal internalization, and impulsiveness. Both the original CB model and the extended model provided good fits to the data. Although structural equation modeling analyses suggested that the original CB model was most parsimonious, hierarchical regression analyses indicated that the additional variables accounted for significantly more variance. Additional analyses showed that the model fit could be improved by adding a path from concern about shape and weight, and deleting the path from dieting, to bulimic symptoms. Expanding upon the factors considered in the model may better capture the scope of variables maintaining bulimic symptoms in young women with a range of severity of bulimic symptoms. Copyright © 2012 Elsevier Ltd. All rights reserved.

Diet History Questionnaire: Database Revision History

Cancer.gov

The following details all additions and revisions made to the DHQ nutrient and food database. This revision history is provided as a reference for investigators who may have performed analyses with a previous release of the database.

Downscaling future climate scenarios to fine scales for hydrologic and ecological modeling and analysis

USGS Publications Warehouse

Flint, Lorraine E.; Flint, Alan L.

2012-01-01

The methodology, which includes a sequence of rigorous analyses and calculations, is intended to reduce the addition of uncertainty to the climate data as a result of the downscaling while providing the fine-scale climate information necessary for ecological analyses. It results in new but consistent data sets for the US at 4 km, the southwest US at 270 m, and California at 90 m and illustrates the utility of fine-scale downscaling to analyses of ecological processes influenced by topographic complexity.

A Sparse Matrix Approach for Simultaneous Quantification of Nystagmus and Saccade

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.; Stone, Lee; Boyle, Richard D.

2012-01-01

The vestibulo-ocular reflex (VOR) consists of two intermingled non-linear subsystems; namely, nystagmus and saccade. Typically, nystagmus is analysed using a single sufficiently long signal or a concatenation of them. Saccade information is not analysed and discarded due to insufficient data length to provide consistent and minimum variance estimates. This paper presents a novel sparse matrix approach to system identification of the VOR. It allows for the simultaneous estimation of both nystagmus and saccade signals. We show via simulation of the VOR that our technique provides consistent and unbiased estimates in the presence of output additive noise.

Thinking critically about the occurrence of widespread participation in poor nursing care.

PubMed

Roberts, Marc; Ion, Robin

2015-04-01

A discussion of how Arendt's work can be productively re-contextualized to provide a critical analysis of the occurrence of widespread participation in poor nursing care and what the implications of this are for the providers of nursing education. While the recent participation of nurses in healthcare failings, such as that detailed in the Francis report, has been universally condemned, there has been an absence of critical analyses in the literature that attempt to understand the occurrence of such widespread participation in poor nursing care. This is a significant omission in so far as such analyses will form an integral part of the strategy to limit the occurrence of such widespread participation of nurses in future healthcare failings. Discussion paper. Arendt's 'Eichmann in Jerusalem: A Report on the Banality of Evil' and 'Thinking and Moral Considerations: A Lecture'. In addition, a literature search was conducted and articles published in English relating to the terms care, compassion, ethics, judgement and thinking between 2004-2014 were included. It is anticipated that this discussion will stimulate further critical debate about the role of Arendt's work for an understanding of the occurrence of poor nursing care, and encouraging additional detailed analyses of the widespread participation of nurses in healthcare failings more generally. This article provides a challenging analysis of the widespread participation of nurses in poor care and discusses the opportunities confronting the providers of nursing education in limiting future healthcare failings. © 2014 John Wiley & Sons Ltd.

Using EFSO/PQC to Improve the Quality of Observations and Analyses

NASA Astrophysics Data System (ADS)

Chen, T. C.; Kalnay, E.

2017-12-01

Massive amounts of observations are assimilated every day into modern Numerical Weather Prediction (NWP) systems. This makes difficult to estimate the impact of a new observing system using the current approach (Observing System Experiments, OSEs) because there is already so much information provided by existing observations. In addition, the large volume of data also prevents monitoring the impact of each assimilated observation with OSEs. We demonstrate here how using Ensemble Forecast Sensitivity to Observations (EFSO) allows monitoring and improving the impact of observations on the analyses and forecasts in the Hybrid GSI/LETKF system. In addition, we show how EFSO can identify flow dependent detrimental observations from observing systems that, on the average, are beneficial. For example, using EFSO we find that positive zonal wind innovations in MODIS polar winds are generally detrimental, whereas no such bias is present in other satellite wind systems. We also show how EFSO can be used to identify and reject very detrimental observations (Proactive Quality Control, PQC). The withdrawal of these detrimental observations leads to improved analyses and 5-day forecasts, which also serves as a verification of EFSO. The operational implementation of PQC/EFSO is computationally very feasible, and will provide detailed QC monitoring of every observing system. Finally, we provide a theoretical justification of the PQC and its connection to dynamical instabilities with a simple Lorenz 96 model.

Geothermal Case Studies

DOE Data Explorer

Young, Katherine

2014-09-30

database.) In fiscal year 2015, NREL is working with universities to populate additional case studies on OpenEI. The goal is to provide a large enough dataset to start conducting analyses of exploration programs to identify correlations between successful exploration plans for areas with similar geologic occurrence models.

Structural neurobiological correlates of Mayer-Salovery-Caruso Emotional Intelligence Test performance in early course schizophrenia.

PubMed

Wojtalik, Jessica A; Eack, Shaun M; Keshavan, Matcheri S

2013-01-10

The Mayer-Salovey-Caruso Emotional Intelligence Test (MSCEIT) is a key measure of social cognition in schizophrenia that has good psychometric properties and is recommended by the MATRICS committee. As a way to further investigate the validity of the MSCEIT, this study sought to examine the neurobiological correlates of MSCEIT performance in patients with early course schizophrenia. A total of 51 patients diagnosed with early course, stabilized schizophrenia or schizoaffective disorder completed structural magnetic resonance imaging (MRI) scans and the MSCEIT. Investigation of the associations between MSCEIT performance and gray matter morphology was examined by conducting voxel-based morphometry (VBM) analyses across hypothesized social-cognitive regions of interest using automated anatomical labeling in Statistical Parametric Mapping Software, version 5 (SPM5). All VBM analyses utilized general linear models examining gray matter density partitioned images, adjusting for demographic and illness-related confounds. VBM results were then followed up with confirmatory volumetric analyses. Patients with poorer overall and Facilitating, Understanding, and Managing Emotions subscale performances on the MSCEIT showed significantly reduced gray matter density in the left parahippocampal gyrus. Additionally, attenuated performance on the Facilitating and Managing Emotions subscales was significantly associated with reduced right posterior cingulate gray matter density. All associations observed between MSCEIT performance and gray matter density were supported with confirmatory gray matter volumetric analyses, with the exception of the association between the right posterior cingulate and the facilitation of emotions. These findings provide additional evidence for the MSCEIT as a valid social-cognitive measure by elucidating its correlates with neurobiological structures commonly implicated in emotion processing. These findings provide additional biological evidence supporting the use of the MSCEIT in cognitive enhancing clinical trials in schizophrenia. Copyright © 2012 Elsevier Inc. All rights reserved.

Healthcare

ERIC Educational Resources Information Center

Carnevale, Anthony P.; Smith, Nicole; Gulish, Artem; Beach, Bennett H.

2012-01-01

This report, provides detailed analyses and projections of occupations in healthcare fields, and wages earned. In addition, the important skills and work values associated with workers in those fields of healthcare are discussed. Finally, the authors analyze the implications of research findings for the racial, ethnic, and class diversity of the…

Markov Chain Monte Carlo: an introduction for epidemiologists

PubMed Central

Hamra, Ghassan; MacLehose, Richard; Richardson, David

2013-01-01

Markov Chain Monte Carlo (MCMC) methods are increasingly popular among epidemiologists. The reason for this may in part be that MCMC offers an appealing approach to handling some difficult types of analyses. Additionally, MCMC methods are those most commonly used for Bayesian analysis. However, epidemiologists are still largely unfamiliar with MCMC. They may lack familiarity either with he implementation of MCMC or with interpretation of the resultant output. As with tutorials outlining the calculus behind maximum likelihood in previous decades, a simple description of the machinery of MCMC is needed. We provide an introduction to conducting analyses with MCMC, and show that, given the same data and under certain model specifications, the results of an MCMC simulation match those of methods based on standard maximum-likelihood estimation (MLE). In addition, we highlight examples of instances in which MCMC approaches to data analysis provide a clear advantage over MLE. We hope that this brief tutorial will encourage epidemiologists to consider MCMC approaches as part of their analytic tool-kit. PMID:23569196

Global analysis of the Burkholderia thailandensis quorum sensing-controlled regulon.

PubMed

Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard; Greenberg, E Peter

2014-04-01

Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei.

The Active for Life Year 5 (AFLY5) school-based cluster randomised controlled trial protocol: detailed statistical analysis plan.

PubMed

Lawlor, Debbie A; Peters, Tim J; Howe, Laura D; Noble, Sian M; Kipping, Ruth R; Jago, Russell

2013-07-24

The Active For Life Year 5 (AFLY5) randomised controlled trial protocol was published in this journal in 2011. It provided a summary analysis plan. This publication is an update of that protocol and provides a detailed analysis plan. This update provides a detailed analysis plan of the effectiveness and cost-effectiveness of the AFLY5 intervention. The plan includes details of how variables will be quality control checked and the criteria used to define derived variables. Details of four key analyses are provided: (a) effectiveness analysis 1 (the effect of the AFLY5 intervention on primary and secondary outcomes at the end of the school year in which the intervention is delivered); (b) mediation analyses (secondary analyses examining the extent to which any effects of the intervention are mediated via self-efficacy, parental support and knowledge, through which the intervention is theoretically believed to act); (c) effectiveness analysis 2 (the effect of the AFLY5 intervention on primary and secondary outcomes 12 months after the end of the intervention) and (d) cost effectiveness analysis (the cost-effectiveness of the AFLY5 intervention). The details include how the intention to treat and per-protocol analyses were defined and planned sensitivity analyses for dealing with missing data. A set of dummy tables are provided in Additional file 1. This detailed analysis plan was written prior to any analyst having access to any data and was approved by the AFLY5 Trial Steering Committee. Its publication will ensure that analyses are in accordance with an a priori plan related to the trial objectives and not driven by knowledge of the data. ISRCTN50133740.

The Roles of Individual and Organizational Factors in Burnout among Community-Based Mental Health Service Providers

PubMed Central

Green, Amy E.; Albanese, Brian J.; Shapiro, Nicole M.; Aarons, Gregory A.

2014-01-01

Public sector mental health care providers are at high risk for burnout which negatively affects not only provider well-being but also the quality of services for clients and the functioning of organizations. This study examines the influence of demographics, work characteristic, and organizational variables on levels of burnout among child and adolescent mental health service providers operating within a public sector mental health service system. Additionally, given the dearth of research examining differences in burnout levels among mental health sub-disciplines (e.g., social work, psychology, marital and family therapy) and mental health programs (e.g., outpatient, day treatment, Wraparound, case management), analyses were conducted to compare levels of burnout among multiple mental health disciplines and program types. Surveys were completed by 285 providers across 49 mental health programs in a large urban public mental health system. Variables representing dimensions of organizational climate and transformational leadership accounted for the greatest amount of variance in provider reported burnout. Analyses demonstrated significantly lower levels of depersonalization among Wraparound providers compared to traditional case managers. Age was the only demographic variable related to burnout. Additionally, no significant effects were found for provider discipline or for agency tenure and caseload size. Results suggest the need to consider organizational development strategies aimed at creating more functional and less stressful climates and increasing levels of transformational leadership behaviors in order to reduce levels of burnout among clinicians working in public mental health settings for youth and families. PMID:24564442

Causal Mediation Analysis of Survival Outcome with Multiple Mediators.

PubMed

Huang, Yen-Tsung; Yang, Hwai-I

2017-05-01

Mediation analyses have been a popular approach to investigate the effect of an exposure on an outcome through a mediator. Mediation models with multiple mediators have been proposed for continuous and dichotomous outcomes. However, development of multimediator models for survival outcomes is still limited. We present methods for multimediator analyses using three survival models: Aalen additive hazard models, Cox proportional hazard models, and semiparametric probit models. Effects through mediators can be characterized by path-specific effects, for which definitions and identifiability assumptions are provided. We derive closed-form expressions for path-specific effects for the three models, which are intuitively interpreted using a causal diagram. Mediation analyses using Cox models under the rare-outcome assumption and Aalen additive hazard models consider effects on log hazard ratio and hazard difference, respectively; analyses using semiparametric probit models consider effects on difference in transformed survival time and survival probability. The three models were applied to a hepatitis study where we investigated effects of hepatitis C on liver cancer incidence mediated through baseline and/or follow-up hepatitis B viral load. The three methods show consistent results on respective effect scales, which suggest an adverse estimated effect of hepatitis C on liver cancer not mediated through hepatitis B, and a protective estimated effect mediated through the baseline (and possibly follow-up) of hepatitis B viral load. Causal mediation analyses of survival outcome with multiple mediators are developed for additive hazard and proportional hazard and probit models with utility demonstrated in a hepatitis study.

Using Toulmin analysis to analyse an instructor's proof presentation in abstract algebra

NASA Astrophysics Data System (ADS)

Fukawa-connelly, Timothy

2014-01-01

This paper provides a method for analysing undergraduate teaching of proof-based courses using Toulmin's model (1969) of argumentation. It presents a case study of one instructor's presentation of proofs. The analysis shows that the instructor presents different levels of detail in different proofs; thus, the students have an inconsistent set of written models for their work. Similarly, the analysis shows that the details the instructor says aloud differ from what she writes down. Although her verbal commentary provides additional detail and appears to have pedagogical value, for instance, by modelling thinking that supports proof writing, this value might be better realized if she were to change her teaching practices.

78 FR 57587 - Environmental Impact and Related Procedures-Programmatic Agreements and Additional Categorical...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-19

... administrative and NEPA processing by encouraging grant applicants to design proposed projects so that... geotechnical and other investigations to provide information for preliminary design and for environmental... information for preliminary design and for environmental analyses and permitting purposes and is found...

40 CFR 98.186 - Data reporting procedures.

Code of Federal Regulations, 2014 CFR

2014-07-01

... section (e.g., supplier provided information, analyses of representative samples you collected). (9) If... addition to the information required by § 98.3(c), each annual report must contain the information... the relevant information required by § 98.36 and the information specified in paragraphs (a)(1...

40 CFR 98.186 - Data reporting procedures.

Code of Federal Regulations, 2010 CFR

2010-07-01

... section (e.g., supplier provided information, analyses of representative samples you collected). (9) If... addition to the information required by § 98.3(c), each annual report must contain the information... the relevant information required by § 98.36 and the information specified in paragraphs (a)(1...

40 CFR 98.116 - Data reporting requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... provided information, analyses of representative samples you collected). (7) If you use the missing data... addition to the information required by § 98.3(c), each annual report must contain the information... relevant information required by § 98.36 for the Tier 4 Calculation Methodology and the following...

40 CFR 98.116 - Data reporting requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... provided information, analyses of representative samples you collected). (7) If you use the missing data... addition to the information required by § 98.3(c), each annual report must contain the information... relevant information required by § 98.36 for the Tier 4 Calculation Methodology and the following...

40 CFR 98.186 - Data reporting procedures.

Code of Federal Regulations, 2013 CFR

2013-07-01

... section (e.g., supplier provided information, analyses of representative samples you collected). (9) If... addition to the information required by § 98.3(c), each annual report must contain the information... the relevant information required by § 98.36 and the information specified in paragraphs (a)(1...

40 CFR 98.186 - Data reporting procedures.

Code of Federal Regulations, 2012 CFR

2012-07-01

... section (e.g., supplier provided information, analyses of representative samples you collected). (9) If... addition to the information required by § 98.3(c), each annual report must contain the information... the relevant information required by § 98.36 and the information specified in paragraphs (a)(1...

40 CFR 98.116 - Data reporting requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... provided information, analyses of representative samples you collected). (7) If you use the missing data... addition to the information required by § 98.3(c), each annual report must contain the information... relevant information required by § 98.36 for the Tier 4 Calculation Methodology and the following...

40 CFR 98.186 - Data reporting procedures.

Code of Federal Regulations, 2011 CFR

2011-07-01

... section (e.g., supplier provided information, analyses of representative samples you collected). (9) If... addition to the information required by § 98.3(c), each annual report must contain the information... the relevant information required by § 98.36 and the information specified in paragraphs (a)(1...

40 CFR 98.116 - Data reporting requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... reported in paragraph (e)(5) of this section (e.g., supplier provided information, analyses of... addition to the information required by § 98.3(c), each annual report must contain the information... relevant information required by § 98.36 for the Tier 4 Calculation Methodology and the following...

Transterm: a database to aid the analysis of regulatory sequences in mRNAs

PubMed Central

Jacobs, Grant H.; Chen, Augustine; Stevens, Stewart G.; Stockwell, Peter A.; Black, Michael A.; Tate, Warren P.; Brown, Chris M.

2009-01-01

Messenger RNAs, in addition to coding for proteins, may contain regulatory elements that affect how the protein is translated. These include protein and microRNA-binding sites. Transterm (http://mRNA.otago.ac.nz/Transterm.html) is a database of regions and elements that affect translation with two major unique components. The first is integrated results of analysis of general features that affect translation (initiation, elongation, termination) for species or strains in Genbank, processed through a standard pipeline. The second is curated descriptions of experimentally determined regulatory elements that function as translational control elements in mRNAs. Transterm focuses on protein binding sites, particularly those in 3′-untranslated regions (3′-UTR). For this release the interface has been extensively updated based on user feedback. The data is now accessible by strain rather than species, for example there are 10 Escherichia coli strains (genomes) analysed separately. In addition to providing a repository of data, the database also provides tools for users to query their own mRNA sequences. Users can search sequences for Transterm or user defined regulatory elements, including protein or miRNA targets. Transterm also provides a central core of links to related resources for complementary analyses. PMID:18984623

Planning, Conducting, and Documenting Data Analysis for Program Improvement

ERIC Educational Resources Information Center

Winer, Abby; Taylor, Cornelia; Derrington, Taletha; Lucas, Anne

2015-01-01

This 2015 document was developed to help technical assistance (TA) providers and state staff define and limit the scope of data analysis for program improvement efforts, including the State Systemic Improvement Plan (SSIP); develop a plan for data analysis; document alternative hypotheses and additional analyses as they are generated; and…

Simple street tree sampling

Treesearch

David J. Nowak; Jeffrey T. Walton; James Baldwin; Jerry Bond

2015-01-01

Information on street trees is critical for management of this important resource. Sampling of street tree populations provides an efficient means to obtain street tree population information. Long-term repeat measures of street tree samples supply additional information on street tree changes and can be used to report damages from catastrophic events. Analyses of...

High School Graduation Minimum Competency Requirements. Final Technical Report.

ERIC Educational Resources Information Center

Austin Independent School District, TX. Office of Research and Evaluation.

This technical report details the testing results and analyses supporting the evaluation findings related to the Austin (Texas) Independent School District (AISD) minimum competency graduation requirements. The graduation competency status of all AISD students in grades 8 to 12 are documented. The report provides additional information on the data…

Misclassification bias in areal estimates

Treesearch

Raymond L. Czaplewski

1992-01-01

In addition to thematic maps, remote sensing provides estimates of area in different thematic categories. Areal estimates are frequently used for resource inventories, management planning, and assessment analyses. Misclassification causes bias in these statistical areal estimates. For example, if a small percentage of a common cover type is misclassified as a rare...

Integrated approach for quantification of fractured tight reservoir rocks: Porosity, permeability analyses and 3D fracture network characterisation on fractured dolomite samples

NASA Astrophysics Data System (ADS)

Voorn, Maarten; Barnhoorn, Auke; Exner, Ulrike; Baud, Patrick; Reuschlé, Thierry

2015-04-01

Fractured reservoir rocks make up an important part of the hydrocarbon reservoirs worldwide. A detailed analysis of fractures and fracture networks in reservoir rock samples is thus essential to determine the potential of these fractured reservoirs. However, common analyses on drill core and plug samples taken from such reservoirs (including hand specimen analysis, thin section analysis and laboratory porosity and permeability determination) suffer from various problems, such as having a limited resolution, providing only 2D and no internal structure information, being destructive on the samples and/or not being representative for full fracture networks. In this study, we therefore explore the use of an additional method - non-destructive 3D X-ray micro-Computed Tomography (μCT) - to obtain more information on such fractured samples. Seven plug-sized samples were selected from narrowly fractured rocks of the Hauptdolomit formation, taken from wellbores in the Vienna Basin, Austria. These samples span a range of different fault rocks in a fault zone interpretation, from damage zone to fault core. 3D μCT data is used to extract porosity, fracture aperture, fracture density and fracture orientations - in bulk as well as locally. The 3D analyses are complemented with thin sections made to provide some 2D information with a much higher detail than the μCT data. Finally, gas- and water permeability measurements under confining pressure provide an important link (at least in order of magnitude) of the µCT results towards more realistic reservoir conditions. Our results show that 3D μCT can be applied efficiently on plug-sized samples of naturally fractured rocks, and that several important parameters can be extracted. μCT can therefore be a useful addition to studies on such reservoir rocks, and provide valuable input for modelling and simulations. Also permeability experiments under confining pressure provide important additional insights. Combining these and other methods can therefore be a powerful approach in microstructural analysis of reservoir rocks, especially when applying the concepts that we present (on a small set of samples) in a larger study, in an automated and standardised manner.

Enhancing Bottom-up and Top-down Proteomic Measurements with Ion Mobility Separations

DOE PAGES

Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Ibrahim, Yehia M.; ...

2015-07-03

Proteomic measurements with greater throughput, sensitivity and additional structural information enhance the in-depth characterization of complex mixtures and targeted studies with additional information and higher confidence. While liquid chromatography separation coupled with mass spectrometry (LC-MS) measurements have provided information on thousands of proteins in different sample types, the additional of another rapid separation stage providing structural information has many benefits for analyses. Technical advances in ion funnels and multiplexing have enabled ion mobility separations to be easily and effectively coupled with LC-MS proteomics to enhance the information content of measurements. Finally, herein, we report on applications illustrating increased sensitivity, throughput,more » and structural information by utilizing IMS-MS and LC-IMS-MS measurements for both bottom-up and top-down proteomics measurements.« less

Chemical Analyses of Pre-Holocene Rocks from Medicine Lake Volcano and Vicinity, Northern California

USGS Publications Warehouse

Donnelly-Nolan, Julie M.

2008-01-01

Chemical analyses are presented in an accompanying table (Table 1) for more than 600 pre-Holocene rocks collected at and near Medicine Lake Volcano, northern California. The data include major-element X-ray fluorescence (XRF) analyses for all of the rocks plus XRF trace element data for most samples, and instrumental neutron activation analysis (INAA) trace element data for many samples. In addition, a limited number of analyses of Na2O and K2O by flame photometry (FP) are included as well assome wet chemical analyses of FeO, H2O+/-, and CO2. Latitude and longitude location information is provided for all samples. This data set is intended to accompany the geologic map of Medicine Lake Volcano (Donnelly-Nolan, in press); map unit designations are given for each sample collected from the map area.

Space Station communications and tracking system

NASA Technical Reports Server (NTRS)

Dietz, Reinhold H.

1987-01-01

A comprehensive description of the existing Space Station communications and tracking system requirements, architecture, and design concepts is provided. Areas which will require innovative solutions to provide cost-effective flight systems are emphasized. Among these are the space-to-space links, the differential global positioning system for determining relative position with free-flying vehicles, multitarget radar, packet/isochronous signal processing, and laser docking systems. In addition, the importance of advanced development, tests, and analyses is summarized.

The roles of individual and organizational factors in burnout among community-based mental health service providers.

PubMed

Green, Amy E; Albanese, Brian J; Shapiro, Nicole M; Aarons, Gregory A

2014-02-01

Public-sector mental health care providers are at high risk for burnout, which negatively affects not only provider well-being but also the quality of services for clients and the functioning of organizations. This study examines the influence of demographics, work characteristic, and organizational variables on levels of burnout among child and adolescent mental health service providers operating within a public-sector mental health service system. Additionally, given the dearth of research examining differences in burnout levels among mental health subdisciplines (e.g., social work, psychology, marital and family therapy) and mental health programs (e.g., outpatient, day treatment, wraparound, case management), analyses were conducted to compare levels of burnout among multiple mental health disciplines and program types. Surveys were completed by 285 providers across 49 mental health programs in a large urban public mental health system. Variables representing dimensions of organizational climate and transformational leadership accounted for the greatest amount of variance in provider reported burnout. Analyses demonstrated significantly lower levels of depersonalization among wraparound providers compared to traditional case managers. Age was the only demographic variable related to burnout. Additionally, no significant effects were found for provider discipline or for agency tenure and caseload size. Results suggest the need to consider organizational development strategies aimed at creating more functional and less stressful climates and increasing levels of transformational leadership behaviors in order to reduce levels of burnout among clinicians working in public mental health settings for youth and families. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Screening HIV-Infected Patients with Low CD4 Counts for Cryptococcal Antigenemia prior to Initiation of Antiretroviral Therapy: Cost Effectiveness of Alternative Screening Strategies in South Africa.

PubMed

Larson, Bruce A; Rockers, Peter C; Bonawitz, Rachael; Sriruttan, Charlotte; Glencross, Deborah K; Cassim, Naseem; Coetzee, Lindi M; Greene, Gregory S; Chiller, Tom M; Vallabhaneni, Snigdha; Long, Lawrence; van Rensburg, Craig; Govender, Nelesh P

2016-01-01

In 2015 South Africa established a national cryptococcal antigenemia (CrAg) screening policy targeted at HIV-infected patients with CD4+ T-lymphocyte (CD4) counts <100 cells/ μl who are not yet on antiretroviral treatment (ART). Two screening strategies are included in national guidelines: reflex screening, where a CrAg test is performed on remnant blood samples from CD4 testing; and provider-initiated screening, where providers order a CrAg test after a patient returns for CD4 test results. The objective of this study was to compare costs and effectiveness of these two screening strategies. We developed a decision analytic model to compare reflex and provider-initiated screening in terms of programmatic and health outcomes (number screened, number identified for preemptive treatment, lives saved, and discounted years of life saved) and screening and treatment costs (2015 USD). We estimated a base case with prevalence and other parameters based on data collected during CrAg screening pilot projects integrated into routine HIV care in Gauteng, Free State, and Western Cape Provinces. We conducted sensitivity analyses to explore how results change with underlying parameter assumptions. In the base case, for each 100,000 CD4 tests, the reflex strategy compared to the provider-initiated strategy has higher screening costs ($37,536 higher) but lower treatment costs ($55,165 lower), so overall costs of screening and treatment are $17,629 less with the reflex strategy. The reflex strategy saves more lives (30 lives, 647 additional years of life saved). Sensitivity analyses suggest that reflex screening dominates provider-initiated screening (lower total costs and more lives saved) or saves additional lives for small additional costs (< $125 per life year) across a wide range of conditions (CrAg prevalence, patient and provider behavior, patient survival without treatment, and effectiveness of preemptive fluconazole treatment). In countries with substantial numbers of people with untreated, advanced HIV disease such as South Africa, CrAg screening before initiation of ART has the potential to reduce cryptococcal meningitis and save lives. Reflex screening compared to provider-initiated screening saves more lives and is likely to be cost saving or have low additional costs per additional year of life saved.

Screening HIV-Infected Patients with Low CD4 Counts for Cryptococcal Antigenemia prior to Initiation of Antiretroviral Therapy: Cost Effectiveness of Alternative Screening Strategies in South Africa

PubMed Central

Rockers, Peter C.; Bonawitz, Rachael; Sriruttan, Charlotte; Glencross, Deborah K.; Cassim, Naseem; Coetzee, Lindi M.; Greene, Gregory S.; Chiller, Tom M.; Vallabhaneni, Snigdha; Long, Lawrence; van Rensburg, Craig; Govender, Nelesh P.

2016-01-01

Background In 2015 South Africa established a national cryptococcal antigenemia (CrAg) screening policy targeted at HIV-infected patients with CD4+ T-lymphocyte (CD4) counts <100 cells/ μl who are not yet on antiretroviral treatment (ART). Two screening strategies are included in national guidelines: reflex screening, where a CrAg test is performed on remnant blood samples from CD4 testing; and provider-initiated screening, where providers order a CrAg test after a patient returns for CD4 test results. The objective of this study was to compare costs and effectiveness of these two screening strategies. Methods We developed a decision analytic model to compare reflex and provider-initiated screening in terms of programmatic and health outcomes (number screened, number identified for preemptive treatment, lives saved, and discounted years of life saved) and screening and treatment costs (2015 USD). We estimated a base case with prevalence and other parameters based on data collected during CrAg screening pilot projects integrated into routine HIV care in Gauteng, Free State, and Western Cape Provinces. We conducted sensitivity analyses to explore how results change with underlying parameter assumptions. Results In the base case, for each 100,000 CD4 tests, the reflex strategy compared to the provider-initiated strategy has higher screening costs ($37,536 higher) but lower treatment costs ($55,165 lower), so overall costs of screening and treatment are $17,629 less with the reflex strategy. The reflex strategy saves more lives (30 lives, 647 additional years of life saved). Sensitivity analyses suggest that reflex screening dominates provider-initiated screening (lower total costs and more lives saved) or saves additional lives for small additional costs (< $125 per life year) across a wide range of conditions (CrAg prevalence, patient and provider behavior, patient survival without treatment, and effectiveness of preemptive fluconazole treatment). Conclusions In countries with substantial numbers of people with untreated, advanced HIV disease such as South Africa, CrAg screening before initiation of ART has the potential to reduce cryptococcal meningitis and save lives. Reflex screening compared to provider-initiated screening saves more lives and is likely to be cost saving or have low additional costs per additional year of life saved. PMID:27390864

Early Versus Delayed Motion After Rotator Cuff Repair: A Systematic Review of Overlapping Meta-analyses.

PubMed

Houck, Darby A; Kraeutler, Matthew J; Schuette, Hayden B; McCarty, Eric C; Bravman, Jonathan T

2017-10-01

Previous meta-analyses have been conducted to compare outcomes of early versus delayed motion after rotator cuff repair. To conduct a systematic review of overlapping meta-analyses comparing early versus delayed motion rehabilitation protocols after rotator cuff repair to determine which meta-analyses provide the best available evidence. Systematic review. A systematic review was performed by searching PubMed and Cochrane Library databases. Search terms included "rotator cuff repair," "early passive motion," "immobilization," "rehabilitation protocol," and "meta-analysis." Results were reviewed to determine study eligibility. Patient outcomes and structural healing were extracted from these meta-analyses. Meta-analysis quality was assessed using the Oxman-Guyatt and Quality of Reporting of Meta-analyses (QUOROM) systems. The Jadad decision algorithm was then used to determine which meta-analyses provided the best level of evidence. Seven meta-analyses containing a total of 5896 patients met the eligibility criteria (1 Level I evidence, 4 Level II evidence, 2 Level III evidence). None of these meta-analyses found immobilization to be superior to early motion; however, most studies suggested that early motion would increase range of motion (ROM), thereby reducing time of recovery. Three of these studies suggested that tear size contributed to the choice of rehabilitation to ensure proper healing of the shoulder. A study by Chan et al in 2014 received the highest QUOROM and Oxman-Guyatt scores, and therefore this meta-analysis appeared to have the highest level of evidence. Additionally, a study by Riboh and Garrigues in 2014 was selected as the highest quality study in this systematic review according to the Jadad decision algorithm. The current, best available evidence suggests that early motion improves ROM after rotator cuff repair but increases the risk of rotator cuff retear. Lower quality meta-analyses indicate that tear size may provide a better strategy in determining the correct rehabilitation protocol.

Quantifying stream nutrient uptake from ambient to saturation with instantaneous tracer additions

NASA Astrophysics Data System (ADS)

Covino, T. P.; McGlynn, B. L.; McNamara, R.

2009-12-01

Stream nutrient tracer additions and spiraling metrics are frequently used to quantify stream ecosystem behavior. However, standard approaches limit our understanding of aquatic biogeochemistry. Specifically, the relationship between in-stream nutrient concentration and stream nutrient spiraling has not been characterized. The standard constant rate (steady-state) approach to stream spiraling parameter estimation, either through elevating nutrient concentration or adding isotopically labeled tracers (e.g. 15N), provides little information regarding the stream kinetic curve that represents the uptake-concentration relationship analogous to the Michaelis-Menten curve. These standard approaches provide single or a few data points and often focus on estimating ambient uptake under the conditions at the time of the experiment. Here we outline and demonstrate a new method using instantaneous nutrient additions and dynamic analyses of breakthrough curve (BTC) data to characterize the full relationship between spiraling metrics and nutrient concentration. We compare the results from these dynamic analyses to BTC-integrated, and standard steady-state approaches. Our results indicate good agreement between these three approaches but we highlight the advantages of our dynamic method. Specifically, our new dynamic method provides a cost-effective and efficient approach to: 1) characterize full concentration-spiraling metric curves; 2) estimate ambient spiraling metrics; 3) estimate Michaelis-Menten parameters maximum uptake (Umax) and the half-saturation constant (Km) from developed uptake-concentration kinetic curves, and; 4) measure dynamic nutrient spiraling in larger rivers where steady-state approaches are impractical.

Nonindependence and sensitivity analyses in ecological and evolutionary meta-analyses.

PubMed

Noble, Daniel W A; Lagisz, Malgorzata; O'dea, Rose E; Nakagawa, Shinichi

2017-05-01

Meta-analysis is an important tool for synthesizing research on a variety of topics in ecology and evolution, including molecular ecology, but can be susceptible to nonindependence. Nonindependence can affect two major interrelated components of a meta-analysis: (i) the calculation of effect size statistics and (ii) the estimation of overall meta-analytic estimates and their uncertainty. While some solutions to nonindependence exist at the statistical analysis stages, there is little advice on what to do when complex analyses are not possible, or when studies with nonindependent experimental designs exist in the data. Here we argue that exploring the effects of procedural decisions in a meta-analysis (e.g. inclusion of different quality data, choice of effect size) and statistical assumptions (e.g. assuming no phylogenetic covariance) using sensitivity analyses are extremely important in assessing the impact of nonindependence. Sensitivity analyses can provide greater confidence in results and highlight important limitations of empirical work (e.g. impact of study design on overall effects). Despite their importance, sensitivity analyses are seldom applied to problems of nonindependence. To encourage better practice for dealing with nonindependence in meta-analytic studies, we present accessible examples demonstrating the impact that ignoring nonindependence can have on meta-analytic estimates. We also provide pragmatic solutions for dealing with nonindependent study designs, and for analysing dependent effect sizes. Additionally, we offer reporting guidelines that will facilitate disclosure of the sources of nonindependence in meta-analyses, leading to greater transparency and more robust conclusions. © 2017 John Wiley & Sons Ltd.

Design Review and Analysis | Water Power | NREL

Science.gov Websites

Design Review and Analysis Design Review and Analysis NREL is leveraging its 35 years of experience devices and components. As part of this effort, NREL researchers provide industry partners with design reviews and analyses. In addition to design reviews, NREL offers technical assistance to solve specific

Group Cohesion DEOCS 4.1 Construct Validity Summary

DTIC Science & Technology

2017-08-01

Group Cohesion DEOCS 4.1 Construct Validity Summary DEFENSE EQUAL OPPORTUNITY MANAGEMENT INSTITUTE DIRECTORATE...See Table 4 for more information regarding item reliabilities. The relationship between the original four-point scale (Organizational Cohesion) and...future analyses, including those using the seven-point scale. Tables 4 and 5 provide additional information regarding the reliability and descriptive

SOCIAL AND EMOTIONAL BEHAVIOR IN INFANCY--SOME DEVELOPMENTAL ISSUES AND PROBLEMS.

ERIC Educational Resources Information Center

RICCIUTI, HENRY N.

INVESTIGATIONS INTO THE NATURE AND DEVELOPMENT OF SOCIAL AND EMOTIONAL BEHAVIOR IN HUMAN INFANCY HAVE RAISED MANY RESEARCH ISSUES AND HAVE INDICATED MANY ADDITIONAL AREAS OF INQUIRY. EARLY AND CONTEMPORARY STUDIES HAVE BOTH BEEN CONCERNED WITH PROVIDING MORE PRECISE ANALYSES OF STIMULUS AND SITUATIONAL DETERMINANTS OF SOCIAL AND EMOTIONAL…

Quantitative genetic tools for insecticide resistance risk assessment: estimating the heritability of resistance

Treesearch

Michael J. Firko; Jane Leslie Hayes

1990-01-01

Quantitative genetic studies of resistance can provide estimates of genetic parameters not available with other types of genetic analyses. Three methods are discussed for estimating the amount of additive genetic variation in resistance to individual insecticides and subsequent estimation of heritability (h2) of resistance. Sibling analysis and...

Formulating Social Policy vis-a-vis Immigrants: Win-Win or Zero-Sum Game?

ERIC Educational Resources Information Center

Kissam, Ed

This paper examines the effectiveness of social services provided to Mexican immigrants in rural California. In addition, the paper offers recommendations for service delivery models and for rethinking the objectives of immigrant social policy. At the most basic level, current social program planning and associated analyses of policy options fail…

A comparative analysis of exome capture.

PubMed

Parla, Jennifer S; Iossifov, Ivan; Grabill, Ian; Spector, Mona S; Kramer, Melissa; McCombie, W Richard

2011-09-29

Human exome resequencing using commercial target capture kits has been and is being used for sequencing large numbers of individuals to search for variants associated with various human diseases. We rigorously evaluated the capabilities of two solution exome capture kits. These analyses help clarify the strengths and limitations of those data as well as systematically identify variables that should be considered in the use of those data. Each exome kit performed well at capturing the targets they were designed to capture, which mainly corresponds to the consensus coding sequences (CCDS) annotations of the human genome. In addition, based on their respective targets, each capture kit coupled with high coverage Illumina sequencing produced highly accurate nucleotide calls. However, other databases, such as the Reference Sequence collection (RefSeq), define the exome more broadly, and so not surprisingly, the exome kits did not capture these additional regions. Commercial exome capture kits provide a very efficient way to sequence select areas of the genome at very high accuracy. Here we provide the data to help guide critical analyses of sequencing data derived from these products.

Teacher, parent, and peer reports of early aggression as screening measures for long-term maladaptive outcomes: who provides the most useful information?

PubMed

Clemans, Katherine H; Musci, Rashelle J; Leoutsakos, Jeannie-Marie S; Ialongo, Nicholas S

2014-04-01

This study compared the ability of teacher, parent, and peer reports of aggressive behavior in early childhood to accurately classify cases of maladaptive outcomes in late adolescence and early adulthood. Weighted kappa analyses determined optimal cut points and relative classification accuracy among teacher, parent, and peer reports of aggression assessed for 691 students (54% male; 84% African American and 13% White) in the fall of first grade. Outcomes included antisocial personality, substance use, incarceration history, risky sexual behavior, and failure to graduate from high school on time. Peer reports were the most accurate classifier of all outcomes in the full sample. For most outcomes, the addition of teacher or parent reports did not improve overall classification accuracy once peer reports were accounted for. Additional gender-specific and adjusted kappa analyses supported the superior classification utility of the peer report measure. The results suggest that peer reports provided the most useful classification information of the 3 aggression measures. Implications for targeted intervention efforts in which screening measures are used to identify at-risk children are discussed.

Global Analysis of the Burkholderia thailandensis Quorum Sensing-Controlled Regulon

PubMed Central

Majerczyk, Charlotte; Brittnacher, Mitchell; Jacobs, Michael; Armour, Christopher D.; Radey, Mathew; Schneider, Emily; Phattarasokul, Somsak; Bunt, Richard

2014-01-01

Burkholderia thailandensis contains three acyl-homoserine lactone quorum sensing circuits and has two additional LuxR homologs. To identify B. thailandensis quorum sensing-controlled genes, we carried out transcriptome sequencing (RNA-seq) analyses of quorum sensing mutants and their parent. The analyses were grounded in the fact that we identified genes coding for factors shown previously to be regulated by quorum sensing among a larger set of quorum-controlled genes. We also found that genes coding for contact-dependent inhibition were induced by quorum sensing and confirmed that specific quorum sensing mutants had a contact-dependent inhibition defect. Additional quorum-controlled genes included those for the production of numerous secondary metabolites, an uncharacterized exopolysaccharide, and a predicted chitin-binding protein. This study provides insights into the roles of the three quorum sensing circuits in the saprophytic lifestyle of B. thailandensis, and it provides a foundation on which to build an understanding of the roles of quorum sensing in the biology of B. thailandensis and the closely related pathogenic Burkholderia pseudomallei and Burkholderia mallei. PMID:24464461

Love Canal Emergency Declaration Area habitability study. Volume 5. Peer review summary: TRC (Technical Review Committee) responses. Final report

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

Not Available

Environmental studies were conducted to provide data that could be used by the Commissioner of Health for the State of New York in determining whether the Emergency Declaration Area surrounding the Love Canal hazardous-waste site is habitable. These volumes (II through IV) were reviewed by a peer-review panel of expert scientists. The scientists concluded that each of the three environmental studies was well planned and well executed. Volume V summarizes the peer review and gives additional information or clarifications as requested during the peer review. Volume V also provides additional supplemental statistical analyses requested by the peer reviewer panel.

Analysis and Application of European Genetic Substructure Using 300 K SNP Information

PubMed Central

Tian, Chao; Plenge, Robert M; Ransom, Michael; Lee, Annette; Villoslada, Pablo; Selmi, Carlo; Klareskog, Lars; Pulver, Ann E; Qi, Lihong; Gregersen, Peter K; Seldin, Michael F

2008-01-01

European population genetic substructure was examined in a diverse set of >1,000 individuals of European descent, each genotyped with >300 K SNPs. Both STRUCTURE and principal component analyses (PCA) showed the largest division/principal component (PC) differentiated northern from southern European ancestry. A second PC further separated Italian, Spanish, and Greek individuals from those of Ashkenazi Jewish ancestry as well as distinguishing among northern European populations. In separate analyses of northern European participants other substructure relationships were discerned showing a west to east gradient. Application of this substructure information was critical in examining a real dataset in whole genome association (WGA) analyses for rheumatoid arthritis in European Americans to reduce false positive signals. In addition, two sets of European substructure ancestry informative markers (ESAIMs) were identified that provide substantial substructure information. The results provide further insight into European population genetic substructure and show that this information can be used for improving error rates in association testing of candidate genes and in replication studies of WGA scans. PMID:18208329

[Molecular and immunohistochemical diagnostics in melanoma].

PubMed

Schilling, B; Griewank, K G

2016-07-01

To provide appropriate therapy and follow-up to patients with malignant melanoma, proper diagnostics are of critical importance. Targeted therapy of advanced melanoma is based on the molecular genetic analyses of tumor tissue. In addition, sequencing of genes and other genetic approaches can provide insight into the origin of melanocytic tumors and can aid in distinguishing benign from malignant lesions. In this regard, spizoid neoplasms remain a challenging entity. Aside from genetic analyses of tumor tissue, immunohistochemistry remains an essential tool in melanoma diagnostics and TNM classification. With new immunotherapies being approved for advanced melanoma, immunohistochemistry to determine PD-L1 expression has gained clinical interest. While PD-L1 expression is associated with response to PD-1 blockade, a substantial number of patients without PD-L1 expression can still experience tumor remission upon treatment. In this review, current and future developments in melanoma diagnostics with regard to molecular genetics and immunohistochemistry are summarized. The utilization of such analyses in clinical decision making is also discussed.

Children's understanding of the immune system: Integrating the cognitive-developmental and intuitive theories' perspectives

NASA Astrophysics Data System (ADS)

Landry-Boozer, Kristine L.

Traditional cognitive-developmental researchers have provided a large body of evidence supporting the stage-like progression of children's cognitive development. Further, from this body of research comes evidence that children's understanding of HIV/AIDS develops in much the same way as their understanding of other illness-related concepts. Researchers from a newer perspective assert that biological concepts develop from intuitive theories. In general, as children are exposed to relevant content and have opportunities to organize this information, their theories become more accurate and differentiated. According to this perspective, there are no broad structural constraints on developing concepts, as asserted by cognitive developmental theorists. The purpose of the current study was two-fold: to provide support for both theoretical perspectives, while at the same time to explore children's conceptualizations of the immune system, which has not been done previously in the cognitive-developmental literature. One hundred ninety children ranging in age from 4 years old through 11 years old, and a group of adults, participated. Each participant was interviewed regarding health concepts and the body's function in maintaining health. Participants were also asked to report if they had certain experiences that would have led to relevant content exposure. Qualitative analyses were utilized to code the interviews with rubrics based on both theoretical perspectives. Quantitative analyses consisted of a series of univariate ANOVAs (and post hoc tests when appropriate) examining all three coding variables (accuracy, differentiation, and developmental level) across various age-group combinations and exposure groups. Results of these analyses provided support for both theoretical perspectives. When the data were analyzed for developmental level by all ages, a stage-like progression consistent with Piagetian stages emerged. When accuracy and differentiation were examined (intuitive theories perspective), discrete groups could not be formed. Instead, a gradual increase in accuracy and differentiation was observed. Additional support for this perspective was found when the responses of participants who had additional exposure provided responses that were more accurate, differentiated, and sophisticated than those of participants with no additional exposure. Theoretical and educational implications of these findings are discussed.

Lidar-Based Rock-Fall Hazard Characterization of Cliffs

USGS Publications Warehouse

Collins, Brian D.; Greg M.Stock,

2017-01-01

Rock falls from cliffs and other steep slopes present numerous challenges for detailed geological characterization. In steep terrain, rock-fall source areas are both dangerous and difficult to access, severely limiting the ability to make detailed structural and volumetric measurements necessary for hazard assessment. Airborne and terrestrial lidar survey methods can provide high-resolution data needed for volumetric, structural, and deformation analyses of rock falls, potentially making these analyses straightforward and routine. However, specific methods to collect, process, and analyze lidar data of steep cliffs are needed to maximize analytical accuracy and efficiency. This paper presents observations showing how lidar data sets should be collected, filtered, registered, and georeferenced to tailor their use in rock fall characterization. Additional observations concerning surface model construction, volumetric calculations, and deformation analysis are also provided.

75 FR 7440 - Oil and Gas Leasing on Lands Administered by the Dixie National Forest, Supplemental Information...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-19

... climate change and to provide the opportunity for public comment on the additional information. DATES: To.... Comments regarding the SIR should be directed to the issues of air resources and climate change and are for... on including climate change in the environmental analyses for future planning decisions. In...

The Consistency of "TOEIC"® Speaking Scores across Ratings and Tasks. Research Report. ETS RR-17-46

ERIC Educational Resources Information Center

Schmidgall, Jonathan E.

2017-01-01

This report briefly reviews the design and scoring procedure for the "TOEIC"® Speaking test and summarizes existing evidence about the consistency of TOEIC Speaking test scores. It then describes several analyses conducted using generalizability theory to provide additional information about the consistency of scores across different…

Structural Tailoring of Advanced Turboprops (STAT)

NASA Technical Reports Server (NTRS)

Brown, Kenneth W.

1988-01-01

This interim report describes the progress achieved in the structural Tailoring of Advanced Turboprops (STAT) program which was developed to perform numerical optimizations on highly swept propfan blades. The optimization procedure seeks to minimize an objective function, defined as either direct operating cost or aeroelastic differences between a blade and its scaled model, by tuning internal and external geometry variables that must satisfy realistic blade design constraints. This report provides a detailed description of the input, optimization procedures, approximate analyses and refined analyses, as well as validation test cases for the STAT program. In addition, conclusions and recommendations are summarized.

MannDB: A microbial annotation database for protein characterization

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

Zhou, C; Lam, M; Smith, J

2006-05-19

MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-sourcemore » tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports.« less

Is cost effectiveness sustained after weekend inpatient rehabilitation? 12 month follow up from a randomized controlled trial.

PubMed

Brusco, Natasha Kareem; Watts, Jennifer J; Shields, Nora; Taylor, Nicholas F

2015-04-18

Our previous work showed that providing additional rehabilitation on a Saturday was cost effective in the short term from the perspective of the health service provider. This study aimed to evaluate if providing additional rehabilitation on a Saturday was cost effective at 12 months, from a health system perspective inclusive of private costs. Cost effectiveness analyses alongside a single-blinded randomized controlled trial with 12 months follow up inclusive of informal care. Participants were adults admitted to two publicly funded inpatient rehabilitation facilities. The control group received usual care rehabilitation services from Monday to Friday and the intervention group received usual care plus additional Saturday rehabilitation. Incremental cost effectiveness ratios were reported as cost per quality adjusted life year (QALY) gained and for a minimal clinical important difference (MCID) in functional independence. A total of 996 patients [mean age 74 years (SD 13)] were randomly assigned to the intervention (n = 496) or control group (n = 500). The intervention was associated with improvements in QALY and MCID in function, as well as a non-significant reduction in cost from admission to 12 months (mean difference (MD) AUD$6,325; 95% CI -4,081 to 16,730; t test p = 0.23 and MWU p = 0.06), and a significant reduction in cost from admission to 6 months (MD AUD$6,445; 95% CI 3,368 to 9,522; t test p = 0.04 and MWU p = 0.01). There is a high degree of certainty that providing additional rehabilitation services on Saturday is cost effective. Sensitivity analyses varying the cost of informal carers and self-reported health service utilization, favored the intervention. From a health system perspective inclusive of private costs the provision of additional Saturday rehabilitation for inpatients is likely to have sustained cost savings per QALY gained and for a MCID in functional independence, for the inpatient stay and 12 months following discharge, without a cost shift into the community. Australian and New Zealand Clinical Trials Registry November 2009 ACTRN12609000973213.

A study of transonic aerodynamic analysis methods for use with a hypersonic aircraft synthesis code

NASA Technical Reports Server (NTRS)

Sandlin, Doral R.; Davis, Paul Christopher

1992-01-01

A means of performing routine transonic lift, drag, and moment analyses on hypersonic all-body and wing-body configurations were studied. The analysis method is to be used in conjunction with the Hypersonic Vehicle Optimization Code (HAVOC). A review of existing techniques is presented, after which three methods, chosen to represent a spectrum of capabilities, are tested and the results are compared with experimental data. The three methods consist of a wave drag code, a full potential code, and a Navier-Stokes code. The wave drag code, representing the empirical approach, has very fast CPU times, but very limited and sporadic results. The full potential code provides results which compare favorably to the wind tunnel data, but with a dramatic increase in computational time. Even more extreme is the Navier-Stokes code, which provides the most favorable and complete results, but with a very large turnaround time. The full potential code, TRANAIR, is used for additional analyses, because of the superior results it can provide over empirical and semi-empirical methods, and because of its automated grid generation. TRANAIR analyses include an all body hypersonic cruise configuration and an oblique flying wing supersonic transport.

Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus.

PubMed

Jo, Yeonhwa; Choi, Hoseong; Kim, Sang-Min; Kim, Sun-Lim; Lee, Bong Choon; Cho, Won Kyong

2016-08-09

Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study. We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes. Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination.

Hanford waste-form release and sediment interaction: A status report with rationale and recommendations for additional studies

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

Serne, R.J.; Wood, M.I.

1990-05-01

This report documents the currently available geochemical data base for release and retardation for actual Hanford Site materials (wastes and/or sediments). The report also recommends specific laboratory tests and presents the rationale for the recommendations. The purpose of this document is threefold: to summarize currently available information, to provide a strategy for generating additional data, and to provide recommendations on specific data collection methods and tests matrices. This report outlines a data collection approach that relies on feedback from performance analyses to ascertain when adequate data have been collected. The data collection scheme emphasizes laboratory testing based on empiricism. 196more » refs., 4 figs., 36 tabs.« less

Assessment of the Impact of Scheduled Postmarketing Safety Summary Analyses on Regulatory Actions

PubMed Central

Sekine, S; Pinnow, EE; Wu, E; Kurtzig, R; Hall, M; Dal Pan, GJ

2016-01-01

In addition to standard postmarketing drug safety monitoring, Section 915 of the Food and Drug Administration Amendments Act of 2007 (FDAAA) requires the US Food and Drug Administration (FDA) to conduct a summary analysis of adverse event reports to identify risks of a drug or biologic product 18 months after product approval, or after 10,000 patients have used the product, whichever is later. We assessed the extent to which these analyses identified new safety signals and resultant safety-related label changes. Among 458 newly approved products, 300 were the subjects of a scheduled analysis; a new safety signal that resulted in a safety-related label change was found for 11 of these products. Less than 2% of 713 safety-related label changes were based on the scheduled analyses. Our study suggests that the safety summary analyses provide only marginal value over other pharmacovigilance activities. PMID:26853718

yStreX: yeast stress expression database

PubMed Central

Wanichthanarak, Kwanjeera; Nookaew, Intawat; Petranovic, Dina

2014-01-01

Over the past decade genome-wide expression analyses have been often used to study how expression of genes changes in response to various environmental stresses. Many of these studies (such as effects of oxygen concentration, temperature stress, low pH stress, osmotic stress, depletion or limitation of nutrients, addition of different chemical compounds, etc.) have been conducted in the unicellular Eukaryal model, yeast Saccharomyces cerevisiae. However, the lack of a unifying or integrated, bioinformatics platform that would permit efficient and rapid use of all these existing data remain an important issue. To facilitate research by exploiting existing transcription data in the field of yeast physiology, we have developed the yStreX database. It is an online repository of analyzed gene expression data from curated data sets from different studies that capture genome-wide transcriptional changes in response to diverse environmental transitions. The first aim of this online database is to facilitate comparison of cross-platform and cross-laboratory gene expression data. Additionally, we performed different expression analyses, meta-analyses and gene set enrichment analyses; and the results are also deposited in this database. Lastly, we constructed a user-friendly Web interface with interactive visualization to provide intuitive access and to display the queried data for users with no background in bioinformatics. Database URL: http://www.ystrexdb.com PMID:25024351

Improving small-angle X-ray scattering data for structural analyses of the RNA world

PubMed Central

Rambo, Robert P.; Tainer, John A.

2010-01-01

Defining the shape, conformation, or assembly state of an RNA in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to X-ray crystallography. A key addition to this toolbox is small-angle X-ray scattering (SAXS). SAXS provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of RNA structures with minimal requirements for sample concentration and volumes. In principle, SAXS can provide reliable data on small and large RNA molecules. In practice, SAXS investigations of RNA samples can show inconsistencies that suggest limitations in the SAXS experimental analyses or problems with the samples. Here, we show through investigations on the SAM-I riboswitch, the Group I intron P4-P6 domain, 30S ribosomal subunit from Sulfolobus solfataricus (30S), brome mosaic virus tRNA-like structure (BMV TLS), Thermotoga maritima asd lysine riboswitch, the recombinant tRNAval, and yeast tRNAphe that many problems with SAXS experiments on RNA samples derive from heterogeneity of the folded RNA. Furthermore, we propose and test a general approach to reducing these sample limitations for accurate SAXS analyses of RNA. Together our method and results show that SAXS with synchrotron radiation has great potential to provide accurate RNA shapes, conformations, and assembly states in solution that inform RNA biological functions in fundamental ways. PMID:20106957

Dyadic confirmatory factor analysis of the inflammatory bowel disease family responsibility questionnaire.

PubMed

Greenley, Rachel Neff; Reed-Knight, Bonney; Blount, Ronald L; Wilson, Helen W

2013-09-01

Evaluate the factor structure of youth and maternal involvement ratings on the Inflammatory Bowel Disease Family Responsibility Questionnaire, a measure of family allocation of condition management responsibilities in pediatric inflammatory bowel disease. Participants included 251 youth aged 11-18 years with inflammatory bowel disease and their mothers. Item-level descriptive analyses, subscale internal consistency estimates, and confirmatory factor analyses of youth and maternal involvement were conducted using a dyadic data-analytic approach. Results supported the validity of 4 conceptually derived subscales including general health maintenance, social aspects, condition management tasks, and nutrition domains. Additionally, results indicated adequate support for the factor structure of a 21-item youth involvement measure and strong support for a 16-item maternal involvement measure. Additional empirical support for the validity of the Inflammatory Bowel Disease Family Responsibility Questionnaire was provided. Future research to replicate current findings and to examine the measure's clinical utility is warranted.

24 CFR 81.65 - Other information and analyses.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Other information and analyses. 81... information and analyses. When deemed appropriate and requested in writing, on a case by-case basis, by the... conduct additional analyses concerning any such report. A GSE shall submit additional reports or other...

24 CFR 81.65 - Other information and analyses.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Other information and analyses. 81... information and analyses. When deemed appropriate and requested in writing, on a case by-case basis, by the... conduct additional analyses concerning any such report. A GSE shall submit additional reports or other...

24 CFR 81.65 - Other information and analyses.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Other information and analyses. 81... information and analyses. When deemed appropriate and requested in writing, on a case by-case basis, by the... conduct additional analyses concerning any such report. A GSE shall submit additional reports or other...

24 CFR 81.65 - Other information and analyses.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Other information and analyses. 81... information and analyses. When deemed appropriate and requested in writing, on a case by-case basis, by the... conduct additional analyses concerning any such report. A GSE shall submit additional reports or other...

24 CFR 81.65 - Other information and analyses.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Other information and analyses. 81... information and analyses. When deemed appropriate and requested in writing, on a case by-case basis, by the... conduct additional analyses concerning any such report. A GSE shall submit additional reports or other...

An entropy-based analysis of lane changing behavior: An interactive approach.

PubMed

Kosun, Caglar; Ozdemir, Serhan

2017-05-19

As a novelty, this article proposes the nonadditive entropy framework for the description of driver behaviors during lane changing. The authors also state that this entropy framework governs the lane changing behavior in traffic flow in accordance with the long-range vehicular interactions and traffic safety. The nonadditive entropy framework is the new generalized theory of thermostatistical mechanics. Vehicular interactions during lane changing are considered within this framework. The interactive approach for the lane changing behavior of the drivers is presented in the traffic flow scenarios presented in the article. According to the traffic flow scenarios, 4 categories of traffic flow and driver behaviors are obtained. Through the scenarios, comparative analyses of nonadditive and additive entropy domains are also provided. Two quadrants of the categories belong to the nonadditive entropy; the rest are involved in the additive entropy domain. Driving behaviors are extracted and the scenarios depict that nonadditivity matches safe driving well, whereas additivity corresponds to unsafe driving. Furthermore, the cooperative traffic system is considered in nonadditivity where the long-range interactions are present. However, the uncooperative traffic system falls into the additivity domain. The analyses also state that there would be possible traffic flow transitions among the quadrants. This article shows that lane changing behavior could be generalized as nonadditive, with additivity as a special case, based on the given traffic conditions. The nearest and close neighbor models are well within the conventional additive entropy framework. In this article, both the long-range vehicular interactions and safe driving behavior in traffic are handled in the nonadditive entropy domain. It is also inferred that the Tsallis entropy region would correspond to mandatory lane changing behavior, whereas additive and either the extensive or nonextensive entropy region would match discretionary lane changing behavior. This article states that driver behaviors would be in the nonadditive entropy domain to provide a safe traffic stream and hence with vehicle accident prevention in mind.

An Assessment of the State-of-the-Art in Multidisciplinary Aeromechanical Analyses

DTIC Science & Technology

2008-01-01

monolithic formulations. In summary, for aerospace structures, partitioned formulations provide fundamental advantages over fully coupled ones, in addition...important frequencies of local analysis directly to global analysis using detailed modeling. Performed ju- diciously, based on a fundamental understanding of...in 2000 has com- prehensively described the problem, and reviewed the status of fundamental understanding, experimental data, and analytical

PARAMETRIC AND NON PARAMETRIC (MARS: MULTIVARIATE ADDITIVE REGRESSION SPLINES) LOGISTIC REGRESSIONS FOR PREDICTION OF A DICHOTOMOUS RESPONSE VARIABLE WITH AN EXAMPLE FOR PRESENCE/ABSENCE OF AMPHIBIANS

EPA Science Inventory

The purpose of this report is to provide a reference manual that could be used by investigators for making informed use of logistic regression using two methods (standard logistic regression and MARS). The details for analyses of relationships between a dependent binary response ...

Skylab explores the Earth

NASA Technical Reports Server (NTRS)

1977-01-01

Data from visual observations are integrated with results of analyses of approxmately 600 of the nearly 2000 photographs taken of Earth during the 84-day Skylab 4 mission to provide additional information on (1) Earth features and processes; (2) operational procedures and constraints in observing and photographing the planet; and (3) the use of man in real-time analysis of oceanic and atmospheric phenomena.

Laser System Reliability

DTIC Science & Technology

1977-03-01

system acquisition cycle since they provide necessary inputs to comparative analyses, cost/benefit trade -offs, and system simulations. In addition, the...Management Program from above performs the function of analyzing the system trade -offs with respect to reliability to determine a reliability goal...one encounters the problem of comparing present dollars with future dollars. In this analysis, we are trading off costs expended initially (or at

75 FR 33615 - Draft EPA's Reanalysis of Key Issues Related to Dioxin Toxicity and Response to NAS Comments (EPA...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-14

... the IRIS Program, EPA provides the highest quality science-based human health assessments to support... comments included in the National Academy of Sciences (NAS) 2006 report. In addition, it includes new analyses on potential human effects that may result from exposure to 2,3,7,8- tetrachlorodibenzo-p-dioxin...

Towards interoperable and reproducible QSAR analyses: Exchange of datasets.

PubMed

Spjuth, Ola; Willighagen, Egon L; Guha, Rajarshi; Eklund, Martin; Wikberg, Jarl Es

2010-06-30

QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but also allows for analyzing the effect descriptors have on the statistical model's performance. The presented Bioclipse plugins equip scientists with graphical tools that make QSAR-ML easily accessible for the community.

Phase 1 environmental report for the Advanced Neutron Source at Oak Ridge National Laboratory

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

Blasing, T.J.; Brown, R.A.; Cada, G.F.

1992-02-01

The US Department of Energy (DOE) has proposed the construction and operation of the Advanced Neutron Source (ANS), a 330-MW(f) reactor, at Oak Ridge National Laboratory (ORNL) to support neutron scattering and nuclear physics experiments. ANS would provide a steady-state source of neutrons that are thermalized to produce sources of hot, cold, and very coal neutrons. The use of these neutrons in ANS experiment facilities would be an essential component of national research efforts in basic materials science. Additionally, ANS capabilities would include production of transplutonium isotopes, irradiation of potential fusion and fission reactor materials, activation analysis, and production ofmore » medical and industrial isotopes such as {sup 252}Cf. Although ANS would not require licensing by the US Nuclear Regulatory Commission (NRC), DOE regards the design, construction, and operation of ANS as activities that would produce a licensable facility; that is, DOE is following the regulatory guidelines that NRC would apply if NRC were licensing the facility. Those guidelines include instructions for the preparation of an environmental report (ER), a compilation of available data and preliminary analyses regarding the environmental impacts of nuclear facility construction and operation. The ER, described and outlined in NRC Regulatory Guide 4.2, serves as a background document to facilitate the preparation of environmental impact statements (EISs). Using Regulatory Guide 4.2 as a model, this ANS ER provides analyses and information specific to the ANS site and area that can be adopted (and modified, if necessary) for the ANS EIS. The ER is being prepared in two phases. Phase 1 ER includes many of the data and analyses needed to prepare the EIS but does not include data or analyses of alternate sites or alternate technologies. Phase 2 ER will include the additional data and analyses stipulated by Regulatory Guide 4.2.« less

Towards interoperable and reproducible QSAR analyses: Exchange of datasets

PubMed Central

2010-01-01

Background QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. Results We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Conclusions Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but also allows for analyzing the effect descriptors have on the statistical model's performance. The presented Bioclipse plugins equip scientists with graphical tools that make QSAR-ML easily accessible for the community. PMID:20591161

CytoCom: a Cytoscape app to visualize, query and analyse disease comorbidity networks.

PubMed

Moni, Mohammad Ali; Xu, Haoming; Liò, Pietro

2015-03-15

CytoCom is an interactive plugin for Cytoscape that can be used to search, explore, analyse and visualize human disease comorbidity network. It represents disease-disease associations in terms of bipartite graphs and provides International Classification of Diseases, Ninth Revision (ICD9)-centric and disease name centric views of disease information. It allows users to find associations between diseases based on the two measures: Relative Risk (RR) and [Formula: see text]-correlation values. In the disease network, the size of each node is based on the prevalence of that disease. CytoCom is capable of clustering disease network based on the ICD9 disease category. It provides user-friendly access that facilitates exploration of human diseases, and finds additional associated diseases by double-clicking a node in the existing network. Additional comorbid diseases are then connected to the existing network. It is able to assist users for interpretation and exploration of the human diseases by a variety of built-in functions. Moreover, CytoCom permits multi-colouring of disease nodes according to standard disease classification for expedient visualization. © The Author 2014. Published by Oxford University Press.

Teacher, parent, and peer reports of early aggression as screening measures for long-term maladaptive outcomes: Who provides the most useful information?

PubMed Central

Clemans, Katherine H.; Musci, Rashelle J.; Leoutsakos, Jeannie-Marie S.; Ialongo, Nicholas S.

2014-01-01

Objective This study compared the ability of teacher, parent, and peer reports of aggressive behavior in early childhood to accurately classify cases of maladaptive outcomes in late adolescence and early adulthood. Method Weighted kappa analyses determined optimal cut points and relative classification accuracy among teacher, parent, and peer reports of aggression assessed for 691 students (54% male; 84% African American, 13% White) in the fall of first grade. Outcomes included antisocial personality, substance use, incarceration history, risky sexual behavior, and failure to graduate from high school on time. Results Peer reports were the most accurate classifier of all outcomes in the full sample. For most outcomes, the addition of teacher or parent reports did not improve overall classification accuracy once peer reports were accounted for. Additional gender-specific and adjusted kappa analyses supported the superior classification utility of the peer report measure. Conclusion The results suggest that peer reports provided the most useful classification information of the three aggression measures. Implications for targeted intervention efforts which use screening measures to identify at-risk children are discussed. PMID:24512126

Design and development of a web-based application for diabetes patient data management.

PubMed

Deo, S S; Deobagkar, D N; Deobagkar, Deepti D

2005-01-01

A web-based database management system developed for collecting, managing and analysing information of diabetes patients is described here. It is a searchable, client-server, relational database application, developed on the Windows platform using Oracle, Active Server Pages (ASP), Visual Basic Script (VB Script) and Java Script. The software is menu-driven and allows authorized healthcare providers to access, enter, update and analyse patient information. Graphical representation of data can be generated by the system using bar charts and pie charts. An interactive web interface allows users to query the database and generate reports. Alpha- and beta-testing of the system was carried out and the system at present holds records of 500 diabetes patients and is found useful in diagnosis and treatment. In addition to providing patient data on a continuous basis in a simple format, the system is used in population and comparative analysis. It has proved to be of significant advantage to the healthcare provider as compared to the paper-based system.

A marked correlation function for constraining modified gravity models

NASA Astrophysics Data System (ADS)

White, Martin

2016-11-01

Future large scale structure surveys will provide increasingly tight constraints on our cosmological model. These surveys will report results on the distance scale and growth rate of perturbations through measurements of Baryon Acoustic Oscillations and Redshift-Space Distortions. It is interesting to ask: what further analyses should become routine, so as to test as-yet-unknown models of cosmic acceleration? Models which aim to explain the accelerated expansion rate of the Universe by modifications to General Relativity often invoke screening mechanisms which can imprint a non-standard density dependence on their predictions. This suggests density-dependent clustering as a `generic' constraint. This paper argues that a density-marked correlation function provides a density-dependent statistic which is easy to compute and report and requires minimal additional infrastructure beyond what is routinely available to such survey analyses. We give one realization of this idea and study it using low order perturbation theory. We encourage groups developing modified gravity theories to see whether such statistics provide discriminatory power for their models.

Integrative Approaches to Understanding the Pathogenic Role of Genetic Variation in Rheumatic Diseases.

PubMed

Laufer, Vincent A; Chen, Jake Y; Langefeld, Carl D; Bridges, S Louis

2017-08-01

The use of high-throughput omics may help to understand the contribution of genetic variants to the pathogenesis of rheumatic diseases. We discuss the concept of missing heritability: that genetic variants do not explain the heritability of rheumatoid arthritis and related rheumatologic conditions. In addition to an overview of how integrative data analysis can lead to novel insights into mechanisms of rheumatic diseases, we describe statistical approaches to prioritizing genetic variants for future functional analyses. We illustrate how analyses of large datasets provide hope for improved approaches to the diagnosis, treatment, and prevention of rheumatic diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

Spectral and fractal analyses of geomagnetic and riometric antarctic observations and a multidimensional index of activity

NASA Astrophysics Data System (ADS)

de Santis, A.; de Franceschi, G.; Perrone, L.

1997-06-01

The Istituto Nazionale di Geofisica under the P.N.R.A. (National Program of Research in Antarctica) has the responsibility of acquiring geophysical observations at the Italian Antarctic Base of Terra Nova Bay. Among others, geomagnetic and riometric data can provide some new insights into local and global activity of the magnetosphere-ionosphere coupling. This article investigates some properties of these kinds of data by means of spectral and fractal analyses. In addition, a multidimensional index is derived from this single-point dataset to represent not only the local but also the global state of the magnetospheric activity.

Going above and beyond for implementation: the development and validity testing of the Implementation Citizenship Behavior Scale (ICBS).

PubMed

Ehrhart, Mark G; Aarons, Gregory A; Farahnak, Lauren R

2015-05-07

In line with recent research on the role of the inner context of organizations in implementation effectiveness, this study extends research on organizational citizenship behavior (OCB) to the domain of evidence-based practice (EBP) implementation. OCB encompasses those behaviors that go beyond what is required for a given job that contribute to greater organizational effectiveness. The goal of this study was to develop and test a measure of implementation citizenship behavior (ICB) or those behaviors that employees perform that go above and beyond what is required in order to support EBP implementation. The primary participants were 68 supervisors from ten mental health agencies throughout California. Items measuring ICB were developed based on past research on OCB and in consultation with experts on EBP implementation in mental health settings. Supervisors rated 357 of their subordinates on ICB and implementation success. In addition, 292 of the subordinates provided data on self-rated performance, attitudes towards EBPs, work experience, and full-time status. The supervisor sample was randomly split, with half used for exploratory factor analyses and the other half for confirmatory factor analyses. The entire sample of supervisors and subordinates was utilized for analyses assessing the reliability and construct validity of the measure. Exploratory factor analyses supported the proposed two-factor structure of the Implementation Citizenship Behavior Scale (ICBS): (1) Helping Others and (2) Keeping Informed. Confirmatory factor analyses with the other half of the sample supported the factor structure. Additional analyses supported the reliability and construct validity for the ICBS. The ICBS is a pragmatic brief measure (six items) that captures critical behaviors employees perform to go above and beyond the call of duty to support EBP implementation, including helping their fellow employees on implementation-related activities and keeping informed about issues related to EBP and implementation efforts. The ICBS can be used by researchers to better understand the outcomes of improved organizational support for implementation (i.e., implementation climate) and the proximal predictors of implementation effectiveness. The ICBS can also provide insight for organizations, practitioners, and managers by focusing on key employee behaviors that should increase the probability of implementation success.

Using computer graphics to design Space Station Freedom viewing

NASA Technical Reports Server (NTRS)

Goldsberry, Betty S.; Lippert, Buddy O.; Mckee, Sandra D.; Lewis, James L., Jr.; Mount, Francis E.

1993-01-01

Viewing requirements were identified early in the Space Station Freedom program for both direct viewing via windows and indirect viewing via cameras and closed-circuit television (CCTV). These requirements reside in NASA Program Definition and Requirements Document (PDRD), Section 3: Space Station Systems Requirements. Currently, analyses are addressing the feasibility of direct and indirect viewing. The goal of these analyses is to determine the optimum locations for the windows, cameras, and CCTV's in order to meet established requirements, to adequately support space station assembly, and to operate on-board equipment. PLAID, a three-dimensional computer graphics program developed at NASA JSC, was selected for use as the major tool in these analyses. PLAID provides the capability to simulate the assembly of the station as well as to examine operations as the station evolves. This program has been used successfully as a tool to analyze general viewing conditions for many Space Shuttle elements and can be used for virtually all Space Station components. Additionally, PLAID provides the ability to integrate an anthropometric scale-modeled human (representing a crew member) with interior and exterior architecture.

Conceptual and statistical problems associated with the use of diversity indices in ecology.

PubMed

Barrantes, Gilbert; Sandoval, Luis

2009-09-01

Diversity indices, particularly the Shannon-Wiener index, have extensively been used in analyzing patterns of diversity at different geographic and ecological scales. These indices have serious conceptual and statistical problems which make comparisons of species richness or species abundances across communities nearly impossible. There is often no a single statistical method that retains all information needed to answer even a simple question. However, multivariate analyses could be used instead of diversity indices, such as cluster analyses or multiple regressions. More complex multivariate analyses, such as Canonical Correspondence Analysis, provide very valuable information on environmental variables associated to the presence and abundance of the species in a community. In addition, particular hypotheses associated to changes in species richness across localities, or change in abundance of one, or a group of species can be tested using univariate, bivariate, and/or rarefaction statistical tests. The rarefaction method has proved to be robust to standardize all samples to a common size. Even the simplest method as reporting the number of species per taxonomic category possibly provides more information than a diversity index value.

COCAP: a carbon dioxide analyser for small unmanned aircraft systems

NASA Astrophysics Data System (ADS)

Kunz, Martin; Lavric, Jost V.; Gerbig, Christoph; Tans, Pieter; Neff, Don; Hummelgård, Christine; Martin, Hans; Rödjegård, Henrik; Wrenger, Burkhard; Heimann, Martin

2018-03-01

Unmanned aircraft systems (UASs) could provide a cost-effective way to close gaps in the observation of the carbon cycle, provided that small yet accurate analysers are available. We have developed a COmpact Carbon dioxide analyser for Airborne Platforms (COCAP). The accuracy of COCAP's carbon dioxide (CO2) measurements is ensured by calibration in an environmental chamber, regular calibration in the field and by chemical drying of sampled air. In addition, the package contains a lightweight thermal stabilisation system that reduces the influence of ambient temperature changes on the CO2 sensor by 2 orders of magnitude. During validation of COCAP's CO2 measurements in simulated and real flights we found a measurement error of 1.2 µmol mol-1 or better with no indication of bias. COCAP is a self-contained package that has proven well suited for the operation on board small UASs. Besides carbon dioxide dry air mole fraction it also measures air temperature, humidity and pressure. We describe the measurement system and our calibration strategy in detail to support others in tapping the potential of UASs for atmospheric trace gas measurements.

Molecular characterization of breast cancer cell lines through multiple omic approaches.

PubMed

Smith, Shari E; Mellor, Paul; Ward, Alison K; Kendall, Stephanie; McDonald, Megan; Vizeacoumar, Frederick S; Vizeacoumar, Franco J; Napper, Scott; Anderson, Deborah H

2017-06-05

Breast cancer cell lines are frequently used as model systems to study the cellular properties and biology of breast cancer. Our objective was to characterize a large, commonly employed panel of breast cancer cell lines obtained from the American Type Culture Collection (ATCC 30-4500 K) to enable researchers to make more informed decisions in selecting cell lines for specific studies. Information about these cell lines was obtained from a wide variety of sources. In addition, new information about cellular pathways that are activated within each cell line was generated. We determined key protein expression data using immunoblot analyses. In addition, two analyses on serum-starved cells were carried out to identify cellular proteins and pathways that are activated in these cells. These analyses were performed using a commercial PathScan array and a novel and more extensive phosphopeptide-based kinome analysis that queries 1290 phosphorylation events in major signaling pathways. Data about this panel of breast cancer cell lines was also accessed from several online sources, compiled and summarized for the following areas: molecular classification, mRNA expression, mutational status of key proteins and other possible cancer-associated mutations, and the tumorigenic and metastatic capacity in mouse xenograft models of breast cancer. The cell lines that were characterized included 10 estrogen receptor (ER)-positive, 12 human epidermal growth factor receptor 2 (HER2)-amplified and 18 triple negative breast cancer cell lines, in addition to 4 non-tumorigenic breast cell lines. Within each subtype, there was significant genetic heterogeneity that could impact both the selection of model cell lines and the interpretation of the results obtained. To capture the net activation of key signaling pathways as a result of these mutational combinations, profiled pathway activation status was examined. This provided further clarity for which cell lines were particularly deregulated in common or unique ways. These two new kinase or "Kin-OMIC" analyses add another dimension of important data about these frequently used breast cancer cell lines. This will assist researchers in selecting the most appropriate cell lines to use for breast cancer studies and provide context for the interpretation of the emerging results.

Recommendations for Conduct, Methodological Practices, and Reporting of Cost-effectiveness Analyses: Second Panel on Cost-Effectiveness in Health and Medicine.

PubMed

Sanders, Gillian D; Neumann, Peter J; Basu, Anirban; Brock, Dan W; Feeny, David; Krahn, Murray; Kuntz, Karen M; Meltzer, David O; Owens, Douglas K; Prosser, Lisa A; Salomon, Joshua A; Sculpher, Mark J; Trikalinos, Thomas A; Russell, Louise B; Siegel, Joanna E; Ganiats, Theodore G

2016-09-13

Since publication of the report by the Panel on Cost-Effectiveness in Health and Medicine in 1996, researchers have advanced the methods of cost-effectiveness analysis, and policy makers have experimented with its application. The need to deliver health care efficiently and the importance of using analytic techniques to understand the clinical and economic consequences of strategies to improve health have increased in recent years. To review the state of the field and provide recommendations to improve the quality of cost-effectiveness analyses. The intended audiences include researchers, government policy makers, public health officials, health care administrators, payers, businesses, clinicians, patients, and consumers. In 2012, the Second Panel on Cost-Effectiveness in Health and Medicine was formed and included 2 co-chairs, 13 members, and 3 additional members of a leadership group. These members were selected on the basis of their experience in the field to provide broad expertise in the design, conduct, and use of cost-effectiveness analyses. Over the next 3.5 years, the panel developed recommendations by consensus. These recommendations were then reviewed by invited external reviewers and through a public posting process. The concept of a "reference case" and a set of standard methodological practices that all cost-effectiveness analyses should follow to improve quality and comparability are recommended. All cost-effectiveness analyses should report 2 reference case analyses: one based on a health care sector perspective and another based on a societal perspective. The use of an "impact inventory," which is a structured table that contains consequences (both inside and outside the formal health care sector), intended to clarify the scope and boundaries of the 2 reference case analyses is also recommended. This special communication reviews these recommendations and others concerning the estimation of the consequences of interventions, the valuation of health outcomes, and the reporting of cost-effectiveness analyses. The Second Panel reviewed the current status of the field of cost-effectiveness analysis and developed a new set of recommendations. Major changes include the recommendation to perform analyses from 2 reference case perspectives and to provide an impact inventory to clarify included consequences.

1995 Annual epidemiologic surveillance report for Pantex Plant

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

NONE

This report provides a summary of epidemiologic surveillance data collected from the Pantex Plant from January 1, 1995 through December 31,1995. The data were collected by a coordinator at Pantex and submitted to the Epidemiologic Surveillance Data Center,located at Oak Ridge Institute for Science and Education, where quality control procedures and data analyses were carried out. The data presented apply only to Pantex. The main sections of the report are the same as in previous years; the 1995 report provides additional information describing the work force by age and occupational groups.

Report endorses data sharing

NASA Astrophysics Data System (ADS)

The potential benefits of sharing data so outweigh its costs that investigators should be required to include plans for sharing data as part of their grant proposals, according to recommendations issued recently by the Committee on National Statistics (CNSTAT) of the National Research Council (NRC).In their report Sharing Research Data, CNSTAT also recommended that “Journals should give more emphasis to reports of secondary analyses and to replications,” provided that the original collections of data receive full credit. In addition, “Journal editors should require authors to provide access to data during the peer review process.”

Sockeye: A 3D Environment for Comparative Genomics

PubMed Central

Montgomery, Stephen B.; Astakhova, Tamara; Bilenky, Mikhail; Birney, Ewan; Fu, Tony; Hassel, Maik; Melsopp, Craig; Rak, Marcin; Robertson, A. Gordon; Sleumer, Monica; Siddiqui, Asim S.; Jones, Steven J.M.

2004-01-01

Comparative genomics techniques are used in bioinformatics analyses to identify the structural and functional properties of DNA sequences. As the amount of available sequence data steadily increases, the ability to perform large-scale comparative analyses has become increasingly relevant. In addition, the growing complexity of genomic feature annotation means that new approaches to genomic visualization need to be explored. We have developed a Java-based application called Sockeye that uses three-dimensional (3D) graphics technology to facilitate the visualization of annotation and conservation across multiple sequences. This software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects are displayed in Sockeye by using custom 3D models. Ensembl-derived and imported sequences can be analyzed by using a suite of multiple and pair-wise alignment algorithms. The results of these comparative analyses are also displayed in the 3D environment of Sockeye. By using the Java3D API to visualize genomic data in a 3D environment, we are able to compactly display cross-sequence comparisons. This provides the user with a novel platform for visualizing and comparing genomic feature organization. PMID:15123592

Children's patterns of reasoning about reading and addition concepts.

PubMed

Farrington-Flint, Lee; Canobi, Katherine H; Wood, Clare; Faulkner, Dorothy

2010-06-01

Children's reasoning was examined within two educational contexts (word reading and addition) so as to understand the factors that contribute to relational reasoning in the two domains. Sixty-seven 5- to 7-year-olds were given a series of related words to read or single-digit addition items to solve (interspersed with unrelated items). The frequency, accuracy, and response times of children's self-reports on the conceptually related items provided a measure of relational reasoning, while performance on the unrelated addition and reading items provided a measure of procedural skill. The results indicated that the children's ability to use conceptual relations to solve both reading and addition problems enhanced speed and accuracy levels, increased with age, and was related to procedural skill. However, regression analyses revealed that domain-specific competencies can best explain the use of conceptual relations in both reading and addition. Moreover, a cluster analysis revealed that children differ according to the academic domain in which they first apply conceptual relations and these differences are related to individual variation in their procedural skills within these particular domains. These results highlight the developmental significance of relational reasoning in the context of reading and addition and underscore the importance of concept-procedure links in explaining children's literacy and arithmetical development.

MHD Advanced Power Train Phase I, Final Report, Volume 7

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

A. R. Jones

This appendix provides additional data in support of the MHD/Steam Power Plant Analyses reported in report Volume 5. The data is in the form of 3PA/SUMARY computer code printouts. The order of presentation in all four cases is as follows: (1) Overall Performance; (2) Component/Subsystem Information; (3) Plant Cost Accounts Summary; and (4) Plant Costing Details and Cost of Electricity.

CALiPER Report 20.5: Chromaticity Shift Modes of LED PAR38 Lamps Operated in Steady-State Conditions

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

Davis, J. Lynn; Young, Joseph; Royer, Michael

2016-02-26

This report builds on CALiPER Report 20.4, focusing on the same 32 PAR38 lamps but investigating causes of color shift and parametric failures. It provides a tear-down analysis of the lamp models and performs additional analyses on the spectroradiometric data obtained using a specially developed automated long-term test apparatus.

Advanced Aeroservoelastic Testing and Data Analysis (Les Essais Aeroservoelastiques et l’Analyse des Donnees).

DTIC Science & Technology

1995-11-01

network - based AFS concepts. Neural networks can addition of vanes in each engine exhaust for thrust provide...parameter estimation programs 19-11 8.6 Neural Network Based Methods unknown parameters of the postulated state space model Artificial neural network ...Forward Neural Network the network that the applicability of the recurrent neural and ii) Recurrent Neural Network [117-119]. network to

The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics.

PubMed

Fernández, Rosa; Sharma, Prashant P; Tourinho, Ana Lúcia; Giribet, Gonzalo

2017-02-22

Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group. © 2017 The Author(s).

The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics

PubMed Central

Sharma, Prashant P.; Tourinho, Ana Lúcia

2017-01-01

Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group. PMID:28228511

Unraveling the evolutionary radiation of the families of the Zingiberales using morphological and molecular evidence.

PubMed

Kress, W J; Prince, L M; Hahn, W J; Zimmer, E A

2001-01-01

The Zingiberales are a tropical group of monocotyledons that includes bananas, gingers, and their relatives. The phylogenetic relationships among the eight families currently recognized are investigated here by using parsimony and maximum likelihood analyses of four character sets: morphological features (1), and sequence data of the (2) chloroplast rbcL gene, (3) chloroplast atpB gene, and (4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most-parsimonious tree. None of the molecular datasets alone completely resolves interfamilial relationships. The analyses of the combined molecular dataset provide more resolution than do those of individual genes, and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggests that the Zingiberales originated in the Early Cretaceous and underwent a rapid radiation in the mid-Cretaceous, by which time most extant family lineages had diverged.

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways.

PubMed

Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian'an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O'Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tõnu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

2012-09-01

Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have increased the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin concentration showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional analysis of these newly discovered loci will further improve our understanding of glycemic control.

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways

PubMed Central

Scott, Robert A; Lagou, Vasiliki; Welch, Ryan P; Wheeler, Eleanor; Montasser, May E; Luan, Jian’an; Mägi, Reedik; Strawbridge, Rona J; Rehnberg, Emil; Gustafsson, Stefan; Kanoni, Stavroula; Rasmussen-Torvik, Laura J; Yengo, Loïc; Lecoeur, Cecile; Shungin, Dmitry; Sanna, Serena; Sidore, Carlo; Johnson, Paul C D; Jukema, J Wouter; Johnson, Toby; Mahajan, Anubha; Verweij, Niek; Thorleifsson, Gudmar; Hottenga, Jouke-Jan; Shah, Sonia; Smith, Albert V; Sennblad, Bengt; Gieger, Christian; Salo, Perttu; Perola, Markus; Timpson, Nicholas J; Evans, David M; Pourcain, Beate St; Wu, Ying; Andrews, Jeanette S; Hui, Jennie; Bielak, Lawrence F; Zhao, Wei; Horikoshi, Momoko; Navarro, Pau; Isaacs, Aaron; O’Connell, Jeffrey R; Stirrups, Kathleen; Vitart, Veronique; Hayward, Caroline; Esko, Tönu; Mihailov, Evelin; Fraser, Ross M; Fall, Tove; Voight, Benjamin F; Raychaudhuri, Soumya; Chen, Han; Lindgren, Cecilia M; Morris, Andrew P; Rayner, Nigel W; Robertson, Neil; Rybin, Denis; Liu, Ching-Ti; Beckmann, Jacques S; Willems, Sara M; Chines, Peter S; Jackson, Anne U; Kang, Hyun Min; Stringham, Heather M; Song, Kijoung; Tanaka, Toshiko; Peden, John F; Goel, Anuj; Hicks, Andrew A; An, Ping; Müller-Nurasyid, Martina; Franco-Cereceda, Anders; Folkersen, Lasse; Marullo, Letizia; Jansen, Hanneke; Oldehinkel, Albertine J; Bruinenberg, Marcel; Pankow, James S; North, Kari E; Forouhi, Nita G; Loos, Ruth J F; Edkins, Sarah; Varga, Tibor V; Hallmans, Göran; Oksa, Heikki; Antonella, Mulas; Nagaraja, Ramaiah; Trompet, Stella; Ford, Ian; Bakker, Stephan J L; Kong, Augustine; Kumari, Meena; Gigante, Bruna; Herder, Christian; Munroe, Patricia B; Caulfield, Mark; Antti, Jula; Mangino, Massimo; Small, Kerrin; Miljkovic, Iva; Liu, Yongmei; Atalay, Mustafa; Kiess, Wieland; James, Alan L; Rivadeneira, Fernando; Uitterlinden, Andre G; Palmer, Colin N A; Doney, Alex S F; Willemsen, Gonneke; Smit, Johannes H; Campbell, Susan; Polasek, Ozren; Bonnycastle, Lori L; Hercberg, Serge; Dimitriou, Maria; Bolton, Jennifer L; Fowkes, Gerard R; Kovacs, Peter; Lindström, Jaana; Zemunik, Tatijana; Bandinelli, Stefania; Wild, Sarah H; Basart, Hanneke V; Rathmann, Wolfgang; Grallert, Harald; Maerz, Winfried; Kleber, Marcus E; Boehm, Bernhard O; Peters, Annette; Pramstaller, Peter P; Province, Michael A; Borecki, Ingrid B; Hastie, Nicholas D; Rudan, Igor; Campbell, Harry; Watkins, Hugh; Farrall, Martin; Stumvoll, Michael; Ferrucci, Luigi; Waterworth, Dawn M; Bergman, Richard N; Collins, Francis S; Tuomilehto, Jaakko; Watanabe, Richard M; de Geus, Eco J C; Penninx, Brenda W; Hofman, Albert; Oostra, Ben A; Psaty, Bruce M; Vollenweider, Peter; Wilson, James F; Wright, Alan F; Hovingh, G Kees; Metspalu, Andres; Uusitupa, Matti; Magnusson, Patrik K E; Kyvik, Kirsten O; Kaprio, Jaakko; Price, Jackie F; Dedoussis, George V; Deloukas, Panos; Meneton, Pierre; Lind, Lars; Boehnke, Michael; Shuldiner, Alan R; van Duijn, Cornelia M; Morris, Andrew D; Toenjes, Anke; Peyser, Patricia A; Beilby, John P; Körner, Antje; Kuusisto, Johanna; Laakso, Markku; Bornstein, Stefan R; Schwarz, Peter E H; Lakka, Timo A; Rauramaa, Rainer; Adair, Linda S; Smith, George Davey; Spector, Tim D; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Gudnason, Vilmundur; Kivimaki, Mika; Hingorani, Aroon; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Boomsma, Dorret I; Stefansson, Kari; van der Harst, Pim; Dupuis, Josée; Pedersen, Nancy L; Sattar, Naveed; Harris, Tamara B; Cucca, Francesco; Ripatti, Samuli; Salomaa, Veikko; Mohlke, Karen L; Balkau, Beverley; Froguel, Philippe; Pouta, Anneli; Jarvelin, Marjo-Riitta; Wareham, Nicholas J; Bouatia-Naji, Nabila; McCarthy, Mark I; Franks, Paul W; Meigs, James B; Teslovich, Tanya M; Florez, Jose C; Langenberg, Claudia; Ingelsson, Erik; Prokopenko, Inga; Barroso, Inês

2012-01-01

Through genome-wide association meta-analyses of up to 133,010 individuals of European ancestry without diabetes, including individuals newly genotyped using the Metabochip, we have raised the number of confirmed loci influencing glycemic traits to 53, of which 33 also increase type 2 diabetes risk (q < 0.05). Loci influencing fasting insulin showed association with lipid levels and fat distribution, suggesting impact on insulin resistance. Gene-based analyses identified further biologically plausible loci, suggesting that additional loci beyond those reaching genome-wide significance are likely to represent real associations. This conclusion is supported by an excess of directionally consistent and nominally significant signals between discovery and follow-up studies. Functional follow-up of these newly discovered loci will further improve our understanding of glycemic control. PMID:22885924

BrainAGE score indicates accelerated brain aging in schizophrenia, but not bipolar disorder.

PubMed

Nenadić, Igor; Dietzek, Maren; Langbein, Kerstin; Sauer, Heinrich; Gaser, Christian

2017-08-30

BrainAGE (brain age gap estimation) is a novel morphometric parameter providing a univariate score derived from multivariate voxel-wise analyses. It uses a machine learning approach and can be used to analyse deviation from physiological developmental or aging-related trajectories. Using structural MRI data and BrainAGE quantification of acceleration or deceleration of in individual aging, we analysed data from 45 schizophrenia patients, 22 bipolar I disorder patients (mostly with previous psychotic symptoms / episodes), and 70 healthy controls. We found significantly higher BrainAGE scores in schizophrenia, but not bipolar disorder patients. Our findings indicate significantly accelerated brain structural aging in schizophrenia. This suggests, that despite the conceptualisation of schizophrenia as a neurodevelopmental disorder, there might be an additional progressive pathogenic component. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

STS-1 operational flight profile. Volume 5: Descent, cycle 3. Appendix C: Monte Carlo dispersion analysis

NASA Technical Reports Server (NTRS)

1980-01-01

The results of three nonlinear the Monte Carlo dispersion analyses for the Space Transportation System 1 Flight (STS-1) Orbiter Descent Operational Flight Profile, Cycle 3 are presented. Fifty randomly selected simulation for the end of mission (EOM) descent, the abort once around (AOA) descent targeted line are steep target line, and the AOA descent targeted to the shallow target line are analyzed. These analyses compare the flight environment with system and operational constraints on the flight environment and in some cases use simplified system models as an aid in assessing the STS-1 descent flight profile. In addition, descent flight envelops are provided as a data base for use by system specialists to determine the flight readiness for STS-1. The results of these dispersion analyses supersede results of the dispersion analysis previously documented.

Alterations to Functional Analysis Methodology to Clarify the Functions of Low Rate, High Intensity Problem Behavior

PubMed Central

Davis, Barbara J; Schmidt, Jonathan; Bowman, Lynn G; Boelter, Eric W

2012-01-01

Current research provides few suggestions for modifications to functional analysis procedures to accommodate low rate, high intensity problem behavior. This study examined the results of the extended duration functional analysis procedures of Kahng, Abt, and Schonbachler (2001) with six children admitted to an inpatient hospital for the treatment of severe problem behavior. Results of initial functional analyses (Iwata, Dorsey, Slifer, Bauman, & Richman, 1982/1994) were inconclusive for all children because of low levels of responding. The altered functional analyses, which changed multiple variables including the duration of the functional analysis (i.e., 6 or 7 hrs), yielded clear behavioral functions for all six participants. These results add additional support for the utility of an altered analysis of low rate, high intensity problem behavior when standard functional analyses do not yield differentiated results. PMID:23326628

Alterations to functional analysis methodology to clarify the functions of low rate, high intensity problem behavior.

PubMed

Davis, Barbara J; Kahng, Sungwoo; Schmidt, Jonathan; Bowman, Lynn G; Boelter, Eric W

2012-01-01

Current research provides few suggestions for modifications to functional analysis procedures to accommodate low rate, high intensity problem behavior. This study examined the results of the extended duration functional analysis procedures of Kahng, Abt, and Schonbachler (2001) with six children admitted to an inpatient hospital for the treatment of severe problem behavior. Results of initial functional analyses (Iwata, Dorsey, Slifer, Bauman, & Richman, 1982/1994) were inconclusive for all children because of low levels of responding. The altered functional analyses, which changed multiple variables including the duration of the functional analysis (i.e., 6 or 7 hrs), yielded clear behavioral functions for all six participants. These results add additional support for the utility of an altered analysis of low rate, high intensity problem behavior when standard functional analyses do not yield differentiated results.

Multilevel modeling: overview and applications to research in counseling psychology.

PubMed

Kahn, Jeffrey H

2011-04-01

Multilevel modeling (MLM) is rapidly becoming the standard method of analyzing nested data, for example, data from students within multiple schools, data on multiple clients seen by a smaller number of therapists, and even longitudinal data. Although MLM analyses are likely to increase in frequency in counseling psychology research, many readers of counseling psychology journals have had only limited exposure to MLM concepts. This paper provides an overview of MLM that blends mathematical concepts with examples drawn from counseling psychology. This tutorial is intended to be a first step in learning about MLM; readers are referred to other sources for more advanced explorations of MLM. In addition to being a tutorial for understanding and perhaps even conducting MLM analyses, this paper reviews recent research in counseling psychology that has adopted a multilevel framework, and it provides ideas for MLM approaches to future research in counseling psychology. 2011 APA, all rights reserved

Measuring Critical Care Providers' Attitudes About Controlled Donation After Circulatory Death.

PubMed

Rodrigue, James R; Luskin, Richard; Nelson, Helen; Glazier, Alexandra; Henderson, Galen V; Delmonico, Francis L

2018-06-01

Unfavorable attitudes and insufficient knowledge about donation after cardiac death among critical care providers can have important consequences for the appropriate identification of potential donors, consistent implementation of donation after cardiac death policies, and relative strength of support for this type of donation. The lack of reliable and valid assessment measures has hampered research to capture providers' attitudes. Design and Research Aims: Using stakeholder engagement and an iterative process, we developed a questionnaire to measure attitudes of donation after cardiac death in critical care providers (n = 112) and examined its psychometric properties. Exploratory factor analysis, internal consistency, and validity analyses were conducted to examine the measure. A 34-item questionnaire consisting of 4 factors (Personal Comfort, Process Satisfaction, Family Comfort, and System Trust) provided the most parsimonious fit. Internal consistency was acceptable for each of the subscales and the total questionnaire (Cronbach α > .70). A strong association between more favorable attitudes overall and knowledge ( r = .43, P < .001) provides evidence of convergent validity. Multivariable regression analyses showed that white race ( P = .002) and more experience with donation after cardiac death ( P < .001) were significant predictors of more favorable attitudes. Study findings support the utility, reliability, and validity of a questionnaire for measuring attitudes in critical care providers and for isolating targets for additional education on donation after cardiac death.

Manpower Mix for Health Services

PubMed Central

Shuman, Larry J.; Young, John P.; Naddor, Eliezer

1971-01-01

A model is formulated to determine the mix of manpower and technology needed to provide health services of acceptable quality at a minimum total cost to the community. Total costs include both the direct costs associated with providing the services and with developing additional manpower and the indirect costs (shortage costs) resulting from not providing needed services. The model is applied to a hypothetical neighborhood health center, and its sensitivity to alternative policies is investigated by cost-benefit analyses. Possible extensions of the model to include dynamic elements in health delivery systems are discussed, as is its adaptation for use in hospital planning, with a changed objective function. PMID:5095652

Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes.

PubMed

Niu, Sheng-Yong; Yang, Jinyu; McDermaid, Adam; Zhao, Jing; Kang, Yu; Ma, Qin

2017-05-08

Metagenomic and metatranscriptomic sequencing approaches are more frequently being used to link microbiota to important diseases and ecological changes. Many analyses have been used to compare the taxonomic and functional profiles of microbiota across habitats or individuals. While a large portion of metagenomic analyses focus on species-level profiling, some studies use strain-level metagenomic analyses to investigate the relationship between specific strains and certain circumstances. Metatranscriptomic analysis provides another important insight into activities of genes by examining gene expression levels of microbiota. Hence, combining metagenomic and metatranscriptomic analyses will help understand the activity or enrichment of a given gene set, such as drug-resistant genes among microbiome samples. Here, we summarize existing bioinformatics tools of metagenomic and metatranscriptomic data analysis, the purpose of which is to assist researchers in deciding the appropriate tools for their microbiome studies. Additionally, we propose an Integrated Meta-Function mapping pipeline to incorporate various reference databases and accelerate functional gene mapping procedures for both metagenomic and metatranscriptomic analyses. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Item response theory analysis of the life orientation test-revised: age and gender differential item functioning analyses.

PubMed

Steca, Patrizia; Monzani, Dario; Greco, Andrea; Chiesi, Francesca; Primi, Caterina

2015-06-01

This study is aimed at testing the measurement properties of the Life Orientation Test-Revised (LOT-R) for the assessment of dispositional optimism by employing item response theory (IRT) analyses. The LOT-R was administered to a large sample of 2,862 Italian adults. First, confirmatory factor analyses demonstrated the theoretical conceptualization of the construct measured by the LOT-R as a single bipolar dimension. Subsequently, IRT analyses for polytomous, ordered response category data were applied to investigate the items' properties. The equivalence of the items across gender and age was assessed by analyzing differential item functioning. Discrimination and severity parameters indicated that all items were able to distinguish people with different levels of optimism and adequately covered the spectrum of the latent trait. Additionally, the LOT-R appears to be gender invariant and, with minor exceptions, age invariant. Results provided evidence that the LOT-R is a reliable and valid measure of dispositional optimism. © The Author(s) 2014.

Phylogenetic relationships of South American lizards of the genus Stenocercus (Squamata: Iguania): A new approach using a general mixture model for gene sequence data.

PubMed

Torres-Carvajal, Omar; Schulte, James A; Cadle, John E

2006-04-01

The South American iguanian lizard genus Stenocercus includes 54 species occurring mostly in the Andes and adjacent lowland areas from northern Venezuela and Colombia to central Argentina at elevations of 0-4000m. Small taxon or character sampling has characterized all phylogenetic analyses of Stenocercus, which has long been recognized as sister taxon to the Tropidurus Group. In this study, we use mtDNA sequence data to perform phylogenetic analyses that include 32 species of Stenocercus and 12 outgroup taxa. Monophyly of this genus is strongly supported by maximum parsimony and Bayesian analyses. Evolutionary relationships within Stenocercus are further analyzed with a Bayesian implementation of a general mixture model, which accommodates variability in the pattern of evolution across sites. These analyses indicate a basal split of Stenocercus into two clades, one of which receives very strong statistical support. In addition, we test previous hypotheses using non-parametric and parametric statistical methods, and provide a phylogenetic classification for Stenocercus.

Comparisons of aerosol optical depth provided by seviri satellite observations and CAMx air quality modelling

NASA Astrophysics Data System (ADS)

Fernandes, A.; Riffler, M.; Ferreira, J.; Wunderle, S.; Borrego, C.; Tchepel, O.

2015-04-01

Satellite data provide high spatial coverage and characterization of atmospheric components for vertical column. Additionally, the use of air pollution modelling in combination with satellite data opens the challenging perspective to analyse the contribution of different pollution sources and transport processes. The main objective of this work is to study the AOD over Portugal using satellite observations in combination with air pollution modelling. For this purpose, satellite data provided by Spinning Enhanced Visible and Infra-Red Imager (SEVIRI) on-board the geostationary Meteosat-9 satellite on AOD at 550 nm and modelling results from the Chemical Transport Model (CAMx - Comprehensive Air quality Model) were analysed. The study period was May 2011 and the aim was to analyse the spatial variations of AOD over Portugal. In this study, a multi-temporal technique to retrieve AOD over land from SEVIRI was used. The proposed method takes advantage of SEVIRI's high temporal resolution of 15 minutes and high spatial resolution. CAMx provides the size distribution of each aerosol constituent among a number of fixed size sections. For post processing, CAMx output species per size bin have been grouped into total particulate sulphate (PSO4), total primary and secondary organic aerosols (POA + SOA), total primary elemental carbon (PEC) and primary inert material per size bin (CRST1 to CRST_4) to be used in AOD quantification. The AOD was calculated by integration of aerosol extinction coefficient (Qext) on the vertical column. The results were analysed in terms of temporal and spatial variations. The analysis points out that the implemented methodology provides a good spatial agreement between modelling results and satellite observation for dust outbreak studied (10th -17th of May 2011). A correlation coefficient of r=0.79 was found between the two datasets. This work provides relevant background to start the integration of these two different types of the data in order to improve air pollution assessment.

Design and Execution of make-like, distributed Analyses based on Spotify’s Pipelining Package Luigi

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, B.; Fischer, R.; Rieger, M.

2017-10-01

In high-energy particle physics, workflow management systems are primarily used as tailored solutions in dedicated areas such as Monte Carlo production. However, physicists performing data analyses are usually required to steer their individual workflows manually which is time-consuming and often leads to undocumented relations between particular workloads. We present a generic analysis design pattern that copes with the sophisticated demands of end-to-end HEP analyses and provides a make-like execution system. It is based on the open-source pipelining package Luigi which was developed at Spotify and enables the definition of arbitrary workloads, so-called Tasks, and the dependencies between them in a lightweight and scalable structure. Further features are multi-user support, automated dependency resolution and error handling, central scheduling, and status visualization in the web. In addition to already built-in features for remote jobs and file systems like Hadoop and HDFS, we added support for WLCG infrastructure such as LSF and CREAM job submission, as well as remote file access through the Grid File Access Library. Furthermore, we implemented automated resubmission functionality, software sandboxing, and a command line interface with auto-completion for a convenient working environment. For the implementation of a t \\overline{{{t}}} H cross section measurement, we created a generic Python interface that provides programmatic access to all external information such as datasets, physics processes, statistical models, and additional files and values. In summary, the setup enables the execution of the entire analysis in a parallelized and distributed fashion with a single command.

Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code.

PubMed

Yinda, Claude Kwe; Ghogomu, Stephen Mbigha; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Vanhulle, Emiel; Maes, Piet; Van Ranst, Marc; Matthijnssens, Jelle

2018-01-01

Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems.

ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs).

PubMed

Mishra, Smriti; Shah, Mohammad I; Sarkar, Malay; Asati, Nimisha; Rout, Chittaranjan

2018-01-01

Interstitial lung diseases (ILDs) are a diverse group of ∼200 acute and chronic pulmonary disorders that are characterized by variable amounts of inflammation, fibrosis and architectural distortion with substantial morbidity and mortality. Inaccurate and delayed diagnoses increase the risk, especially in developing countries. Studies have indicated the significant roles of genetic elements in ILDs pathogenesis. Therefore, the first genetic knowledge resource, ILDgenDB, has been developed with an objective to provide ILDs genetic data and their integrated analyses for the better understanding of disease pathogenesis and identification of diagnostics-based biomarkers. This resource contains literature-curated disease candidate genes (DCGs) enriched with various regulatory elements that have been generated using an integrated bioinformatics workflow of databases searches, literature-mining and DCGs-microRNA (miRNAs)-single nucleotide polymorphisms (SNPs) association analyses. To provide statistical significance to disease-gene association, ILD-specificity index and hypergeomatric test scores were also incorporated. Association analyses of miRNAs, SNPs and pathways responsible for the pathogenesis of different sub-classes of ILDs were also incorporated. Manually verified 299 DCGs and their significant associations with 1932 SNPs, 2966 miRNAs and 9170 miR-polymorphisms were also provided. Furthermore, 216 literature-mined and proposed biomarkers were identified. The ILDgenDB resource provides user-friendly browsing and extensive query-based information retrieval systems. Additionally, this resource also facilitates graphical view of predicted DCGs-SNPs/miRNAs and literature associated DCGs-ILDs interactions for each ILD to facilitate efficient data interpretation. Outcomes of analyses suggested the significant involvement of immune system and defense mechanisms in ILDs pathogenesis. This resource may potentially facilitate genetic-based disease monitoring and diagnosis.Database URL: http://14.139.240.55/ildgendb/index.php.

A landscape ecology approach to assessing development impacts in the tropics: A geothermal energy example in Hawaii

USGS Publications Warehouse

Griffith, J.A.; Trettin, C.C.; O'Neill, R. V.

2002-01-01

Geographic information systems (GIS) are increasingly being used in environmental impact assessments (EIA) because GIS is useful for analysing spatial impacts of various development scenarios. Spatially representing these impacts provides another tool for landscape ecology in environmental and geographical investigations by facilitating analysis of the effects of landscape patterns on ecological processes and examining change over time. Landscape ecological principles are applied in this study to a hypothetical geothermal development project on the Island of Hawaii. Some common landscape pattern metrics were used to analyse dispersed versus condensed development scenarios and their effect on landscape pattern. Indices of fragmentation and patch shape did not appreciably change with additional development. The amount of forest to open edge, however, greatly increased with the dispersed development scenario. In addition, landscape metrics showed that a human disturbance had a greater simplifying effect on patch shape and also increased fragmentation than a natural disturbance. The use of these landscape pattern metrics can advance the methodology of applying GIS to EIA.

Tafamidis delays disease progression in patients with early stage transthyretin familial amyloid polyneuropathy: additional supportive analyses from the pivotal trial.

PubMed

Keohane, Denis; Schwartz, Jeffrey; Gundapaneni, Balarama; Stewart, Michelle; Amass, Leslie

2017-03-01

Tafamidis, a non-NSAID highly specific transthyretin stabilizer, delayed neurologic disease progression as measured by Neuropathy Impairment Score-Lower Limbs (NIS-LL) in an 18-month, double-blind, placebo-controlled randomized trial in 128 patients with early-stage transthyretin V30M familial amyloid polyneuropathy (ATTRV30M-FAP). The current post hoc analyses aimed to further evaluate the effects of tafamidis in delaying ATTRV30M-FAP progression in this trial. Pre-specified, repeated-measures analysis of change from baseline in NIS-LL in this trial (ClinicalTrials.gov NCT00409175) was repeated with addition of baseline as covariate and multiple imputation analysis for missing data by treatment group. Change in NIS-LL plus three small-fiber nerve tests (NIS-LL + Σ3) and NIS-LL plus seven nerve tests (NIS-LL + Σ7) were assessed without baseline as covariate. Treatment outcomes over the NIS-LL, Σ3, Σ7, modified body mass index and Norfolk Quality of Life-Diabetic Neuropathy Total Quality of Life Score were also examined using multivariate analysis techniques. Neuropathy progression based on NIS-LL change from baseline to Month 18 remained significantly reduced for tafamidis versus placebo in the baseline-adjusted and multiple imputation analyses. NIS-LL + Σ3 and NIS-LL + Σ7 captured significant treatment group differences. Multivariate analyses provided strong statistical evidence for a superior tafamidis treatment effect. These supportive analyses confirm that tafamidis delays neurologic progression in early-stage ATTRV30M-FAP. NCT00409175.

MANOVA vs nonlinear mixed effects modeling: The comparison of growth patterns of female and male quail

NASA Astrophysics Data System (ADS)

Gürcan, Eser Kemal

2017-04-01

The most commonly used methods for analyzing time-dependent data are multivariate analysis of variance (MANOVA) and nonlinear regression models. The aim of this study was to compare some MANOVA techniques and nonlinear mixed modeling approach for investigation of growth differentiation in female and male Japanese quail. Weekly individual body weight data of 352 male and 335 female quail from hatch to 8 weeks of age were used to perform analyses. It is possible to say that when all the analyses are evaluated, the nonlinear mixed modeling is superior to the other techniques because it also reveals the individual variation. In addition, the profile analysis also provides important information.

Big Data Bioinformatics

PubMed Central

GREENE, CASEY S.; TAN, JIE; UNG, MATTHEW; MOORE, JASON H.; CHENG, CHAO

2017-01-01

Recent technological advances allow for high throughput profiling of biological systems in a cost-efficient manner. The low cost of data generation is leading us to the “big data” era. The availability of big data provides unprecedented opportunities but also raises new challenges for data mining and analysis. In this review, we introduce key concepts in the analysis of big data, including both “machine learning” algorithms as well as “unsupervised” and “supervised” examples of each. We note packages for the R programming language that are available to perform machine learning analyses. In addition to programming based solutions, we review webservers that allow users with limited or no programming background to perform these analyses on large data compendia. PMID:27908398

Big Data Bioinformatics

PubMed Central

GREENE, CASEY S.; TAN, JIE; UNG, MATTHEW; MOORE, JASON H.; CHENG, CHAO

2017-01-01

Recent technological advances allow for high throughput profiling of biological systems in a cost-efficient manner. The low cost of data generation is leading us to the “big data” era. The availability of big data provides unprecedented opportunities but also raises new challenges for data mining and analysis. In this review, we introduce key concepts in the analysis of big data, including both “machine learning” algorithms as well as “unsupervised” and “supervised” examples of each. We note packages for the R programming language that are available to perform machine learning analyses. In addition to programming based solutions, we review webservers that allow users with limited or no programming background to perform these analyses on large data compendia. PMID:24799088

Preparation of a 1:1 cocrystal of genistein with 4,4‧-bipyridine

NASA Astrophysics Data System (ADS)

Zhang, Yu-Nan; Yin, He-Mei; Zhang, Yu; Zhang, Da-Jun; Su, Xin; Kuang, Hai-Xue

2017-01-01

Based on analysing the relationship between the possible number of intermolecular O-H···N hydrogen bonds and the stoichiometric ratio, a 1:1 C15H10O5·C10H8N2 (genistein-4,4‧-bipyridine) cocrystal has been prepared by solution evaporation and characterized. This work successfully demonstrates that the stoichiometric ratio could be inferred by analysing the possible number of intermolecular hydrogen bonds between flavonoids and amines. The strategy provides a facile route for rational designing cocrystal of flavonoids with amines. Additionally, the title cocrystal shows advantages in terms of solubility and antibacterial properties in comparison to pure genistein.

Big data bioinformatics.

PubMed

Greene, Casey S; Tan, Jie; Ung, Matthew; Moore, Jason H; Cheng, Chao

2014-12-01

Recent technological advances allow for high throughput profiling of biological systems in a cost-efficient manner. The low cost of data generation is leading us to the "big data" era. The availability of big data provides unprecedented opportunities but also raises new challenges for data mining and analysis. In this review, we introduce key concepts in the analysis of big data, including both "machine learning" algorithms as well as "unsupervised" and "supervised" examples of each. We note packages for the R programming language that are available to perform machine learning analyses. In addition to programming based solutions, we review webservers that allow users with limited or no programming background to perform these analyses on large data compendia. © 2014 Wiley Periodicals, Inc.

A software platform for statistical evaluation of patient respiratory patterns in radiation therapy.

PubMed

Dunn, Leon; Kenny, John

2017-10-01

The aim of this work was to design and evaluate a software tool for analysis of a patient's respiration, with the goal of optimizing the effectiveness of motion management techniques during radiotherapy imaging and treatment. A software tool which analyses patient respiratory data files (.vxp files) created by the Varian Real-Time Position Management System (RPM) was developed to analyse patient respiratory data. The software, called RespAnalysis, was created in MATLAB and provides four modules, one each for determining respiration characteristics, providing breathing coaching (biofeedback training), comparing pre and post-training characteristics and performing a fraction-by-fraction assessment. The modules analyse respiratory traces to determine signal characteristics and specifically use a Sample Entropy algorithm as the key means to quantify breathing irregularity. Simulated respiratory signals, as well as 91 patient RPM traces were analysed with RespAnalysis to test the viability of using the Sample Entropy for predicting breathing regularity. Retrospective assessment of patient data demonstrated that the Sample Entropy metric was a predictor of periodic irregularity in respiration data, however, it was found to be insensitive to amplitude variation. Additional waveform statistics assessing the distribution of signal amplitudes over time coupled with Sample Entropy method were found to be useful in assessing breathing regularity. The RespAnalysis software tool presented in this work uses the Sample Entropy method to analyse patient respiratory data recorded for motion management purposes in radiation therapy. This is applicable during treatment simulation and during subsequent treatment fractions, providing a way to quantify breathing irregularity, as well as assess the need for breathing coaching. It was demonstrated that the Sample Entropy metric was correlated to the irregularity of the patient's respiratory motion in terms of periodicity, whilst other metrics, such as percentage deviation of inhale/exhale peak positions provided insight into respiratory amplitude regularity. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Orbital service module systems analysis study documentation. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1978-01-01

Potentially feasible system concepts for providing additional power, thermal control, and attitude to the baseline orbiter were investigated in order to support a greater variety of space missions and to extend the orbiter's ability to remain in orbit. Results of these analyses include an incremental growth plan that offers the flexibility of adding capability as, and when, it is needed in order to satisfy emerging user requirements.

Quantum cryptography: individual eavesdropping with the knowledge of the error-correcting protocol

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

Horoshko, D B

2007-12-31

The quantum key distribution protocol BB84 combined with the repetition protocol for error correction is analysed from the point of view of its security against individual eavesdropping relying on quantum memory. It is shown that the mere knowledge of the error-correcting protocol changes the optimal attack and provides the eavesdropper with additional information on the distributed key. (fifth seminar in memory of d.n. klyshko)

Combining ISO/IEC 17025:2005 and European Commission Decision 2002/657 audit requirements: a practical way forward.

PubMed

Kay, Jack F

2012-08-01

Laboratories involved in the analyses of veterinary drug residues are under increasing pressure to demonstrate that they produce meaningful and reliable data. Quality assurance and quality control systems are implemented in laboratories to provide evidence of this and these are subject to external assessment to ensure that they are effective. Audits to ISO/IEC 17025:2005, an internationally accepted standard, and subsequent accreditation provide laboratories and their customers with a degree of assurance that the laboratories are operating in control and the data they report can be relied on. However, national or regional authorities may place additional requirements on laboratories to ensure quality data are reported. For example, in the European Union, all official control laboratories involved in veterinary drug residue analyses must also meet the requirements of European Commission Decision 2002/657/EC which sets performance criteria for analytical methods used in this area and these are subject to additional audits by national or regional authorities. All audits place considerable time and resource demands on laboratories and this paper discusses the burden audits place on laboratories and describes a UK initiative to combine these audits to the benefit of both the regulatory authority and the laboratory. © 2012 John Wiley & Sons, Ltd.

Proteogenomics connects somatic mutations to signalling in breast cancer.

PubMed

Mertins, Philipp; Mani, D R; Ruggles, Kelly V; Gillette, Michael A; Clauser, Karl R; Wang, Pei; Wang, Xianlong; Qiao, Jana W; Cao, Song; Petralia, Francesca; Kawaler, Emily; Mundt, Filip; Krug, Karsten; Tu, Zhidong; Lei, Jonathan T; Gatza, Michael L; Wilkerson, Matthew; Perou, Charles M; Yellapantula, Venkata; Huang, Kuan-lin; Lin, Chenwei; McLellan, Michael D; Yan, Ping; Davies, Sherri R; Townsend, R Reid; Skates, Steven J; Wang, Jing; Zhang, Bing; Kinsinger, Christopher R; Mesri, Mehdi; Rodriguez, Henry; Ding, Li; Paulovich, Amanda G; Fenyö, David; Ellis, Matthew J; Carr, Steven A

2016-06-02

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. Here we describe quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers, of which 77 provided high-quality data. Integrated analyses provided insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. Interrogation of the 5q trans-effects against the Library of Integrated Network-based Cellular Signatures, connected loss of CETN3 and SKP1 to elevated expression of epidermal growth factor receptor (EGFR), and SKP1 loss also to increased SRC tyrosine kinase. Global proteomic data confirmed a stromal-enriched group of proteins in addition to basal and luminal clusters, and pathway analysis of the phosphoproteome identified a G-protein-coupled receptor cluster that was not readily identified at the mRNA level. In addition to ERBB2, other amplicon-associated highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates the functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets.

After initial treatment for primary breast cancer: information needs, health literacy, and the role of health care workers.

PubMed

Schmidt, Anna; Ernstmann, Nicole; Wesselmann, Simone; Pfaff, Holger; Wirtz, Markus; Kowalski, Christoph

2016-02-01

After a short hospital stay of just some days follows long-term outpatient care for breast cancer patients. The aim of the study is to describe the information needs of breast cancer outpatients and to get in touch with aspects of health literacy, as well as contact various health care workers. In a multicenter study, patients were asked about their information needs 10 weeks after surgery. The analysis on hand includes data about 1248 female patients. In addition to descriptive analyses identifying the most prevalent information needs, logistic regression analyses were calculated to identify factors associated with these. The results show that information needs of breast cancer outpatients are mainly in "follow-up after acute treatment", "coping with long-term side effects", and "heredity of breast cancer". In addition to sociodemographic patient characteristics, perceived helpful contacts with various health care workers as well as a satisfactory patient's level of health literacy reduced the probability of unmet information needs. Breast cancer outpatients have numerous information needs. In addition to provide information at the right time regarding a specific disease phase, it is important that health professionals' support affected breast cancer patients in coping with the new situation.

AL Pictoris and FR Piscium: Two Regular Blazhko RR Lyrae Stars

NASA Astrophysics Data System (ADS)

de Ponthière, P.; Hambsch, F.-J.; Menzies, K.; Sabo, R.

2014-12-01

The results presented are a continuation of observing campaigns conducted by a small group of amateur astronomers interested in the Blazhko effect of RR Lyrae stars. The goal of these observations is to confirm the RR Lyrae Blazhko effect and to detect any additional Blazhko modulation which cannot be identified from all sky survey data-mining. The Blazhko effect of the two observed stars is confirmed, but no additional Blazhko modulations have been detected. The observation of the RR Lyrae star AL Pictoris during 169 nights was conducted from San Pedro de Atacama (Chile). From the observed light curve, 49 pulsation maxima have been measured. Fourier analyses of (O-C), magnitude at maximum light (Mmax), and the complete light curve have provided a confirmation of published pulsation and Blazhko periods, 0.548622 and 34.07 days, respectively. The second multi-longitude observation campaign focused on the RR Lyrae star FR Piscium and was performed from Europe, the United States, and Chile. Fourier analyses of the light curve and of 59 measured brightness maxima have improved the accuracy of pulsation and Blazhko periods to 0.45568 and 51.31 days, respectively. For both stars, no additional Blazhko modulations have been detected.

A Systematic Review of Health Economic Analyses of Housing Improvement Interventions and Insecticide-Treated Bednets in the Home

PubMed Central

Pega, Frank; Wilson, Nick

2016-01-01

Background Housing improvements have considerable potential for improving health. So does the provision of insecticide-treated bednets for malaria prevention. Therefore we aimed to conduct updated systematic reviews of health economic analyses in both these intervention domains. Methods and findings The search strategy included economic analyses of housing improvement interventions and use of insecticide-treated bednets for community-dwelling, healthy populations (published between 1 January 2000 and 15 April 2014). We searched the Cochrane Database of Systematic Reviews, MEDLINE, PubMed, EMBASE, and three health economics databases. Thirty-five economic analyses of seven types of intervention fulfilled the inclusion criteria. Most included studies adopted a health sector perspective and were cost-effectiveness analyses using decision analytic modeling or conducted alongside trials. The overall quality of the studies was generally likely to be adequate for informing policy-making (albeit with limitations in some areas). There was fairly consistent evidence for the cost-effectiveness/favorable cost-benefit of removing indoor lead to prevent lead poisoning and sequelae, and retrofitting insulation to prevent lung disease. But the value of assessing and improving home safety and providing smoke alarms to prevent injuries was more mixed and the economic evidence was inconclusive or insufficient for: home ventilation to prevent lung disease, installing heaters to prevent lung disease and regulating tap water temperatures to prevent scalding. Few studies (n = 4) considered health equity. The 12 studies of providing insecticide-treated bednets or hammocks to prevent malaria found these interventions to be moderately to highly cost-effective. Conclusions This systematic review provides updated evidence that several housing improvement interventions (such as removing indoor lead and retrofitting insulation) and also the provision of insecticide-treated bednets are cost-effective interventions. Nevertheless, for some interventions additional analyses are required to better clarify their health economic and health equity value. PMID:27249419

Additional considerations are required when preparing a protocol for a systematic review with multiple interventions.

PubMed

Chaimani, Anna; Caldwell, Deborah M; Li, Tianjing; Higgins, Julian P T; Salanti, Georgia

2017-03-01

The number of systematic reviews that aim to compare multiple interventions using network meta-analysis is increasing. In this study, we highlight aspects of a standard systematic review protocol that may need modification when multiple interventions are to be compared. We take the protocol format suggested by Cochrane for a standard systematic review as our reference and compare the considerations for a pairwise review with those required for a valid comparison of multiple interventions. We suggest new sections for protocols of systematic reviews including network meta-analyses with a focus on how to evaluate their assumptions. We provide example text from published protocols to exemplify the considerations. Standard systematic review protocols for pairwise meta-analyses need extensions to accommodate the increased complexity of network meta-analysis. Our suggested modifications are widely applicable to both Cochrane and non-Cochrane systematic reviews involving network meta-analyses. Copyright © 2017 Elsevier Inc. All rights reserved.

The origin of parasitism gene in nematodes: evolutionary analysis through the construction of domain trees.

PubMed

Yang, Yizi; Luo, Damin

2013-01-01

Inferring evolutionary history of parasitism genes is important to understand how evolutionary mechanisms affect the occurrences of parasitism genes. In this study, we constructed multiple domain trees for parasitism genes and genes under free-living conditions. Further analyses of horizontal gene transfer (HGT)-like phylogenetic incongruences, duplications, and speciations were performed based on these trees. By comparing these analyses, the contributions of pre-adaptations were found to be more important to the evolution of parasitism genes than those of duplications, and pre-adaptations are as crucial as previously reported HGTs to parasitism. Furthermore, speciation may also affect the evolution of parasitism genes. In addition, Pristionchus pacificus was suggested to be a common model organism for studies of parasitic nematodes, including root-knot species. These analyses provided information regarding mechanisms that may have contributed to the evolution of parasitism genes.

The evolution of high-alumina basalts of the Klyuchevskoy volcano, Kamchatka, Russia, based on microprobe analyses of mineral inclusions

NASA Astrophysics Data System (ADS)

Ozerov, Alexei Y.

2000-01-01

The origin of calc-alkaline high-alumina basalts (HAB) of the Klyuchevskoy volcano, Kamchatka, was examined using electron microprobe analyses of phenocrysts and mineral phases included in the phenocrysts. Continuous trends on major-element variation diagrams suggest the HAB were derived from high-magnesia basalt (HMB) by fractional crystallization. Phenocrysts in the HAB are strongly zoned: olivine (Mg# 91-64), clinopyroxene (Wo 45-38En 40-51Fs 5-20) and chrome—spinel/magnetite inclusions in them (Cr 2O 3 45-0 wt.%, TiO 2 0.5-11%). Microprobe analyses of minerals included in the phenocrysts provide additional constraints on the mineral crystallization trends in the HAB. Fe/Mg partitioning data, when applied to the phenocrysts cores, show they crystallized from a HMB. The similarity of phenocryst core compositions in HAB with those in HMB strongly suggests a genetic relationship between the two magma types.

Elemental abundance analyses with Complejo Astronomico El Leoncito REOSC echelle spectrograms. IV. Extensions of nine previous analyses

NASA Astrophysics Data System (ADS)

Adelman, S. J.; Pintado, O. I.

2000-02-01

Using new CASLEO echelle spectrograms, we extended our elemental abundances of the sharp-lined Mercury-Manganese stars mu Lep, 14 Hya, kappa Cnc, HR 4487, HR 4817, 28 Her, and HR 7245, the closely related star 3 Cen A, and 7 Sex an A0 V star with Population I abundances, but with Population II star space motions. The lambda lambda 4500-6200 region contains a sufficient number of lines to derive high-quality abundances of these stars. For most stars, the new spectra provide additional lines for the analyses which improve their quality as well as help fill in the periodic table. Table~5 is only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr(130.79.128.5) or via http://cdsweb.u-strabg.fr/Abstract.html}

Assessing potential effects of highway runoff on receiving-water quality at selected sites in Oregon with the Stochastic Empirical Loading and Dilution Model (SELDM)

USGS Publications Warehouse

Risley, John C.; Granato, Gregory E.

2014-01-01

6. An analysis of the use of grab sampling and nonstochastic upstream modeling methods was done to evaluate the potential effects on modeling outcomes. Additional analyses using surrogate water-quality datasets for the upstream basin and highway catchment were provided for six Oregon study sites to illustrate the risk-based information that SELDM will produce. These analyses show that the potential effects of highway runoff on receiving-water quality downstream of the outfall depends on the ratio of drainage areas (dilution), the quality of the receiving water upstream of the highway, and the concentration of the criteria of the constituent of interest. These analyses also show that the probability of exceeding a water-quality criterion may depend on the input statistics used, thus careful selection of representative values is important.

Comparison of NOAA/NMC stratospheric wind analyses with UARS high resolution Doppler Imager wind measurements

NASA Technical Reports Server (NTRS)

Miller, A. J.; Hays, P. B.; Abreu, V.; Long, C.; Kann, D.

1994-01-01

The NOAA National Weather Service currently derives global stratospheric wind analyses via several procedures. The first is the operational data assimilation system that extends from the surface up to about 50 mb and is in process of being tested to about 10 mb. In addition, a balanced wind is determined from the available Climate Analysis Center stratospheric height analyses that encompass the 70-0.4 mb region. The High Resolution Doppler Imager (HRDI) recently launched as a member of the Upper Atmosphere Research Satellite (UARS) is the first satellite instrument designed to measure winds in this stratospheric region and, thus, provide a basic evaluation of the NMC derived products. The HRDI accomplishes this by utilizing a triple-etalon Fabry-Perot interferometer that allows one to measure the Doppler shift of O2 absorption and emission features of the atmosphere, from which the wind field can be determined.

Additional Sr Isotopic Heterogeneity in Zagami Olivine-Rich Lithology

NASA Technical Reports Server (NTRS)

Misawa, K.; Niihara, T.; Shih, C.-Y; Reese, Y. D.; Nyquist, L. E.; Yoneda, S.; Yamashita, H.

2012-01-01

Prior isotopic analyses of Zagami have established differing initial Sr-87/Sr-86 (ISr) ratios of among Zagami lithologies, fine-grained (FG), coarse-grained (CG), and dark mottled lithologies (DML)]. The Zagami sample (KPM-NLH000057) newly allocated from the Kanagawa Prefectural Museum of Natural History contained DML and the Ol-rich lithology which included more ferroan olivines (Ol-rich: Fa(sub 97- 99) vs late-stage melt pockets: Fa(sub 90-97)]). We have combined mineralogy-petrology and Rb-Sr isotopic studies on the Kanagawa Zagami sample, which will provide additional clues to the genesis of enriched shergottites and to the evolution of Martian crust and mantle

ERTS data user investigation to develop a multistage forest sampling inventory system

NASA Technical Reports Server (NTRS)

Langley, P. G.; Vanroessel, J. W. (Principal Investigator); Wert, S. L.

1973-01-01

The author has identified the following significant results. A system to provide precision annotation of predetermined forest inventory sampling units on the ERTS-1 MSS images was developed. In addition, an annotation system for high altitude U2 photographs was completed. MSS bulk image accuracy is good enough to allow the use of one square mile sampling units. IMANCO image analyzer interpretation work for small scale images demonstrated the need for much additional analyses. Continuing image interpretation work for the next reporting period is concentrated on manual image interpretation work as well as digital interpretation system development using the computer compatible tapes.

Can Economic Model Transparency Improve Provider Interpretation of Cost-effectiveness Analysis? Evaluating Tradeoffs Presented by the Second Panel on Cost-effectiveness in Health and Medicine.

PubMed

Padula, William V; McQueen, Robert Brett; Pronovost, Peter J

2017-11-01

The Second Panel on Cost-Effectiveness in Health and Medicine convened on December 7, 2016 at the National Academy of Medicine to disseminate their recommendations for conduct, methodological practices, and reporting of cost-effectiveness analyses (CEAs). Following its summary, panel proceedings included lengthy discussions including the field's struggle to disseminate findings efficiently through peer-reviewed literature to target audiences. With editors of several medical and outcomes research journals in attendance, there was consensus that findings of cost-effectiveness analyses do not effectively reach other researchers or health care providers. The audience members suggested several solutions including providing additional training to clinicians in cost-effectiveness research and requiring that cost-effectiveness models are made publicly available. However, there remains the questions of whether making economic modelers' work open-access through journals is fair under the defense that these models remain one's own intellectual property, or whether journals can properly manage the peer-review process specifically for cost-effectiveness analyses. In this article, we elaborate on these issues and provide some suggested solutions that may increase the dissemination and application of cost-effectiveness literature to reach its intended audiences and ultimately benefit the patient. Ultimately, it is our combined view as economic modelers and clinicians that cost-effectiveness results need to reach the clinician to improve the efficiency of medical practice, but that open-access models do not improve clinician access or interpretation of the economics of medicine.

A review of the genus Saccharicoccus Ferris, 1950 (Hemiptera: Coccomorpha: Pseudococcidae) in China, with description of a new species.

PubMed

Zhang, Jiang-Tao; Wu, Bo-Wen; Wu, San-An

2018-01-23

The mealybug genus Saccharicoccus Ferris includes three species: S. isfarensis (Borchsenius, 1949), S. sacchari (Cockerell, 1895) and a new species, S. chinensis Zhang, Wu Wu sp. n. The new species, collected on Miscanthus sp. (Poaceae) and other poaceous weeds in China, is described and illustrated, and molecular analyses based on the mitochondrial gene cytochrome c oxidase subunit I (COI) are provided. Additional data on the distribution and host-plants of each species are given, and a key to the adult females of Saccharicoccus species is provided.

KERNELHR: A program for estimating animal home ranges

USGS Publications Warehouse

Seaman, D.E.; Griffith, B.; Powell, R.A.

1998-01-01

Kernel methods are state of the art for estimating animal home-range area and utilization distribution (UD). The KERNELHR program was developed to provide researchers and managers a tool to implement this extremely flexible set of methods with many variants. KERNELHR runs interactively or from the command line on any personal computer (PC) running DOS. KERNELHR provides output of fixed and adaptive kernel home-range estimates, as well as density values in a format suitable for in-depth statistical and spatial analyses. An additional package of programs creates contour files for plotting in geographic information systems (GIS) and estimates core areas of ranges.

Morphogenesis in bat wings: linking development, evolution and ecology.

PubMed

Adams, Rick A

2008-01-01

The evolution of powered flight in mammals required specific developmental shifts from an ancestral limb morphology to one adapted for flight. Through studies of comparative morphogenesis, investigators have quantified points and rates of divergence providing important insights into how wings evolved in mammals. Herein I compare growth,development and skeletogenesis of forelimbs between bats and the more ancestral state provided by the rat (Rattus norvegicus)and quantify growth trajectories that illustrate morphological divergence both developmentally and evolutionarily. In addition, I discuss how wing shape is controlled during morphogenesis by applying multivariate analyses of wing bones and wing membranes and discuss how flight dynamics are stabilized during flight ontogeny. Further, I discuss the development of flight in bats in relation to the ontogenetic niche and how juveniles effect populational foraging patterns. In addition, I provide a hypothetical ontogenetic landscape model that predicts how and when selection is most intense during juvenile morphogenesis and test this model with data from a population of the little brown bat, Myotis lucifugus. (c) 2007 S. Karger AG, Basel

Dynamics of representational change: entropy, action, and cognition.

PubMed

Stephen, Damian G; Dixon, James A; Isenhower, Robert W

2009-12-01

Explaining how the cognitive system can create new structures has been a major challenge for cognitive science. Self-organization from the theory of nonlinear dynamics offers an account of this remarkable phenomenon. Two studies provide an initial test of the hypothesis that the emergence of new cognitive structure follows the same universal principles as emergence in other domains (e.g., fluids, lasers). In both studies, participants initially solved gear-system problems by manually tracing the force across a system of gears. Subsequently, they discovered that the gears form an alternating sequence, thereby demonstrating a new cognitive structure. In both studies, dynamical analyses of action during problem solving predicted the spontaneous emergence of the new cognitive structure. Study 1 showed that a peak in entropy, followed by negentropy, key indicators of self-organization, predicted discovery of alternation. Study 2 replicated these effects, and showed that increasing environmental entropy accelerated discovery, a classic prediction from dynamics. Additional analyses based on the relationship between phase transitions and power-law behavior provide converging evidence. The studies provide an initial demonstration of the emergence of cognitive structure through self-organization.

Can rheumatoid arthritis (RA) registries provide contextual safety data for modern RA clinical trials? The case for mortality and cardiovascular disease.

PubMed

Michaud, Kaleb; Berglind, Niklas; Franzén, Stefan; Frisell, Thomas; Garwood, Christopher; Greenberg, Jeffrey D; Ho, Meilien; Holmqvist, Marie; Horne, Laura; Inoue, Eisuke; Nyberg, Fredrik; Pappas, Dimitrios A; Reed, George; Symmons, Deborah; Tanaka, Eiichi; Tran, Trung N; Verstappen, Suzanne M M; Wesby-van Swaay, Eveline; Yamanaka, Hisashi; Askling, Johan

2016-10-01

We implemented a novel method for providing contextual adverse event rates for a randomised controlled trial (RCT) programme through coordinated analyses of five RA registries, focusing here on cardiovascular disease (CVD) and mortality. Each participating registry (Consortium of Rheumatology Researchers of North America (CORRONA) (USA), Swedish Rheumatology Quality of Care Register (SRR) (Sweden), Norfolk Arthritis Register (NOAR) (UK), CORRONA International (East Europe, Latin America, India) and Institute of Rheumatology, Rheumatoid Arthritis (IORRA) (Japan)) defined a main cohort from January 2000 onwards. To address comparability and potential bias, we harmonised event definitions and defined several subcohorts for sensitivity analyses based on disease activity, treatment, calendar time, duration of follow-up and RCT exclusions. Rates were standardised for age, sex and, in one sensitivity analysis, also HAQ. The combined registry cohorts included 57 251 patients with RA (234 089 person-years)-24.5% men, mean (SD) baseline age 58.2 (13.8) and RA duration 8.2 (11.7) years. Standardised registry mortality rates (per 100 person-years) varied from 0.42 (CORRONA) to 0.80 (NOAR), with 0.60 for RCT patients. Myocardial infarction and major adverse cardiovascular events (MACE) rates ranged from 0.09 and 0.31 (IORRA) to 0.39 and 0.77 (SRR), with RCT rates intermediate (0.18 and 0.42), respectively. Additional subcohort analyses showed small and mostly consistent changes across registries, retaining reasonable consistency in rates across the Western registries. Additional standardisation for HAQ returned higher mortality and MACE registry rates. This coordinated approach to contextualising RA RCT safety data demonstrated reasonable differences and consistency in rates for mortality and CVD across registries, and comparable RCT rates, and may serve as a model method to supplement clinical trial analyses for drug development programmes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Association analyses of East Asian individuals and trans-ancestry analyses with European individuals reveal new loci associated with cholesterol and triglyceride levels.

PubMed

Spracklen, Cassandra N; Chen, Peng; Kim, Young Jin; Wang, Xu; Cai, Hui; Li, Shengxu; Long, Jirong; Wu, Ying; Wang, Ya Xing; Takeuchi, Fumihiko; Wu, Jer-Yuarn; Jung, Keum-Ji; Hu, Cheng; Akiyama, Koichi; Zhang, Yonghong; Moon, Sanghoon; Johnson, Todd A; Li, Huaixing; Dorajoo, Rajkumar; He, Meian; Cannon, Maren E; Roman, Tamara S; Salfati, Elias; Lin, Keng-Hung; Guo, Xiuqing; Sheu, Wayne H H; Absher, Devin; Adair, Linda S; Assimes, Themistocles L; Aung, Tin; Cai, Qiuyin; Chang, Li-Ching; Chen, Chien-Hsiun; Chien, Li-Hsin; Chuang, Lee-Ming; Chuang, Shu-Chun; Du, Shufa; Fan, Qiao; Fann, Cathy S J; Feranil, Alan B; Friedlander, Yechiel; Gordon-Larsen, Penny; Gu, Dongfeng; Gui, Lixuan; Guo, Zhirong; Heng, Chew-Kiat; Hixson, James; Hou, Xuhong; Hsiung, Chao Agnes; Hu, Yao; Hwang, Mi Yeong; Hwu, Chii-Min; Isono, Masato; Juang, Jyh-Ming Jimmy; Khor, Chiea-Chuen; Kim, Yun Kyoung; Koh, Woon-Puay; Kubo, Michiaki; Lee, I-Te; Lee, Sun-Ju; Lee, Wen-Jane; Liang, Kae-Woei; Lim, Blanche; Lim, Sing-Hui; Liu, Jianjun; Nabika, Toru; Pan, Wen-Harn; Peng, Hao; Quertermous, Thomas; Sabanayagam, Charumathi; Sandow, Kevin; Shi, Jinxiu; Sun, Liang; Tan, Pok Chien; Tan, Shu-Pei; Taylor, Kent D; Teo, Yik-Ying; Toh, Sue-Anne; Tsunoda, Tatsuhiko; van Dam, Rob M; Wang, Aili; Wang, Feijie; Wang, Jie; Wei, Wen Bin; Xiang, Yong-Bing; Yao, Jie; Yuan, Jian-Min; Zhang, Rong; Zhao, Wanting; Chen, Yii-Der Ida; Rich, Stephen S; Rotter, Jerome I; Wang, Tzung-Dau; Wu, Tangchun; Lin, Xu; Han, Bok-Ghee; Tanaka, Toshihiro; Cho, Yoon Shin; Katsuya, Tomohiro; Jia, Weiping; Jee, Sun-Ha; Chen, Yuan-Tsong; Kato, Norihiro; Jonas, Jost B; Cheng, Ching-Yu; Shu, Xiao-Ou; He, Jiang; Zheng, Wei; Wong, Tien-Yin; Huang, Wei; Kim, Bong-Jo; Tai, E-Shyong; Mohlke, Karen L; Sim, Xueling

2017-05-01

Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan. These meta-analyses identified (P < 5 × 10-8) three novel loci associated with HDL-C near CD163-APOBEC1 (P = 7.4 × 10-9), NCOA2 (P = 1.6 × 10-8), and NID2-PTGDR (P = 4.2 × 10-8), and one novel locus associated with TG near WDR11-FGFR2 (P = 2.7 × 10-10). Conditional analyses identified a second signal near CD163-APOBEC1. We then combined results from the East Asian meta-analysis with association results from up to 187,365 European individuals from the Global Lipids Genetics Consortium in a trans-ancestry meta-analysis. This analysis identified (log10Bayes Factor ≥6.1) eight additional novel lipid loci. Among the twelve total loci identified, the index variants at eight loci have demonstrated at least nominal significance with other metabolic traits in prior studies, and two loci exhibited coincident eQTLs (P < 1 × 10-5) in subcutaneous adipose tissue for BPTF and PDGFC. Taken together, these analyses identified multiple novel lipid loci, providing new potential therapeutic targets. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Real-time new satellite product demonstration from microwave sensors and GOES-16 at NRL TC web

NASA Astrophysics Data System (ADS)

Cossuth, J.; Richardson, K.; Surratt, M. L.; Bankert, R.

2017-12-01

The Naval Research Laboratory (NRL) Tropical Cyclone (TC) satellite webpage (https://www.nrlmry.navy.mil/TC.html) provides demonstration analyses of storm imagery to benefit operational TC forecast centers around the world. With the availability of new spectral information provided by GOES-16 satellite data and recent research into improved visualization methods of microwave data, experimental imagery was operationally tested to visualize the structural changes of TCs during the 2017 hurricane season. This presentation provides an introduction into these innovative satellite analysis methods, NRL's next generation satellite analysis system (the Geolocated Information Processing System, GeoIPSTM), and demonstration the added value of additional spectral frequencies when monitoring storms in near-realtime.

77 FR 39959 - Draft Guidance To Implement Requirements for the Treatment of Air Quality Monitoring Data...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-06

... of the revised draft High Winds Guidance document, the EPA identifies example technical analyses that... identified analyses and any additional technical analyses that air agencies could use to demonstrate that the... Web site at http://www.epa.gov/ttn/analysis/exevents.htm for additional details on the draft non...

The Influence of Metabolic Syndrome and Sex on the DNA Methylome in Schizophrenia

PubMed Central

Lines, Brittany N.

2018-01-01

Introduction The mechanism by which metabolic syndrome occurs in schizophrenia is not completely known; however, previous work suggests that changes in DNA methylation may be involved which is further influenced by sex. Within this study, the DNA methylome was profiled to identify altered methylation associated with metabolic syndrome in a schizophrenia population on atypical antipsychotics. Methods Peripheral blood from schizophrenia subjects was utilized for DNA methylation analyses. Discovery analyses (n = 96) were performed using an epigenome-wide analysis on the Illumina HumanMethylation450K BeadChip based on metabolic syndrome diagnosis. A secondary discovery analysis was conducted based on sex. The top hits from the discovery analyses were assessed in an additional validation set (n = 166) using site-specific methylation pyrosequencing. Results A significant increase in CDH22 gene methylation in subjects with metabolic syndrome was identified in the overall sample. Additionally, differential methylation was found within the MAP3K13 gene in females and the CCDC8 gene within males. Significant differences in methylation were again observed for the CDH22 and MAP3K13 genes, but not CCDC8, in the validation sample set. Conclusions This study provides preliminary evidence that DNA methylation may be associated with metabolic syndrome and sex in schizophrenia. PMID:29850476

Cost-benefit analyses of supplementary measles immunisation in the highly immunized population of New Zealand.

PubMed

Hayman, D T S; Marshall, J C; French, N P; Carpenter, T E; Roberts, M G; Kiedrzynski, T

2017-09-05

As endemic measles is eliminated from countries through increased immunisation, the economic benefits of enhanced immunisation programs may come into question. New Zealand has suffered from outbreaks after measles introductions from abroad and we use it as a model system to understand the benefits of catch up immunisation in highly immunised populations. We provide cost-benefit analyses for measles supplementary immunisation in New Zealand. We model outbreaks based on estimates of the basic reproduction number in the vaccinated population (R v , the number of secondary infections in a partially immunised population), based on the number of immunologically-naïve people at district and national levels, considering both pre- and post-catch up vaccination scenarios. Our analyses suggest that measles R v often includes or exceeds one (0.18-3.92) despite high levels of population immunity. We calculate the cost of the first 187 confirmed and probable measles cases in 2014 to be over NZ$1 million (∼US$864,200) due to earnings lost, case management and hospitalization costs. The benefit-cost ratio analyses suggest additional vaccination beyond routine childhood immunisation is economically efficient. Supplemental vaccination-related costs are required to exceed approximately US$66 to US$1877 per person, depending on different scenarios, before supplemental vaccination is economically inefficient. Thus, our analysis suggests additional immunisation beyond childhood programs to target naïve individuals is economically beneficial even when childhood immunisation rates are high. Copyright © 2017 Elsevier Ltd. All rights reserved.

Maser: one-stop platform for NGS big data from analysis to visualization

PubMed Central

Kinjo, Sonoko; Monma, Norikazu; Misu, Sadahiko; Kitamura, Norikazu; Imoto, Junichi; Yoshitake, Kazutoshi; Gojobori, Takashi; Ikeo, Kazuho

2018-01-01

Abstract A major challenge in analyzing the data from high-throughput next-generation sequencing (NGS) is how to handle the huge amounts of data and variety of NGS tools and visualize the resultant outputs. To address these issues, we developed a cloud-based data analysis platform, Maser (Management and Analysis System for Enormous Reads), and an original genome browser, Genome Explorer (GE). Maser enables users to manage up to 2 terabytes of data to conduct analyses with easy graphical user interface operations and offers analysis pipelines in which several individual tools are combined as a single pipeline for very common and standard analyses. GE automatically visualizes genome assembly and mapping results output from Maser pipelines, without requiring additional data upload. With this function, the Maser pipelines can graphically display the results output from all the embedded tools and mapping results in a web browser. Therefore Maser realized a more user-friendly analysis platform especially for beginners by improving graphical display and providing the selected standard pipelines that work with built-in genome browser. In addition, all the analyses executed on Maser are recorded in the analysis history, helping users to trace and repeat the analyses. The entire process of analysis and its histories can be shared with collaborators or opened to the public. In conclusion, our system is useful for managing, analyzing, and visualizing NGS data and achieves traceability, reproducibility, and transparency of NGS analysis. Database URL: http://cell-innovation.nig.ac.jp/maser/ PMID:29688385

mySyntenyPortal: an application package to construct websites for synteny block analysis.

PubMed

Lee, Jongin; Lee, Daehwan; Sim, Mikang; Kwon, Daehong; Kim, Juyeon; Ko, Younhee; Kim, Jaebum

2018-06-05

Advances in sequencing technologies have facilitated large-scale comparative genomics based on whole genome sequencing. Constructing and investigating conserved genomic regions among multiple species (called synteny blocks) are essential in the comparative genomics. However, they require significant amounts of computational resources and time in addition to bioinformatics skills. Many web interfaces have been developed to make such tasks easier. However, these web interfaces cannot be customized for users who want to use their own set of genome sequences or definition of synteny blocks. To resolve this limitation, we present mySyntenyPortal, a stand-alone application package to construct websites for synteny block analyses by using users' own genome data. mySyntenyPortal provides both command line and web-based interfaces to build and manage websites for large-scale comparative genomic analyses. The websites can be also easily published and accessed by other users. To demonstrate the usability of mySyntenyPortal, we present an example study for building websites to compare genomes of three mammalian species (human, mouse, and cow) and show how they can be easily utilized to identify potential genes affected by genome rearrangements. mySyntenyPortal will contribute for extended comparative genomic analyses based on large-scale whole genome sequences by providing unique functionality to support the easy creation of interactive websites for synteny block analyses from user's own genome data.

A seasonal comparison of surface sediment characteristics in Chincoteague Bay, Maryland and Virginia, USA

USGS Publications Warehouse

Ellis, Alisha M.; Marot, Marci E.; Wheaton, Cathryn J.; Bernier, Julie C.; Smith, Christopher G.

2016-02-03

This report is an archive for sedimentological data derived from the surface sediment of Chincoteague Bay. Data are available for the spring (March/April 2014) and fall (October 2014) samples collected. Downloadable data are provided as Excel spreadsheets and as JPEG files. Additional files include ArcGIS shapefiles of the sampling sites, detailed results of sediment grain-size analyses, and formal Federal Geographic Data Committee metadata (data downloads).

Multi-Element Unstructured Analyses of Complex Valve Systems

NASA Technical Reports Server (NTRS)

Sulyma, Peter (Technical Monitor); Ahuja, Vineet; Hosangadi, Ashvin; Shipman, Jeremy

2004-01-01

The safe and reliable operation of high pressure test stands for rocket engine and component testing places an increased emphasis on the performance of control valves and flow metering devices. In this paper, we will present a series of high fidelity computational analyses of systems ranging from cryogenic control valves and pressure regulator systems to cavitating venturis that are used to support rocket engine and component testing at NASA Stennis Space Center. A generalized multi-element framework with sub-models for grid adaption, grid movement and multi-phase flow dynamics has been used to carry out the simulations. Such a framework provides the flexibility of resolving the structural and functional complexities that are typically associated with valve-based high pressure feed systems and have been difficult to deal with traditional CFD methods. Our simulations revealed a rich variety of flow phenomena such as secondary flow patterns, hydrodynamic instabilities, fluctuating vapor pockets etc. In the paper, we will discuss performance losses related to cryogenic control valves, and provide insight into the physics of the dominant multi-phase fluid transport phenomena that are responsible for the choking like behavior in cryogenic control elements. Additionally, we will provide detailed analyses of the modal instability that is observed in the operation of the dome pressure regulator valve. Such instabilities are usually not localized and manifest themselves as a system wide phenomena leading to an undesirable chatter at high flow conditions.

IN SITU FIELD TESTING OF PROCESSES

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

J.S.Y. YANG

2004-11-08

The purpose of this scientific analysis report is to update and document the data and subsequent analyses from ambient field-testing activities performed in underground drifts and surface-based boreholes through unsaturated zone (UZ) tuff rock units. In situ testing, monitoring, and associated laboratory studies are conducted to directly assess and evaluate the waste emplacement environment and the natural barriers to radionuclide transport at Yucca Mountain. This scientific analysis report supports and provides data to UZ flow and transport model reports, which in turn contribute to the Total System Performance Assessment (TSPA) of Yucca Mountain, an important document for the license applicationmore » (LA). The objectives of ambient field-testing activities are described in Section 1.1. This report is the third revision (REV 03), which supercedes REV 02. The scientific analysis of data for inputs to model calibration and validation as documented in REV 02 were developed in accordance with the Technical Work Plan (TWP) ''Technical Work Plan for: Performance Assessment Unsaturated Zone'' (BSC 2004 [DIRS 167969]). This revision was developed in accordance with the ''Technical Work Plan for: Unsaturated Zone Flow Analysis and Model Report Integration'' (BSC 2004 [DIRS 169654], Section 1.2.4) for better integrated, consistent, transparent, traceable, and more complete documentation in this scientific analysis report and associated UZ flow and transport model reports. No additional testing or analyses were performed as part of this revision. The list of relevant acceptance criteria is provided by ''Technical Work Plan for: Unsaturated Zone Flow Analysis and Model Report Integration'' (BSC 2004 [DIRS 169654]), Table 3-1. Additional deviations from the TWP regarding the features, events, and processes (FEPs) list are discussed in Section 1.3. Documentation in this report includes descriptions of how, and under what conditions, the tests were conducted. The descriptions and analyses provide data useful for refining and confirming the understanding of flow, drift seepage, and transport processes in the UZ. The UZ testing activities included measurement of permeability distribution, quantification of the seepage of water into the drifts, evaluation of fracture-matrix interaction, study of flow along faults, testing of flow and transport between drifts, characterization of hydrologic heterogeneity along drifts, estimation of drying effects on the rock surrounding the drifts due to ventilation, monitoring of moisture conditions in open and sealed drifts, and determination of the degree of minimum construction water migration below drift. These field tests were conducted in two underground drifts at Yucca Mountain, the Exploratory Studies Facility (ESF) drift, and the cross-drift for Enhanced Characterization of the Repository Block (ECRB), as described in Section 1.2. Samples collected in boreholes and underground drifts have been used for additional hydrochemical and isotopic analyses for additional understanding of the UZ setting. The UZ transport tests conducted at the nearby Busted Butte site (see Figure 1-4) are also described in this scientific analysis report.« less

Patient-provider communication and hormonal therapy side effects in breast cancer survivors.

PubMed

Lin, Jenny J; Chao, Jennifer; Bickell, Nina A; Wisnivesky, Juan P

2017-09-01

Side effects from hormonal therapy (HT) for breast cancer treatment occur frequently and are associated with worse quality of life and HT non-adherence. Whether improved patient-physician communication is associated with patients' reporting of side effects is unknown. We undertook this study to assess factors associated with women's reports of HT side effects. Between December 2012 and April 2013, we conducted a cross-sectional survey of breast cancer patients undergoing HT in an urban medical center. Descriptive statistics, univariate analyses, and multivariate analyses were used to evaluate associations. Of the 100 participants, 67% reported having HT side effects. However, when prompted, an additional 9% reported experiencing specific HT-related symptoms. Despite very high communication scores, one-third of participants reported they had not discussed side effects with providers. Multivariate analysis showed that after controlling for age, education, race, and medication beliefs, women who had difficulty asking providers for more information were more likely to report side effects (odds ratio 8.27, 95% confidence interval 1.01-69.88). Although HT side effects often occur and are bothersome, patient-provider discussions about side effects remain suboptimal. Providers should actively ask patients about medication side effects so that they can be addressed to improve quality of life and potentially, medication adherence.

Lessons learned from additional research analyses of unsolved clinical exome cases.

PubMed

Eldomery, Mohammad K; Coban-Akdemir, Zeynep; Harel, Tamar; Rosenfeld, Jill A; Gambin, Tomasz; Stray-Pedersen, Asbjørg; Küry, Sébastien; Mercier, Sandra; Lessel, Davor; Denecke, Jonas; Wiszniewski, Wojciech; Penney, Samantha; Liu, Pengfei; Bi, Weimin; Lalani, Seema R; Schaaf, Christian P; Wangler, Michael F; Bacino, Carlos A; Lewis, Richard Alan; Potocki, Lorraine; Graham, Brett H; Belmont, John W; Scaglia, Fernando; Orange, Jordan S; Jhangiani, Shalini N; Chiang, Theodore; Doddapaneni, Harsha; Hu, Jianhong; Muzny, Donna M; Xia, Fan; Beaudet, Arthur L; Boerwinkle, Eric; Eng, Christine M; Plon, Sharon E; Sutton, V Reid; Gibbs, Richard A; Posey, Jennifer E; Yang, Yaping; Lupski, James R

2017-03-21

Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.

An automated data management/analysis system for space shuttle orbiter tiles. [stress analysis

NASA Technical Reports Server (NTRS)

Giles, G. L.; Ballas, M.

1982-01-01

An engineering data management system was combined with a nonlinear stress analysis program to provide a capability for analyzing a large number of tiles on the space shuttle orbiter. Tile geometry data and all data necessary of define the tile loads environment accessed automatically as needed for the analysis of a particular tile or a set of tiles. User documentation provided includes: (1) description of computer programs and data files contained in the system; (2) definitions of all engineering data stored in the data base; (3) characteristics of the tile anaytical model; (4) instructions for preparation of user input; and (5) a sample problem to illustrate use of the system. Description of data, computer programs, and analytical models of the tile are sufficiently detailed to guide extension of the system to include additional zones of tiles and/or additional types of analyses

Reliability of the individual components of the Canadian Armed Forces Physical Employment Standard.

PubMed

Stockbrugger, Barry G; Reilly, Tara J; Blacklock, Rachel E; Gagnon, Patrick J

2018-01-29

This investigation recruited 24 participants from both the Canadian Armed Forces (CAF) and civilian populations to complete 4 separate trials at "best effort" of each of the 4 components in the CAF Physical Employment Standard named the FORCE Evaluation: Fitness for Operational Requirements of CAF Employment. Analyses were performed to examine the level of variability and reliability within each component. The results demonstrate that candidates should be provided with at least 1 retest if they have recently completed at least 2 previous best effort attempts as per the protocol. In addition, the minimal detectable difference is given for each of the 4 components in seconds which identifies the threshold for subsequent action, either retest or remedial training, for those unable to meet the minimum standard. These results will educate the delivery of this employment standard, function as a method of accommodation, in addition to providing direction for physical training programs.

Rising dough and baking bread at the Australian synchrotron

NASA Astrophysics Data System (ADS)

Mayo, S. C.; McCann, T.; Day, L.; Favaro, J.; Tuhumury, H.; Thompson, D.; Maksimenko, A.

2016-01-01

Wheat protein quality and the amount of common salt added in dough formulation can have a significant effect on the microstructure and loaf volume of bread. High-speed synchrotron micro-CT provides an ideal tool for observing the three dimensional structure of bread dough in situ during proving (rising) and baking. In this work, the synchrotron micro-CT technique was used to observe the structure and time evolution of doughs made from high and low protein flour and three different salt additives. These experiments showed that, as expected, high protein flour produces a higher volume loaf compared to low protein flour regardless of salt additives. Furthermore the results show that KCl in particular has a very negative effect on dough properties resulting in much reduced porosity. The hundreds of datasets produced and analysed during this experiment also provided a valuable test case for handling large quantities of data using tools on the Australian Synchrotron's MASSIVE cluster.

High performance flight computer developed for deep space applications

NASA Technical Reports Server (NTRS)

Bunker, Robert L.

1993-01-01

The development of an advanced space flight computer for real time embedded deep space applications which embodies the lessons learned on Galileo and modern computer technology is described. The requirements are listed and the design implementation that meets those requirements is described. The development of SPACE-16 (Spaceborne Advanced Computing Engine) (where 16 designates the databus width) was initiated to support the MM2 (Marine Mark 2) project. The computer is based on a radiation hardened emulation of a modern 32 bit microprocessor and its family of support devices including a high performance floating point accelerator. Additional custom devices which include a coprocessor to improve input/output capabilities, a memory interface chip, and an additional support chip that provide management of all fault tolerant features, are described. Detailed supporting analyses and rationale which justifies specific design and architectural decisions are provided. The six chip types were designed and fabricated. Testing and evaluation of a brass/board was initiated.

How individual participant data meta-analyses have influenced trial design, conduct, and analysis.

PubMed

Tierney, Jayne F; Pignon, Jean-Pierre; Gueffyier, Francois; Clarke, Mike; Askie, Lisa; Vale, Claire L; Burdett, Sarah

2015-11-01

To demonstrate how individual participant data (IPD) meta-analyses have impacted directly on the design and conduct of trials and highlight other advantages IPD might offer. Potential examples of the impact of IPD meta-analyses on trials were identified at an international workshop, attended by individuals with experience in the conduct of IPD meta-analyses and knowledge of trials in their respective clinical areas. Experts in the field who did not attend were asked to provide any further examples. We then examined relevant trial protocols, publications, and Web sites to verify the impacts of the IPD meta-analyses. A subgroup of workshop attendees sought further examples and identified other aspects of trial design and conduct that may inform IPD meta-analyses. We identified 52 examples of IPD meta-analyses thought to have had a direct impact on the design or conduct of trials. After screening relevant trial protocols and publications, we identified 28 instances where IPD meta-analyses had clearly impacted on trials. They have influenced the selection of comparators and participants, sample size calculations, analysis and interpretation of subsequent trials, and the conduct and analysis of ongoing trials, sometimes in ways that would not possible with systematic reviews of aggregate data. We identified additional potential ways that IPD meta-analyses could be used to influence trials. IPD meta-analysis could be better used to inform the design, conduct, analysis, and interpretation of trials. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

How individual participant data meta-analyses have influenced trial design, conduct, and analysis

PubMed Central

Tierney, Jayne F.; Pignon, Jean-Pierre; Gueffyier, Francois; Clarke, Mike; Askie, Lisa; Vale, Claire L.; Burdett, Sarah; Alderson, P.; Askie, L.; Bennett, D.; Burdett, S.; Clarke, M.; Dias, S.; Emberson, J.; Gueyffier, F.; Iorio, A.; Macleod, M.; Mol, B.W.; Moons, C.; Parmar, M.; Perera, R.; Phillips, R.; Pignon, J.P.; Rees, J.; Reitsma, H.; Riley, R.; Rovers, M.; Rydzewska, L.; Schmid, C.; Shepperd, S.; Stenning, S.; Stewart, L.; Tierney, J.; Tudur Smith, C.; Vale, C.; Welge, J.; White, I.; Whiteley, W.

2015-01-01

Objectives To demonstrate how individual participant data (IPD) meta-analyses have impacted directly on the design and conduct of trials and highlight other advantages IPD might offer. Study Design and Setting Potential examples of the impact of IPD meta-analyses on trials were identified at an international workshop, attended by individuals with experience in the conduct of IPD meta-analyses and knowledge of trials in their respective clinical areas. Experts in the field who did not attend were asked to provide any further examples. We then examined relevant trial protocols, publications, and Web sites to verify the impacts of the IPD meta-analyses. A subgroup of workshop attendees sought further examples and identified other aspects of trial design and conduct that may inform IPD meta-analyses. Results We identified 52 examples of IPD meta-analyses thought to have had a direct impact on the design or conduct of trials. After screening relevant trial protocols and publications, we identified 28 instances where IPD meta-analyses had clearly impacted on trials. They have influenced the selection of comparators and participants, sample size calculations, analysis and interpretation of subsequent trials, and the conduct and analysis of ongoing trials, sometimes in ways that would not possible with systematic reviews of aggregate data. We identified additional potential ways that IPD meta-analyses could be used to influence trials. Conclusions IPD meta-analysis could be better used to inform the design, conduct, analysis, and interpretation of trials. PMID:26186982

Cost Analysis of Channeled, Distal Chip Laryngoscope for In-office Laryngopharyngeal Biopsies.

PubMed

Marcus, Sonya; Timen, Micah; Dion, Gregory R; Fritz, Mark A; Branski, Ryan C; Amin, Milan R

2018-02-19

Given that financial considerations play an increasingly prominent role in clinical decision-making, we sought (1) to determine the cost-effectiveness of in-office biopsy for the patient, the provider, and the health-care system, and (2) to determine the diagnostic accuracy of in-office biopsy. Retrospective, financial analyses were performed. Patients who underwent in-office (Current Procedural Terminology Code 31576) or operative biopsy (CPT Code 31535) for laryngopharyngeal lesions were included. Two financial analyses were performed: (1) the average cost of operating room (OR) versus in-office biopsy was calculated, and (2) a break-even analysis was calculated to determine the cost-effectiveness of in-office biopsy for the provider. In addition, the diagnostic accuracy of in-office biopsies and need for additional biopsies or procedures was recorded. Of the 48 patients included in the current study, 28 underwent in-office biopsy. A pathologic sample was obtained in 26 of 28 (92.9%) biopsies performed in the office. Of these patients, 16 avoided subsequent OR procedures. The average per patient cost was $7000 and $11,000 for in-office and OR biopsy, respectively. Break-even analysis demonstrated that the provider could achieve a profit 2 years after purchase of the necessary equipment. In-office laryngopharyngeal biopsies are accurate and, overall, more cost-effective than OR biopsies. Purchase of the channeled, distal chip laryngoscope and biopsy forceps to perform in-office biopsies can be profitable for a provider with a videolaryngoscopy tower. In-office biopsy should be considered the initial diagnostic tool for suspected laryngopharyngeal malignancies noted on videolaryngoscopy. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

The interplay between customer participation and difficulty of design examples in the online designing process and its effect on customer satisfaction: mediational analyses.

PubMed

Chang, Chia-Chi; Chen, Hui-Yun; Huang, I-Chiang

2009-04-01

In the current consumer-centric economy, consumers increasingly desire the opportunity to design their own products in order to express more effectively their self-image. Mass customization, based on efficient and flexible modulization designs, has provided individualized products to satisfy this desire. This work presents an experiment employed to demonstrate that customer participation leads to higher satisfaction. Specifically, the increment in customer satisfaction due to participation is greater when an easy example is provided than when either no example or a difficult one is provided. Additionally, self-congruity plays a mediating role on the customer participation-satisfaction relationship, and this mediating effect varies across different levels of the design example provided in the design process. When an easy design example is present, customer participation has a direct effect on satisfaction, in addition to the indirect effect of self-congruity. When a difficult example is provided, customer participation does not have incremental effects on either self-congruity or customer satisfaction. Finally, when no design example is shown to customers, contrary to our expectation, participation still enhances customer satisfaction due to an increased sense of self-congruity.

Results of the Excreta Bioassay Quality Control Program for April 1, 2009 through March 31, 2010

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

Antonio, Cheryl L.

2012-07-19

A total of 58 urine samples and 10 fecal samples were submitted during the report period (April 1, 2009 through March 31, 2010) to General Engineering Laboratories, South Carolina by the Hanford Internal Dosimetry Program (IDP) to check the accuracy, precision, and detection levels of their analyses. Urine analyses for Sr, 238Pu, 239Pu, 241Am, 243Am 235U, 238U, elemental uranium and fecal analyses for 241Am, 238Pu and 239Pu were tested this year as well as four tissue samples for 238Pu, 239Pu, 241Am and 241Pu. The number of QC urine samples submitted during the report period represented 1.3% of the total samplesmore » submitted. In addition to the samples provided by IDP, GEL was also required to conduct their own QC program, and submit the results of analyses to IDP. About 33% of the analyses processed by GEL during the third year of this contract were quality control samples. GEL tested the performance of 21 radioisotopes, all of which met or exceeded the specifications in the Statement of Work within statistical uncertainty (Table 4).« less

Results of The Excreta Bioassay Quality Control Program For April 1, 2010 Through March 31, 2011

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

Antonio, Cheryl L.

2012-07-19

A total of 76 urine samples and 10 spiked fecal samples were submitted during the report period (April 1, 2010 through March 31, 2011) to GEL Laboratories, LLC in South Carolina by the Hanford Internal Dosimetry Program (IDP) to check the accuracy, precision, and detection levels of their analyses. Urine analyses for 14C, Sr, for 238Pu, 239Pu, 241Am, 243Am, 235U, 238U, 238U-mass and fecal analyses for 241Am, 238Pu and 239Pu were tested this year. The number of QC urine samples submitted during the report period represented 1.1% of the total samples submitted. In addition to the samples provided by IDP,more » GEL was also required to conduct their own QC program, and submit the results of analyses to IDP. About 31% of the analyses processed by GEL during the first year of contract 112512 were quality control samples. GEL tested the performance of 23 radioisotopes, all of which met or exceeded the specifications in the Statement of Work within statistical uncertainty except the slightly elevated relative bias for 243,244Cm (Table 4).« less

Algorithms and analyses for stochastic optimization for turbofan noise reduction using parallel reduced-order modeling

NASA Astrophysics Data System (ADS)

Yang, Huanhuan; Gunzburger, Max

2017-06-01

Simulation-based optimization of acoustic liner design in a turbofan engine nacelle for noise reduction purposes can dramatically reduce the cost and time needed for experimental designs. Because uncertainties are inevitable in the design process, a stochastic optimization algorithm is posed based on the conditional value-at-risk measure so that an ideal acoustic liner impedance is determined that is robust in the presence of uncertainties. A parallel reduced-order modeling framework is developed that dramatically improves the computational efficiency of the stochastic optimization solver for a realistic nacelle geometry. The reduced stochastic optimization solver takes less than 500 seconds to execute. In addition, well-posedness and finite element error analyses of the state system and optimization problem are provided.

Metagenomic analyses of the late Pleistocene permafrost - additional tools for reconstruction of environmental conditions

NASA Astrophysics Data System (ADS)

Rivkina, Elizaveta; Petrovskaya, Lada; Vishnivetskaya, Tatiana; Krivushin, Kirill; Shmakova, Lyubov; Tutukina, Maria; Meyers, Arthur; Kondrashov, Fyodor

2016-04-01

A comparative analysis of the metagenomes from two 30 000-year-old permafrost samples, one of lake-alluvial origin and the other from late Pleistocene Ice Complex sediments, revealed significant differences within microbial communities. The late Pleistocene Ice Complex sediments (which have been characterized by the absence of methane with lower values of redox potential and Fe2+ content) showed a low abundance of methanogenic archaea and enzymes from both the carbon and nitrogen cycles, but a higher abundance of enzymes associated with the sulfur cycle. The metagenomic and geochemical analyses described in the paper provide evidence that the formation of the sampled late Pleistocene Ice Complex sediments likely took place under much more aerobic conditions than lake-alluvial sediments.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

Cameroonian fruit bats harbor divergent viruses, including rotavirus H, bastroviruses, and picobirnaviruses using an alternative genetic code

PubMed Central

Ghogomu, Stephen Mbigha; Conceição-Neto, Nádia; Beller, Leen; Deboutte, Ward; Maes, Piet; Van Ranst, Marc

2018-01-01

Abstract Most human emerging infectious diseases originate from wildlife and bats are a major reservoir of viruses, a few of which have been highly pathogenic to humans. In some regions of Cameroon, bats are hunted and eaten as a delicacy. This close proximity between human and bats provides ample opportunity for zoonotic events. To elucidate the viral diversity of Cameroonian fruit bats, we collected and metagenomically screened eighty-seven fecal samples of Eidolon helvum and Epomophorus gambianus fruit bats. The results showed a plethora of known and novel viruses. Phylogenetic analyses of the eleven gene segments of the first complete bat rotavirus H genome, showed clearly separated clusters of human, porcine, and bat rotavirus H strains, not indicating any recent interspecies transmission events. Additionally, we identified and analyzed a bat bastrovirus genome (a novel group of recently described viruses, related to astroviruses and hepatitis E viruses), confirming their recombinant nature, and provide further evidence of additional recombination events among bat bastroviruses. Interestingly, picobirnavirus-like RNA-dependent RNA polymerase gene segments were identified using an alternative mitochondrial genetic code, and further principal component analyses suggested that they may have a similar lifestyle to mitoviruses, a group of virus-like elements known to infect the mitochondria of fungi. Although identified bat coronavirus, parvovirus, and cyclovirus strains belong to established genera, most of the identified partitiviruses and densoviruses constitute putative novel genera in their respective families. Finally, the results of the phage community analyses of these bats indicate a very diverse geographically distinct bat phage population, probably reflecting different diets and gut bacterial ecosystems. PMID:29644096

Cost-Utility of Quadrivalent Versus Trivalent Influenza Vaccine in Germany, Using an Individual-Based Dynamic Transmission Model.

PubMed

Dolk, Christiaan; Eichner, Martin; Welte, Robert; Anastassopoulou, Anastassia; Van Bellinghen, Laure-Anne; Poulsen Nautrup, Barbara; Van Vlaenderen, Ilse; Schmidt-Ott, Ruprecht; Schwehm, Markus; Postma, Maarten

2016-12-01

Seasonal influenza infection is primarily caused by circulation of two influenza A strain subtypes and strains from two B lineages that vary each year. Trivalent influenza vaccine (TIV) contains only one of the two B-lineage strains, resulting in mismatches between vaccine strains and the predominant circulating B lineage. Quadrivalent influenza vaccine (QIV) includes both B-lineage strains. The objective was to estimate the cost-utility of introducing QIV to replace TIV in Germany. An individual-based dynamic transmission model (4Flu) using German data was used to provide realistic estimates of the impact of TIV and QIV on age-specific influenza infections. Cases were linked to health and economic outcomes to calculate the cost-utility of QIV versus TIV, from both a societal and payer perspective. Costs and effects were discounted at 3.0 and 1.5 % respectively, with 2014 as the base year. Univariate and probabilistic sensitivity analyses were conducted. Using QIV instead of TIV resulted in additional quality-adjusted life-years (QALYs) and cost savings from the societal perspective (i.e. it represents the dominant strategy) and an incremental cost-utility ratio (ICUR) of €14,461 per QALY from a healthcare payer perspective. In all univariate analyses, QIV remained cost-effective (ICUR <€50,000). In probabilistic sensitivity analyses, QIV was cost-effective in >98 and >99 % of the simulations from the societal and payer perspective, respectively. This analysis suggests that QIV in Germany would provide additional health gains while being cost-saving to society or costing €14,461 per QALY gained from the healthcare payer perspective, compared with TIV.

Assessing the treatment effect in a randomized controlled trial with extensive non-adherence: the EVOLVE trial.

PubMed

Kubo, Yumi; Sterling, Lulu Ren; Parfrey, Patrick S; Gill, Karminder; Mahaffey, Kenneth W; Gioni, Ioanna; Trotman, Marie-Louise; Dehmel, Bastian; Chertow, Glenn M

2015-01-01

Intention-to-treat (ITT) analysis is widely used to establish efficacy in randomized clinical trials. However, in a long-term outcomes study where non-adherence to study drug is substantial, the on-treatment effect of the study drug may be underestimated using the ITT analysis. The analyses presented herein are from the EVOLVE trial, a double-blind, placebo-controlled, event-driven cardiovascular outcomes study conducted to assess whether a treatment regimen including cinacalcet compared with placebo in addition to other conventional therapies reduces the risk of mortality and major cardiovascular events in patients receiving hemodialysis with secondary hyperparathyroidism. Pre-specified sensitivity analyses were performed to assess the impact of non-adherence on the estimated effect of cinacalcet. These analyses included lag-censoring, inverse probability of censoring weights (IPCW), rank preserving structural failure time model (RPSFTM) and iterative parameter estimation (IPE). The relative hazard (cinacalcet versus placebo) of mortality and major cardiovascular events was 0.93 (95% confidence interval 0.85, 1.02) using the ITT analysis; 0.85 (0.76, 0.95) using lag-censoring analysis; 0.81 (0.70, 0.92) using IPCW; 0.85 (0.66, 1.04) using RPSFTM and 0.85 (0.75, 0.96) using IPE. These analyses, while not providing definitive evidence, suggest that the intervention may have an effect while subjects are receiving treatment. The ITT method remains the established method to evaluate efficacy of a new treatment; however, additional analyses should be considered to assess the on-treatment effect when substantial non-adherence to study drug is expected or observed. Copyright © 2015 John Wiley & Sons, Ltd.

Missing heritability in the tails of quantitative traits? A simulation study on the impact of slightly altered true genetic models.

PubMed

Pütter, Carolin; Pechlivanis, Sonali; Nöthen, Markus M; Jöckel, Karl-Heinz; Wichmann, Heinz-Erich; Scherag, André

2011-01-01

Genome-wide association studies have identified robust associations between single nucleotide polymorphisms and complex traits. As the proportion of phenotypic variance explained is still limited for most of the traits, larger and larger meta-analyses are being conducted to detect additional associations. Here we investigate the impact of the study design and the underlying assumption about the true genetic effect in a bimodal mixture situation on the power to detect associations. We performed simulations of quantitative phenotypes analysed by standard linear regression and dichotomized case-control data sets from the extremes of the quantitative trait analysed by standard logistic regression. Using linear regression, markers with an effect in the extremes of the traits were almost undetectable, whereas analysing extremes by case-control design had superior power even for much smaller sample sizes. Two real data examples are provided to support our theoretical findings and to explore our mixture and parameter assumption. Our findings support the idea to re-analyse the available meta-analysis data sets to detect new loci in the extremes. Moreover, our investigation offers an explanation for discrepant findings when analysing quantitative traits in the general population and in the extremes. Copyright © 2011 S. Karger AG, Basel.

Systematic literature reviews and meta-analyses: part 6 of a series on evaluation of scientific publications.

PubMed

Ressing, Meike; Blettner, Maria; Klug, Stefanie J

2009-07-01

Because of the rising number of scientific publications, it is important to have a means of jointly summarizing and assessing different studies on a single topic. Systematic literature reviews, meta-analyses of published data, and meta-analyses of individual data (pooled reanalyses) are now being published with increasing frequency. We here describe the essential features of these methods and discuss their strengths and weaknesses. This article is based on a selective literature search. The different types of review and meta-analysis are described, the methods used in each are outlined so that they can be evaluated, and a checklist is given for the assessment of reviews and meta-analyses of scientific articles. Systematic literature reviews provide an overview of the state of research on a given topic and enable an assessment of the quality of individual studies. They also allow the results of different studies to be evaluated together when these are inconsistent. Meta-analyses additionally allow calculation of pooled estimates of an effect. The different types of review and meta-analysis are discussed with examples from the literature on one particular topic. Systematic literature reviews and meta-analyses enable the research findings and treatment effects obtained in different individual studies to be summed up and evaluated.

Genomic Repeat Abundances Contain Phylogenetic Signal

PubMed Central

Dodsworth, Steven; Chase, Mark W.; Kelly, Laura J.; Leitch, Ilia J.; Macas, Jiří; Novák, Petr; Piednoël, Mathieu; Weiss-Schneeweiss, Hanna; Leitch, Andrew R.

2015-01-01

A large proportion of genomic information, particularly repetitive elements, is usually ignored when researchers are using next-generation sequencing. Here we demonstrate the usefulness of this repetitive fraction in phylogenetic analyses, utilizing comparative graph-based clustering of next-generation sequence reads, which results in abundance estimates of different classes of genomic repeats. Phylogenetic trees are then inferred based on the genome-wide abundance of different repeat types treated as continuously varying characters; such repeats are scattered across chromosomes and in angiosperms can constitute a majority of nuclear genomic DNA. In six diverse examples, five angiosperms and one insect, this method provides generally well-supported relationships at interspecific and intergeneric levels that agree with results from more standard phylogenetic analyses of commonly used markers. We propose that this methodology may prove especially useful in groups where there is little genetic differentiation in standard phylogenetic markers. At the same time as providing data for phylogenetic inference, this method additionally yields a wealth of data for comparative studies of genome evolution. PMID:25261464

Cost analyses of peer health worker and mHealth support interventions for improving AIDS care in Rakai, Uganda

PubMed Central

Chang, Larry W.; Kagaayi, Joseph; Nakigozi, Gertrude; Serwadda, David; Quinn, Thomas C.; Gray, Ronald H.; Bollinger, Robert C.; Reynolds, Steven J.; Holtgrave, David

2012-01-01

A cost analysis study calculates resources needed to deliver an intervention and can provide useful information on affordability for service providers and policy makers. We conducted cost analyses of both a peer health worker (PHW) and a mHealth (mobile phone) support intervention. Excluding supervisory staffing costs, total yearly costs for the PHW intervention was $8,475, resulting in a yearly cost per patient of $8.74, per virologic failure averted cost of $189, and per patient lost to follow-up averted cost of $1025. Including supervisory staffing costs increased total yearly costs to $14,991. Yearly costs of the mHealth intervention were an additional $1046, resulting in a yearly cost per patient of $2.35. In a threshold analysis, the PHW intervention was found to be cost saving if it was able to avert 1.50 patients per year from switching to second-line antiretroviral therapy. Other AIDS care programs may find these intervention costs affordable. PMID:22971113

A novel eQTL-based analysis reveals the biology of breast cancer risk loci

PubMed Central

Li, Qiyuan; Seo, Ji-Heui; Stranger, Barbara; McKenna, Aaron; Pe'er, Itsik; LaFramboise, Thomas; Brown, Myles; Tyekucheva, Svitlana; Freedman, Matthew L.

2014-01-01

Summary Germline determinants of gene expression in tumors are less studied due to the complexity of transcript regulation caused by somatically acquired alterations. We performed expression quantitative trait locus (eQTL) based analyses using the multi-level information provided in The Cancer Genome Atlas (TCGA). Of the factors we measured, cis-acting eQTL saccounted for 1.2% of the total variation of tumor gene expression, while somatic copy number alteration and CpG methylation accounted for 7.3% and 3.3%, respectively. eQTL analyses of 15 previously reported breast cancer risk loci resulted in discovery of three variants that are significantly associated with transcript levels (FDR<0.1). In a novel trans- based analysis, an additional three risk loci were identified to act through ESR1, MYC, and KLF4. These findings provide a more comprehensive picture of gene expression determinants in breast cancer as well as insights into the underlying biology of breast cancer risk loci. PMID:23374354

Grapheme-color synesthetes show peculiarities in their emotional brain: cortical and subcortical evidence from VBM analysis of 3D-T1 and DTI data.

PubMed

Melero, Helena; Peña-Melián, Ángel; Ríos-Lago, Marcos; Pajares, Gonzalo; Hernández-Tamames, Juan Antonio; Álvarez-Linera, Juan

2013-06-01

Grapheme-color synesthesia is a neurological phenomenon in which viewing achromatic letters/numbers leads to automatic and involuntary color experiences. In this study, voxel-based morphometry analyses were performed on T1 images and fractional anisotropy measures to examine the whole brain in associator grapheme-color synesthetes. These analyses provide new evidence of variations in emotional areas (both at the cortical and subcortical levels), findings that help understand the emotional component as a relevant aspect of the synesthetic experience. Additionally, this study replicates previous findings in the left intraparietal sulcus and, for the first time, reports the existence of anatomical differences in subcortical gray nuclei of developmental grapheme-color synesthetes, providing a link between acquired and developmental synesthesia. This empirical evidence, which goes beyond modality-specific areas, could lead to a better understanding of grapheme-color synesthesia as well as of other modalities of the phenomenon.

pc8.1, a major QTL for pigment content in pepper fruit, is associated with variation in plastid compartment size.

PubMed

Brand, Arnon; Borovsky, Yelena; Meir, Sagit; Rogachev, Ilana; Aharoni, Asaph; Paran, Ilan

2012-03-01

Studies on the genetic control of pigment content in pepper fruit have focused mainly on monogenic mutations leading to changes in fruit color. In addition to the qualitative variation in fruit color, quantitative variation in pigment content and color intensity exists in pepper giving rise to a range of color intensities. However, the genetic basis for this variation is poorly understood, hindering the development of peppers that are rich in these beneficial compounds. In this paper, quantitative variation in pigment content was studied in a cross between a dark-green Capsicum annuum pepper and a light-green C. chinense pepper. Two major pigment content QTLs that control chlorophyll content were identified, pc8.1 and pc10.1. The major QTL pc8.1, also affected carotenoid content in the ripe fruit. However, additional analyses in subsequent generations did not reveal a consistent effect of this QTL on carotenoid content in ripe fruit. Confocal microscopy analyses of green immature fruits of the parents and of near-isogenic lines for pc8.1 indicated that the QTL exerts its effect via increasing chloroplast compartment size in the dark-green genotypes, predominantly in a fruit-specific manner. Metabolic analyses indicated that in addition to chlorophyll, chloroplast-associated tocopherols and carotenoids are also elevated. Future identification of the genes controlling pigment content QTLs in pepper will provide a better understanding of this important trait and new opportunities for breeding peppers and other Solanaceae species with enhanced nutritional value.

Supporting employees' work-family needs improves health care quality: Longitudinal evidence from long-term care.

PubMed

Okechukwu, Cassandra A; Kelly, Erin L; Bacic, Janine; DePasquale, Nicole; Hurtado, David; Kossek, Ellen; Sembajwe, Grace

2016-05-01

We analyzed qualitative and quantitative data from U.S.-based employees in 30 long-term care facilities. Analysis of semi-structured interviews from 154 managers informed quantitative analyses. Quantitative data include 1214 employees' scoring of their supervisors and their organizations on family supportiveness (individual scores and aggregated to facility level), and three outcomes: (1), care quality indicators assessed at facility level (n = 30) and collected monthly for six months after employees' data collection; (2), employees' dichotomous survey response on having additional off-site jobs; and (3), proportion of employees with additional jobs at each facility. Thematic analyses revealed that managers operate within the constraints of an industry that simultaneously: (a) employs low-wage employees with multiple work-family challenges, and (b) has firmly institutionalized goals of prioritizing quality of care and minimizing labor costs. Managers universally described providing work-family support and prioritizing care quality as antithetical to each other. Concerns surfaced that family-supportiveness encouraged employees to work additional jobs off-site, compromising care quality. Multivariable linear regression analysis of facility-level data revealed that higher family-supportive supervision was associated with significant decreases in residents' incidence of all pressure ulcers (-2.62%) and other injuries (-9.79%). Higher family-supportive organizational climate was associated with significant decreases in all falls (-17.94%) and falls with injuries (-7.57%). Managers' concerns about additional jobs were not entirely unwarranted: multivariable logistic regression of employee-level data revealed that among employees with children, having family-supportive supervision was associated with significantly higher likelihood of additional off-site jobs (RR 1.46, 95%CI 1.08-1.99), but family-supportive organizational climate was associated with lower likelihood (RR 0.76, 95%CI 0.59-0.99). However, proportion of workers with additional off-site jobs did not significantly predict care quality at facility levels. Although managers perceived providing work-family support and ensuring high care quality as conflicting goals, results suggest that family-supportiveness is associated with better care quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

Supporting employees’ work-family needs improves health care quality: longitudinal evidence from long-term care

PubMed Central

Okechukwu, Cassandra A.; Kelly, Erin L.; Bacic, Janine; DePasquale, Nicole; Hurtado, David; Kossek, Ellen; Sembajwe, Grace

2016-01-01

We analyzed qualitative and quantitative data from U.S.-based employees in 30 long-term care facilities. Analysis of semi-structured interviews from 154 managers informed quantitative analyses. Quantitative data include 1,214 employees’ scoring of their supervisors and their organizations on family supportiveness (individual scores and aggregated to facility level), and three outcomes: (1), care quality indicators assessed at facility level (n=30) and collected monthly for six months after employees’ data collection; (2), employees’ dichotomous survey response on having additional off-site jobs; and (3), proportion of employees with additional jobs at each facility. Thematic analyses revealed that managers operate within the constraints of an industry that simultaneously: (a) employs low-wage employees with multiple work-family challenges, and (b) has firmly institutionalized goals of prioritizing quality of care and minimizing labor costs. Managers universally described providing work-family support and prioritizing care quality as antithetical to each other. Concerns surfaced that family-supportiveness encouraged employees to work additional jobs off-site, compromising care quality. Multivariable linear regression analysis of facility-level data revealed that higher family-supportive supervision was associated with significant decreases in residents’ incidence of all pressure ulcers (−2.62%) and other injuries (−9.79%). Higher family-supportive organizational climate was associated with significant decreases in all falls (−17.94%) and falls with injuries (−7.57%). Managers’ concerns about additional jobs were not entirely unwarranted: multivariable logistic regression of employee-level data revealed that among employees with children, having family-supportive supervision was associated with significantly higher likelihood of additional off-site jobs (RR 1.46, 95%CI 1.08-1.99), but family-supportive organizational climate was associated with lower likelihood (RR 0.76, 95%CI 0.59-0.99). However, proportion of workers with additional off-site jobs did not significantly predict care quality at facility levels. Although managers perceived providing work-family support and ensuring high care quality as conflicting goals, results suggest that family-supportiveness is associated with better care quality. PMID:27082022

Topographic ERP analyses: a step-by-step tutorial review.

PubMed

Murray, Micah M; Brunet, Denis; Michel, Christoph M

2008-06-01

In this tutorial review, we detail both the rationale for as well as the implementation of a set of analyses of surface-recorded event-related potentials (ERPs) that uses the reference-free spatial (i.e. topographic) information available from high-density electrode montages to render statistical information concerning modulations in response strength, latency, and topography both between and within experimental conditions. In these and other ways these topographic analysis methods allow the experimenter to glean additional information and neurophysiologic interpretability beyond what is available from canonical waveform analyses. In this tutorial we present the example of somatosensory evoked potentials (SEPs) in response to stimulation of each hand to illustrate these points. For each step of these analyses, we provide the reader with both a conceptual and mathematical description of how the analysis is carried out, what it yields, and how to interpret its statistical outcome. We show that these topographic analysis methods are intuitive and easy-to-use approaches that can remove much of the guesswork often confronting ERP researchers and also assist in identifying the information contained within high-density ERP datasets.

Constitutive Analyses of Nontraditional Stabilization Additives

DTIC Science & Technology

2004-11-01

cm-I Figure 29. FTIRIATR spectrum of Ven-Set 950 soil stabilization agent Based on the information provided in the MSDS and the FTIR analysis above...emulsion. The MSDS states that it is composed of an acrylic polymer (52 percent) with zinc oxide (2 percent), activated carbon (8 to 9 percent), and...water. The polymer as yet is unidentified. However, it appears to be an acrylate/ methacrylate with some aromaticity (peak about 1,635 c-f’). The

Defense Contracting: Actions Needed to Explore Additional Opportunities to Gain Efficiencies in Acquiring Foreign Language Support

DTIC Science & Technology

2013-02-25

Directive 5160.41E, Defense Language Program . 10GAO-11-456. Page 5 GAO-13-251R Defense Contracting types of foreign language support that DOD has acquired...Language Transformation Roadmap, (January 2005), and Department of Defense Directive 5160.41E, Defense Language Program . Page 15 GAO-13-251R Defense...examines the use of public funds; evaluates federal programs and policies; and provides analyses, recommendations, and other assistance to help

Thinking lean: implementing DMAIC methods to improve efficiency within a cystic fibrosis clinic.

PubMed

Smith, Chad; Wood, Suzanne; Beauvais, Bradley

2011-01-01

The timely coordination of care in clinics that require frequent assessments by multiple specialists can be challenging for both patients and providers. The cornerstone of care at cystic fibrosis (CF) centers with superior clinical outcomes, as with reduced acuity of episodic disease and incidence of hospitalizations, is frequent clinical encounters coupled with aggressive therapies. However, inefficiencies in the clinical practice structure prevent optimal utilization of resources. To decrease non-value-added time, defined as time a patient spends alone in an examination room, without altering the time providers spend caring for a patient, the application of Lean methods was used to see whether reducing variation could significantly decrease lead time, considered the length of a patient visit, within a CF clinic setting. Baseline capability analyses revealed only 19.3% of patient visits were completed in 60min or less, with mean and median visit times of 84 and 81min, respectively. Final capability analyses demonstrated that 41.5% of patient visits were completed in 60min or less, 23% greater than the baseline capability. Mean and median visit times decreased by 10min per visit. Research efforts increased the available capacity by 500 patient visits per year, representing additional revenue of over US$165,000 annually with no additional administrative costs incurred. © 2011 National Association for Healthcare Quality.

The Utility of Stage-specific Mid-to-late Drosophila Follicle Isolation

PubMed Central

Spracklen, Andrew J.; Tootle, Tina L.

2013-01-01

Drosophila oogenesis or follicle development has been widely used to advance the understanding of complex developmental and cell biologic processes. This methods paper describes how to isolate mid-to-late stage follicles (Stage 10B-14) and utilize them to provide new insights into the molecular and morphologic events occurring during tight windows of developmental time. Isolated follicles can be used for a variety of experimental techniques, including in vitro development assays, live imaging, mRNA expression analysis and western blot analysis of proteins. Follicles at Stage 10B (S10B) or later will complete development in culture; this allows one to combine genetic or pharmacologic perturbations with in vitro development to define the effects of such manipulations on the processes occurring during specific periods of development. Additionally, because these follicles develop in culture, they are ideally suited for live imaging studies, which often reveal new mechanisms that mediate morphological events. Isolated follicles can also be used for molecular analyses. For example, changes in gene expression that result from genetic perturbations can be defined for specific developmental windows. Additionally, protein level, stability, and/or posttranslational modification state during a particular stage of follicle development can be examined through western blot analyses. Thus, stage-specific isolation of Drosophila follicles provides a rich source of information into widely conserved processes of development and morphogenesis. PMID:24326735

Kinetic analyses of vasculogenesis inform mechanistic studies

PubMed Central

Winfree, Seth; Chu, Chenghao; Tu, Wanzhu; Blue, Emily K.; Gohn, Cassandra R.; Dunn, Kenneth W.

2017-01-01

Vasculogenesis is a complex process by which endothelial stem and progenitor cells undergo de novo vessel formation. Quantitative assessment of vasculogenesis is a central readout of endothelial progenitor cell functionality. However, current assays lack kinetic measurements. To address this issue, new approaches were developed to quantitatively assess in vitro endothelial colony-forming cell (ECFC) network formation in real time. Eight parameters of network structure were quantified using novel Kinetic Analysis of Vasculogenesis (KAV) software. KAV assessment of structure complexity identified two phases of network formation. This observation guided the development of additional vasculogenic readouts. A tissue cytometry approach was established to quantify the frequency and localization of dividing ECFCs. Additionally, Fiji TrackMate was used to quantify ECFC displacement and speed at the single-cell level during network formation. These novel approaches were then implemented to identify how intrauterine exposure to maternal diabetes mellitus (DM) impairs fetal ECFC vasculogenesis. Fetal ECFCs exposed to maternal DM form fewer initial network structures, which are not stable over time. Correlation analyses demonstrated that ECFC samples with greater division in branches form fewer closed network structures. Additionally, reductions in average ECFC movement over time decrease structural connectivity. Identification of these novel phenotypes utilizing the newly established methodologies provides evidence for the cellular mechanisms contributing to aberrant ECFC vasculogenesis. PMID:28100488

The differentiation of tuna (family: Scombridae) products through the PCR-based analysis of the cytochrome b gene and parvalbumin introns.

PubMed

Abdullah, Asadatun; Rehbein, Hartmut

2016-01-30

In spite of the many studies performed over the years, there are still problems in the authentication of closely related tuna species, not only for canned fish but also for raw products. With the aim of providing screening methods to identify different tuna species and related scombrids, segments of mitochondrial cytochrome b (cyt b) and nuclear parvalbumin genes were amplified and sequenced or subjected to single-strand conformation polymorphism (SSCP) and restriction fragment length polymorphism (RFLP) analyses. The nucleotide diagnostic sites in the cyt b gene of five tuna species from Indonesia were determined in this study and used to construct a phylogenetic tree. In addition, the suitability of the nuclear gene that encodes parvalbumin for the differentiation of tuna species was determined by SSCP and RFLP analyses of an intron segment. RFLP differentiated Thunnus albacares and from T. obesus, and fish species in the Thunnus genus could be distinguished from bullet tuna (Auxis rochei) by SSCP. Parvalbumin-based polymerase chain reaction systems could serve as an additional tool in the detection and identification of tuna and other Scombridae fish species for routine seafood control. This reaction can be performed in addition to the cyt b analysis as previously described. © 2015 Society of Chemical Industry.

Non-invasive measurement of pulse wave velocity using transputer-based analysis of Doppler flow audio signals.

PubMed

Stewart, W R; Ramsey, M W; Jones, C J

1994-08-01

A system for the measurement of arterial pulse wave velocity is described. A personal computer (PC) plug-in transputer board is used to process the audio signals from two pocket Doppler ultrasound units. The transputer is used to provide a set of bandpass digital filters on two channels. The times of excursion of power through thresholds in each filter are recorded and used to estimate the onset of systolic flow. The system does not require an additional spectrum analyser and can work in real time. The transputer architecture provides for easy integration into any wider physiological measurement system.

Substance misuse prevention and economic analysis: challenges and opportunities regarding international utility.

PubMed

Guyll, Max; Spoth, Richard; Cornish, Marilyn A

2012-01-01

Economic analyses of substance misuse prevention assess the intervention cost necessary to achieve a particular outcome, and thereby provide an additional dimension for evaluating prevention programming. This article reviews several types of economic analysis, considers how they can be applied to substance misuse prevention, and discusses challenges to enhancing their international relevance, particularly their usefulness for informing policy decisions. Important first steps taken to address these challenges are presented, including the disease burden concept and the development of generalized cost-effectiveness, advances that facilitate international policy discussions by providing a common framework for evaluating health care needs and program effects.

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

Green, D.W.; Heinrich, R.R.; Graczyk, D.G.

The purpose of this report is to summarize the activities of the Analytical Chemistry Laboratory (ACL) at Argonne National Laboratory (ANL) for fiscal year 1988 (October 1987 through September 1988). The Analytical Chemistry Laboratory is a full-cost recovery service center, with the primary mission of providing a broad range of analytical chemistry support services to the scientific and engineering programs at ANL. In addition, the ACL conducts a research program in analytical chemistry, works on instrumental and methods development, and provides analytical services for governmental, educational, and industrial organizations. The ACL handles a wide range of analytical problems, from routinemore » standard analyses to unique problems that require significant development of methods and techniques.« less

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

Green, D.W.; Heinrich, R.R.; Graczyk, D.G.

The purpose of this report is to summarize the activities of the Analytical Chemistry Laboratory (ACL) at Argonne National Laboratory (ANL) for Fiscal Year 1989 (October 1988 through September 1989). The Analytical Chemistry Laboratory is a full-cost-recovery service center, with the primary mission of providing a broad range of analytical chemistry support services to the scientific and engineering programs at ANL. In addition, the ACL conducts a research program in analytical chemistry, works on instrumental and methods development, and provides analytical services for governmental, educational, and industrial organizations. The ACL handles a wide range of analytical problems, from routine standardmore » analyses to unique problems that require significant development of methods and techniques.« less

2012 drug packaging review: many dangerous, reportable flaws.

PubMed

2013-05-01

Drug packaging plays an important role in protecting and providing information to patients. The packaging examined by Prescrire in 2012, on the whole, still fails to perform all of these functions effectively. Two issues are especially worrisome. First, packaging too often poses a danger to children. In addition, too many patient leaflets provide incomplete information about adverse effects, thus failing to properly protect the most vulnerable patients. Yet, the method Prescrire used to analyse drug packaging shows that it is not difficult to detect and anticipate risks. It is up to healthcare professionals to take advantage of the method, to protect patients from, and report, dangerous packaging.

Assessment of the Neutronic and Fuel Cycle Performance of the Transatomic Power Molten Salt Reactor Design

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

Robertson, Sean; Dewan, Leslie; Massie, Mark

This report presents results from a collaboration between Transatomic Power Corporation (TAP) and Oak Ridge National Laboratory (ORNL) to provide neutronic and fuel cycle analysis of the TAP core design through the Department of Energy Gateway for Accelerated Innovation in Nuclear (GAIN) Nuclear Energy Voucher program. The TAP concept is a molten salt reactor using configurable zirconium hydride moderator rod assemblies to shift the neutron spectrum in the core from mostly epithermal at beginning of life to thermal at end of life. Additional developments in the ChemTriton modeling and simulation tool provide the critical moderator-to-fuel ratio searches and time-dependent parametersmore » necessary to simulate the continuously changing physics in this complex system. The implementation of continuous-energy Monte Carlo transport and depletion tools in ChemTriton provide for full-core three-dimensional modeling and simulation. Results from simulations with these tools show agreement with TAP-calculated performance metrics for core lifetime, discharge burnup, and salt volume fraction, verifying the viability of reducing actinide waste production with this concept. Additional analyses of mass feed rates and enrichments, isotopic removals, tritium generation, core power distribution, core vessel helium generation, moderator rod heat deposition, and reactivity coeffcients provide additional information to make informed design decisions. This work demonstrates capabilities of ORNL modeling and simulation tools for neutronic and fuel cycle analysis of molten salt reactor concepts.« less

Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways.

PubMed

Obayashi, Takeshi; Kinoshita, Kengo

2010-05-01

Gene coexpression analyses are a powerful method to predict the function of genes and/or to identify genes that are functionally related to query genes. The basic idea of gene coexpression analyses is that genes with similar functions should have similar expression patterns under many different conditions. This approach is now widely used by many experimental researchers, especially in the field of plant biology. In this review, we will summarize recent successful examples obtained by using our gene coexpression database, ATTED-II. Specifically, the examples will describe the identification of new genes, such as the subunits of a complex protein, the enzymes in a metabolic pathway and transporters. In addition, we will discuss the discovery of a new intercellular signaling factor and new regulatory relationships between transcription factors and their target genes. In ATTED-II, we provide two basic views of gene coexpression, a gene list view and a gene network view, which can be used as guide gene approach and narrow-down approach, respectively. In addition, we will discuss the coexpression effectiveness for various types of gene sets.

Updating signal typing in voice: addition of type 4 signals.

PubMed

Sprecher, Alicia; Olszewski, Aleksandra; Jiang, Jack J; Zhang, Yu

2010-06-01

The addition of a fourth type of voice to Titze's voice classification scheme is proposed. This fourth voice type is characterized by primarily stochastic noise behavior and is therefore unsuitable for both perturbation and correlation dimension analysis. Forty voice samples were classified into the proposed four types using narrowband spectrograms. Acoustic, perceptual, and correlation dimension analyses were completed for all voice samples. Perturbation measures tended to increase with voice type. Based on reliability cutoffs, the type 1 and type 2 voices were considered suitable for perturbation analysis. Measures of unreliability were higher for type 3 and 4 voices. Correlation dimension analyses increased significantly with signal type as indicated by a one-way analysis of variance. Notably, correlation dimension analysis could not quantify the type 4 voices. The proposed fourth voice type represents a subset of voices dominated by noise behavior. Current measures capable of evaluating type 4 voices provide only qualitative data (spectrograms, perceptual analysis, and an infinite correlation dimension). Type 4 voices are highly complex and the development of objective measures capable of analyzing these voices remains a topic of future investigation.

Disambiguating brain functional connectivity.

PubMed

Duff, Eugene P; Makin, Tamar; Cottaar, Michiel; Smith, Stephen M; Woolrich, Mark W

2018-06-01

Functional connectivity (FC) analyses of correlations of neural activity are used extensively in neuroimaging and electrophysiology to gain insights into neural interactions. However, analyses assessing changes in correlation fail to distinguish effects produced by sources as different as changes in neural signal amplitudes or noise levels. This ambiguity substantially diminishes the value of FC for inferring system properties and clinical states. Network modelling approaches may avoid ambiguities, but require specific assumptions. We present an enhancement to FC analysis with improved specificity of inferences, minimal assumptions and no reduction in flexibility. The Additive Signal Change (ASC) approach characterizes FC changes into certain prevalent classes of signal change that involve the input of additional signal to existing activity. With FMRI data, the approach reveals a rich diversity of signal changes underlying measured changes in FC, suggesting that it could clarify our current understanding of FC changes in many contexts. The ASC method can also be used to disambiguate other measures of dependency, such as regression and coherence, providing a flexible tool for the analysis of neural data. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Remote Monitoring of Groundwater Overdraft Using GRACE and InSAR

NASA Astrophysics Data System (ADS)

Scher, C.; Saah, D.

2017-12-01

Gravity Recovery and Climate Experiment (GRACE) data paired with radar-derived analyses of volumetric changes in aquifer storage capacity present a viable technique for remote monitoring of aquifer depletion. Interferometric Synthetic Aperture Radar (InSAR) analyses of ground level subsidence can account for a significant portion of mass loss observed in GRACE data and provide information on point-sources of overdraft. This study summed one water-year of GRACE monthly mass change grids and delineated regions with negative water storage anomalies for further InSAR analyses. Magnitude of water-storage anomalies observed by GRACE were compared to InSAR-derived minimum volumetric changes in aquifer storage capacity as a result of measurable compaction at the surface. Four major aquifers were selected within regions where GRACE observed a net decrease in water storage (Central Valley, California; Mekong Delta, Vietnam; West Bank, occupied Palestinian Territory; and the Indus Basin, South Asia). Interferogram imagery of the extent and magnitude of subsidence within study regions provided estimates for net minimum volume of groundwater extracted between image acquisitions. These volumetric estimates were compared to GRACE mass change grids to resolve a percent contribution of mass change observed by GRACE likely due to groundwater overdraft. Interferograms revealed characteristic cones of depression within regions of net mass loss observed by GRACE, suggesting point-source locations of groundwater overdraft and demonstrating forensic potential for the use of InSAR and GRACE data in remote monitoring of aquifer depletion. Paired GRACE and InSAR analyses offer a technique to increase the spatial and temporal resolution of remote applications for monitoring groundwater overdraft in addition to providing a novel parameter - measurable vertical deformation at the surface - to global groundwater models.

Are In Vitro Methods for the Detection of Endocrine Potentials in the Aquatic Environment Predictive for In Vivo Effects? Outcomes of the Projects SchussenAktiv and SchussenAktivplus in the Lake Constance Area, Germany

PubMed Central

Henneberg, Anja; Bender, Katrin; Blaha, Ludek; Giebner, Sabrina; Kuch, Bertram; Köhler, Heinz-R.; Maier, Diana; Oehlmann, Jörg; Richter, Doreen; Scheurer, Marco; Schulte-Oehlmann, Ulrike; Sieratowicz, Agnes; Ziebart, Simone; Triebskorn, Rita

2014-01-01

Many studies about endocrine pollution in the aquatic environment reveal changes in the reproduction system of biota. We analysed endocrine activities in two rivers in Southern Germany using three approaches: (1) chemical analyses, (2) in vitro bioassays, and (3) in vivo investigations in fish and snails. Chemical analyses were based on gas chromatography coupled with mass spectrometry. For in vitro analyses of endocrine potentials in water, sediment, and waste water samples, we used the E-screen assay (human breast cancer cells MCF-7) and reporter gene assays (human cell line HeLa-9903 and MDA-kb2). In addition, we performed reproduction tests with the freshwater mudsnail Potamopyrgus antipodarum to analyse water and sediment samples. We exposed juvenile brown trout (Salmo trutta f. fario) to water downstream of a wastewater outfall (Schussen River) or to water from a reference site (Argen River) to investigate the vitellogenin production. Furthermore, two feral fish species, chub (Leuciscus cephalus) and spirlin (Alburnoides bipunctatus), were caught in both rivers to determine their gonadal maturity and the gonadosomatic index. Chemical analyses provided only little information about endocrine active substances, whereas the in vitro assays revealed endocrine potentials in most of the samples. In addition to endocrine potentials, we also observed toxic potentials (E-screen/reproduction test) in waste water samples, which could interfere with and camouflage endocrine effects. The results of our in vivo tests were mostly in line with the results of the in vitro assays and revealed a consistent reproduction-disrupting (reproduction tests) and an occasional endocrine action (vitellogenin levels) in both investigated rivers, with more pronounced effects for the Schussen river (e.g. a lower gonadosomatic index). We were able to show that biological in vitro assays for endocrine potentials in natural stream water reasonably reflect reproduction and endocrine disruption observed in snails and field-exposed fish, respectively. PMID:24901835

Preferred Reporting Items for Systematic Review and Meta-Analyses of individual participant data: the PRISMA-IPD Statement.

PubMed

Stewart, Lesley A; Clarke, Mike; Rovers, Maroeska; Riley, Richard D; Simmonds, Mark; Stewart, Gavin; Tierney, Jayne F

2015-04-28

Systematic reviews and meta-analyses of individual participant data (IPD) aim to collect, check, and reanalyze individual-level data from all studies addressing a particular research question and are therefore considered a gold standard approach to evidence synthesis. They are likely to be used with increasing frequency as current initiatives to share clinical trial data gain momentum and may be particularly important in reviewing controversial therapeutic areas. To develop PRISMA-IPD as a stand-alone extension to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) Statement, tailored to the specific requirements of reporting systematic reviews and meta-analyses of IPD. Although developed primarily for reviews of randomized trials, many items will apply in other contexts, including reviews of diagnosis and prognosis. Development of PRISMA-IPD followed the EQUATOR Network framework guidance and used the existing standard PRISMA Statement as a starting point to draft additional relevant material. A web-based survey informed discussion at an international workshop that included researchers, clinicians, methodologists experienced in conducting systematic reviews and meta-analyses of IPD, and journal editors. The statement was drafted and iterative refinements were made by the project, advisory, and development groups. The PRISMA-IPD Development Group reached agreement on the PRISMA-IPD checklist and flow diagram by consensus. Compared with standard PRISMA, the PRISMA-IPD checklist includes 3 new items that address (1) methods of checking the integrity of the IPD (such as pattern of randomization, data consistency, baseline imbalance, and missing data), (2) reporting any important issues that emerge, and (3) exploring variation (such as whether certain types of individual benefit more from the intervention than others). A further additional item was created by reorganization of standard PRISMA items relating to interpreting results. Wording was modified in 23 items to reflect the IPD approach. PRISMA-IPD provides guidelines for reporting systematic reviews and meta-analyses of IPD.

Small Aircraft Transportation System Simulation Analysis of the HVO and ERO Concepts

NASA Technical Reports Server (NTRS)

Millsaps, Gary D.; Yackovetsky, Robert E. (Technical Monitor)

2003-01-01

It is acknowledged that the aviation and aerospace industries are primary forces influencing the industrial development and economic well being of the United States and many countries around the world. For decades the US national air transportation system has been the model of success - safely and efficiently moving people, cargo, goods and services and generating countless benefits throughout the global community; however, the finite nature of the system and many of its components is becoming apparent. Without measurable increases in the capacity of the national air transportation system, delays and service delivery failures will eventually become intolerable. Although the recent economic slowdown has lowered immediate travel demands, that trend is reversing and cargo movement remains high. Research data indicates a conservative 2.5-3.0% annual increase in aircraft operations nationwide through 2017. Such growth will place additional strains upon a system already experiencing capacity constraints. The stakeholders of the system will continue to endure ever-increasing delays and abide lesser levels of service to many lower population density areas of the country unless more efficient uses of existing and new transportation resources are implemented. NASA s Small Aircraft Transportation System program (SATS) is one of several technologies under development that are aimed at using such resources more effectively. As part of this development effort, this report is the first in a series outlining the findings and recommendations resulting from a comprehensive program of multi-level analyses and system engineering efforts undertaken by NASA Langley Research Center s Systems Analysis Branch (SAB). These efforts are guided by a commitment to provide systems-level analysis support for the SATS program. Subsequent efforts will build upon this early work to produce additional analyses and benefits studies needed to provide the technical and economic basis for national investment and policy decisions related to further development and potential deployment of a small aircraft transportation system. This report primarily serves two purposes. First, it presents results attained from an initial evaluation and analysis of the Higher Volume Operations (HVO) and EnRoute Operations (ERO) concepts - both designated operational capabilities within the SATS Program s Concept of Operations (CONOPS) document. It further outlines areas of the concepts that would benefit from follow-on analyses and system engineering efforts. It is intended that these processes will aid continued maturation of the concepts and promote additional studies of their effects and influences in combination with other designated CONOPS currently under development. In essence, it establishes a baseline of data upon which subsequent analyses and studies can be built and identifies performance characteristics the concept must exhibit in order to provide, at minimum, levels of safety and usage equal to or better than the current system.

Pharmacoeconomic spotlight on rotavirus vaccine RIX4414 (Rotarix™) in developed countries.

PubMed

Plosker, Greg L

2012-12-01

The most common cause of severe diarrhea in infants and young children is rotavirus gastroenteritis (RVGE), which is associated with significant morbidity, healthcare resource use, and direct and indirect costs in industrialized nations. The monovalent rotavirus vaccine RIX4414 (Rotarix™) is administered as a two-dose oral series in infants and has demonstrated protective efficacy against RVGE in clinical trials conducted in developed countries. In addition, various naturalistic studies have demonstrated 'real-world' effectiveness after the introduction of widespread rotavirus vaccination programs in the community setting. Numerous cost-effectiveness analyses have been conducted in developed countries in which a universal rotavirus vaccination program using RIX4414 was compared with no universal rotavirus vaccination program. There was a high degree of variability in base-case results across studies even when the studies were conducted in the same country, often reflecting differences in the selection of data sources or assumptions used to populate the models. In addition, results were sensitive to plausible changes in a number of key input parameters. As such, it is not possible to definitively state whether a universal rotavirus vaccination program with RIX4414 is cost effective in developed countries, although results of some analyses in some countries suggest this is the case. In addition, international guidelines advocate universal vaccination of infants and children against rotavirus. It is also difficult to draw conclusions regarding the cost effectiveness of rotavirus vaccine RIX4414 relative to that of the pentavalent rotavirus vaccine, which is administered as a three-dose oral series. Although indirect comparisons in cost-effectiveness analyses indicate that RIX4414 provided more favorable incremental cost-effectiveness ratios when each vaccine was compared with no universal rotavirus vaccination program, results were generally sensitive to vaccine costs. Actual tender prices of a full vaccination course for each vaccine were not known at the time of the analyses and therefore had to be estimated.

Psychometric properties of the Epworth Sleepiness Scale: A factor analysis and item-response theory approach.

PubMed

Pilcher, June J; Switzer, Fred S; Munc, Alec; Donnelly, Janet; Jellen, Julia C; Lamm, Claus

2018-04-01

The purpose of this study is to examine the psychometric properties of the Epworth Sleepiness Scale (ESS) in two languages, German and English. Students from a university in Austria (N = 292; 55 males; mean age = 18.71 ± 1.71 years; 237 females; mean age = 18.24 ± 0.88 years) and a university in the US (N = 329; 128 males; mean age = 18.71 ± 0.88 years; 201 females; mean age = 21.59 ± 2.27 years) completed the ESS. An exploratory-factor analysis was completed to examine dimensionality of the ESS. Item response theory (IRT) analyses were used to provide information about the response rates on the items on the ESS and provide differential item functioning (DIF) analyses to examine whether the items were interpreted differently between the two languages. The factor analyses suggest that the ESS measures two distinct sleepiness constructs. These constructs indicate that the ESS is probing sleepiness in settings requiring active versus passive responding. The IRT analyses found that overall, the items on the ESS perform well as a measure of sleepiness. However, Item 8 and to a lesser extent Item 6 were being interpreted differently by respondents in comparison to the other items. In addition, the DIF analyses showed that the responses between German and English were very similar indicating that there are only minor measurement differences between the two language versions of the ESS. These findings suggest that the ESS provides a reliable measure of propensity to sleepiness; however, it does convey a two-factor approach to sleepiness. Researchers and clinicians can use the German and English versions of the ESS but may wish to exclude Item 8 when calculating a total sleepiness score.

Two-Dimensional Neutronic and Fuel Cycle Analysis of the Transatomic Power Molten Salt Reactor

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

Betzler, Benjamin R.; Powers, Jeffrey J.; Worrall, Andrew

2017-01-15

This status report presents the results from the first phase of the collaboration between Transatomic Power Corporation (TAP) and Oak Ridge National Laboratory (ORNL) to provide neutronic and fuel cycle analysis of the TAP core design through the Department of Energy Gateway for Accelerated Innovation in Nuclear, Nuclear Energy Voucher program. The TAP design is a molten salt reactor using movable moderator rods to shift the neutron spectrum in the core from mostly epithermal at beginning of life to thermal at end of life. Additional developments in the ChemTriton modeling and simulation tool provide the critical moderator-to-fuel ratio searches andmore » time-dependent parameters necessary to simulate the continuously changing physics in this complex system. Results from simulations with these tools show agreement with TAP-calculated performance metrics for core lifetime, discharge burnup, and salt volume fraction, verifying the viability of reducing actinide waste production with this design. Additional analyses of time step sizes, mass feed rates and enrichments, and isotopic removals provide additional information to make informed design decisions. This work further demonstrates capabilities of ORNL modeling and simulation tools for analysis of molten salt reactor designs and strongly positions this effort for the upcoming three-dimensional core analysis.« less

Validation of chlorine and oxygen isotope ratio analysis to differentiate perchlorate sources and to document perchlorate biodegradation

USGS Publications Warehouse

Paul B. Hatzinger,; Böhlke, John Karl; Sturchio, Neil C.; Gu, Baohua

2013-01-01

Increased health concerns about perchlorate (ClO4-) during the past decade and subsequent regulatory considerations have generated appreciable interest in source identification. The key objective of the isotopic techniques described in this guidance manual is to provide evidence concerning the origin of ClO4- in soils and groundwater and, more specifically, whether that ClO4- is synthetic or natural. Chlorine and oxygen isotopic analyses of ClO4- provide the primary direct approach whereby different sources of ClO4- can be distinguished from each other. These techniques measure the relative abundances of the stable isotopes of chlorine (37Cl and 35Cl) and oxygen (18O, 17O, and 16O) in ClO4- using isotope-ratio mass spectrometry (IRMS). In addition, the relative abundance of the radioactive chlorine isotope 36Cl is measured using accelerator mass spectrometry (AMS). Taken together, these measurements provide four independent quantities that can be used to distinguish natural and synthetic ClO4- sources, to discriminate different types of natural ClO4-, and to detect ClO4- biodegradation in the environment. Other isotopic, chemical, and geochemical techniques that can be applied in conjunction with isotopic analyses of ClO4- to provide supporting data in forensic studies are also described.

Measurement of DSM-5 section II personality disorder constructs using the MMPI-2-RF in clinical and forensic samples.

PubMed

Anderson, Jaime L; Sellbom, Martin; Pymont, Carly; Smid, Wineke; De Saeger, Hilde; Kamphuis, Jan H

2015-09-01

In the current study, we evaluated the associations between the Minnesota Multiphasic Personality Inventory-2 Restructured Form (MMPI-2-RF; Ben-Porath & Tellegen, 2008) scale scores and the Diagnostic and Statistical Manual of Mental Disorders (5th ed.; DSM-5; American Psychiatric Association, 2013) Section II personality disorder (PD) criterion counts in inpatient and forensic psychiatric samples from The Netherlands using structured clinical interviews to operationalize PDs. The inpatient psychiatric sample included 190 male and female patients and the forensic sample included 162 male psychiatric patients. We conducted correlation and count regression analyses to evaluate the utility of relevant MMPI-2-RF scales in predicting PD criterion count scores. Generally, results from these analyses emerged as conceptually expected and provided evidence that MMPI-2-RF scales can be useful in assessing PDs. At the zero-order level, most hypothesized associations between Section II disorders and MMPI-2-RF scales were supported. Similarly, in the regression analyses, a unique set of predictors emerged for each PD that was generally in line with conceptual expectations. Additionally, the results provided general evidence that PDs can be captured by dimensional psychopathology constructs, which has implications for both DSM-5 Section III specifically and the personality psychopathology literature more broadly. (c) 2015 APA, all rights reserved.

Analysis of Soccer Players’ Positional Variability During the 2012 UEFA European Championship: A Case Study

PubMed Central

Moura, Felipe Arruda; Santana, Juliana Exel; Vieira, Nathália Arnosti; Santiago, Paulo Roberto Pereira; Cunha, Sergio Augusto

2015-01-01

The purpose of this study was to analyse players’ positional variability during the 2012 UEFA European Championship by applying principal component analysis (PCA) to data gathered from heat maps posted on the UEFA website. We analysed the teams that reached the finals and semi-finals of the competition. The players’ 2D coordinates from each match were obtained by applying an image-processing algorithm to the heat maps. With all the players’ 2D coordinates for each match, we applied PCA to identify the directions of greatest variability. Then, two orthogonal segments were centred on each player’s mean position for all matches. The segments’ directions were driven by the eigenvectors of the PCA, and the length of each segment was defined as one standard deviation around the mean. Finally, an ellipse was circumscribed around both segments. To represent player variability, segment lengths and elliptical areas were analysed. The results demonstrate that Portugal exhibited the lowest variability, followed by Germany, Spain and Italy. Additionally, a graphical representation of every player’s ellipse provided insight into the teams’ organisational features throughout the competition. The presented study provides important information regarding soccer teams’ tactical strategy in high-level championships that allows coaches to better control team organisation on the pitch. PMID:26557206

Altitudinal and climatic associations of seed dormancy and flowering traits evidence adaptation of annual life cycle timing in Arabidopsis thaliana.

PubMed

Vidigal, Deborah S; Marques, Alexandre C S S; Willems, Leo A J; Buijs, Gonda; Méndez-Vigo, Belén; Hilhorst, Henk W M; Bentsink, Leónie; Picó, F Xavier; Alonso-Blanco, Carlos

2016-08-01

The temporal control or timing of the life cycle of annual plants is presumed to provide adaptive strategies to escape harsh environments for survival and reproduction. This is mainly determined by the timing of germination, which is controlled by the level of seed dormancy, and of flowering initiation. However, the environmental factors driving the evolution of plant life cycles remain largely unknown. To address this question we have analysed nine quantitative life history traits, in a native regional collection of 300 wild accessions of Arabidopsis thaliana. Seed dormancy and flowering time were negatively correlated, indicating that these traits have coevolved. In addition, environmental-phenotypic analyses detected strong altitudinal and climatic clines for most life history traits. Overall, accessions showing life cycles with early flowering, small seeds, high seed dormancy and slow germination rate were associated with locations exposed to high temperature, low summer precipitation and high radiation. Furthermore, we analysed the expression level of the positive regulator of seed dormancy DELAY OF GERMINATION 1 (DOG1), finding similar but weaker altitudinal and climatic patterns than seed dormancy. Therefore, DOG1 regulatory mutations are likely to provide a quantitative molecular mechanism for the adaptation of A. thaliana life cycle to altitude and climate. © 2016 John Wiley & Sons Ltd.

Numerical framework for the modeling of electrokinetic flows

NASA Astrophysics Data System (ADS)

Deshpande, Manish; Ghaddar, Chahid; Gilbert, John R.; St. John, Pamela M.; Woudenberg, Timothy M.; Connell, Charles R.; Molho, Joshua; Herr, Amy; Mungal, Godfrey; Kenny, Thomas W.

1998-09-01

This paper presents a numerical framework for design-based analyses of electrokinetic flow in interconnects. Electrokinetic effects, which can be broadly divided into electrophoresis and electroosmosis, are of importance in providing a transport mechanism in microfluidic devices for both pumping and separation. Models for the electrokinetic effects can be derived and coupled to the fluid dynamic equations through appropriate source terms. In the design of practical microdevices, however, accurate coupling of the electrokinetic effects requires the knowledge of several material and physical parameters, such as the diffusivity and the mobility of the solute in the solvent. Additionally wall-based effects such as chemical binding sites might exist that affect the flow patterns. In this paper, we address some of these issues by describing a synergistic numerical/experimental process to extract the parameters required. Experiments were conducted to provide the numerical simulations with a mechanism to extract these parameters based on quantitative comparisons with each other. These parameters were then applied in predicting further experiments to validate the process. As part of this research, we have created NetFlow, a tool for micro-fluid analyses. The tool can be validated and applied in existing technologies by first creating test structures to extract representations of the physical phenomena in the device, and then applying them in the design analyses to predict correct behavior.

COLORcation: A new application to phenotype exploratory behavior models of anxiety in mice.

PubMed

Dagan, Shachar Y; Tsoory, Michael M; Fainzilber, Mike; Panayotis, Nicolas

2016-09-01

Behavioral analyses in rodents have successfully delineated the function of many genes and signaling pathways in the brain. Behavioral testing uses highly defined experimental conditions to identify abnormalities in a given mouse strain or genotype. The open field (OF) is widely used to assess both locomotion and anxiety in rodents. In this test, the more a mouse explores and spend time in the center of the arena, the less anxious it is considered to be. However, the simplistic distinction between center and border substantially reduces the information content of the analysis and may fail to detect biologically meaningful differences. Here we describe COLORcation, a new application for improved analyses of mouse behavior in the OF. The application analyses animal exploration patterns in detailed spatial resolution (e.g. 10×10 bins) to provide a color-encoded heat map of mouse activity. In addition, COLORcation provides new parameters to track activity and locomotion of the test animals. We demonstrate the use of COLORcation in different experimental paradigms, including pharmacological and restraint-based induction of stress and anxiety. COLORcation is compatible with multiple acquisition systems, giving users the option to make the most of their raw data organized text files containing time and coordinates of animal locations as input. These analyses validate the utility of the software and establish its reliability and potential as a new tool to analyze OF data. Copyright © 2016 Elsevier B.V. All rights reserved.

The Aqueous Chemistry of the Soils at the Phoenix Landing Site

NASA Astrophysics Data System (ADS)

Kounaves, S. P.; Hecht, M. H.; Quinn, R.; West, S. J.; Young, S. M.; Clark, B. C.; Ming, D. W.; Boynton, W. V.; Gospodinova, K.; Kapit, J.; Deflores, L. P.; Smith, P. H.; Team, A

2008-12-01

The MECA Wet Chemistry Laboratory (WCL) analyses on the Phoenix Mars Lander have provided the first direct evidence of the soluble ionic components of the Martian soil. The analyses were performed on samples acquired from the surface (Rosy Red) and at the soil/ice interface approximately 4-5 cm under the surface (Sorceress). Even though the samples are from a rather unique site because of the high polar latitude and the polygon-patterned ground, they present a picture of a geochemical environment different from some previously hypothesized. Addition of 25mL of a water/calibrant solution to approximately 1cc of each of the soil samples resulted in the detection of a variety of ionic species, increased solution conductivity, and a slightly alkaline pH. The major constituent cations identified and quantified to date include Na+, K+, Mg2+, and Ca2+, while the anions included Cl- and ClO4-. Sulfate analysis was performed using a Ba2+ titration method. Even though carbonate and bicarbonate were not directly measured, their presence and quantification is supported by the alkaline pH of the solution, its buffering capacity after the addition of an acid, common ion effects, conductivity, and the modeled equilibrium species distribution of the system. The species distribution resulting from the modeling and consideration of additional interactions; dissolution, precipitation, ion exchange, ads/desorption, charge balance, the behavior over the several hours of monitoring, provided constraints for carbonate speciation and concentration and was used to formulate and test soil simulants. Results from the Thermal and Evolved Gas Analyzer (TEGA) also support the presence of a significant amount of calcite in the soil.

Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles

PubMed Central

Arndt, Birgit; Kalinina, Svetlana A.; Houterman, Petra M.; Ahn, Il-Pyung; Tonti, Stefano; Sieber, Christian M. K.

2017-01-01

Fusarium fujikuroi causes bakanae (“foolish seedling”) disease of rice which is characterized by hyper-elongation of seedlings resulting from production of gibberellic acids (GAs) by the fungus. This plant pathogen is also known for production of harmful mycotoxins, such as fusarins, fusaric acid, apicidin F and beauvericin. Recently, we generated the first de novo genome sequence of F. fujikuroi strain IMI 58289 combined with extensive transcriptional, epigenetic, proteomic and chemical product analyses. GA production was shown to provide a selective advantage during infection of the preferred host plant rice. Here, we provide genome sequences of eight additional F. fujikuroi isolates from distant geographic regions. The isolates differ in the size of chromosomes, most likely due to variability of subtelomeric regions, the type of asexual spores (microconidia and/or macroconidia), and the number and expression of secondary metabolite gene clusters. Whilst most of the isolates caused the typical bakanae symptoms, one isolate, B14, caused stunting and early withering of infected seedlings. In contrast to the other isolates, B14 produced no GAs but high amounts of fumonisins during infection on rice. Furthermore, it differed from the other isolates by the presence of three additional polyketide synthase (PKS) genes (PKS40, PKS43, PKS51) and the absence of the F. fujikuroi-specific apicidin F (NRPS31) gene cluster. Analysis of additional field isolates confirmed the strong correlation between the pathotype (bakanae or stunting/withering), and the ability to produce either GAs or fumonisins. Deletion of the fumonisin and fusaric acid-specific PKS genes in B14 reduced the stunting/withering symptoms, whereas deletion of the PKS51 gene resulted in elevated symptom development. Phylogenetic analyses revealed two subclades of F. fujikuroi strains according to their pathotype and secondary metabolite profiles. PMID:29073267

The human alimentary tract transfer and body retention of environmental polonium-210.

PubMed

Hunt, G J; Rumney, H S

2007-12-01

This paper presents the results of a 4 year study to investigate the human alimentary tract transfer factor (f(A) value) and body retention of 210 Po in shellfish. In the first 3 years, mussels (Mytilus edulis L.), cockles (Cerastoderma edule L.) and brown meat from crab (Cancer pagurus L.) were successively studied. In each year five volunteers (from a pool of seven) ate a suitable portion of the shellfish and provided 24 h samples of excreta usually for 3 days before and for at least 7 days during and after eating. Subsamples of shellfish were analysed to determine the intakes of 210 Po. Faeces were analysed and the data used to assess apparent fA values. Urine samples were analysed in the mussel and crab studies to provide urinary excretion parameters. Pb-210 was also analysed during the mussel study; the levels were low, leading to large uncertainties, but confirming the negligible effect of radioactive decay to its granddaughter 210 Po in the main study. In the fourth year, larger samples of brown crab meat were eaten by five volunteers and faecal samples were taken at suitable times over periods of up to 43 days to study body retention of 210 Po. The first approximately 7 days provided additional data on fA values. Pooled results for the apparent fA for the whole study lay in the range 0.15-0.65 with a mean of 0.46; corrections for endogenous excretion suggest a true fA value of approximately 0.51, supporting the value of 0.5 currently used by the International Commission on Radiological Protection (ICRP). The retention data suggest a biological half-time of about 40 days, in broad consistency with the 50 days currently used by the ICRP. Thus there is no strong evidence from this study suggesting a change in dose coefficient for 210 Po. Full experimental data are provided to allow independent further interpretation.

Stationarity is undead: Uncertainty dominates the distribution of extremes

NASA Astrophysics Data System (ADS)

Serinaldi, Francesco; Kilsby, Chris G.

2015-03-01

The increasing effort to develop and apply nonstationary models in hydrologic frequency analyses under changing environmental conditions can be frustrated when the additional uncertainty related to the model complexity is accounted for along with the sampling uncertainty. In order to show the practical implications and possible problems of using nonstationary models and provide critical guidelines, in this study we review the main tools developed in this field (such as nonstationary distribution functions, return periods, and risk of failure) highlighting advantages and disadvantages. The discussion is supported by three case studies that revise three illustrative examples reported in the scientific and technical literature referring to the Little Sugar Creek (at Charlotte, North Carolina), Red River of the North (North Dakota/Minnesota), and the Assunpink Creek (at Trenton, New Jersey). The uncertainty of the results is assessed by complementing point estimates with confidence intervals (CIs) and emphasizing critical aspects such as the subjectivity affecting the choice of the models' structure. Our results show that (1) nonstationary frequency analyses should not only be based on at-site time series but require additional information and detailed exploratory data analyses (EDA); (2) as nonstationary models imply that the time-varying model structure holds true for the entire future design life period, an appropriate modeling strategy requires that EDA identifies a well-defined deterministic mechanism leading the examined process; (3) when the model structure cannot be inferred in a deductive manner and nonstationary models are fitted by inductive inference, model structure introduces an additional source of uncertainty so that the resulting nonstationary models can provide no practical enhancement of the credibility and accuracy of the predicted extreme quantiles, whereas possible model misspecification can easily lead to physically inconsistent results; (4) when the model structure is uncertain, stationary models and a suitable assessment of the uncertainty accounting for possible temporal persistence should be retained as more theoretically coherent and reliable options for practical applications in real-world design and management problems; (5) a clear understanding of the actual probabilistic meaning of stationary and nonstationary return periods and risk of failure is required for a correct risk assessment and communication.

Is Operative Treatment of Achilles Tendon Ruptures Superior to Nonoperative Treatment?

PubMed Central

Erickson, Brandon J.; Mascarenhas, Randy; Saltzman, Bryan M.; Walton, David; Lee, Simon; Cole, Brian J.; Bach, Bernard R.

2015-01-01

Background: Multiple meta-analyses have been published in efforts to determine whether operative or nonoperative treatment of Achilles tendon ruptures affords superior outcomes. Purpose: To perform a systematic review of overlapping meta-analyses comparing operative and nonoperative treatment of Achilles tendon ruptures to determine which meta-analyses provide the highest level of evidence for treatment recommendations. Study Design: Systematic review; Level of evidence, 3. Methods: A systematic review of the literature was performed to identify meta-analyses that fit the study inclusion criteria. Data were extracted from these meta-analyses regarding patient outcomes and reruptures. Meta-analysis quality was assessed using the Oxman-Guyatt and QUOROM (Quality of Reporting of Meta-analyses) systems. The Jadad algorithm was applied to determine the meta-analyses with the highest level of evidence. Results: Nine meta-analyses met the eligibility criteria, with all but 1 study including level 1 evidence. A total of 5842 patients were included. Seven studies found a higher rate of rerupture in the nonoperative group but a higher rate of complications in the operative group. One study found no differences in rerupture or complication rates, and 1 study found surgery decreased rerupture rates only when compared with nonoperative treatment without a functional brace. Three studies also identified an earlier return to work in the operative group. Almost all (8 of 9) of the meta-analyses had Oxman-Guyatt scores >3, indicating no major flaws. Conclusion: Operative treatment of Achilles tendon ruptures decreases rerupture rates but increases the risk for minor complications when compared with nonoperative treatment. Additionally, surgical treatment may allow earlier return to work. PMID:26665055

Genomic Evidence of Widespread Admixture from Polar Bears into Brown Bears during the Last Ice Age.

PubMed

Cahill, James A; Heintzman, Peter D; Harris, Kelley; Teasdale, Matthew D; Kapp, Joshua; Soares, Andre E R; Stirling, Ian; Bradley, Daniel; Edwards, Ceiridwen J; Graim, Kiley; Kisleika, Aliaksandr A; Malev, Alexander V; Monaghan, Nigel; Green, Richard E; Shapiro, Beth

2018-05-01

Recent genomic analyses have provided substantial evidence for past periods of gene flow from polar bears (Ursus maritimus) into Alaskan brown bears (Ursus arctos), with some analyses suggesting a link between climate change and genomic introgression. However, because it has mainly been possible to sample bears from the present day, the timing, frequency, and evolutionary significance of this admixture remains unknown. Here, we analyze genomic DNA from three additional and geographically distinct brown bear populations, including two that lived temporally close to the peak of the last ice age. We find evidence of admixture in all three populations, suggesting that admixture between these species has been common in their recent evolutionary history. In addition, analyses of ten fossil bears from the now-extinct Irish population indicate that admixture peaked during the last ice age, whereas brown bear and polar bear ranges overlapped. Following this peak, the proportion of polar bear ancestry in Irish brown bears declined rapidly until their extinction. Our results support a model in which ice age climate change created geographically widespread conditions conducive to admixture between polar bears and brown bears, as is again occurring today. We postulate that this model will be informative for many admixing species pairs impacted by climate change. Our results highlight the power of paleogenomics to reveal patterns of evolutionary change that are otherwise masked in contemporary data.

Integrative Taxonomy and Species Delimitation in Harvestmen: A Revision of the Western North American Genus Sclerobunus (Opiliones: Laniatores: Travunioidea)

PubMed Central

Derkarabetian, Shahan; Hedin, Marshal

2014-01-01

Alpha taxonomy, and specifically the delimitation of species, is becoming increasingly objective and integrative. The use of coalescent-based methods applied to genetic data is providing new tools for the discovery and delimitation of species. Here, we use an integrative approach via a combination of discovery-based multivariate morphological analyses to detect potential new species. These potential species are then used as a priori species in hypothesis-driven validation analyses with genetic data. This research focuses on the harvestmen genus Sclerobunus found throughout the mountainous regions of western North America. Based on our analyses, we conduct a revision of Sclerobunus resulting in synonymy of Cyptobunus with Sclerobunus including transfer of S. cavicolens comb. nov. and elevation of both subspecies of S. ungulatus: S. ungulatus comb. nov. and S. madhousensis comb. nov., stat. nov. The three subspecies of S. robustus are elevated, S. robustus, S. glorietus stat. nov., and S. idahoensis stat. nov. Additionally, five new species of Sclerobunus are described from New Mexico and Colorado, including S. jemez sp. nov., S. klomax sp. nov., S. skywalkeri sp. nov., S. speoventus sp. nov., and S. steinmanni sp. nov. Several of the newly described species are single-cave endemics, and our findings suggest that further exploration of western North American cave habitats will likely yield additional new species. PMID:25144370

Combined Magnetic Resonance Imaging and Spectroscopic Imaging Approach to Molecular Imaging of Prostate Cancer

PubMed Central

Kurhanewicz, John; Swanson, Mark G.; Nelson, Sarah J.; Vigneron, Daniel B.

2005-01-01

Magnetic resonance spectroscopic imaging (MRSI) provides a noninvasive method of detecting small molecular markers (historically the metabolites choline and citrate) within the cytosol and extracellular spaces of the prostate, and is performed in conjunction with high-resolution anatomic imaging. Recent studies in pre-prostatectomy patients have indicated that the metabolic information provided by MRSI combined with the anatomical information provided by MRI can significantly improve the assessment of cancer location and extent within the prostate, extracapsular spread, and cancer aggressiveness. Additionally, pre- and post-therapy studies have demonstrated the potential of MRI/MRSI to provide a direct measure of the presence and spatial extent of prostate cancer after therapy, a measure of the time course of response, and information concerning the mechanism of therapeutic response. In addition to detecting metabolic biomarkers of disease behavior and therapeutic response, MRI/MRSI guidance can improve tissue selection for ex vivo analysis. High-resolution magic angle spinning (1H HR-MAS) spectroscopy provides a full chemical analysis of MRI/MRSI-targeted tissues prior to pathologic and immunohistochemical analyses of the same tissue. Preliminary 1H HR-MAS spectroscopy studies have already identified unique spectral patterns for healthy glandular and stromal tissues and prostate cancer, determined the composition of the composite in vivo choline peak, and identified the polyamine spermine as a new metabolic marker of prostate cancer. The addition of imaging sequences that provide other functional information within the same exam (dynamic contrast uptake imaging and diffusion-weighted imaging) have also demonstrated the potential to further increase the accuracy of prostate cancer detection and characterization. PMID:12353259

Functional PET Evaluation of the Photosensitive Baboon

PubMed Central

Szabó, C. Ákos; Salinas, Felipe S; Narayana, Shalini

2011-01-01

The baboon provides a unique, natural model of epilepsy in nonhuman primates. Additionally, photosensitivity of the epileptic baboon provides an important window into the mechanism of human idiopathic generalized epilepsies. In order to better understand the networks underlying this model, our group utilized functional positron emission tomography (PET) to compare cerebral blood flow (CBF) changes occurring during intermittent light stimulation (ILS) and rest between baboons photosensitive, epileptic (PS) and asymptomatic, control (CTL) animals. Our studies utilized subtraction and covariance analyses to evaluate CBF changes occurring during ILS across activation and resting states, but also evaluated CBF correlations with ketamine doses and interictal epileptic discharge (IED) rate during the resting state. Furthermore, our group also assessed the CBF responses related to variation of ILS in PS and CTL animals. CBF changes in the subtraction and covariance analyses reveal the physiological response and visual connectivity in CTL animals and pathophysiological networks underlying responses associated with the activation of ictal and interictal epileptic discharges in PS animals. The correlation with ketamine dose is essential to understanding differences in CBF responses between both groups, and correlations with IED rate provides an insight into an epileptic network independent of visual activation. Finally, the ILS frequency dependent changes can help develop a framework to study not only spatial connectivity but also the temporal sequence of regional activations and deactivations related to ILS. The maps generated by the CBF analyses will be used to target specific nodes in the epileptic network for electrophysiological evaluation using intracranial electrodes. PMID:22276085

Transfer of patients from health care centres to special care services: analysis of travel distances in Nordic countries.

PubMed

Vuori, Jari; Kylänen, Marika; Tritter, Jonathan

2010-12-01

This paper highlights the importance of analysing patient transportation in Nordic circumpolar areas. The research questions we asked are as follows: How many Finnish patients have been transferred to special care intra-country and inter-country in 2009? Does it make any difference to health care policymakers if patients are transferred inter-country? We analysed the differences in distances from health care centres to special care services within Finland, Sweden and Norway and considered the health care policy implications. An analysis of the time required to drive between service providers using the "Google distance meter" (http://maps.google.com/); conducting interviews with key Finnish stakeholders; and undertaking a quantitative analyses of referral data from the Lapland Hospital District. Finnish patients are generally not transferred for health care services across national borders even if the distances are shorter. Finnish patients have limited access to health care services in circumpolar areas across the Nordic countries for 2 reasons. First, health professionals in Norway and Sweden do not speak Finnish, which presents a language problem. Second, the Social Insurance Institution of Finland does not cover the expenditures of travel or the costs of medicine. In addition, it seems that in circumpolar areas the density of Finnish service providers is greater than Swedish ones, causing many Swedish citizens to transfer to Finnish health care providers every year. However, future research is needed to determine the precise reasons for this.

Storage requirements for Georgia streams

USGS Publications Warehouse

Carter, Robert F.

1983-01-01

The suitability of a stream as a source of water supply or for waste disposal may be severely limited by low flow during certain periods. A water user may be forced to provide storage facilities to supplement the natural flow if the low flow is insufficient for his needs. This report provides data for evaluating the feasibility of augmenting low streamflow by means of storage facilities. It contains tabular data on storage requirements for draft rates that are as much as 60 percent of the mean annual flow at 99 continuous-record gaging stations, and draft-storage diagrams for estimating storage requirements at many additional sites. Through analyses of streamflow data, the State was divided into four regions. Draft-storage diagrams for each region provide a means of estimating storage requirements for sites on streams where data are scant, provided the drainage area, mean annual flow, and the 7-day, 10-year low flow are known or can be estimated. These data are tabulated for the 99 gaging stations used in the analyses and for 102 partial-record sites where only base-flow measurements have been made. The draft-storage diagrams are useful not only for estimating in-channel storage required for low-flow augmentation, but also can be used for estimating the volume of off-channel storage required to retain wastewater during low-flow periods for later release. In addition, these relationships can be helpful in estimating the volume of wastewater to be disposed of by spraying on land, provided that the water disposed of in this manner is only that for which streamflow dilution water is not currently available. Mean annual flow can be determined for any stream within the State by using the runoff map in this report. Low-flow indices can be estimated by several methods, including correlation of base-flow measurements with concurrent flow at nearby continuous-record gaging stations where low-flow indices have been determined.

Taste and pheromone perception in the fruit fly Drosophila melanogaster.

PubMed

Ebbs, Michelle L; Amrein, Hubert

2007-08-01

Taste is an essential sense for detection of nutrient-rich food and avoidance of toxic substances. The Drosophila melanogaster gustatory system provides an excellent model to study taste perception and taste-elicited behaviors. "The fly" is unique in the animal kingdom with regard to available experimental tools, which include a wide repertoire of molecular-genetic analyses (i.e., efficient production of transgenics and gene knockouts), elegant behavioral assays, and the possibility to conduct electrophysiological investigations. In addition, fruit flies, like humans, recognize sugars as a food source, but avoid bitter tasting substances that are often toxic to insects and mammals alike. This paper will present recent research progress in the field of taste and contact pheromone perception in the fruit fly. First, we shall describe the anatomical properties of the Drosophila gustatory system and survey the family of taste receptors to provide an appropriate background. We shall then review taste and pheromone perception mainly from a molecular genetic perspective that includes behavioral, electrophysiological and imaging analyses of wild type flies and flies with genetically manipulated taste cells. Finally, we shall provide an outlook of taste research in this elegant model system for the next few years.

Spatiotemporal analysis of changes in lode mining claims around the McDermitt Caldera, northern Nevada and southern Oregon

USGS Publications Warehouse

Coyan, Joshua; Zientek, Michael L.; Mihalasky, Mark J.

2017-01-01

Resource managers and agencies involved with planning for future federal land needs are required to complete an assessment of and forecast for future land use every ten years. Predicting mining activities on federal lands is difficult as current regulations do not require disclosure of exploration results. In these cases, historic mining claims may serve as a useful proxy for determining where mining-related activities may occur. We assess the utility of using a space–time cube (STC) and associated analyses to evaluate and characterize mining claim activities around the McDermitt Caldera in northern Nevada and southern Oregon. The most significant advantage of arranging the mining claim data into a STC is the ability to visualize and compare the data, which allows scientists to better understand patterns and results. Additional analyses of the STC (i.e., Trend, Emerging Hot Spot, Hot Spot, and Cluster and Outlier Analyses) provide extra insights into the data and may aid in predicting future mining claim activities.

Remote sensing data acquisition, analysis and archival. Volume 1. Final report

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

Stringer, W.J.; Dean, K.G.; Groves, J.E.

1993-03-25

The project specialized in the acquisition and dissemination of satellite imagery and its utilization for case-specific and statistical analyses of offshore environmental conditions, particularly those involving sea ice. During the duration of this contract, 854 Landsat Multispectral Scanner and 2 Landsat Thematic Mapper scenes, 8,576 Advanced Very High Resolution Radiometer images, and 31,000 European, Earth Resources Satellite, Synthetic Aperture Radar images were archived. Direct assistance was provided to eight Minerals Management Service (MMS)-sponsored studies, including analyses of Port Moller circulation, Bowhead whale migration, distribution, population and behavioral studies, Beaufort Sea fisheries, oil spill trajectory model development, and Kasegaluk Lagoon environmentalmore » assessments. In addition, under this Cooperative Agreement several complete studies were undertaken based on analysis of satellite imagery. The topics included: Kasegaluk Lagoon transport, the effect of winter storms on arctic ice, the relationship between ice surface temperatures as measured by buoys and passive microwave imagery, unusual cloud forms following lead-openings, and analyses of Chukchi and Bering sea polynyas.« less

ParallelStructure: A R Package to Distribute Parallel Runs of the Population Genetics Program STRUCTURE on Multi-Core Computers

PubMed Central

Besnier, Francois; Glover, Kevin A.

2013-01-01

This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/. PMID:23923012

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool

PubMed Central

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-01-01

Background It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. Results This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. Conclusion SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes. PMID:18706080

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

PubMed

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-08-15

It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

Data Mining as a Service (DMaaS)

NASA Astrophysics Data System (ADS)

Tejedor, E.; Piparo, D.; Mascetti, L.; Moscicki, J.; Lamanna, M.; Mato, P.

2016-10-01

Data Mining as a Service (DMaaS) is a software and computing infrastructure that allows interactive mining of scientific data in the cloud. It allows users to run advanced data analyses by leveraging the widely adopted Jupyter notebook interface. Furthermore, the system makes it easier to share results and scientific code, access scientific software, produce tutorials and demonstrations as well as preserve the analyses of scientists. This paper describes how a first pilot of the DMaaS service is being deployed at CERN, starting from the notebook interface that has been fully integrated with the ROOT analysis framework, in order to provide all the tools for scientists to run their analyses. Additionally, we characterise the service backend, which combines a set of IT services such as user authentication, virtual computing infrastructure, mass storage, file synchronisation, development portals or batch systems. The added value acquired by the combination of the aforementioned categories of services is discussed, focusing on the opportunities offered by the CERNBox synchronisation service and its massive storage backend, EOS.

An infectious way to teach students about outbreaks.

PubMed

Cremin, Íde; Watson, Oliver; Heffernan, Alastair; Imai, Natsuko; Ahmed, Norin; Bivegete, Sandra; Kimani, Teresia; Kyriacou, Demetris; Mahadevan, Preveina; Mustafa, Rima; Pagoni, Panagiota; Sophiea, Marisa; Whittaker, Charlie; Beacroft, Leo; Riley, Steven; Fisher, Matthew C

2018-06-01

The study of infectious disease outbreaks is required to train today's epidemiologists. A typical way to introduce and explain key epidemiological concepts is through the analysis of a historical outbreak. There are, however, few training options that explicitly utilise real-time simulated stochastic outbreaks where the participants themselves comprise the dataset they subsequently analyse. In this paper, we present a teaching exercise in which an infectious disease outbreak is simulated over a five-day period and subsequently analysed. We iteratively developed the teaching exercise to offer additional insight into analysing an outbreak. An R package for visualisation, analysis and simulation of the outbreak data was developed to accompany the practical to reinforce learning outcomes. Computer simulations of the outbreak revealed deviations from observed dynamics, highlighting how simplifying assumptions conventionally made in mathematical models often differ from reality. Here we provide a pedagogical tool for others to use and adapt in their own settings. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Ensembl Plants: Integrating Tools for Visualizing, Mining, and Analyzing Plant Genomics Data.

PubMed

Bolser, Dan; Staines, Daniel M; Pritchard, Emily; Kersey, Paul

2016-01-01

Ensembl Plants ( http://plants.ensembl.org ) is an integrative resource presenting genome-scale information for a growing number of sequenced plant species (currently 33). Data provided includes genome sequence, gene models, functional annotation, and polymorphic loci. Various additional information are provided for variation data, including population structure, individual genotypes, linkage, and phenotype data. In each release, comparative analyses are performed on whole genome and protein sequences, and genome alignments and gene trees are made available that show the implied evolutionary history of each gene family. Access to the data is provided through a genome browser incorporating many specialist interfaces for different data types, and through a variety of additional methods for programmatic access and data mining. These access routes are consistent with those offered through the Ensembl interface for the genomes of non-plant species, including those of plant pathogens, pests, and pollinators.Ensembl Plants is updated 4-5 times a year and is developed in collaboration with our international partners in the Gramene ( http://www.gramene.org ) and transPLANT projects ( http://www.transplantdb.org ).

Extracting Fitness Relationships and Oncogenic Patterns among Driver Genes in Cancer.

PubMed

Zhang, Xindong; Gao, Lin; Jia, Songwei

2017-12-25

Driver mutation provides fitness advantage to cancer cells, the accumulation of which increases the fitness of cancer cells and accelerates cancer progression. This work seeks to extract patterns accumulated by driver genes ("fitness relationships") in tumorigenesis. We introduce a network-based method for extracting the fitness relationships of driver genes by modeling the network properties of the "fitness" of cancer cells. Colon adenocarcinoma (COAD) and skin cutaneous malignant melanoma (SKCM) are employed as case studies. Consistent results derived from different background networks suggest the reliability of the identified fitness relationships. Additionally co-occurrence analysis and pathway analysis reveal the functional significance of the fitness relationships with signaling transduction. In addition, a subset of driver genes called the "fitness core" is recognized for each case. Further analyses indicate the functional importance of the fitness core in carcinogenesis, and provide potential therapeutic opportunities in medicinal intervention. Fitness relationships characterize the functional continuity among driver genes in carcinogenesis, and suggest new insights in understanding the oncogenic mechanisms of cancers, as well as providing guiding information for medicinal intervention.

A study of the comparative effects of various means of motion cueing during a simulated compensatory tracking task

NASA Technical Reports Server (NTRS)

Mckissick, B. T.; Ashworth, B. R.; Parrish, R. V.; Martin, D. J., Jr.

1980-01-01

NASA's Langley Research Center conducted a simulation experiment to ascertain the comparative effects of motion cues (combinations of platform motion and g-seat normal acceleration cues) on compensatory tracking performance. In the experiment, a full six-degree-of-freedom YF-16 model was used as the simulated pursuit aircraft. The Langley Visual Motion Simulator (with in-house developed wash-out), and a Langley developed g-seat were principal components of the simulation. The results of the experiment were examined utilizing univariate and multivariate techniques. The statistical analyses demonstrate that the platform motion and g-seat cues provide additional information to the pilot that allows substantial reduction of lateral tracking error. Also, the analyses show that the g-seat cue helps reduce vertical error.

What We Talk About When We Talk About Drought: Tree-ring Perspectives on Model-Data Comparisons in Hydroclimate Research

NASA Astrophysics Data System (ADS)

Cook, B.; Anchukaitis, K. J.

2017-12-01

Comparative analyses of paleoclimate reconstructions and climate model simulations can provide valuable insights into past and future climate events. Conducting meaningful and quantitative comparisons, however, can be difficult for a variety of reasons. Here, we use tree-ring based hydroclimate reconstructions to discuss some best practices for paleoclimate-model comparisons, highlighting recent studies that have successfully used this approach. These analyses have improved our understanding of the Medieval-era megadroughts, ocean forcing of large scale drought patterns, and even climate change contributions to future drought risk. Additional work is needed, however, to better reconcile and formalize uncertainties across observed, modeled, and reconstructed variables. In this regard, process based forward models of proxy-systems will likely be a critical tool moving forward.

FERRET-SAND II physics-dosimetry analysis for N Reactor Pressure Tubes 2954, 3053 and 1165 using a WIMS calculated input spectrum

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

McElroy, W.N.; Kellogg, L.S.; Matsumoto, W.Y.

1988-05-01

This report is in response to a request from Westinghouse Hanford Company (WHC) that the PNL National Dosimetry Center (NDC) perform physics-dosimetry analyses (E > MeV) for N Reactor Pressure Tubes 2954 and 3053. As a result of these analyses, and recommendations for additional studies, two physics-dosimetry re-evaluations for Pressure Tube 1165 were also accomplished. The primary objective of Pacific Northwest Laboratories' (PNL) National Dosimetry Center (NDC) physics-dosimetry work for N Reactor was to provide FERRET-SAND II physics-dosimetry results to assist in the assessment of neutron radiation-induced changes in the physical and mechanical properties of N Reactor pressure tubes. 15more » refs., 6 figs., 5 tabs.« less

Orthodontic archwire composition and phase analyses by neutron spectroscopy.

PubMed

Tian, Kun V; Festa, Giulia; Basoli, Francesco; Laganà, Giuseppina; Scherillo, Antonella; Andreani, Carla; Bollero, Patrizio; Licoccia, Silvia; Senesi, Roberto; Cozza, Paola

2017-05-31

Quantitative metallurgical and phase analyses employing neutron diffraction technique were conducted on two as-received commercial rectangular austenitic stainless steel orthodontic archwires, G&H and Azdent, 0.43×0.64 mm (0.017×0.025 inch). Results showed a bi-phase structure containing martensitic phase (45.67% for G&H and 6.62% for Azdent) in addition to the expected metastable austenite. The former may be a strain-induced phase-transformation arising during the cold working process of wire fabrication. Further neutron resonance capture analysis determinations provided atomic and isotopic compositions, including alloying elements in each sample, complementary to the results of traditional energy dispersive X-ray spectroscopy. Together, these results assist in relating commercial alloying recipes and processing histories with mechanical performance, strength and ductility in particular.

Strengthen forensic entomology in court--the need for data exploration and the validation of a generalised additive mixed model.

PubMed

Baqué, Michèle; Amendt, Jens

2013-01-01

Developmental data of juvenile blow flies (Diptera: Calliphoridae) are typically used to calculate the age of immature stages found on or around a corpse and thus to estimate a minimum post-mortem interval (PMI(min)). However, many of those data sets don't take into account that immature blow flies grow in a non-linear fashion. Linear models do not supply a sufficient reliability on age estimates and may even lead to an erroneous determination of the PMI(min). According to the Daubert standard and the need for improvements in forensic science, new statistic tools like smoothing methods and mixed models allow the modelling of non-linear relationships and expand the field of statistical analyses. The present study introduces into the background and application of these statistical techniques by analysing a model which describes the development of the forensically important blow fly Calliphora vicina at different temperatures. The comparison of three statistical methods (linear regression, generalised additive modelling and generalised additive mixed modelling) clearly demonstrates that only the latter provided regression parameters that reflect the data adequately. We focus explicitly on both the exploration of the data--to assure their quality and to show the importance of checking it carefully prior to conducting the statistical tests--and the validation of the resulting models. Hence, we present a common method for evaluating and testing forensic entomological data sets by using for the first time generalised additive mixed models.

Formative assessment in mathematics for engineering students

NASA Astrophysics Data System (ADS)

Ní Fhloinn, Eabhnat; Carr, Michael

2017-07-01

In this paper, we present a range of formative assessment types for engineering mathematics, including in-class exercises, homework, mock examination questions, table quizzes, presentations, critical analyses of statistical papers, peer-to-peer teaching, online assessments and electronic voting systems. We provide practical tips for the implementation of such assessments, with a particular focus on time or resource constraints and large class sizes, as well as effective methods of feedback. In addition, we consider the benefits of such formative assessments for students and staff.

Providing Additional Support for MNA by Including Quantitative Lines of Evidence for Abiotic Degradation and Co-metabolic Oxidation of Chlorinated Ethylenes

DTIC Science & Technology

2017-02-08

cost benefit of the technology. 7.1 COST MODEL A simple cost model for the technology is presented so that a remediation professional can understand...reporting costs . The benefit of the qPCR analyses is that they allow the user to determine if aerobic cometabolism is possible. Because the PHE and...of Chlorinated Ethylenes February 2017 This document has been cleared for public release; Distribution Statement A Page Intentionally Left

Accommodating complexity and human behaviors in decision analysis.

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

Backus, George A.; Siirola, John Daniel; Schoenwald, David Alan

2007-11-01

This is the final report for a LDRD effort to address human behavior in decision support systems. One sister LDRD effort reports the extension of this work to include actual human choices and additional simulation analyses. Another provides the background for this effort and the programmatic directions for future work. This specific effort considered the feasibility of five aspects of model development required for analysis viability. To avoid the use of classified information, healthcare decisions and the system embedding them became the illustrative example for assessment.

First records of Hippocampus algiricus in the Canary Islands (north-east Atlantic Ocean) with an observation of hybridization with Hippocampus hippocampus.

PubMed

Otero-Ferrer, F; Herrera, R; López, A; Socorro, J; Molina, L; Bouza, C

2015-10-01

Morphometric and genetic analyses confirmed the first records of the West African seahorse Hippocampus algiricus at Gran Canaria Island (north-east Atlantic Ocean), and also the first evidence of interspecific hybridization in seahorses. These results provide additional data on the distribution of H. algiricus that may help to establish future conservation strategies, and uncover a new potential sympatric scenario between H. algiricus and Hippocampus hippocampus. © 2015 The Fisheries Society of the British Isles.

Scattering by Artificial Wind and Rain Roughened Water Surfaces at Oblique Incidences

NASA Technical Reports Server (NTRS)

Craeye, C.; Sobieski, P. W.; Bliven, L. F.

1997-01-01

Rain affects wind retrievals from scatterometric measurements of the sea surface. To depict the additional roughness caused by rain on a wind driven surface, we use a ring-wave spectral model. This enables us to analyse the rain effect on K(u) band scatterometric observations from two laboratory experiments. Calculations based on the small perturbation method provide good simulation of scattering measurements for the rain-only case, whereas for combined wind and rain cases, the boundary perturbation method is appropriate.

Life Sciences Implications of Lunar Surface Operations

NASA Technical Reports Server (NTRS)

Chappell, Steven P.; Norcross, Jason R.; Abercromby, Andrew F.; Gernhardt, Michael L.

2010-01-01

The purpose of this report is to document preliminary, predicted, life sciences implications of expected operational concepts for lunar surface extravehicular activity (EVA). Algorithms developed through simulation and testing in lunar analog environments were used to predict crew metabolic rates and ground reaction forces experienced during lunar EVA. Subsequently, the total metabolic energy consumption, the daily bone load stimulus, total oxygen needed, and other variables were calculated and provided to Human Research Program and Exploration Systems Mission Directorate stakeholders. To provide context to the modeling, the report includes an overview of some scenarios that have been considered. Concise descriptions of the analog testing and development of the algorithms are also provided. This document may be updated to remain current with evolving lunar or other planetary surface operations, assumptions and concepts, and to provide additional data and analyses collected during the ongoing analog research program.

Summary of Meta-Analyses Dealing with Single-Row versus Double-Row Repair Techniques for Rotator Cuff Tears

PubMed Central

Spiegl, U.J.; Euler, S.A.; Millett, P.J.; Hepp, P.

2016-01-01

Background: Several meta-analyses of randomized clinical trials have been performed to analyze whether double-row (DR) rotator cuff repair (RCR) provides superior clinical outcomes and structural healing compared to single-row (SR) repair. The purpose of this study was to sum up the results of meta-analysis comparing SR and DR repair with respect on clinical outcomes and re-tear rates. Methods: A literature search was undertaken to identify all meta-analyses dealing with randomized controlled trials comparing clinical und structural outcomes after SR versus DR RCR. Results: Eight meta-analyses met the eligibility criteria: two including Level I studies only, five including both Level I and Level II studies, and one including additional Level III studies. Four meta-analyses found no differences between SR and DR RCR for patient outcomes, whereas four favored DR RCR for tears greater than 3 cm. Two meta-analyses found no structural healing differences between SR and DR RCR, whereas six found DR repair to be superior for tears greater than 3 cm tears. Conclusion: No clinical differences are seen between single-row and double-row repair for small and medium rotator cuff tears after a short-term follow-up period with a higher re-tear rate following single-row repairs. There seems to be a trend to superior results with double-row repair in large to massive tear sizes. PMID:27708735

Unsteady Aerodynamic Models for Turbomachinery Aeroelastic and Aeroacoustic Applications

NASA Technical Reports Server (NTRS)

Verdon, Joseph M.; Barnett, Mark; Ayer, Timothy C.

1995-01-01

Theoretical analyses and computer codes are being developed for predicting compressible unsteady inviscid and viscous flows through blade rows of axial-flow turbomachines. Such analyses are needed to determine the impact of unsteady flow phenomena on the structural durability and noise generation characteristics of the blading. The emphasis has been placed on developing analyses based on asymptotic representations of unsteady flow phenomena. Thus, high Reynolds number flows driven by small amplitude unsteady excitations have been considered. The resulting analyses should apply in many practical situations and lead to a better understanding of the relevant flow physics. In addition, they will be efficient computationally, and therefore, appropriate for use in aeroelastic and aeroacoustic design studies. Under the present effort, inviscid interaction and linearized inviscid unsteady flow models have been formulated, and inviscid and viscid prediction capabilities for subsonic steady and unsteady cascade flows have been developed. In this report, we describe the linearized inviscid unsteady analysis, LINFLO, the steady inviscid/viscid interaction analysis, SFLOW-IVI, and the unsteady viscous layer analysis, UNSVIS. These analyses are demonstrated via application to unsteady flows through compressor and turbine cascades that are excited by prescribed vortical and acoustic excitations and by prescribed blade vibrations. Recommendations are also given for the future research needed for extending and improving the foregoing asymptotic analyses, and to meet the goal of providing efficient inviscid/viscid interaction capabilities for subsonic and transonic unsteady cascade flows.

Grain-Scale Analyses of Curiosity Data at Marias Pass, Gale Crater, Mars: Methods Comparison and Depositional Interpretation

NASA Astrophysics Data System (ADS)

Sacks, L. E.; Edgar, L. A.; Edwards, C. S.; Anderson, R. B.

2016-12-01

Images acquired by the Mars Hand Lens Imager (MAHLI) and the ChemCam Remote Micro Imager (RMI) onboard the Mars Science Laboratory (MSL) Curiosity rover provide grain-scale data that are critical for interpreting sedimentary deposits. At the location informally known as Marias Pass, Curiosity used both cameras to image the nine rock targets used in this study. We used manual point-counts to measure grain size distributions from those images to compare the abilities of the two cameras. The manually derived results were compared to automated grain size data obtained using pyDGS (Digital Grain Size), an open-source python program. Grain size analyses were used to test the lacustrine and aeolian depositional hypotheses for the Murray and Stimson formations at Marias Pass. Results indicate that the MAHLI and RMI instruments, despite their different fields of view and properties, provide comparable grain size measurements. Additionally, pyDGS does not account for grains smaller than a few pixels and thus does not report representative grain size data and should not be used on images with a large fraction of unresolved grains. Finally, the data collected at Marias Pass are consistent with the existing interpretations of the Murray and Stimson formations. The fine-grained results of the Murray formation analyses support lacustrine deposition, while the mean grain size of the Stimson formation is fine to medium sized sand, consistent with aeolian deposition. However, directly above the contact with the Murray formation, larger rip-up clasts of the Murray formation are present in the Stimson formation. It is possible that water was involved at this stage of erosion and re-deposition, prior to aeolian deposition. Additionally, the grain-scale analyses conducted in this study show that the Dust Removal Tool on Curiosity should be used prior to capturing images for grain-scale analysis. Two images of the target informally named Ronan, taken before and after brushing, resulted in dramatically different grain size results, suggesting that the common, thin layer of dust obscured the true grain size distribution. These grain-scale analyses at Marias Pass have important implications for the collection and processing of image data, as well as the depositional environments recorded in Gale crater. Funded by NSF Grant AST-1461200

Volcanic Chemostratigraphy on the Outcrop Using Field-Portable X-Ray Fluorescence: An Example from the Basaltic Flows of Hewitt's Cove, MA.

NASA Astrophysics Data System (ADS)

Wall, A. M.; Brabander, D. J.

2005-05-01

The area of Hewitt's Cove, Hingham, Massachusetts structurally represents the southern extent of the Boston Basin, and as such, provides the opportunity to identify and recognize basin-wide events. While the stratigraphy of the Boston Basin has been developed since the advent of U-Pb geochronology and formal stratigraphic facies descriptions (Socci and Smith, 2001), the stratigraphy of the Hewitt's Cove area has not been thoroughly addressed since the work of William O. Crosby in 1894 (Billings, 1976, Bailey and Bland, 2001). Hewitt's Cove consists of an andesitic basaltic flow, approximately 150 m thick, overlain by siltstone and conglomeratic sequences. Field-Portable X-Ray Fluorescence (FP-XRF) was used on fresh and weathered surfaces on the outcrop and in hand samples, and these analyses were compared with conventional laboratory XRF analyses. The in situ field-based analyses produced a reproducible chemostratigraphy that is consistent with subsequent laboratory-based analyses. These data suggest that the series of andesitic basalt flows at Hewitt's Cove are the result of compositionally different magmatic pulses. Additional analyses must be completed to determine the extent of these pulses and the extent of variation in this area before further conclusions can be made. This study particularly demonstrates the utility of using FP-XRF in igneous geologic applications.

Analysis of ozone precursor data from Baton Rouge, Houston, El Paso, and Dallas

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

Sather, M.E.; Kemp, M.G.

1998-12-31

Ongoing analyses of ozone precursor data continue to be performed for Baton Rouge, Louisiana, and Houston, El Paso, and Dallas, Texas. All four areas have collected ambient monitoring data for ozone, nitrogen oxides (NO{sub x}), and over 50 volatile organic compound (VOC) species in accordance with the Photochemical Assessment Monitoring Stations (PAMS) requirements. The PAMS program was initiated to provide more detailed VOC, NO{sub x}, and meteorological data for scientists, modelers, and managers working toward eliminating violations of the ozone National Ambient Air Quality Standards (NAAQS). This paper will focus on several useful analyses of PAMS data for the fourmore » study areas including: (1) a trends analysis of Total Non-Methane Organic Compounds (TNMOC), NO{sub x}, and ozone data from two Baton Rouge sites, (2) results of TNMOC/NO{sub x} ratio analyses for the three Baton Rouge PAMS sites which can provide a starting point for evaluating specific site sensitivity to changes in VOC or NO{sub x} ambient concentrations, (3) results of benzene/toluene ratio analyses which supply information on aged/fresh air masses, and (4) results of ethylene/acetylene ratio analyses which are useful in determining the impacts of catalytic/noncatalytic vehicles. This paper will also discuss the continuing maturation of the PAMS program in Baton Rouge, Houston, and El Paso. The Dallas area is expected to formally begin implementing a PAMS program in 1998 after the area is reclassified to a serious status for ozone pollution. In addition, the Beaumont, Texas area is currently scheduled to be reclassified to a serious status for ozone pollution in the 1998/1999 time period, and thus would also need to begin implementing a PAMS program.« less

Meta-Analyses and Orthodontic Evidence-Based Clinical Practice in the 21st Century

PubMed Central

Papadopoulos, Moschos A.

2010-01-01

Introduction: Aim of this systematic review was to assess the orthodontic related issues which currently provide the best evidence as documented by meta-analyses, by critically evaluating and discussing the methodology used in these studies. Material and Methods: Several electronic databases were searched and handsearching was also performed in order to identify the corresponding meta-analyses investigating orthodontic related subjects. In total, 197 studies were retrieved initially. After applying specific inclusion and exclusion criteria, 27 articles were identified as meta-analyses treating orthodontic-related subjects. Results: Many of these 27 papers presented sufficient quality and followed appropriate meta-analytic approaches to quantitatively synthesize data and presented adequately supported evidence. However, the methodology used in some of them presented weaknesses, limitations or deficiencies. Consequently, the topics in orthodontics which currently provide the best evidence, include some issues related to Class II or Class III treatment, treatment of transverse problems, external apical root resorption, dental anomalies, such as congenital missing teeth and tooth transposition, frequency of severe occlusal problems, nickel hypersensitivity, obstructive sleep apnea syndrome, and computer-assisted learning in orthodontic education. Conclusions: Only a few orthodontic related issues have been so far investigated by means of MAs. In addition, for some of these issues investigated in the corresponding MAs no definite conclusions could be drawn, due to significant methodological deficiencies of these studies. According to this investigation, it can be concluded that at the begin of the 21st century there is evidence for only a few orthodontic related issues as documented by meta-analyses, and more well-conducted high quality research studies are needed to produce strong evidence in order to support evidence-based clinical practice in orthodontics. PMID:21673839

Preliminary performance assessment for the Waste Isolation Pilot Plant, December 1992. Volume 5, Uncertainty and sensitivity analyses of gas and brine migration for undisturbed performance

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

Not Available

1993-08-01

Before disposing of transuranic radioactive waste in the Waste Isolation Pilot Plant (WIPP), the United States Department of Energy (DOE) must evaluate compliance with applicable long-term regulations of the United States Environmental Protection Agency (EPA). Sandia National Laboratories is conducting iterative performance assessments (PAs) of the WIPP for the DOE to provide interim guidance while preparing for a final compliance evaluation. This volume of the 1992 PA contains results of uncertainty and sensitivity analyses with respect to migration of gas and brine from the undisturbed repository. Additional information about the 1992 PA is provided in other volumes. Volume 1 containsmore » an overview of WIPP PA and results of a preliminary comparison with 40 CFR 191, Subpart B. Volume 2 describes the technical basis for the performance assessment, including descriptions of the linked computational models used in the Monte Carlo analyses. Volume 3 contains the reference data base and values for input parameters used in consequence and probability modeling. Volume 4 contains uncertainty and sensitivity analyses with respect to the EPA`s Environmental Standards for the Management and Disposal of Spent Nuclear Fuel, High-Level and Transuranic Radioactive Wastes (40 CFR 191, Subpart B). Finally, guidance derived from the entire 1992 PA is presented in Volume 6. Results of the 1992 uncertainty and sensitivity analyses indicate that, conditional on the modeling assumptions and the assigned parameter-value distributions, the most important parameters for which uncertainty has the potential to affect gas and brine migration from the undisturbed repository are: initial liquid saturation in the waste, anhydrite permeability, biodegradation-reaction stoichiometry, gas-generation rates for both corrosion and biodegradation under inundated conditions, and the permeability of the long-term shaft seal.« less

Metagenomic analyses of bacteria on human hairs: a qualitative assessment for applications in forensic science.

PubMed

Tridico, Silvana R; Murray, Dáithí C; Addison, Jayne; Kirkbride, Kenneth P; Bunce, Michael

2014-01-01

Mammalian hairs are one of the most ubiquitous types of trace evidence collected in the course of forensic investigations. However, hairs that are naturally shed or that lack roots are problematic substrates for DNA profiling; these hair types often contain insufficient nuclear DNA to yield short tandem repeat (STR) profiles. Whilst there have been a number of initial investigations evaluating the value of metagenomics analyses for forensic applications (e.g. examination of computer keyboards), there have been no metagenomic evaluations of human hairs-a substrate commonly encountered during forensic practice. This present study attempts to address this forensic capability gap, by conducting a qualitative assessment into the applicability of metagenomic analyses of human scalp and pubic hair. Forty-two DNA extracts obtained from human scalp and pubic hairs generated a total of 79,766 reads, yielding 39,814 reads post control and abundance filtering. The results revealed the presence of unique combinations of microbial taxa that can enable discrimination between individuals and signature taxa indigenous to female pubic hairs. Microbial data from a single co-habiting couple added an extra dimension to the study by suggesting that metagenomic analyses might be of evidentiary value in sexual assault cases when other associative evidence is not present. Of all the data generated in this study, the next-generation sequencing (NGS) data generated from pubic hair held the most potential for forensic applications. Metagenomic analyses of human hairs may provide independent data to augment other forensic results and possibly provide association between victims of sexual assault and offender when other associative evidence is absent. Based on results garnered in the present study, we believe that with further development, bacterial profiling of hair will become a valuable addition to the forensic toolkit.

Cetuximab in treatment of metastatic colorectal cancer: final survival analyses and extended RAS data from the NORDIC-VII study.

PubMed

Guren, Tormod Kyrre; Thomsen, Maria; Kure, Elin H; Sorbye, Halfdan; Glimelius, Bengt; Pfeiffer, Per; Österlund, Pia; Sigurdsson, Fridbjörn; Lothe, Inger Marie Bowitz; Dalsgaard, Astrid Marie; Skovlund, Eva; Christoffersen, Thoralf; Tveit, Kjell Magne

2017-05-09

The NORDIC-VII study is a randomised phase III trial of cetuximab plus continuous or intermittent fluorouracil, folinic acid, and oxaliplatin (Nordic FLOX) vs FLOX alone in first-line treatment of metastatic colorectal cancer. The present report presents an updated and final survival analysis with BRAF and extended RAS mutational status, 5 years after the primary analysis. A total of 566 patients were included in the intention-to-treat (ITT) population of the NORDIC-VII study. Updated survival status was obtained from 176 patients who were alive in the primary survival analyses. Samples from 223 tumours previously found to be KRAS (exon 2) and BRAF (V600E) wild-type, were re-analysed for KRAS (exons 3 and 4) and NRAS (exons 2-4) mutations. Including the extended RAS analyses, RAS and BRAF mutational status was available from 457 patients (81% of the ITT population). RAS was mutated in 46% and BRAF in 12% of the tumours. RAS and BRAF, if mutated, were negative prognostic factors. The updated analyses confirmed the finding of the primary report that cetuximab did not provide any additional benefit when added to FLOX in patients with RAS/BRAF wild-type tumours, neither on progression-free nor overall survival. However, the outcomes in a subset of patients, which, after the first eight treatment cycles, received cetuximab alone, suggested a beneficial effect of cetuximab monotherapy. Adding cetuximab to Nordic FLOX did not provide any clinical benefit, but the data suggested an effect of cetuximab monotherapy in patients with RAS/BRAF wild-type tumours in the NORDIC-VII cohort. The data were compatible with a negative interaction between cetuximab and the Nordic FLOX chemotherapy backbone.

40 CFR 194.15 - Content of compliance re-certification application(s).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Content of compliance re-certification...-certification Applications § 194.15 Content of compliance re-certification application(s). (a) In submitting...; (2) All additional monitoring data, analyses and results; (3) All additional analyses and results of...

Ground-water and water-chemistry data for the Willamette basin, Oregon

USGS Publications Warehouse

Orzol, Leonard L.; Wozniak, Karl C.; Meissner, Tiffany R.; Lee, Douglas B.

2000-01-01

This report presents ground-water data collected and compiled as part of a study of the ground-water resources of the Willamette River Basin, Oregon. The report includes tabulated information and a location map for 1,234 field-located water wells and 6 springs, hydrographs showing water-level fluctuations during various time periods for 265 of the wells, borehole geophysical data for 16 wells, and water-chemistry analyses from 125 wells and 6 springs. These data, as well as data for 4,752 additional fieldlocated wells and 1 spring, are included on a CD-ROM. In addition, the locations of the field-located wells and springs are provided in geographic information system formats on the CD-ROM.

CEOS SEO and GISS Meeting

NASA Technical Reports Server (NTRS)

Killough, Brian; Stover, Shelley

2008-01-01

The Committee on Earth Observation Satellites (CEOS) provides a brief to the Goddard Institute for Space Studies (GISS) regarding the CEOS Systems Engineering Office (SEO) and current work on climate requirements and analysis. A "system framework" is provided for the Global Earth Observation System of Systems (GEOSS). SEO climate-related tasks are outlined including the assessment of essential climate variable (ECV) parameters, use of the "systems framework" to determine relevant informational products and science models and the performance of assessments and gap analyses of measurements and missions for each ECV. Climate requirements, including instruments and missions, measurements, knowledge and models, and decision makers, are also outlined. These requirements would establish traceability from instruments to products and services allowing for benefit evaluation of instruments and measurements. Additionally, traceable climate requirements would provide a better understanding of global climate models.

[Involvement of scientific societies in early benefit assessment: Simulated participation or valuable additional input?

PubMed

Bleß, Hans-Holger; Seidlitz, Cornelia; Ohlmeier, Christoph; de Millas, Christoph

2018-02-01

The German framework of early benefit assessment (EBA) of drugs also provides for the participation of scientific medical societies. The aim of their inclusion is to assure that care providers can critically assess all aspects of the EBA and provide insights into relevant aspects regarding the provision of care. This study systematically reviews the frequency of participation of the scientific medical societies (FGs) and the Drug Commission of the German Medical Association (AkdÄ) within the scope of the EBA. In addition, the positioning of AkdÄ/FG is compared to the Institute for Quality and Efficiency in Health Care (IQWiG) and the Federal Joint Committee (G-BA) with a focus on antidiabetic drugs and cancer drugs. A literature analysis was performed based on the comprehensive documentation of benefit assessments published by G-BA. All proceedings of antidiabetic drugs and cancer drugs were included, for which a decision was published by August 6, 2015. In addition, statements of FGs or AkdÄ were identified by an exploratory literature review and included in the analysis. The statements considered were assessed with regard to three categories: (1) additional benefit, (2) appropriate comparator (ZVT) and (3) suitability of the endpoints. For each procedure and category, it was assessed whether there was agreement or disagreement between IGWiG/G-BA and AkdÄ/FGs statements. Regarding the additional benefit, a deviating position was further differentiated according to the level of additional benefit (higher/lower). Afterwards, the proportion of favorable and unfavorable positions was calculated, stratified by FGs and AkdÄ and, separately, for proceedings of antidiabetics and cancer drugs. The literature review revealed 41 proceedings of cancer drugs and 21 proceedings of antidiabetic drugs which were included in the analyses. Statements by AkdÄ/FGs were identified in 90 % of the proceedings for antidiabetic drugs and in 98 % of the proceedings for cancer drugs. In general, the AkdÄ was more often in agreement with the IQWiG than with the FGs' positions. In addition, a different position was more frequent in the proceedings concerning antidiabetic drugs than in the proceedings concerning cancer drugs. Furthermore, the G-BA decision was more frequently in line with the AkdÄ position than with the FGs' position, and this applies to both indications. There was a high willingness to participate in the commenting procedure of the EBA. At the same time, the analyses revealed partially heterogeneous positions, both between FGs/AkdÄ and IQWiG/G-BA, as well as between FGs and AkdÄ. The results thus emphasize the need for such discussions within the framework of the EBA. Copyright © 2018. Published by Elsevier GmbH.

Developing advanced X-ray scattering methods combined with crystallography and computation.

PubMed

Perry, J Jefferson P; Tainer, John A

2013-03-01

The extensive use of small angle X-ray scattering (SAXS) over the last few years is rapidly providing new insights into protein interactions, complex formation and conformational states in solution. This SAXS methodology allows for detailed biophysical quantification of samples of interest. Initial analyses provide a judgment of sample quality, revealing the potential presence of aggregation, the overall extent of folding or disorder, the radius of gyration, maximum particle dimensions and oligomerization state. Structural characterizations include ab initio approaches from SAXS data alone, and when combined with previously determined crystal/NMR, atomistic modeling can further enhance structural solutions and assess validity. This combination can provide definitions of architectures, spatial organizations of protein domains within a complex, including those not determined by crystallography or NMR, as well as defining key conformational states of a protein interaction. SAXS is not generally constrained by macromolecule size, and the rapid collection of data in a 96-well plate format provides methods to screen sample conditions. This includes screening for co-factors, substrates, differing protein or nucleotide partners or small molecule inhibitors, to more fully characterize the variations within assembly states and key conformational changes. Such analyses may be useful for screening constructs and conditions to determine those most likely to promote crystal growth of a complex under study. Moreover, these high throughput structural determinations can be leveraged to define how polymorphisms affect assembly formations and activities. This is in addition to potentially providing architectural characterizations of complexes and interactions for systems biology-based research, and distinctions in assemblies and interactions in comparative genomics. Thus, SAXS combined with crystallography/NMR and computation provides a unique set of tools that should be considered as being part of one's repertoire of biophysical analyses, when conducting characterizations of protein and other macromolecular interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Stereotactic Radiosurgery in the Management of Limited (1-4) Brain Metasteses: Systematic Review and International Stereotactic Radiosurgery Society Practice Guideline.

PubMed

Chao, Samuel T; De Salles, Antonio; Hayashi, Motohiro; Levivier, Marc; Ma, Lijun; Martinez, Roberto; Paddick, Ian; Régis, Jean; Ryu, Samuel; Slotman, Ben J; Sahgal, Arjun

2017-11-03

Guidelines regarding stereotactic radiosurgery (SRS) for brain metastases are missing recently published evidence. To conduct a systematic review and provide an objective summary of publications regarding SRS in managing patients with 1 to 4 brain metastases. Using Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, a systematic review was conducted using PubMed and Medline up to November 2016. A separate search was conducted for SRS for larger brain metastases. Twenty-seven prospective studies, critical reviews, meta-analyses, and published consensus guidelines were reviewed. Four key points came from these studies. First, there is no detriment to survival by withholding whole brain radiation (WBRT) in the upfront management of brain metastases with SRS. Second, while SRS on its own provides a high rate of local control (LC), WBRT may provide further increase in LC. Next, WBRT does provide distant brain control with less need for salvage therapy. Finally, the addition of WBRT does affect neurocognitive function and quality of life more than SRS alone. For larger brain metastases, surgical resection should be considered, especially when factoring lower LC with single-session radiosurgery. There is emerging data showing good LC and/or decreased toxicity with multisession radiosurgery. A number of well-conducted prospective and meta-analyses studies demonstrate good LC, without compromising survival, using SRS alone for patients with a limited number of brain metastases. Some also demonstrated less impact on neurocognitive function with SRS alone. Practice guidelines were developed using these data with International Stereotactic Radiosurgery Society consensus. Copyright © 2017 by the Congress of Neurological Surgeons

An analysis of context-based similarity tasks in textbooks from Brazil and the United States

NASA Astrophysics Data System (ADS)

Barcelos Amaral, Rúbia; Hollebrands, Karen

2017-11-01

Three textbooks from Brazil and three textbooks from the United States were analysed with a focus on similarity and context-based tasks. Students' opportunities to learn similarity were examined by considering whether students were provided context-based tasks of high cognitive demand and whether those tasks included missing or superfluous information. Although books in the United States included more tasks, the proportion of tasks focused on similarity were about the same. Context-based similarity tasks accounted for 9%-29% of the similarity tasks, and many of these contextual tasks were of low cognitive demand. In addition, the types of contexts that were included in the textbooks were critiqued and examples provided.

Debris/Ice/TPS Assessment and Integrated Photographic Analysis of Shuttle Mission STS-109

NASA Technical Reports Server (NTRS)

Oliu, Armando

2005-01-01

The Debris Team has developed and implemented measures to control damage from debris in the Shuttle operational environment and to make the control measures a part of routine launch flows. These measures include engineering surveillance during vehicle processing and closeout operations, facility and flight hardware inspections before and after launch, and photographic analysis of mission events. Photographic analyses of mission imagery from launch, on-orbit, and landing provide significant data in verifying proper operation of systems and evaluating anomalies. In addition to the Kennedy Space Center Photo/Video Analysis, reports from Johnson Space Center and Marshall Space Flight Center are also included in this document to provide an integrated assessment of the mission.

Debris/Ice/TPS Assessment and Integrated Photographic Analysis of Shuttle Mission STS-110

NASA Technical Reports Server (NTRS)

Oliu, Armando

2005-01-01

The Debris Team has developed and implemented measures to control damage from debris in the Shuttle operational environment and to make the control measures a part of routine launch flows. These measures include engineering surveillance during vehicle processing and closeout operations, facility and flight hardware inspections before and after launch, and photographic analysis of mission events. Photographic analyses of mission imagery from launch, on-orbit, and landing provide significant data in verifying proper operation of systems and evaluating anomalies. In addition to the Kennedy Space Center Photo/Video Analysis, reports from Johnson Space Center and Marshall Space Flight Center are also included in this document to provide an integrated assessment of the mission.

Debris/Ice/TPS Assessment and Integrated Photographic Analysis of Shuttle Mission STS-105

NASA Technical Reports Server (NTRS)

Oliu, Armando

2005-01-01

The Debris Team has developed and implemented measures to control damage from debris in the Shuttle operational environment and to make the control measures a part of routine launch flows. These measures include engineering surveillance during vehicle processing and closeout operations, facility and flight hardware inspections before and after launch, and photographic analysis of mission events. Photographic analyses of mission imagery from launch, on-orbit, and landing provide significant data in verifying proper operation of systems and evaluating anomalies. In addition to the Kennedy Space Center Photo/Video Analysis, reports from Johnson Space Center and Marshall Space Flight Center are also included in this document to provide an integrated assessment of the mission.

Debris/Ice/TPS Assessment and Integrated Photographic Analysis of Shuttle Mission STS-104

NASA Technical Reports Server (NTRS)

Oliu, Armando

2005-01-01

The Debris Team has developed and implemented measures to control damage from debris in the Shuttle operational environment and to make the control measures a part of routine launch flows. These measures include engineering surveillance during vehicle processing and closeout operations, facility and flight hardware inspections before and after launch, and photographic analysis of mission events. Photographic analyses of mission imagery from launch, on-orbit, and landing provide significant data in verifying proper operation of systems and evaluating anomalies. In addition to the Kennedy Space Center Photo/Video Analysis, reports from Johnson Space Center and Marshall Space Flight Center are also included in this document to provide an integrated assessment of the mission.

Debris/Ice/TPS Assessment and Integrated Photographic Analysis of Shuttle Mission STS-108

NASA Technical Reports Server (NTRS)

Oliu, Armando

2005-01-01

The Debris Team has developed and implemented measures to control damage from debris in the Shuttle operational environment and to make the control measures a part of routine launch flows. These measures include engineering surveillance during vehicle processing and closeout operations, facility and flight hardware inspections before and after launch, and photographic analysis of mission events. Photographic analyses of mission imagery from launch, on-orbit, and landing provide significant data in verifying proper operation of systems and evaluating anomalies. In addition to the Kennedy Space Center Photo/Video Analysis, reports from Johnson Space Center and Marshall Space Flight Center are also included in this document to provide an integrated assessment of the mission.

Central Processing of the Chemical Senses: An Overview

PubMed Central

2010-01-01

Our knowledge regarding the neural processing of the three chemical senses has been considerably lagging behind that of our other senses. It is only during the last 25 years that significant advances have been made in our understanding of where in the human brain odors, tastants, and trigeminal stimuli are processed. Here, we provide an overview of the current knowledge of how the human brain processes chemical stimuli based on findings in neuroimaging studies using positron emission tomography and functional magnetic resonance imaging. Additionally, we provide new insights from recent meta-analyses, on the basis of all published neuroimaging studies of the chemical senses, of where the chemical senses converge in the brain. PMID:21503268

Feasibility of an EHF (40/50 GHz) mobile satellite system using highly inclined orbits

NASA Technical Reports Server (NTRS)

Falciasecca, G.; Paraboni, A.; Ruggieri, M.; Valdoni, F.; Vatalaro, F.

1990-01-01

The pan-European L-band terrestrial cellular system (GSM) is expected to provide service to more than 10 million users by the year 2000. Discussed here is the feasibility of a new satellite system at EHF (40/50 GHz) to complement, at the end of the decade, the GSM system or its decendants in order to provide additional services at 64 kbits/s, or so. The main system aspects, channel characteristics, technology issues, and both on-board and earth terminal architectures are highlighted. Based on the performed analyses, a proposal was addressed to the Italian Space Agency (ASI), aimed at the implementation of a national plan.

A cross-sectional study on person-centred communication in the care of older people: the COMHOME study protocol

PubMed Central

Hafskjold, Linda; Sundler, Annelie J; Holmström, Inger K; Sundling, Vibeke; van Dulmen, Sandra

2015-01-01

Introduction This paper presents an international cross-sectional study on person-centred communication with older people receiving healthcare (COMHOME). Person-centred care relies on effective communication, but few studies have explored this with a specific focus on older people. The main aim of the COMHOME study is to generate knowledge on person-centred communication with older people (>65 years) in home healthcare services, radiographic and optometric practice. Methods and analysis This study will explore the communication between care providers and older persons in home care services. Home healthcare visits will be audiorecorded (n=500) in Norway, the Netherlands and Sweden. Analyses will be performed with the Verona Coding Definitions for Emotional Sequences (VR-CoDES), the Roter Interaction Analysis System (RIAS) and qualitative methods. The content of the communication, communicative challenging situations as well as empathy, power distance, decision-making, preservation of dignity and respect will be explored. In Norway, an additional 100 encounters, 50 in optometric practice (video recorded) and 50 in radiographic practice (audiorecorded), will be analysed. Furthermore, healthcare providers’ self-reported communication skills, empathy, mindfulness and emotional intelligence in relation to observed person-centred communication skills will be assessed using well-established standardised instruments. Ethics and dissemination Depending on national legislation, approval of either the central ethical committees (eg, nation or university), the national data protection officials or the local ethical committees (eg, units of home healthcare) was obtained. Study findings will be disseminated widely through peer-reviewed publications and conference presentations. The research findings will add knowledge to improve services provided to this vulnerable group of patients. Additionally, the findings will underpin a training programme for healthcare students and care providers focusing on communication with older people. PMID:25877282

Chemical fingerprinting of naphthenic acids and oil sands process waters-A review of analytical methods for environmental samples.

PubMed

Headley, J V; Peru, K M; Mohamed, M H; Frank, R A; Martin, J W; Hazewinkel, R R O; Humphries, D; Gurprasad, N P; Hewitt, L M; Muir, D C G; Lindeman, D; Strub, R; Young, R F; Grewer, D M; Whittal, R M; Fedorak, P M; Birkholz, D A; Hindle, R; Reisdorph, R; Wang, X; Kasperski, K L; Hamilton, C; Woudneh, M; Wang, G; Loescher, B; Farwell, A; Dixon, D G; Ross, M; Pereira, A Dos Santos; King, E; Barrow, M P; Fahlman, B; Bailey, J; McMartin, D W; Borchers, C H; Ryan, C H; Toor, N S; Gillis, H M; Zuin, L; Bickerton, G; Mcmaster, M; Sverko, E; Shang, D; Wilson, L D; Wrona, F J

2013-01-01

This article provides a review of the routine methods currently utilized for total naphthenic acid analyses. There is a growing need to develop chemical methods that can selectively distinguish compounds found within industrially derived oil sands process affected waters (OSPW) from those derived from the natural weathering of oil sands deposits. Attention is thus given to the characterization of other OSPW components such as oil sands polar organic compounds, PAHs, and heavy metals along with characterization of chemical additives such as polyacrylamide polymers and trace levels of boron species. Environmental samples discussed cover the following matrices: OSPW containments, on-lease interceptor well systems, on- and off-lease groundwater, and river and lake surface waters. There are diverse ranges of methods available for analyses of total naphthenic acids. However, there is a need for inter-laboratory studies to compare their accuracy and precision for routine analyses. Recent advances in high- and medium-resolution mass spectrometry, concomitant with comprehensive mass spectrometry techniques following multi-dimensional chromatography or ion-mobility separations, have allowed for the speciation of monocarboxylic naphthenic acids along with a wide range of other species including humics. The distributions of oil sands polar organic compounds, particularly the sulphur containing species (i.e., OxS and OxS2) may allow for distinguishing sources of OSPW. The ratios of oxygen- (i.e., Ox) and nitrogen-containing species (i.e., NOx, and N2Ox) are useful for differentiating organic components derived from OSPW from natural components found within receiving waters. Synchronous fluorescence spectroscopy also provides a powerful screening technique capable of quickly detecting the presence of aromatic organic acids contained within oil sands naphthenic acid mixtures. Synchronous fluorescence spectroscopy provides diagnostic profiles for OSPW and potentially impacted groundwater that can be compared against reference groundwater and surface water samples. Novel applications of X-ray absorption near edge spectroscopy (XANES) are emerging for speciation of sulphur-containing species (both organic and inorganic components) as well as industrially derived boron-containing species. There is strong potential for an environmental forensics application of XANES for chemical fingerprinting of weathered sulphur-containing species and industrial additives in OSPW.

Ion Mobility Spectrometry-Mass Spectrometry Coupled with Gas-Phase Hydrogen/Deuterium Exchange for Metabolomics Analyses

NASA Astrophysics Data System (ADS)

Maleki, Hossein; Karanji, Ahmad K.; Majuta, Sandra; Maurer, Megan M.; Valentine, Stephen J.

2018-02-01

Ion mobility spectrometry-mass spectrometry (IMS-MS) in combination with gas-phase hydrogen/deuterium exchange (HDX) and collision-induced dissociation (CID) is evaluated as an analytical method for small-molecule standard and mixture characterization. Experiments show that compound ions exhibit unique HDX reactivities that can be used to distinguish different species. Additionally, it is shown that gas-phase HDX kinetics can be exploited to provide even further distinguishing capabilities by using different partial pressures of reagent gas. The relative HDX reactivity of a wide variety of molecules is discussed in light of the various molecular structures. Additionally, hydrogen accessibility scoring (HAS) and HDX kinetics modeling of candidate ( in silico) ion structures is utilized to estimate the relative ion conformer populations giving rise to specific HDX behavior. These data interpretation methods are discussed with a focus on developing predictive tools for HDX behavior. Finally, an example is provided in which ion mobility information is supplemented with HDX reactivity data to aid identification efforts of compounds in a metabolite extract.

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS

PubMed Central

Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

2016-01-01

As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optimizations1 to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor a , an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions. PMID:27896971

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.

PubMed

Kaushik, Gaurav; Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

2017-01-01

As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.

Age-Related Macular Degeneration: Genetics and Biology Coming Together

PubMed Central

Fritsche, Lars G.; Fariss, Robert N.; Stambolian, Dwight; Abecasis, Gonçalo R.; Curcio, Christine A.

2014-01-01

Genetic and genomic studies have enhanced our understanding of complex neurodegenerative diseases that exert a devastating impact on individuals and society. One such disease, age-related macular degeneration (AMD), is a major cause of progressive and debilitating visual impairment. Since the pioneering discovery in 2005 of complement factor H (CFH) as a major AMD susceptibility gene, extensive investigations have confirmed 19 additional genetic risk loci, and more are anticipated. In addition to common variants identified by now-conventional genome-wide association studies, targeted genomic sequencing and exome-chip analyses are uncovering rare variant alleles of high impact. Here, we provide a critical review of the ongoing genetic studies and of common and rare risk variants at a total of 20 susceptibility loci, which together explain 40–60% of the disease heritability but provide limited power for diagnostic testing of disease risk. Identification of these susceptibility loci has begun to untangle the complex biological pathways underlying AMD pathophysiology, pointing to new testable paradigms for treatment. PMID:24773320

Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus

PubMed Central

Harr, Bettina; Karakoc, Emre; Neme, Rafik; Teschke, Meike; Pfeifle, Christine; Pezer, Željka; Babiker, Hiba; Linnenbrink, Miriam; Montero, Inka; Scavetta, Rick; Abai, Mohammad Reza; Molins, Marta Puente; Schlegel, Mathias; Ulrich, Rainer G.; Altmüller, Janine; Franitza, Marek; Büntge, Anna; Künzel, Sven; Tautz, Diethard

2016-01-01

Wild populations of the house mouse (Mus musculus) represent the raw genetic material for the classical inbred strains in biomedical research and are a major model system for evolutionary biology. We provide whole genome sequencing data of individuals representing natural populations of M. m. domesticus (24 individuals from 3 populations), M. m. helgolandicus (3 individuals), M. m. musculus (22 individuals from 3 populations) and M. spretus (8 individuals from one population). We use a single pipeline to map and call variants for these individuals and also include 10 additional individuals of M. m. castaneus for which genomic data are publically available. In addition, RNAseq data were obtained from 10 tissues of up to eight adult individuals from each of the three M. m. domesticus populations for which genomic data were collected. Data and analyses are presented via tracks viewable in the UCSC or IGV genome browsers. We also provide information on available outbred stocks and instructions on how to keep them in the laboratory. PMID:27622383

Stable isotopes in the atmospheric marine boundary layer water vapour over the Atlantic Ocean, 2012–2015

PubMed Central

Benetti, Marion; Steen-Larsen, Hans Christian; Reverdin, Gilles; Sveinbjörnsdóttir, Árný Erla; Aloisi, Giovanni; Berkelhammer, Max B.; Bourlès, Bernard; Bourras, Denis; de Coetlogon, Gaëlle; Cosgrove, Ann; Faber, Anne-Katrine; Grelet, Jacques; Hansen, Steffen Bo; Johnson, Rod; Legoff, Hervé; Martin, Nicolas; Peters, Andrew J.; Popp, Trevor James; Reynaud, Thierry; Winther, Malte

2017-01-01

The water vapour isotopic composition (1H216O, H218O and 1H2H16O) of the Atlantic marine boundary layer has been measured from 5 research vessels between 2012 and 2015. Using laser spectroscopy analysers, measurements have been carried out continuously on samples collected 10–20 meter above sea level. All the datasets have been carefully calibrated against the international VSMOW-SLAP scale following the same protocol to build a homogeneous dataset covering the Atlantic Ocean between 4°S to 63°N. In addition, standard meteorological variables have been measured continuously, including sea surface temperatures using calibrated Thermo-Salinograph for most cruises. All calibrated observations are provided with 15-minute resolution. We also provide 6-hourly data to allow easier comparisons with simulations from the isotope-enabled Global Circulation Models. In addition, backwards trajectories from the HYSPLIT model are supplied every 6-hours for the position of our measurements. PMID:28094798

Analysing how negative emotions emerge and are addressed in veterinary consultations, using the Verona Coding Definitions of Emotional Sequences (VR-CoDES).

PubMed

Vijfhuizen, Malou; Bok, Harold; Matthew, Susan M; Del Piccolo, Lidia; McArthur, Michelle

2017-04-01

To explore the applicability, need for modifications and reliability of the VR-CoDES in a veterinary setting while also gaining a deeper understanding of clients' expressions of negative emotion and how they are addressed by veterinarians. The Verona Coding Definitions of Emotional Sequences for client cues and concerns (VR-CoDES-CC) and health provider responses (VR-CoDES-P) were used to analyse 20 audiotaped veterinary consultations. Inter-rater reliability was established. The applicability of definitions of the VR-CoDES was identified, together with the need for specific modifications to suit veterinary consultations. The VR-CoDES-CC and VR-CoDES-P generally applied to veterinary consultations. Cue and concern reliability was found satisfactory for most types of cues, but not for concerns. Response reliability was satisfactory for explicitness, and for providing and reducing space for further disclosure. Modifications to the original coding system were necessary to accurately reflect the veterinary context and included minor additions to the VR-CoDES-CC. Using minor additions to the VR-CoDES including guilt, reassurance and cost discussions it can be reliably adopted to assess clients' implicit expressions of negative emotion and veterinarians' responses. The modified VR-CoDES could be of great value when combined with existing frameworks used for teaching and researching veterinary communication. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Rural patients' experiences of the open disclosure of adverse events.

PubMed

Piper, Donella; Iedema, Rick; Bower, Kate

2014-08-01

To analyse rural patients' and their families' experiences of open disclosure and offer recommendations to improve disclosure in rural areas. Retrospective qualitative study based on a subset of 13 semistructured, in-depth interviews with rural patients from a larger dataset. The larger data set form a nationwide, multisite, retrospective-qualitative study that included 100 semistructured, in-depth interviews with 119 patients and family members who were involved in high-severity health care incidents and incident disclosure. The larger study is known as the '100 Patient Stories' study. Interviews were transcribed verbatim and analysed by one analyst (D.P.) for recurrent experiences and concerns. Acute care. A sub-set of 13 of the 100 participants from the '100 Patient Stories' study who identified as experiencing an adverse incident in a rural or regional area. Patients' and family members' perceptions and experiences of health care incident disclosure, as expressed in interviews. Rural patients and clinicians experience additional challenges to metropolitan patients and clinicians in their experiences of health care incidents. These additional barriers include: a lack of resources at small hospitals; delays in diagnosis and transfer; distance between services; and a lack of communication between providers. These challenges impact not only upon how patients and their families experience incidents, but also how open disclosure is implemented. This analysis of 13 of the 100 Patient Stories interviews provides guidance to rural health services on how to conduct open disclosure. © 2014 National Rural Health Alliance Inc.

Completing the third person's perspective on patients' involvement in medical decision-making: approaching the full picture.

PubMed

Kasper, Jürgen; Hoffmann, Frauke; Heesen, Christoph; Köpke, Sascha; Geiger, Friedemann

2012-01-01

Shared decision making is based on the idea of cooperation and partnership between patients and doctors. In this concept both parties may initiate and perform specific decision-making steps. However, the common observation-based instruments focus solely on doctors' behaviour. Content and quality of information provided to involve patients in medical decisions are hardly considered in evaluation of SDM. This study investigates the advantages of a revised observer inventory taking into account these aspects. Based on the OPTION scale, a more comprehensive observation-based inventory was developed, additionally considering both the patient-sided indicators for patient involvement and the criteria of evidence-based patient information. The inventory comprises three scales (doctor, patient, doctor-patient dyad) and 15 indicators each. Rater training and re-analyses of 76 consultations previously analysed using the OPTION scale were conducted. Convergent validities were calculated between the observer-based scales and the patients' ratings on the Shared Decision Making Questionnaire, the Decisional Conflict Scale and the Control Preference Scale. Interrater reliabilities of the revised scales were high (r=.87 to .74) and even higher when only the dyadic perspective was coded (.86). The revised inventory provided additional information on the involvement taking place. No substantive correlations were found between observation-based and patients' subjective judgments. The observers' perspective on patient involvement needs to consider patient activities. Inconsistencies of patients' and observers' judgements concerning patient participation need further investigation. Copyright © 2012. Published by Elsevier GmbH.

Sequencing and annotation of mitochondrial genomes from individual parasitic helminths.

PubMed

Jex, Aaron R; Littlewood, D Timothy; Gasser, Robin B

2015-01-01

Mitochondrial (mt) genomics has significant implications in a range of fundamental areas of parasitology, including evolution, systematics, and population genetics as well as explorations of mt biochemistry, physiology, and function. Mt genomes also provide a rich source of markers to aid molecular epidemiological and ecological studies of key parasites. However, there is still a paucity of information on mt genomes for many metazoan organisms, particularly parasitic helminths, which has often related to challenges linked to sequencing from tiny amounts of material. The advent of next-generation sequencing (NGS) technologies has paved the way for low cost, high-throughput mt genomic research, but there have been obstacles, particularly in relation to post-sequencing assembly and analyses of large datasets. In this chapter, we describe protocols for the efficient amplification and sequencing of mt genomes from small portions of individual helminths, and highlight the utility of NGS platforms to expedite mt genomics. In addition, we recommend approaches for manual or semi-automated bioinformatic annotation and analyses to overcome the bioinformatic "bottleneck" to research in this area. Taken together, these approaches have demonstrated applicability to a range of parasites and provide prospects for using complete mt genomic sequence datasets for large-scale molecular systematic and epidemiological studies. In addition, these methods have broader utility and might be readily adapted to a range of other medium-sized molecular regions (i.e., 10-100 kb), including large genomic operons, and other organellar (e.g., plastid) and viral genomes.

Development of unconfined conditions in multi-aquifer flow systems: a case study in the Rajshahi Barind, Bangladesh

NASA Astrophysics Data System (ADS)

Rushton, K. R.; Zaman, M. Asaduz

2017-01-01

Identifying flow processes in multi-aquifer flow systems is a considerable challenge, especially if substantial abstraction occurs. The Rajshahi Barind groundwater flow system in Bangladesh provides an example of the manner in which flow processes can change with time. At some locations there has been a decrease with time in groundwater heads and also in the magnitude of the seasonal fluctuations. This report describes the important stages in a detailed field and modelling study at a specific location in this groundwater flow system. To understand more about the changing conditions, piezometers were constructed in 2015 at different depths but the same location; water levels in these piezometers indicate the formation of an additional water table. Conceptual models are described which show how conditions have changed between the years 2000 and 2015. Following the formation of the additional water table, the aquifer system is conceptualised as two units. A pumping test is described with data collected during both the pumping and recovery phases. Pumping test data for the Lower Unit are analysed using a computational model with estimates of the aquifer parameters; the model also provided estimates of the quantity of water moving from the ground surface, through the Upper Unit, to provide an input to the Lower Unit. The reasons for the substantial changes in the groundwater heads are identified; monitoring of the recently formed additional water table provides a means of testing whether over-abstraction is occurring.

Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection.

PubMed

Careau, Vincent; Wolak, Matthew E; Carter, Patrick A; Garland, Theodore

2013-11-01

Replicated selection experiments provide a powerful way to study how "multiple adaptive solutions" may lead to differences in the quantitative-genetic architecture of selected traits and whether this may translate into differences in the timing at which evolutionary limits are reached. We analyze data from 31 generations (n=17,988) of selection on voluntary wheel running in house mice. The rate of initial response, timing of selection limit, and height of the plateau varied significantly between sexes and among the four selected lines. Analyses of litter size and realized selection differentials seem to rule out counterposing natural selection as a cause of the selection limits. Animal-model analyses showed that although the additive genetic variance was significantly lower in selected than control lines, both before and after the limits, the decrease was not sufficient to explain the limits. Moreover, directional selection promoted a negative covariance between additive and maternal genetic variance over the first 10 generations. These results stress the importance of replication in selection studies of higher-level traits and highlight the fact that long-term predictions of response to selection are not necessarily expected to be linear because of the variable effects of selection on additive genetic variance and maternal effects. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

Bioinformatics on the cloud computing platform Azure.

PubMed

Shanahan, Hugh P; Owen, Anne M; Harrison, Andrew P

2014-01-01

We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development.

Bioinformatics on the Cloud Computing Platform Azure

PubMed Central

Shanahan, Hugh P.; Owen, Anne M.; Harrison, Andrew P.

2014-01-01

We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse a large amount of microarray expression data deposited at the public database ArrayExpress. We provide a walk through to demonstrate explicitly how Azure can be used to perform these analyses in Appendix S1 and we offer a comparison with a local computation. We note that the use of the Platform as a Service (PaaS) offering of Azure can represent a steep learning curve for bioinformatics developers who will usually have a Linux and scripting language background. On the other hand, the presence of an additional set of libraries makes it easier to deploy software in a parallel (scalable) fashion and explicitly manage such a production run with only a few hundred lines of code, most of which can be incorporated from a template. We propose that this environment is best suited for running stable bioinformatics software by users not involved with its development. PMID:25050811

Reference manual for the Thermal Analyst's Help Desk Expert System

NASA Technical Reports Server (NTRS)

Ormsby, Rachel A.

1994-01-01

This document provides technical information and programming guidance for the maintenance and future development of the Thermal Analyst's Help Desk. Help Desk is an expert system that operates within the EXSYSTM expert system shell, and is used to determine first approximations of thermal capacity for spacecraft and instruments. The five analyses supported in Help Desk are: (1) surface area required for a radiating surface, (2) equilibrium temperature of a surface, (3) enclosure temperature and heat loads for a defined position in orbit, (4) enclosure temperature and heat loads over a complete orbit and, (5) selection of appropriate surface properties. The two geometries supported by Help Desk are a single flat plate and a rectangular box enclosure. The technical information includes the mathematical approach and analytical derivations used in the analyses such as: radiation heat balance, view factor calculation, and orbit determination with coordinate transformation. The programming guide for developers describes techniques for enhancement of Help Desk. Examples are provided showing the addition of new features, user interface development and enhancement, and external program interfaces.

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.

PubMed

Buttigieg, Pier Luigi; Ramette, Alban

2014-12-01

The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community. © 2014 The Authors. FEMS Microbiology Ecology published by John Wiley & Sons Ltd on behalf of Federation of European Microbiological Societies.

Evaluating the Utility of Web-Based Consumer Support Tools Using Rough Sets

NASA Astrophysics Data System (ADS)

Maciag, Timothy; Hepting, Daryl H.; Slezak, Dominik; Hilderman, Robert J.

On the Web, many popular e-commerce sites provide consumers with decision support tools to assist them in their commerce-related decision-making. Many consumers will rank the utility of these tools quite highly. Data obtained from web usage mining analyses, which may provide knowledge about a user's online experiences, could help indicate the utility of these tools. This type of analysis could provide insight into whether provided tools are adequately assisting consumers in conducting their online shopping activities or if new or additional enhancements need consideration. Although some research in this regard has been described in previous literature, there is still much that can be done. The authors of this paper hypothesize that a measurement of consumer decision accuracy, i.e. a measurement preferences, could help indicate the utility of these tools. This paper describes a procedure developed towards this goal using elements of rough set theory. The authors evaluated the procedure using two support tools, one based on a tool developed by the US-EPA and the other developed by one of the authors called cogito. Results from the evaluation did provide interesting insights on the utility of both support tools. Although it was shown that the cogito tool obtained slightly higher decision accuracy, both tools could be improved from additional enhancements. Details of the procedure developed and results obtained from the evaluation will be provided. Opportunities for future work are also discussed.

Gene-set and multivariate genome-wide association analysis of oppositional defiant behavior subtypes in attention-deficit/hyperactivity disorder.

PubMed

Aebi, Marcel; van Donkelaar, Marjolein M J; Poelmans, Geert; Buitelaar, Jan K; Sonuga-Barke, Edmund J S; Stringaris, Argyris; Consortium, Image; Faraone, Stephen V; Franke, Barbara; Steinhausen, Hans-Christoph; van Hulzen, Kimm J E

2016-07-01

Oppositional defiant disorder (ODD) is a frequent psychiatric disorder seen in children and adolescents with attention-deficit-hyperactivity disorder (ADHD). ODD is also a common antecedent to both affective disorders and aggressive behaviors. Although the heritability of ODD has been estimated to be around 0.60, there has been little research into the molecular genetics of ODD. The present study examined the association of irritable and defiant/vindictive dimensions and categorical subtypes of ODD (based on latent class analyses) with previously described specific polymorphisms (DRD4 exon3 VNTR, 5-HTTLPR, and seven OXTR SNPs) as well as with dopamine, serotonin, and oxytocin genes and pathways in a clinical sample of children and adolescents with ADHD. In addition, we performed a multivariate genome-wide association study (GWAS) of the aforementioned ODD dimensions and subtypes. Apart from adjusting the analyses for age and sex, we controlled for "parental ability to cope with disruptive behavior." None of the hypothesis-driven analyses revealed a significant association with ODD dimensions and subtypes. Inadequate parenting behavior was significantly associated with all ODD dimensions and subtypes, most strongly with defiant/vindictive behaviors. In addition, the GWAS did not result in genome-wide significant findings but bioinformatics and literature analyses revealed that the proteins encoded by 28 of the 53 top-ranked genes functionally interact in a molecular landscape centered around Beta-catenin signaling and involved in the regulation of neurite outgrowth. Our findings provide new insights into the molecular basis of ODD and inform future genetic studies of oppositional behavior. © 2015 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc. © 2015 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc.

An economic evaluation based on a randomized placebo-controlled trial of varenicline in smokers with cardiovascular disease: results for Belgium, Spain, Portugal, and Italy.

PubMed

Wilson, Koo; Hettle, Robert; Marbaix, Sophie; Diaz Cerezo, Silvia; Ines, Monica; Santoni, Laura; Annemans, Lieven; Prignot, Jacques; Lopez de Sa, Esteban

2012-10-01

An estimated 17.2% of patients continue to smoke following diagnosis of cardiovascular disease (CVD). To reduce the risk of further morbidity or mortality in cardiovascular patients, smoking cessation has been shown to reduce the risk of mortality by 36% and myocardial infarction by 32%. The objective of this study was to evaluate the long-term health and economic consequences of smoking cessation in patients with CVD. Results of a randomized clinical trial comparing varenicline plus counselling vs. placebo plus counselling were extrapolated using a Markov model to simulate the lifetime costs and health consequences of smoking cessation in patients with stable CVD. For the base case, we considered a payer's perspective including direct costs attributed to the healthcare provider, measuring cumulative life years (LY) and quality adjusted life (QALY) years as outcome measures. Secondary analyses were conducted from a societal perspective, evaluating lost productivity due to premature mortality. Sensitivity and subgroup analyses were also undertaken. Results were analysed for Belgium, Spain, Portugal, and Italy. Varenicline plus counselling was associated with a gain in LY and QALY across all countries; relative to placebo plus counselling. From a payer's perspective, incremental cost effectiveness ratios were € 6120 (Belgium), € 5151 (Spain), € 5357 (Portugal), and € 5433 (Italy) per QALY gained. From a societal perspective, varenicline in addition to counselling was less costly than placebo and counselling in all cases. Sensitivity analyses showed little sensitivity in outcomes to model assumptions or uncertainty in model parameters. Varenicline in addition to counselling is cost-effective compared to placebo and counselling in smokers with CVD.

The new guidelines for paternity analysis in Germany-how many STR loci are necessary when investigating duo cases?

PubMed

Poetsch, Micaela; Preusse-Prange, Andrea; Schwark, Thorsten; von Wurmb-Schwark, Nicole

2013-07-01

The requirements in the new German guidelines for paternity analysis have not only changed according to the so-called Gendiagnostikgesetz, the new German law regulating human genetic as well as paternity analyses, but also regarding the minimal number of short tandem repeats (STRs) which should be investigated (15 STRs) and the minimal required average exclusion chance (99.999 %). Even in paternity analyses involving only two people (e.g., father and child or mother and child), this exclusion chance is mandatory. A retrospective analysis of 330 father-child cases from our routine investigations showed in 142 cases (43 %) an individual exclusion chance below 99.999 % when using 15 STRs as required, in our routine work provided by the Powerplex® 16 kit which is reported to have an average exclusion chance of 99.988 %. Therefore, these same 330 father-child pairs were additionally analysed using the Powerplex® 21 kit and 120 of these duos were additionally analysed using the Powerplex® ESX17 kit enabling the analysis of 20 or 16 loci respectively. Now, an individual exclusion chance of more than 99.999 % could be achieved in 95.5 % (Powerplex® 21; calculation without the results of D6S1043), 98.8 % (Powerplex® 21; calculation with the results of D6S1043, using allele frequencies established in this study for a German and a West African population) and 98.3 % (Powerplex® ESX17). These data clearly demonstrate that in duo cases, more than the required 15 STR loci have to be investigated to obtain sufficient results.

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

PubMed Central

Bushley, Kathryn E.; Raja, Rajani; Jaiswal, Pankaj; Cumbie, Jason S.; Nonogaki, Mariko; Boyd, Alexander E.; Owensby, C. Alisha; Knaus, Brian J.; Elser, Justin; Miller, Daniel; Di, Yanming; McPhail, Kerry L.; Spatafora, Joseph W.

2013-01-01

The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of cyclosporin and other secondary metabolites in T. inflatum and related taxa. Phylogenomic analyses reveal previously undetected and complex patterns of homology between the nonribosomal peptide synthetase (NRPS) that encodes for cyclosporin synthetase (simA) and those of other secondary metabolites with activities against insects (e.g., beauvericin, destruxins, etc.), and demonstrate the roles of module duplication and gene fusion in diversification of NRPSs. The secondary metabolite gene cluster responsible for cyclosporin biosynthesis is described. In addition to genes necessary for cyclosporin biosynthesis, it harbors a gene for a cyclophilin, which is a member of a family of immunophilins known to bind cyclosporin. Comparative analyses support a lineage specific origin of the cyclosporin gene cluster rather than horizontal gene transfer from bacteria or other fungi. RNA-Seq transcriptome analyses in a cyclosporin-inducing medium delineate the boundaries of the cyclosporin cluster and reveal high levels of expression of the gene cluster cyclophilin. In medium containing insect hemolymph, weaker but significant upregulation of several genes within the cyclosporin cluster, including the highly expressed cyclophilin gene, was observed. T. inflatum also represents the first reference draft genome of Ophiocordycipitaceae, a third family of insect pathogenic fungi within the fungal order Hypocreales, and supports parallel and qualitatively distinct radiations of insect pathogens. The T. inflatum genome provides additional insight into the evolution and biosynthesis of cyclosporin and lays a foundation for further investigations of the role of secondary metabolite gene clusters and their metabolites in fungal biology. PMID:23818858

Gene‐set and multivariate genome‐wide association analysis of oppositional defiant behavior subtypes in attention‐deficit/hyperactivity disorder

PubMed Central

van Donkelaar, Marjolein M. J.; Poelmans, Geert; Buitelaar, Jan K.; Sonuga‐Barke, Edmund J. S.; Stringaris, Argyris; consortium, IMAGE; Faraone, Stephen V.; Franke, Barbara; Steinhausen, Hans‐Christoph; van Hulzen, Kimm J. E.

2015-01-01

Oppositional defiant disorder (ODD) is a frequent psychiatric disorder seen in children and adolescents with attention‐deficit‐hyperactivity disorder (ADHD). ODD is also a common antecedent to both affective disorders and aggressive behaviors. Although the heritability of ODD has been estimated to be around 0.60, there has been little research into the molecular genetics of ODD. The present study examined the association of irritable and defiant/vindictive dimensions and categorical subtypes of ODD (based on latent class analyses) with previously described specific polymorphisms (DRD4 exon3 VNTR, 5‐HTTLPR, and seven OXTR SNPs) as well as with dopamine, serotonin, and oxytocin genes and pathways in a clinical sample of children and adolescents with ADHD. In addition, we performed a multivariate genome‐wide association study (GWAS) of the aforementioned ODD dimensions and subtypes. Apart from adjusting the analyses for age and sex, we controlled for “parental ability to cope with disruptive behavior.” None of the hypothesis‐driven analyses revealed a significant association with ODD dimensions and subtypes. Inadequate parenting behavior was significantly associated with all ODD dimensions and subtypes, most strongly with defiant/vindictive behaviors. In addition, the GWAS did not result in genome‐wide significant findings but bioinformatics and literature analyses revealed that the proteins encoded by 28 of the 53 top‐ranked genes functionally interact in a molecular landscape centered around Beta‐catenin signaling and involved in the regulation of neurite outgrowth. Our findings provide new insights into the molecular basis of ODD and inform future genetic studies of oppositional behavior. © 2015 The Authors. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics Published by Wiley Periodicals, Inc. PMID:26184070

Effect of nutrient and selective inhibitor amendments on methane oxidation, nitrous oxide production, and key gene presence and expression in landfill cover soils: characterization of the role of methanotrophs, nitrifiers, and denitrifiers.

PubMed

Lee, Sung-Woo; Im, Jeongdae; Dispirito, Alan A; Bodrossy, Levente; Barcelona, Michael J; Semrau, Jeremy D

2009-11-01

Methane and nitrous oxide are both potent greenhouse gasses, with global warming potentials approximately 25 and 298 times that of carbon dioxide. A matrix of soil microcosms was constructed with landfill cover soils collected from the King Highway Landfill in Kalamazoo, Michigan and exposed to geochemical parameters known to affect methane consumption by methanotrophs while also examining their impact on biogenic nitrous oxide production. It was found that relatively dry soils (5% moisture content) along with 15 mg NH (4) (+) (kg soil)(-1) and 0.1 mg phenylacetylene(kg soil)(-1) provided the greatest stimulation of methane oxidation while minimizing nitrous oxide production. Microarray analyses of pmoA showed that the methanotrophic community structure was dominated by Type II organisms, but Type I genera were more evident with the addition of ammonia. When phenylacetylene was added in conjunction with ammonia, the methanotrophic community structure was more similar to that observed in the presence of no amendments. PCR analyses showed the presence of amoA from both ammonia-oxidizing bacteria and archaea, and that the presence of key genes associated with these cells was reduced with the addition of phenylacetylene. Messenger RNA analyses found transcripts of pmoA, but not of mmoX, nirK, norB, or amoA from either ammonia-oxidizing bacteria or archaea. Pure culture analyses showed that methanotrophs could produce significant amounts of nitrous oxide, particularly when expressing the particulate methane monooxygenase (pMMO). Collectively, these data suggest that methanotrophs expressing pMMO played a role in nitrous oxide production in these microcosms.

A preliminary quality of life questionnaire-bronchiectasis: a patient-reported outcome measure for bronchiectasis.

PubMed

Quittner, Alexandra L; Marciel, Kristen K; Salathe, Matthias A; O'Donnell, Anne E; Gotfried, Mark H; Ilowite, Jonathan S; Metersky, Mark L; Flume, Patrick A; Lewis, Sandra A; McKevitt, Matthew; Montgomery, A Bruce; O'Riordan, Thomas G; Barker, Alan F

2014-08-01

The Quality of Life Questionnaire-Bronchiectasis (QOL-B) is the first disease-specific, patient-reported outcome measure for patients with bronchiectasis. Content validity, cognitive testing, responsivity to open-label treatment, and psychometric analyses are presented. Reviews of literature, existing measures, and physician input were used to generate the initial QOL-B. Modifications following preliminary cognitive testing (N = 35 patients with bronchiectasis) generated version (V) 1.0. An open-ended patient interview study (N = 28) provided additional information and was content analyzed to derive saturation matrices, which summarized all disease-related topics mentioned by each participant. This resulted in QOL-B V2.0. Psychometric analyses were carried out using results from an open-label phase 2 trial, in which 89 patients were enrolled and treated with aztreonam for inhalation solution. Responsivity to open-label treatment was observed. Additional analyses generated QOL-B V3.0, with 37 items on eight scales: respiratory symptoms; physical, role, emotional, and social functioning; vitality; health perceptions; and treatment burden. For each scale, scores are standardized on a 0-to-100-point scale; higher scores indicate better health-related quality of life. No total score is calculated. A final cognitive testing study (N = 40) resulted in a minor change to one social functioning scale item (QOL-B V3.1). Content validity, cognitive testing, responsivity to open-label treatment, and initial psychometric analyses supported QOL-B items and structure. This interim QOL-B is a promising tool for evaluating the efficacy of new therapies for patients with bronchiectasis and for measuring symptoms, functioning, and quality of life in these patients on a routine basis. A final psychometric validation study is needed and is forthcoming. ClinicalTrials.gov; No.: NCT00805025; URL: www.clinicaltrials.gov.

Coping in context: sociocultural determinants of responses to sexual harassment.

PubMed

Wasti, S Arzu; Cortina, Lilia M

2002-08-01

The authors investigated coping responses to sexual harassment across 4 samples of working women from 3 cultures and 2 occupational classes. Complete-link cluster analyses provide preliminary support for D. E. Knapp, R. H. Faley, S. E. Ekeberg, and C. L. Z. Dubois's (1997) coping framework, suggesting that avoidance, denial, negotiation, advocacy seeking, and social coping are universal responses to sexual harassment. Further, L. F. Fitzgerald's (1990) internal-external dichotomy appears to capture higher order relationships among coping responses. In addition, regression analyses suggest that Turkish and Hispanic American women engage in more avoidance than Anglo American women, and Hispanic women also use more denial but less advocacy seeking. No differences emerged in social coping. The authors discuss these results in the context of coping theory, individualism-collectivism, power distance, and patriarchal gender norms.

Colorimetric determination of nitrate plus nitrite in water by enzymatic reduction, automated discrete analyzer methods

USGS Publications Warehouse

Patton, Charles J.; Kryskalla, Jennifer R.

2011-01-01

In addition to operational details and performance benchmarks for these new DA-AtNaR2 nitrate + nitrite assays, this report also provides results of interference studies for common inorganic and organic matrix constituents at 1, 10, and 100 times their median concentrations in surface-water and groundwater samples submitted annually to the NWQL for nitrate + nitrite analyses. Paired t-test and Wilcoxon signed-rank statistical analyses of results determined by CFA-CdR methods and DA-AtNaR2 methods indicate that nitrate concentration differences between population means or sign ranks were either statistically equivalent to zero at the 95 percent confidence level (p ≥ 0.05) or analytically equivalent to zero-that is, when p < 0.05, concentration differences between population means or medians were less than MDLs.

Mediation analysis in nursing research: a methodological review.

PubMed

Liu, Jianghong; Ulrich, Connie

2016-12-01

Mediation statistical models help clarify the relationship between independent predictor variables and dependent outcomes of interest by assessing the impact of third variables. This type of statistical analysis is applicable for many clinical nursing research questions, yet its use within nursing remains low. Indeed, mediational analyses may help nurse researchers develop more effective and accurate prevention and treatment programs as well as help bridge the gap between scientific knowledge and clinical practice. In addition, this statistical approach allows nurse researchers to ask - and answer - more meaningful and nuanced questions that extend beyond merely determining whether an outcome occurs. Therefore, the goal of this paper is to provide a brief tutorial on the use of mediational analyses in clinical nursing research by briefly introducing the technique and, through selected empirical examples from the nursing literature, demonstrating its applicability in advancing nursing science.

Reduced-Order Modeling: Cooperative Research and Development at the NASA Langley Research Center

NASA Technical Reports Server (NTRS)

Silva, Walter A.; Beran, Philip S.; Cesnik, Carlos E. S.; Guendel, Randal E.; Kurdila, Andrew; Prazenica, Richard J.; Librescu, Liviu; Marzocca, Piergiovanni; Raveh, Daniella E.

2001-01-01

Cooperative research and development activities at the NASA Langley Research Center (LaRC) involving reduced-order modeling (ROM) techniques are presented. Emphasis is given to reduced-order methods and analyses based on Volterra series representations, although some recent results using Proper Orthogonal Deco in position (POD) are discussed as well. Results are reported for a variety of computational and experimental nonlinear systems to provide clear examples of the use of reduced-order models, particularly within the field of computational aeroelasticity. The need for and the relative performance (speed, accuracy, and robustness) of reduced-order modeling strategies is documented. The development of unsteady aerodynamic state-space models directly from computational fluid dynamics analyses is presented in addition to analytical and experimental identifications of Volterra kernels. Finally, future directions for this research activity are summarized.

California GAMA Special Study: Analysis of Carbamazepine, Oxcarbazepine and Metabolites as Wastewater Tracers in Water Resource Studies

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

Owens, J. E.; Vu, A. K.; Esser, B. K.

2010-08-20

The Groundwater Ambient Monitoring and Assessment (GAMA) Program is a comprehensive groundwater quality monitoring program managed by the California State Water Resources Control Board (SWRCB). The GAMA Special Studies project provides analyses and interpretation of constituents of concern that allow assessment of current groundwater conditions. In addition, the Special Studies project develops analyses that will enhance the monitoring and assessment effort by focusing on specific constituents of concern and water quality parameters, such as disinfection byproducts (DBP), wastewater indicators, and redox conditions, as it relates to irrigation and groundwater management. This study developed a robust analytical method for the quantitationmore » of CBZ, OXC, CBZ-E, CBZ-DiOH, and CBZ-10-OH in wastewater treatement plant (WWTP) effluent and in groundwater in the parts per trillion range.« less

Analyses of fatalities from natural catastrophes in different income groups over time

NASA Astrophysics Data System (ADS)

Grimm, Tobias

2017-04-01

Identifying not only economic and insured losses but also numbers of fatalities from natural catastrophes provides new information on resilience and prevention measures in the countries affected. In this talk, we examine how fatalities from Munich Re's NatCatSERVICE database, caused by natural disasters have developed. In addition to the standard approach based on fatalities by country, we introduced a new measure, "fatalities per million inhabitants", and factored in population development over time. The World Bank definition was used to determine the wealth classification of individual countries. This methodology enables us to compare countries with different population sizes and thus produce an index for humanitarian impact. The analyses are key information on ascertaining whether prevention measures or early-warning systems have in fact reduced the number of fatalities in recent decades (1980-2016).

Landsat 4 and 5 status and results from Thematic Mapper data analyses

NASA Technical Reports Server (NTRS)

Salomonson, V. V.

1984-01-01

Landsat-1, 2, and 3 have functioned successfully well beyond their design lifetimes of one year and provided a very sizable collection of data. On July 16, 1982 with the successful launch of Landsat-4, a second generation of Landsat satellites was introduced. Landsat-4 continues to make available the observational services which had been provided by the Multispectral Scanner (MSS) on Landsats 1-3. In addition, the new satellite is provided with an improved observational capability which is based on a utilization of the Thematic Mapper (TM). The system status (March 1984) of Landsat-4 is considered along with an evaluation of the MSS, and a description of the design and performance of the TM. Attention is also given to the satellite Landsat-5, which was launched successfully on March 1, 1984, taking into account design modifications leading to improved performance and some scenes provided by the new spacecraft.

OdorMapComparer: an application for quantitative analyses and comparisons of fMRI brain odor maps.

PubMed

Liu, Nian; Xu, Fuqiang; Miller, Perry L; Shepherd, Gordon M

2007-01-01

Brain odor maps are reconstructed flat images that describe the spatial activity patterns in the glomerular layer of the olfactory bulbs in animals exposed to different odor stimuli. We have developed a software application, OdorMapComparer, to carry out quantitative analyses and comparisons of the fMRI odor maps. This application is an open-source window program that first loads two odor map images being compared. It allows image transformations including scaling, flipping, rotating, and warping so that the two images can be appropriately aligned to each other. It performs simple subtraction, addition, and average of signals in the two images. It also provides comparative statistics including the normalized correlation (NC) and spatial correlation coefficient. Experimental studies showed that the rodent fMRI odor maps for aliphatic aldehydes displayed spatial activity patterns that are similar in gross outlines but somewhat different in specific subregions. Analyses with OdorMapComparer indicate that the similarity between odor maps decreases with increasing difference in the length of carbon chains. For example, the map of butanal is more closely related to that of pentanal (with a NC = 0.617) than to that of octanal (NC = 0.082), which is consistent with animal behavioral studies. The study also indicates that fMRI odor maps are statistically odor-specific and repeatable across both the intra- and intersubject trials. OdorMapComparer thus provides a tool for quantitative, statistical analyses and comparisons of fMRI odor maps in a fashion that is integrated with the overall odor mapping techniques.

An artifact caused by undersampling optimal trees in supermatrix analyses of locally sampled characters.

PubMed

Simmons, Mark P; Goloboff, Pablo A

2013-10-01

Empirical and simulated examples are used to demonstrate an artifact caused by undersampling optimal trees in data matrices that consist mostly or entirely of locally sampled (as opposed to globally, for most or all terminals) characters. The artifact is that unsupported clades consisting entirely of terminals scored for the same locally sampled partition may be resolved and assigned high resampling support-despite their being properly unsupported (i.e., not resolved in the strict consensus of all optimal trees). This artifact occurs despite application of random-addition sequences for stepwise terminal addition. The artifact is not necessarily obviated with thorough conventional branch swapping methods (even tree-bisection-reconnection) when just a single tree is held, as is sometimes implemented in parsimony bootstrap pseudoreplicates, and in every GARLI, PhyML, and RAxML pseudoreplicate and search for the most likely tree for the matrix as a whole. Hence GARLI, RAxML, and PhyML-based likelihood results require extra scrutiny, particularly when they provide high resolution and support for clades that are entirely unsupported by methods that perform more thorough searches, as in most parsimony analyses. Copyright © 2013 Elsevier Inc. All rights reserved.

Metaproteomics of complex microbial communities in biogas plants

PubMed Central

Heyer, Robert; Kohrs, Fabian; Reichl, Udo; Benndorf, Dirk

2015-01-01

Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed. PMID:25874383

On the nexus of air pollution and health expenditures: new empirical evidence.

PubMed

Blázquez-Fernández, Carla; Cantarero-Prieto, David; Pascual-Sáez, Marta

2018-05-21

To analyse the impact of per capita income and environmental air quality variables on health expenditure determinants. In this study, we analyse the relationship between air pollution and health expenditure in 29 OECD countries over the period 1995-2014. In addition, we test whether our findings differ between countries with higher or lower incomes. The econometric results show that per capita income has a positive effect on health expenditure, but is not as statistically significant as expected when lag-time is incorporated. In addition, an anchorage effect is observed, which implies that about 80%-90% of previous expenditure explain current expenditure. Our empirical results are quite consistent between groups and when compared with the full sample. Nevertheless, there appear to be some differences when broken down by financing scheme (total, public, and private). Overall, our findings could be used to clarify the appropriate health expenditure level or to obtain better environmental quality and social well-being. That is, empirical support is provided on how health management and policy makers should include more considerations for the use of cleaner fuels in developed countries. Copyright © 2018 SESPAS. Publicado por Elsevier España, S.L.U. All rights reserved.

Psychometric assessment of the craving to tan questionnaire.

PubMed

Ashrafioun, Lisham; Bonar, Erin E

2015-01-01

Researchers and clinicians suggest that excessive tanning may be a behavioral addiction. Given the significance of craving in substance use, craving may be a useful construct to assess in those who tan. We designed this study to assess the psychometric properties of an alcohol craving measure adapted to measure past-week craving to tan. Undergraduate students (n = 421) who reported past-month tanning completed a battery of questionnaires that assessed demographics, tanning-related characteristics, and psychopathology, in addition to the Craving to Tan Questionnaire (CTQ). Analyses provided support for a single factor CTQ with good internal consistency, construct validity and convergent validity. CTQ scores were significantly higher among problematic versus non-problematic and dependent versus non-dependent tanners. CTQ scores were also associated with several tanning-related characteristics, such money spent on tanning in a typical month, frequency of tanning, and frequency of tanning-related problems. Additional analyses found that past-week craving to tan was significantly associated with greater obsessive compulsive and body dysmorphic symptoms. It may be useful in clinical settings to identify those experiencing problems with tanning and in research to further clarify the conceptualization of addiction-like tanning. However, the CTQ needs further evaluation.

A new framework for analysing automated acoustic species-detection data: occupancy estimation and optimization of recordings post-processing

USGS Publications Warehouse

Chambert, Thierry A.; Waddle, J. Hardin; Miller, David A.W.; Walls, Susan; Nichols, James D.

2018-01-01

The development and use of automated species-detection technologies, such as acoustic recorders, for monitoring wildlife are rapidly expanding. Automated classification algorithms provide a cost- and time-effective means to process information-rich data, but often at the cost of additional detection errors. Appropriate methods are necessary to analyse such data while dealing with the different types of detection errors.We developed a hierarchical modelling framework for estimating species occupancy from automated species-detection data. We explore design and optimization of data post-processing procedures to account for detection errors and generate accurate estimates. Our proposed method accounts for both imperfect detection and false positive errors and utilizes information about both occurrence and abundance of detections to improve estimation.Using simulations, we show that our method provides much more accurate estimates than models ignoring the abundance of detections. The same findings are reached when we apply the methods to two real datasets on North American frogs surveyed with acoustic recorders.When false positives occur, estimator accuracy can be improved when a subset of detections produced by the classification algorithm is post-validated by a human observer. We use simulations to investigate the relationship between accuracy and effort spent on post-validation, and found that very accurate occupancy estimates can be obtained with as little as 1% of data being validated.Automated monitoring of wildlife provides opportunity and challenges. Our methods for analysing automated species-detection data help to meet key challenges unique to these data and will prove useful for many wildlife monitoring programs.

ETE: a python Environment for Tree Exploration.

PubMed

Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

2010-01-13

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

A cross-sectional study on person-centred communication in the care of older people: the COMHOME study protocol.

PubMed

Hafskjold, Linda; Sundler, Annelie J; Holmström, Inger K; Sundling, Vibeke; van Dulmen, Sandra; Eide, Hilde

2015-04-15

This paper presents an international cross-sectional study on person-centred communication with older people receiving healthcare (COMHOME). Person-centred care relies on effective communication, but few studies have explored this with a specific focus on older people. The main aim of the COMHOME study is to generate knowledge on person-centred communication with older people (>65 years) in home healthcare services, radiographic and optometric practice. This study will explore the communication between care providers and older persons in home care services. Home healthcare visits will be audiorecorded (n=500) in Norway, the Netherlands and Sweden. Analyses will be performed with the Verona Coding Definitions for Emotional Sequences (VR-CoDES), the Roter Interaction Analysis System (RIAS) and qualitative methods. The content of the communication, communicative challenging situations as well as empathy, power distance, decision-making, preservation of dignity and respect will be explored. In Norway, an additional 100 encounters, 50 in optometric practice (video recorded) and 50 in radiographic practice (audiorecorded), will be analysed. Furthermore, healthcare providers' self-reported communication skills, empathy, mindfulness and emotional intelligence in relation to observed person-centred communication skills will be assessed using well-established standardised instruments. Depending on national legislation, approval of either the central ethical committees (eg, nation or university), the national data protection officials or the local ethical committees (eg, units of home healthcare) was obtained. Study findings will be disseminated widely through peer-reviewed publications and conference presentations. The research findings will add knowledge to improve services provided to this vulnerable group of patients. Additionally, the findings will underpin a training programme for healthcare students and care providers focusing on communication with older people. 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.

Surgical and medical emergencies on board European aircraft: a retrospective study of 10189 cases.

PubMed

Sand, Michael; Bechara, Falk-Georges; Sand, Daniel; Mann, Benno

2009-01-01

In-flight medical and surgical emergencies (IMEs) onboard commercial aircrafts occur quite commonly. However, little epidemiological research exists concerning these incidents. Thirty-two European airlines were asked to provide anonymous data on medical flight reports of IMEs for the years 2002 to 2007. The total number of incidents was correlated to revenue passenger kilometers (rpk). Additionally, on-board births and deaths, flight diversions, flight routes (continental/intercontinental) and involvement of a physician or medical professional in providing therapy were analysed. Only four airlines, of which two participated in this study, were able to provide the necessary data. A total of 10,189 cases of IMEs were analysed. Syncope was the most common medical condition reported (5307 cases, 53.5%) followed by gastrointestinal disorders (926 cases, 8.9%) and cardiac conditions (509 cases, 4.9%). The most common surgical conditions were thrombosis (47 cases, 0.5%) and appendicitis (27 cases, 0.25%). In 2.8% of all IMEs, an aircraft diversion was performed. In 86% of cases, a physician or medical professional was involved in providing therapy. A mean (standard deviation) of 14 (+/- 2.3, 10.8 to 16.6 interquartile range) IMEs per billion rpk was calculated. The study demonstrates that although aviation is regulated by a variety of national and international laws, standardised documentation of IMEs is inadequate and needs further development.

Surgical and medical emergencies on board European aircraft: a retrospective study of 10189 cases

PubMed Central

Sand, Michael; Bechara, Falk-Georges; Sand, Daniel; Mann, Benno

2009-01-01

Introduction In-flight medical and surgical emergencies (IMEs) onboard commercial aircrafts occur quite commonly. However, little epidemiological research exists concerning these incidents. Methods Thirty-two European airlines were asked to provide anonymous data on medical flight reports of IMEs for the years 2002 to 2007. The total number of incidents was correlated to revenue passenger kilometers (rpk). Additionally, on-board births and deaths, flight diversions, flight routes (continental/intercontinental) and involvement of a physician or medical professional in providing therapy were analysed. Results Only four airlines, of which two participated in this study, were able to provide the necessary data. A total of 10,189 cases of IMEs were analysed. Syncope was the most common medical condition reported (5307 cases, 53.5%) followed by gastrointestinal disorders (926 cases, 8.9%) and cardiac conditions (509 cases, 4.9%). The most common surgical conditions were thrombosis (47 cases, 0.5%) and appendicitis (27 cases, 0.25%). In 2.8% of all IMEs, an aircraft diversion was performed. In 86% of cases, a physician or medical professional was involved in providing therapy. A mean (standard deviation) of 14 (+/- 2.3, 10.8 to 16.6 interquartile range) IMEs per billion rpk was calculated. Conclusions The study demonstrates that although aviation is regulated by a variety of national and international laws, standardised documentation of IMEs is inadequate and needs further development. PMID:19154581

GC-MS and LC-MS analysis of nerve agents in body fluids: intra-laboratory verification test using spiked plasma and urine samples.

PubMed

Koller, Marianne; Becker, Christian; Thiermann, Horst; Worek, Franz

2010-05-15

The purpose of this study was to check the applicability of different analytical methods for the identification of unknown nerve agents in human body fluids. Plasma and urine samples were spiked with nerve agents (plasma) or with their metabolites (urine) or were left blank. Seven random samples (35% of all samples) were selected for the verification test. Plasma was worked up for unchanged nerve agents and for regenerated nerve agents after fluoride-induced reactivation of nerve agent-inhibited butyrylcholinesterase. Both extracts were analysed by GC-MS. Metabolites were extracted from plasma and urine, respectively, and were analysed by LC-MS. The urinary metabolites and two blank samples could be identified without further measurements, plasma metabolites and blanks were identified in six of seven samples. The analysis of unchanged nerve agent provided five agents/blanks and the sixth agent after further investigation. The determination of the regenerated agents also provided only five clear findings during the first screening because of a rather noisy baseline. Therefore, the sample preparation was extended by a size exclusion step performed before addition of fluoride which visibly reduced baseline noise and thus improved identification of the two missing agents. The test clearly showed that verification should be performed by analysing more than one biomarker to ensure identification of the agent(s). Copyright (c) 2010 Elsevier B.V. All rights reserved.

The Efficacy of Cognitive Behavioral Therapy: A Review of Meta-analyses

PubMed Central

Hofmann, Stefan G.; Asnaani, Anu; Vonk, Imke J.J.; Sawyer, Alice T.; Fang, Angela

2012-01-01

Cognitive behavioral therapy (CBT) refers to a popular therapeutic approach that has been applied to a variety of problems. The goal of this review was to provide a comprehensive survey of meta-analyses examining the efficacy of CBT. We identified 269 meta-analytic studies and reviewed of those a representative sample of 106 meta-analyses examining CBT for the following problems: substance use disorder, schizophrenia and other psychotic disorders, depression and dysthymia, bipolar disorder, anxiety disorders, somatoform disorders, eating disorders, insomnia, personality disorders, anger and aggression, criminal behaviors, general stress, distress due to general medical conditions, chronic pain and fatigue, distress related to pregnancy complications and female hormonal conditions. Additional meta-analytic reviews examined the efficacy of CBT for various problems in children and elderly adults. The strongest support exists for CBT of anxiety disorders, somatoform disorders, bulimia, anger control problems, and general stress. Eleven studies compared response rates between CBT and other treatments or control conditions. CBT showed higher response rates than the comparison conditions in 7 of these reviews and only one review reported that CBT had lower response rates than comparison treatments. In general, the evidence-base of CBT is very strong. However, additional research is needed to examine the efficacy of CBT for randomized-controlled studies. Moreover, except for children and elderly populations, no meta-analytic studies of CBT have been reported on specific subgroups, such as ethnic minorities and low income samples. PMID:23459093

Seismic response of Pacific Park Plaza. I. Data and preliminary analysis

USGS Publications Warehouse

Celebi, M.; Safak, E.

1992-01-01

The objective of this paper is to present analyses of a set of acceleration response records obtained during the October 17, 1989 Loma Prieta earthquake (Ms = 7.1) from the 30-story, three-winged, ductile moment-resistant reinforced-concrete-framed Pacific Park Plaza Building, located in Emeryville, east of San Francisco, Calif. The building was constructed in 1983, and instrumented in 1985 with 21 channels of synchronized uniaxial accelerometers deployed throughout the structure, and three channels of accelerometers located at free-field outside on the north side of the building, all connected to a central recording system. In addition, a triaxial strong-motion accelerograph is deployed at free-field on the south side of the building. The predominant response modes of the building and the associated frequencies at approximately 0.4 Hz and 1.0 Hz are identified visually from the unprocessed records, and also from Fourier amplitude spectra of the processed records, which, as expected, reveal significant torsional motion. In addition, the response spectra of the free-field and basement motions are very similar. These spectra show that significant structural resonances at higher modes influence both the ground level and the free-field motions, thus rising the question as to the definition of free-field motion, at least at this site. This part of the paper includes the preliminary analyses of the data acquired from this building. Part 2 of the paper provides detailed analyses of the data using system identification techniques.

iDNA screening: Disease vectors as vertebrate samplers.

PubMed

Kocher, Arthur; de Thoisy, Benoit; Catzeflis, François; Valière, Sophie; Bañuls, Anne-Laure; Murienne, Jérôme

2017-11-01

In the current context of global change and human-induced biodiversity decline, there is an urgent need for developing sampling approaches able to accurately describe the state of biodiversity. Traditional surveys of vertebrate fauna involve time-consuming and skill-demanding field methods. Recently, the use of DNA derived from invertebrate parasites (leeches and blowflies) was suggested as a new tool for vertebrate diversity assessment. Bloodmeal analyses of arthropod disease vectors have long been performed to describe their feeding behaviour, for epidemiological purposes. On the other hand, this existing expertise has not yet been applied to investigate vertebrate fauna per se. Here, we evaluate the usefulness of hematophagous dipterans as vertebrate samplers. Blood-fed sand flies and mosquitoes were collected in Amazonian forest sites and analysed using high-throughput sequencing of short mitochondrial markers. Bloodmeal identifications highlighted contrasting ecological features and feeding behaviour among dipteran species, which allowed unveiling arboreal and terrestrial mammals of various body size, as well as birds, lizards and amphibians. Additionally, lower vertebrate diversity was found in sites undergoing higher levels of human-induced perturbation. These results suggest that, in addition to providing precious information on disease vector host use, dipteran bloodmeal analyses may represent a useful tool in the study of vertebrate communities. Although further effort is required to validate the approach and consider its application to large-scale studies, this first work opens up promising perspectives for biodiversity monitoring and eco-epidemiology. © 2017 John Wiley & Sons Ltd.

Multielement geochemical dataset of surficial materials for the northern Great Basin

USGS Publications Warehouse

Coombs, Mary Jane; Kotlyar, Boris B.; Ludington, Steve; Folger, Helen W.; Mossotti, Victor G.

2002-01-01

This report presents geochemical data generated during mineral and environmental assessments for the Bureau of Land Management in northern Nevada, northeastern California, southeastern Oregon, and southwestern Idaho, along with metadata and map representations of selected elements. The dataset presented here is a compilation of chemical analyses of over 10,200 stream-sediment and soil samples originally collected during the National Uranium Resource Evaluation's (NURE) Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) program of the Department of Energy and its predecessors and reanalyzed to support a series of mineral-resource assessments by the U.S. Geological Survey (USGS). The dataset also includes the analyses of additional samples collected by the USGS in 1992. The sample sites are in southeastern Oregon, southwestern Idaho, northeastern California, and, primarily, in northern Nevada. These samples were collected from 1977 to 1983, before the development of most of the present-day large-scale mining infrastructure in northern Nevada. As such, these data may serve as an important baseline for current and future geoenvironmental studies. Largely because of the very diverse analytical methods used by the NURE HSSR program, the original NURE analyses in this area yielded little useful geochemical information. The Humboldt, Malheur-Jordan-Andrews, and Winnemucca-Surprise studies were designed to provide useful geochemical data via improved analytical methods (lower detection levels and higher precision) and, in the Malheur-Jordan-Andrews and Winnemucca Surprise areas, to collect additional stream-sediment samples to increase sampling coverage. The data are provided in *.xls (Microsoft Excel) and *.csv (comma-separated-value) format. We also present graphically 35 elements, interpolated ("gridded") in a geographic information system (GIS) and overlain by major geologic trends, so that users may view the variation in elemental concentrations over the landscape and reach their own conclusions regarding correlation among geochemistry, geologic features, and known mineral deposits. Quality-control issues are discussed for the grids and data.

A simulation-based approach for estimating premining water quality: Red Mountain Creek, Colorado

USGS Publications Warehouse

Runkel, Robert L.; Kimball, Briant A; Walton-Day, Katherine; Verplanck, Philip L.

2007-01-01

Regulatory agencies are often charged with the task of setting site-specific numeric water quality standards for impaired streams. This task is particularly difficult for streams draining highly mineralized watersheds with past mining activity. Baseline water quality data obtained prior to mining are often non-existent and application of generic water quality standards developed for unmineralized watersheds is suspect given the geology of most watersheds affected by mining. Various approaches have been used to estimate premining conditions, but none of the existing approaches rigorously consider the physical and geochemical processes that ultimately determine instream water quality. An approach based on simulation modeling is therefore proposed herein. The approach utilizes synoptic data that provide spatially-detailed profiles of concentration, streamflow, and constituent load along the study reach. This field data set is used to calibrate a reactive stream transport model that considers the suite of physical and geochemical processes that affect constituent concentrations during instream transport. A key input to the model is the quality and quantity of waters entering the study reach. This input is based on chemical analyses available from synoptic sampling and observed increases in streamflow along the study reach. Given the calibrated model, additional simulations are conducted to estimate premining conditions. In these simulations, the chemistry of mining-affected sources is replaced with the chemistry of waters that are thought to be unaffected by mining (proximal, premining analogues). The resultant simulations provide estimates of premining water quality that reflect both the reduced loads that were present prior to mining and the processes that affect these loads as they are transported downstream. This simulation-based approach is demonstrated using data from Red Mountain Creek, Colorado, a small stream draining a heavily-mined watershed. Model application to the premining problem for Red Mountain Creek is based on limited field reconnaissance and chemical analyses; additional field work and analyses may be needed to develop definitive, quantitative estimates of premining water quality.

Five new species of grass cicadas in the genus Graminitigrina (Hemiptera: Cicadidae: Cicadettinae: Cicadettini) from Queensland and Northern Territory, Australia: comparative morphology, songs, behaviour and distributions.

PubMed

Ewart, A; Popple, L W; Hill, K B R

2017-02-07

Five new species of small grass cicadas belonging to the genus Graminitigrina Ewart and Marques are described, together with detailed analyses of their calling songs. Four species occur in Queensland, G. aurora n. sp. from eastern central Queensland near Fairbairn Dam; G. flindensis n. sp. from central Queensland between Hughenden northwards for at least 108 km; G. einasleighi n. sp. from near The Lynd, Einasleigh River, northeastern Queensland; G. selwynensis n. sp. from the Selwyn Range, northwestern Queensland, at locations about 40 km east of Mount Isa and 25 km southwest of Cloncurry, this latter here transferred from G. bowensis Ewart and Marques; G. uluruensis n. sp. from Uluru and the Olgas in southwestern Northern Territory, extending northwards through Tennant Creek and apparently further north to near Larrimah, a linear distance of approximately 1190 km. These new species bring the known Graminitigrina species to ten, all superficially similar in colour and morphology. A key to male specimens is provided for the 10 species. Additional distribution records and additional aural song recordings are presented for G. bowensis, these requiring the transfer of populations previously identified as G. bowensis from Croydon and Georgetown, northern Gulf region, to G. karumbae Ewart and Marques. Detailed comparative analyses, including NMDS analyses, of the songs of all 10 species are provided, which show that the song parameters are appropriate to distinguish the species, although some partial overlap is noted in the waveform plots between the songs of G. uluruensis n. sp. and G. flindensis n. sp. Regional variations of song parameters are noted in the calling songs of most of the species described.

Contour plot assessment of existing meta-analyses confirms robust association of statin use and acute kidney injury risk.

PubMed

Chevance, Aurélie; Schuster, Tibor; Steele, Russell; Ternès, Nils; Platt, Robert W

2015-10-01

Robustness of an existing meta-analysis can justify decisions on whether to conduct an additional study addressing the same research question. We illustrate the graphical assessment of the potential impact of an additional study on an existing meta-analysis using published data on statin use and the risk of acute kidney injury. A previously proposed graphical augmentation approach is used to assess the sensitivity of the current test and heterogeneity statistics extracted from existing meta-analysis data. In addition, we extended the graphical augmentation approach to assess potential changes in the pooled effect estimate after updating a current meta-analysis and applied the three graphical contour definitions to data from meta-analyses on statin use and acute kidney injury risk. In the considered example data, the pooled effect estimates and heterogeneity indices demonstrated to be considerably robust to the addition of a future study. Supportingly, for some previously inconclusive meta-analyses, a study update might yield statistically significant kidney injury risk increase associated with higher statin exposure. The illustrated contour approach should become a standard tool for the assessment of the robustness of meta-analyses. It can guide decisions on whether to conduct additional studies addressing a relevant research question. Copyright © 2015 Elsevier Inc. All rights reserved.

Tripal: a construction toolkit for online genome databases.

PubMed

Ficklin, Stephen P; Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net.

Tripal: a construction toolkit for online genome databases

PubMed Central

Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E.; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E.; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net PMID:21959868

An exploration of screening protocols for intimate partner violence in healthcare facilities: a qualitative study.

PubMed

Williams, Jessica R; Halstead, Valerie; Salani, Deborah; Koermer, Natasha

2017-08-01

Explore different methods by which intimate partner violence screening practices are implemented in clinic and emergency settings and better understand barriers and facilitators. Healthcare visits provide an opportunity for providers to identify and provide assistance to victims of intimate partner violence. However, wide variation exists in the implementation of screening and response protocols. In addition, providers experience barriers and facilitators to intimate partner violence screening and response. A comprehensive understanding of these factors is necessary to improve the role that providers play in detection and intervention of intimate partner violence. Qualitative descriptive research design. Sixteen healthcare facilities were recruited from a large metropolitan area in the USA. Data were collected through semi-structured, in-depth interviews with individuals knowledgeable about intimate partner violence screening and response within their facility. Data were analysed using directive content analysis. Major themes and patterns concerning intimate partner violence screening and response were identified within the following areas: procedural characteristics, barriers, facilitators and additional needs. Patient-provider communication and operational/facility characteristics emerged as critical aspects that impact the successful implementation of intimate partner violence screening and response programmes. Differences were found between clinic and emergency settings stemming from variations in health delivery models. Results provide important information on how healthcare facilities implement intimate partner violence screening and response, suggestions for practice improvement and directions for future interventions. Additional guidance is needed to ensure intimate partner violence identification, and response procedures are effective and tailored to needs of patients, providers and the facility. Nurses are in a strategic position to play a pivotal role in identification of and response to intimate partner violence. It is essential that nurses are cognizant of this, and understand the actions they can take to assist patients who have been victims of intimate partner violence. Recommendations on how to do this are provided. © 2016 John Wiley & Sons Ltd.

The Presentation of Animals in English as an Additional Language Coursebooks

ERIC Educational Resources Information Center

Jacobs, George M.; Jiexin, Teh; Michael, Joyce J.

2016-01-01

Education materials can be analysed in many ways. The current study analysed EAL (English as an Additional Language) coursebooks as to the presentation of nonhuman animals in the books. The study examined 22 EAL coursebooks. The research looked at the percentage of activities that contained animals in the coursebooks, what types of animals were…

Implementation of Head Start Planned Variation: 1970-1971. Part II.

ERIC Educational Resources Information Center

Lukas, Carol Van Deusen; Wohlleb, Cynthia

This volume of appendices is Part II of a study of program implementation in 12 models of Head Start Planned Variation. It presents details of the data analysis, copies of data collection instruments, and additional analyses and statistics. The appendices are: (A) Analysis of Variance Designs, (B) Copies of Instruments, (C) Additional Analyses,…

The GSFC NASTRAN thermal analyzer new capabilities

NASA Technical Reports Server (NTRS)

Lee, H. P.; Harder, R. L.

1976-01-01

An overview of four analysis capabilities, which developed and integrated into the NASTRAN Thermal Analyzer, is given. To broaden the scope of applications, these additions provide the NTA users with the following capabilities: (1) simulating a thermal louver as a means of the passive thermal control, (2) simulating a fluid loop for transporting energy as a means of the active thermal control, (3) condensing a large sized finite element model for an efficient transient thermal analysis, and (4) entering multiple boundary condition sets in a single submission for execution in steady state thermal analyses.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

PubMed

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Megastudies, crowdsourcing, and large datasets in psycholinguistics: An overview of recent developments.

PubMed

Keuleers, Emmanuel; Balota, David A

2015-01-01

This paper introduces and summarizes the special issue on megastudies, crowdsourcing, and large datasets in psycholinguistics. We provide a brief historical overview and show how the papers in this issue have extended the field by compiling new databases and making important theoretical contributions. In addition, we discuss several studies that use text corpora to build distributional semantic models to tackle various interesting problems in psycholinguistics. Finally, as is the case across the papers, we highlight some methodological issues that are brought forth via the analyses of such datasets.

HTGR technology economic/ business analysis and trade studies impacts. Impacts of HTGR commericialization on the U.S. economy

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

Silady, Fred

The approach to this task was to initially review the 2012 Business Plan and supporting analyses for the above impacts. With that understanding as a base, the Business Plan impacts are updated in terms of the GDP and job creation as a result of additional studies and inputs such as the revised market assessment from Task 1.1. For the impacts on U.S. competitiveness, the NGNP Industry Alliance team members have been utilized to provide inputs on supplier infrastructure development and on vendor capability.

Handling qualities criteria for the space shuttle orbiter during the terminal phase of flight

NASA Technical Reports Server (NTRS)

Stapleford, R. L.; Klein, R. H.; Hob, R. H.

1972-01-01

It was found that large portions of the military handling qualities specification are directly applicable. However a number of additional and substitute criteria are recommended for areas not covered or inadequately covered in the military specification. Supporting pilot/vehicle analyses and simulation experiments were conducted and are described. Results are also presented of analytical and simulator evaluations of three specific interim Orbiter designs which provided a test of the proposed handling qualities criteria. The correlations between the analytical and experimental evaluations were generally excellent.

OCLC for the hospital library: the justification plan for hospital administration.

PubMed

Allen, C W; Branson, J R

1982-07-01

This paper delineates the necessary steps to provide hospital administrators with the information needed to evaluate an automated system, OCLC, for addition to the medical library. Based on experience at the Norton-Children's Hospitals, included are: (1) cost analyses of present technical processing systems and cost comparisons with OCLC; (2) delineation of start-up costs for installing OCLC; (3) budgetary requirements for 1981; (4) the impact of automation on library systems, personnel, and services; (5) potential as a shared service; and (6) preparation of the proposal for administrative review.

OCLC for the hospital library: the justification plan for hospital administration.

PubMed Central

Allen, C W; Branson, J R

1982-01-01

This paper delineates the necessary steps to provide hospital administrators with the information needed to evaluate an automated system, OCLC, for addition to the medical library. Based on experience at the Norton-Children's Hospitals, included are: (1) cost analyses of present technical processing systems and cost comparisons with OCLC; (2) delineation of start-up costs for installing OCLC; (3) budgetary requirements for 1981; (4) the impact of automation on library systems, personnel, and services; (5) potential as a shared service; and (6) preparation of the proposal for administrative review. PMID:7116018

Energy-efficient electric motors study

NASA Astrophysics Data System (ADS)

1981-03-01

A survey conducted of purchasers of integral horsepower polyphase motors measured current knowledge of and awareness of energy efficient motors, decision making criteria, information sources, purchase and usage patterns, and related factors. The data obtained were used for the electric motor market penetration analysis. Additionally, a telephone survey was made. The study also provides analyses of distribution channels, commercialization constraints, and the impacts of government programs and rising energy prices. Study findings, conclusions, and recommendations are presented. Sample questionnaires and copies of letters to respondents are presented in appendices as well as descriptions of the methods used.

Recollimation shocks in the relativistic outflows of active galactic nuclei. Doctoral Thesis Award Lecture 2014

NASA Astrophysics Data System (ADS)

Fromm, C. M.

2015-06-01

We analysed the single-dish radio light curves of the blazar CTA 102 during its major flare around April 2006. The modelling of these data revealed a possible travelling shock-recollimation shock interaction during the flare. To verify this hypothesis, we used multi-epoch and multi-frequency very-long baseline interferometry (VLBI) observations and performed a detailed kinematic and spectral analysis. The results confirmed the hypothesis of a shock-shock interaction causing the 2006 radio flare and provided indications for additional recollimation shocks farther downstream.

In situ spectroradiometric quantification of ERTS data. [Prescott and Phoenix, Arizona

NASA Technical Reports Server (NTRS)

Yost, E. F. (Principal Investigator)

1975-01-01

The author has identified the following significant results. Analyses of ERTS-1 photographic data were made to quantitatively relate ground reflectance measurements to photometric characteristics of the images. Digital image processing of photographic data resulted in a nomograph to correct for atmospheric effects over arid terrain. Optimum processing techniques to derive maximum geologic information from desert areas were established. Additive color techniques to provide quantitative measurements of surface water between different orbits were developed which were accepted as the standard flood mapping techniques using ERTS.

Infusing Reliability Techniques into Software Safety Analysis

NASA Technical Reports Server (NTRS)

Shi, Ying

2015-01-01

Software safety analysis for a large software intensive system is always a challenge. Software safety practitioners need to ensure that software related hazards are completely identified, controlled, and tracked. This paper discusses in detail how to incorporate the traditional reliability techniques into the entire software safety analysis process. In addition, this paper addresses how information can be effectively shared between the various practitioners involved in the software safety analyses. The author has successfully applied the approach to several aerospace applications. Examples are provided to illustrate the key steps of the proposed approach.

Nuclear techniques for the on-line bulk analysis of carbon in coal-fired power stations.

PubMed

Sowerby, B D

2009-09-01

Carbon trading schemes usually require large emitters of CO(2), such as coal-fired power stations, to monitor, report and be audited on their CO(2) emissions. The emission price provides a significant additional incentive for power stations to improve efficiency. In the present paper, previous work on the bulk determination of carbon in coal is reviewed and assessed. The most favourable method is that based on neutron inelastic scattering. The potential role of on-line carbon analysers in improving boiler efficiency and in carbon accounting is discussed.

Evidence for the Continuous Latent Structure of Mania in the Epidemiologic Catchment Area from Multiple Latent Structure and Construct Validation Methodologies

PubMed Central

Prisciandaro, James J.; Roberts, John E.

2011-01-01

Background Although psychiatric diagnostic systems have conceptualized mania as a discrete phenomenon, appropriate latent structure investigations testing this conceptualization are lacking. In contrast to these diagnostic systems, several influential theories of mania have suggested a continuous conceptualization. The present study examined whether mania has a continuous or discrete latent structure using a comprehensive approach including taxometric, information-theoretic latent distribution modeling (ITLDM), and predictive validity methodologies in the Epidemiologic Catchment Area (ECA) study. Methods Eight dichotomous manic symptom items were submitted to a variety of latent structural analyses; including factor analyses, taxometric procedures, and ITLDM; in 10,105 ECA community participants. Additionally, a variety of continuous and discrete models of mania were compared in terms of their relative abilities to predict outcomes (i.e., health service utilization, internalizing and externalizing disorders, and suicidal behavior). Results Taxometric and ITLDM analyses consistently supported a continuous conceptualization of mania. In ITLDM analyses, a continuous model of mania demonstrated 6:52:1 odds over the best fitting latent class model of mania. Factor analyses suggested that the continuous structure of mania was best represented by a single latent factor. Predictive validity analyses demonstrated a consistent superior ability of continuous models of mania relative to discrete models. Conclusions The present study provided three independent lines of support for a continuous conceptualization of mania. The implications of a continuous model of mania are discussed. PMID:20507671

Analysis of phase II methodologies for single-arm clinical trials with multiple endpoints in rare cancers: An example in Ewing's sarcoma.

PubMed

Dutton, P; Love, S B; Billingham, L; Hassan, A B

2018-05-01

Trials run in either rare diseases, such as rare cancers, or rare sub-populations of common diseases are challenging in terms of identifying, recruiting and treating sufficient patients in a sensible period. Treatments for rare diseases are often designed for other disease areas and then later proposed as possible treatments for the rare disease after initial phase I testing is complete. To ensure the trial is in the best interests of the patient participants, frequent interim analyses are needed to force the trial to stop promptly if the treatment is futile or toxic. These non-definitive phase II trials should also be stopped for efficacy to accelerate research progress if the treatment proves to be particularly promising. In this paper, we review frequentist and Bayesian methods that have been adapted to incorporate two binary endpoints and frequent interim analyses. The Eurosarc Trial of Linsitinib in advanced Ewing Sarcoma (LINES) is used as a motivating example and provides a suitable platform to compare these approaches. The Bayesian approach provides greater design flexibility, but does not provide additional value over the frequentist approaches in a single trial setting when the prior is non-informative. However, Bayesian designs are able to borrow from any previous experience, using prior information to improve efficiency.

MOLSIM: A modular molecular simulation software

PubMed Central

Jurij, Reščič

2015-01-01

The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:25994597

Huntington's Disease and its therapeutic target genes: a global functional profile based on the HD Research Crossroads database

PubMed Central

2012-01-01

Background Huntington’s disease (HD) is a fatal progressive neurodegenerative disorder caused by the expansion of the polyglutamine repeat region in the huntingtin gene. Although the disease is triggered by the mutation of a single gene, intensive research has linked numerous other genes to its pathogenesis. To obtain a systematic overview of these genes, which may serve as therapeutic targets, CHDI Foundation has recently established the HD Research Crossroads database. With currently over 800 cataloged genes, this web-based resource constitutes the most extensive curation of genes relevant to HD. It provides us with an unprecedented opportunity to survey molecular mechanisms involved in HD in a holistic manner. Methods To gain a synoptic view of therapeutic targets for HD, we have carried out a variety of bioinformatical and statistical analyses to scrutinize the functional association of genes curated in the HD Research Crossroads database. In particular, enrichment analyses were performed with respect to Gene Ontology categories, KEGG signaling pathways, and Pfam protein families. For selected processes, we also analyzed differential expression, using published microarray data. Additionally, we generated a candidate set of novel genetic modifiers of HD by combining information from the HD Research Crossroads database with previous genome-wide linkage studies. Results Our analyses led to a comprehensive identification of molecular mechanisms associated with HD. Remarkably, we not only recovered processes and pathways, which have frequently been linked to HD (such as cytotoxicity, apoptosis, and calcium signaling), but also found strong indications for other potentially disease-relevant mechanisms that have been less intensively studied in the context of HD (such as the cell cycle and RNA splicing, as well as Wnt and ErbB signaling). For follow-up studies, we provide a regularly updated compendium of molecular mechanism, that are associated with HD, at http://hdtt.sysbiolab.eu Additionally, we derived a candidate set of 24 novel genetic modifiers, including histone deacetylase 3 (HDAC3), metabotropic glutamate receptor 1 (GRM1), CDK5 regulatory subunit 2 (CDK5R2), and coactivator 1ß of the peroxisome proliferator-activated receptor gamma (PPARGC1B). Conclusions The results of our study give us an intriguing picture of the molecular complexity of HD. Our analyses can be seen as a first step towards a comprehensive list of biological processes, molecular functions, and pathways involved in HD, and may provide a basis for the development of more holistic disease models and new therapeutics. PMID:22741533

Care in subsequent pregnancies following stillbirth: an international survey of parents.

PubMed

Wojcieszek, A M; Boyle, F M; Belizán, J M; Cassidy, J; Cassidy, P; Erwich, Jjhm; Farrales, L; Gross, M M; Heazell, Aep; Leisher, S H; Mills, T; Murphy, M; Pettersson, K; Ravaldi, C; Ruidiaz, J; Siassakos, D; Silver, R M; Storey, C; Vannacci, A; Middleton, P; Ellwood, D; Flenady, V

2018-01-01

To assess the frequency of additional care, and parents' perceptions of quality, respectful care, in pregnancies subsequent to stillbirth. Multi-language web-based survey. International. A total of 2716 parents, from 40 high- and middle-income countries. Data were obtained from a broader survey of parents' experiences following stillbirth. Data were analysed using descriptive statistics and stratified by geographic region. Subgroup analyses explored variation in additional care by gestational age at index stillbirth. Frequency of additional care, and perceptions of quality, respectful care. The majority (66%) of parents conceived their subsequent pregnancy within 1 year of stillbirth. Additional antenatal care visits and ultrasound scans were provided for 67% and 70% of all parents, respectively, although there was wide variation across geographic regions. Care addressing psychosocial needs was less frequently provided, such as additional visits to a bereavement counsellor (10%) and access to named care provider's phone number (27%). Compared with parents whose stillbirth occurred at ≤ 29 weeks of gestation, parents whose stillbirth occurred at ≥ 30 weeks of gestation were more likely to receive various forms of additional care, particularly the option for early delivery after 37 weeks. Around half (47-63%) of all parents felt that elements of quality, respectful care were consistently applied, such as spending enough time with parents and involving parents in decision-making. Greater attention is required to providing thoughtful, empathic and collaborative care in all pregnancies following stillbirth. Specific education and training for health professionals is needed. More support for providing quality care in pregnancies after stillbirth is needed. Study rationale and design More than two million babies are stillborn every year. Most parents will conceive again soon after having a stillborn baby. These parents are more likely to have another stillborn baby in the next pregnancy than parents who have not had a stillborn baby before. The next pregnancy after stillbirth is often an extremely anxious time for parents, as they worry about whether their baby will survive. In this study we asked 2716 parents from 40 countries about the care they received during their first pregnancy after stillbirth. Parents were recruited mainly through the International Stillbirth Alliance and completed on online survey that was available in six languages. Findings Parents often had extra antenatal visits and extra ultrasound scans in the next pregnancy, but they rarely had extra emotional support. Also, many parents felt their care providers did not always listen to them and spend enough time with them, involve them in decisions, and take their concerns seriously. Parents were more likely to receive various forms of extra care in the next pregnancy if their baby had died later in pregnancy compared to earlier in pregnancy. Limitations In this study we only have information from parents who were able and willing to complete an online survey. Most of the parents were involved in charity and support groups and most parents lived in developed countries. We do not know how well the findings relate to other parents. Finally, our study does not include parents who may have tried for another pregnancy but were not able to conceive. Potential impact This study can help to improve care through the development of best practice guidelines for pregnancies following stillbirth. The results suggest that parents need better emotional support in these pregnancies, and more opportunities to participate actively in decisions about care. Extra support should be available no matter how far along in pregnancy the previous stillborn baby died. © 2016 Royal College of Obstetricians and Gynaecologists.

Evolutionary game theory for physical and biological scientists. II. Population dynamics equations can be associated with interpretations

PubMed Central

Liao, David; Tlsty, Thea D.

2014-01-01

The use of mathematical equations to analyse population dynamics measurements is being increasingly applied to elucidate complex dynamic processes in biological systems, including cancer. Purely ‘empirical’ equations may provide sufficient accuracy to support predictions and therapy design. Nevertheless, interpretation of fitting equations in terms of physical and biological propositions can provide additional insights that can be used both to refine models that prove inconsistent with data and to understand the scope of applicability of models that validate. The purpose of this tutorial is to assist readers in mathematically associating interpretations with equations and to provide guidance in choosing interpretations and experimental systems to investigate based on currently available biological knowledge, techniques in mathematical and computational analysis and methods for in vitro and in vivo experiments. PMID:25097752

Crop identification technology assessment for remote sensing (CITARS). Volume 6: Data processing at the laboratory for applications of remote sensing

NASA Technical Reports Server (NTRS)

Bauer, M. E.; Cary, T. K.; Davis, B. J.; Swain, P. H.

1975-01-01

The results of classifications and experiments for the crop identification technology assessment for remote sensing are summarized. Using two analysis procedures, 15 data sets were classified. One procedure used class weights while the other assumed equal probabilities of occurrence for all classes. Additionally, 20 data sets were classified using training statistics from another segment or date. The classification and proportion estimation results of the local and nonlocal classifications are reported. Data also describe several other experiments to provide additional understanding of the results of the crop identification technology assessment for remote sensing. These experiments investigated alternative analysis procedures, training set selection and size, effects of multitemporal registration, spectral discriminability of corn, soybeans, and other, and analyses of aircraft multispectral data.

The anatomy, affinity, and phylogenetic significance of Markuelia.

PubMed

Dong, Xi-Ping; Donoghue, Philip C J; Cunningham, John A; Liu, Jian-Bo; Cheng, Hong

2005-01-01

The fossil record provides a paucity of data on the development of extinct organisms, particularly for their embryology. The recovery of fossilized embryos heralds new insight into the evolution of development but advances are limited by an almost complete absence of phylogenetic constraint. Markuelia is an exception to this, known from cleavage and pre-hatchling stages as a vermiform and profusely annulated direct-developing bilaterian with terminal circumoral and posterior radial arrays of spines. Phylogenetic analyses have hitherto suggested assignment to stem-Scalidophora (phyla Kinorhyncha, Loricifera, Priapulida). We test this assumption with additional data and through the inclusion of additional taxa. The available evidence supports stem-Scalidophora affinity, leading to the conclusion that scalidophorans, cyclonerualians, and ecdysozoans are primitive direct developers, and the likelihood that scalidophorans are primitively metameric.

Cost-Utility Analysis of Cancer Prevention, Treatment, and Control: A Systematic Review.

PubMed

Winn, Aaron N; Ekwueme, Donatus U; Guy, Gery P; Neumann, Peter J

2016-02-01

Substantial innovation related to cancer prevention and treatment has occurred in recent decades. However, these innovations have often come at a significant cost. Cost-utility analysis provides a useful framework to assess if the benefits from innovation are worth the additional cost. This systematic review on published cost-utility analyses related to cancer care is from 1988 through 2013. Analyses were conducted in 2013-2015. This review analyzed data from the Tufts Medical Center Cost-Effectiveness Analysis Registry (www.cearegistry.org), a comprehensive registry with detailed information on 4,339 original cost-utility analyses published in the peer-reviewed medical and economic literature through 2013. There were 721 cancer-related cost-utility analyses published from 1998 through 2013, with roughly 12% of studies focused on primary prevention and 17% focused on secondary prevention. The most often studied cancers were breast cancer (29%); colorectal cancer (11%); and prostate cancer (8%). The median reported incremental cost-effectiveness ratios (in 2014 U.S. dollars) were $25,000 for breast cancer, $24,000 for colorectal cancer, and $34,000 for prostate cancer. The current evidence indicates that there are many interventions that are cost effective across cancer sites and levels of prevention. However, the results highlight the relatively small number of cancer cost-utility analyses devoted to primary prevention compared with secondary or tertiary prevention. Copyright © 2016 American Journal of Preventive Medicine. All rights reserved.

Cost-Utility Analysis of Cancer Prevention, Treatment, and Control

PubMed Central

Winn, Aaron N.; Ekwueme, Donatus U.; Guy, Gery P.; Neumann, Peter J.

2018-01-01

Context Substantial innovation related to cancer prevention and treatment has occurred in recent decades. However, these innovations have often come at a significant cost. Cost-utility analysis provides a useful framework to assess if the benefits from innovation are worth the additional cost. This systematic review on published cost-utility analyses related to cancer care is from 1988 through 2013. Analyses were conducted in 2013–2015. Evidence acquisition This review analyzed data from the Tufts Medical Center Cost-Effectiveness Analysis Registry (www.cearegistry.org), a comprehensive registry with detailed information on 4,339 original cost-utility analyses published in the peer-reviewed medical and economic literature through 2013. Evidence synthesis There were 721 cancer-related cost-utility analyses published from 1998 through 2013, with roughly 12% of studies focused on primary prevention and 17% focused on secondary prevention. The most often studied cancers were breast cancer (29%); colorectal cancer (11%); and prostate cancer (8%). The median reported incremental cost-effectiveness ratios (in 2014 U.S. dollars) were $25,000 for breast cancer, $24,000 for colorectal cancer, and $34,000 for prostate cancer. Conclusions The current evidence indicates that there are many interventions that are cost effective across cancer sites and levels of prevention. However, the results highlight the relatively small number of cancer cost-utility analyses devoted to primary prevention compared with secondary or tertiary prevention. PMID:26470806

SPARC Intercomparison of Middle Atmosphere Climatologies

NASA Technical Reports Server (NTRS)

Randel, William; Fleming, Eric; Geller, Marvin; Hamilton, Kevin; Karoly, David; Ortland, Dave; Pawson, Steve; Swinbank, Richard; Udelhofen, Petra

2002-01-01

This atlas presents detailed incomparisons of several climatological wind and temperature data sets which cover the middle atmosphere (over altitudes approx. 10-80 km). A number of middle atmosphere climatologies have been developed in the research community based on a variety of meteorological analyses and satellite data sets. Here we present comparisons between these climatological data sets for a number of basic circulation statistics, such as zonal mean temperature, winds and eddy flux statistics. Special attention is focused on tropical winds and temperatures, where large differences exist among separate analyses. We also include comparisons between the global climatologies and historical rocketsonde wind and temperature measurements, and also with more recent lidar temperature data. These comparisons highlight differences and uncertainties in contemporary middle atmosphere data sets, and allow biases in particular analyses to be isolated. In addition, a brief atlas of zonal mean temperature and wind statistics is provided to highlight data availability and as a quick-look reference. This technical report is intended as a companion to the climatological data sets held in archive at the SPARC Data Center (http://www.sparc.sunysb.edu).

Rasch analysis for psychometric improvement of science attitude rating scales

NASA Astrophysics Data System (ADS)

Oon, Pey-Tee; Fan, Xitao

2017-04-01

Students' attitude towards science (SAS) is often a subject of investigation in science education research. Survey of rating scale is commonly used in the study of SAS. The present study illustrates how Rasch analysis can be used to provide psychometric information of SAS rating scales. The analyses were conducted on a 20-item SAS scale used in an existing dataset of The Trends in International Mathematics and Science Study (TIMSS) (2011). Data of all the eight-grade participants from Hong Kong and Singapore (N = 9942) were retrieved for analyses. Additional insights from Rasch analysis that are not commonly available from conventional test and item analyses were discussed, such as invariance measurement of SAS, unidimensionality of SAS construct, optimum utilization of SAS rating categories, and item difficulty hierarchy in the SAS scale. Recommendations on how TIMSS items on the measurement of SAS can be better designed were discussed. The study also highlights the importance of using Rasch estimates for statistical parametric tests (e.g. ANOVA, t-test) that are common in science education research for group comparisons.

Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics

PubMed Central

Zhou, Tao; Zhou, Zuo-Min; Guo, Xue-Jiang

2013-01-01

Proteomics strategies have been widely used in the field of male reproduction, both in basic and clinical research. Bioinformatics methods are indispensable in proteomics-based studies and are used for data presentation, database construction and functional annotation. In the present review, we focus on the functional annotation of gene lists obtained through qualitative or quantitative methods, summarizing the common and male reproduction specialized proteomics databases. We introduce several integrated tools used to find the hidden biological significance from the data obtained. We further describe in detail the information on male reproduction derived from Gene Ontology analyses, pathway analyses and biomedical analyses. We provide an overview of bioinformatics annotations in spermatogenesis, from gene function to biological function and from biological function to clinical application. On the basis of recently published proteomics studies and associated data, we show that bioinformatics methods help us to discover drug targets for sperm motility and to scan for cancer-testis genes. In addition, we summarize the online resources relevant to male reproduction research for the exploration of the regulation of spermatogenesis. PMID:23852026

[Statistical analysis using freely-available "EZR (Easy R)" software].

PubMed

Kanda, Yoshinobu

2015-10-01

Clinicians must often perform statistical analyses for purposes such evaluating preexisting evidence and designing or executing clinical studies. R is a free software environment for statistical computing. R supports many statistical analysis functions, but does not incorporate a statistical graphical user interface (GUI). The R commander provides an easy-to-use basic-statistics GUI for R. However, the statistical function of the R commander is limited, especially in the field of biostatistics. Therefore, the author added several important statistical functions to the R commander and named it "EZR (Easy R)", which is now being distributed on the following website: http://www.jichi.ac.jp/saitama-sct/. EZR allows the application of statistical functions that are frequently used in clinical studies, such as survival analyses, including competing risk analyses and the use of time-dependent covariates and so on, by point-and-click access. In addition, by saving the script automatically created by EZR, users can learn R script writing, maintain the traceability of the analysis, and assure that the statistical process is overseen by a supervisor.

Biotic and abiotic degradation of 1,1,2,2-tetrachloroethane in wetland sediments: Geochemical and microbial community analyses

USGS Publications Warehouse

Lorah, M.M.; Voytek, M.A.; Kirshtein, J.

2000-01-01

Additional microcosm experiments with the wetland sediment and groundwater at the Aberdeen Proving Ground, MD, site was presented to assist in elucidating the conditions under which these potentially competing biotic and abiotic degradation reactions for 1,1,2,2-tetrachloroethane (PCA) occur in the environment and to evaluate potential seasonal changes in degradation reactions. PCA concentration decreased to below detection within 21 days in the March 1999 experiment, while PCA was still present at day 35 in the July 1999 experiment. Compared to March 1999 experiment, peak concentrations of all daughter products except trichloroethylene (TCE) were delayed in the July 1999 experiment. The relative intensity of the peaks was directly related to the biomass present for each fragment length (bp, base pair). The relative intensities were lower in sediment collected in August 1999 than in March 1999, especially in the bp size range of ??? 160??-240??. These microbial community analyses, along with the geochemical analyses of the microcosms, provide evidence that abiotic production of TCE from PCA degradation is more significant under conditions of low bacterial biomass in the wetland sediments.

Explosive detection using a novel dielectric barrier discharge ionisation source for mass spectrometry.

PubMed

Fletcher, Carl; Sleeman, Richard; Luke, John; Luke, Peter; Bradley, James W

2018-03-01

The detection of explosives is of great importance, as is the need for sensitive, reliable techniques that require little or no sample preparation and short run times for high throughput analysis. In this work, a novel ionisation source is presented based on a dielectric barrier discharge (DBD). This not only affects desorption and ionisation but also forms an ionic wind, providing mass transportation of ions towards the mass spectrometer. Furthermore, the design incorporates 2 asymmetric alumina sheets, each containing 3 DBDs, so that a large surface area can be analysed. The DBD operates in ambient air, overcoming the limitation of other plasma-based techniques which typically analyse smaller surface areas and require solvents or gases. A range of explosives across 4 different functional groups was analysed using the DBD with low limits of detection for cyclotrimethylene trinitramine (RDX) (100 pg), pentaerythritol trinitrate (PETN) (100 pg), hexamethylene triperoxide diamide (HMTD) (1 ng), and trinitrotoluene (TNT) (5 ng). Detection was achieved without any sample preparation or the addition of reagents to facilitate adduct formation. Copyright © 2017 John Wiley & Sons, Ltd.

Quality of surface water at selected sites in the Suwannee River basin, Florida

USGS Publications Warehouse

Coffin, J.E.

1982-01-01

This report presents the results of analyses of water-quality samples collected from 14 surface-water sites in the Suwannee River basin in Florida from January through December 1980. The analyses of samples collected routinely included: nutrients, total organic carbon, and 5-day biochemical oxygen demand, bimonthly; and trace metals, annually. The array of constituents sampled was expanded in October 1978 at three of the original nine stations to provide quality-of-water information for streams draining an industrial area: Rocky Creek near Belmont, Hunter Creek near Belmont, and Swift Creek at Facil. Data collected at these three sites now include: major chemical constituents, six times per year: radium-226, two times per year; and trace metals, one time per year. These constituents are determined in addition to nutrients, total organic carbon, and bio-chemical oxygen demand which continue to be analyzed six times per year. All results of analyses of the water-quality samples collected from January through December 1980 remained within, or near, previously measured ranges and water-quality fluctuations were similar to those noted from data collected since 1971. (USGS)

Phylogenetic relationships in Taxodiaceae and Cupressaceae sensu stricto based on matK gene, chlL gene, trnL-trnF IGS region, and trnL intron sequences.

PubMed

Kusumi, J; Tsumura, Y; Yoshimaru, H; Tachida, H

2000-10-01

Nucleotide sequences from four chloroplast genes, the matK, chlL, intergenic spacer (IGS) region between trnL and trnF, and an intron of trnL, were determined from all species of Taxodiaceae and five species of Cupressaceae sensu stricto (s.s.). Phylogenetic trees were constructed using the maximum parsimony and the neighbor-joining methods with Cunninghamia as an outgroup. These analyses provided greater resolution of relationships among genera and higher bootstrap supports for clades compared to previous analyses. Results indicate that Taiwania diverged first, and then Athrotaxis diverged from the remaining genera. Metasequoia, Sequoia, and Sequoiadendron form a clade. Taxodium and Glyptostrobus form a clade, which is the sister to Cryptomeria. Cupressaceae s.s. are derived from within Taxodiaceae, being the most closely related to the Cryptomeria/Taxodium/Glyptostrobus clade. These relationships are consistent with previous morphological groupings and the analyses of molecular data. In addition, we found acceleration of evolutionary rates in Cupressaceae s.s. Possible causes for the acceleration are discussed.

Reaffirmed limitations of meta-analytic methods in the study of mild traumatic brain injury: a response to Rohling et al.

PubMed

Bigler, Erin D; Farrer, Thomas J; Pertab, Jon L; James, Kelly; Petrie, Jo Ann; Hedges, Dawson W

2013-01-01

In 2009 Pertab, James, and Bigler published a critique of two prior meta-analyses by Binder, Rohling, and Larrabee (1997) and Frencham, Fox, and Maybery (2005) that showed small effect size difference at least 3 months post-injury in individuals who had sustained a mild traumatic brain injury (mTBI). The Binder et al. and Frencham et al. meta-analyses have been widely cited as showing no lasting effect of mTBI. In their critique Pertab et al. (2009) point out many limitations of these two prior meta-analyses, demonstrating that depending on how inclusion/exclusion criteria were defined different meta-analytic findings occur, some supporting the persistence of neuropsychological impairments beyond 3 months. Rohling et al. (2011) have now critiqued Pertab et al. (2009). Herein we respond to the Rolling et al. (2011) critique reaffirming the original findings of Pertab et al. (2009), providing additional details concerning the flaws in prior meta-analytic mTBI studies and the effects on neuropsychological performance.

Multi-Criteria GIS Analyses with the Use of Uavs for the Needs of Spatial Planning

NASA Astrophysics Data System (ADS)

Zawieska, D.; Markiewicz, J.; Turek, A.; Bakuła, K.; Kowalczyk, M.; Kurczyński, Z.; Ostrowski, W.; Podlasiak, P.

2016-06-01

Utilization of Unmanned Aerial Systems (UAVs) in agriculture, forestry, or other environmental contexts has recently become common. However, in the case of spatial planning, the role of UAVs still seems to be underestimated. At present, sections of municipal development use UAVs mainly for promotional purposes (films, folders, brochures, etc.). The use of UAVs for spatial management provides results, first of all, in the form of savings in human resources and time; however, more frequently, it is also connected with financial savings (given the decreasing cost of UAVs and photogrammetric software). The performed research presented here relates to the possibilities of using UAVs to update planning documents, and, in particular, to update the study of conditions and directions of spatial management and preparation of local plans for physical management. Based on acquired photographs with a resolution of 3 cm, a cloud of points is generated, as well as 3D models and the true orthophotomap. These data allow multi-criteria spatial analyses. Additionally, directions of development and changes in physical management are analysed for the given area.

Network meta-analyses performed by contracting companies and commissioned by industry.

PubMed

Schuit, Ewoud; Ioannidis, John Pa

2016-11-25

Industry commissions contracting companies to perform network meta-analysis for health technology assessment (HTA) and reimbursement submissions. Our objective was to estimate the number of network meta-analyses performed by consulting companies contracted by industry, to assess whether they were published, and to explore reasons for non-publication. We searched MEDLINE for network meta-analyses of randomized trials. Papers were included if they had authors affiliated with any contracting company. All identified contracting companies as well as additional ones from the list of the exhibitors at the International Society for Pharmacoeconomics and Outcomes Research, an annual meeting that representatives from many contracting companies attend and exhibit at, were surveyed regarding conduct and publication of network meta-analyses. In 162 of 822 (20%) network meta-analysis papers, authors were affiliated to 66 contracting companies. Another 36 contracting companies were identified by the exhibitors list. Three companies had no contact information and six merged with others, therefore 93 companies were contacted. Thirty seven out of ninety three (40%) companies responded, and 19 indicated that they had performed a total of 476 network meta-analyses, but only 102 (21%) papers were published. Thirteen companies that disclosed to have conducted 174 network meta-analyses (45 published) provided reasons for non-publication. Of the 129 still unpublished meta-analyses, for 40 there were plans for future publication, for 37 the sponsor did not allow publication, for 16 the contracting companies did not plan to publish the meta-analysis, for another 23 plans were unclear, and the remaining 13 were used as HTA submission. The protocol of the network meta-analysis was publically available from 11/162 (6.8%) network meta-analyses published by authors affiliated with contracting companies. There is a prolific sector of professional contracting companies that perform network meta-analyses. Industry commissions many network meta-analyses, but most are not registered before or published after analyses in the scientific literature. Mechanisms to improve publication rates of network meta-analysis commissioned by industry are warranted.

Interprofessional student clinics: an economic evaluation of collaborative clinical placement education.

PubMed

Haines, Terry P; Kent, Fiona; Keating, Jennifer L

2014-07-01

Interprofessional student clinics can be used to create clinical education placements for health professional students in addition to traditional hospital-based placements and present an opportunity to provide interprofessional learning experiences in a clinical context. To date, little consideration has been given in research literature as to whether such clinics are economically viable for a university to run. We conducted an economic evaluation based upon data generated during a pilot of an interprofessional student clinic based in Australia. Cost-minimization analyses of the student clinic as opposed to traditional profession-specific clinical education in hospitals were conducted from university, Commonwealth Government, state government and societal perspectives. Cost data gathered during the pilot study and market prices were used where available, while $AUD currency at 2011 values were used. Per student day of clinical education, the student clinic cost an additional $289, whereas the state government saved $49 and the Commonwealth Government saved $66. Overall, society paid an additional $175 per student day of clinical education using the student clinic as opposed to conventional hospital-based placements, indicating that traditional hospital-based placements are a cost-minimizing approach overall for providing clinical education. Although interprofessional student clinics have reported positive patient and student learning outcomes, further research is required to determine if these benefits can justify the additional cost of this model of education. Considerations for clinic sustainability are proposed.

Ecological Momentary Assessments and Automated Time Series Analysis to Promote Tailored Health Care: A Proof-of-Principle Study.

PubMed

van der Krieke, Lian; Emerencia, Ando C; Bos, Elisabeth H; Rosmalen, Judith Gm; Riese, Harriëtte; Aiello, Marco; Sytema, Sjoerd; de Jonge, Peter

2015-08-07

Health promotion can be tailored by combining ecological momentary assessments (EMA) with time series analysis. This combined method allows for studying the temporal order of dynamic relationships among variables, which may provide concrete indications for intervention. However, application of this method in health care practice is hampered because analyses are conducted manually and advanced statistical expertise is required. This study aims to show how this limitation can be overcome by introducing automated vector autoregressive modeling (VAR) of EMA data and to evaluate its feasibility through comparisons with results of previously published manual analyses. We developed a Web-based open source application, called AutoVAR, which automates time series analyses of EMA data and provides output that is intended to be interpretable by nonexperts. The statistical technique we used was VAR. AutoVAR tests and evaluates all possible VAR models within a given combinatorial search space and summarizes their results, thereby replacing the researcher's tasks of conducting the analysis, making an informed selection of models, and choosing the best model. We compared the output of AutoVAR to the output of a previously published manual analysis (n=4). An illustrative example consisting of 4 analyses was provided. Compared to the manual output, the AutoVAR output presents similar model characteristics and statistical results in terms of the Akaike information criterion, the Bayesian information criterion, and the test statistic of the Granger causality test. Results suggest that automated analysis and interpretation of times series is feasible. Compared to a manual procedure, the automated procedure is more robust and can save days of time. These findings may pave the way for using time series analysis for health promotion on a larger scale. AutoVAR was evaluated using the results of a previously conducted manual analysis. Analysis of additional datasets is needed in order to validate and refine the application for general use.

Explaining seemingly paradoxical consumer experiences: conjoining weekly road rage and church attendance.

PubMed

Gau, Li-Shiue; Woodside, Arch G; Martin, Drew

2015-02-01

The purposes of the current study are threefold: Provide evidence that an extreme paradoxical group exists-people frequently attending church and exhibiting road rage, profile this group, and frame possible explanations for the seemingly paradoxical behaviors. This study employs data from a national (USA) lifestyle survey conducted by Market Facts with 3,350 American respondents. The major questions asked about church participation and road-rage behavior ("giving a finger" and "flashing headlights"). Nomologically, relevant activities include 3 items for church goers and 3 items for road-rage givers. Additionally, 14 items profiled the lifestyles of the unique paradoxical behavior segment. Utilizing cross-tabulation tables, property space analyses identify the double extreme (XX) group (18 people) and other 6 groups with a significant chi-square test, confirming the extreme group exists. Analyses of variance test results show that comparing nomologically relevant activities among the seven groups is all statistically significant, indicating the nomological validity is met. Overall, the XX group tends to have more males, be younger, and have a higher proportion of people working in sales. The profile of lifestyle analyses shows the XX group members have both high ambitions and expectations, might be very frustrated individuals, and equip with the adventurous and masculine traits related to aggression. The XX behavior group's demographic and psychographic characteristics portray similar lifestyles that differ from other groups. Case-based analyses provide further contextual information of nuances to XX segment individuals. The limited energy theory, the Eagleman's theory of unconscious mind, and justification theory help to explain why people conjointly go to church and commit road rage. Addressing chronic paradoxical behaviors provides implications for social de-marketing to reduce aggressive anti-social behavior such as road rage. Frequent church attendance may help make people more sensitive to their wrongdoings and gradually revise the anti-social behavior.

Benefits and applications of interdisciplinary digital tools for environmental meta-reviews and analyses

NASA Astrophysics Data System (ADS)

Grubert, Emily; Siders, Anne

2016-09-01

Digitally-aided reviews of large bodies of text-based information, such as academic literature, are growing in capability but are not yet common in environmental fields. Environmental sciences and studies can benefit from application of digital tools to create comprehensive, replicable, interdisciplinary reviews that provide rapid, up-to-date, and policy-relevant reports of existing work. This work reviews the potential for applications of computational text mining and analysis tools originating in the humanities to environmental science and policy questions. Two process-oriented case studies of digitally-aided environmental literature reviews and meta-analyses illustrate potential benefits and limitations. A medium-sized, medium-resolution review (∼8000 journal abstracts and titles) focuses on topic modeling as a rapid way to identify thematic changes over time. A small, high-resolution review (∼300 full text journal articles) combines collocation and network analysis with manual coding to synthesize and question empirical field work. We note that even small digitally-aided analyses are close to the upper limit of what can be done manually. Established computational methods developed in humanities disciplines and refined by humanities and social science scholars to interrogate large bodies of textual data are applicable and useful in environmental sciences but have not yet been widely applied. Two case studies provide evidence that digital tools can enhance insight. Two major conclusions emerge. First, digital tools enable scholars to engage large literatures rapidly and, in some cases, more comprehensively than is possible manually. Digital tools can confirm manually identified patterns or identify additional patterns visible only at a large scale. Second, digital tools allow for more replicable and transparent conclusions to be drawn from literature reviews and meta-analyses. The methodological subfields of digital humanities and computational social sciences will likely continue to create innovative tools for analyzing large bodies of text, providing opportunities for interdisciplinary collaboration with the environmental fields.

Ecological Momentary Assessments and Automated Time Series Analysis to Promote Tailored Health Care: A Proof-of-Principle Study

PubMed Central

Emerencia, Ando C; Bos, Elisabeth H; Rosmalen, Judith GM; Riese, Harriëtte; Aiello, Marco; Sytema, Sjoerd; de Jonge, Peter

2015-01-01

Background Health promotion can be tailored by combining ecological momentary assessments (EMA) with time series analysis. This combined method allows for studying the temporal order of dynamic relationships among variables, which may provide concrete indications for intervention. However, application of this method in health care practice is hampered because analyses are conducted manually and advanced statistical expertise is required. Objective This study aims to show how this limitation can be overcome by introducing automated vector autoregressive modeling (VAR) of EMA data and to evaluate its feasibility through comparisons with results of previously published manual analyses. Methods We developed a Web-based open source application, called AutoVAR, which automates time series analyses of EMA data and provides output that is intended to be interpretable by nonexperts. The statistical technique we used was VAR. AutoVAR tests and evaluates all possible VAR models within a given combinatorial search space and summarizes their results, thereby replacing the researcher’s tasks of conducting the analysis, making an informed selection of models, and choosing the best model. We compared the output of AutoVAR to the output of a previously published manual analysis (n=4). Results An illustrative example consisting of 4 analyses was provided. Compared to the manual output, the AutoVAR output presents similar model characteristics and statistical results in terms of the Akaike information criterion, the Bayesian information criterion, and the test statistic of the Granger causality test. Conclusions Results suggest that automated analysis and interpretation of times series is feasible. Compared to a manual procedure, the automated procedure is more robust and can save days of time. These findings may pave the way for using time series analysis for health promotion on a larger scale. AutoVAR was evaluated using the results of a previously conducted manual analysis. Analysis of additional datasets is needed in order to validate and refine the application for general use. PMID:26254160

Phylogenomic analysis of the Chilean clade of Liolaemus lizards (Squamata: Liolaemidae) based on sequence capture data.

PubMed

Panzera, Alejandra; Leaché, Adam D; D'Elía, Guillermo; Victoriano, Pedro F

2017-01-01

The genus Liolaemus is one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless, Liolaemus lizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenus Liolaemus sensu stricto ), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic. Liolaemus tenuis tenuis is difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion of L. t. tenuis from analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships between L. fuscus , L. monticola , L. nigroviridis and L. nitidus , and L. platei and L. velosoi . Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade of Liolaemus that will help future work aimed at resolving the Liolaemus phylogeny.

An analysis of narratives to identify critical thinking contexts in psychiatric clinical practice.

PubMed

Mun, Mi Suk

2010-02-01

The development of students' critical thinking abilities is one of the greatest challenges facing contemporary nursing educators. Nursing educators should know about what kind of contents or situations need critical thinking. The research was undertaken to identify the critical thinking contexts that nursing students confront in psychiatric clinical practices. Students were asked to document their everyday experience. The narratives were analysed and interpreted from the philosophical notion of hermeneutics. Four themes emerged as critical thinking contexts: anxiety, conflict, hyper-awareness, dilemmas. Writing narratives appear to provide opportunities for reflection in addition to facilitating critical thinking and communicative skills in students. Also, for the instructor, students' clinical narratives could provide insight to understand how students are thinking and to share student's personal difficulties.

Wind-Tunnel Evaluation of the Effect of Blade Nonstructural Mass Distribution on Helicopter Fixed-System Loads

NASA Technical Reports Server (NTRS)

Wilbur, Matthew L.; Yeager, William T., Jr.; Singleton, Jeffrey D.; Mirick, Paul H.; Wilkie, W. Keats

1998-01-01

This report provides data obtained during a wind-tunnel test conducted to investigate parametrically the effect of blade nonstructural mass on helicopter fixed-system vibratory loads. The data were obtained with aeroelastically scaled model rotor blades that allowed for the addition of concentrated nonstructural masses at multiple locations along the blade radius. Testing was conducted for advance ratios ranging from 0.10 to 0.35 for 10 blade-mass configurations. Three thrust levels were obtained at representative full-scale shaft angles for each blade-mass configuration. This report provides the fixed-system forces and moments measured during testing. The comprehensive database obtained is well-suited for use in correlation and development of advanced rotorcraft analyses.

Modular space station

NASA Technical Reports Server (NTRS)

1972-01-01

The modular space station comprising small, shuttle-launched modules, and characterized by low initial cost and incremental manning, is described. The initial space station is designed to be delivered into orbit by three space shuttles and assembled in space. The three sections are the power/subsystems module, the crew/operations module, and the general purpose laboratory module. It provides for a crew of six. Subsequently duplicate/crew/operations and power/subsystems modules will be mated to the original modules, and provide for an additional six crewmen. A total of 17 research and applications modules is planned, three of which will be free-flying modules. Details are given on the program plan, modular characteristics, logistics, experiment support capability and requirements, operations analysis, design support analyses, and shuttle interfaces.

LIMO EEG: a toolbox for hierarchical LInear MOdeling of ElectroEncephaloGraphic data.

PubMed

Pernet, Cyril R; Chauveau, Nicolas; Gaspar, Carl; Rousselet, Guillaume A

2011-01-01

Magnetic- and electric-evoked brain responses have traditionally been analyzed by comparing the peaks or mean amplitudes of signals from selected channels and averaged across trials. More recently, tools have been developed to investigate single trial response variability (e.g., EEGLAB) and to test differences between averaged evoked responses over the entire scalp and time dimensions (e.g., SPM, Fieldtrip). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data. In addition, LIMO EEG provides robust parametric tests, therefore providing a new and complementary tool in the analysis of neural evoked responses.

LIMO EEG: A Toolbox for Hierarchical LInear MOdeling of ElectroEncephaloGraphic Data

PubMed Central

Pernet, Cyril R.; Chauveau, Nicolas; Gaspar, Carl; Rousselet, Guillaume A.

2011-01-01

Magnetic- and electric-evoked brain responses have traditionally been analyzed by comparing the peaks or mean amplitudes of signals from selected channels and averaged across trials. More recently, tools have been developed to investigate single trial response variability (e.g., EEGLAB) and to test differences between averaged evoked responses over the entire scalp and time dimensions (e.g., SPM, Fieldtrip). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data. In addition, LIMO EEG provides robust parametric tests, therefore providing a new and complementary tool in the analysis of neural evoked responses. PMID:21403915

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

Green, D.W.; Heinrich, R.R.; Graczyk, D.G.

The purpose of this report is to summarize the activities of the Analytical Chemistry Laboratory (ACL) at Argonne National Laboratory (ANL) for Fiscal Year 1991 (October 1990 through September 1991). This is the eighth annual report for the ACL. The Analytical Chemistry Laboratory is a full-cost-recovery service center, with the primary mission of providing a broad range of analytical chemistry support services to the scientific and engineering programs at ANL. In addition, the ACL conducts a research program in analytical chemistry, works on instrumental and methods development, and provides analytical services for governmental, educational, and industrial organizations. The ACL handlesmore » a wide range of analytical problems, from routine standard analyses to unique problems that require significant development of methods and techniques.« less

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

Green, D.W.; Heinrich, R.R.; Jensen, K.J.

The Analytical Chemistry Laboratory is a full-cost-recovery service center, with the primary mission of providing a broad range of technical support services to the scientific and engineering programs at ANL. In addition, ACL conducts a research program in analytical chemistry, works on instrumental and methods development, and provides analytical services for governmental, educational, and industrial organizations. The ACL handles a wide range of analytical problems, from routine standard analyses to unique problems that require significant development of methods and techniques. The purpose of this report is to summarize the technical and administrative activities of the Analytical Chemistry Laboratory (ACL) atmore » Argonne National Laboratory (ANL) for Fiscal Year 1985 (October 1984 through September 1985). This is the second annual report for the ACL. 4 figs., 1 tab.« less

Debris/ice/TPS assessment and integrated photographic analysis for Shuttle Mission STS-45

NASA Technical Reports Server (NTRS)

Katnik, Gregory N.; Higginbotham, Scott A.; Davis, J. Bradley

1992-01-01

The Debris Team has developed and implemented measures to control damage from debris in the Shuttle operational environment and to make the control measures a part of routine launch flows. These measures include engineering surveillance during vehicle processing and closeout operations, facility and flight hardware inspections before and after launch, and photographic analysis of mission events. Photographic analyses of mission imagery from launch, on-orbit, and landing provide significant data in verifying proper operation of systems and evaluating anomalies. In addition to the Kennedy Space Center (KSC) Photo/Video Analysis, reports from Johnson Space Center, Marshall Space Flight Center, and Rockwell International-Downey are also included to provide an integrated assessment of each Shuttle mission.

AgMIP's Transdisciplinary Agricultural Systems Approach to Regional Integrated Assessment of Climate Impacts, Vulnerability, and Adaptation

NASA Technical Reports Server (NTRS)

Antle, John M.; Valdivia, Roberto O.; Boote, Kenneth J.; Janssen, Sander; Jones, James W.; Porter, Cheryl H.; Rosenzweig, Cynthia; Ruane, Alexander C.; Thorburn, Peter J.

2015-01-01

This chapter describes methods developed by the Agricultural Model Intercomparison and Improvement Project (AgMIP) to implement a transdisciplinary, systems-based approach for regional-scale (local to national) integrated assessment of agricultural systems under future climate, biophysical, and socio-economic conditions. These methods were used by the AgMIP regional research teams in Sub-Saharan Africa and South Asia to implement the analyses reported in their respective chapters of this book. Additional technical details are provided in Appendix 1.The principal goal that motivates AgMIP's regional integrated assessment (RIA) methodology is to provide scientifically rigorous information needed to support improved decision-making by various stakeholders, ranging from local to national and international non-governmental and governmental organizations.

Postoptimality Analysis in the Selection of Technology Portfolios

NASA Technical Reports Server (NTRS)

Adumitroaie, Virgil; Shelton, Kacie; Elfes, Alberto; Weisbin, Charles R.

2006-01-01

This slide presentation reviews a process of postoptimally analysing the selection of technology portfolios. The rationale for the analysis stems from the need for consistent, transparent and auditable decision making processes and tools. The methodology is used to assure that project investments are selected through an optimization of net mission value. The main intent of the analysis is to gauge the degree of confidence in the optimal solution and to provide the decision maker with an array of viable selection alternatives which take into account input uncertainties and possibly satisfy non-technical constraints. A few examples of the analysis are reviewed. The goal of the postoptimality study is to enhance and improve the decision-making process by providing additional qualifications and substitutes to the optimal solution.

Improving phylogenetic analyses by incorporating additional information from genetic sequence databases.

PubMed

Liang, Li-Jung; Weiss, Robert E; Redelings, Benjamin; Suchard, Marc A

2009-10-01

Statistical analyses of phylogenetic data culminate in uncertain estimates of underlying model parameters. Lack of additional data hinders the ability to reduce this uncertainty, as the original phylogenetic dataset is often complete, containing the entire gene or genome information available for the given set of taxa. Informative priors in a Bayesian analysis can reduce posterior uncertainty; however, publicly available phylogenetic software specifies vague priors for model parameters by default. We build objective and informative priors using hierarchical random effect models that combine additional datasets whose parameters are not of direct interest but are similar to the analysis of interest. We propose principled statistical methods that permit more precise parameter estimates in phylogenetic analyses by creating informative priors for parameters of interest. Using additional sequence datasets from our lab or public databases, we construct a fully Bayesian semiparametric hierarchical model to combine datasets. A dynamic iteratively reweighted Markov chain Monte Carlo algorithm conveniently recycles posterior samples from the individual analyses. We demonstrate the value of our approach by examining the insertion-deletion (indel) process in the enolase gene across the Tree of Life using the phylogenetic software BALI-PHY; we incorporate prior information about indels from 82 curated alignments downloaded from the BAliBASE database.

Rural and remote dementia care challenges and needs: perspectives of formal and informal care providers residing in Saskatchewan, Canada.

PubMed

Dal Bello-Haas, Vanina P M; Cammer, Allison; Morgan, Debra; Stewart, Norma; Kosteniuk, Julie

2014-01-01

Rural and remote settings pose particular healthcare and service delivery challenges. Providing appropriate care and support for individuals with dementia and their families living in these communities is especially difficult, and can only be accomplished when the needs of care providers and the context and complexity of care provision are understood. This paper describes formal and informal caregivers' perceptions of the challenges and needs in providing care and support for individuals with dementia living in rural and remote areas of Saskatchewan, Canada. A mixed-methods exploratory approach was used to examine caregivers' needs. This research was a component of a broader process evaluation designed to inform the initial and ongoing development of a community-based participatory research program in rural dementia care, which included the development of the Rural and Remote Memory Clinic (RRMC). Four approaches were used for data collection and analyses: (1) thematic analysis of consultation meetings with rural healthcare providers: documented discussions from consultation meetings that occurred in 2003-2004 with rural physicians and healthcare providers regarding plans for a new RRMC were analysed thematically; (2) telephone and mail questionnaires: consultation meeting participants completed a subsequent telephone or mail questionnaire (2003-2004) that was analysed descriptively; (3) thematic analysis of referral letters to the Rural and Remote Memory Clinic: physician referral letters over a five-year period (2003-2008) were analysed descriptively and thematically; and (4) examination of family caregiver satisfaction: four specific baseline questionnaire questions completed by family caregivers (2007-2010) were analysed descriptively and thematically. Both physician and non-physician healthcare providers identified increased facilities and care programs as needs. Physicians were much more likely than other providers to report available support services for patients and families as adequate. Non-physician providers identified improved services, better coordination of services, travel and travel burden related needs, and staff training and education needs as priorities. Physician needs, as determined via referral letters, included confirmation of diagnosis or treatment, request for further management suggestions, patient or family request, and consultation regarding difficult cases. One-third of informal caregivers expressed not being satisfied with the care received prior to the Rural and Remote Memory Clinic assessment visit, and identified lack of diagnosis and long wait times for services as key issues. Delivering services and providing care and support for individuals with dementia living in rural and remote communities are especially challenging. The need for increased extent of services was a commonality among formal and informal caregivers. Primary care physicians may seek confirmation of their diagnosis or may need assistance when dealing with difficult aspects of care, as identified by referral letters. Differences between the needs identified via referral letters and questionnaire responses of physicians may be a reflection of the rural or remote context of care provision. Informal caregiver needs were more aligned with non-physician healthcare providers with respect to the need for improved access to additional healthcare professionals and services. The findings have implications for regional policy development that addresses human and other resource shortages.

Mental Health Providers' Decision-Making Around the Implementation of Evidence-Based Treatment for PTSD.

PubMed

Osei-Bonsu, Princess E; Bolton, Rendelle E; Wiltsey Stirman, Shannon; Eisen, Susan V; Herz, Lawrence; Pellowe, Maura E

2017-04-01

It is estimated that <15% of veterans with posttraumatic stress disorder (PTSD) have engaged in two evidence-based psychotherapies highly recommended by VA-cognitive processing therapy (CPT) and prolonged exposure (PE). CPT and PE guidelines specify which patients are appropriate, but research suggests that providers may be more selective than the guidelines. In addition, PTSD clinical guidelines encourage "shared decision-making," but there is little research on what processes providers use to make decisions about CPT/PE. Sixteen licensed psychologists and social workers from two VA medical centers working with ≥1 patient with PTSD were interviewed about patient factors considered and decision-making processes for CPT/PE use. Qualitative analyses revealed that patient readiness and comorbid conditions influenced decisions to use or refer patients with PTSD for CPT/PE. Providers reported mentally derived and instances of patient-involved decision-making around CPT/PE use. Continued efforts to assist providers in making informed and collaborative decisions about CPT/PE use are discussed.

Genetic Association and Gene-Gene Interaction Analyses in African American Dialysis Patients With Nondiabetic Nephropathy

PubMed Central

Bostrom, Meredith A.; Kao, W.H. Linda; Li, Man; Abboud, Hanna E.; Adler, Sharon G.; Iyengar, Sudha K.; Kimmel, Paul L.; Hanson, Robert L.; Nicholas, Susanne B.; Rasooly, Rebekah S.; Sedor, John R.; Coresh, Josef; Kohn, Orly F.; Leehey, David J.; Thornley-Brown, Denyse; Bottinger, Erwin P.; Lipkowitz, Michael S.; Meoni, Lucy A.; Klag, Michael J.; Lu, Lingyi; Hicks, Pamela J.; Langefeld, Carl D.; Parekh, Rulan S.; Bowden, Donald W.; Freedman, Barry I.

2011-01-01

Background African Americans (AAs) have increased susceptibility to non-diabetic nephropathy relative to European Americans. Study Design Follow-up of a pooled genome-wide association study (GWAS) in AA dialysis patients with nondiabetic nephropathy; novel gene-gene interaction analyses. Setting & Participants Wake Forest sample: 962 AA nondiabetic nephropathy cases; 931 non-nephropathy controls. Replication sample: 668 Family Investigation of Nephropathy and Diabetes (FIND) AA nondiabetic nephropathy cases; 804 non-nephropathy controls. Predictors Individual genotyping of top 1420 pooled GWAS-associated single nucleotide polymorphisms (SNPs) and 54 SNPs in six nephropathy susceptibility genes. Outcomes APOL1 genetic association and additional candidate susceptibility loci interacting with, or independently from, APOL1. Results The strongest GWAS associations included two non-coding APOL1 SNPs, rs2239785 (odds ratio [OR], 0.33; dominant; p = 5.9 × 10−24) and rs136148 (OR, 0.54; additive; p = 1.1 × 10−7) with replication in FIND (p = 5.0 × 10−21 and 1.9 × 10−05, respectively). Rs2239785 remained significantly associated after controlling for the APOL1 G1 and G2 coding variants. Additional top hits included a CFH SNP(OR from meta-analysis in above 3367 AA cases and controls, 0.81; additive; p = 6.8 × 10−4). The 1420 SNPs were tested for interaction with APOL1 G1 and G2 variants. Several interactive SNPs were detected, the most significant was rs16854341 in the podocin gene (NPHS2) (p = 0.0001). Limitations Non-pooled GWAS have not been performed in AA nondiabetic nephropathy. Conclusions This follow-up of a pooled GWAS provides additional and independent evidence that APOL1 variants contribute to nondiabetic nephropathy in AAs and identified additional associated and interactive non-diabetic nephropathy susceptibility genes. PMID:22119407

The Effect of Exposure to Ultraviolet Radiation in Infancy on Melanoma Risk.

PubMed

Gefeller, Olaf; Fiessler, Cornelia; Radespiel-Tröger, Martin; Uter, Wolfgang; Pfahlberg, Annette B

2016-01-01

Evidence on the effect of ultraviolet radiation (UVR) exposure in infancy on melanoma risk in later life is scarce. Three recent studies suffering from methodological shortcomings suggested that people born in spring carry a higher melanoma risk. Data from the Bavarian population-based cancer registry on 28374 incident melanoma cases between 2002 and 2012 were analyzed to reexamine this finding. Crude and adjusted analyses - using negative binomial regression models - were performed addressing the relationship. In the crude analysis, the birth months March - May were significantly overrepresented among melanoma cases. However, after additionally adjusting for the birth month distribution of the Bavarian population, the ostensible seasonal effect disappeared. Similar results emerged in all subgroup analyses. Our large registry-based study provides no evidence that people born in spring carry a higher risk for developing melanoma in later life and thus lends no support to the hypothesis of higher UVR-susceptibility during the first months of life.

Spatial quantile regression using INLA with applications to childhood overweight in Malawi.

PubMed

Mtambo, Owen P L; Masangwi, Salule J; Kazembe, Lawrence N M

2015-04-01

Analyses of childhood overweight have mainly used mean regression. However, using quantile regression is more appropriate as it provides flexibility to analyse the determinants of overweight corresponding to quantiles of interest. The main objective of this study was to fit a Bayesian additive quantile regression model with structured spatial effects for childhood overweight in Malawi using the 2010 Malawi DHS data. Inference was fully Bayesian using R-INLA package. The significant determinants of childhood overweight ranged from socio-demographic factors such as type of residence to child and maternal factors such as child age and maternal BMI. We observed significant positive structured spatial effects on childhood overweight in some districts of Malawi. We recommended that the childhood malnutrition policy makers should consider timely interventions based on risk factors as identified in this paper including spatial targets of interventions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dissecting effects of complex mixtures: who's afraid of informative priors?

PubMed

Thomas, Duncan C; Witte, John S; Greenland, Sander

2007-03-01

Epidemiologic studies commonly investigate multiple correlated exposures, which are difficult to analyze appropriately. Hierarchical modeling provides a promising approach for analyzing such data by adding a higher-level structure or prior model for the exposure effects. This prior model can incorporate additional information on similarities among the correlated exposures and can be parametric, semiparametric, or nonparametric. We discuss the implications of applying these models and argue for their expanded use in epidemiology. While a prior model adds assumptions to the conventional (first-stage) model, all statistical methods (including conventional methods) make strong intrinsic assumptions about the processes that generated the data. One should thus balance prior modeling assumptions against assumptions of validity, and use sensitivity analyses to understand their implications. In doing so - and by directly incorporating into our analyses information from other studies or allied fields - we can improve our ability to distinguish true causes of disease from noise and bias.

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

TSUNAMI Primer: A Primer for Sensitivity/Uncertainty Calculations with SCALE

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

Rearden, Bradley T; Mueller, Don; Bowman, Stephen M

2009-01-01

This primer presents examples in the application of the SCALE/TSUNAMI tools to generate k{sub eff} sensitivity data for one- and three-dimensional models using TSUNAMI-1D and -3D and to examine uncertainties in the computed k{sub eff} values due to uncertainties in the cross-section data used in their calculation. The proper use of unit cell data and need for confirming the appropriate selection of input parameters through direct perturbations are described. The uses of sensitivity and uncertainty data to identify and rank potential sources of computational bias in an application system and TSUNAMI tools for assessment of system similarity using sensitivity andmore » uncertainty criteria are demonstrated. Uses of these criteria in trending analyses to assess computational biases, bias uncertainties, and gap analyses are also described. Additionally, an application of the data adjustment tool TSURFER is provided, including identification of specific details of sources of computational bias.« less

Analysis of Solar Potential of Roofs Based on Digital Terrain Model

NASA Astrophysics Data System (ADS)

Gorički, M.; Poslončec-Petrić, V.; Frangeš, S.; Bačić, Ž.

2017-09-01

One of the basic goals of the smart city concept is to create a high-quality environment that is long sustainable and economically justifiable. The priority and concrete goal today is to promote and provide sustainable sources of energy (SSE). Croatia is rich with sun energy and as one of the sunniest European countries, it has a huge insufficiently used solar potential at its disposal. The paper describes the procedure of analysing the solar potential of a pilot area Sveti Križ Začretje by means of digital surface model (DSM) and based on the data available in the Meteorological and Hydrological Service of the Republic of Croatia. Although a more detailed analysis would require some additional factors, it is clear that the installation of 19,6m2 of solar panels in each household could cover annual requirements of the household in the analysed area, the locality Sveti Križ Začretje.

Geologic Field Notes, Geochemical Analyses, and Field Photographs of Outcrops and Rock Samples from the Big Delta B-1 Quadrangle, East-Central Alaska

USGS Publications Warehouse

Day, Warren C.; O'Neill, J. Michael

2008-01-01

The U.S. Geological Survey, in cooperation with the Alaska Department of Natural Resources Division of Mining, Land, and Water, has released a geologic map of the Big Delta B-1 quadrangle of east-central Alaska (Day and others, 2007). This companion report presents the major element oxide and trace element geochemical analyses, including those for gold, silver, and base metals, for representative rock units and for grab samples from quartz veins and mineralized zones within the quadrangle. Also included are field station locations, field notes, structural data, and field photographs based primarily on observations by W.C. Day with additions by J.M. O'Neill and B.M. Gamble, all of the U.S. Geological Survey. The data are provided in both Microsoft Excel spread sheet format and as a Microsoft Access database.

Molecular systematics and global phylogeography of angel sharks (genus Squatina).

PubMed

Stelbrink, Björn; von Rintelen, Thomas; Cliff, Geremy; Kriwet, Jürgen

2010-02-01

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe-North Africa-Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events. Copyright (c) 2009. Published by Elsevier Inc.

Distributed representations in memory: Insights from functional brain imaging

PubMed Central

Rissman, Jesse; Wagner, Anthony D.

2015-01-01

Forging new memories for facts and events, holding critical details in mind on a moment-to-moment basis, and retrieving knowledge in the service of current goals all depend on a complex interplay between neural ensembles throughout the brain. Over the past decade, researchers have increasingly leveraged powerful analytical tools (e.g., multi-voxel pattern analysis) to decode the information represented within distributed fMRI activity patterns. In this review, we discuss how these methods can sensitively index neural representations of perceptual and semantic content, and how leverage on the engagement of distributed representations provides unique insights into distinct aspects of memory-guided behavior. We emphasize that, in addition to characterizing the contents of memories, analyses of distributed patterns shed light on the processes that influence how information is encoded, maintained, or retrieved, and thus inform memory theory. We conclude by highlighting open questions about memory that can be addressed through distributed pattern analyses. PMID:21943171

The Dissociative Subtype of PTSD Scale (DSPS): Initial Evaluation in a National Sample of Trauma-Exposed Veterans

PubMed Central

Wolf, Erika J.; Mitchell, Karen S.; Sadeh, Naomi; Hein, Christina; Fuhrman, Isaac; Pietrzak, Robert H.; Miller, Mark W.

2015-01-01

The fifth edition of the Diagnostic and Statistical Manual (DSM-5) includes a dissociative subtype of posttraumatic stress disorder (PTSD), but no existing measures specifically assess it. This paper describes the initial evaluation of a 15-item self-report measure of the subtype called the Dissociative Subtype of PTSD Scale (DSPS) in an on-line survey of 697 trauma-exposed military veterans representative of the US veteran population. Exploratory factor analyses of the lifetime DSPS items supported the intended structure of the measure consisting of three factors reflecting derealization/depersonalization, loss of awareness, and psychogenic amnesia. Consistent with prior research, latent profile analyses assigned 8.3% of the sample to a highly dissociative class distinguished by pronounced symptoms of derealization and depersonalization. Overall, results provide initial psychometric support for the lifetime DSPS scales; additional research in clinical and community samples is needed to further validate the measure. PMID:26603115

The Dissociative Subtype of PTSD Scale: Initial Evaluation in a National Sample of Trauma-Exposed Veterans.

PubMed

Wolf, Erika J; Mitchell, Karen S; Sadeh, Naomi; Hein, Christina; Fuhrman, Isaac; Pietrzak, Robert H; Miller, Mark W

2017-06-01

The fifth edition of the Diagnostic and Statistical Manual includes a dissociative subtype of posttraumatic stress disorder, but no existing measures specifically assess it. This article describes the initial evaluation of a 15-item self-report measure of the subtype called the Dissociative Subtype of Posttraumatic Stress Disorder Scale (DSPS) in an online survey of 697 trauma-exposed military veterans representative of the U.S. veteran population. Exploratory factor analyses of the lifetime DSPS items supported the intended structure of the measure consisting of three factors reflecting derealization/depersonalization, loss of awareness, and psychogenic amnesia. Consistent with prior research, latent profile analyses assigned 8.3% of the sample to a highly dissociative class distinguished by pronounced symptoms of derealization and depersonalization. Overall, results provide initial psychometric support for the lifetime DSPS scales; additional research in clinical and community samples is needed to further validate the measure.

Coastal and wetland ecosystems of the Chesapeake Bay watershed: Applying palynology to understand impacts of changing climate, sea level, and land use

USGS Publications Warehouse

Willard, Debra A.; Bernhardt, Christopher E.; Hupp, Cliff R.; Newell, Wayne L.

2015-01-01

The mid-Atlantic region and Chesapeake Bay watershed have been influenced by fluctuations in climate and sea level since the Cretaceous, and human alteration of the landscape began ~12,000 years ago, with greatest impacts since colonial times. Efforts to devise sustainable management strategies that maximize ecosystem services are integrating data from a range of scientific disciplines to understand how ecosystems and habitats respond to different climatic and environmental stressors. Palynology has played an important role in improving understanding of the impact of changing climate, sea level, and land use on local and regional vegetation. Additionally, palynological analyses have provided biostratigraphic control for surficial mapping efforts and documented agricultural activities of both Native American populations and European colonists. This field trip focuses on sites where palynological analyses have supported efforts to understand the impacts of changing climate and land use on the Chesapeake Bay ecosystem.

Reanalysis of the Stratosphere in GEOS-5: Lessons Learned from MERRA and Future Prospects

NASA Technical Reports Server (NTRS)

Pawson, Steven

2011-01-01

The MERRA configuration of GEOS-5 includes about 30 layers in the middle atmosphere, with an upper boundary near 80km. Stratospheric Sounding Unit (SSU) and Advanced microwave sounding unit ( AMSU) radiance data are assimilated, which yield good constraints on the analyses up to the upper stratosphere. This paper examines the performance of MERRA, with foci on: the somewhat erratic system behavior in the 1980s, as numerous SSU instruments were available for short periods; the transition from SSU to AMSU radiances; conflicts between equivalent instruments on different platforms, given in the context of bias correction and the diurnal cycle; and, the relative stability of the analyses in the 21st Century. The results from MERRA provide guidance for how to use the operational polar-orbiting datasets in future reanalyses. Additional discussion will be directed at the possible use of research data sets, from limb-sounding instruments, in future multi-decadal products.

Natural Hazards and the press in the western Mediterranean region

NASA Astrophysics Data System (ADS)

Llasat-Botija, M.; Llasat, M. C.; López, L.

2007-07-01

This study analyses press articles published between 1982 and 2005 in an attempt to describe the social perception of natural hazards in Catalonia. The articles included in the database have been classified according to different types of risk. In addition, the study examines the evolution of each type of risk in the press coverage during the study period. Finally, the results have been compared to data provided by insurance companies with respect to compensations paid out for damages. Conclusions show that floods are the most important natural hazard in the region, but that the number of headlines for each event is greater in the case of snowfalls and forest fires. Factors such as the season of the year, the proximity of the affected region to the capital, the topical issues at the time, and the presence of other important news must be considered when the impact in the press is analysed.

CASAS: Cancer Survival Analysis Suite, a web based application

PubMed Central

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/. PMID:28928946

NASA Lewis Helps Company With New Single-Engine Business Turbojet

NASA Technical Reports Server (NTRS)

1998-01-01

Century Aerospace Corporation, a small company in Albuquerque, New Mexico, is developing a six-seat aircraft powered by a single turbofan engine for general aviation. The company had completed a preliminary design of the jet but needed analyses and testing to proceed with detailed design and subsequent fabrication of a prototype aircraft. NASA Lewis Research Center used computational fluid dynamics (CFD) analyses to ferret out areas of excessive curvature in the inlet where separation might occur. A preliminary look at the results indicated very good inlet performance; and additional calculations, performed with vortex generators installed in the inlet, led to even better results. When it was initially determined that the airflow distortion pattern at the compressor face fell outside of the limits set by the engine manufacturer, the Lewis team studied possible solutions, selected the best, and provided recommendations. CFD results for the inlet system were so good that wind tunnel tests were unnecessary.

Microfluidics for Single-Cell Genetic Analysis

PubMed Central

Thompson, A. M.; Paguirigan, A. L.; Kreutz, J. E.; Radich, J. P.; Chiu, D. T.

2014-01-01

The ability to correlate single-cell genetic information to cellular phenotypes will provide the kind of detailed insight into human physiology and disease pathways that is not possible to infer from bulk cell analysis. Microfluidic technologies are attractive for single-cell manipulation due to precise handling and low risk of contamination. Additionally, microfluidic single-cell techniques can allow for high-throughput and detailed genetic analyses that increase accuracy and decreases reagent cost compared to bulk techniques. Incorporating these microfluidic platforms into research and clinical laboratory workflows can fill an unmet need in biology, delivering the highly accurate, highly informative data necessary to develop new therapies and monitor patient outcomes. In this perspective, we describe the current and potential future uses of microfluidics at all stages of single-cell genetic analysis, including cell enrichment and capture, single-cell compartmentalization and manipulation, and detection and analyses. PMID:24789374

CASAS: Cancer Survival Analysis Suite, a web based application.

PubMed

Rupji, Manali; Zhang, Xinyan; Kowalski, Jeanne

2017-01-01

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/.

Analysis of Umami Taste Compounds in a Fermented Corn Sauce by Means of Sensory-Guided Fractionation.

PubMed

Charve, Joséphine; Manganiello, Sonia; Glabasnia, Arne

2018-02-28

Corn sauce, an ingredient obtained from the fermentation of enzymatically hydrolyzed corn starch and used in culinary applications to provide savory taste, was investigated in this study. The links between its sensory properties and taste compounds were assessed using a combination of analytical and sensory approaches. The analyses revealed that glutamic acid, sodium chloride, and acetic acid were the most abundant compounds, but they could not explain entirely the savory taste. The addition of other compounds, found at subthreshold concentrations (alanine, glutamyl peptides, and one Amadori compound), contributed partly to close the sensory gap between the re-engineered sample and the original product. Further chemical breakdown, by a sensory-guided fractionation approach, led to the isolation of two fractions with taste-modulating effects. Analyses by mass spectrometry and nuclear magnetic resonance showed that the fractions contained glutamyl peptides, pyroglutamic acid, glutamic acid, valine, N-formyl-glutamic acid, and N-acetyl-glutamine.

Radioactive Waste Management Complex low-level waste radiological performance assessment

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

Maheras, S.J.; Rood, A.S.; Magnuson, S.O.

This report documents the projected radiological dose impacts associated with the disposal of radioactive low-level waste at the Radioactive Waste Management Complex at the Idaho National Engineering Laboratory. This radiological performance assessment was conducted to evaluate compliance with applicable radiological criteria of the US Department of Energy and the US Environmental Protection Agency for protection of the public and the environment. The calculations involved modeling the transport of radionuclides from buried waste, to surface soil and subsurface media, and eventually to members of the public via air, groundwater, and food chain pathways. Projections of doses were made for both offsitemore » receptors and individuals inadvertently intruding onto the site after closure. In addition, uncertainty and sensitivity analyses were performed. The results of the analyses indicate compliance with established radiological criteria and provide reasonable assurance that public health and safety will be protected.« less

Mediation analysis in nursing research: a methodological review

PubMed Central

Liu, Jianghong; Ulrich, Connie

2017-01-01

Mediation statistical models help clarify the relationship between independent predictor variables and dependent outcomes of interest by assessing the impact of third variables. This type of statistical analysis is applicable for many clinical nursing research questions, yet its use within nursing remains low. Indeed, mediational analyses may help nurse researchers develop more effective and accurate prevention and treatment programs as well as help bridge the gap between scientific knowledge and clinical practice. In addition, this statistical approach allows nurse researchers to ask – and answer – more meaningful and nuanced questions that extend beyond merely determining whether an outcome occurs. Therefore, the goal of this paper is to provide a brief tutorial on the use of mediational analyses in clinical nursing research by briefly introducing the technique and, through selected empirical examples from the nursing literature, demonstrating its applicability in advancing nursing science. PMID:26176804

Geographically Sourcing Cocaine's Origin - Delineation of the Nineteen Major Coca Growing Regions in South America.

PubMed

Mallette, Jennifer R; Casale, John F; Jordan, James; Morello, David R; Beyer, Paul M

2016-03-23

Previously, geo-sourcing to five major coca growing regions within South America was accomplished. However, the expansion of coca cultivation throughout South America made sub-regional origin determinations increasingly difficult. The former methodology was recently enhanced with additional stable isotope analyses ((2)H and (18)O) to fully characterize cocaine due to the varying environmental conditions in which the coca was grown. An improved data analysis method was implemented with the combination of machine learning and multivariate statistical analysis methods to provide further partitioning between growing regions. Here, we show how the combination of trace cocaine alkaloids, stable isotopes, and multivariate statistical analyses can be used to classify illicit cocaine as originating from one of 19 growing regions within South America. The data obtained through this approach can be used to describe current coca cultivation and production trends, highlight trafficking routes, as well as identify new coca growing regions.

Geographically Sourcing Cocaine’s Origin - Delineation of the Nineteen Major Coca Growing Regions in South America

NASA Astrophysics Data System (ADS)

Mallette, Jennifer R.; Casale, John F.; Jordan, James; Morello, David R.; Beyer, Paul M.

2016-03-01

Previously, geo-sourcing to five major coca growing regions within South America was accomplished. However, the expansion of coca cultivation throughout South America made sub-regional origin determinations increasingly difficult. The former methodology was recently enhanced with additional stable isotope analyses (2H and 18O) to fully characterize cocaine due to the varying environmental conditions in which the coca was grown. An improved data analysis method was implemented with the combination of machine learning and multivariate statistical analysis methods to provide further partitioning between growing regions. Here, we show how the combination of trace cocaine alkaloids, stable isotopes, and multivariate statistical analyses can be used to classify illicit cocaine as originating from one of 19 growing regions within South America. The data obtained through this approach can be used to describe current coca cultivation and production trends, highlight trafficking routes, as well as identify new coca growing regions.

Catalog of Mount St. Helens 2004 - 2005 Tephra Samples with Major- and Trace-Element Geochemistry

USGS Publications Warehouse

Rowe, Michael C.; Thornber, Carl R.; Gooding, Daniel J.; Pallister, John S.

2008-01-01

This open-file report presents a catalog of information about 135 ash samples along with geochemical analyses of bulk ash, glass and individual mineral grains from tephra deposited as a result of volcanic activity at Mount St. Helens, Washington, from October 1, 2004 until August 15, 2005. This data, in conjunction with that in a companion report on 2004?2007 Mount St. Helens dome samples by Thornber and others (2008a) are presented in support of the contents of the U.S. Geological Survey Professional Paper 1750 (Sherrod and others, ed., 2008). Readers are referred to appropriate chapters in USGS Professional Paper 1750 for detailed narratives of eruptive activity during this time period and for interpretations of sample characteristics and geochemical data presented here. All ash samples reported herein are currently archived at the David A. Johnston Cascades Volcano Observatory in Vancouver, Washington. The Mount St. Helens 2004?2005 Tephra Sample Catalogue along with bulk, glass and mineral geochemistry are tabulated in 6 worksheets of the accompanying Microsoft Excel file, of2008-1131.xls. Samples in all tables are organized by collection date. Table 1 is a detailed catalog of sample information for tephra deposited downwind of Mount St. Helens between October 1, 2004 and August 18, 2005. Table 2 provides major- and trace-element analyses of 8 bulk tephra samples collected throughout that interval. Major-element compositions of 82 groundmass glass fragments, 420 feldspar grains, and 213 mafic (clinopyroxene, amphibole, hypersthene, and olivine) mineral grains from 12 ash samples collected between October 1, 2004 and March 8, 2005 are presented in tables 3 through 5. In addition, trace-element abundances of 198 feldspars from 11 ash samples (same samples as major-element analyses) are provided in table 6. Additional mineral and bulk ash analyses from 2004 and 2005 ash samples are published in chapters 30 (oxide thermometry; Pallister and others, 2008), 32 (amphibole major elements; Thornber and others, 2008b) and 37 (210Pb; 210Pb/226Pa; Reagan and others, 2008) of U.S. Geological Survey Professional Paper 1750 (Sherrod and others, 2008). A brief overview of sample collection methods is given below as an aid to deciphering the tephra sample catalog. This is followed by an explanation of the categories of sample information (column headers) in table 1. A summary of the analytical methods used to obtain the geochemical data in this report introduces the presentation of major- and trace-element geochemistry of Mount St. Helens 2004?2005 tephra samples in tables 2?6. Rhyolite glass standard analyses are reported (Appendix 1) to demonstrate the accuracy and precision of similar glass analyses presented herein.

On the Structure of Personality Disorder Traits: Conjoint Analyses of the CAT-PD, PID-5, and NEO-PI-3 Trait Models

PubMed Central

Wright, Aidan G.C.; Simms, Leonard J.

2014-01-01

The current study examines the relations among contemporary models of pathological and normal range personality traits. Specifically, we report on (a) conjoint exploratory factor analyses of the Computerized Adaptive Test of Personality Disorder static form (CAT-PD-SF) with the Personality Inventory for the DSM-5 (PID-5; Krueger et al., 2012) and NEO Personality Inventory-3 First Half (NEI-PI-3FH; McCrae & Costa, 2007), and (b) unfolding hierarchical analyses of the three measures in a large general psychiatric outpatient sample (N = 628; 64% Female). A five-factor solution provided conceptually coherent alignment among the CAT-PD-SF, PID-5, and NEO-PI-3FH scales. Hierarchical solutions suggested that higher-order factors bear strong resemblance to dimensions that emerge from structural models of psychopathology (e.g., Internalizing and Externalizing spectra). These results demonstrate that the CAT-PD-SF adheres to the consensual structure of broad trait domains at the five-factor level. Additionally, patterns of scale loadings further inform questions of structure and bipolarity of facet and domain level constructs. Finally, hierarchical analyses strengthen the argument for using broad dimensions that span normative and pathological functioning to scaffold a quantitatively derived phenotypic structure of psychopathology to orient future research on explanatory, etiological, and maintenance mechanisms. PMID:24588061

On the structure of personality disorder traits: conjoint analyses of the CAT-PD, PID-5, and NEO-PI-3 trait models.

PubMed

Wright, Aidan G C; Simms, Leonard J

2014-01-01

The current study examines the relations among contemporary models of pathological and normal range personality traits. Specifically, we report on (a) conjoint exploratory factor analyses of the Computerized Adaptive Test of Personality Disorder static form (CAT-PD-SF) with the Personality Inventory for the Diagnostic and Statistical Manual of Mental Disorders, fifth edition and NEO Personality Inventory-3 First Half, and (b) unfolding hierarchical analyses of the three measures in a large general psychiatric outpatient sample (n = 628; 64% Female). A five-factor solution provided conceptually coherent alignment among the CAT-PD-SF, PID-5, and NEO-PI-3FH scales. Hierarchical solutions suggested that higher-order factors bear strong resemblance to dimensions that emerge from structural models of psychopathology (e.g., Internalizing and Externalizing spectra). These results demonstrate that the CAT-PD-SF adheres to the consensual structure of broad trait domains at the five-factor level. Additionally, patterns of scale loadings further inform questions of structure and bipolarity of facet and domain level constructs. Finally, hierarchical analyses strengthen the argument for using broad dimensions that span normative and pathological functioning to scaffold a quantitatively derived phenotypic structure of psychopathology to orient future research on explanatory, etiological, and maintenance mechanisms.

Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa

PubMed Central

Campos, Alexandre; Turkina, Maria V.; Ribeiro, Tiago; Osorio, Hugo; Vasconcelos, Vítor; Antunes, Agostinho

2018-01-01

Cnidarian toxic products, particularly peptide toxins, constitute a promising target for biomedicine research. Indeed, cnidarians are considered as the largest phylum of generally toxic animals. However, research on peptides and toxins of sea anemones is still limited. Moreover, most of the toxins from sea anemones have been discovered by classical purification approaches. Recently, high-throughput methodologies have been used for this purpose but in other Phyla. Hence, the present work was focused on the proteomic analyses of whole-body extract from the unexplored sea anemone Bunodactis verrucosa. The proteomic analyses applied were based on two methods: two-dimensional gel electrophoresis combined with MALDI-TOF/TOF and shotgun proteomic approach. In total, 413 proteins were identified, but only eight proteins were identified from gel-based analyses. Such proteins are mainly involved in basal metabolism and biosynthesis of antibiotics as the most relevant pathways. In addition, some putative toxins including metalloproteinases and neurotoxins were also identified. These findings reinforce the significance of the production of antimicrobial compounds and toxins by sea anemones, which play a significant role in defense and feeding. In general, the present study provides the first proteome map of the sea anemone B. verrucosa stablishing a reference for future studies in the discovery of new compounds. PMID:29364843

Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa.

PubMed

Domínguez-Pérez, Dany; Campos, Alexandre; Alexei Rodríguez, Armando; Turkina, Maria V; Ribeiro, Tiago; Osorio, Hugo; Vasconcelos, Vítor; Antunes, Agostinho

2018-01-24

Cnidarian toxic products, particularly peptide toxins, constitute a promising target for biomedicine research. Indeed, cnidarians are considered as the largest phylum of generally toxic animals. However, research on peptides and toxins of sea anemones is still limited. Moreover, most of the toxins from sea anemones have been discovered by classical purification approaches. Recently, high-throughput methodologies have been used for this purpose but in other Phyla. Hence, the present work was focused on the proteomic analyses of whole-body extract from the unexplored sea anemone Bunodactis verrucosa . The proteomic analyses applied were based on two methods: two-dimensional gel electrophoresis combined with MALDI-TOF/TOF and shotgun proteomic approach. In total, 413 proteins were identified, but only eight proteins were identified from gel-based analyses. Such proteins are mainly involved in basal metabolism and biosynthesis of antibiotics as the most relevant pathways. In addition, some putative toxins including metalloproteinases and neurotoxins were also identified. These findings reinforce the significance of the production of antimicrobial compounds and toxins by sea anemones, which play a significant role in defense and feeding. In general, the present study provides the first proteome map of the sea anemone B. verrucosa stablishing a reference for future studies in the discovery of new compounds.

Gender consistency and flexibility: using dynamics to understand the relationship between gender and adjustment.

PubMed

DiDonato, Matthew D; Martin, Carol L; Hessler, Eric E; Amazeen, Polemnia G; Hanish, Laura D; Fabes, Richard A

2012-04-01

Controversy surrounds questions regarding the influence of being gender consistent (i.e., having and expressing gendered characteristics that are consistent with one's biological sex) versus being gender flexible (i.e., having and expressing gendered characteristics that vary from masculine to feminine as circumstances arise) on children's adjustment outcomes, such as self-esteem, positive emotion, or behavior problems. Whereas evidence supporting the consistency hypothesis is abundant, little support exists for the flexibility hypothesis. To shed new light on the flexibility hypothesis, we explored children's gendered behavior from a dynamical perspective that highlighted variability and flexibility in addition to employing a conventional approach that emphasized stability and consistency. Conventional mean-level analyses supported the consistency hypothesis by revealing that gender atypical behavior was related to greater maladjustment, and dynamical analyses supported the flexibility hypothesis by showing that flexibility of gendered behavior over time was related to positive adjustment. Integrated analyses showed that gender typical behavior was related to the adjustment of children who were behaviorally inflexible, but not for those who were flexible. These results provided a more comprehensive understanding of the relation between gendered behavior and adjustment in young children and illustrated for the first time the feasibility of applying dynamical analyses to the study of gendered behavior.

Systematics and diversification of Anindobothrium Marques, Brooks & Lasso, 2001 (Eucestoda: Rhinebothriidea)

PubMed Central

Primon, Juliana F.

2017-01-01

Tapeworms of the genus Anindobothrium Marques, Brooks & Lasso, 2001 are found in both marine and Neotropical freshwater stingrays of the family Potamotrygonidae. The patterns of host association within the genus support the most recent hypothesis about the history of diversification of potamotrygonids, which suggests that the ancestor of freshwater lineages of the Potamotrygonidae colonized South American river systems through marine incursion events. Despite the relevance of the genus Anindobothrium to understand the history of colonization and diversification of potamotrygonids, no additional efforts were done to better investigate the phylogenetic relationship of this taxon with other lineages of cestodes since its erection. This study is a result of recent collecting efforts to sample members of the genus in marine and freshwater potamotrygonids that enabled the most extensive documentation of the fauna of Anindobothrium parasitizing species of Styracura de Carvalho, Loboda & da Silva, Potamotrygon schroederi Fernández-Yépez, P. orbignyi (Castelnau) and P. yepezi Castex & Castello from six different countries, representing the eastern Pacific Ocean, Caribbean Sea, and river basins in South America (Rio Negro, Orinoco, and Maracaibo). The newly collected material provided additional specimens for morphological studies and molecular samples for subsequent phylogenetic analyses that allowed us to address the phylogenetic position of Anindobothrium and provide molecular and morphological evidence to recognize two additional species for the genus. The taxonomic actions that followed our analyses included the proposition of a new family, Anindobothriidae fam. n., to accommodate the genus Anindobothrium in the order Rhinebothriidea Healy, Caira, Jensen, Webster & Littlewood, 2009 and the description of two new species—one from the eastern Pacific Ocean, A. carrioni sp. n., and the other from the Caribbean Sea, A. inexpectatum sp. n. In addition, we also present a redescription of the type species of the genus, A. anacolum (Brooks, 1977) Marques, Brooks & Lasso, 2001, and of A. lisae Marques, Brooks & Lasso, 2001. Finally, we discuss the paleogeographical events mostly linked with the diversification of the genus and the protocols adopted to uncover cryptic diversity in Anindobothrium. PMID:28953933

Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly.

PubMed

Kim, Soonok; Cho, Yun Sung; Kim, Hak-Min; Chung, Oksung; Kim, Hyunho; Jho, Sungwoong; Seomun, Hong; Kim, Jeongho; Bang, Woo Young; Kim, Changmu; An, Junghwa; Bae, Chang Hwan; Bhak, Youngjune; Jeon, Sungwon; Yoon, Hyejun; Kim, Yumi; Jun, JeHoon; Lee, HyeJin; Cho, Suan; Uphyrkina, Olga; Kostyria, Aleksey; Goodrich, John; Miquelle, Dale; Roelke, Melody; Lewis, John; Yurchenko, Andrey; Bankevich, Anton; Cho, Juok; Lee, Semin; Edwards, Jeremy S; Weber, Jessica A; Cook, Jo; Kim, Sangsoo; Lee, Hang; Manica, Andrea; Lee, Ilbeum; O'Brien, Stephen J; Bhak, Jong; Yeo, Joo-Hong

2016-10-11

There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild Amur leopard whole genomes. In addition to a clear contraction in gene families for starch and sucrose metabolism, the carnivore genomes showed evidence of shared evolutionary adaptations in genes associated with diet, muscle strength, agility, and other traits responsible for successful hunting and meat consumption. Additionally, an analysis of highly conserved regions at the family level revealed molecular signatures of dietary adaptation in each of Felidae, Hominidae, and Bovidae. However, unlike carnivores, omnivores and herbivores showed fewer shared adaptive signatures, indicating that carnivores are under strong selective pressure related to diet. Finally, felids showed recent reductions in genetic diversity associated with decreased population sizes, which may be due to the inflexible nature of their strict diet, highlighting their vulnerability and critical conservation status. Our study provides a large-scale family level comparative genomic analysis to address genomic changes associated with dietary specialization. Our genomic analyses also provide useful resources for diet-related genetic and health research.

EnGeoMAP - geological applications within the EnMAP hyperspectral satellite science program

NASA Astrophysics Data System (ADS)

Boesche, N. K.; Mielke, C.; Rogass, C.; Guanter, L.

2016-12-01

Hyperspectral investigations from near field to space substantially contribute to geological exploration and mining monitoring of raw material and mineral deposits. Due to their spectral characteristics, large mineral occurrences and minefields can be identified from space and the spatial distribution of distinct proxy minerals be mapped. In the frame of the EnMAP hyperspectral satellite science program a mineral and elemental mapping tool was developed - the EnGeoMAP. It contains a basic mineral mapping and a rare earth element mapping approach. This study shows the performance of EnGeoMAP based on simulated EnMAP data of the rare earth element bearing Mountain Pass Carbonatite Complex, USA, and the Rodalquilar and Lomilla Calderas, Spain, which host the economically relevant gold-silver, lead-zinc-silver-gold and alunite deposits. The mountain pass image data was simulated on the basis of AVIRIS Next Generation images, while the Rodalquilar data is based on HyMap images. The EnGeoMAP - Base approach was applied to both images, while the mountain pass image data were additionally analysed using the EnGeoMAP - REE software tool. The results are mineral and elemental maps that serve as proxies for the regional lithology and deposit types. The validation of the maps is based on chemical analyses of field samples. Current airborne sensors meet the spatial and spectral requirements for detailed mineral mapping and future hyperspectral space borne missions will additionally provide a large coverage. For those hyperspectral missions, EnGeoMAP is a rapid data analysis tool that is provided to spectral geologists working in mineral exploration.

Sequential karyotyping in Burkitt lymphoma reveals a linear clonal evolution with increase in karyotype complexity and a high frequency of recurrent secondary aberrations.

PubMed

Aukema, Sietse M; Theil, Laura; Rohde, Marius; Bauer, Benedikt; Bradtke, Jutta; Burkhardt, Birgit; Bonn, Bettina R; Claviez, Alexander; Gattenlöhner, Stefan; Makarova, Olga; Nagel, Inga; Oschlies, Ilske; Pott, Christiane; Szczepanowski, Monika; Traulsen, Arne; Kluin, Philip M; Klapper, Wolfram; Siebert, Reiner; Murga Penas, Eva M

2015-09-01

Typical Burkitt lymphoma is characterized by an IG-MYC translocation and overall low genomic complexity. Clinically, Burkitt lymphoma has a favourable prognosis with very few relapses. However, the few patients experiencing disease progression and/or relapse have a dismal outcome. Here we report cytogenetic findings of seven cases of Burkitt lymphoma in which sequential karyotyping was performed at time of diagnosis and/or disease progression/relapse(s). After case selection, karyotype re-review and additional molecular analyses were performed in six paediatric cases, treated in Berlin-Frankfurt-Münster-Non-Hodgkin lymphoma study group trials, and one additional adult patient. Moreover, we analysed 18 cases of Burkitt lymphoma from the Mitelman database in which sequential karyotyping was performed. Our findings show secondary karyotypes to have a significant increase in load of cytogenetic aberrations with a mean number of 2, 5 and 8 aberrations for primary, secondary and third investigations. Importantly, this increase in karyotype complexity seemed to result from recurrent secondary chromosomal changes involving mainly trisomy 21, gains of 1q and 7q, losses of 6q, 11q, 13q, and 17p. In addition, our findings indicate a linear clonal evolution to be the predominant manner of cytogenetic evolution. Our data may provide a biological framework for the dismal outcome of progressive and relapsing Burkitt lymphoma. © 2015 John Wiley & Sons Ltd.

The International Space Station Urine Monitoring System (UMS)

NASA Technical Reports Server (NTRS)

Feeback, Daniel L.; Cibuzar, Branelle R.; Milstead, Jeffery R.; Pietrzyk,, Robert A.; Clark, Mark S.F.

2009-01-01

A device capable of making in-flight volume measurements of single void urine samples, the Urine Monitoring System (UMS), was developed and flown on seven U.S. Space Shuttle missions. This device provided volume data for each urine void from multiple crewmembers and allowed samples of each to be taken and returned to Earth for post-flight analysis. There were a number of design flaws in the original instrument including the presence of liquid carry-over producing invalid "actual" micturition volumes and cross-contamination between successive users from residual urine in "dead" spots". Additionally, high or low volume voids could not be accurately measured, the on-orbit calibration and nominal use sequence was time intensive, and the unit had to be returned and disassembled to retrieve the volume data. These problems have been resolved in a new version, the International Space Station (ISS) UMS, that has been designed to provide real-time in-flight volume data with accuracy and precision equivalent to measurements made on Earth and the ability to provide urine samples that are unadulterated by the device. Originally conceived to be interfaced with a U.S.-built Waste Collection System (WCS), the unit now has been modified to interface with the Russian-supplied Sanitary Hygiene Device (ASY). The ISS UMS provides significant advantages over the current method of collecting urine samples into Urine Collection Devices (UCDs), from which samples are removed and returned to Earth for analyses. A significant future advantage of the UMS is that it can provide an interface to analytical instrumentation that will allow real-time measurement of urine bioanalytes allowing monitoring of crewmember health status during flight and the ability to provide medical interventions based on the results of these measurements. Currently, the ISS UMS is scheduled to launch along with Node-3 on STS-130 (20A) in December 2009. UMS will be installed and scientific/functional verification completed prior to placing the instrument into operation. Samples collected during the verification sequence will be returned for analyses on STS-131 (19A) currently scheduled for launch in March 2010. The presence of a UMS on ISS will provide the capability to conduct additional collaborative human life science investigations among the ISS International Partners.

Is more better than less? An analysis of children's mental health services.

PubMed Central

Foster, E M

2000-01-01

OBJECTIVE: To assess the dose-response relationship for outpatient therapy received by children and adolescents-that is, to determine the impact of added outpatient visits on key mental health outcomes (functioning and symptomatology). DATA SOURCES/STUDY SETTING: The results presented involve analyses of data from the Fort Bragg Demonstration and are based on a sample of 301 individuals using outpatient services. STUDY DESIGN: This article provides estimates of the impact of outpatient therapy based on comparisons of individuals receiving differing treatment doses. Those comparisons involve standard multiple regression analyses as well as instrumental variables estimation. The latter provides a means of adjusting comparisons for unobserved or unmeasured differences among individuals receiving differing doses, differences that would otherwise be confounded with the impact of treatment dose. DATA COLLECTION/EXTRACTION METHODS: Using structured diagnostic interviews and behavior checklists completed by the child and his or her caretaker, detailed data on psychopathology, symptomatology, and psychosocial functioning were collected on individuals included in these analyses. Information on the use of mental health services was taken from insurance claims and a management information system. Services data were used to describe the use of outpatient therapy within the year following entry into the study. PRINCIPAL FINDINGS/CONCLUSIONS: Instrumental variables estimation indicates that added outpatient therapy improves functioning among children and adolescents. The effect is statistically significant and of moderate practical magnitude. These results imply that conventional analyses of the dose-response relationship may understate the impact of additional treatment on functioning. This finding is robust to choice of functional form, length of time over which outcomes are measured, and model specification. Dose does not appear to influence symptomatology. PMID:11130814

Multi-locus phylogeny of dolphins in the subfamily Lissodelphininae: character synergy improves phylogenetic resolution

PubMed Central

Harlin-Cognato, April D; Honeycutt, Rodney L

2006-01-01

Background Dolphins of the genus Lagenorhynchus are anti-tropically distributed in temperate to cool waters. Phylogenetic analyses of cytochrome b sequences have suggested that the genus is polyphyletic; however, many relationships were poorly resolved. In this study, we present a combined-analysis phylogenetic hypothesis for Lagenorhynchus and members of the subfamily Lissodelphininae, which is derived from two nuclear and two mitochondrial data sets and the addition of 34 individuals representing 9 species. In addition, we characterize with parsimony and Bayesian analyses the phylogenetic utility and interaction of characters with statistical measures, including the utility of highly consistent (non-homoplasious) characters as a conservative measure of phylogenetic robustness. We also explore the effects of removing sources of character conflict on phylogenetic resolution. Results Overall, our study provides strong support for the monophyly of the subfamily Lissodelphininae and the polyphyly of the genus Lagenorhynchus. In addition, the simultaneous parsimony analysis resolved and/or improved resolution for 12 nodes including: (1) L. albirostris, L. acutus; (2) L. obscurus and L. obliquidens; and (3) L. cruciger and L. australis. In addition, the Bayesian analysis supported the monophyly of the Cephalorhynchus, and resolved ambiguities regarding the relationship of L. australis/L. cruciger to other members of the genus Lagenorhynchus. The frequency of highly consistent characters varied among data partitions, but the rate of evolution was consistent within data partitions. Although the control region was the greatest source of character conflict, removal of this data partition impeded phylogenetic resolution. Conclusion The simultaneous analysis approach produced a more robust phylogenetic hypothesis for Lagenorhynchus than previous studies, thus supporting a phylogenetic approach employing multiple data partitions that vary in overall rate of evolution. Even in cases where there was apparent conflict among characters, our data suggest a synergistic interaction in the simultaneous analysis, and speak against a priori exclusion of data because of potential conflicts, primarily because phylogenetic results can be less robust. For example, the removal of the control region, the putative source of character conflict, produced spurious results with inconsistencies among and within topologies from parsimony and Bayesian analyses. PMID:17078887

Review Article: Multi-criteria decision making for flood risk management: a survey of the current state-of-the-art

NASA Astrophysics Data System (ADS)

de Brito, M. M.; Evers, M.

2015-11-01

This paper provides a review of Multi-Criteria Decision Making (MCDM) applications to flood risk management, seeking to highlight trends and identify research gaps. Totally, 128 peer-reviewed papers published from 1995 to June 2015 were systematically analysed and classified into the following application areas: (1) ranking of alternatives for flood mitigation, (2) reservoir flood control, (3) susceptibility, (4) hazard, (5) vulnerability, (6) risk, (7) coping capacity, and (8) emergency management. Additionally, the articles were categorized based on the publication year, MCDM method, whether they were or were not carried out in a participatory process, and if uncertainty and sensitivity analysis were performed. Results showed that the number of flood MCDM publications has exponentially grown during this period, with over 82 % of all papers published since 2009. The Analytical Hierarchy Process (AHP) was the most popular technique, followed by Technique for Order Preference by Similarity to an Ideal Solution (TOPSIS), and Simple Additive Weighting (SAW). Although there is greater interest on MCDM, uncertainty analysis remains an issue and is seldom applied in flood-related studies. In addition, participation of multiple stakeholders has been generally fragmented, focusing on particular stages of the decision-making process, especially on the definition of criteria weights. Based on the survey, some suggestions for further investigation are provided.

Simplified spacecraft vulnerability assessments at component level in early design phase at the European Space Agency's Concurrent Design Facility

NASA Astrophysics Data System (ADS)

Kempf, Scott; Schäfer, Frank K.; Cardone, Tiziana; Ferreira, Ivo; Gerené, Sam; Destefanis, Roberto; Grassi, Lilith

2016-12-01

During recent years, the state-of-the-art risk assessment of the threat posed to spacecraft by micrometeoroids and space debris has been expanded to the analysis of failure modes of internal spacecraft components. This method can now be used to perform risk analyses for satellites to assess various failure levels - from failure of specific sub-systems to catastrophic break-up. This new assessment methodology is based on triple-wall ballistic limit equations (BLEs), specifically the Schäfer-Ryan-Lambert (SRL) BLE, which is applicable for describing failure threshold levels for satellite components following a hypervelocity impact. The methodology is implemented in the form of the software tool Particle Impact Risk and vulnerability Analysis Tool (PIRAT). During a recent European Space Agency (ESA) funded study, the PIRAT functionality was expanded in order to provide an interface to ESA's Concurrent Design Facility (CDF). The additions include a geometry importer and an OCDT (Open Concurrent Design Tool) interface. The new interface provides both the expanded geometrical flexibility, which is provided by external computer aided design (CAD) modelling, and an ease of import of existing data without the need for extensive preparation of the model. The reduced effort required to perform vulnerability analyses makes it feasible for application during early design phase, at which point modifications to satellite design can be undertaken with relatively little extra effort. The integration of PIRAT in the CDF represents the first time that vulnerability analyses can be performed in-session in ESA's CDF and the first time that comprehensive vulnerability studies can be applied cost-effectively in early design phase in general.

Stranding Events of Kogia Whales along the Brazilian Coast.

PubMed

Moura, Jailson F; Acevedo-Trejos, Esteban; Tavares, Davi C; Meirelles, Ana C O; Silva, Cristine P N; Oliveira, Larissa R; Santos, Roberta A; Wickert, Janaína C; Machado, Rodrigo; Siciliano, Salvatore; Merico, Agostino

2016-01-01

The genus Kogia, which comprises only two extant species, Kogia sima and Kogia breviceps, represents one of the least known groups of cetaceans in the global ocean. In some coastal regions, however, stranding events of these species have been relatively common over the last decades. Stranding provides the opportunity to investigate the biology of these cetaceans and to explore the epidemiological aspects associated with the mortality of the organisms found on the beach. A number of disturbances (including pelagic fisheries, chemical pollution, boat strikes, and noise pollution) have been confirmed to pose a particular threat to the Kogia species. However, no study has yet investigated potential relationships between environmental conditions and stranding events. Here we analyse how a collection of environmental, physical, and biological variables, such as wind, sea surface temperature (SST), water depth, and chlorophyll-a, correlate to Kogia stranding events along the Brazilian coast. The results of our statistical analyses suggest that K. sima is more likely found in warm tropical waters, which provide an explanation for the high frequency of stranding in northeastern Brazilian coast. In contrast, K. breviceps appears to have a preference for temperate and productive waters. Wind speed results to be also an important factor for predicting Kogia strandings in Brazilian coast. Additionally, literature information in combination with our own data and analyses of stomach contents confirms that oceanic cephalopods constitute the primary nutritional source of both Kogia species. By using the available information as a qualitative proxy for habitat preference and feeding ecology, our study provides a novel and comprehensive assessment of Kogia stranding data in relation to environmental conditions along the Brazilian coast.

Evaluating the provenance of Permian-Triassic and Palaeocene-Eocene ash beds by high precision U-Pb and Lu-Hf isotopic analyses of zircons: linking local sedimentary records to global events

NASA Astrophysics Data System (ADS)

Eivind Augland, Lars; Jones, Morgan; Planke, Sverre; Svensen, Henrik; Tegner, Christian

2016-04-01

Zircons are a powerful tool in geochronology and isotope geochemistry, as their affinity for U and Hf in the crystal structure and the low initial Pb and Lu allow for precise and accurate dating by U-Pb ID-TIMS and precise and accurate determination of initial Hf isotopic composition by solution MC-ICP-MS analysis. The U-Pb analyses provide accurate chronostratigraphic controls on the sedimentary successions and absolute age frames for the biotic evolution across geological boundaries. Moreover, the analyses of Lu-Hf by solution MC-ICP-MS after Hf-purification column chemistry provide a powerful and robust fingerprinting tool to test the provenance of individual ash beds. Here we focus on ash beds from Permian-Triassic and Palaeocene successions in Svalbard and from the Palaeocene-Eocene Thermal Maximum (PETM) in Fur, Denmark. Used in combination with whole rock geochemistry from the ash layers and the available geochemical and isotopic data from potential source volcanoes, these data are used to evaluate the provenance of the Permian-Triassic and Palaeocene ashes preserved in Svalbard and PETM ashes in Denmark. If explosive eruptions from volcanic centres such as the Siberian Traps and the North Atlantic Igneous Province (NAIP) can be traced to distal basins as ash layers, they provide robust tests of hypotheses of global synchronicity of environmental changes and biotic crises. In addition, the potential correlation of ash layers with source volcanoes will aid in constraining the extent of explosive volcanism in the respective volcanic centres. The new integrated data sets will also contribute to establish new reference sections for the study of these boundary events when combined with stable isotope data and biostratigraphy.

PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences

PubMed Central

Machida, Ryuji J.; Knowlton, Nancy

2012-01-01

Background Metagenetic analyses, which amplify and sequence target marker DNA regions from environmental samples, are increasingly employed to assess the biodiversity of communities of small organisms. Using this approach, our understanding of microbial diversity has expanded greatly. In contrast, only a few studies using this approach to characterize metazoan diversity have been reported, despite the fact that many metazoan species are small and difficult to identify or are undescribed. One of the reasons for this discrepancy is the availability of universal primers for the target taxa. In microbial studies, analysis of the 16S ribosomal DNA is standard. In contrast, the best gene for metazoan metagenetics is less clear. In the present study, we have designed primers that amplify the nuclear 18S and 28S ribosomal DNA sequences of most metazoan species with the goal of providing effective approaches for metagenetic analyses of metazoan diversity in environmental samples, with a particular emphasis on marine biodiversity. Methodology/Principal Findings Conserved regions suitable for designing PCR primers were identified using 14,503 and 1,072 metazoan sequences of the nuclear 18S and 28S rDNA regions, respectively. The sequence similarity of both these newly designed and the previously reported primers to the target regions of these primers were compared for each phylum to determine the expected amplification efficacy. The nucleotide diversity of the flanking regions of the primers was also estimated for genera or higher taxonomic groups of 11 phyla to determine the variable regions within the genes. Conclusions/Significance The identified nuclear ribosomal DNA primers (five primer pairs for 18S and eleven for 28S) and the results of the nucleotide diversity analyses provide options for primer combinations for metazoan metagenetic analyses. Additionally, advantages and disadvantages of not only the 18S and 28S ribosomal DNA, but also other marker regions as targets for metazoan metagenetic analyses, are discussed. PMID:23049971

Variable effectiveness of stepwise implementation of nudge-type interventions to improve provider compliance with intraoperative low tidal volume ventilation.

PubMed

O'Reilly-Shah, Vikas N; Easton, George S; Jabaley, Craig S; Lynde, Grant C

2018-05-18

Identifying mechanisms to improve provider compliance with quality metrics is a common goal across medical disciplines. Nudge interventions are minimally invasive strategies that can influence behavioural changes and are increasingly used within healthcare settings. We hypothesised that nudge interventions may improve provider compliance with lung-protective ventilation (LPV) strategies during general anaesthesia. We developed an audit and feedback dashboard that included information on both provider-level and department-level compliance with LPV strategies in two academic hospitals, two non-academic hospitals and two academic surgery centres affiliated with a single healthcare system. Dashboards were emailed to providers four times over the course of the 9-month study. Additionally, the default setting on anaesthesia machines for tidal volume was decreased from 700 mL to 400 mL. Data on surgical cases performed between 1 September 2016 and 31 May 2017 were examined for compliance with LPV. The impact of the interventions was assessed via pairwise logistic regression analysis corrected for multiple comparisons. A total of 14 793 anaesthesia records were analysed. Absolute compliance rates increased from 59.3% to 87.8%preintervention to postintervention. Introduction of attending physician dashboards resulted in a 41% increase in the odds of compliance (OR 1.41, 95% CI 1.17 to 1.69, p=0.002). Subsequently, the addition of advanced practice provider and resident dashboards lead to an additional 93% increase in the odds of compliance (OR 1.93, 95% CI 1.52 to 2.46, p<0.001). Lastly, modifying ventilator defaults led to a 376% increase in the odds of compliance (OR 3.76, 95% CI 3.1 to 4.57, p<0.001). Audit and feedback tools in conjunction with default changes improve provider compliance. © 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.

Applications of NMR and computational methodologies to study protein dynamics.

PubMed

Narayanan, Chitra; Bafna, Khushboo; Roux, Louise D; Agarwal, Pratul K; Doucet, Nicolas

2017-08-15

Overwhelming evidence now illustrates the defining role of atomic-scale protein flexibility in biological events such as allostery, cell signaling, and enzyme catalysis. Over the years, spin relaxation nuclear magnetic resonance (NMR) has provided significant insights on the structural motions occurring on multiple time frames over the course of a protein life span. The present review article aims to illustrate to the broader community how this technique continues to shape many areas of protein science and engineering, in addition to being an indispensable tool for studying atomic-scale motions and functional characterization. Continuing developments in underlying NMR technology alongside software and hardware developments for complementary computational approaches now enable methodologies to routinely provide spatial directionality and structural representations traditionally harder to achieve solely using NMR spectroscopy. In addition to its well-established role in structural elucidation, we present recent examples that illustrate the combined power of selective isotope labeling, relaxation dispersion experiments, chemical shift analyses, and computational approaches for the characterization of conformational sub-states in proteins and enzymes. Copyright © 2017 Elsevier Inc. All rights reserved.

Controlling Methane Emissions in the Natural Gas Sector. A Review of Federal and State Regulatory Frameworks Governing Production, Gathering, Processing, Transmission, and Distribution

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

Paranhos, Elizabeth; Kozak, Tracy G.; Boyd, William

This report provides an overview of the regulatory frameworks governing natural gas supply chain infrastructure siting, construction, operation, and maintenance. Information was drawn from a number of sources, including published analyses, government reports, in addition to relevant statutes, court decisions and regulatory language, as needed. The scope includes all onshore facilities that contribute to methane emissions from the natural gas sector, focusing on three areas of state and federal regulations: (1) natural gas pipeline infrastructure siting and transportation service (including gathering, transmission, and distribution pipelines), (2) natural gas pipeline safety, and (3) air emissions associated with the natural gas supplymore » chain. In addition, the report identifies the incentives under current regulatory frameworks to invest in measures to reduce leakage, as well as the barriers facing investment in infrastructure improvement to reduce leakage. Policy recommendations regarding how federal or state authorities could regulate methane emissions are not provided; rather, existing frameworks are identified and some of the options for modifying existing regulations or adopting new regulations to reduce methane leakage are discussed.« less

31P-edited diffusion-ordered 1H NMR spectroscopy for the spectral isolation and identification of organophosphorus compounds related to chemical weapons agents and their degradation products.

PubMed

Mayer, Brian P; Valdez, Carlos A; Hok, Saphon; Chinn, Sarah C; Hart, Bradley R

2012-12-04

Organophosphorus compounds represent a large class of molecules that include pesticides, flame-retardants, biologically relevant molecules, and chemical weapons agents (CWAs). The detection and identification of organophosphorus molecules, particularly in the cases of pesticides and CWAs, are paramount to the verification of international treaties by various organizations. To that end, novel analytical methodologies that can provide additional support to traditional analyses are important for unambiguous identification of these compounds. We have developed an NMR method that selectively edits for organophosphorus compounds via (31)P-(1)H heteronuclear single quantum correlation (HSQC) and provides an additional chromatographic-like separation based on self-diffusivities of the individual species via (1)H diffusion-ordered spectroscopy (DOSY): (1)H-(31)P HSQC-DOSY. The technique is first validated using the CWA VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) by traditional two-dimensional DOSY spectra. We then extend this technique to a complex mixture of VX degradation products and identify all the main phosphorus-containing byproducts generated after exposure to a zinc-cyclen organometallic homogeneous catalyst.

Honoring the Past and Looking to the Future: Updates on Seminal Behavior Therapy Publications on Current Therapies and Future Directions.

PubMed

Newman, Michelle G

2016-11-01

This is the introduction to the second of two special issues in honor of the 50 th anniversary of the Association for Behavioral and Cognitive Therapies. The goal of this issue is to pay tribute to prior seminal Behavior Therapy publications on current therapies and future directions, to provide an updated review of important topics covered by these papers, and to make recommendations for the future. Each invited paper in this issue highlights a particular Behavior Therapy publication's contribution to our understanding and also provides an updated review or meta-analysis on the topic of the original paper. The topics covered here include review papers on current therapies such as cognitive and behavioral therapies, youth and family psychotherapy, unified protocols, and third-wave therapies. In addition, we include a review paper on implementation science, and meta-analyses on individualized psychotherapy, and culturally adapted interventions. With the two 50 th anniversary issues of Behavior Therapy, we hope to inspire additional research and discussion. Copyright © 2016. Published by Elsevier Ltd.

Value and usability of unpublished data sources for systematic reviews and network meta-analyses.

PubMed

Halfpenny, Nicholas James Anthony; Quigley, Joan Mary; Thompson, Juliette Catherine; Scott, David Alexander

2016-12-01

Peer-reviewed publications and conference proceedings are the mainstay of data sources for systematic reviews and network meta-analyses (NMA), but access to informative unpublished data is now becoming commonplace. To explore the usefulness of three types of 'grey' literature-clinical trials registries, clinical study reports and data from regulatory authorities-we conducted four case studies. The reporting of outcome data in peer-reviewed publications, the clinical trials registries and the clinical study reports for two clinical trials-one in melanoma, one in juvenile idiopathic arthritis (JIA)-was examined. In addition, we assessed the value of including unpublished data from the European Medicines Agency (EMA) and US Food and Drug Administration (FDA) in evidence syntheses of hepatitis C virus (HCV) and chronic obstructive pulmonary disease (COPD), respectively. For the clinical trials in melanoma and JIA, we identified outcome parameters on ClinicalTrials.gov additional to those reported in the peer-reviewed publications: subgroup data and additional efficacy end points/extended follow-up, respectively. The clinical study report also provided results for several subgroups unavailable elsewhere. For HCV and COPD, additional outcome data were obtained from the EMA European Public Assessment Report (EPAR) and the FDA, respectively, including data on subgroups and mortality. We conclude that data from these grey literature sources have the potential to influence results of systematic reviews and NMAs, and may thus have implications for healthcare decisions. However, it is important to consider carefully the availability, reliability and consequent usability of these data sources in systematic reviews and NMAs. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Impact and Cost-effectiveness of 3 Doses of 9-Valent Human Papillomavirus (HPV) Vaccine Among US Females Previously Vaccinated With 4-Valent HPV Vaccine.

PubMed

Chesson, Harrell W; Laprise, Jean-François; Brisson, Marc; Markowitz, Lauri E

2016-06-01

We estimated the potential impact and cost-effectiveness of providing 3-doses of nonavalent human papillomavirus (HPV) vaccine (9vHPV) to females aged 13-18 years who had previously completed a series of quadrivalent HPV vaccine (4vHPV), a strategy we refer to as "additional 9vHPV vaccination." We used 2 distinct models: (1) the simplified model, which is among the most basic of the published dynamic HPV models, and (2) the US HPV-ADVISE model, a complex, stochastic, individual-based transmission-dynamic model. When assuming no 4vHPV cross-protection, the incremental cost per quality-adjusted life-year (QALY) gained by additional 9vHPV vaccination was $146 200 in the simplified model and $108 200 in the US HPV-ADVISE model ($191 800 when assuming 4vHPV cross-protection). In 1-way sensitivity analyses in the scenario of no 4vHPV cross-protection, the simplified model results ranged from $70 300 to $182 000, and the US HPV-ADVISE model results ranged from $97 600 to $118 900. The average cost per QALY gained by additional 9vHPV vaccination exceeded $100 000 in both models. However, the results varied considerably in sensitivity and uncertainty analyses. Additional 9vHPV vaccination is likely not as efficient as many other potential HPV vaccination strategies, such as increasing primary 9vHPV vaccine coverage. Published by Oxford University Press for the Infectious Diseases Society of America 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Terminal Olefin Profiles and Phylogenetic Analyses of Olefin Synthases of Diverse Cyanobacterial Species.

PubMed

Zhu, Tao; Scalvenzi, Thibault; Sassoon, Nathalie; Lu, Xuefeng; Gugger, Muriel

2018-07-01

Cyanobacteria can synthesize alkanes and alkenes, which are considered to be infrastructure-compatible biofuels. In terms of physiological function, cyanobacterial hydrocarbons are thought to be essential for membrane flexibility for cell division, size, and growth. The genetic basis for the biosynthesis of terminal olefins (1-alkenes) is a modular type I polyketide synthase (PKS) termed olefin synthase (Ols). The modular architectures of Ols and structural characteristics of alkenes have been investigated only in a few species of the small percentage (approximately 10%) of cyanobacteria that harbor putative Ols pathways. In this study, investigations of the domains, modular architectures, and phylogenies of Ols in 28 cyanobacterial strains suggested distinctive pathway evolution. Structural feature analyses revealed 1-alkenes with three carbon chain lengths (C 15 , C 17 , and C 19 ). In addition, the total cellular fatty acid profile revealed the diversity of the carbon chain lengths, while the fatty acid feeding assay indicated substrate carbon chain length specificity of cyanobacterial Ols enzymes. Finally, in silico analyses suggested that the N terminus of the modular Ols enzyme exhibited characteristics typical of a fatty acyl-adenylate ligase (FAAL), suggesting a mechanism of fatty acid activation via the formation of acyl-adenylates. Our results shed new light on the diversity of cyanobacterial terminal olefins and a mechanism for substrate activation in the biosynthesis of these olefins. IMPORTANCE Cyanobacterial terminal olefins are hydrocarbons with promising applications as advanced biofuels. Despite the basic understanding of the genetic basis of olefin biosynthesis, the structural diversity and phylogeny of the key modular olefin synthase (Ols) have been poorly explored. An overview of the chemical structural traits of terminal olefins in cyanobacteria is provided in this study. In addition, we demonstrated by in vivo fatty acid feeding assays that cyanobacterial Ols enzymes might exhibit substrate carbon chain length specificity. Furthermore, by performing bioinformatic analyses, we observed that the substrate activation domain of Ols exhibited features typical of a fatty acyl-adenylate ligase (FAAL), which activates fatty acids by converting them to fatty acyl-adenylates. Our results provide further insight into the chemical structures of terminal olefins and further elucidate the mechanism of substrate activation for terminal olefin biosynthesis in cyanobacteria. Copyright © 2018 American Society for Microbiology.

Computational Analyses in Support of Sub-scale Diffuser Testing for the A-3 Facility. Part 3; Aero-Acoustic Analyses and Experimental Validation

NASA Technical Reports Server (NTRS)

Allgood, Daniel C.; Graham, Jason S.; McVay, Greg P.; Langford, Lester L.

2008-01-01

A unique assessment of acoustic similarity scaling laws and acoustic analogy methodologies in predicting the far-field acoustic signature from a sub-scale altitude rocket test facility at the NASA Stennis Space Center was performed. A directional, point-source similarity analysis was implemented for predicting the acoustic far-field. In this approach, experimental acoustic data obtained from "similar" rocket engine tests were appropriately scaled using key geometric and dynamic parameters. The accuracy of this engineering-level method is discussed by comparing the predictions with acoustic far-field measurements obtained. In addition, a CFD solver was coupled with a Lilley's acoustic analogy formulation to determine the improvement of using a physics-based methodology over an experimental correlation approach. In the current work, steady-state Reynolds-averaged Navier-Stokes calculations were used to model the internal flow of the rocket engine and altitude diffuser. These internal flow simulations provided the necessary realistic input conditions for external plume simulations. The CFD plume simulations were then used to provide the spatial turbulent noise source distributions in the acoustic analogy calculations. Preliminary findings of these studies will be discussed.

Back to BaySICS: a user-friendly program for Bayesian Statistical Inference from Coalescent Simulations.

PubMed

Sandoval-Castellanos, Edson; Palkopoulou, Eleftheria; Dalén, Love

2014-01-01

Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.

Cost-Effectiveness Analysis of Regorafenib for Metastatic Colorectal Cancer

PubMed Central

Goldstein, Daniel A.; Ahmad, Bilal B.; Chen, Qiushi; Ayer, Turgay; Howard, David H.; Lipscomb, Joseph; El-Rayes, Bassel F.; Flowers, Christopher R.

2015-01-01

Purpose Regorafenib is a standard-care option for treatment-refractory metastatic colorectal cancer that increases median overall survival by 6 weeks compared with placebo. Given this small incremental clinical benefit, we evaluated the cost-effectiveness of regorafenib in the third-line setting for patients with metastatic colorectal cancer from the US payer perspective. Methods We developed a Markov model to compare the cost and effectiveness of regorafenib with those of placebo in the third-line treatment of metastatic colorectal cancer. Health outcomes were measured in life-years and quality-adjusted life-years (QALYs). Drug costs were based on Medicare reimbursement rates in 2014. Model robustness was addressed in univariable and probabilistic sensitivity analyses. Results Regorafenib provided an additional 0.04 QALYs (0.13 life-years) at a cost of $40,000, resulting in an incremental cost-effectiveness ratio of $900,000 per QALY. The incremental cost-effectiveness ratio for regorafenib was > $550,000 per QALY in all of our univariable and probabilistic sensitivity analyses. Conclusion Regorafenib provides minimal incremental benefit at high incremental cost per QALY in the third-line management of metastatic colorectal cancer. The cost-effectiveness of regorafenib could be improved by the use of value-based pricing. PMID:26304904

Modelling Coastal Cliff Recession Based on the GIM-DDD Method

NASA Astrophysics Data System (ADS)

Gong, Bin; Wang, Shanyong; Sloan, Scott William; Sheng, Daichao; Tang, Chun'an

2018-04-01

The unpredictable and instantaneous collapse behaviour of coastal rocky cliffs may cause damage that extends significantly beyond the area of failure. Gravitational movements that occur during coastal cliff recession involve two major stages: the small deformation stage and the large displacement stage. In this paper, a method of simulating the entire progressive failure process of coastal rocky cliffs is developed based on the gravity increase method (GIM), the rock failure process analysis method and the discontinuous deformation analysis method, and it is referred to as the GIM-DDD method. The small deformation stage, which includes crack initiation, propagation and coalescence processes, and the large displacement stage, which includes block translation and rotation processes during the rocky cliff collapse, are modelled using the GIM-DDD method. In addition, acoustic emissions, stress field variations, crack propagation and failure mode characteristics are further analysed to provide insights that can be used to predict, prevent and minimize potential economic losses and casualties. The calculation and analytical results are consistent with previous studies, which indicate that the developed method provides an effective and reliable approach for performing rocky cliff stability evaluations and coastal cliff recession analyses and has considerable potential for improving the safety and protection of seaside cliff areas.

Large eddy simulations and direct numerical simulations of high speed turbulent reacting flows

NASA Technical Reports Server (NTRS)

Givi, P.; Frankel, S. H.; Adumitroaie, V.; Sabini, G.; Madnia, C. K.

1993-01-01

The primary objective of this research is to extend current capabilities of Large Eddy Simulations (LES) and Direct Numerical Simulations (DNS) for the computational analyses of high speed reacting flows. Our efforts in the first two years of this research have been concentrated on a priori investigations of single-point Probability Density Function (PDF) methods for providing subgrid closures in reacting turbulent flows. In the efforts initiated in the third year, our primary focus has been on performing actual LES by means of PDF methods. The approach is based on assumed PDF methods and we have performed extensive analysis of turbulent reacting flows by means of LES. This includes simulations of both three-dimensional (3D) isotropic compressible flows and two-dimensional reacting planar mixing layers. In addition to these LES analyses, some work is in progress to assess the extent of validity of our assumed PDF methods. This assessment is done by making detailed companions with recent laboratory data in predicting the rate of reactant conversion in parallel reacting shear flows. This report provides a summary of our achievements for the first six months of the third year of this program.

Modeling barrier island response to sea-level rise in the Outer Banks, North Carolina

USGS Publications Warehouse

Moore, Laura J.; List, Jeffrey H.; Williams, S. Jeffress; Stolper, David

2007-01-01

An 8500-year Holocene simulation developed in GEOMBEST provides a possible scenario to explain the evolution of barrier coast between Rodanthe and Cape Hatteras, NC. Sensitivity analyses suggest that in the Outer Banks, the rate of sea-level rise is the most important factor in determining how barrier islands evolve. The Holocene simulation provides a basis for future simulations, which suggest that if sea level rises up to 0.88 m by AD 2100, as predicted by the highest estimates of the Intergovernmental Panel on Climate Change, the barrier in the study area may migrate on the order of 2.5 times more rapidly than at present. If sea level rises beyond IPCC predictions to reach 1.4–1.9 m above modern sea level by AD 2100, model results suggest that barrier islands in the Outer Banks may become vulnerable to threshold collapse, disintegrating during storm events, by the end of the next century. Consistent with sensitivity analyses, additional simulations indicate that anthropogenic activities, such as increasing the rate of sediment supply through beach nourishment, will only slightly affect barrier island migration rates and barrier island vulnerability to collapse.

Development of cost estimation tools for total occupational safety and health activities and occupational health services: cost estimation from a corporate perspective.

PubMed

Nagata, Tomohisa; Mori, Koji; Aratake, Yutaka; Ide, Hiroshi; Ishida, Hiromi; Nobori, Junichiro; Kojima, Reiko; Odagami, Kiminori; Kato, Anna; Tsutsumi, Akizumi; Matsuda, Shinya

2014-01-01

The aim of the present study was to develop standardized cost estimation tools that provide information to employers about occupational safety and health (OSH) activities for effective and efficient decision making in Japanese companies. We interviewed OSH staff members including full-time professional occupational physicians to list all OSH activities. Using activity-based costing, cost data were obtained from retrospective analyses of occupational safety and health costs over a 1-year period in three manufacturing workplaces and were obtained from retrospective analyses of occupational health services costs in four manufacturing workplaces. We verified the tools additionally in four workplaces including service businesses. We created the OSH and occupational health standardized cost estimation tools. OSH costs consisted of personnel costs, expenses, outsourcing costs and investments for 15 OSH activities. The tools provided accurate, relevant information on OSH activities and occupational health services. The standardized information obtained from our OSH and occupational health cost estimation tools can be used to manage OSH costs, make comparisons of OSH costs between companies and organizations and help occupational health physicians and employers to determine the best course of action.

Developing a self-rating measure of patient competence in the context of oncology: a multi-center study.

PubMed

Giesler, Jürgen M; Weis, Joachim

2008-11-01

Concepts of patient competence (PC) are being increasingly used, but seldom clearly defined in the context of shared medical treatment decision making and coping with cancer. The meaning of such concepts should therefore be clarified, and measures developed that permit the assessment of different facets of this patient characteristic. Consequently, this study attempted to contribute to the definition and measurement of PC. Employing literature reviews and qualitative interviews, we developed a working definition of PC in the context of cancer from which we designed a self-rating measure of this patient characteristic that was then tested for validity and reliability in a sample of N=536 patients with cancer. Using factor analyses, we developed five problem- and three emotion-focused subscales that measure distinct facets of PC with satisfactory reliability. Additional analyses provide preliminary evidence of the instruments' validity. This study represents an essential first step in developing a reliable self-rating measure of PC in the context of cancer. Although further refinement of this measure is clearly required, it provides a preliminary methodological basis for empirically investigating the determinants and potential health effects of PC. (c) 2008 John Wiley & Sons, Ltd.

Psychophysiological Assessment of Fatigue in Commercial Aviation Operations

NASA Technical Reports Server (NTRS)

Hernandez, Norma; Cowings, Patricia; Toscano, William

2012-01-01

The overall goal of this study is to improve our understanding of crew work hours, workload, sleep, fatigue, and performance, and the relationships between these variables on actual flight deck performance. Specifically, this study will provide objective measures of physiology and performance, which may benefit investigators in identifying fatigue levels of operators in commercial aviation and provide a way to better design strategies to limit crew fatigue. This research was supported by an agreement between NASA Ames Research Center and easyJet Airline Company, Ltd., Luton, UK. Twenty commercial pilots volunteered to participant in the study that included 15 flight duty days. Participants wore a Zephyr Bioharness ambulatory physiological monitor each flight day, which measured their heart rate, respiration rate, skin temperature, activity and posture. In addition, pilots completed sleep log diaries, self-report scales of mood, sleepiness and workload, and a Performance Vigilance Task (PVT). All data were sent to NASA researchers for processing and analyses. Heart rate variability data of several subjects were subjected to a spectral analysis to examine power in specific frequency bands. Increased power in low frequency band was associated with reports of higher subjective sleepinesss in some subjects. Analyses of other participants data are currently underway.

A software-based tool for video motion tracking in the surgical skills assessment landscape.

PubMed

Ganni, Sandeep; Botden, Sanne M B I; Chmarra, Magdalena; Goossens, Richard H M; Jakimowicz, Jack J

2018-01-16

The use of motion tracking has been proved to provide an objective assessment in surgical skills training. Current systems, however, require the use of additional equipment or specialised laparoscopic instruments and cameras to extract the data. The aim of this study was to determine the possibility of using a software-based solution to extract the data. 6 expert and 23 novice participants performed a basic laparoscopic cholecystectomy procedure in the operating room. The recorded videos were analysed using Kinovea 0.8.15 and the following parameters calculated the path length, average instrument movement and number of sudden or extreme movements. The analysed data showed that experts had significantly shorter path length (median 127 cm vs. 187 cm, p = 0.01), smaller average movements (median 0.40 cm vs. 0.32 cm, p = 0.002) and fewer sudden movements (median 14.00 vs. 21.61, p = 0.001) than their novice counterparts. The use of software-based video motion tracking of laparoscopic cholecystectomy is a simple and viable method enabling objective assessment of surgical performance. It provides clear discrimination between expert and novice performance.

A new intelligent electronic nose system for measuring and analysing livestock and poultry farm odours.

PubMed

Pan, Leilei; Yang, Simon X

2007-12-01

This paper introduces a new portable intelligent electronic nose system developed especially for measuring and analysing livestock and poultry farm odours. It can be used in both laboratory and field. The sensor array of the proposed electronic nose consists of 14 gas sensors, a humidity sensor, and a temperature sensor. The gas sensors were especially selected for the main compounds from the livestock farm odours. An expert system called "Odour Expert" was developed to support researchers' and farmers' decision making on odour control strategies for livestock and poultry operations. "Odour Expert" utilises several advanced artificial intelligence technologies tailored to livestock and poultry farm odours. It can provide more advanced odour analysis than existing commercially available products. In addition, a rank of odour generation factors is provided, which refines the focus of odour control research. Field experiments were conducted downwind from the barns on 14 livestock and poultry farms. Experimental results show that the predicted odour strengths by the electronic nose yield higher consistency in comparison to the perceived odour intensity by human panel. The "Odour Expert" is a useful tool for assisting farmers' odour management practises.

Modelling and simulating a crisis management system: an organisational perspective

NASA Astrophysics Data System (ADS)

Chaawa, Mohamed; Thabet, Inès; Hanachi, Chihab; Ben Said, Lamjed

2017-04-01

Crises are complex situations due to the dynamism of the environment, its unpredictability and the complexity of the interactions among several different and autonomous involved organisations. In such a context, establishing an organisational view as well as structuring organisations' communications and their functioning is a crucial requirement. In this article, we propose a multi-agent organisational model (OM) to abstract, simulate and analyse a crisis management system (CMS). The objective is to evaluate the CMS from an organisational view, to assess its strength as well as its weakness and to provide deciders with some recommendations for a more flexible and reactive CMS. The proposed OM is illustrated through a real case study: a snowstorm in a Tunisian region. More precisely, we made the following contribution: firstly, we provide an environmental model that identifies the concepts involved in the crisis. Then, we define a role model that copes with the involved actors. In addition, we specify the organisational structure and the interaction model that rule communications and structure actors' functioning. Those models, built following the GAIA methodology, abstract the CMS from an organisational perspective. Finally, we implemented a customisable multi-agent simulator based on the Janus platform to analyse, through several performed simulations, the organisational model.

Longitudinal change mechanisms for substance use and illegal activity for adolescents in treatment.

PubMed

Hunter, Brooke D; Godley, Susan H; Hesson-McInnis, Matthew S; Roozen, Hendrik G

2014-06-01

The current study investigated: (a) the relationships of exposure to the Adolescent Community Reinforcement Approach (A-CRA) with reductions in substance use, illegal activity, and juvenile justice system involvement in adolescents diagnosed with a substance use disorder, and (b) the pathways by which reductions in the target behaviors were achieved. This study is a secondary data analysis of longitudinal data from a large-scale implementation effort for A-CRA. The sample consisted of 1,467 adolescents who presented to substance use treatment and reported past-year engagement in illegal activity. Participants had an average age of 15.8 years (SD = 1.3) and were 25% female, 14% African American, 29% Hispanic, 35% Caucasian, 16% mixed ethnicity, and 6% other ethnicity. Path analyses provided support that participation in A-CRA had a significant, direct association with reduced substance use; a significant, indirect association with reduced illegal activity through reductions in substance use; and a significant indirect association with reduced juvenile justice system involvement through reductions in both substance use and illegal activity. In addition, post hoc analyses using a bootstrapping strategy provided evidence that reductions in substance use partially mediated the relationship between A-CRA and illegal activity.

10 CFR 436.24 - Uncertainty analyses.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... impact of uncertainty on the calculation of life cycle cost effectiveness or the assignment of rank order... and probabilistic analysis. If additional analysis casts substantial doubt on the life cycle cost...

10 CFR 436.24 - Uncertainty analyses.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... impact of uncertainty on the calculation of life cycle cost effectiveness or the assignment of rank order... and probabilistic analysis. If additional analysis casts substantial doubt on the life cycle cost...

10 CFR 436.24 - Uncertainty analyses.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... impact of uncertainty on the calculation of life cycle cost effectiveness or the assignment of rank order... and probabilistic analysis. If additional analysis casts substantial doubt on the life cycle cost...

10 CFR 436.24 - Uncertainty analyses.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Procedures for Life Cycle Cost Analyses § 436.24 Uncertainty analyses. If particular items of cost data or... impact of uncertainty on the calculation of life cycle cost effectiveness or the assignment of rank order... and probabilistic analysis. If additional analysis casts substantial doubt on the life cycle cost...

Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) Tutorial

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

C. L. Smith; S. T. Beck; S. T. Wood

2008-08-01

The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) refers to a set of computer programs that were developed to create and analyze probabilistic risk assessment (PRAs). This volume is the tutorial manual for the SAPHIRE system. In this document, a series of lessons are provided that guide the user through basic steps common to most analyses preformed with SAPHIRE. The tutorial is divided into two major sections covering both basic and advanced features. The section covering basic topics contains lessons that lead the reader through development of a probabilistic hypothetical problem involving a vehicle accident, highlighting the program’smore » most fundamental features. The advanced features section contains additional lessons that expand on fundamental analysis features of SAPHIRE and provide insights into more complex analysis techniques. Together, these two elements provide an overview into the operation and capabilities of the SAPHIRE software.« less

Integrated Flight Performance Analysis of a Launch Abort System Concept

NASA Technical Reports Server (NTRS)

Tartabini, Paul V.

2007-01-01

This paper describes initial flight performance analyses conducted early in the Orion Project to support concept feasibility studies for the Crew Exploration Vehicle s Launch Abort System (LAS). Key performance requirements that significantly affect abort capability are presented. These requirements have implications on sizing the Abort Motor, tailoring its thrust profile to meet escape requirements for both launch pad and high drag/high dynamic pressure ascent aborts. Additional performance considerations are provided for the Attitude Control Motor, a key element of the Orion LAS design that eliminates the need for ballast and provides performance robustness over a passive control approach. Finally, performance of the LAS jettison function is discussed, along with implications on Jettison Motor sizing and the timing of the jettison event during a nominal mission. These studies provide an initial understanding of LAS performance that will continue to evolve as the Orion design is matured.

Stillbirths: economic and psychosocial consequences.

PubMed

Heazell, Alexander E P; Siassakos, Dimitrios; Blencowe, Hannah; Burden, Christy; Bhutta, Zulfiqar A; Cacciatore, Joanne; Dang, Nghia; Das, Jai; Flenady, Vicki; Gold, Katherine J; Mensah, Olivia K; Millum, Joseph; Nuzum, Daniel; O'Donoghue, Keelin; Redshaw, Maggie; Rizvi, Arjumand; Roberts, Tracy; Toyin Saraki, H E; Storey, Claire; Wojcieszek, Aleena M; Downe, Soo

2016-02-06

Despite the frequency of stillbirths, the subsequent implications are overlooked and underappreciated. We present findings from comprehensive, systematic literature reviews, and new analyses of published and unpublished data, to establish the effect of stillbirth on parents, families, health-care providers, and societies worldwide. Data for direct costs of this event are sparse but suggest that a stillbirth needs more resources than a livebirth, both in the perinatal period and in additional surveillance during subsequent pregnancies. Indirect and intangible costs of stillbirth are extensive and are usually met by families alone. This issue is particularly onerous for those with few resources. Negative effects, particularly on parental mental health, might be moderated by empathic attitudes of care providers and tailored interventions. The value of the baby, as well as the associated costs for parents, families, care providers, communities, and society, should be considered to prevent stillbirths and reduce associated morbidity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantitative interpretation of the magnetic susceptibility frequency dependence

NASA Astrophysics Data System (ADS)

Ustra, Andrea; Mendonça, Carlos A.; Leite, Aruã; Jovane, Luigi; Trindade, Ricardo I. F.

2018-05-01

Low-field mass-specific magnetic susceptibility (MS) measurements using multifrequency alternating fields are commonly used to evaluate concentration of ferrimagnetic particles in the transition of superparamagnetic (SP) to stable single domain (SSD). In classical palaeomagnetic analyses, this measurement serves as a preliminary assessment of rock samples providing rapid, non-destructive, economical and easy information of magnetic properties. The SP-SSD transition is relevant in environmental studies because it has been associated with several geological and biogeochemical processes affecting magnetic mineralogy. MS is a complex function of mineral-type and grain-size distribution, as well as measuring parameters such as external field magnitude and frequency. In this work, we propose a new technique to obtain quantitative information on grain-size variations of magnetic particles in the SP-SSD transition by inverting frequency-dependent susceptibility. We introduce a descriptive parameter named as `limiting frequency effect' that provides an accurate estimation of MS loss with frequency. Numerical simulations show the methodology capability in providing data fitting and model parameters in many practical situations. Real-data applications with magnetite nanoparticles and core samples from sediments of Poggio le Guaine section of Umbria-Marche Basin (Italy) provide additional information not clearly recognized when interpreting cruder MS data. Caution is needed when interpreting frequency dependence in terms of single relaxation processes, which are not universally applicable and depend upon the nature of magnetic mineral in the material. Nevertheless, the proposed technique is a promising tool for SP-SSD content analyses.

Soil functional diversity analysis of a bauxite-mined restoration chronosequence.

PubMed

Lewis, Dawn E; White, John R; Wafula, Denis; Athar, Rana; Dickerson, Tamar; Williams, Henry N; Chauhan, Ashvini

2010-05-01

Soil microorganisms are sensitive to environmental perturbations such that changes in microbial community structure and function can provide early signs of anthropogenic disturbances and even predict restoration success. We evaluated the bacterial functional diversity of un-mined and three chronosequence sites at various stages of rehabilitation (0, 10, and 20 years old) located in the Mocho Mountains of Jamaica. Samples were collected during the dry and wet seasons and analyzed for metal concentrations, microbial biomass carbon, bacterial numbers, and functional responses of soil microbiota using community-level physiological profile (CLPP) assays. Regardless of the season, un-mined soils consisted of higher microbial biomass and numbers than any of the rehabilitated sites. Additionally, the number and rate of substrates utilized and substrate evenness (the distribution of color development between the substrates) were significantly greater in the un-mined soils with carbohydrates being preferentially utilized than amino acids, polymers, carboxylic acids, and esters. To some extent, functional responses varied with the seasons but the least physiological activity was shown by the site rehabilitated in 1987 indicating long-term perturbation to this ecosystem. Small subunit ribosomal DNA (SSUrDNA)-denaturing gradient-gel electrophoresis analyses on the microbiota collected from the most preferred CLPP substrates followed by taxonomic analyses showed Proteobacteria, specifically the gamma-proteobacteria, as the most functionally active phyla, indicating a propensity of this phyla to out-compete other groups under the prevailing conditions. Additionally, multivariate statistical analyses, Shannon's diversity, and evenness indices, principal component analysis, biplot and un-weighted-pair-group method with arithmetic averages dendrograms further confirmed that un-mined sites were distinctly different from the rehabilitated soils.

Expanding Lipidome Coverage Using LC-MS/MS Data-Dependent Acquisition with Automated Exclusion List Generation

NASA Astrophysics Data System (ADS)

Koelmel, Jeremy P.; Kroeger, Nicholas M.; Gill, Emily L.; Ulmer, Candice Z.; Bowden, John A.; Patterson, Rainey E.; Yost, Richard A.; Garrett, Timothy J.

2017-05-01

Untargeted omics analyses aim to comprehensively characterize biomolecules within a biological system. Changes in the presence or quantity of these biomolecules can indicate important biological perturbations, such as those caused by disease. With current technological advancements, the entire genome can now be sequenced; however, in the burgeoning fields of lipidomics, only a subset of lipids can be identified. The recent emergence of high resolution tandem mass spectrometry (HR-MS/MS), in combination with ultra-high performance liquid chromatography, has resulted in an increased coverage of the lipidome. Nevertheless, identifications from MS/MS are generally limited by the number of precursors that can be selected for fragmentation during chromatographic elution. Therefore, we developed the software IE-Omics to automate iterative exclusion (IE), where selected precursors using data-dependent topN analyses are excluded in sequential injections. In each sequential injection, unique precursors are fragmented until HR-MS/MS spectra of all ions above a user-defined intensity threshold are acquired. IE-Omics was applied to lipidomic analyses in Red Cross plasma and substantia nigra tissue. Coverage of the lipidome was drastically improved using IE. When applying IE-Omics to Red Cross plasma and substantia nigra lipid extracts in positive ion mode, 69% and 40% more molecular identifications were obtained, respectively. In addition, applying IE-Omics to a lipidomics workflow increased the coverage of trace species, including odd-chained and short-chained diacylglycerides and oxidized lipid species. By increasing the coverage of the lipidome, applying IE to a lipidomics workflow increases the probability of finding biomarkers and provides additional information for determining etiology of disease.

Factors influencing quit attempts among male daily smokers in China.

PubMed

Zhao, Luhua; Song, Yang; Xiao, Lin; Palipudi, Krishna; Asma, Samira

2015-12-01

China has the largest population of smokers in the world, yet the quit rate is low. We used data from the 2010 Global Adult Tobacco Survey China to identify factors influencing quit attempts among male Chinese daily smokers. The study sample included 3303 male daily smokers. To determine the factors that were significantly associated with making a quit attempt, we conducted logistic regression analyses. In addition, mediation analyses were carried out to investigate how the intermediate association among demographics (age, education, urbanicity) and smoking-related variables affected making a quit attempt. An estimated 11.0% of male daily smokers tried to quit smoking in the 12 months prior to the survey. Logistic regression analysis indicated that younger age (15-24 years), being advised to quit by a health care provider (HCP) in the past 12 months, lower cigarette cost per pack, monthly or less frequent exposure to smoking at home, and awareness of the harms of tobacco use were significantly associated with making a quit attempt. Additional mediation analyses showed that having knowledge of the harm of tobacco, exposure to smoking at home, and having been advised to quit by an HCP were mediators of making a quit attempt for other independent variables. Evidence-based tobacco control measures such as conducting educational campaigns on the harms of tobacco use, establishing smoke-free policies at home, and integrating tobacco cessation advice into primary health care services can increase quit attempts and reduce smoking among male Chinese daily smokers. Copyright © 2015 Elsevier Inc. All rights reserved.

Analyses of Injection-Coupled Combustion Instability from J-2X Gas Generator Development

NASA Technical Reports Server (NTRS)

Hulka, James R.; Kenny, R. Jeremy; Protz, Chris; Casiano, Matthew

2011-01-01

During development of the gas generator for the liquid oxygen/liquid hydrogen propellant J-2X rocket engine, combustion instabilities were observed near the frequency of the first longitudinal acoustic mode of the hot gas combustion chamber duct. These instabilities were similar to intermediate-frequency or buzz-type instabilities as described in historical programs, except for several aspects: 1) the frequencies were low, in the realm of chug; 2) at times the instability oscillation amplitudes were quite large, with peak-to-peak amplitudes exceeding 50% of the mean chamber pressure along with the appearance of harmonics; 3) the chamber excitation was related to but not exactly at the first longitudinal combustion chamber acoustic mode; and 4) the injector provided mass flow rate oscillations induced by capacitance and inertance effects in the injector rather than by organ pipe resonances of the coaxial oxidizer posts. This type of combustion instability is referred to as "injection coupling" because one critical driving source of the instability is mass flow rate oscillations from the injector. However, the type of injection coupling observed here is different than observed in previous instances of buzz instability with coaxial injectors, because of the lower frequencies and lack of influence from the oxidizer post organ pipe resonances. Test data and preliminary analyses of the initial combustion instabilities were presented in several papers at the 5th Liquid Propulsion Subcommittee meeting. Since that time, additional hot-fire tests with several new hardware configurations have been conducted, and additional analyses have been completed. The analytical models described in previous papers have been updated to include the influences of new geometrical configurations, including a different oxidizer injector manifold configuration and a branch pipe in the hot gas duct that supplies gaseous helium during the start transient to pre-spin the turbine. In addition, the analysis methodology has been revisited to evaluate the potential influence of a combustion response as well as an injection response.

1-D Compression Behaviour of Acid Sulphate Soils Treated with Alkali-Activated Slag

PubMed Central

Islam, Shahidul; Haque, Asadul; Bui, Ha Hong

2016-01-01

Improvements of soft soils by mechanically mixing cementitious additives have been widely practised for construction of infrastructure. Mixing of additives improves strength and compressibility properties of soils through the development of soil structure. This study investigates the 1-D compression behaviour of alkali-activated slag treated acid sulphate soils (ASS) cured up to 365 days. The void ratio-logarithm of pressure (e-logσ′) behaviour of treated ASS, including the destructuration behaviour, with additive contents and curing time have been analysed. X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses have been undertaken to explain the observed variations of the 1-D compression behaviour. This paper presents the results of these analyses in view of obtaining an insight into the 1-D compression behaviour of treated ASS with the help of mineralogical analysis. PMID:28773415

1-D Compression Behaviour of Acid Sulphate Soils Treated with Alkali-Activated Slag.

PubMed

Islam, Shahidul; Haque, Asadul; Bui, Ha Hong

2016-04-15

Improvements of soft soils by mechanically mixing cementitious additives have been widely practised for construction of infrastructure. Mixing of additives improves strength and compressibility properties of soils through the development of soil structure. This study investigates the 1-D compression behaviour of alkali-activated slag treated acid sulphate soils (ASS) cured up to 365 days. The void ratio-logarithm of pressure (e-logσ') behaviour of treated ASS, including the destructuration behaviour, with additive contents and curing time have been analysed. X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses have been undertaken to explain the observed variations of the 1-D compression behaviour. This paper presents the results of these analyses in view of obtaining an insight into the 1-D compression behaviour of treated ASS with the help of mineralogical analysis.

Mind the Scales: Harnessing Spatial Big Data for Infectious Disease Surveillance and Inference

PubMed Central

Lee, Elizabeth C.; Asher, Jason M.; Goldlust, Sandra; Kraemer, John D.; Lawson, Andrew B.; Bansal, Shweta

2016-01-01

Spatial big data have the velocity, volume, and variety of big data sources and contain additional geographic information. Digital data sources, such as medical claims, mobile phone call data records, and geographically tagged tweets, have entered infectious diseases epidemiology as novel sources of data to complement traditional infectious disease surveillance. In this work, we provide examples of how spatial big data have been used thus far in epidemiological analyses and describe opportunities for these sources to improve disease-mitigation strategies and public health coordination. In addition, we consider the technical, practical, and ethical challenges with the use of spatial big data in infectious disease surveillance and inference. Finally, we discuss the implications of the rising use of spatial big data in epidemiology to health risk communication, and public health policy recommendations and coordination across scales. PMID:28830109

Cost-Effectiveness Analysis Comparing Pre-diagnosis Autism Spectrum Disorder (ASD)-Targeted Intervention with Ontario's Autism Intervention Program.

PubMed

Penner, Melanie; Rayar, Meera; Bashir, Naazish; Roberts, S Wendy; Hancock-Howard, Rebecca L; Coyte, Peter C

2015-09-01

Novel management strategies for autism spectrum disorder (ASD) propose providing interventions before diagnosis. We performed a cost-effectiveness analysis comparing the costs and dependency-free life years (DFLYs) generated by pre-diagnosis intensive Early Start Denver Model (ESDM-I); pre-diagnosis parent-delivered ESDM (ESDM-PD); and the Ontario Status Quo (SQ). The analyses took government and societal perspectives to age 65. We assigned probabilities of Independent, Semi-dependent or Dependent living based on projected IQ. Costs per person (in Canadian dollars) were ascribed to each living setting. From a government perspective, the ESDM-PD produced an additional 0.17 DFLYs for $8600 less than SQ. From a societal perspective, the ESDM-I produced an additional 0.53 DFLYs for $45,000 less than SQ. Pre-diagnosis interventions targeting ASD symptoms warrant further investigation.

Emission FTIR analyses of thin microscopic patches of jet fuel residues deposited on heated metal surfaces

NASA Technical Reports Server (NTRS)

Lauer, J. L.; Vogel, P.

1986-01-01

The relationship of fuel stability to fuel composition and the development of mechanisms for deposit formation were investigated. Fuel deposits reduce heat transfer efficiency and increase resistance to fuel flow and are highly detrimental to aircraft performance. Infrared emission Fourier transform spectroscopy was chosen as the primary method of analysis because it was sensitive enough to be used in-situ on tiny patches of monolayers or of only a few molecular layers of deposits which generally proved completely insoluble in any nondestructive solvents. Deposits of four base fuels were compared; dodecane, a dodecane/tetralin blend, commercial Jet A fuel, and a broadened-properties jet fuel particularly rich in polynuclear aromatics. Every fuel in turn was provided with and without small additions of such additives as thiophene, furan, pyrrole, and copper and iron naphthenates.

Facile and Chemically Pure Preparation of YVO4:Eu3+ Colloid with Novel Nanostructure via Laser Ablation in Water

PubMed Central

Wang, Haohao; Odawara, Osamu; Wada, Hiroyuki

2016-01-01

A YVO4:Eu3+ colloid with an interesting nanostructure was formed by pulsed laser ablation in deionized water without any additives or surfactants. Analyses of particle morphology, composition and optical properties were accomplished by SEM, TEM, EDS PL and UV-vis. Ovoid-like particles formed by the agglomeration of numerous nanocrystals were observed by SEM and TEM, while EDS with area-mode analysis revealed that the content of dopant ion was well retained within the nanoparticles. In addition, the formation mechanism is deduced and discussed for the first time in this research. The findings of this study could provide new insights into the understanding of laser-induced oxide materials and offer an opportunity for other research groups to pursue red emitting nanophosphors with outstandingly purity. PMID:26842419

[Working memory and executive control: inhibitory processes in updating and random generation tasks].

PubMed

Macizo, Pedro; Bajo, Teresa; Soriano, Maria Felipa

2006-02-01

Working Memory (WM) span predicts subjects' performance in control executive tasks and, in addition, it has been related to the capacity to inhibit irrelevant information. In this paper we investigate the role of WM span in two executive tasks focusing our attention on inhibitory components of both tasks. High and low span participants recalled targets words rejecting irrelevant items at the same time (Experiment 1) and they generated random numbers (Experiment 2). Results showed a clear relation between WM span and performance in both tasks. In addition, analyses of intrusion errors (Experiment 1) and stereotyped responses (Experiment 2) indicated that high span individuals were able to efficiently use the inhibitory component implied in both tasks. The pattern of data provides support to the relation between WM span and control executive tasks through an inhibitory mechanism.

Isotopic Composition of Oxygen in Lunar Zircons

NASA Technical Reports Server (NTRS)

Nemchin, A. A.; Whitehouse, M. J.; Pidgeon, R. T.; Meyer, C.

2005-01-01

The recent discovery of heavy oxygen in zircons from the Jack Hills conglomerates Wilde et al. and Mojzsis et al. was interpreted as an indication of presence of liquid water on the surface of Early Earth. The distribution of ages of Jack Hills zircons and lunar zircons appears to be very similar and therefore analysis of oxygen in the lunar grains may provide a reference frame for further study of the early history of the Earth as well as give additional information regarding processes that operated on the Moon. In the present study we have analysed the oxygen isotopic composition of zircon grains from three lunar samples using the Swedish Museum of Natural History CAMECA 1270 ion microprobe. The samples were selected as likely tests for variations in lunar oxygen isotopic composition. Additional information is included in the original extended abstract.

Genomic and transcriptomic approaches to study immunology in cyprinids: What is next?

PubMed

Petit, Jules; David, Lior; Dirks, Ron; Wiegertjes, Geert F

2017-10-01

Accelerated by the introduction of Next-Generation Sequencing (NGS), a number of genomes of cyprinid fish species have been drafted, leading to a highly valuable collective resource of comparative genome information on cyprinids (Cyprinidae). In addition, NGS-based transcriptome analyses of different developmental stages, organs, or cell types, increasingly contribute to the understanding of complex physiological processes, including immune responses. Cyprinids are a highly interesting family because they comprise one of the most-diversified families of teleosts and because of their variation in ploidy level, with diploid, triploid, tetraploid, hexaploid and sometimes even octoploid species. The wealth of data obtained from NGS technologies provides both challenges and opportunities for immunological research, which will be discussed here. Correct interpretation of ploidy effects on immune responses requires knowledge of the degree of functional divergence between duplicated genes, which can differ even between closely-related cyprinid fish species. We summarize NGS-based progress in analysing immune responses and discuss the importance of respecting the presence of (multiple) duplicated gene sequences when performing transcriptome analyses for detailed understanding of complex physiological processes. Progressively, advances in NGS technology are providing workable methods to further elucidate the implications of gene duplication events and functional divergence of duplicates genes and proteins involved in immune responses in cyprinids. We conclude with discussing how future applications of NGS technologies and analysis methods could enhance immunological research and understanding. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Characteristics of Violent Deaths Among Homeless People in Maryland, 2003-2011.

PubMed

Stanley, Jennifer L; Jansson, Alexandra V; Akinyemi, Adebola A; Mitchell, Clifford S

2016-11-01

People experiencing homelessness are susceptible to many adverse health events, including violence. The purpose of this study was to provide a descriptive analysis of homeless individuals who suffered a violent death in Maryland. Characterizing these deaths will provide a basis for additional analyses that can inform violence prevention activities. This study used data from the Maryland Violent Death Reporting System to examine violent deaths of homeless people occurring from 2003 through 2011. This surveillance system collects information on all violent deaths occurring in Maryland. Victim demographics, injury and death information, precipitating circumstances contributing to deaths, and toxicology information were examined. All analyses were conducted in 2014 and 2015. Among all violent death victims from 2003 through 2011 (N=14,327), a total of 279 (2.0%) were identified as homeless victims. More than half (65.2%) of deaths were of undetermined intent, 21.2% were homicides, and 13.6% were suicides. The most common method of injury was poisoning (59.0%). Substance abuse and having a current mental health problem were among the most commonly reported circumstances relating to death. This study found substance abuse and mental health problems to be major circumstances precipitating violent death among people experiencing homelessness. This study will serve as a starting point for more in-depth analyses on experiences of violent death among homeless people that can inform violence prevention policy and programming. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

On the allopolyploid origin and genome structure of the closely related species Hordeum secalinum and Hordeum capense inferred by molecular karyotyping.

PubMed

Cuadrado, Ángeles; de Bustos, Alfredo; Jouve, Nicolás

2017-08-01

To provide additional information to the many phylogenetic analyses conducted within Hordeum , here the origin and interspecific affinities of the allotetraploids Hordeum secalinum and Hordeum capense were analysed by molecular karyotyping. Karyotypes were determined using genomic in situ hybridization (GISH) to distinguish the sub-genomes and , plus fluorescence in situ hybridization (FISH)/non-denaturing (ND)-FISH to determine the distribution of ten tandem repetitive DNA sequences and thus provide chromosome markers. Each chromosome pair in the six accessions analysed was identified, allowing the establishment of homologous and putative homeologous relationships. The low-level polymorphism observed among the H. secalinum accessions contrasted with the divergence recorded for the sub-genome of the H. capense accessions. Although accession H335 carries an intergenomic translocation, its chromosome structure was indistinguishable from that of H. secalinum . Hordeum secalinum and H. capense accession H335 share a hybrid origin involving Hordeum marinum subsp. gussoneanum as the genome donor and an unidentified genome progenitor. Hordeum capense accession BCC2062 either diverged, with remodelling of the sub-genome, or its genome was donated by a now extinct ancestor. A scheme of probable evolution shows the intricate pattern of relationships among the Hordeum species carrying the genome (including all H. marinum taxa and the hexaploid Hordeum brachyantherum ). © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Forced Response Analysis of a Fan with Boundary Layer Inlet Distortion

NASA Technical Reports Server (NTRS)

Bakhle, Milind A.; Reddy, T. S. R.; Coroneos, Rula M.

2014-01-01

Boundary layer ingesting propulsion systems have the potential to significantly reduce fuel burn for future generations of commercial aircraft, but these systems must be designed to overcome the challenge of high dynamic stresses in fan blades due to forced response. High dynamic stresses can lead to high cycle fatigue failures. High-fidelity computational analysis of the fan aeromechanics is integral to an ongoing effort to design a boundary layer ingesting inlet and fan for a wind-tunnel test. An unsteady flow solution from a Reynoldsaveraged Navier Stokes analysis of a coupled inlet-fan system is used to calculate blade unsteady loading and assess forced response of the fan to distorted inflow. Conducted prior to the mechanical design of a fan, the initial forced response analyses performed in this study provide an early look at the levels of dynamic stresses that are likely to be encountered. For the boundary layer ingesting inlet, the distortion contains strong engine order excitations that act simultaneously. The combined effect of these harmonics was considered in the calculation of the forced response stresses. Together, static and dynamic stresses can provide the information necessary to evaluate whether the blades are likely to fail due to high cycle fatigue. Based on the analyses done, the overspeed condition is likely to result in the smallest stress margin in terms of the mean and alternating stresses. Additional work is ongoing to expand the analyses to off-design conditions, on-resonance conditions, and to include more detailed modeling of the blade structure.

European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing Among Diverse European Ethnic Groups

PubMed Central

Tian, Chao; Kosoy, Roman; Nassir, Rami; Lee, Annette; Villoslada, Pablo; Klareskog, Lars; Hammarström, Lennart; Garchon, Henri-Jean; Pulver, Ann E.; Ransom, Michael; Gregersen, Peter K.; Seldin, Michael F.

2009-01-01

The definition of European population genetic substructure and its application to understanding complex phenotypes is becoming increasingly important. In the current study using over 4000 subjects genotyped for 300 thousand SNPs we provide further insight into relationships among European population groups and identify sets of SNP ancestry informative markers (AIMs) for application in genetic studies. In general, the graphical description of these principal components analyses (PCA) of diverse European subjects showed a strong correspondence to the geographical relationships of specific countries or regions of origin. Clearer separation of different ethnic and regional populations was observed when northern and southern European groups were considered separately and the PCA results were influenced by the inclusion or exclusion of different self-identified population groups including Ashkenazi Jewish, Sardinian and Orcadian ethnic groups. SNP AIM sets were identified that could distinguish the regional and ethnic population groups. Moreover, the studies demonstrated that most allele frequency differences between different European groups could be effectively controlled in analyses using these AIM sets. The European substructure AIMs should be widely applicable to ongoing studies to confirm and delineate specific disease susceptibility candidate regions without the necessity to perform additional genome-wide SNP studies in additional subject sets. PMID:19707526

European population genetic substructure: further definition of ancestry informative markers for distinguishing among diverse European ethnic groups.

PubMed

Tian, Chao; Kosoy, Roman; Nassir, Rami; Lee, Annette; Villoslada, Pablo; Klareskog, Lars; Hammarström, Lennart; Garchon, Henri-Jean; Pulver, Ann E; Ransom, Michael; Gregersen, Peter K; Seldin, Michael F

2009-01-01

The definition of European population genetic substructure and its application to understanding complex phenotypes is becoming increasingly important. In the current study using over 4,000 subjects genotyped for 300,000 single-nucleotide polymorphisms (SNPs), we provide further insight into relationships among European population groups and identify sets of SNP ancestry informative markers (AIMs) for application in genetic studies. In general, the graphical description of these principal components analyses (PCA) of diverse European subjects showed a strong correspondence to the geographical relationships of specific countries or regions of origin. Clearer separation of different ethnic and regional populations was observed when northern and southern European groups were considered separately and the PCA results were influenced by the inclusion or exclusion of different self-identified population groups including Ashkenazi Jewish, Sardinian, and Orcadian ethnic groups. SNP AIM sets were identified that could distinguish the regional and ethnic population groups. Moreover, the studies demonstrated that most allele frequency differences between different European groups could be controlled effectively in analyses using these AIM sets. The European substructure AIMs should be widely applicable to ongoing studies to confirm and delineate specific disease susceptibility candidate regions without the necessity of performing additional genome-wide SNP studies in additional subject sets.

Role of thought-related beliefs and coping strategies in the escalation of intrusive thoughts: an analog to obsessive-compulsive disorder.

PubMed

Marcks, Brook A; Woods, Douglas W

2007-11-01

Cognitive-behavioral models of obsessive-compulsive disorder (OCD) assume that obsessions have their origin in normal intrusive thoughts. These models propose that certain beliefs, such as thought-action fusion (TAF) beliefs, combined with the use of ineffective coping strategies, such as thought suppression, lead to the development of OCD. The purpose of the current study was to examine the relationship between these variables in a non-clinical sample in addition to exploring the effects of an alternative, acceptance-based coping strategy. This study explored the relationship between TAF beliefs, thought suppression, and OC-consistent symptoms via mediational analyses. Results showed that thought suppression mediated the relationship between TAF beliefs and OC-consistent symptoms. This study also experimentally examined the effects of various coping strategies (suppression, acceptance, or monitor-only) on the frequency of a distressing intrusion and appraisal ratings (e.g., anxiety, guilt, responsibility) after a TAF induction. Spontaneous suppression in the monitor-only group made comparisons of the experimental data difficult. However, analyses provided preliminary evidence suggesting that thought suppression is related to more intrusions, higher levels of anxiety, and negative appraisals, whereas an acceptance-based approach may be a useful alternative. Additional findings, limitations of the current study, and directions for future research are discussed.

Can they dig it? Functional morphology and semifossoriality among small-eared shrews, genus Cryptotis (Mammalia, Soricidae)

USGS Publications Warehouse

Woodman, Neal; Gaffney, Sarah A.

2014-01-01

Small-eared shrews (Mammalia: Soricidae: Cryptotis), exhibit modifications of the forelimb skeleton that have been interpreted as adaptations for semifossoriality. Most species inhabit remote regions, however, and their locomotory and foraging behaviors remain mostly speculative. To better understand the morphological modifications in the absence of direct observations, we quantified variation in these species by measuring 151 individuals representing 18 species and populations of Cryptotis and two species of moles (Talpidae) for comparison. From our measurements, we calculated 22 indices, most of which have been used previously to characterize substrate use among rodents and other taxa. We analyzed the indices using 1) average percentile ranks, 2) principal components analysis, and 3) cluster analysis. From these analyses, we determined that three basic modes of substrate adaptation are present within Cryptotis: 1) a primarily terrestrial mode, with species that are capable of burrowing, but lack adaptations to increase digging efficiency, 2) a semifossorial mode, with species whose forelimbs bones show strong muscle attachment areas and increased mechanical advantage, and 3) an intermediate mode. In addition to identifying new morphological characters and contributing to our understanding of the functional morphology of soricids, these analyses provide additional insight into the ecology of the species of interest.

The composition of the atmosphere of Venus below 100 km altitude: An overview

NASA Astrophysics Data System (ADS)

de Bergh, C.; Moroz, V. I.; Taylor, F. W.; Crisp, D.; Bézard, B.; Zasova, L. V.

2006-11-01

We review the progress in our understanding of the composition of the Venus atmosphere since the publication of the COSPAR Venus International Reference Atmosphere volume in 1985. Results presented there were derived from data compiled in 1982-1983. More recent progress has resulted in large part from Earth-based studies of the near-infrared radiation from the nightside of the planet. These observations allow us to probe the atmosphere between the cloud tops and the surface. Additional insight has been gained through: (i) the analysis of ultraviolet radiation by satellites and rockets; (ii) data collected by the Vega 1 and 2 landers; (iii) complementary analyses of Venera 15 and 16 data; (iv) ground-based and Magellan radio occultation measurements, and (v) re-analyses of some spacecraft measurements made before 1983, in particular the Pioneer Venus and Venera 11, 13 and 14 data. These new data, and re-interpretations of older data, provide a much better knowledge of the vertical profile of water vapor, and more information on sulfur species above and below the clouds, including firm detections of OCS and SO. In addition, some spatial and/or temporal variations have been observed for CO, H 2O, H 2SO 4, SO 2, and OCS. New values of the D/H ratio have also been obtained.

Quantitative methods for analysing cumulative effects on fish migration success: a review.

PubMed

Johnson, J E; Patterson, D A; Martins, E G; Cooke, S J; Hinch, S G

2012-07-01

It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Simulating smoke transport from wildland fires with a regional-scale air quality model: sensitivity to spatiotemporal allocation of fire emissions.

PubMed

Garcia-Menendez, Fernando; Hu, Yongtao; Odman, Mehmet T

2014-09-15

Air quality forecasts generated with chemical transport models can provide valuable information about the potential impacts of fires on pollutant levels. However, significant uncertainties are associated with fire-related emission estimates as well as their distribution on gridded modeling domains. In this study, we explore the sensitivity of fine particulate matter concentrations predicted by a regional-scale air quality model to the spatial and temporal allocation of fire emissions. The assessment was completed by simulating a fire-related smoke episode in which air quality throughout the Atlanta metropolitan area was affected on February 28, 2007. Sensitivity analyses were carried out to evaluate the significance of emission distribution among the model's vertical layers, along the horizontal plane, and into hourly inputs. Predicted PM2.5 concentrations were highly sensitive to emission injection altitude relative to planetary boundary layer height. Simulations were also responsive to the horizontal allocation of fire emissions and their distribution into single or multiple grid cells. Additionally, modeled concentrations were greatly sensitive to the temporal distribution of fire-related emissions. The analyses demonstrate that, in addition to adequate estimates of emitted mass, successfully modeling the impacts of fires on air quality depends on an accurate spatiotemporal allocation of emissions. Copyright © 2014 Elsevier B.V. All rights reserved.

The effect of bracing availability on one-hand isometric force exertion capability.

PubMed

Jones, Monica L H; Reed, Matthew P; Chaffin, Don B

2013-01-01

Environmental obstructions that workers encounter can kinematically limit the postures that they can achieve. However, such obstructions can also provide an opportunity for additional support by bracing with the hand, thigh or other body part. The reaction forces on bracing surfaces, which are in addition to those acting at the feet and task hand, are hypothesised to improve force exertion capability, and become required inputs to biomechanical analysis of tasks with bracing. The effects of kinematic constraints and associated bracing opportunities on isometric hand force were quantified in a laboratory study of 22 men and women. Analyses of one-hand maximal push, pull and lift tasks demonstrated that bracing surfaces available at the thighs and non-task hand enabled participants to exert an average of 43% more force at the task hand. Task hand force direction deviated significantly from the nominal direction for exertions performed with bracing at both medium and low task hand locations. This study quantifies the effect of bracing on kinematically constrained force exertions. Knowledge that appropriate bracing surfaces can substantially increase hand force is critical to the evaluation of task-oriented strength capability. Force estimates may also involve large off-axis components, which have clear implications for ergonomic analyses of manual tasks.

Display size effects in visual search: analyses of reaction time distributions as mixtures.

PubMed

Reynolds, Ann; Miller, Jeff

2009-05-01

In a reanalysis of data from Cousineau and Shiffrin (2004) and two new visual search experiments, we used a likelihood ratio test to examine the full distributions of reaction time (RT) for evidence that the display size effect is a mixture-type effect that occurs on only a proportion of trials, leaving RT in the remaining trials unaffected, as is predicted by serial self-terminating search models. Experiment 1 was a reanalysis of Cousineau and Shiffrin's data, for which a mixture effect had previously been established by a bimodal distribution of RTs, and the results confirmed that the likelihood ratio test could also detect this mixture. Experiment 2 applied the likelihood ratio test within a more standard visual search task with a relatively easy target/distractor discrimination, and Experiment 3 applied it within a target identification search task within the same types of stimuli. Neither of these experiments provided any evidence for the mixture-type display size effect predicted by serial self-terminating search models. Overall, these results suggest that serial self-terminating search models may generally be applicable only with relatively difficult target/distractor discriminations, and then only for some participants. In addition, they further illustrate the utility of analysing full RT distributions in addition to mean RT.

Multiple optimality criteria support Ornithoscelida

NASA Astrophysics Data System (ADS)

Parry, Luke A.; Baron, Matthew G.; Vinther, Jakob

2017-10-01

A recent study of early dinosaur evolution using equal-weights parsimony recovered a scheme of dinosaur interrelationships and classification that differed from historical consensus in a single, but significant, respect; Ornithischia and Saurischia were not recovered as monophyletic sister-taxa, but rather Ornithischia and Theropoda formed a novel clade named Ornithoscelida. However, these analyses only used maximum parsimony, and numerous recent simulation studies have questioned the accuracy of parsimony under equal weights. Here, we provide additional support for this alternative hypothesis using Bayesian implementation of the Mkv model, as well as through number of additional parsimony analyses, including implied weighting. Using Bayesian inference and implied weighting, we recover the same fundamental topology for Dinosauria as the original study, with a monophyletic Ornithoscelida, demonstrating that the main suite of methods used in morphological phylogenetics recover this novel hypothesis. This result was further scrutinized through the systematic exclusion of different character sets. Novel characters from the original study (those not taken or adapted from previous phylogenetic studies) were found to be more important for resolving the relationships within Dinosauromorpha than the relationships within Dinosauria. Reanalysis of a modified version of the character matrix that supports the Ornithischia-Saurischia dichotomy under maximum parsimony also supports this hypothesis under implied weighting, but not under the Mkv model, with both Theropoda and Sauropodomorpha becoming paraphyletic with respect to Ornithischia.

Additive effects of word frequency and stimulus quality: the influence of trial history and data transformations.

PubMed

Balota, David A; Aschenbrenner, Andrew J; Yap, Melvin J

2013-09-01

A counterintuitive and theoretically important pattern of results in the visual word recognition literature is that both word frequency and stimulus quality produce large but additive effects in lexical decision performance. The additive nature of these effects has recently been called into question by Masson and Kliegl (in press), who used linear mixed effects modeling to provide evidence that the additive effects were actually being driven by previous trial history. Because Masson and Kliegl also included semantic priming as a factor in their study and recent evidence has shown that semantic priming can moderate the additivity of word frequency and stimulus quality (Scaltritti, Balota, & Peressotti, 2012), we reanalyzed data from 3 published studies to determine if previous trial history moderated the additive pattern when semantic priming was not also manipulated. The results indicated that previous trial history did not influence the joint influence of word frequency and stimulus quality. More important, and independent of Masson and Kliegl's conclusions, we also show how a common transformation used in linear mixed effects analyses to normalize the residuals can systematically alter the way in which two variables combine to influence performance. Specifically, using transformed, rather than raw reaction times, consistently produces more underadditive patterns. PsycINFO Database Record (c) 2013 APA, all rights reserved.