DMINDA: an integrated web server for DNA motif identification and analyses

PubMed Central

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-01-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. PMID:24753419

From pre-registration to publication: a non-technical primer for conducting a meta-analysis to synthesize correlational data

PubMed Central

Quintana, Daniel S.

2015-01-01

Meta-analysis synthesizes a body of research investigating a common research question. Outcomes from meta-analyses provide a more objective and transparent summary of a research area than traditional narrative reviews. Moreover, they are often used to support research grant applications, guide clinical practice, and direct health policy. The aim of this article is to provide a practical and non-technical guide for psychological scientists that outlines the steps involved in planning and performing a meta-analysis of correlational datasets. I provide a supplementary R script to demonstrate each analytical step described in the paper, which is readily adaptable for researchers to use for their analyses. While the worked example is the analysis of a correlational dataset, the general meta-analytic process described in this paper is applicable for all types of effect sizes. I also emphasize the importance of meta-analysis protocols and pre-registration to improve transparency and help avoid unintended duplication. An improved understanding this tool will not only help scientists to conduct their own meta-analyses but also improve their evaluation of published meta-analyses. PMID:26500598

From pre-registration to publication: a non-technical primer for conducting a meta-analysis to synthesize correlational data.

PubMed

Quintana, Daniel S

2015-01-01

Meta-analysis synthesizes a body of research investigating a common research question. Outcomes from meta-analyses provide a more objective and transparent summary of a research area than traditional narrative reviews. Moreover, they are often used to support research grant applications, guide clinical practice, and direct health policy. The aim of this article is to provide a practical and non-technical guide for psychological scientists that outlines the steps involved in planning and performing a meta-analysis of correlational datasets. I provide a supplementary R script to demonstrate each analytical step described in the paper, which is readily adaptable for researchers to use for their analyses. While the worked example is the analysis of a correlational dataset, the general meta-analytic process described in this paper is applicable for all types of effect sizes. I also emphasize the importance of meta-analysis protocols and pre-registration to improve transparency and help avoid unintended duplication. An improved understanding this tool will not only help scientists to conduct their own meta-analyses but also improve their evaluation of published meta-analyses.

Dynamics of spiral waves rotating around an obstacle and the existence of a minimal obstacle

NASA Astrophysics Data System (ADS)

Gao, Xiang; Feng, Xia; Li, Teng-Chao; Qu, Shixian; Wang, Xingang; Zhang, Hong

2017-05-01

Pinning of vortices by obstacles plays an important role in various systems. In the heart, anatomical reentry is created when a vortex, also known as the spiral wave, is pinned to an anatomical obstacle, leading to a class of physiologically very important arrhythmias. Previous analyses of its dynamics and instability provide fine estimates in some special circumstances, such as large obstacles or weak excitabilities. Here, to expand theoretical analyses to all circumstances, we propose a general theory whose results quantitatively agree with direct numerical simulations. In particular, when obstacles are small and pinned spiral waves are destabilized, an accurate explanation of the instability in two-dimensional media is provided by the usage of a mapping rule and dimension reduction. The implications of our results are to better understand the mechanism of arrhythmia and thus improve its early prevention.

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.

The relative importance of mangroves and seagrass beds as feeding habitats for resident and transient fishes from Florida and Belize:: evidence from dietary and stable isotope analyses

EPA Science Inventory

In the western Atlantic region, the contribution of mangrove food-sources to fish diets has been considered of more limited importance then previously expected due to their constant flooding and proximity to adjacent coastal habitats such as seagrass beds which provide potential ...

Paragenesis and Geochronology of the Nopal I Uranium Deposit, Mexico

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

M. Fayek; M. Ren

2007-02-14

Uranium deposits can, by analogy, provide important information on the long-term performance of radioactive waste forms and radioactive waste repositories. Their complex mineralogy and variable elemental and isotopic compositions can provide important information, provided that analyses are obtained on the scale of several micrometers. Here, we present a structural model of the Nopal I deposit as well as petrography at the nanoscale coupled with preliminary U-Th-Pb ages and O isotopic compositions of uranium-rich minerals obtained by Secondary Ion Mass Spectrometry (SIMS). This multi-technique approach promises to provide ''natural system'' data on the corrosion rate of uraninite, the natural analogue ofmore » spent nuclear fuel.« less

Characteristics of meta-analyses and their component studies in the Cochrane Database of Systematic Reviews: a cross-sectional, descriptive analysis

PubMed Central

2011-01-01

Background Cochrane systematic reviews collate and summarise studies of the effects of healthcare interventions. The characteristics of these reviews and the meta-analyses and individual studies they contain provide insights into the nature of healthcare research and important context for the development of relevant statistical and other methods. Methods We classified every meta-analysis with at least two studies in every review in the January 2008 issue of the Cochrane Database of Systematic Reviews (CDSR) according to the medical specialty, the types of interventions being compared and the type of outcome. We provide descriptive statistics for numbers of meta-analyses, numbers of component studies and sample sizes of component studies, broken down by these categories. Results We included 2321 reviews containing 22,453 meta-analyses, which themselves consist of data from 112,600 individual studies (which may appear in more than one meta-analysis). Meta-analyses in the areas of gynaecology, pregnancy and childbirth (21%), mental health (13%) and respiratory diseases (13%) are well represented in the CDSR. Most meta-analyses address drugs, either with a control or placebo group (37%) or in a comparison with another drug (25%). The median number of meta-analyses per review is six (inter-quartile range 3 to 12). The median number of studies included in the meta-analyses with at least two studies is three (inter-quartile range 2 to 6). Sample sizes of individual studies range from 2 to 1,242,071, with a median of 91 participants. Discussion It is clear that the numbers of studies eligible for meta-analyses are typically very small for all medical areas, outcomes and interventions covered by Cochrane reviews. This highlights the particular importance of suitable methods for the meta-analysis of small data sets. There was little variation in number of studies per meta-analysis across medical areas, across outcome data types or across types of interventions being compared. PMID:22114982

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.

`Learning Experience' Provided by Science Teaching Practice in a Classroom and the Development of Students' Competences

NASA Astrophysics Data System (ADS)

Lopes, J. Bernardino; Branco, Julia; Jimenez-Aleixandre, Maria Pilar

2011-11-01

According to the literature, there is a very important corpus of knowledge that allows for the investigation of some dimensions of `learning experience' provided to students, in relation to epistemic, pedagogical and meta-cognitive practices. However, in the literature, there is little investigation into the invariance (or not) of the characteristics of students' learning experience while being taught a scientific subject by the same teacher. This paper suggests that the relationship between the learning experience provided and the competences developed is not properly highlighted. This paper analyses the learning experience provided to students in epistemic, pedagogical and meta-cognitive terms. The students were taught the proprieties and applications of light by one teacher, in three classes, over 7 weeks. We analysed the data in each referred learning experience, using a pre-defined category system. The students' competences were evaluated by a competence test. The epistemic demand of each item and the students' performances were also analysed. Our findings point to the non invariance of learning experiences provided to students and the influence of some dimensions of learning experiences provided in the development of certain competences. These findings and their implications are contextualized and discussed.

Access to finance from different finance provider types: Farmer knowledge of the requirements.

PubMed

Wulandari, Eliana; Meuwissen, Miranda P M; Karmana, Maman H; Oude Lansink, Alfons G J M

2017-01-01

Analysing farmer knowledge of the requirements of finance providers can provide valuable insights to policy makers about ways to improve farmers' access to finance. This study compares farmer knowledge of the requirements to obtain finance with the actual requirements set by different finance provider types, and investigates the relation between demographic and socioeconomic factors and farmer knowledge of finance requirements. We use a structured questionnaire to collect data from a sample of finance providers and farmers in Java Island, Indonesia. We find that the most important requirements to acquire finance vary among different finance provider types. We also find that farmers generally have little knowledge of the requirements, which are important to each type of finance provider. Awareness campaigns are needed to increase farmer knowledge of the diversity of requirements among the finance provider types.

Access to finance from different finance provider types: Farmer knowledge of the requirements

PubMed Central

Meuwissen, Miranda P. M.; Karmana, Maman H.; Oude Lansink, Alfons G. J. M.

2017-01-01

Analysing farmer knowledge of the requirements of finance providers can provide valuable insights to policy makers about ways to improve farmers’ access to finance. This study compares farmer knowledge of the requirements to obtain finance with the actual requirements set by different finance provider types, and investigates the relation between demographic and socioeconomic factors and farmer knowledge of finance requirements. We use a structured questionnaire to collect data from a sample of finance providers and farmers in Java Island, Indonesia. We find that the most important requirements to acquire finance vary among different finance provider types. We also find that farmers generally have little knowledge of the requirements, which are important to each type of finance provider. Awareness campaigns are needed to increase farmer knowledge of the diversity of requirements among the finance provider types. PMID:28877174

Importance analysis for Hudson River PCB transport and fate model parameters using robust sensitivity studies

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

Zhang, S.; Toll, J.; Cothern, K.

1995-12-31

The authors have performed robust sensitivity studies of the physico-chemical Hudson River PCB model PCHEPM to identify the parameters and process uncertainties contributing the most to uncertainty in predictions of water column and sediment PCB concentrations, over the time period 1977--1991 in one segment of the lower Hudson River. The term ``robust sensitivity studies`` refers to the use of several sensitivity analysis techniques to obtain a more accurate depiction of the relative importance of different sources of uncertainty. Local sensitivity analysis provided data on the sensitivity of PCB concentration estimates to small perturbations in nominal parameter values. Range sensitivity analysismore » provided information about the magnitude of prediction uncertainty associated with each input uncertainty. Rank correlation analysis indicated which parameters had the most dominant influence on model predictions. Factorial analysis identified important interactions among model parameters. Finally, term analysis looked at the aggregate influence of combinations of parameters representing physico-chemical processes. The authors scored the results of the local and range sensitivity and rank correlation analyses. The authors considered parameters that scored high on two of the three analyses to be important contributors to PCB concentration prediction uncertainty, and treated them probabilistically in simulations. They also treated probabilistically parameters identified in the factorial analysis as interacting with important parameters. The authors used the term analysis to better understand how uncertain parameters were influencing the PCB concentration predictions. The importance analysis allowed us to reduce the number of parameters to be modeled probabilistically from 16 to 5. This reduced the computational complexity of Monte Carlo simulations, and more importantly, provided a more lucid depiction of prediction uncertainty and its causes.« less

Job Tasks and the Participation of Low-Skilled Employees in Employer-Provided Continuing Training in Germany

ERIC Educational Resources Information Center

Mohr, Sabine; Troltsch, Klaus; Gerhards, Christian

2016-01-01

This study analyses the participation of low-skilled employees in employer-provided training and examines the mechanisms that encourage the training participation of low-skilled employees. Building on theoretical considerations of human capital theory and the task-based approach, we seek to show that job tasks play an important role in explaining…

The Professional Translator and Information Literacy: Perceptions and Needs

ERIC Educational Resources Information Center

Sales, Dora; Pinto, Maria

2011-01-01

This paper is part of a broader research project, the main goal of which is to provide translators with solid instruction in information literacy (IL). For this, it is important to know the views of the community of professional translators. The results of the ongoing research which we analyse in this paper provide this view, by means of a…

Measuring the Regional Economic Significance of Airports.

DTIC Science & Technology

1986-10-01

of the economic importance of airports. It is not intended for use in financial feasibility studies or cost/benefit analyses. Rather, it provides...activities involving aviation above and beyond the carriage of passengers. Air cargo accounts for several distinct businesses, including air freight and...selected for the analysis take regional imports into account . More economically self- S-.. sufficient regions have higher multipliers than do regions that

Investigating Predictors of Listening Comprehension in Third-, Seventh-, and Tenth-Grade Students: A Dominance Analysis Approach

PubMed Central

Tighe, Elizabeth L.; Spencer, Mercedes; Schatschneider, Christopher

2015-01-01

This study rank ordered the contributive importance of several predictors of listening comprehension for third, seventh, and tenth graders. Principal components analyses revealed that a three-factor solution with fluency, reasoning, and working memory components provided the best fit across grade levels. Dominance analyses indicated that fluency and reasoning were the strongest predictors of third grade listening comprehension. Reasoning emerged as the strongest predictor of seventh and tenth grade listening comprehension. These findings suggest a shift in the contributive importance of predictors to listening comprehension across development (i.e., grade levels). The implications of our findings for educators and researchers are discussed. PMID:26877573

Calculating and reporting effect sizes to facilitate cumulative science: a practical primer for t-tests and ANOVAs

PubMed Central

Lakens, Daniël

2013-01-01

Effect sizes are the most important outcome of empirical studies. Most articles on effect sizes highlight their importance to communicate the practical significance of results. For scientists themselves, effect sizes are most useful because they facilitate cumulative science. Effect sizes can be used to determine the sample size for follow-up studies, or examining effects across studies. This article aims to provide a practical primer on how to calculate and report effect sizes for t-tests and ANOVA's such that effect sizes can be used in a-priori power analyses and meta-analyses. Whereas many articles about effect sizes focus on between-subjects designs and address within-subjects designs only briefly, I provide a detailed overview of the similarities and differences between within- and between-subjects designs. I suggest that some research questions in experimental psychology examine inherently intra-individual effects, which makes effect sizes that incorporate the correlation between measures the best summary of the results. Finally, a supplementary spreadsheet is provided to make it as easy as possible for researchers to incorporate effect size calculations into their workflow. PMID:24324449

Exploring Teacher Intervention in the Intersection of Digital Resources, Peer Collaboration, and Instructional Design.

PubMed

Strømme, Torunn Aa; Furberg, Anniken

2015-09-01

This paper reports on a case study of the teacher's role as facilitator in computer-supported collaborative learning (CSCL) settings in science. In naturalistic classroom settings, the teacher most often acts as an important resource and provides various forms of guidance during students' learning activities. Few studies, however, have focused on the role of teacher intervention in CSCL settings. By analyzing the interactions between secondary school students and their teacher during a science project, the current study provides insight into the concerns that teachers might encounter when facilitating students' learning processes in these types of settings. The analyses show that one main concern was creating a balance between providing the requested information and supporting students in utilizing each other's knowledge and understanding. Another concern was balancing support on an individual versus group level, and a third concern was directing the students' attention to coexisting conceptual perspectives. Most importantly, however, the analyses show how teacher intervention constitutes the pivotal "glue" that aids students in linking and using coexisting aspects of support such as peer collaboration, digital tools, and instructional design.

Exploring Teacher Intervention in the Intersection of Digital Resources, Peer Collaboration, and Instructional Design

PubMed Central

FURBERG, ANNIKEN

2015-01-01

ABSTRACT This paper reports on a case study of the teacher's role as facilitator in computer‐supported collaborative learning (CSCL) settings in science. In naturalistic classroom settings, the teacher most often acts as an important resource and provides various forms of guidance during students’ learning activities. Few studies, however, have focused on the role of teacher intervention in CSCL settings. By analyzing the interactions between secondary school students and their teacher during a science project, the current study provides insight into the concerns that teachers might encounter when facilitating students’ learning processes in these types of settings. The analyses show that one main concern was creating a balance between providing the requested information and supporting students in utilizing each other's knowledge and understanding. Another concern was balancing support on an individual versus group level, and a third concern was directing the students’ attention to coexisting conceptual perspectives. Most importantly, however, the analyses show how teacher intervention constitutes the pivotal “glue” that aids students in linking and using coexisting aspects of support such as peer collaboration, digital tools, and instructional design. PMID:26900182

Explosive Cyclogenesis Over the Eastern United States.

NASA Astrophysics Data System (ADS)

MacDonald, Bruce Calvin

Cases of explosive cyclogenesis occurring over the east central United States are identified and analyzed. Other selected cases of weak or nonintensifying cyclones over the same area are identified and studied for comparative purposes. Signatures of explosively deepening cyclones (bombs) are derived from the analyses, including vertical profiles of vorticity, divergence, and latent heating, and also the relative importance of terms in the vorticity tendency equation and the relative importance of convective and stable latent heating. Composite analyses for the differing phases of bomb development and for regular cyclones are presented. Analyses of individual cases reveal the importance of a low-level jet streak, low-level moisture content, and moisture gradients in the lower troposphere. A numerical model is used to further examine the important processes in explosive cyclogenesis. A mesoscale feature is introduced to improve the prediction of sea -level pressure. This feature is based on the tendency of the large scale height field and vorticity field to adjust concurrently at each time step. The model is also used to provide air parcel trajectories to indicate the importance of parcels with high vorticity and moisture content as an ingredient in explosive cyclogenesis. Sensitivity studies are carried out with the model in order to determine the effect of changes in the initial vorticity and moisture field on cyclogenesis.

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.

Analysis of Cross-Sectional Univariate Measurements for Family Dyads Using Linear Mixed Modeling

PubMed Central

Knafl, George J.; Dixon, Jane K.; O'Malley, Jean P.; Grey, Margaret; Deatrick, Janet A.; Gallo, Agatha M.; Knafl, Kathleen A.

2010-01-01

Outcome measurements from members of the same family are likely correlated. Such intrafamilial correlation (IFC) is an important dimension of the family as a unit but is not always accounted for in analyses of family data. This article demonstrates the use of linear mixed modeling to account for IFC in the important special case of univariate measurements for family dyads collected at a single point in time. Example analyses of data from partnered parents having a child with a chronic condition on their child's adaptation to the condition and on the family's general functioning and management of the condition are provided. Analyses of this kind are reasonably straightforward to generate with popular statistical tools. Thus, it is recommended that IFC be reported as standard practice reflecting the fact that a family dyad is more than just the aggregate of two individuals. Moreover, not accounting for IFC can affect the conclusions. PMID:19307316

DMINDA: an integrated web server for DNA motif identification and analyses.

PubMed

Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

2014-07-01

DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Capturing Budget Impact Considerations Within Economic Evaluations: A Systematic Review of Economic Evaluations of Rotavirus Vaccine in Low- and Middle-Income Countries and a Proposed Assessment Framework.

PubMed

Carvalho, Natalie; Jit, Mark; Cox, Sarah; Yoong, Joanne; Hutubessy, Raymond C W

2018-01-01

In low- and middle-income countries, budget impact is an important criterion for funding new interventions, particularly for large public health investments such as new vaccines. However, budget impact analyses remain less frequently conducted and less well researched than cost-effectiveness analyses. The objective of this study was to fill the gap in research on budget impact analyses by assessing (1) the quality of stand-alone budget impact analyses, and (2) the feasibility of extending cost-effectiveness analyses to capture budget impact. We developed a budget impact analysis checklist and scoring system for budget impact analyses, which we then adapted for cost-effectiveness analyses, based on current International Society for Pharmacoeconomics and Outcomes Research Task Force recommendations. We applied both budget impact analysis and cost-effectiveness analysis checklists and scoring systems to examine the extent to which existing economic evaluations provide sufficient evidence about budget impact to enable decision making. We used rotavirus vaccination as an illustrative case in which low- and middle-income countries uptake has been limited despite demonstrated cost effectiveness. A systematic literature review was conducted to identify economic evaluations of rotavirus vaccine in low- and middle-income countries published between January 2000 and February 2017. We critically appraised the quality of budget impact analyses, and assessed the extension of cost-effectiveness analyses to provide useful budget impact information. Six budget impact analyses and 60 cost-effectiveness analyses were identified. Budget impact analyses adhered to most International Society for Pharmacoeconomics and Outcomes Research recommendations, with key exceptions being provision of undiscounted financial streams for each budget period and model validation. Most cost-effectiveness analyses could not be extended to provide useful budget impact information; cost-effectiveness analyses also rarely presented undiscounted annual costs, or estimated financial streams during the first years of programme scale-up. Cost-effectiveness analyses vastly outnumber budget impact analyses of rotavirus vaccination, despite both being critical for policy decision making. Straightforward changes to the presentation of cost-effectiveness analyses results could facilitate their adaptation into budget impact analyses.

Factors Important for Work Participation Among Older Workers with Depression, Cardiovascular Disease, and Osteoarthritis: A Mixed Method Study.

PubMed

Boot, Cécile R L; de Kruif, Anja Th C M; Shaw, William S; van der Beek, Allard J; Deeg, Dorly J; Abma, Tineke

2016-06-01

Purpose The aim of this study was to gain insight into differences and similarities in factors important for work participation in older (58-65 years) workers among three different chronic diseases: depression (D), cardiovascular disease (C), and osteoarthritis (O). Methods A mixed method design was used, with a qualitative part (in-depth interviews) with 14 patients with D, C or O and a quantitative part based on the 2002-2003 cohort of the Longitudinal Aging Study Amsterdam. We analysed and compared 3-year (response 93 %) predictors of paid work in 239 participants with D, C, or O using regression analyses. The qualitative findings were integrated with the quantitative findings aiming at complementarity. Results Common factors important for work participation were: working at baseline; male gender; lower age; partner with paid work; better physical and mental health; and higher mastery scores. The qualitative analyses added autonomy in work and provided contextual information regarding the perceived importance of working as factors important for participation in paid work. For D and C, work gave purpose in life and enhanced social contacts. Participation in work was perceived as necessary to structure life only for D. Conclusion Most factors important for work participation were similar for D, C, and O. However, the interviews revealed that for D, the context and the meaning attributed to these factors differed.

Exploring and Harnessing Haplotype Diversity to Improve Yield Stability in Crops.

PubMed

Qian, Lunwen; Hickey, Lee T; Stahl, Andreas; Werner, Christian R; Hayes, Ben; Snowdon, Rod J; Voss-Fels, Kai P

2017-01-01

In order to meet future food, feed, fiber, and bioenergy demands, global yields of all major crops need to be increased significantly. At the same time, the increasing frequency of extreme weather events such as heat and drought necessitates improvements in the environmental resilience of modern crop cultivars. Achieving sustainably increase yields implies rapid improvement of quantitative traits with a very complex genetic architecture and strong environmental interaction. Latest advances in genome analysis technologies today provide molecular information at an ultrahigh resolution, revolutionizing crop genomic research, and paving the way for advanced quantitative genetic approaches. These include highly detailed assessment of population structure and genotypic diversity, facilitating the identification of selective sweeps and signatures of directional selection, dissection of genetic variants that underlie important agronomic traits, and genomic selection (GS) strategies that not only consider major-effect genes. Single-nucleotide polymorphism (SNP) markers today represent the genotyping system of choice for crop genetic studies because they occur abundantly in plant genomes and are easy to detect. SNPs are typically biallelic, however, hence their information content compared to multiallelic markers is low, limiting the resolution at which SNP-trait relationships can be delineated. An efficient way to overcome this limitation is to construct haplotypes based on linkage disequilibrium, one of the most important features influencing genetic analyses of crop genomes. Here, we give an overview of the latest advances in genomics-based haplotype analyses in crops, highlighting their importance in the context of polyploidy and genome evolution, linkage drag, and co-selection. We provide examples of how haplotype analyses can complement well-established quantitative genetics frameworks, such as quantitative trait analysis and GS, ultimately providing an effective tool to equip modern crops with environment-tailored characteristics.

Strategic action grids: a study in Indian hospitals.

PubMed

Padma, Panchapakesan; Lokachari, Prakash Sai; Chandrasekharan, Rajendran

2014-01-01

The purpose of this paper is to provide strategic recommendations to Indian hospital administrators for improving service quality by analysing performance dimensions and the importance attached to them by patients and attendants. Patient and attendant perceptions were collected using a questionnaire. Patients and attendants have different perceptions. Different customers have different needs of which providers need to be aware to better serve their consumers. The study captured only 408 patient and attendants' perceptions--a 32 per cent response rate. Results enable hospital administrators to develop appropriate strategies to improve their structure and function by analysing their strengths and weaknesses regarding their tangible and intangible assets. The study included attendants, specifically in an Indian healthcare context.

Taking stock: A meta-analysis of studies on the media's coverage of science.

PubMed

Schäfer, Mike S

2012-08-01

The presentation of science in the mass media is one of the most important questions facing social scientists who analyse science. Accordingly, media coverage of science has been a constant focal point in the respective literature, and a flurry of such publications has appeared in the past few years. Yet the activity and growth of the respective research have not been accompanied by systematic overviews. This article aims to provide such an overview by means of a meta-analysis: it analyses existing studies systematically and provides an empirical overview of the literature. The analysis shows that while the research field grew significantly in the past few years and employs a variety of research strategies and methods, it has been biased in three ways: mainly natural sciences (and namely biosciences and medicine), Western countries, and print media have been analysed.

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…

Urban water - a new frontier in isotope hydrology.

PubMed

Ehleringer, James R; Barnette, Janet E; Jameel, Yusuf; Tipple, Brett J; Bowen, Gabriel J

2016-01-01

Isotope hydrology has focused largely on landscapes away from densely inhabited regions. In coming decades, it will become increasingly more important to focus on water supplies and dynamics within urban systems. Stable isotope analyses provide important information to water managers within large cities, particularly in arid regions where evaporative histories of water sources, vulnerabilities, and reliabilities of the water supplies can be major issues. Here the spatial and vertical understanding of water supporting urban systems that comes from stable isotope analyses can serve as a useful management tool. We explore this research frontier using the coupled natural-human landscape of the Salt Lake Valley, USA, with its greater than one million inhabitants. We first provide data on the stable isotope ratios of the hydrologic system's primary components: precipitation, incoming surface waters, and terminus waters in this closed basin. We then explore the spatial and temporal patterns of drinking waters within the urban landscape and the new opportunities to better link isotope ratio data with short- and long-term management interests of water managers.

Advanced concepts in biomass production and pretreatment. Annual report, April 1986-March 1987

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

Hiler, E.A.; Miller, F.R.; Dominy, R.E.

1987-04-01

The objective of the research is to develop an integrated system for methane production utilizing terrestrial biomass as the feedstock. The report provides specifics of research activities in the Texas A and M biomass program sponsored by Gas Research Institute and co-funded by Texas Agricultural Experiment Station. Researchers in the program include plant geneticists, plant physiologists, chemists, agronomists, ruminant physiologists, agricultural engineers, biochemical engineers, and agricultural economists. Major research emphases are genetic manipulation, physiology and production systems, harvesting, storage, processing and conversion systems, inhibitors, and economic and system analyses. During the past year, increasing emphasis was placed on the biologicalmore » pretreatment aspects of the program because of the critical importance of the area to the improved efficiency of the overall system. In the breeding, tissue culture, and production programs, continued substantial progress was made in identifying and characterizing sorghums that will produce high biomass yields and have improved lodging resistance and high uniformity. Economic and systems analyses provided important information regarding optimal overall systems.« less

Energetic and flexibility properties captured by long molecular dynamics simulations of a membrane-embedded pMHCII-TCR complex.

PubMed

Bello, Martiniano; Correa-Basurto, José

2016-04-01

Although crystallographic data have provided important molecular insight into the interactions in the pMHC-TCR complex, the inherent features of this structural approach cause it to only provide a static picture of the interactions. While unbiased molecular dynamics simulations (UMDSs) have provided important information about the dynamic structural behavior of the pMHC-TCR complex, most of them have modeled the pMHC-TCR complex as soluble, when in physiological conditions, this complex is membrane bound; therefore, following this latter UMDS protocol might hamper important dynamic results. In this contribution, we performed three independent 300 ns-long UMDSs of the pMHCII-TCR complex anchored in two opposing membranes to explore the structural and energetic properties of the recognition of pMHCII by the TCR. The conformational ensemble generated through UMDSs was subjected to clustering and Cartesian principal component analyses (cPCA) to explore the dynamical behavior of the pMHCII-TCR association. Furthermore, based on the conformational population sampled through UMDSs, the effective binding free energy, per-residue free energy decomposition, and alanine scanning mutations were explored for the native pMHCII-TCR complex, as well as for 12 mutations (p1-p12MHCII-TCR) introduced in the native peptide. Clustering analyses and cPCA provide insight into the rocking motion of the TCR onto pMHCII, together with the presence of new electrostatic interactions not observed through crystallographic methods. Energetic results provide evidence of the main contributors to the pMHC-TCR complex formation as well as the key residues involved in this molecular recognition process.

MolabIS--an integrated information system for storing and managing molecular genetics data.

PubMed

Truong, Cong V C; Groeneveld, Linn F; Morgenstern, Burkhard; Groeneveld, Eildert

2011-10-31

Long-term sample storage, tracing of data flow and data export for subsequent analyses are of great importance in genetics studies. Therefore, molecular labs do need a proper information system to handle an increasing amount of data from different projects. We have developed a molecular labs information management system (MolabIS). It was implemented as a web-based system allowing the users to capture original data at each step of their workflow. MolabIS provides essential functionality for managing information on individuals, tracking samples and storage locations, capturing raw files, importing final data from external files, searching results, accessing and modifying data. Further important features are options to generate ready-to-print reports and convert sequence and microsatellite data into various data formats, which can be used as input files in subsequent analyses. Moreover, MolabIS also provides a tool for data migration. MolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org.

MolabIS - An integrated information system for storing and managing molecular genetics data

PubMed Central

2011-01-01

Background Long-term sample storage, tracing of data flow and data export for subsequent analyses are of great importance in genetics studies. Therefore, molecular labs do need a proper information system to handle an increasing amount of data from different projects. Results We have developed a molecular labs information management system (MolabIS). It was implemented as a web-based system allowing the users to capture original data at each step of their workflow. MolabIS provides essential functionality for managing information on individuals, tracking samples and storage locations, capturing raw files, importing final data from external files, searching results, accessing and modifying data. Further important features are options to generate ready-to-print reports and convert sequence and microsatellite data into various data formats, which can be used as input files in subsequent analyses. Moreover, MolabIS also provides a tool for data migration. Conclusions MolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org. PMID:22040322

Importance of contraction history on muscle force of porcine urinary bladder smooth muscle.

PubMed

Menzel, Robin; Böl, Markus; Siebert, Tobias

2017-02-01

The purpose of this study was to provide a comprehensive dataset of porcine urinary bladder smooth muscle properties. Particularly, the history dependence of force production, namely force depression (FD) following shortening and force enhancement (FE) following stretch, was analysed. During active micturition, the circumference of the urinary bladder changes enormously. Thus, FD might be an important phenomenon during smooth muscle contraction. Electrically stimulated, intact urinary bladder strips from pigs (n = 10) were suspended in an aerated-filled organ bath, and different isometric, isotonic, and isokinetic contraction protocols were performed to determine the force-length and the force-velocity relation. FD and FE were assessed in concentric and eccentric contractions with different ramp lengths and ramp velocities. Bladder smooth muscles exhibit considerable amounts of FD and FE. The amount of FD increased significantly with ramp length, while FE did not change. However, FE and FD were independent of ramp velocity. The results imply that smooth muscle bladder strips exhibit similar muscle properties and history-dependent behaviour compared to striated muscles. The provided dataset of muscle properties is important for bladder modelling as well as for the analyses and interpretation of dynamic bladder filling and voiding.

A python framework for environmental model uncertainty analysis

USGS Publications Warehouse

White, Jeremy; Fienen, Michael N.; Doherty, John E.

2016-01-01

We have developed pyEMU, a python framework for Environmental Modeling Uncertainty analyses, open-source tool that is non-intrusive, easy-to-use, computationally efficient, and scalable to highly-parameterized inverse problems. The framework implements several types of linear (first-order, second-moment (FOSM)) and non-linear uncertainty analyses. The FOSM-based analyses can also be completed prior to parameter estimation to help inform important modeling decisions, such as parameterization and objective function formulation. Complete workflows for several types of FOSM-based and non-linear analyses are documented in example notebooks implemented using Jupyter that are available in the online pyEMU repository. Example workflows include basic parameter and forecast analyses, data worth analyses, and error-variance analyses, as well as usage of parameter ensemble generation and management capabilities. These workflows document the necessary steps and provides insights into the results, with the goal of educating users not only in how to apply pyEMU, but also in the underlying theory of applied uncertainty quantification.

HIGHLIGHTS FROM TECHNICAL MANUAL ON HOOD SYSTEM CAPTURE OF PROCESS FUGITIVE PARTICULATE EMISSIONS

EPA Science Inventory

The paper discusses a technical manual whose emphasis is on the design and evaluation of actual hood systems used to control various fugitive particulate emission sources. Engineering analyses of the most important hood types are presented to provide a conceptual understanding of...

A Cell Wall Proteome and Targeted Cell Wall Analyses Provide Novel Information on Hemicellulose Metabolism in Flax.

PubMed

Chabi, Malika; Goulas, Estelle; Leclercq, Celine C; de Waele, Isabelle; Rihouey, Christophe; Cenci, Ugo; Day, Arnaud; Blervacq, Anne-Sophie; Neutelings, Godfrey; Duponchel, Ludovic; Lerouge, Patrice; Hausman, Jean-François; Renaut, Jenny; Hawkins, Simon

2017-09-01

Experimentally-generated (nanoLC-MS/MS) proteomic analyses of four different flax organs/tissues (inner-stem, outer-stem, leaves and roots) enriched in proteins from 3 different sub-compartments (soluble-, membrane-, and cell wall-proteins) was combined with publically available data on flax seed and whole-stem proteins to generate a flax protein database containing 2996 nonredundant total proteins. Subsequent multiple analyses (MapMan, CAZy, WallProtDB and expert curation) of this database were then used to identify a flax cell wall proteome consisting of 456 nonredundant proteins localized in the cell wall and/or associated with cell wall biosynthesis, remodeling and other cell wall related processes. Examination of the proteins present in different flax organs/tissues provided a detailed overview of cell wall metabolism and highlighted the importance of hemicellulose and pectin remodeling in stem tissues. Phylogenetic analyses of proteins in the cell wall proteome revealed an important paralogy in the class IIIA xyloglucan endo-transglycosylase/hydrolase (XTH) family associated with xyloglucan endo-hydrolase activity.Immunolocalisation, FT-IR microspectroscopy, and enzymatic fingerprinting indicated that flax fiber primary/S1 cell walls contained xyloglucans with typical substituted side chains as well as glucuronoxylans in much lower quantities. These results suggest a likely central role of xyloglucans and endotransglucosylase/hydrolase activity in flax fiber formation and cell wall remodeling processes. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Lessons on RNA Silencing Mechanisms in Plants from Eukaryotic Argonaute Structures[W

PubMed Central

Poulsen, Christian; Vaucheret, Hervé; Brodersen, Peter

2013-01-01

RNA silencing refers to a collection of gene regulatory mechanisms that use small RNAs for sequence specific repression. These mechanisms rely on ARGONAUTE (AGO) proteins that directly bind small RNAs and thereby constitute the central component of the RNA-induced silencing complex (RISC). AGO protein function has been probed extensively by mutational analyses, particularly in plants where large allelic series of several AGO proteins have been isolated. Structures of entire human and yeast AGO proteins have only very recently been obtained, and they allow more precise analyses of functional consequences of mutations obtained by forward genetics. To a large extent, these analyses support current models of regions of particular functional importance of AGO proteins. Interestingly, they also identify previously unrecognized parts of AGO proteins with profound structural and functional importance and provide the first hints at structural elements that have important functions specific to individual AGO family members. A particularly important outcome of the analysis concerns the evidence for existence of Gly-Trp (GW) repeat interactors of AGO proteins acting in the plant microRNA pathway. The parallel analysis of AGO structures and plant AGO mutations also suggests that such interactions with GW proteins may be a determinant of whether an endonucleolytically competent RISC is formed. PMID:23303917

Lessons on RNA silencing mechanisms in plants from eukaryotic argonaute structures.

PubMed

Poulsen, Christian; Vaucheret, Hervé; Brodersen, Peter

2013-01-01

RNA silencing refers to a collection of gene regulatory mechanisms that use small RNAs for sequence specific repression. These mechanisms rely on ARGONAUTE (AGO) proteins that directly bind small RNAs and thereby constitute the central component of the RNA-induced silencing complex (RISC). AGO protein function has been probed extensively by mutational analyses, particularly in plants where large allelic series of several AGO proteins have been isolated. Structures of entire human and yeast AGO proteins have only very recently been obtained, and they allow more precise analyses of functional consequences of mutations obtained by forward genetics. To a large extent, these analyses support current models of regions of particular functional importance of AGO proteins. Interestingly, they also identify previously unrecognized parts of AGO proteins with profound structural and functional importance and provide the first hints at structural elements that have important functions specific to individual AGO family members. A particularly important outcome of the analysis concerns the evidence for existence of Gly-Trp (GW) repeat interactors of AGO proteins acting in the plant microRNA pathway. The parallel analysis of AGO structures and plant AGO mutations also suggests that such interactions with GW proteins may be a determinant of whether an endonucleolytically competent RISC is formed.

Explicit versus implicit motivations: Clarifying how experiences affect turkey hunter satisfaction using revised importance-performance, importance grid, and penalty-reward-contrast analyses

USGS Publications Warehouse

Schroeder, Susan A.; Cornicelli, Louis; Fulton, David C.; Merchant, Steven S.

2018-01-01

Although research has advanced methods for clarifying factors that relate to customer satisfaction, they have not been embraced by leisure researchers. Using results from a survey of wild turkey hunters, we applied traditional and revised importance-performance (IPA/RIPA), importance-grid analysis (IGA), and penalty-reward-contrast analysis (PRCA) to examine how activity-specific factors influenced satisfaction. Results suggested differences between the explicit and implicit importance of factors related to turkey hunting. Opportunities to kill turkeys were explicitly rated as less important than seeing, hearing, or calling in turkeys, but opportunities for harvest had relatively higher levels of implicit importance. PRCA identified “calling turkeys in” and “hearing gobbling” as minimum requirements that cause dissatisfaction if not fulfilled, but do not provide satisfaction, whereas “seeing turkeys” and an “opportunity to kill a turkey” related to both satisfaction and dissatisfaction. RIPA, IGA, and PRCA could provide valuable insights about factors that may improve satisfaction for leisure participants.

Authentication of Valeriana procera Kunth and comparative account of five Valeriana species.

PubMed

Joshi, Vaishali C; Navarrete, Andres; Khan, Ikhlas A

2005-01-01

Valeriana procera Kunth (Mexican Valerian) is a commercially important species, sometimes used as a substitute for Valeriana officinalis L., an important sedative in herbal medicine. A detailed macroscopic and microscopic account was provided for V. procera Kunth and a comparison was made between the wild and cultivated samples of V. procera Kunth. Macro- and microscopic comparative analyses were performed to differentiate V. procera Kunth from V. officinalis L. and other commercially important Valerian species such as V. jatamansi Jones, Valeriana edulis Nutt, and V. sitchensis Bong.

Does climate directly influence NPP globally?

PubMed

Chu, Chengjin; Bartlett, Megan; Wang, Youshi; He, Fangliang; Weiner, Jacob; Chave, Jérôme; Sack, Lawren

2016-01-01

The need for rigorous analyses of climate impacts has never been more crucial. Current textbooks state that climate directly influences ecosystem annual net primary productivity (NPP), emphasizing the urgent need to monitor the impacts of climate change. A recent paper challenged this consensus, arguing, based on an analysis of NPP for 1247 woody plant communities across global climate gradients, that temperature and precipitation have negligible direct effects on NPP and only perhaps have indirect effects by constraining total stand biomass (Mtot ) and stand age (a). The authors of that study concluded that the length of the growing season (lgs ) might have a minor influence on NPP, an effect they considered not to be directly related to climate. In this article, we describe flaws that affected that study's conclusions and present novel analyses to disentangle the effects of stand variables and climate in determining NPP. We re-analyzed the same database to partition the direct and indirect effects of climate on NPP, using three approaches: maximum-likelihood model selection, independent-effects analysis, and structural equation modeling. These new analyses showed that about half of the global variation in NPP could be explained by Mtot combined with climate variables and supported strong and direct influences of climate independently of Mtot , both for NPP and for net biomass change averaged across the known lifetime of the stands (ABC = average biomass change). We show that lgs is an important climate variable, intrinsically correlated with, and contributing to mean annual temperature and precipitation (Tann and Pann ), all important climatic drivers of NPP. Our analyses provide guidance for statistical and mechanistic analyses of climate drivers of ecosystem processes for predictive modeling and provide novel evidence supporting the strong, direct role of climate in determining vegetation productivity at the global scale. © 2015 John Wiley & Sons Ltd.

Genetic structure and domestication of carrot (Daucus carota subsp. sativus L.) (Apiaceae)

USDA-ARS?s Scientific Manuscript database

Analyses of genetic structure and phylogenetic relationships illuminate the origin and domestication of modern crops. Despite being an important world-wide vegetable, the genetic structure and domestication of carrot (Daucus carota L.) is poorly understood. We provide the first such study using a la...

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...

Identification and characterization of plasmids from Xylella fastidiosa using next generation sequencing analyses

USDA-ARS?s Scientific Manuscript database

Xylella fastidiosa causes diseases in many economically important crops, e.g. Pierce’s disease (PD) of grapevines and blueberry bacterial leaf scorch (BBLS) disease in the U.S. Biological research on X. fastidiosa has been difficult due to its nutritional fastidiousness. Genomic research provides a ...

The Critical Importance of Costs for Education Decisions. REL 2017-274

ERIC Educational Resources Information Center

Hollands, Fiona M.; Levin, Henry M.

2017-01-01

This brief provides guidance to decision makers in schools, districts, state education departments, and intermediary organizations about ways that cost analyses can help inform their decisions about program choices, budgets, and strategies. It addresses questions about: (1) why cost information matters in education; (2) what cost metrics are…

Why Does Collaboration Work? Linking Positive Psychology and Collaboration

ERIC Educational Resources Information Center

Conoley, Jane Close; Conoley, Collie Wyatt

2010-01-01

Authors in this special issue edited by Cook and Friend provide analyses of many important relationships within a school: teacher to teacher; teacher to paraprofessional, educators, and home caregivers; and whole-building systems. Their focus on collaboration prompted these authors to reflect on a possible theoretical mechanism behind the success…

Genome wide association analyses based on a multiple trait approach for modeling feed efficiency

USDA-ARS?s Scientific Manuscript database

Genome wide association (GWA) of feed efficiency (FE) could help target important genomic regions influencing FE. Data provided by an international dairy FE research consortium consisted of phenotypic records on dry matter intakes (DMI), milk energy (MILKE), and metabolic body weight (MBW) on 6,937 ...

Comparative Cognitive Task Analyses of Experimental Science and Instructional Laboratory Courses

ERIC Educational Resources Information Center

Wieman, Carl

2015-01-01

Undergraduate instructional labs in physics generate intense opinions. Their advocates are passionate as to their importance for teaching physics as an experimental activity and providing "hands-on" learning experiences, while their detractors (often but not entirely students) offer harsh criticisms that they are pointless, confusing and…

Safe Planet. The Guide to Environmental Film and Video.

ERIC Educational Resources Information Center

Media Network, New York, NY.

Innovative and incisive films and videotapes exist which address the issues of toxic waste, agricultural pollutants, land and water use, energy production, and other important environmental topics. They provide in-depth analyses, alternative points of view, and specific suggestions for what ordinary citizens can do to help stop environmental…

The geochemical landscape of northwestern Wisconsin and adjacent parts of northern Michigan and Minnesota (geochemical data files)

USGS Publications Warehouse

Cannon, William F.; Woodruff, Laurel G.

2003-01-01

This data set consists of nine files of geochemical information on various types of surficial deposits in northwestern Wisconsin and immediately adjacent parts of Michigan and Minnesota. The files are presented in two formats: as dbase files in dbaseIV form and Microsoft Excel form. The data present multi-element chemical analyses of soils, stream sediments, and lake sediments. Latitude and longitude values are provided in each file so that the dbf files can be readily imported to GIS applications. Metadata files are provided in outline form, question and answer form and text form. The metadata includes information on procedures for sample collection, sample preparation, and chemical analyses including sensitivity and precision.

Monitoring the southwestern Wyoming landscape—A foundation for management and science

USGS Publications Warehouse

Manier, Daniel J.; Anderson, Patrick J.; Assal, Timothy J.; Chong, Geneva W.; Melcher, Cynthia P.

2017-08-29

Natural resource monitoring involves repeated collections of resource condition data and analyses to detect possible changes and identify underlying causes of changes. For natural resource agencies, monitoring provides the foundation for management and science. Specifically, analyses of monitoring data allow managers to better understand effects of land-use and other changes on important natural resources and to achieve their conservation and management goals. Examples of natural resources monitored on public lands include wildlife habitats, plant productivity, animal movements and population trends, soil chemistry, and water quality and quantity. Broader definitions of monitoring also recognize the need for scientifically valid data to help support planning efforts and informed decisions, to develop adaptive management strategies, and to provide the means for evaluating management outcomes.

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

Molecular biology of bladder cancer.

PubMed

Martin-Doyle, William; Kwiatkowski, David J

2015-04-01

Classic as well as more recent large-scale genomic analyses have uncovered multiple genes and pathways important for bladder cancer development. Genes involved in cell-cycle control, chromatin regulation, and receptor tyrosine and PI3 kinase-mammalian target of rapamycin signaling pathways are commonly mutated in muscle-invasive bladder cancer. Expression-based analyses have identified distinct types of bladder cancer that are similar to subsets of breast cancer, and have prognostic and therapeutic significance. These observations are leading to novel therapeutic approaches in bladder cancer, providing optimism for therapeutic progress. Copyright © 2015 Elsevier Inc. All rights reserved.

Research on Visual Analysis Methods of Terrorism Events

NASA Astrophysics Data System (ADS)

Guo, Wenyue; Liu, Haiyan; Yu, Anzhu; Li, Jing

2016-06-01

Under the situation that terrorism events occur more and more frequency throughout the world, improving the response capability of social security incidents has become an important aspect to test governments govern ability. Visual analysis has become an important method of event analysing for its advantage of intuitive and effective. To analyse events' spatio-temporal distribution characteristics, correlations among event items and the development trend, terrorism event's spatio-temporal characteristics are discussed. Suitable event data table structure based on "5W" theory is designed. Then, six types of visual analysis are purposed, and how to use thematic map and statistical charts to realize visual analysis on terrorism events is studied. Finally, experiments have been carried out by using the data provided by Global Terrorism Database, and the results of experiments proves the availability of the methods.

Traumatic brain injuries in the construction industry.

PubMed

Colantonio, Angela; McVittie, Doug; Lewko, John; Yin, Junlang

2009-10-01

This study analyses factors associated with work-related traumatic brain injury (TBI), specifically in the construction industry in Ontario, Canada. This cross-sectional study utilized data extracted from the Ontario Workplace Safety and Insurance Board (WSIB) records indicating concussion/intracranial injury that resulted in days off work in 2004-2005. Analyses of 218 TBI cases revealed that falls were the most common cause of injury, followed by being struck by or against an object. Mechanisms of injury and the temporal profile of injury also varied by age. For instance, a significantly higher proportion of injuries occurred in the mornings for young workers compared to older workers. The results of this study provide important information for prevention of TBI which suggest important age-specific strategies for workers in the construction industry.

Understanding unemployed people's job search behaviour, unemployment experience and well-being: a comparison of expectancy-value theory and self-determination theory.

PubMed

Vansteenkiste, Maarten; Lens, Willy; De Witte, Hans; Feather, N T

2005-06-01

Previous unemployment research has directly tested hypotheses derived from expectancy-value theory (EVT; Feather, 1982, 1990), but no comparative analysis has been executed with another motivational framework. In one large study with 446 unemployed people, separate analyses provided good evidence for predictions derived from both EVT and self-determination theory (SDT; Deci & Ryan, 1985, 2000). Comparative analyses indicated that the type of people's job search motivation, as conceptualized through the notions of autonomous versus controlled motivation within SDT, is an important predictor of people's unemployment experience and wellbeing, beyond people's strength of motivation assessed within EVT through expectancies of finding a job and employment value. The importance of simultaneously testing two theoretical frameworks is discussed.

Dynamic systems approaches and levels of analysis in the nervous system

PubMed Central

Parker, David; Srivastava, Vipin

2013-01-01

Various analyses are applied to physiological signals. While epistemological diversity is necessary to address effects at different levels, there is often a sense of competition between analyses rather than integration. This is evidenced by the differences in the criteria needed to claim understanding in different approaches. In the nervous system, neuronal analyses that attempt to explain network outputs in cellular and synaptic terms are rightly criticized as being insufficient to explain global effects, emergent or otherwise, while higher-level statistical and mathematical analyses can provide quantitative descriptions of outputs but can only hypothesize on their underlying mechanisms. The major gap in neuroscience is arguably our inability to translate what should be seen as complementary effects between levels. We thus ultimately need approaches that allow us to bridge between different spatial and temporal levels. Analytical approaches derived from critical phenomena in the physical sciences are increasingly being applied to physiological systems, including the nervous system, and claim to provide novel insight into physiological mechanisms and opportunities for their control. Analyses of criticality have suggested several important insights that should be considered in cellular analyses. However, there is a mismatch between lower-level neurophysiological approaches and statistical phenomenological analyses that assume that lower-level effects can be abstracted away, which means that these effects are unknown or inaccessible to experimentalists. As a result experimental designs often generate data that is insufficient for analyses of criticality. This review considers the relevance of insights from analyses of criticality to neuronal network analyses, and highlights that to move the analyses forward and close the gap between the theoretical and neurobiological levels, it is necessary to consider that effects at each level are complementary rather than in competition. PMID:23386835

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.

Easier said than done: a qualitative study conducted in the USA exploring Latino family child care home providers as role models for healthy eating and physical activity behaviours.

PubMed

Lindsay, Ana Cristina; Greaney, Mary L; Wallington, Sherrie F; Wright, Julie A

2017-11-12

Latinos are the largest and most rapidly growing minority population group in the USA and are disproportionally affected by obesity and related chronic diseases. Child care providers likely influence the eating and physical activity behaviours of children in their care, and therefore are important targets for interventions designed to prevent childhood obesity. Nonetheless, there is a paucity of research examining the behaviours of family child care home (FCCH) providers and whether they model healthy eating and physical activity behaviours. Therefore, this study explored Latino FCCH providers' beliefs and practices related to healthy eating, physical activity and sedentary behaviours, and how they view their ability to serve as role models for these behaviours for young children in their care. This is a qualitative study consisting of six focus groups conducted in Spanish with a sample of 44 state-licensed Latino FCCH providers in the state of Massachusetts. Translated transcripts were analysed using thematic analyses to identify meaningful patterns. Analyses revealed that Latino FCCH providers have positive beliefs and attitudes about the importance of healthy eating and physical activity for children in their care, but personally struggle with these same behaviours and with maintaining a healthy weight status. The ability of Latino FCCH providers to model healthy eating and physical activity may be limited by their low self-efficacy in their ability to be physically active, eat a healthy diet and maintain a healthy weight. Interventions designed to improve healthy eating and physical activity behaviours of children enrolled in FCCHs should address providers' own health behaviours as well as their modelling of these health behaviours. Future research can build on the findings of this qualitative study by quantifying Latino FCCH providers' eating and physical activity behaviours, and determining how these behaviours influence behaviours and health outcomes of children in their care. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

PubMed Central

Yu, Ke; Bælum, Jacob; Gao, Ying; Tremblay, Julien; Prestat, Emmanuel; Stenuit, Ben; Tringe, Susannah G.; Jansson, Janet; Zhang, Tong; Alvarez-Cohen, Lisa

2017-01-01

ABSTRACT The aim of this study is to obtain a systems-level understanding of the interactions between Dehalococcoides and corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in the Veillonellaceae bin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin was not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoid de novo biosynthesis pathway was also assigned to the Veillonellaceae bin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway of Dehalococcoides was upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. IMPORTANCE The key chloroethene-dechlorinating bacterium Dehalococcoides mccartyi is a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions between Dehalococcoides and the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles of Veillonellaceae species in the communities compared to other coexisting community members in producing and providing corrinoids for Dehalococcoides species under cobalamin-limited conditions. PMID:28188205

HIV testing of pregnant women: an ethical analysis.

PubMed

Johansson, Kjell Arne; Pedersen, Kirsten Bjerkreim; Andersson, Anna-Karin

2011-12-01

Recent global advances in available technology to prevent mother-to-child HIV transmission necessitate a rethinking of contemporary and previous ethical debates on HIV testing as a means to preventing vertical transmission. In this paper, we will provide an ethical analysis of HIV-testing strategies of pregnant women. First, we argue that provider-initiated opt-out HIV testing seems to be the most effective HIV test strategy. The flip-side of an opt-out strategy is that it may end up as involuntary testing in a clinical setting. We analyse this ethical puzzle from a novel perspective, taking into account the moral importance of certain hypothetical preferences of the child, as well as the moral importance of certain actual preferences of the mother. Finally, we balance the conflicting concerns and try to arrive at an ethically sound solution to this dilemma. Our aim is to introduce a novel perspective from which to analyse testing strategies, and to explore the implications and possible benefits of our proposal. The conclusion from our analysis is that policies that recommend provider-initiated opt-out HIV testing of pregnant mothers, with a risk of becoming involuntary testing in a clinical setting, are acceptable. The rationale behind this is that the increased availability of very effective and inexpensive life-saving drugs makes the ethical problems raised by the possible intrusiveness of HIV testing less important than the child's hypothetical preferences to be born healthy. Health care providers, therefore, have a duty to offer both opt-out HIV testing and available PMTCT (preventing mother-to-child transmission) interventions. © 2011 Blackwell Publishing Ltd.

Analyses and forecasts with LAWS winds

NASA Technical Reports Server (NTRS)

Wang, Muyin; Paegle, Jan

1994-01-01

Horizontal fluxes of atmospheric water vapor are studied for summer months during 1989 and 1992 over North and South America based on analyses from European Center for Medium Range Weather Forecasts, US National Meteorological Center, and United Kingdom Meteorological Office. The calculations are performed over 20 deg by 20 deg box-shaped midlatitude domains located to the east of the Rocky Mountains in North America, and to the east of the Andes Mountains in South America. The fluxes are determined from operational center gridded analyses of wind and moisture. Differences in the monthly mean moisture flux divergence determined from these analyses are as large as 7 cm/month precipitable water equivalent over South America, and 3 cm/month over North America. Gridded analyses at higher spatial and temporal resolution exhibit better agreement in the moisture budget study. However, significant discrepancies of the moisture flux divergence computed from different gridded analyses still exist. The conclusion is more pessimistic than Rasmusson's estimate based on station data. Further analysis reveals that the most significant sources of error result from model surface elevation fields, gaps in the data archive, and uncertainties in the wind and specific humidity analyses. Uncertainties in the wind analyses are the most important problem. The low-level jets, in particular, are substantially different in the different data archives. Part of the reason for this may be due to the way the different analysis models parameterized physical processes affecting low-level jets. The results support the inference that the noise/signal ratio of the moisture budget may be improved more rapidly by providing better wind observations and analyses than by providing better moisture data.

Personality Strengths as Resilience: A One-Year Multiwave Study.

PubMed

Goodman, Fallon R; Disabato, David J; Kashdan, Todd B; Machell, Kyla A

2017-06-01

We examined how personality strengths prospectively predict reactions to negative life events. Participants were 797 community adults from 42 countries. At five points over the course of 1 year, participants completed a series of questionnaires measuring seven personality strengths (hope, grit, meaning in life, curiosity, gratitude, control beliefs, and use of strengths), subjective well-being, and frequency and severity of negative life events. Using hierarchical linear modeling with assessment periods nested within participants, results from lagged analyses found that only hope emerged as a resilience factor. To illustrate the importance of using appropriate lagged analyses in resilience research, we ran nonlagged analyses; these results suggest that all seven personality strengths moderated the effect of negative life events on subjective well-being, with greater strengths associated with healthier outcomes. To provide evidence that personality strengths confer resilience, a prospective examination is needed with the inclusion of events and responses to them. The use of concurrent methodologies and analyses, which is the norm in psychology, often leads to erroneous conclusions. Hope, the ability to generate routes to reach goals and the motivation to use those routes, was shown to be particularly important in promoting resilience. © 2016 Wiley Periodicals, Inc.

Use of Health Care Claims Data to Study Patients with Ophthalmologic Conditions

PubMed Central

Stein, Joshua D.; Lum, Flora; Lee, Paul P.; Rich, William L.; Coleman, Anne L.

2014-01-01

Objective To describe what information is or is not included in health care claims data, provide an overview of the main advantages and limitations of performing analyses using health care claims data, and offer general guidance on how to report and interpret findings of ophthalmology-related claims data analyses. Design Systematic review. Participants Not applicable. Methods A literature review and synthesis of methods for claims-based data analyses. Main Outcome Measures Not applicable. Results Some advantages of using claims data for analyses include large, diverse sample sizes, longitudinal follow-up, lack of selection bias, and potential for complex, multivariable modeling. The disadvantages include (a) the inherent limitations of claims data, such as incomplete, inaccurate, or missing data, or the lack of specific billing codes for some conditions; and (b) the inability, in some circumstances, to adequately evaluate the appropriateness of care. In general, reports of claims data analyses should include clear descriptions of the following methodological elements: the data source, the inclusion and exclusion criteria, the specific billing codes used, and the potential confounding factors incorporated in the multivariable models. Conclusions The use of claims data for research is expected to increase with the enhanced availability of data from Medicare and other sources. The use of claims data to evaluate resource use and efficiency and to determine the basis for supplementary payment methods for physicians is anticipated. Thus, it will be increasingly important for eye care providers to use accurate and descriptive codes for billing. Adherence to general guidance on the reporting of claims data analyses, as outlined in this article, is important to enhance the credibility and applicability of findings. Guidance on optimal ways to conduct and report ophthalmology-related investigations using claims data will likely continue to evolve as health services researchers refine the metrics to analyze large administrative data sets. PMID:24433971

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals

PubMed Central

Atanassov, Ilian; Kuznetsova, Irina; Hinze, Yvonne; Mourier, Arnaud; Filipovska, Aleksandra

2017-01-01

Dysfunction of the oxidative phosphorylation (OXPHOS) system is a major cause of human disease and the cellular consequences are highly complex. Here, we present comparative analyses of mitochondrial proteomes, cellular transcriptomes and targeted metabolomics of five knockout mouse strains deficient in essential factors required for mitochondrial DNA gene expression, leading to OXPHOS dysfunction. Moreover, we describe sequential protein changes during post-natal development and progressive OXPHOS dysfunction in time course analyses in control mice and a middle lifespan knockout, respectively. Very unexpectedly, we identify a new response pathway to OXPHOS dysfunction in which the intra-mitochondrial synthesis of coenzyme Q (ubiquinone, Q) and Q levels are profoundly decreased, pointing towards novel possibilities for therapy. Our extensive omics analyses provide a high-quality resource of altered gene expression patterns under severe OXPHOS deficiency comparing several mouse models, that will deepen our understanding, open avenues for research and provide an important reference for diagnosis and treatment. PMID:29132502

Analysing the external supply chain risk driver competitiveness: a risk mitigation framework and business continuity plan.

PubMed

Blos, Mauricio F; Wee, Hui-Ming; Yang, Joshua

2010-11-01

Innovation challenges for handling supply chain risks have become one of the most important drivers in business competitiveness and differentiation. This study analyses competitiveness at the external supply chain level as a driver of risks and provides a framework for mitigating these risks. The mitigation framework, also called the supply chain continuity framework, provides insight into six stages of the business continuity planning (BCP) process life cycle (risk mitigation management, business impact analysis, supply continuity strategy development, supply continuity plan development, supply continuity plan testing and supply continuity plan maintenance), together with the operational constructs: customer service, inventory management, flexibility, time to market, ordering cycle time and quality. The purpose of the BCP process life cycle and operational constructs working together is to emphasise the way in which a supply chain can deal with disruption risks and, consequently, bring competitive advantage. Future research will consider the new risk scenarios and analyse the consequences to promote the improvement of supply chain resilience.

[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.

Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder.

PubMed

Takata, Atsushi; Miyake, Noriko; Tsurusaki, Yoshinori; Fukai, Ryoko; Miyatake, Satoko; Koshimizu, Eriko; Kushima, Itaru; Okada, Takashi; Morikawa, Mako; Uno, Yota; Ishizuka, Kanako; Nakamura, Kazuhiko; Tsujii, Masatsugu; Yoshikawa, Takeo; Toyota, Tomoko; Okamoto, Nobuhiko; Hiraki, Yoko; Hashimoto, Ryota; Yasuda, Yuka; Saitoh, Shinji; Ohashi, Kei; Sakai, Yasunari; Ohga, Shouichi; Hara, Toshiro; Kato, Mitsuhiro; Nakamura, Kazuyuki; Ito, Aiko; Seiwa, Chizuru; Shirahata, Emi; Osaka, Hitoshi; Matsumoto, Ayumi; Takeshita, Saoko; Tohyama, Jun; Saikusa, Tomoko; Matsuishi, Toyojiro; Nakamura, Takumi; Tsuboi, Takashi; Kato, Tadafumi; Suzuki, Toshifumi; Saitsu, Hirotomo; Nakashima, Mitsuko; Mizuguchi, Takeshi; Tanaka, Fumiaki; Mori, Norio; Ozaki, Norio; Matsumoto, Naomichi

2018-01-16

Recent studies have established important roles of de novo mutations (DNMs) in autism spectrum disorders (ASDs). Here, we analyze DNMs in 262 ASD probands of Japanese origin and confirm the "de novo paradigm" of ASDs across ethnicities. Based on this consistency, we combine the lists of damaging DNMs in our and published ASD cohorts (total number of trios, 4,244) and perform integrative bioinformatics analyses. Besides replicating the findings of previous studies, our analyses highlight ATP-binding genes and fetal cerebellar/striatal circuits. Analysis of individual genes identified 61 genes enriched for damaging DNMs, including ten genes for which our dataset now contributes to statistical significance. Screening of compounds altering the expression of genes hit by damaging DNMs reveals a global downregulating effect of valproic acid, a known risk factor for ASDs, whereas cardiac glycosides upregulate these genes. Collectively, our integrative approach provides deeper biological and potential medical insights into ASDs. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Training and Developing Non-Irish Workers: The Perspectives of Interested Stakeholders

ERIC Educational Resources Information Center

Prendergast, Mary

2016-01-01

Purpose: This paper aims to explore the challenges facing Irish organisations in the training and development of non-Irish workers. It analyses the importance of fluency in the host country's language and the approach taken by organisations in relation to language training. In-depth semi-structured interviews provide significant insights for the…

American Women: Three Decades of Change. Special Demographic Analyses, CDS-80-8.

ERIC Educational Resources Information Center

Bianchi, Suzanne M.; Spain, Daphne

One of a series of reports which use Census Bureau data to provide perspective on important demographic and socioeconomic trends and patterns, this analysis describes changes that have affected women's roles in the last 30 years. Topics discussed are: marriage, divorce, widowhood, childbearing, household and family living arrangements, education,…

The Interface of Opinion, Understanding and Evaluation While Learning about a Socioscientific Issue

ERIC Educational Resources Information Center

Witzig, Stephen B.; Halverson, Kristy L.; Siegel, Marcelle A.; Freyermuth, Sharyn K.

2013-01-01

Scientific literacy is an important goal for science education, especially within controversial socioscientific issues. In this study, we analysed 143 students' research reports about stem cell research (SCR) for how they addressed specific source evaluation criteria provided within the assignment. We investigated students' opinions about SCR, how…

Automated Analysis of Text in Graduate School Recommendations. Research Report. ETS RR-15-23

ERIC Educational Resources Information Center

Heilman, Michael; Breyer, F. Jay; Williams, Frank; Klieger, David; Flor, Michael

2015-01-01

Graduate school recommendations are an important part of admissions in higher education, and natural language processing may be able to provide objective and consistent analyses of recommendation texts to complement readings by faculty and admissions staff. However, these sorts of high-stakes, personal recommendations are different from the…

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

USDA-ARS?s Scientific Manuscript database

Genetic and genomic analyses of Upland cotton (Gossypium hirsutum) are difficult because it has a complex allotetraploid (AADD; 2n = 4x = 52) genome. Here we sequenced, assembled and analyzed the world's most important cultivated cotton genome with 246.2 gigabase (Gb) clean data obtained using whol...

The Use of Structure Coefficients to Address Multicollinearity in Sport and Exercise Science

ERIC Educational Resources Information Center

Yeatts, Paul E.; Barton, Mitch; Henson, Robin K.; Martin, Scott B.

2017-01-01

A common practice in general linear model (GLM) analyses is to interpret regression coefficients (e.g., standardized ß weights) as indicators of variable importance. However, focusing solely on standardized beta weights may provide limited or erroneous information. For example, ß weights become increasingly unreliable when predictor variables are…

Multiple-Try Feedback and Higher-Order Learning Outcomes

ERIC Educational Resources Information Center

Clariana, Roy B.; Koul, Ravinder

2005-01-01

Although feedback is an important component of computer-based instruction (CBI), the effects of feedback on higher-order learning outcomes are not well understood. Several meta-analyses provide two rules of thumb: any feedback is better than no feedback and feedback with more information is better than feedback with less information. …

Webinar summary: Important findings for managers [Chapter 2

Treesearch

Claudia Regan

2014-01-01

This chapter summarizes key findings and offers take-home messages of the Future Forest Webinar Series with regard to resource management planning, analyses, and project design. In the wake of the mountain pine beetle (MPB) epidemic, resource managers are especially concerned with developing more resilient forests, providing for the sustainability of wildlife and fish...

Ideas for a Teaching Sequence for the Concept of Energy

ERIC Educational Resources Information Center

Duit, Reinders; Neumann, Knut

2014-01-01

The energy concept is one of the most important ideas for students to understand. Looking at phenomena through the lens of energy provides powerful tools to model, analyse and predict phenomena in the scientific disciplines. The cross-disciplinary nature of the energy concept enables students to look at phenomena from different angles, helping…

Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora.

PubMed

Sharma, Rahul; Xia, Xiaojuan; Cano, Liliana M; Evangelisti, Edouard; Kemen, Eric; Judelson, Howard; Oome, Stan; Sambles, Christine; van den Hoogen, D Johan; Kitner, Miloslav; Klein, Joël; Meijer, Harold J G; Spring, Otmar; Win, Joe; Zipper, Reinhard; Bode, Helge B; Govers, Francine; Kamoun, Sophien; Schornack, Sebastian; Studholme, David J; Van den Ackerveken, Guido; Thines, Marco

2015-10-05

Downy mildews are the most speciose group of oomycetes and affect crops of great economic importance. So far, there is only a single deeply-sequenced downy mildew genome available, from Hyaloperonospora arabidopsidis. Further genomic resources for downy mildews are required to study their evolution, including pathogenicity effector proteins, such as RxLR effectors. Plasmopara halstedii is a devastating pathogen of sunflower and a potential pathosystem model to study downy mildews, as several Avr-genes and R-genes have been predicted and unlike Arabidopsis downy mildew, large quantities of almost contamination-free material can be obtained easily. Here a high-quality draft genome of Plasmopara halstedii is reported and analysed with respect to various aspects, including genome organisation, secondary metabolism, effector proteins and comparative genomics with other sequenced oomycetes. Interestingly, the present analyses revealed further variation of the RxLR motif, suggesting an important role of the conservation of the dEER-motif. Orthology analyses revealed the conservation of 28 RxLR-like core effectors among Phytophthora species. Only six putative RxLR-like effectors were shared by the two sequenced downy mildews, highlighting the fast and largely independent evolution of two of the three major downy mildew lineages. This is seemingly supported by phylogenomic results, in which downy mildews did not appear to be monophyletic. The genome resource will be useful for developing markers for monitoring the pathogen population and might provide the basis for new approaches to fight Phytophthora and downy mildew pathogens by targeting core pathogenicity effectors.

Making comparative performance information more comprehensible: an experimental evaluation of the impact of formats on consumer understanding

PubMed Central

Damman, Olga C; De Jong, Anco; Hibbard, Judith H; Timmermans, Danielle R M

2016-01-01

Study objectives We aimed to investigate how different presentation formats influence comprehension and use of comparative performance information (CPI) among consumers. Methods An experimental between-subjects and within-subjects design with manipulations of CPI presentation formats. We enrolled both consumers with lower socioeconomic status (SES)/cognitive skills and consumers with higher SES/cognitive skills, recruited through an online access panel. Respondents received fictitious CPI and completed questions about interpretation and information use. Between subjects, we tested (1) displaying an overall performance score (yes/no); (2) displaying a small number of quality indicators (5 vs 9); and (3) displaying different types of evaluative symbols (star ratings, coloured dots and word icons vs numbers and bar graphs). Within subjects, we tested the effect of a reduced number of healthcare providers (5 vs 20). Data were analysed using descriptive analysis, analyses of variance and paired-sampled t tests. Results A total of 902 (43%) respondents participated. Displaying an overall performance score and the use of coloured dots and word icons particularly enhanced consumer understanding. Importantly, respondents provided with coloured dots most often correctly selected the top three healthcare providers (84.3%), compared with word icons (76.6% correct), star ratings (70.6% correct), numbers (62.0%) and bars (54.2%) when viewing performance scores of 20 providers. Furthermore, a reduced number of healthcare providers appeared to support consumers, for example, when provided with 20 providers, 69.5% correctly selected the top three, compared with 80.2% with five providers. Discussion Particular presentation formats enhanced consumer understanding of CPI, most importantly the use of overall performance scores, word icons and coloured dots, and a reduced number of providers displayed. Public report efforts should use these formats to maximise impact on consumers. PMID:26543066

Economic importance of bats in agriculture

USGS Publications Warehouse

Boyles, Justin G.; Cryan, Paul M.; McCracken, Gary F.; Kunz, Thomas H.

2011-01-01

White-nose syndrome (WNS) and the increased development of wind-power facilities are threatening populations of insectivorous bats in North America. Bats are voracious predators of nocturnal insects, including many crop and forest pests. We present here analyses suggesting that loss of bats in North America could lead to agricultural losses estimated at more than $3.7 billion/year. Urgent efforts are needed to educate the public and policy-makers about the ecological and economic importance of insectivorous bats and to provide practical conservation solutions.

Factors associated with the practice of nursing staff sharing information about patients' nutritional status with their colleagues in hospitals.

PubMed

Kawasaki, Y; Tamaura, Y; Akamatsu, R; Sakai, M; Fujiwara, K

2018-01-01

Nursing staff have an important role in patients' nutritional care. The aim of this study was to demonstrate how the practice of sharing a patient's nutritional status with colleagues was affected by the nursing staff's attitude, knowledge and their priority to provide nutritional care. The participants were 492 nursing staff. We obtained participants' demographic data, the practice of sharing patients' nutritional information and information about participants' knowledge, attitude and priority of providing nutritional care by the questionnaire. We performed partial correlation analyses and linear regression analyses to describe the relationship between the total scores of the practice of sharing patients' nutritional information based on their knowledge, attitude and priority to provide nutritional care. Among the 492 participants, 396 nursing staff (80.5%) completed the questionnaire and were included in analyses. Mean±s.d. of total score of the 396 participants was 8.4±3.1. Nursing staff shared information when they had a high nutritional knowledge (r=0.36, P<0.01) and attitude (r=0.13, P<0.05); however, their correlation coefficients were low. In the linear regression analyses, job categories (β=-0.28, P<0.01), knowledge (β=0.33, P<0.01) and attitude (β=0.10, P<0.05) were independently associated with the practice of sharing information. Nursing staff's priority to provide nutritional care practice was not significantly associated with the practice of sharing information. Knowledge and attitude were independently associated with the practice of sharing patients' nutrition information with colleagues, regardless of their priority to provide nutritional care. An effective approach should be taken to improve the practice of providing nutritional care practice.

Healthcare preferences of lesbian, gay, bisexual, transgender and questioning youth.

PubMed

Hoffman, Neal D; Freeman, Katherine; Swann, Stephanie

2009-09-01

Lesbian, gay, bisexual, transgender and questioning (LGBTQ) youth appear to be at higher risk for certain adverse health outcomes, and to have several personal, cultural and structural barriers to accessing healthcare. Little is known, however, about the experiences of LGBTQ youth with healthcare providers and healthcare services. Our goal was to recruit a sample of LGBTQ youth and to determine their preferences regarding healthcare providers, healthcare settings and the health issues that they consider important to discuss with a healthcare provider. We conducted a cross-sectional Internet-based survey. Respondents ages 13-21 years and living in the U.S. or Canada were asked to review three lists of items pertaining to qualities of healthcare providers, qualities of offices or health centers, and concerns or problems to discuss with a healthcare provider, and then to assign for each item a relative importance. Items in each of the three lists were then ranked, and differences among ranks were assessed. Inter-group differences by age, gender, and race/ethnicity were also assessed. 733 youth met eligibility criteria. Youth indicated as most important competence overall and specifically in issues unique to taking care of youth and LGBTQ persons, as well as being respected and treated by providers the same as other youth. Notably, youth ranked as least important the provider's gender and sexual orientation. Youth ranked accessibility issues higher than specific services provided. As health concerns to discuss with a provider, youth ranked preventive healthcare, nutrition, safe sex, and family as important as common morbidities. Youth placed as much importance on provider qualities and interpersonal skills as provider knowledge and experience, and placed little importance on a provider's gender and sexual orientation. Youth indicated the importance of providers addressing not only health risks, but also wellness and health promotion, and to do so within the context of home and family. Subgroup analyses underscore the need for greater sensitivity to both cultural and developmental differences among LGBTQ youth. These results provide a foundation for further research about healthcare services and delivery systems for youth, training initiatives for healthcare providers, and the role of utilizing the Internet for health research purposes to access and recruit hard-to-reach youth.

The genetic architecture of sexually selected traits in two natural populations of Drosophila montana

PubMed Central

Veltsos, P; Gregson, E; Morrissey, B; Slate, J; Hoikkala, A; Butlin, R K; Ritchie, M G

2015-01-01

We investigated the genetic architecture of courtship song and cuticular hydrocarbon traits in two phygenetically distinct populations of Drosophila montana. To study natural variation in these two important traits, we analysed within-population crosses among individuals sampled from the wild. Hence, the genetic variation analysed should represent that available for natural and sexual selection to act upon. In contrast to previous between-population crosses in this species, no major quantitative trait loci (QTLs) were detected, perhaps because the between-population QTLs were due to fixed differences between the populations. Partitioning the trait variation to chromosomes suggested a broadly polygenic genetic architecture of within-population variation, although some chromosomes explained more variation in one population compared with the other. Studies of natural variation provide an important contrast to crosses between species or divergent lines, but our analysis highlights recent concerns that segregating variation within populations for important quantitative ecological traits may largely consist of small effect alleles, difficult to detect with studies of moderate power. PMID:26198076

Nurses' and patients' perceptions of privacy protection behaviours and information provision.

PubMed

Kim, Kyunghee; Han, Yonghee; Kim, Ji-Su

2017-08-01

With increased attention to patient privacy and autonomy, privacy protection and information provision for patients are becoming increasingly important. The aim of this study was to identify and analyse nurses' and patients' perceptions of the importance and performance of protecting patients' privacy and providing them with relevant information. This study is a descriptive cross-sectional investigation. Participants and research context: Participants were 168 patients hospitalised in medical and surgical wards and 176 nurses who cared for them. Ethical consideration: This study was approved by the Chung-Ang University Bioethics Committee, and informed written consent was collected from all participants. Nurses' recognition of the importance of protecting patients' privacy and providing adequate information was higher compared to their actual performance, and the nurses' level of performance was higher in comparison with the patients' recognition of its importance. Although a holistic approach to patient privacy protection and information provision is needed, the medical field has not embraced this model of care. These findings provide empirical data to create an ethical environment for the future, as considerable attention has been devoted to patients' rights and medical institutions' liability for providing explanations to patients.

A conceptual model for analysing informal learning in online social networks for health professionals.

PubMed

Li, Xin; Gray, Kathleen; Chang, Shanton; Elliott, Kristine; Barnett, Stephen

2014-01-01

Online social networking (OSN) provides a new way for health professionals to communicate, collaborate and share ideas with each other for informal learning on a massive scale. It has important implications for ongoing efforts to support Continuing Professional Development (CPD) in the health professions. However, the challenge of analysing the data generated in OSNs makes it difficult to understand whether and how they are useful for CPD. This paper presents a conceptual model for using mixed methods to study data from OSNs to examine the efficacy of OSN in supporting informal learning of health professionals. It is expected that using this model with the dataset generated in OSNs for informal learning will produce new and important insights into how well this innovation in CPD is serving professionals and the healthcare system.

Analyzing endocrine system conservation and evolution.

PubMed

Bonett, Ronald M

2016-08-01

Analyzing variation in rates of evolution can provide important insights into the factors that constrain trait evolution, as well as those that promote diversification. Metazoan endocrine systems exhibit apparent variation in evolutionary rates of their constituent components at multiple levels, yet relatively few studies have quantified these patterns and analyzed them in a phylogenetic context. This may be in part due to historical and current data limitations for many endocrine components and taxonomic groups. However, recent technological advancements such as high-throughput sequencing provide the opportunity to collect large-scale comparative data sets for even non-model species. Such ventures will produce a fertile data landscape for evolutionary analyses of nucleic acid and amino acid based endocrine components. Here I summarize evolutionary rate analyses that can be applied to categorical and continuous endocrine traits, and also those for nucleic acid and protein-based components. I emphasize analyses that could be used to test whether other variables (e.g., ecology, ontogenetic timing of expression, etc.) are related to patterns of rate variation and endocrine component diversification. The application of phylogenetic-based rate analyses to comparative endocrine data will greatly enhance our understanding of the factors that have shaped endocrine system evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Health economics and outcomes methods in risk-based decision-making for blood safety.

PubMed

Custer, Brian; Janssen, Mart P

2015-08-01

Analytical methods appropriate for health economic assessments of transfusion safety interventions have not previously been described in ways that facilitate their use. Within the context of risk-based decision-making (RBDM), health economics can be important for optimizing decisions among competing interventions. The objective of this review is to address key considerations and limitations of current methods as they apply to blood safety. Because a voluntary blood supply is an example of a public good, analyses should be conducted from the societal perspective when possible. Two primary study designs are recommended for most blood safety intervention assessments: budget impact analysis (BIA), which measures the cost to implement an intervention both to the blood operator but also in a broader context, and cost-utility analysis (CUA), which measures the ratio between costs and health gain achieved, in terms of reduced morbidity and mortality, by use of an intervention. These analyses often have important limitations because data that reflect specific aspects, for example, blood recipient population characteristics or complication rates, are not available. Sensitivity analyses play an important role. The impact of various uncertain factors can be studied conjointly in probabilistic sensitivity analyses. The use of BIA and CUA together provides a comprehensive assessment of the costs and benefits from implementing (or not) specific interventions. RBDM is multifaceted and impacts a broad spectrum of stakeholders. Gathering and analyzing health economic evidence as part of the RBDM process enhances the quality, completeness, and transparency of decision-making. © 2015 AABB.

The science is in the data.

PubMed

Helliwell, John R; McMahon, Brian; Guss, J Mitchell; Kroon-Batenburg, Loes M J

2017-11-01

Understanding published research results should be through one's own eyes and include the opportunity to work with raw diffraction data to check the various decisions made in the analyses by the original authors. Today, preserving raw diffraction data is technically and organizationally viable at a growing number of data archives, both centralized and distributed, which are empowered to register data sets and obtain a preservation descriptor, typically a 'digital object identifier'. This introduces an important role of preserving raw data, namely understanding where we fail in or could improve our analyses. Individual science area case studies in crystallography are provided.

Bayou Choctaw Well Integrity Grading Component Based on Geomechanical Simulation

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

Park, Byoung

2016-09-08

This letter report provides a Bayou Choctaw (BC) Strategic Petroleum Reserve (SPR) well grading system based on the geomechanical simulation. The analyses described in this letter were used to evaluate the caverns’ geomechanical effect on wellbore integrity, which is an important component in the well integrity grading system recently developed by Roberts et al. [2015]. Using these analyses, the wellbores for caverns BC-17 and 20 are expected to be significantly impacted by cavern geomechanics, BC-18 and 19 are expected to be medium impacted; and the other caverns are expected to be less impacted.

The science is in the data

PubMed Central

Kroon-Batenburg, Loes M. J.

2017-01-01

Understanding published research results should be through one’s own eyes and include the opportunity to work with raw diffraction data to check the various decisions made in the analyses by the original authors. Today, preserving raw diffraction data is technically and organizationally viable at a growing number of data archives, both centralized and distributed, which are empowered to register data sets and obtain a preservation descriptor, typically a ‘digital object identifier’. This introduces an important role of preserving raw data, namely understanding where we fail in or could improve our analyses. Individual science area case studies in crystallography are provided. PMID:29123672

Multi-country health surveys: are the analyses misleading?

PubMed

Masood, Mohd; Reidpath, Daniel D

2014-05-01

The aim of this paper was to review the types of approaches currently utilized in the analysis of multi-country survey data, specifically focusing on design and modeling issues with a focus on analyses of significant multi-country surveys published in 2010. A systematic search strategy was used to identify the 10 multi-country surveys and the articles published from them in 2010. The surveys were selected to reflect diverse topics and foci; and provide an insight into analytic approaches across research themes. The search identified 159 articles appropriate for full text review and data extraction. The analyses adopted in the multi-country surveys can be broadly classified as: univariate/bivariate analyses, and multivariate/multivariable analyses. Multivariate/multivariable analyses may be further divided into design- and model-based analyses. Of the 159 articles reviewed, 129 articles used model-based analysis, 30 articles used design-based analyses. Similar patterns could be seen in all the individual surveys. While there is general agreement among survey statisticians that complex surveys are most appropriately analyzed using design-based analyses, most researchers continued to use the more common model-based approaches. Recent developments in design-based multi-level analysis may be one approach to include all the survey design characteristics. This is a relatively new area, however, and there remains statistical, as well as applied analytic research required. An important limitation of this study relates to the selection of the surveys used and the choice of year for the analysis, i.e., year 2010 only. There is, however, no strong reason to believe that analytic strategies have changed radically in the past few years, and 2010 provides a credible snapshot of current practice.

Evaluating the Dimensionality of Self-Determination Theory's Relative Autonomy Continuum.

PubMed

Sheldon, Kennon M; Osin, Evgeny N; Gordeeva, Tamara O; Suchkov, Dmitry D; Sychev, Oleg A

2017-09-01

We conducted a theoretical and psychometric evaluation of self-determination theory's "relative autonomy continuum" (RAC), an important aspect of the theory whose validity has recently been questioned. We first derived a Comprehensive Relative Autonomy Index (C-RAI) containing six subscales and 24 items, by conducting a paired paraphrase content analysis of existing RAI measures. We administered the C-RAI to multiple U.S. and Russian samples, assessing motivation to attend class, study a major, and take responsibility. Item-level and scale-level multidimensional scaling analyses, confirmatory factor analyses, and simplex/circumplex modeling analyses reaffirmed the validity of the RAC, across multiple samples, stems, and studies. Validation analyses predicting subjective well-being and trait autonomy from the six separate subscales, in combination with various higher order composites (weighted and unweighted), showed that an aggregate unweighted RAI score provides the most unbiased and efficient indicator of the overall quality of motivation within the behavioral domain being assessed.

Construction of masculinities among men aged 85 and older in the north of Sweden.

PubMed

Aléx, Lena; Hammarström, Anne; Norberg, Astrid; Lundman, Berit

2008-02-01

The aim was to analyse the construction of masculinities among men aged 85 and older. All societies have a gender order, constructed from multiple ideas of what is seen as feminine and masculine. As the group of men aged 85 and older is increasing in size and their demand for care will increase, we must recognize the importance of studying these men and various discourses of masculinities. Qualitative explorative. Qualitative content analysis was used to analyse thematic narratives. Masculinity theories provided the point of departure for the analysis. The analysis coalesced into three masculinities. 'Being in the male centre', developed from subthemes as: taking pride in one's work and economic situation; being in the centre in relation to others; regarding women as sexual objects; and belonging to a select group. 'Striving to maintain the male facade' developed from subthemes as: emphasizing 'important' connections; having feelings of loss; striving to maintain old norms and rejecting the fact of being old. 'Being related' was formulated from subthemes as: feeling at home with domestic duties; being concerned; accepting one's own aging; and reflecting on life. Our study indicates the importance of being aware of the existence of multiple masculinities, in contrast to the generally unproblematic and unsubtle particular healthcare approaches which consider men as simply belonging to one masculinity. Relevance to clinical practice. Diverse masculinities probably affect encounters between men and healthcare providers and others who work with an older population and therefore our results are of importance in a caring context.

Kepler observations of the asteroseismic binary HD 176465

NASA Astrophysics Data System (ADS)

White, T. R.; Benomar, O.; Silva Aguirre, V.; Ball, W. H.; Bedding, T. R.; Chaplin, W. J.; Christensen-Dalsgaard, J.; Garcia, R. A.; Gizon, L.; Stello, D.; Aigrain, S.; Antia, H. M.; Appourchaux, T.; Bazot, M.; Campante, T. L.; Creevey, O. L.; Davies, G. R.; Elsworth, Y. P.; Gaulme, P.; Handberg, R.; Hekker, S.; Houdek, G.; Howe, R.; Huber, D.; Karoff, C.; Marques, J. P.; Mathur, S.; McQuillan, A.; Metcalfe, T. S.; Mosser, B.; Nielsen, M. B.; Régulo, C.; Salabert, D.; Stahn, T.

2017-05-01

Binary star systems are important for understanding stellar structure and evolution, and are especially useful when oscillations can be detected and analysed with asteroseismology. However, only four systems are known in which solar-like oscillations are detected in both components. Here, we analyse the fifth such system, HD 176465, which was observed by Kepler. We carefully analysed the system's power spectrum to measure individual mode frequencies, adapting our methods where necessary to accommodate the fact that both stars oscillate in a similar frequency range. We also modelled the two stars independently by fitting stellar models to the frequencies and complementaryparameters. We are able to cleanly separate the oscillation modes in both systems. The stellar models produce compatible ages and initial compositions for the stars, as is expected from their common and contemporaneous origin. Combining the individual ages, the system is about 3.0 ± 0.5 Gyr old. The two components of HD 176465 are young physically-similar oscillating solar analogues, the first such system to be found, and provide important constraints for stellar evolution and asteroseismology.

Utility of Classical α-Taxonomy for Biodiversity of Aquatic Nematodes

PubMed Central

Decraemer, Wilfrida; Backeljau, Thierry

2015-01-01

“Classical α-taxonomy” has different interpretations. Therefore, within the framework of an integrated taxonomic approach it is not relevant to divide taxonomy in different components, each being allocated a different weight of importance. Preferably, taxonomy should be seen in a holistic way, including the act of delimiting and describing taxa, based on different features and available methods, and taxonomy can not be interpreted without looking at evolutionary relationships. The concept of diversity itself is quite diverse as is the measure of diversity. Taxonomic descriptions of free-living aquatic nematodes are very valuable as they provide basic phenotypic information that is necessary for the functional ecological, behavioral, and evolutionary interpretation of data gathered from molecular analyses and of the organism as a whole. In general, molecular taxonomic analyses have the advantage of being much faster and of being able to deal with a larger number of specimens but also possess the important advantage of dealing with a huge amount of features compared to the morphology-based approach. However, just as morphological studies, molecular analyses deal only with partial of an organism. PMID:25861112

Definite Markers, Phi-Features, and Agreement: A Morphosyntactic Investigation of the Amharic DP

ERIC Educational Resources Information Center

Kramer, Ruth

2009-01-01

This dissertation has two inter-related goals: (i) to describe and provide novel analyses of three types of important and difficult phenomena within Amharic DPs and (ii) to explore the properties of the syntax-morphology interface. The core phenomena explicated are the unusual distribution of the definite marker, the gender system (which relies…

[Malassezia related diseases].

PubMed

Sei, Yoshihiro

2012-01-01

Genusmalassezia are now divided to fourteen species. Different species will start or aggravate different skin diseases. In the seborrheic dermatitis, M.restricta will play an important role, in the atopic dermatitis, M.globosa and/or M.restricta are major cutaneous microflora. The availability of new tools such as genomic and proteomic analyses has begun to provide a new insight into the pathogenetic mechanisms involved.

Understanding the transformative aspects of the Wilderness and Protected Lands experience upon human health

Treesearch

Alan Ewert; Jillisa Overholt; Alison Voight; Chun Chieh Wang

2011-01-01

Wilderness and Protected Landscapes (WPLs) have long been considered special areas for a variety of reasons including baseline data, impact analyses, protected zones, and other tangible and intangible values. Another salient, and some would argue, a more important value offered through WPLs is that of human transformation. Accordingly, three theories have provided the...

El Yunque National Forest Atlas

Treesearch

Maya Quiñones; Isabel K. Parés-Ramos; William A. Gould; Grizelle Gonzalez; Kathleen McGinley; Pedro Ríos

2018-01-01

El Yunque National Forest Atlas is a collaborative effort by the International Institute of Tropical Forestry and El Yunque National Forest to provide upto-date maps and analyses of spatial information of an important natural reserve in Puerto Rico and the only tropical forest in the National Forest System of the United States. El Yunque National Forest Atlas serves as...

Evaluation of Northwest University, Kano Post-UTME Test Items Using Item Response Theory

ERIC Educational Resources Information Center

Bichi, Ado Abdu; Hafiz, Hadiza; Bello, Samira Abdullahi

2016-01-01

High-stakes testing is used for the purposes of providing results that have important consequences. Validity is the cornerstone upon which all measurement systems are built. This study applied the Item Response Theory principles to analyse Northwest University Kano Post-UTME Economics test items. The developed fifty (50) economics test items was…

Margin for Excellence and Opportunity. The Impact of Private Investment on Public Colleges and Universities.

ERIC Educational Resources Information Center

National Association of State Universities and Land Grant Colleges, Washington, DC.

This report discusses the trend of private funding to state universities, examines the importance of this area of financial support, and analyses the financial challenge confronting the nation's state and land-grant universities. Examples of what private investment does for the school are provided as is an argument supporting the need for…

A Cross-Cultural Comparison of Belgian and Vietnamese Children's Social Competence and Behavior

ERIC Educational Resources Information Center

Roskam, Isabelle; Hoang, Thi Vân; Schelstraete, Marie-Anne

2017-01-01

Children's social competence and behavioral adjustment are key issues for child development, education, and clinical research. Cross-cultural analyses are necessary to provide relevant methods of assessing them for cross-cultural research. The aim of the current study was to contribute to this important line of research by validating the 3-factor…

Assessing microsatellite linkage disequilibrium in wild, cultivated, and mapping populations of Theobroma cacao L and its impact on association mapping

USDA-ARS?s Scientific Manuscript database

Linkage disequilibrium (LD) is the nonrandom association of alleles and loci within sets of genetic data and when measured over the genomes of a species can provide important indications for how future association analyses should proceed. This information can be advantageous especially for slow-gro...

The World Bank's Position on Early Child Education in Brazil: A Critical Assessment of Contributions and Shortcomings

ERIC Educational Resources Information Center

Fernandes, Sabrina

2014-01-01

In 2010, the World Bank published a policy study on early child education (ECE) developments in Brazil, entitled "Early Child Education: Making Programs Work for Brazil's Most Important Generation. Development." This paper analyses the report's assessment of ECE policy in Brazil as well as the recommendations it provides. A critical…

A Critical Analysis of Concepts Associated with Sustainability in Early Childhood Curriculum Frameworks across Five National Contexts

ERIC Educational Resources Information Center

Weldemariam, Kassahun; Boyd, Diane; Hirst, Nicky; Sageidet, Barbara Maria; Browder, Jamison K.; Grogan, Leanne; Hughes, Fran

2017-01-01

Curriculum frameworks have an important role in providing guidance to early childhood practitioners on how to integrate knowledge about sustainability into their practice. This article examines how ideas about sustainability are integrated in the early childhood curricula for Australia, England, Norway, Sweden and the USA. The analyses were guided…

Exploring Person Fit with an Approach Based on Multilevel Logistic Regression

ERIC Educational Resources Information Center

Walker, A. Adrienne; Engelhard, George, Jr.

2015-01-01

The idea that test scores may not be valid representations of what students know, can do, and should learn next is well known. Person fit provides an important aspect of validity evidence. Person fit analyses at the individual student level are not typically conducted and person fit information is not communicated to educational stakeholders. In…

Critical Thinking: Art Criticism as a Tool for Analysing and Evaluating Art, Instructional Practice and Social Justice Issues

ERIC Educational Resources Information Center

Broome, Jeffrey; Pereira, Adriane; Anderson, Tom

2018-01-01

Recent educational initiatives have emphasised the importance of fostering critical thinking skills in today's students in order to provide strategies for becoming successful problem solvers throughout life. Other scholars advocate the use of critical thinking skills on the grounds that such tools can be used effectively when considering social…

Evaluating the Use of a Wiki for Collaborative Learning

ERIC Educational Resources Information Center

Su, Feng; Beaumont, Chris

2010-01-01

A wiki is able to provide a learning environment which is closely aligned with the social-constructivist approach and is more natural than many tools where open collaboration and the exchange of ideas are important. This case study analyses and evaluates essential aspects for the successful deployment of a wiki in a higher education setting using…

Using Person Response Functions to Investigate Areas of Person Misfit Related to Item Characteristics

ERIC Educational Resources Information Center

Walker, A. Adrienne; Jennings, Jeremy Kyle; Engelhard, George, Jr.

2018-01-01

Individual person fit analyses provide important information regarding the validity of test score inferences for an "individual" test taker. In this study, we use data from an undergraduate statistics test (N = 1135) to illustrate a two-step method that researchers and practitioners can use to examine individual person fit. First, person…

Where to restore ecological connectivity? Detecting barriers and quantifying restoration benefits.

PubMed

McRae, Brad H; Hall, Sonia A; Beier, Paul; Theobald, David M

2012-01-01

Landscape connectivity is crucial for many ecological processes, including dispersal, gene flow, demographic rescue, and movement in response to climate change. As a result, governmental and non-governmental organizations are focusing efforts to map and conserve areas that facilitate movement to maintain population connectivity and promote climate adaptation. In contrast, little focus has been placed on identifying barriers-landscape features which impede movement between ecologically important areas-where restoration could most improve connectivity. Yet knowing where barriers most strongly reduce connectivity can complement traditional analyses aimed at mapping best movement routes. We introduce a novel method to detect important barriers and provide example applications. Our method uses GIS neighborhood analyses in conjunction with effective distance analyses to detect barriers that, if removed, would significantly improve connectivity. Applicable in least-cost, circuit-theoretic, and simulation modeling frameworks, the method detects both complete (impermeable) barriers and those that impede but do not completely block movement. Barrier mapping complements corridor mapping by broadening the range of connectivity conservation alternatives available to practitioners. The method can help practitioners move beyond maintaining currently important areas to restoring and enhancing connectivity through active barrier removal. It can inform decisions on trade-offs between restoration and protection; for example, purchasing an intact corridor may be substantially more costly than restoring a barrier that blocks an alternative corridor. And it extends the concept of centrality to barriers, highlighting areas that most diminish connectivity across broad networks. Identifying which modeled barriers have the greatest impact can also help prioritize error checking of land cover data and collection of field data to improve connectivity maps. Barrier detection provides a different way to view the landscape, broadening thinking about connectivity and fragmentation while increasing conservation options.

Where to Restore Ecological Connectivity? Detecting Barriers and Quantifying Restoration Benefits

PubMed Central

McRae, Brad H.; Hall, Sonia A.; Beier, Paul; Theobald, David M.

2012-01-01

Landscape connectivity is crucial for many ecological processes, including dispersal, gene flow, demographic rescue, and movement in response to climate change. As a result, governmental and non-governmental organizations are focusing efforts to map and conserve areas that facilitate movement to maintain population connectivity and promote climate adaptation. In contrast, little focus has been placed on identifying barriers—landscape features which impede movement between ecologically important areas—where restoration could most improve connectivity. Yet knowing where barriers most strongly reduce connectivity can complement traditional analyses aimed at mapping best movement routes. We introduce a novel method to detect important barriers and provide example applications. Our method uses GIS neighborhood analyses in conjunction with effective distance analyses to detect barriers that, if removed, would significantly improve connectivity. Applicable in least-cost, circuit-theoretic, and simulation modeling frameworks, the method detects both complete (impermeable) barriers and those that impede but do not completely block movement. Barrier mapping complements corridor mapping by broadening the range of connectivity conservation alternatives available to practitioners. The method can help practitioners move beyond maintaining currently important areas to restoring and enhancing connectivity through active barrier removal. It can inform decisions on trade-offs between restoration and protection; for example, purchasing an intact corridor may be substantially more costly than restoring a barrier that blocks an alternative corridor. And it extends the concept of centrality to barriers, highlighting areas that most diminish connectivity across broad networks. Identifying which modeled barriers have the greatest impact can also help prioritize error checking of land cover data and collection of field data to improve connectivity maps. Barrier detection provides a different way to view the landscape, broadening thinking about connectivity and fragmentation while increasing conservation options. PMID:23300719

The power of a collaborative relationship between technical assistance providers and community prevention teams: A correlational and longitudinal study

PubMed Central

Chilenski, Sarah M.; Perkins, Daniel F.; Olson, Jonathan; Hoffman, Lesa; Feinberg, Mark E.; Greenberg, Mark; Welsh, Janet; Crowley, D. Max; Spoth, Richard

2015-01-01

Background Historically, effectiveness of community collaborative prevention efforts has been mixed. Consequently, research has been undertaken to better understand the factors that support their effectiveness; theory and some related empirical research suggests that the provision of technical assistance is one important supporting factor. The current study examines one aspect of technical assistance that may be important in supporting coalition effectiveness, the collaborative relationship between the technical assistance provider and site lead implementer. Methods Four and one-half years of data were collected from technical assistance providers and prevention team members from the 14 community prevention teams involved in the PROSPER project. Results Spearman correlation analyses with longitudinal data show that the levels of the collaborative relationship during one phase of collaborative team functioning associated with characteristics of internal team functioning in future phases. Conclusions Results suggest that community collaborative prevention work should consider the collaborative nature of the technical assistance provider – prevention community team relationship when designing and conducting technical assistance activities, and it may be important to continually assess these dynamics to support high quality implementation. PMID:26476860

Malaria vaccine development and how external forces shape it: an overview.

PubMed

Lorenz, Veronique; Karanis, Gabriele; Karanis, Panagiotis

2014-06-30

The aim of this paper is to analyse the current status and scientific value of malaria vaccine approaches and to provide a realistic prognosis for future developments. We systematically review previous approaches to malaria vaccination, address how vaccine efforts have developed, how this issue may be fixed, and how external forces shape vaccine development. Our analysis provides significant information on the various aspects and on the external factors that shape malaria vaccine development and reveal the importance of vaccine development in our society.

Predictive distributions for between-study heterogeneity and simple methods for their application in Bayesian meta-analysis

PubMed Central

Turner, Rebecca M; Jackson, Dan; Wei, Yinghui; Thompson, Simon G; Higgins, Julian P T

2015-01-01

Numerous meta-analyses in healthcare research combine results from only a small number of studies, for which the variance representing between-study heterogeneity is estimated imprecisely. A Bayesian approach to estimation allows external evidence on the expected magnitude of heterogeneity to be incorporated. The aim of this paper is to provide tools that improve the accessibility of Bayesian meta-analysis. We present two methods for implementing Bayesian meta-analysis, using numerical integration and importance sampling techniques. Based on 14 886 binary outcome meta-analyses in the Cochrane Database of Systematic Reviews, we derive a novel set of predictive distributions for the degree of heterogeneity expected in 80 settings depending on the outcomes assessed and comparisons made. These can be used as prior distributions for heterogeneity in future meta-analyses. The two methods are implemented in R, for which code is provided. Both methods produce equivalent results to standard but more complex Markov chain Monte Carlo approaches. The priors are derived as log-normal distributions for the between-study variance, applicable to meta-analyses of binary outcomes on the log odds-ratio scale. The methods are applied to two example meta-analyses, incorporating the relevant predictive distributions as prior distributions for between-study heterogeneity. We have provided resources to facilitate Bayesian meta-analysis, in a form accessible to applied researchers, which allow relevant prior information on the degree of heterogeneity to be incorporated. © 2014 The Authors. Statistics in Medicine published by John Wiley & Sons Ltd. PMID:25475839

Utilization of Large Scale Surface Models for Detailed Visibility Analyses

NASA Astrophysics Data System (ADS)

Caha, J.; Kačmařík, M.

2017-11-01

This article demonstrates utilization of large scale surface models with small spatial resolution and high accuracy, acquired from Unmanned Aerial Vehicle scanning, for visibility analyses. The importance of large scale data for visibility analyses on the local scale, where the detail of the surface model is the most defining factor, is described. The focus is not only the classic Boolean visibility, that is usually determined within GIS, but also on so called extended viewsheds that aims to provide more information about visibility. The case study with examples of visibility analyses was performed on river Opava, near the Ostrava city (Czech Republic). The multiple Boolean viewshed analysis and global horizon viewshed were calculated to determine most prominent features and visibility barriers of the surface. Besides that, the extended viewshed showing angle difference above the local horizon, which describes angular height of the target area above the barrier, is shown. The case study proved that large scale models are appropriate data source for visibility analyses on local level. The discussion summarizes possible future applications and further development directions of visibility analyses.

Patient reports of the quality of care in community health centers: the importance of having a regular provider.

PubMed

Beal, Anne; Hernandez, Susan

2010-05-01

To examine the importance of having a regular provider in community health centers (CHCs) for high quality care. Analyses of a national survey-the Commonwealth Fund 2006 Health care Quality Survey-among patients with a private doctor's (PMD) office (n=1,743) or CHC (n=275) as their regular source of care. Outcomes include prevention measures, and measures of patient experience. Patients at CHCs are less likely than patients who use a PMD to report having a regular doctor (53% vs. 95%, p

Multilevel multi-informant structure of the authoritative school climate survey.

PubMed

Konold, Timothy; Cornell, Dewey; Huang, Francis; Meyer, Patrick; Lacey, Anna; Nekvasil, Erin; Heilbrun, Anna; Shukla, Kathan

2014-09-01

The Authoritative School Climate Survey was designed to provide schools with a brief assessment of 2 key characteristics of school climate--disciplinary structure and student support--that are hypothesized to influence 2 important school climate outcomes--student engagement and prevalence of teasing and bullying in school. The factor structure of these 4 constructs was examined with exploratory and confirmatory factor analyses in a statewide sample of 39,364 students (Grades 7 and 8) attending 423 schools. Notably, the analyses used a multilevel structural approach to model the nesting of students in schools for purposes of evaluating factor structure, demonstrating convergent and concurrent validity and gauging the structural invariance of concurrent validity coefficients across gender. These findings provide schools with a core group of school climate measures guided by authoritative discipline theory. PsycINFO Database Record (c) 2014 APA, all rights reserved.

U.S. Geological Survey Science Support Strategy for Biscayne National Park and Surrounding Areas in Southeastern Florida

USGS Publications Warehouse

Wolfert-Lohmann, Melinda A.; Langevin, Christian D.; Jones, Sonya A.; Reich, Chris D.; Wingard, Georgina L.; Kuffner, Ilsa B.; Cunningham, Kevin J.

2008-01-01

The U.S. Geological Survey conducts a wide range of research in and around the Biscayne National Park region of southern Florida. This research encompasses the biologic, ecologic, meteorologic, geologic, and hydrologic components of the system, including water-quality analyses, ground-water modeling, hydrogeologic-data collection, ecologic-habitat evaluations, wetlands characterizations, biogeochemistry of ecosystems, and paleo-ecologic analyses. Relevant information is provided herein for researchers and managers interested in the Biscayne Bay area and about current U.S. Geological Survey efforts that address important resource protection and management issues. Specifically, managers and scientists are provided with information on current and recently completed U.S. Geological Survey projects and a sample listing of potential U.S. Geological Survey research projects addressing relevant issues that face the study area.

Red meat, diseases, and healthy alternatives: A critical review.

PubMed

Ekmekcioglu, Cem; Wallner, Peter; Kundi, Michael; Weisz, Ulli; Haas, Willi; Hutter, Hans-Peter

2018-01-22

Meat is an important food for human nutrition, by especially providing high-quality protein and also some essential micronutrients, in front iron, zinc, and vitamin B 12 . However, a high intake of red and processed meat is associated with an increased risk for diseases, especially type 2 diabetes and colorectal cancer, as several epidemiological studies and meta-analyses have shown. This review summarizes meta-analyses of publications studying the association between red and processed meat intake and type 2 diabetes, cardiovascular diseases, colorectal and other cancers, and all-cause mortality. Various potential mechanisms involved in the increased disease risk are discussed. Furthermore, the beneficial effects of healthy alternatives for meat, like fish, nuts, vegetables and fruits, pulses and legumes, whole grains, and dairy products are reviewed by including selected papers and recent meta-analyses.

Enhanced situational awareness in the maritime domain: an agent-based approach for situation management

NASA Astrophysics Data System (ADS)

Brax, Christoffer; Niklasson, Lars

2009-05-01

Maritime Domain Awareness is important for both civilian and military applications. An important part of MDA is detection of unusual vessel activities such as piracy, smuggling, poaching, collisions, etc. Today's interconnected sensorsystems provide us with huge amounts of information over large geographical areas which can make the operators reach their cognitive capacity and start to miss important events. We propose and agent-based situation management system that automatically analyse sensor information to detect unusual activity and anomalies. The system combines knowledge-based detection with data-driven anomaly detection. The system is evaluated using information from both radar and AIS sensors.

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.

Implementing informative priors for heterogeneity in meta-analysis using meta-regression and pseudo data.

PubMed

Rhodes, Kirsty M; Turner, Rebecca M; White, Ian R; Jackson, Dan; Spiegelhalter, David J; Higgins, Julian P T

2016-12-20

Many meta-analyses combine results from only a small number of studies, a situation in which the between-study variance is imprecisely estimated when standard methods are applied. Bayesian meta-analysis allows incorporation of external evidence on heterogeneity, providing the potential for more robust inference on the effect size of interest. We present a method for performing Bayesian meta-analysis using data augmentation, in which we represent an informative conjugate prior for between-study variance by pseudo data and use meta-regression for estimation. To assist in this, we derive predictive inverse-gamma distributions for the between-study variance expected in future meta-analyses. These may serve as priors for heterogeneity in new meta-analyses. In a simulation study, we compare approximate Bayesian methods using meta-regression and pseudo data against fully Bayesian approaches based on importance sampling techniques and Markov chain Monte Carlo (MCMC). We compare the frequentist properties of these Bayesian methods with those of the commonly used frequentist DerSimonian and Laird procedure. The method is implemented in standard statistical software and provides a less complex alternative to standard MCMC approaches. An importance sampling approach produces almost identical results to standard MCMC approaches, and results obtained through meta-regression and pseudo data are very similar. On average, data augmentation provides closer results to MCMC, if implemented using restricted maximum likelihood estimation rather than DerSimonian and Laird or maximum likelihood estimation. The methods are applied to real datasets, and an extension to network meta-analysis is described. The proposed method facilitates Bayesian meta-analysis in a way that is accessible to applied researchers. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

Assessing congenital malformation risk from medications used in pregnancy: The contribution of NBDPS in pregnancy labeling of prescription drug products.

PubMed

Tassinari, Melissa S; Sahin, Leyla; Yao, Lynne P

2015-08-01

Obtaining human pregnancy data to inform product labeling is important for drug and biological products. Collection and analyses of safety data on their use during pregnancy is usually performed after approval. The Centers for Disease Control National Birth Defects Prevention Study has provided important data on the relationship between drug use in pregnancy and birth defects. The Pregnancy and Lactation Labeling Rule will set new and improved standards for the inclusion of information about the use of prescription drugs and biological products during pregnancy; the National Birth Defects Prevention Study, along with other data sources, will be critical for providing safety data to inform product labeling. © 2015 Wiley Periodicals, Inc.

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.

Fundamental principles of conducting a surgery economic analysis study.

PubMed

Kotsis, Sandra V; Chung, Kevin C

2010-02-01

The use of economic evaluation in surgery is scarce. Economic evaluation is used even less so in plastic surgery, in which health-related quality of life is of particular importance. This article, part of a tutorial series on evidence-based medicine, focuses on the fundamental principles of conducting a surgery economic analysis. The authors include the essential aspects of conducting a surgical cost-utility analysis by considering perspectives, costs, outcomes, and utilities. The authors also describe and give examples of how to conduct the analyses (including calculating quality-adjusted life-years and discounting), how to interpret the results, and how to report the results. Although economic analyses are not simple to conduct, a well-conducted one provides many rewards, such as recommending the adoption of a more effective treatment. For comparing and interpreting economic analysis publications, it is important that all studies use consistent methodology and report the results in a similar manner.

Time- & Load-Dependence of Triboelectric Effect.

PubMed

Pan, Shuaihang; Yin, Nian; Zhang, Zhinan

2018-02-06

Time- and load-dependent friction behavior is considered as important for a long time, due to its time-evolution and force-driving characteristics. However, its electronic behavior, mainly considered in triboelectric effect, has almost never been given the full attention and analyses from the above point of view. In this paper, by experimenting with fcc-latticed aluminum and copper friction pairs, the mechanical and electronic behaviors of friction contacts are correlated by time and load analyses, and the behind physical understanding is provided. Most importantly, the difference of "response lag" in force and electricity is discussed, the extreme points of coefficient of friction with the increasing normal loads are observed and explained with the surface properties and dynamical behaviors (i.e. wear), and the micro and macro theories linking tribo-electricity to normal load and wear (i.e. the physical explanation between coupled electrical and mechanical phenomena) are successfully developed and tested.

What Can the Diffusion Model Tell Us About Prospective Memory?

PubMed Central

Horn, Sebastian S.; Bayen, Ute J.; Smith, Rebekah E.

2011-01-01

Cognitive process models, such as Ratcliff’s (1978) diffusion model, are useful tools for examining cost- or interference effects in event-based prospective memory (PM). The diffusion model includes several parameters that provide insight into how and why ongoing-task performance may be affected by a PM task and is ideally suited to analyze performance because both reaction time and accuracy are taken into account. Separate analyses of these measures can easily yield misleading interpretations in cases of speed-accuracy tradeoffs. The diffusion model allows us to measure possible criterion shifts and is thus an important methodological improvement over standard analyses. Performance in an ongoing lexical decision task (Smith, 2003) was analyzed with the diffusion model. The results suggest that criterion shifts play an important role when a PM task is added, but do not fully explain the cost effect on RT. PMID:21443332

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.

Analysis of fluid film lubrication in artificial hip joint replacements with surfaces of high elastic modulus.

PubMed

Jin, Z M; Dowson, D; Fisher, J

1997-01-01

Lubrication mechanisms and contact mechanics have been analysed for total hip joint replacements made from hard bearing surfaces such as metal-on-metal and ceramic-on-ceramic. A similar analysis for ultra-high molecular weight polyethylene (UHMWPE) against a hard bearing surface has also been carried out and used as a reference. The most important factor influencing the predicted lubrication film thickness has been found to be the radial clearance between the ball and the socket. Full fluid film lubrication may be achieved in these hard/hard bearings provided that the surface finish of the bearing surface and the radial clearance are chosen correctly and maintained. Furthermore, there is a close relation between the predicted contact half width and the predicted lubrication film thickness. Therefore, it is important to analyse the contact mechanics in artificial hip joint replacements. Practical considerations of manufacturing these bearing surfaces have also been discussed.

Confounding in statistical mediation analysis: What it is and how to address it.

PubMed

Valente, Matthew J; Pelham, William E; Smyth, Heather; MacKinnon, David P

2017-11-01

Psychology researchers are often interested in mechanisms underlying how randomized interventions affect outcomes such as substance use and mental health. Mediation analysis is a common statistical method for investigating psychological mechanisms that has benefited from exciting new methodological improvements over the last 2 decades. One of the most important new developments is methodology for estimating causal mediated effects using the potential outcomes framework for causal inference. Potential outcomes-based methods developed in epidemiology and statistics have important implications for understanding psychological mechanisms. We aim to provide a concise introduction to and illustration of these new methods and emphasize the importance of confounder adjustment. First, we review the traditional regression approach for estimating mediated effects. Second, we describe the potential outcomes framework. Third, we define what a confounder is and how the presence of a confounder can provide misleading evidence regarding mechanisms of interventions. Fourth, we describe experimental designs that can help rule out confounder bias. Fifth, we describe new statistical approaches to adjust for measured confounders of the mediator-outcome relation and sensitivity analyses to probe effects of unmeasured confounders on the mediated effect. All approaches are illustrated with application to a real counseling intervention dataset. Counseling psychologists interested in understanding the causal mechanisms of their interventions can benefit from incorporating the most up-to-date techniques into their mediation analyses. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis.

PubMed

Kalendar, Ruslan; Lee, David; Schulman, Alan H

2011-08-01

The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator. Copyright © 2011 Elsevier Inc. All rights reserved.

CAPITATION IN HEALTHCARE FINANCING IN GHANA.

PubMed

Aboagye, A Q Q

2013-05-01

To analyse implementation of the pilot study of the per capita system of healthcare financing in Ghana in 2012 for a determination of the likelihood of realising the inherent theoretical benefits when the system is rolled out nationally. First, publicly available information on how the pilot unfolded is presented, followed by the reaction of the health authorities to these developments. We then analysed accrued evidence on costs and developments vis-à-vis the theoretical benefits. It would appear that preparation for the pilot exercise could have been handled better. Concerns include i) the low level of both education and awareness of the capitation system among healthcare subscribers and primary care providers; ii) confusion about service provider to whom subscribers had been assigned for the capitation period; and iii) service providers not understanding differences between capitation financing and financing under the Ghana diagnostic Related Grouping; and iv) some indication of cost savings. Cost savings may be available nationally. This is important because cost containment is the driving force behind the introduction of the capitation system.

A traits-based approach for prioritizing species for monitoring and surrogacy selection

DOE PAGES

Pracheil, Brenda M.; McManamay, Ryan A.; Bevelhimer, Mark S.; ...

2016-11-28

The bar for justifying the use of vertebrate animals for study is being increasingly raised, thus requiring increased rigor for species selection and study design. Although we have power analyses to provide quantitative backing for the numbers of organisms used, quantitative backing for selection of study species is not frequently employed. This can be especially important when measuring the impacts of ecosystem alteration, when study species must be chosen that are both sensitive to the alteration and of sufficient abundance for study. Just as important is providing justification for designation of surrogate species for study, especially when the species ofmore » interest is rare or of conservation concern and selection of an appropriate surrogate can have legal implications. In this study, we use a combination of GIS, a fish traits database and multivariate statistical analyses to quantitatively prioritize species for study and to determine potential study surrogate species. We provide two case studies to illustrate our quantitative, traits-based approach for designating study species and surrogate species. In the first case study, we select broadly representative fish species to understand the effects of turbine passage on adult fishes based on traits that suggest sensitivity to turbine passage. In our second case study, we present a framework for selecting a surrogate species for an endangered species. Lastly, we suggest that our traits-based framework can provide quantitative backing and added justification to selection of study species while expanding the inference space of study results.« less

Effect of longer health service provider delays on stage at diagnosis and mortality in symptomatic breast cancer.

PubMed

Murchie, P; Raja, E A; Lee, A J; Brewster, D H; Campbell, N C; Gray, N M; Ritchie, L D; Robertson, R; Samuel, L

2015-06-01

This study explored whether longer provider delays (between first presentation and treatment) were associated with later stage and poorer survival in women with symptomatic breast cancer. Data from 850 women with symptomatic breast cancer were linked with the Scottish Cancer Registry; Death Registry; and hospital discharge dataset. Logistic regression and Cox survival analyses with restricted cubic splines explored relationships between provider delays, stage and survival, with sequential adjustment for patient and tumour factors. Although confidence intervals were wide in both adjusted analyses, those with the shortest provider delays had more advanced breast cancer at diagnosis. Beyond approximately 20 weeks, the trend suggests longer delays are associated with more advanced stage, but is not statistically significant. Those with symptomatic breast cancer and the shortest presentation to treatment time (within 4 weeks) had the poorest survival. Longer time to treatment was not significantly associated with worsening mortality. Poor prognosis patients with breast cancer are being triaged for rapid treatment with limited effect on outcome. Prolonged time to treatment does not appear to be strongly associated with poorer outcomes for patients with breast cancer, but the power of this study to assess the effect of very long delays (>25 weeks) was limited. Efforts to reduce waiting times are important from a quality of life perspective, but tumour biology may often be a more important determinant of stage at diagnosis and survival outcome. Copyright © 2015 Elsevier Ltd. All rights reserved.

A traits-based approach for prioritizing species for monitoring and surrogacy selection

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

Pracheil, Brenda M.; McManamay, Ryan A.; Bevelhimer, Mark S.

The bar for justifying the use of vertebrate animals for study is being increasingly raised, thus requiring increased rigor for species selection and study design. Although we have power analyses to provide quantitative backing for the numbers of organisms used, quantitative backing for selection of study species is not frequently employed. This can be especially important when measuring the impacts of ecosystem alteration, when study species must be chosen that are both sensitive to the alteration and of sufficient abundance for study. Just as important is providing justification for designation of surrogate species for study, especially when the species ofmore » interest is rare or of conservation concern and selection of an appropriate surrogate can have legal implications. In this study, we use a combination of GIS, a fish traits database and multivariate statistical analyses to quantitatively prioritize species for study and to determine potential study surrogate species. We provide two case studies to illustrate our quantitative, traits-based approach for designating study species and surrogate species. In the first case study, we select broadly representative fish species to understand the effects of turbine passage on adult fishes based on traits that suggest sensitivity to turbine passage. In our second case study, we present a framework for selecting a surrogate species for an endangered species. Lastly, we suggest that our traits-based framework can provide quantitative backing and added justification to selection of study species while expanding the inference space of study results.« less

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

How Variables Uncorrelated with the Dependent Variable Can Actually Make Excellent Predictors: The Important Suppressor Variable Case.

ERIC Educational Resources Information Center

Woolley, Kristin K.

Many researchers are unfamiliar with suppressor variables and how they operate in multiple regression analyses. This paper describes the role suppressor variables play in a multiple regression model and provides practical examples that explain how they can change research results. A variable that when added as another predictor increases the total…

Identification of soybean proteins and genes differentially regulated in near isogenic lines differing in resistance to aphid infestation

USDA-ARS?s Scientific Manuscript database

The soybean aphid, a plant sap sucking insect, is an important soybean pest in the USA causing significant yield losses. The Rag2 gene of soybean provides resistance to soybean aphid biotypes 1 and 2. Transcriptomic and proteomic analyses were performed on near isogenic lines (NILs) with the Rag2 al...

Satisfied Fools: Using J. S. Mill's Notion of Utility to Analyse the Impact of Vocationalism in Education within a Democratic Society

ERIC Educational Resources Information Center

Tarrant, Iona; Tarrant, James

2004-01-01

This paper proposes a new interpretation of John Stuart Mill's notion of utility, which is used to provide a utilitarian justification for an eclectic, rather than a vocational, education. Vocational education is strongly promoted in recent policy documents, which makes it important to raise the question of justification. Many existing…

Education for Sustainable Development and Normativity: A Transactional Analysis of Moral Meaning-Making and Companion Meanings in Classroom Communication

ERIC Educational Resources Information Center

Ostman, Leif

2010-01-01

The purpose of the present article is to present and illustrate two different ways of analysing the normativity and discursivity of classroom communication during education for sustainable development (ESD). The two types of analysis can provide important knowledge for discussions of ESD in relation to morals and democracy. Both methods are based…

Embracing the New Disability Rights Paradigm: The Importance of the Convention on the Rights of Persons with Disabilities

ERIC Educational Resources Information Center

Harpur, Paul

2012-01-01

In 2008 the United Nations Convention on the Rights of Persons with Disabilities (CRPD) commenced operation. The CRPD has created a dynamic new disability rights paradigm that empowers disability people's organizations and creates a new paradigm for disability scholars. This paper analyses the impact of the CRPD and provides practical guidance as…

Positive Beliefs about Errors as an Important Element of Adaptive Individual Dealing with Errors during Academic Learning

ERIC Educational Resources Information Center

Tulis, Maria; Steuer, Gabriele; Dresel, Markus

2018-01-01

Research on learning from errors gives reason to assume that errors provide a high potential to facilitate deep learning if students are willing and able to take these learning opportunities. The first aim of this study was to analyse whether beliefs about errors as learning opportunities can be theoretically and empirically distinguished from…

The K-12 School System in Milwaukee: How Has It Changed and How Does It Measure up to Peers?

ERIC Educational Resources Information Center

Day, Doug; Yeado, Joe; Schmidt, Jeff

2014-01-01

This report provides important perspective on the distinctive and changing features of Milwaukee's K-12 education landscape. The authors conducted two comparative analyses of Milwaukee schools. The first, a trend analysis, traces how Milwaukee schools have changed in the past decade. The second, a peer analysis, shows how Milwaukee schools compare…

Stable isotope probing to study functional components of complex microbial ecosystems.

PubMed

Mazard, Sophie; Schäfer, Hendrik

2014-01-01

This protocol presents a method of dissecting the DNA or RNA of key organisms involved in a specific biochemical process within a complex ecosystem. Stable isotope probing (SIP) allows the labelling and separation of nucleic acids from community members that are involved in important biochemical transformations, yet are often not the most numerically abundant members of a community. This pure culture-independent technique circumvents limitations of traditional microbial isolation techniques or data mining from large-scale whole-community metagenomic studies to tease out the identities and genomic repertoires of microorganisms participating in biological nutrient cycles. SIP experiments can be applied to virtually any ecosystem and biochemical pathway under investigation provided a suitable stable isotope substrate is available. This versatile methodology allows a wide range of analyses to be performed, from fatty-acid analyses, community structure and ecology studies, and targeted metagenomics involving nucleic acid sequencing. SIP experiments provide an effective alternative to large-scale whole-community metagenomic studies by specifically targeting the organisms or biochemical transformations of interest, thereby reducing the sequencing effort and time-consuming bioinformatics analyses of large datasets.

AHRQ series on complex intervention systematic reviews-paper 6: PRISMA-CI extension statement and checklist.

PubMed

Guise, Jeanne-Marie; Butler, Mary E; Chang, Christine; Viswanathan, Meera; Pigott, Terri; Tugwell, Peter

2017-10-01

Complex interventions are widely used in health systems, public health, education, and communities and are increasingly the subject of systematic reviews. Oversimplification and inconsistencies in reporting about complex interventions can limit the usability of review findings. Although guidance exists to ensure that reports of individual studies and systematic reviews adhere to accepted scientific standards, their design-specific focus leaves important reporting gaps relative to complex interventions in health care. This paper provides a stand-alone extension to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting tool for complex interventions-PRISMA-CI-to help authors, publishers, and readers understand and apply to systematic reviews of complex interventions. PRISMA-CI development followed the Enhancing the QUAlity and Transparency Of health Research Network guidance for extensions and focused on adding or modifying only essential items that are truly unique to complex interventions and are not covered by broader interpretation of current PRISMA guidance. PRISMA-CI provides an important structure and guidance for systematic reviews and meta-analyses for the highly prevalent and dynamic field of complex interventions. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants.

PubMed

Samanta, Subhasis; Thakur, Jitendra K

2015-01-01

Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channeling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic, and molecular analyses have unraveled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator's involvement in these processes.

Importance of Mediator complex in the regulation and integration of diverse signaling pathways in plants

PubMed Central

Samanta, Subhasis; Thakur, Jitendra K.

2015-01-01

Basic transcriptional machinery in eukaryotes is assisted by a number of cofactors, which either increase or decrease the rate of transcription. Mediator complex is one such cofactor, and recently has drawn a lot of interest because of its integrative power to converge different signaling pathways before channeling the transcription instructions to the RNA polymerase II machinery. Like yeast and metazoans, plants do possess the Mediator complex across the kingdom, and its isolation and subunit analyses have been reported from the model plant, Arabidopsis. Genetic, and molecular analyses have unraveled important regulatory roles of Mediator subunits at every stage of plant life cycle starting from flowering to embryo and organ development, to even size determination. It also contributes immensely to the survival of plants against different environmental vagaries by the timely activation of its resistance mechanisms. Here, we have provided an overview of plant Mediator complex starting from its discovery to regulation of stoichiometry of its subunits. We have also reviewed involvement of different Mediator subunits in different processes and pathways including defense response pathways evoked by diverse biotic cues. Wherever possible, attempts have been made to provide mechanistic insight of Mediator's involvement in these processes. PMID:26442070

Importance-performance analysis of dental satisfaction among three ethnic groups in malaysia.

PubMed

Dewi, Fellani Danasra; Gundavarapu, Kalyan C; Cugati, Navaneetha

2013-01-01

To find the differences in patient satisfaction related to dental services among three ethnic groups - Chinese, Indian and Malay - at AIMST University Dental Centre and analyse them with an importance-performance grid, identifying the weak and strong points, in order to provide better service. This questionnaire-based study consisted of convenience samples of 174 patients of Chinese, Indian and Malay ethnicity. Importance-performance analysis for 20 attributes were compared using Likert's scale. The data obtained were statistically analysed using the Kruskal-Wallis test. Chinese and Indians both emphasised low performance on the interpersonal relationship attribute in terms of the receptionist's courtesy, whereas the Malay participants were concerned with convenience attributes. All the ethnic groups favoured maintaining existing major attributes towards technical competency, interpersonal relationship and facility factors. This study demonstrated priority differences between the ethnic groups' perception of the quality of dental services, where ethnic Chinese showed the highest gap (measure of dissatisfaction) between importance and performance compared to ethnic Malays, followed by ethnic Indians. The patients from the three major ethnic groups of Malaysia were generally well satisfied. Perhaps more priority should be placed on improving the interpersonal relationship attribute, especially with the receptionists.

Patient-provider relationship predicts mental and physical health indicators for HIV-positive men who have sex with men.

PubMed

Bankoff, Sarah M; McCullough, Mary B; Pantalone, David W

2013-06-01

We used secondary data analysis to examine associations among aspects of patient-provider relationships and mental and physical health indicators. Positive patient perceptions of patient-provider relationships were associated with fewer mental health symptoms in this outpatient sample of HIV-positive men who have sex with men (N = 171). Regression analyses revealed the role of anxiety and depression in explaining associations between two aspects of patient-provider relationships (i.e. quality of information offered and provider interactional style) and health-related quality of life. The findings demonstrated the importance of patient-provider relationships to improving physical health and functioning and maintaining engagement in care, among HIV-positive men who have sex with men.

Metagenomic and Metatranscriptomic Analyses Reveal the Structure and Dynamics of a Dechlorinating Community Containing Dehalococcoides mccartyi and Corrinoid-Providing Microorganisms under Cobalamin-Limited Conditions

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

Men, Yujie; Yu, Ke; Bælum, Jacob

ABSTRACT The aim of this study is to obtain a systems-level understanding of the interactions betweenDehalococcoidesand corrinoid-supplying microorganisms by analyzing community structures and functional compositions, activities, and dynamics in trichloroethene (TCE)-dechlorinating enrichments. Metagenomes and metatranscriptomes of the dechlorinating enrichments with and without exogenous cobalamin were compared. Seven putative draft genomes were binned from the metagenomes. At an early stage (2 days), more transcripts of genes in theVeillonellaceaebin-genome were detected in the metatranscriptome of the enrichment without exogenous cobalamin than in the one with the addition of cobalamin. Among these genes, sporulation-related genes exhibited the highest differential expression when cobalamin wasmore » not added, suggesting a possible release route of corrinoids from corrinoid producers. Other differentially expressed genes include those involved in energy conservation and nutrient transport (including cobalt transport). The most highly expressed corrinoidde novobiosynthesis pathway was also assigned to theVeillonellaceaebin-genome. Targeted quantitative PCR (qPCR) analyses confirmed higher transcript abundances of those corrinoid biosynthesis genes in the enrichment without exogenous cobalamin than in the enrichment with cobalamin. Furthermore, the corrinoid salvaging and modification pathway ofDehalococcoideswas upregulated in response to the cobalamin stress. This study provides important insights into the microbial interactions and roles played by members of dechlorinating communities under cobalamin-limited conditions. IMPORTANCEThe key chloroethene-dechlorinating bacteriumDehalococcoides mccartyiis a cobalamin auxotroph, thus acquiring corrinoids from other community members. Therefore, it is important to investigate the microbe-microbe interactions betweenDehalococcoidesand the corrinoid-providing microorganisms in a community. This study provides systems-level information, i.e., taxonomic and functional compositions and dynamics of the supportive microorganisms in dechlorinating communities under different cobalamin conditions. The findings shed light on the important roles ofVeillonellaceaespecies in the communities compared to other coexisting community members in producing and providing corrinoids forDehalococcoidesspecies under cobalamin-limited conditions.« less

Activation characteristics of candidate structural materials for a near-term Indian fusion reactor and the impact of their impurities on design considerations

NASA Astrophysics Data System (ADS)

H, L. SWAMI; C, DANANI; A, K. SHAW

2018-06-01

Activation analyses play a vital role in nuclear reactor design. Activation analyses, along with nuclear analyses, provide important information for nuclear safety and maintenance strategies. Activation analyses also help in the selection of materials for a nuclear reactor, by providing the radioactivity and dose rate levels after irradiation. This information is important to help define maintenance activity for different parts of the reactor, and to plan decommissioning and radioactive waste disposal strategies. The study of activation analyses of candidate structural materials for near-term fusion reactors or ITER is equally essential, due to the presence of a high-energy neutron environment which makes decisive demands on material selection. This study comprises two parts; in the first part the activation characteristics, in a fusion radiation environment, of several elements which are widely present in structural materials, are studied. It reveals that the presence of a few specific elements in a material can diminish its feasibility for use in the nuclear environment. The second part of the study concentrates on activation analyses of candidate structural materials for near-term fusion reactors and their comparison in fusion radiation conditions. The structural materials selected for this study, i.e. India-specific Reduced Activation Ferritic‑Martensitic steel (IN-RAFMS), P91-grade steel, stainless steel 316LN ITER-grade (SS-316LN-IG), stainless steel 316L and stainless steel 304, are candidates for use in ITER either in vessel components or test blanket systems. Tungsten is also included in this study because of its use for ITER plasma-facing components. The study is carried out using the reference parameters of the ITER fusion reactor. The activation characteristics of the materials are assessed considering the irradiation at an ITER equatorial port. The presence of elements like Nb, Mo, Co and Ta in a structural material enhance the activity level as well as the dose level, which has an impact on design considerations. IN-RAFMS was shown to be a more effective low-activation material than SS-316LN-IG.

Computational biology for ageing

PubMed Central

Wieser, Daniela; Papatheodorou, Irene; Ziehm, Matthias; Thornton, Janet M.

2011-01-01

High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in order to pinpoint the causes and effects of ageing. Here, we provide a description of the existing databases and computational tools on ageing that are available for researchers. We also describe the computational approaches to data interpretation in the field of ageing including gene expression, comparative and pathway analyses, and highlight the challenges for future developments. We review recent biological insights gained from applying bioinformatics methods to analyse and interpret ageing data in different organisms, tissues and conditions. PMID:21115530

Genetics and Cell Morphology Analyses of the Actinomyces oris srtA Mutant.

PubMed

Wu, Chenggang; Reardon-Robinson, Melissa Elizabeth; Ton-That, Hung

2016-01-01

Sortase is a cysteine-transpeptidase that anchors LPXTG-containing proteins on the Gram-positive bacterial cell wall. Previously, sortase was considered to be an important factor for bacterial pathogenesis and fitness, but not cell growth. However, the Actinomyces oris sortase is essential for cell viability, due to its coupling to a glycosylation pathway. In this chapter, we describe the methods to generate conditional srtA deletion mutants and identify srtA suppressors by Tn5 transposon mutagenesis. We also provide procedures for analyzing cell morphology of this mutant by thin-section electron microscopy. These techniques can be applied for analyses of other essential genes in A. oris.

On meta- and mega-analyses for gene–environment interactions

PubMed Central

Huang, Jing; Liu, Yulun; Vitale, Steve; Penning, Trevor M.; Whitehead, Alexander S.; Blair, Ian A.; Vachani, Anil; Clapper, Margie L.; Muscat, Joshua E.; Lazarus, Philip; Scheet, Paul; Moore, Jason H.; Chen, Yong

2017-01-01

Gene-by-environment (G × E) interactions are important in explaining the missing heritability and understanding the causation of complex diseases, but a single, moderately sized study often has limited statistical power to detect such interactions. With the increasing need for integrating data and reporting results from multiple collaborative studies or sites, debate over choice between mega- versus meta-analysis continues. In principle, data from different sites can be integrated at the individual level into a “mega” data set, which can be fit by a joint “mega-analysis.” Alternatively, analyses can be done at each site, and results across sites can be combined through a “meta-analysis” procedure without integrating individual level data across sites. Although mega-analysis has been advocated in several recent initiatives, meta-analysis has the advantages of simplicity and feasibility, and has recently led to several important findings in identifying main genetic effects. In this paper, we conducted empirical and simulation studies, using data from a G × E study of lung cancer, to compare the mega- and meta-analyses in four commonly used G × E analyses under the scenario that the number of studies is small and sample sizes of individual studies are relatively large. We compared the two data integration approaches in the context of fixed effect models and random effects models separately. Our investigations provide valuable insights in understanding the differences between mega- and meta-analyses in practice of combining small number of studies in identifying G × E interactions. PMID:29110346

On meta- and mega-analyses for gene-environment interactions.

PubMed

Huang, Jing; Liu, Yulun; Vitale, Steve; Penning, Trevor M; Whitehead, Alexander S; Blair, Ian A; Vachani, Anil; Clapper, Margie L; Muscat, Joshua E; Lazarus, Philip; Scheet, Paul; Moore, Jason H; Chen, Yong

2017-12-01

Gene-by-environment (G × E) interactions are important in explaining the missing heritability and understanding the causation of complex diseases, but a single, moderately sized study often has limited statistical power to detect such interactions. With the increasing need for integrating data and reporting results from multiple collaborative studies or sites, debate over choice between mega- versus meta-analysis continues. In principle, data from different sites can be integrated at the individual level into a "mega" data set, which can be fit by a joint "mega-analysis." Alternatively, analyses can be done at each site, and results across sites can be combined through a "meta-analysis" procedure without integrating individual level data across sites. Although mega-analysis has been advocated in several recent initiatives, meta-analysis has the advantages of simplicity and feasibility, and has recently led to several important findings in identifying main genetic effects. In this paper, we conducted empirical and simulation studies, using data from a G × E study of lung cancer, to compare the mega- and meta-analyses in four commonly used G × E analyses under the scenario that the number of studies is small and sample sizes of individual studies are relatively large. We compared the two data integration approaches in the context of fixed effect models and random effects models separately. Our investigations provide valuable insights in understanding the differences between mega- and meta-analyses in practice of combining small number of studies in identifying G × E interactions. © 2017 WILEY PERIODICALS, INC.

The Hemolymph Proteome of Fed and Starved Drosophila Larvae

PubMed Central

Goetze, Sandra; Ahrens, Christian H.; Omasits, Ulrich; Marty, Florian; Simigdala, Nikiana; Meyer, Imke; Wollscheid, Bernd; Brunner, Erich; Hafen, Ernst; Lehner, Christian F.

2013-01-01

The co-operation of specialized organ systems in complex multicellular organisms depends on effective chemical communication. Thus, body fluids (like blood, lymph or intraspinal fluid) contain myriads of signaling mediators apart from metabolites. Moreover, these fluids are also of crucial importance for immune and wound responses. Compositional analyses of human body fluids are therefore of paramount diagnostic importance. Further improving their comprehensiveness should increase our understanding of inter-organ communication. In arthropods, which have trachea for gas exchange and an open circulatory system, the single dominating interstitial fluid is the hemolymph. Accordingly, a detailed analysis of hemolymph composition should provide an especially comprehensive picture of chemical communication and defense in animals. Therefore we used an extensive protein fractionation workflow in combination with a discovery-driven proteomic approach to map out the detectable protein composition of hemolymph isolated from Drosophila larvae. Combined mass spectrometric analysis revealed more than 700 proteins extending far beyond the previously known Drosophila hemolymph proteome. Moreover, by comparing hemolymph isolated from either fed or starved larvae, we provide initial provisional insights concerning compositional changes in response to nutritional state. Storage proteins in particular were observed to be strongly reduced by starvation. Our hemolymph proteome catalog provides a rich basis for data mining, as exemplified by our identification of potential novel cytokines, as well as for future quantitative analyses by targeted proteomics. PMID:23840627

Veterans' Pain Management Goals: Changes During the Course of a Peer-led Pain Self-Management Program

PubMed Central

Bauer, Sarah M.; McGuire, Alan B.; Kukla, Marina; McGuire, Shannon; Bair, Matthew J.; Matthias, Marianne S.

2017-01-01

Objective Goal setting is a common element of self-management support programs; however, little is known about the nature of patients' goals or how goals change during pain self-management. The purpose of the current study is to explore how patients' goals and views of goal setting change over the course of a peer-led pain self-management program. Methods Veterans (n = 16) completing a 4-month peer-led pain self-management program completed semi-structured interviews at baseline and follow-up regarding their goals for their pain. Interviews were analyzed using immersion/crystallization. Results Analyses revealed six themes: motivation to do something for their pain, more goal-oriented, actually setting goals, clarity of goal importance, more specific/measurable goal criteria, and more specific/measurable strategies. Conclusion The current analyses illustrate how participants' goals can evolve over the course of a peer-led pain self-management program. Specifically, increased motivation, more openness to using goals, greater clarity of goal importance, more specific and measurable goals and strategies, and the influence of the peer coach relationship were described by participants. Practice implications Pain self-management interventions should emphasize goal setting, and development of specific, measurable goals and plans. Trainings for providers should address the potential for the provider-patient relationship, particularly peer providers, to facilitate motivation and goal setting. PMID:27516437

Veterans' pain management goals: Changes during the course of a peer-led pain self-management program.

PubMed

Bauer, Sarah M; McGuire, Alan B; Kukla, Marina; McGuire, Shannon; Bair, Matthew J; Matthias, Marianne S

2016-12-01

Goal setting is a common element of self-management support programs; however, little is known about the nature of patients' goals or how goals change during pain self-management. The purpose of the current study is to explore how patients' goals and views of goal setting change over the course of a peer-led pain self-management program. Veterans (n=16) completing a 4-month peer-led pain self-management program completed semi-structured interviews at baseline and follow-up regarding their goals for their pain. Interviews were analyzed using immersion/crystallization. Analyses revealed six themes: motivation to do something for their pain, more goal-oriented, actually setting goals, clarity of goal importance, more specific/measurable goal criteria, and more specific/measurable strategies. The current analyses illustrate how participants' goals can evolve over the course of a peer-led pain self-management program. Specifically, increased motivation, more openness to using goals, greater clarity of goal importance, more specific and measurable goals and strategies, and the influence of the peer coach relationship were described by participants. Pain self-management interventions should emphasize goal setting, and development of specific, measurable goals and plans. Trainings for providers should address the potential for the provider-patient relationship, particularly peer providers, to facilitate motivation and goal setting. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The hemolymph proteome of fed and starved Drosophila larvae.

PubMed

Handke, Björn; Poernbacher, Ingrid; Goetze, Sandra; Ahrens, Christian H; Omasits, Ulrich; Marty, Florian; Simigdala, Nikiana; Meyer, Imke; Wollscheid, Bernd; Brunner, Erich; Hafen, Ernst; Lehner, Christian F

2013-01-01

The co-operation of specialized organ systems in complex multicellular organisms depends on effective chemical communication. Thus, body fluids (like blood, lymph or intraspinal fluid) contain myriads of signaling mediators apart from metabolites. Moreover, these fluids are also of crucial importance for immune and wound responses. Compositional analyses of human body fluids are therefore of paramount diagnostic importance. Further improving their comprehensiveness should increase our understanding of inter-organ communication. In arthropods, which have trachea for gas exchange and an open circulatory system, the single dominating interstitial fluid is the hemolymph. Accordingly, a detailed analysis of hemolymph composition should provide an especially comprehensive picture of chemical communication and defense in animals. Therefore we used an extensive protein fractionation workflow in combination with a discovery-driven proteomic approach to map out the detectable protein composition of hemolymph isolated from Drosophila larvae. Combined mass spectrometric analysis revealed more than 700 proteins extending far beyond the previously known Drosophila hemolymph proteome. Moreover, by comparing hemolymph isolated from either fed or starved larvae, we provide initial provisional insights concerning compositional changes in response to nutritional state. Storage proteins in particular were observed to be strongly reduced by starvation. Our hemolymph proteome catalog provides a rich basis for data mining, as exemplified by our identification of potential novel cytokines, as well as for future quantitative analyses by targeted proteomics.

[Management characteristics in charity hospitals in Brazil].

PubMed

Lima, Sheyla Maria Lemos; Barbosa, Pedro Ribeiro; Portela, Margareth C; Ugá, Maria Alicia Dominguez; Vasconcellos, Miguel Murat; Gerschman, Silvia

2004-01-01

This paper presents the management characteristics of charity hospitals in Brazil, based on data from a national survey developed in 2001. The sample accounted for the random inclusion of 66 Brazilian Unified Health System (SUS) inpatient care providers with less than 599 beds and all 26 hospitals with at least 599 beds. It also included 10 institutions assumed as non-providers of services to the SUS. The analyses are descriptive, focusing on the classification of the hospitals according to their managerial development level, as well as selected issues regarding the utilization of specific managerial technologies, human resources, technical services, and services contracting. Distinct managerial levels were identified, but it is important to note that 83% of the SUS providers with less than 599 beds were classified as having incipient management. The authors discuss implications of the findings for inpatient care policies, considering the importance of charity hospitals for the Brazilian Health System.

Seismic risk assessment of architectural heritages in Gyeongju considering local site effects

NASA Astrophysics Data System (ADS)

Park, H.-J.; Kim, D.-S.; Kim, D.-M.

2013-02-01

A seismic risk assessment is conducted for cultural heritage sites in Gyeongju, the capital of Korea's ancient Silla Kingdom. Gyeongju, home to UNESCO World Heritage sites, contains remarkable artifacts of Korean Buddhist art. An extensive geotechnical survey including a series of in situ tests is presented, providing pertinent soil profiles for site response analyses on thirty cultural heritage sites. After the shear wave velocity profiles and dynamic material properties were obtained, site response analyses were carried out at each historical site and the amplification characteristics, site period, and response spectrum of the site were determined for the earthquake levels of 2400 yr and 1000 yr return periods based on the Korean seismic hazard map. Response spectrum and corresponding site coefficients obtained from site response analyses considering geologic conditions differ significantly from the current Korean seismic code. This study confirms the importance of site-specific ground response analyses considering local geological conditions. Results are given in the form of the spatial distribution of bedrock depth, site period, and site amplification coefficients, which are particularly valuable in the context of a seismic vulnerability study. This study presents the potential amplification of hazard maps and provides primary data on the seismic risk assessment of each cultural heritage.

Sampling strategies on Mars: Remote and not-so-remote observations from a surface rover

NASA Technical Reports Server (NTRS)

Singer, R. B.

1988-01-01

The mobility and speed of a semi-autonomous Mars rover are of necessity limited by the need to think and stay out of trouble. This consideration makes it essential that the rover's travels be carefully directed to likely targets of interest for sampling and in situ study. Short range remote sensing conducted from the rover, based on existing technology, can provide significant information about the chemistry and mineralogy of surrounding rocks and soils in support of sampling efforts. These observations are of course of direct scientific importance as well. Because of the small number of samples actually to be returned to Earth, it is also important that candidate samples be analyzed aboard the rover so that diversity can be maximized. It is essential to perform certain types of analyses, such as those involving volatiles, prior to the thermal and physical shocks of the return trip to Earth. In addition, whatever measurements can be made of nonreturned samples will be important to enlarge the context of the detailed analyses to be performed later on the few returned samples. Some considerations related to these objectives are discussed.

The emergence of psychiatric semiology during the Age of Revolution: evolving concepts of 'normal' and 'pathological'.

PubMed

Londoño, Diego Enrique; Dening, Tom

2016-06-01

This article addresses some important questions in psychiatric semiology. The concept of a sign is crucial in psychiatry. How do signs emerge, and what gives them validity and legitimacy? What are the boundaries of 'normal' and 'pathological' behaviour and mental experiences? To address these issues, we analyse the characteristics and rules that govern semiological signs and clinical elements. We examine 'normality' from the perspective of Georges Canguilehm and compare the differences of 'normal' in physiology and psychiatry. We then examine the history and the philosophical, linguistic and medical-psychiatric origins of semiology during the eighteenth and nineteenth centuries (the Age of Revolution). The field of rhetoric and oratory has emphasized the importance of passions, emotions and language as applied to signs of madness. Another perspective on semiology, provided by Michel Foucault, lays stress on the concept of 'instinct' and the axis of voluntary-involuntary behaviour. Finally, we analyse how statistics and eugenics have played an important role in our current conceptualization of the norm and therefore the scientific discourse behind the established clinical signs. © The Author(s) 2016.

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.

The Importance of Species Traits for Species Distribution on Oceanic Islands

PubMed Central

Vazačová, Kristýna; Münzbergová, Zuzana

2014-01-01

Understanding species' ability to colonize new habitats is a key knowledge allowing us to predict species' survival in the changing landscapes. However, most studies exploring this topic observe distribution of species in landscapes which are under strong human influence being fragmented only recently and ignore the fact that the species distribution in these landscapes is far from equilibrium. Oceanic islands seem more appropriate systems for studying the relationship between species traits and its distribution as they are fragmented without human contribution and as they remained unchanged for a long evolutionary time. In our study we compared the values of dispersal as well as persistence traits among 18 species pairs from the Canary Islands differing in their distribution within the archipelago. The data were analyzed both with and without phylogenetic correction. The results demonstrate that no dispersal trait alone can explain the distribution of the species in the system. They, however, also suggest that species with better dispersal compared to their close relatives are better colonizers. Similarly, abundance of species in the archipelago seems to be an important predictor of species colonization ability only when comparing closely related species. This implies that analyses including phylogenetic correction may provide different insights than analyses without such a correction and both types of analyses should be combined to understand the importance of various plant traits for species colonization ability. PMID:25003737

Polyphenism in social insects: insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris

PubMed Central

2011-01-01

Background Understanding polyphenism, the ability of a single genome to express multiple morphologically and behaviourally distinct phenotypes, is an important goal for evolutionary and developmental biology. Polyphenism has been key to the evolution of the Hymenoptera, and particularly the social Hymenoptera where the genome of a single species regulates distinct larval stages, sexual dimorphism and physical castes within the female sex. Transcriptomic analyses of social Hymenoptera will therefore provide unique insights into how changes in gene expression underlie such complexity. Here we describe gene expression in individual specimens of the pre-adult stages, sexes and castes of the key pollinator, the buff-tailed bumblebee Bombus terrestris. Results cDNA was prepared from mRNA from five life cycle stages (one larva, one pupa, one male, one gyne and two workers) and a total of 1,610,742 expressed sequence tags (ESTs) were generated using Roche 454 technology, substantially increasing the sequence data available for this important species. Overlapping ESTs were assembled into 36,354 B. terrestris putative transcripts, and functionally annotated. A preliminary assessment of differences in gene expression across non-replicated specimens from the pre-adult stages, castes and sexes was performed using R-STAT analysis. Individual samples from the life cycle stages of the bumblebee differed in the expression of a wide array of genes, including genes involved in amino acid storage, metabolism, immunity and olfaction. Conclusions Detailed analyses of immune and olfaction gene expression across phenotypes demonstrated how transcriptomic analyses can inform our understanding of processes central to the biology of B. terrestris and the social Hymenoptera in general. For example, examination of immunity-related genes identified high conservation of important immunity pathway components across individual specimens from the life cycle stages while olfactory-related genes exhibited differential expression with a wider repertoire of gene expression within adults, especially sexuals, in comparison to immature stages. As there is an absence of replication across the samples, the results of this study are preliminary but provide a number of candidate genes which may be related to distinct phenotypic stage expression. This comprehensive transcriptome catalogue will provide an important gene discovery resource for directed programmes in ecology, evolution and conservation of a key pollinator. PMID:22185240

Earthquake hazard assessment after Mexico (1985).

PubMed

Degg, M R

1989-09-01

The 1985 Mexican earthquake ranks foremost amongst the major earthquake disasters of the twentieth century. One of the few positive aspects of the disaster is that it provided massive quantities of data that would otherwise have been unobtainable. Every opportunity should be taken to incorporate the findings from these data in earthquake hazard assessments. The purpose of this paper is to provide a succinct summary of some of the more important lessons from Mexico. It stems from detailed field investigations, and subsequent analyses, conducted by the author on the behalf of reinsurance companies.

Grid Architecture 2

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

Taft, Jeffrey D.

The report describes work done on Grid Architecture under the auspices of the Department of Electricity Office of Electricity Delivery and Reliability in 2015. As described in the first Grid Architecture report, the primary purpose of this work is to provide stakeholder insight about grid issues so as to enable superior decision making on their part. Doing this requires the creation of various work products, including oft-times complex diagrams, analyses, and explanations. This report provides architectural insights into several important grid topics and also describes work done to advance the science of Grid Architecture as well.

Mitochondrial DNA and STR analyses for human DNA from maggots crop contents: a forensic entomology case from central-southern China.

PubMed

Li, X; Cai, J F; Guo, Y D; Xiong, F; Zhang, L; Feng, H; Meng, F M; Fu, Y; Li, J B; Chen, Y Q

2011-08-01

Insect larvae and adult insects found on human corpses can provide important forensic evidence however it is useful to be able to prove evidence of association. Without this, it could be claimed that the insect evidence was a contaminant or had been planted on the body. This paper describes how mitochondrial DNA (mtDNA) and STR analysis of the crop contents of larvae of the blowfly Aldrichina grahami collected from separated body parts was used to provide evidence of association.

Whorfian effects on colour memory are not reliable.

PubMed

Wright, Oliver; Davies, Ian R L; Franklin, Anna

2015-01-01

The Whorfian hypothesis suggests that differences between languages cause differences in cognitive processes. Support for this idea comes from studies that find that patterns of colour memory errors made by speakers of different languages align with differences in colour lexicons. The current study provides a large-scale investigation of the relationship between colour language and colour memory, adopting a cross-linguistic and developmental approach. Colour memory on a delayed matching-to-sample (XAB) task was investigated in 2 language groups with differing colour lexicons, for 3 developmental stages and 2 regions of colour space. Analyses used a Bayesian technique to provide simultaneous assessment of two competing hypotheses (H1-Whorfian effect present, H0-Whorfian effect absent). Results of the analyses consistently favoured H0. The findings suggest that Whorfian effects on colour memory are not reliable and that the importance of such effects should not be overestimated.

Quantitative structure-activity relationship models that stand the test of time.

PubMed

Davis, Andrew M; Wood, David J

2013-04-01

The pharmaceutical industry is in a period of intense change. While this has many drivers, attrition through the development process continues to be an important pressure. The emerging definitions of "compound quality" that are based on retrospective analyses of developmental attrition have highlighted a new direction for medicinal chemistry and the paradigm of "quality at the point of design". The time has come for retrospective analyses to catalyze prospective action. Quality at the point of design places pressure on the quality of our predictive models. Empirical QSAR models when built with care provide true predictive control, but their accuracy and precision can be improved. Here we describe AstraZeneca's experience of automation in QSAR model building and validation, and how an informatics system can provide a step-change in predictive power to project design teams, if they choose to use it.

The relationship between employees' perceptions of human resource systems and organizational performance: examining mediating mechanisms and temporal dynamics.

PubMed

Piening, Erk P; Baluch, Alina M; Salge, Torsten Oliver

2013-11-01

Given the limited understanding of temporal issues in extant theorizing about the link between human resource management (HRM) and performance, in this study we aim to shed light on how, when, and why HR interventions affect organizational performance. On the basis of longitudinal, multi-informant and multisource data from public hospital services in England, we provide new insights into the complex interplay between employees' perceptions of HR systems, job satisfaction, and performance outcomes over time. The dynamic panel data analyses provide support for changes in employees' experience of an HR system being related to subsequent changes in customer satisfaction, as mediated by changes in job satisfaction, albeit these effects decrease over time. Moreover, our longitudinal analyses highlight the importance of feedback effects in the HRM-performance chain, which otherwise appears to evolve in a cyclical manner. (c) 2013 APA, all rights reserved.

[The role of meta-analysis in assessing the treatment of advanced non-small cell lung cancer].

PubMed

Pérol, M; Pérol, D

2004-02-01

Meta-analysis is a statistical method allowing an evaluation of the direction and quantitative importance of a treatment effect observed in randomized trials which have tested the treatment but have not provided a definitive conclusion. In the present review, we discuss the methodology and the contribution of meta-analyses to the treatment of advanced-stage or metastatic non-small-cell lung cancer. In this area of cancerology, meta-analyses have provided determining information demonstrating the impact of chemotherapy on patient survival. They have also helped define a two-drug regimen based on cisplatin as the gold standard treatment for patients with a satisfactory general status. Recently, the meta-analysis method was used to measure the influence of gemcitabin in combination with platinium salts and demonstrated a small but significant benefit in survival, confirming that gemcitabin remains the gold standard treatment in combination with cisplatin.

Making comparative performance information more comprehensible: an experimental evaluation of the impact of formats on consumer understanding.

PubMed

Damman, Olga C; De Jong, Anco; Hibbard, Judith H; Timmermans, Danielle R M

2016-11-01

We aimed to investigate how different presentation formats influence comprehension and use of comparative performance information (CPI) among consumers. An experimental between-subjects and within-subjects design with manipulations of CPI presentation formats. We enrolled both consumers with lower socioeconomic status (SES)/cognitive skills and consumers with higher SES/cognitive skills, recruited through an online access panel. Respondents received fictitious CPI and completed questions about interpretation and information use. Between subjects, we tested (1) displaying an overall performance score (yes/no); (2) displaying a small number of quality indicators (5 vs 9); and (3) displaying different types of evaluative symbols (star ratings, coloured dots and word icons vs numbers and bar graphs). Within subjects, we tested the effect of a reduced number of healthcare providers (5 vs 20). Data were analysed using descriptive analysis, analyses of variance and paired-sampled t tests. A total of 902 (43%) respondents participated. Displaying an overall performance score and the use of coloured dots and word icons particularly enhanced consumer understanding. Importantly, respondents provided with coloured dots most often correctly selected the top three healthcare providers (84.3%), compared with word icons (76.6% correct), star ratings (70.6% correct), numbers (62.0%) and bars (54.2%) when viewing performance scores of 20 providers. Furthermore, a reduced number of healthcare providers appeared to support consumers, for example, when provided with 20 providers, 69.5% correctly selected the top three, compared with 80.2% with five providers. Particular presentation formats enhanced consumer understanding of CPI, most importantly the use of overall performance scores, word icons and coloured dots, and a reduced number of providers displayed. Public report efforts should use these formats to maximise impact on consumers. 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/.

The power of a collaborative relationship between technical assistance providers and community prevention teams: A correlational and longitudinal study.

PubMed

Chilenski, Sarah M; Perkins, Daniel F; Olson, Jonathan; Hoffman, Lesa; Feinberg, Mark E; Greenberg, Mark; Welsh, Janet; Crowley, D Max; Spoth, Richard

2016-02-01

Historically, effectiveness of community collaborative prevention efforts has been mixed. Consequently, research has been undertaken to better understand the factors that support their effectiveness; theory and some related empirical research suggests that the provision of technical assistance is one important supporting factor. The current study examines one aspect of technical assistance that may be important in supporting coalition effectiveness, the collaborative relationship between the technical assistance provider and site lead implementer. Four and one-half years of data were collected from technical assistance providers and prevention team members from the 14 community prevention teams involved in the PROSPER project. Spearman correlation analyses with longitudinal data show that the levels of the collaborative relationship during one phase of collaborative team functioning associated with characteristics of internal team functioning in future phases. Results suggest that community collaborative prevention work should consider the collaborative nature of the technical assistance provider - prevention community team relationship when designing and conducting technical assistance activities, and it may be important to continually assess these dynamics to support high quality implementation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Joint modelling of serological and hospitalization data reveals that high levels of pre-existing immunity and school holidays shaped the influenza A pandemic of 2009 in The Netherlands

PubMed Central

te Beest, Dennis E.; Birrell, Paul J; Wallinga, Jacco; De Angelis, Daniela; van Boven, Michiel

2015-01-01

Obtaining a quantitative understanding of the transmission dynamics of influenza A is important for predicting healthcare demand and assessing the likely impact of intervention measures. The pandemic of 2009 provides an ideal platform for developing integrative analyses as it has been studied intensively, and a wealth of data sources is available. Here, we analyse two complementary datasets in a disease transmission framework: cross-sectional serological surveys providing data on infection attack rates, and hospitalization data that convey information on the timing and duration of the pandemic. We estimate key epidemic determinants such as infection and hospitalization rates, and the impact of a school holiday. In contrast to previous approaches, our novel modelling of serological data with mixture distributions provides a probabilistic classification of individual samples (susceptible, immune and infected), propagating classification uncertainties to the transmission model and enabling serological classifications to be informed by hospitalization data. The analyses show that high levels of immunity among persons 20 years and older provide a consistent explanation of the skewed attack rates observed during the pandemic and yield precise estimates of the probability of hospitalization per infection (1–4 years: 0.00096 (95%CrI: 0.00078–0.0012); 5–19 years: 0.00036 (0.00031–0.0044); 20–64 years: 0.0015 (0.00091–0.0020); 65+ years: 0.0084 (0.0028–0.016)). The analyses suggest that in The Netherlands, the school holiday period reduced the number of infectious contacts between 5- and 9-year-old children substantially (estimated reduction: 54%; 95%CrI: 29–82%), thereby delaying the unfolding of the pandemic in The Netherlands by approximately a week. PMID:25540241

Identifying consumer segments in health services markets: an application of conjoint and cluster analyses to the ambulatory care pharmacy market.

PubMed

Carrol, N V; Gagon, J P

1983-01-01

Because of increasing competition, it is becoming more important that health care providers pursue consumer-based market segmentation strategies. This paper presents a methodology for identifying and describing consumer segments in health service markets, and demonstrates the use of the methodology by presenting a study of consumer segments in the ambulatory care pharmacy market.

Detecting Bias in Meta-Analyses of Distance Education Research: Big Pictures We Can Rely On

ERIC Educational Resources Information Center

Bernard, Robert M.; Borokhovski, Eugene; Tamim, Rana M.

2014-01-01

This article has two interrelated purposes. The first is to explain how various forms of bias, if introduced during any stage of a meta-analysis, can provide the consumer with a misimpression of the state of a research literature. Five of the most important bias-producing aspects of a meta-analysis are presented and discussed. Second, armed with…

Understanding protein-nanoparticle interaction: a new gateway to disease therapeutics.

PubMed

Giri, Karuna; Shameer, Khader; Zimmermann, Michael T; Saha, Sounik; Chakraborty, Prabir K; Sharma, Anirudh; Arvizo, Rochelle R; Madden, Benjamin J; Mccormick, Daniel J; Kocher, Jean-Pierre A; Bhattacharya, Resham; Mukherjee, Priyabrata

2014-06-18

Molecular identification of protein molecules surrounding nanoparticles (NPs) may provide useful information that influences NP clearance, biodistribution, and toxicity. Hence, nanoproteomics provides specific information about the environment that NPs interact with and can therefore report on the changes in protein distribution that occurs during tumorigenesis. Therefore, we hypothesized that characterization and identification of protein molecules that interact with 20 nm AuNPs from cancer and noncancer cells may provide mechanistic insights into the biology of tumor growth and metastasis and identify new therapeutic targets in ovarian cancer. Hence, in the present study, we systematically examined the interaction of the protein molecules with 20 nm AuNPs from cancer and noncancerous cell lysates. Time-resolved proteomic profiles of NP-protein complexes demonstrated electrostatic interaction to be the governing factor in the initial time-points which are dominated by further stabilization interaction at longer time-points as determined by ultraviolet-visible spectroscopy (UV-vis), dynamic light scattering (DLS), ζ-potential measurements, transmission electron microscopy (TEM), and tandem mass spectrometry (MS/MS). Reduction in size, charge, and number of bound proteins were observed as the protein-NP complex stabilized over time. Interestingly, proteins related to mRNA processing were overwhelmingly represented on the NP-protein complex at all times. More importantly, comparative proteomic analyses revealed enrichment of a number of cancer-specific proteins on the AuNP surface. Network analyses of these proteins highlighted important hub nodes that could potentially be targeted for maximal therapeutic advantage in the treatment of ovarian cancer. The importance of this methodology and the biological significance of the network proteins were validated by a functional study of three hubs that exhibited variable connectivity, namely, PPA1, SMNDC1, and PI15. Western blot analysis revealed overexpression of these proteins in ovarian cancer cells when compared to normal cells. Silencing of PPA1, SMNDC1, and PI15 by the siRNA approach significantly inhibited proliferation of ovarian cancer cells and the effect correlated with the connectivity pattern obtained from our network analyses.

Online Tools for Bioinformatics Analyses in Nutrition Sciences12

PubMed Central

Malkaram, Sridhar A.; Hassan, Yousef I.; Zempleni, Janos

2012-01-01

Recent advances in “omics” research have resulted in the creation of large datasets that were generated by consortiums and centers, small datasets that were generated by individual investigators, and bioinformatics tools for mining these datasets. It is important for nutrition laboratories to take full advantage of the analysis tools to interrogate datasets for information relevant to genomics, epigenomics, transcriptomics, proteomics, and metabolomics. This review provides guidance regarding bioinformatics resources that are currently available in the public domain, with the intent to provide a starting point for investigators who want to take advantage of the opportunities provided by the bioinformatics field. PMID:22983844

Human Systems Integration: Unmanned Aircraft Control Station Certification Plan Guidance

NASA Technical Reports Server (NTRS)

2005-01-01

This document provides guidance to the FAA on important human factors considerations that can be used to support the certification of a UAS Aircraft Control Station (ACS). This document provides a synopsis of the human factors analysis, design and test activities to be performed to provide a basis for FAA certification. The data from these analyses, design activities, and tests, along with data from certification/qualification tests of other key components should be used to establish the ACS certification basis. It is expected that this information will be useful to manufacturers in developing the ACS Certification Plan,, and in supporting the design of their ACS.

Distinguishing Mediational Models and Analyses in Clinical Psychology: Atemporal Associations Do Not Imply Causation.

PubMed

Winer, E Samuel; Cervone, Daniel; Bryant, Jessica; McKinney, Cliff; Liu, Richard T; Nadorff, Michael R

2016-09-01

A popular way to attempt to discern causality in clinical psychology is through mediation analysis. However, mediation analysis is sometimes applied to research questions in clinical psychology when inferring causality is impossible. This practice may soon increase with new, readily available, and easy-to-use statistical advances. Thus, we here provide a heuristic to remind clinical psychological scientists of the assumptions of mediation analyses. We describe recent statistical advances and unpack assumptions of causality in mediation, underscoring the importance of time in understanding mediational hypotheses and analyses in clinical psychology. Example analyses demonstrate that statistical mediation can occur despite theoretical mediation being improbable. We propose a delineation of mediational effects derived from cross-sectional designs into the terms temporal and atemporal associations to emphasize time in conceptualizing process models in clinical psychology. The general implications for mediational hypotheses and the temporal frameworks from within which they may be drawn are discussed. © 2016 Wiley Periodicals, Inc.

Effects of Sample Selection Bias on the Accuracy of Population Structure and Ancestry Inference

PubMed Central

Shringarpure, Suyash; Xing, Eric P.

2014-01-01

Population stratification is an important task in genetic analyses. It provides information about the ancestry of individuals and can be an important confounder in genome-wide association studies. Public genotyping projects have made a large number of datasets available for study. However, practical constraints dictate that of a geographical/ethnic population, only a small number of individuals are genotyped. The resulting data are a sample from the entire population. If the distribution of sample sizes is not representative of the populations being sampled, the accuracy of population stratification analyses of the data could be affected. We attempt to understand the effect of biased sampling on the accuracy of population structure analysis and individual ancestry recovery. We examined two commonly used methods for analyses of such datasets, ADMIXTURE and EIGENSOFT, and found that the accuracy of recovery of population structure is affected to a large extent by the sample used for analysis and how representative it is of the underlying populations. Using simulated data and real genotype data from cattle, we show that sample selection bias can affect the results of population structure analyses. We develop a mathematical framework for sample selection bias in models for population structure and also proposed a correction for sample selection bias using auxiliary information about the sample. We demonstrate that such a correction is effective in practice using simulated and real data. PMID:24637351

Estimating the Effective Sample Size of Tree Topologies from Bayesian Phylogenetic Analyses

PubMed Central

Lanfear, Robert; Hua, Xia; Warren, Dan L.

2016-01-01

Bayesian phylogenetic analyses estimate posterior distributions of phylogenetic tree topologies and other parameters using Markov chain Monte Carlo (MCMC) methods. Before making inferences from these distributions, it is important to assess their adequacy. To this end, the effective sample size (ESS) estimates how many truly independent samples of a given parameter the output of the MCMC represents. The ESS of a parameter is frequently much lower than the number of samples taken from the MCMC because sequential samples from the chain can be non-independent due to autocorrelation. Typically, phylogeneticists use a rule of thumb that the ESS of all parameters should be greater than 200. However, we have no method to calculate an ESS of tree topology samples, despite the fact that the tree topology is often the parameter of primary interest and is almost always central to the estimation of other parameters. That is, we lack a method to determine whether we have adequately sampled one of the most important parameters in our analyses. In this study, we address this problem by developing methods to estimate the ESS for tree topologies. We combine these methods with two new diagnostic plots for assessing posterior samples of tree topologies, and compare their performance on simulated and empirical data sets. Combined, the methods we present provide new ways to assess the mixing and convergence of phylogenetic tree topologies in Bayesian MCMC analyses. PMID:27435794

Alterations of Intrinsic Brain Connectivity Patterns in Depression and Bipolar Disorders: A Critical Assessment of Magnetoencephalography-Based Evidence

PubMed Central

Alamian, Golnoush; Hincapié, Ana-Sofía; Combrisson, Etienne; Thiery, Thomas; Martel, Véronique; Althukov, Dmitrii; Jerbi, Karim

2017-01-01

Despite being the object of a thriving field of clinical research, the investigation of intrinsic brain network alterations in psychiatric illnesses is still in its early days. Because the pathological alterations are predominantly probed using functional magnetic resonance imaging (fMRI), many questions about the electrophysiological bases of resting-state alterations in psychiatric disorders, particularly among mood disorder patients, remain unanswered. Alongside important research using electroencephalography (EEG), the specific recent contributions and future promise of magnetoencephalography (MEG) in this field are not fully recognized and valued. Here, we provide a critical review of recent findings from MEG resting-state connectivity within major depressive disorder (MDD) and bipolar disorder (BD). The clinical MEG resting-state results are compared with those previously reported with fMRI and EEG. Taken together, MEG appears to be a promising but still critically underexploited technique to unravel the neurophysiological mechanisms that mediate abnormal (both hyper- and hypo-) connectivity patterns involved in MDD and BD. In particular, a major strength of MEG is its ability to provide source-space estimations of neuromagnetic long-range rhythmic synchronization at various frequencies (i.e., oscillatory coupling). The reviewed literature highlights the relevance of probing local and interregional rhythmic synchronization to explore the pathophysiological underpinnings of each disorder. However, before we can fully take advantage of MEG connectivity analyses in psychiatry, several limitations inherent to MEG connectivity analyses need to be understood and taken into account. Thus, we also discuss current methodological challenges and outline paths for future research. MEG resting-state studies provide an important window onto perturbed spontaneous oscillatory brain networks and hence supply an important complement to fMRI-based resting-state measurements in psychiatric populations. PMID:28367127

Comparative analyses of structural features and scaffold diversity for purchasable compound libraries.

PubMed

Shang, Jun; Sun, Huiyong; Liu, Hui; Chen, Fu; Tian, Sheng; Pan, Peichen; Li, Dan; Kong, Dexin; Hou, Tingjun

2017-04-21

Large purchasable screening libraries of small molecules afforded by commercial vendors are indispensable sources for virtual screening (VS). Selecting an optimal screening library for a specific VS campaign is quite important to improve the success rates and avoid wasting resources in later experimental phases. Analysis of the structural features and molecular diversity for different screening libraries can provide valuable information to the decision making process when selecting screening libraries for VS. In this study, the structural features and scaffold diversity of eleven purchasable screening libraries and Traditional Chinese Medicine Compound Database (TCMCD) were analyzed and compared. Their scaffold diversity represented by the Murcko frameworks and Level 1 scaffolds was characterized by the scaffold counts and cumulative scaffold frequency plots, and visualized by Tree Maps and SAR Maps. The analysis demonstrates that, based on the standardized subsets with similar molecular weight distributions, Chembridge, ChemicalBlock, Mucle, TCMCD and VitasM are more structurally diverse than the others. Compared with all purchasable screening libraries, TCMCD has the highest structural complexity indeed but more conservative molecular scaffolds. Moreover, we found that some representative scaffolds were important components of drug candidates against different drug targets, such as kinases and guanosine-binding protein coupled receptors, and therefore the molecules containing pharmacologically important scaffolds found in screening libraries might be potential inhibitors against the relevant targets. This study may provide valuable perspective on which purchasable compound libraries are better for you to screen. Graphical abstract Selecting diverse compound libraries with scaffold analyses.

Impacts of Agricultural Practices and Individual Life Characteristics on Ecosystem Services: A Case Study on Family Farmers in the Context of an Amazonian Pioneer Front.

PubMed

Solen, Le Clec'h; Nicolas, Jégou; de Sartre Xavier, Arnauld; Thibaud, Decaens; Simon, Dufour; Michel, Grimaldi; Johan, Oszwald

2018-05-01

In tropical forests farmers are among the most important agents of deforestation. At the interface between societies and their environment, ecosystem services (ES) is an integrated working framework through which natural and anthropogenic dimensions can be addressed. Here, we aimed to understand to what extent farmers impact ES availability. Based on case studies in three locations in the Brazilian Amazon rainforest, we performed statistical analyses at 135 sampling points and 110 farms to link socioeconomic and ES data, both derived from field work. The socioeconomic data characterized agricultural production, sociological characteristics, and quality of life. ES data were obtained from statistical analyses that yielded a multiple ES indicator for each sampling point and farm. Our results produced three main findings: first, the establishment of ES associations is due more to agricultural production characteristics than to sociological and quality-of-life factors. Second, the impact of agricultural production on ES availability depends on the level of total incomes. An increase in incomes causes a decrease in the forest cover that provides many ES and an increase in other areas that provide fewer ES. Finally, our analyses show a very strong site effect that probably expresses the heterogeneity of the biophysical contexts, but also the importance for ES availability of the historical depth of deforestation and/or the role of specific public policies. Finding ways of producing an alternative impact on ES availability and establishing specific ES associations will therefore depend more on changes in the global political context than in individual practices.

The conscientious retiree: The relationship between conscientiousness, retirement, and volunteering.

PubMed

Mike, Anissa; Jackson, Joshua J; Oltmanns, Thomas F

2014-10-01

The current study examined the relationship between conscientiousness, work status, and volunteering utilizing two large samples, the St. Louis Personality and Aging Network (SPAN) and the Health and Retirement Study (HRS). It was hypothesized that conscientious adults who were retired would be more likely to volunteer because, after retirement, they gain a substantial amount of free time, while losing an outlet for their industrious and achievement-striving tendencies. Cross-sectional and longitudinal analyses revealed that conscientious, retired individuals were more likely to volunteer than conscientious, working individuals. Further analyses revealed that facets of conscientiousness provide differential information from the general trait. These findings indicate that volunteering during retirement fills an important niche for high-striving, conscientious individuals.

Petrographic and Vitrinite Reflectance Analyses of a Suite of High Volatile Bituminous Coal Samples from the United States and Venezuela

USGS Publications Warehouse

Hackley, Paul C.; Kolak, Jonathan J.

2008-01-01

This report presents vitrinite reflectance and detailed organic composition data for nine high volatile bituminous coal samples. These samples were selected to provide a single, internally consistent set of reflectance and composition analyses to facilitate the study of linkages among coal composition, bitumen generation during thermal maturation, and geochemical characteristics of generated hydrocarbons. Understanding these linkages is important for addressing several issues, including: the role of coal as a source rock within a petroleum system, the potential for conversion of coal resources to liquid hydrocarbon fuels, and the interactions between coal and carbon dioxide during enhanced coalbed methane recovery and(or) carbon dioxide sequestration in coal beds.

Geomorphology and seismic risk

NASA Astrophysics Data System (ADS)

Panizza, Mario

1991-07-01

The author analyses the contributions provided by geomorphology in studies suited to the assessment of seismic risk: this is defined as function of the seismic hazard, of the seismic susceptibility, and of the vulnerability. The geomorphological studies applicable to seismic risk assessment can be divided into two sectors: (a) morpho-neotectonic investigations conducted to identify active tectonic structures; (b) geomorphological and morphometric analyses aimed at identifying the particular situations that amplify or reduce seismic susceptibility. The morpho-neotectonic studies lead to the identification, selection and classification of the lineaments that can be linked with active tectonic structures. The most important geomorphological situations that can condition seismic susceptibility are: slope angle, debris, morphology, degradational slopes, paleo-landslides and underground cavities.

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.

'That would have been beneficial': LGBTQ education for home-care service providers.

PubMed

Daley, Andrea; MacDonnell, Judith A

2015-05-01

This paper reports qualitative findings from a pilot study that explored the lesbian, gay, bisexual, transgender and queer (LGBTQ) education needs of home-care service providers working in one large, urban Canadian city. The pilot study builds upon research that has documented barriers to health services for diversely situated LGBTQ people, which function to limit access to good-quality healthcare. LGBTQ activists, organisations and allies have underscored the need for health provider education related to the unique health and service experiences of sexual and gender minority communities. However, the home-care sector is generally overlooked in this important body of research literature. We used purposeful convenience sampling to conduct four focus groups and two individual interviews with a total of 15 professionally diverse home-care service providers. Data collection was carried out from January 2011 to July 2012 and data were analysed using grounded theory methods towards the identification of the overarching theme, 'provider education' and it had two sub-themes: (i) experiences of LGBTQ education; and (ii) recommendations for LGBTQ education. The study findings raise important questions about limited and uneven access to adequate LGBTQ education for home-care service providers, suggest important policy implications for the education and health sectors, and point to the need for anti-oppression principles in the development of education initiatives. © 2014 John Wiley & Sons Ltd.

Validity of Meta-analysis in Diabetes: We Need to Be Aware of Its Limitations

PubMed Central

Home, Philip D.

2013-01-01

To deliver high-quality clinical care to patients with diabetes and other chronic conditions, clinicians must understand the evidence available from studies that have been performed to address important clinical management questions. In an evidence-based approach to clinical care, the evidence from clinical research should be integrated with clinical expertise, pathophysiological knowledge, and an understanding of patient values. As such, in an effort to provide information from many studies, the publication of diabetes meta-analyses has increased markedly in the recent past, using either observational or clinical trial data. In this regard, guidelines have been developed to direct the performance of meta-analysis to provide consistency among contributions. Thus, when done appropriately, meta-analysis can provide estimates from clinically and statistically homogeneous but underpowered studies and is useful in supporting clinical decisions, guidelines, and cost-effectiveness analysis. However, often these conditions are not met, the data considered are unreliable, and the results should not be assumed to be any more valid than the data underlying the included studies. To provide an understanding of both sides of the argument, we provide a discussion of this topic as part of this two-part point-counterpoint narrative. In the point narrative as presented below, Dr. Home provides his opinion and review of the data to date showing that we need to carefully evaluate meta-analyses and to learn what results are reliable. In the counterpoint narrative following Dr. Home’s contribution, Drs. Golden and Bass emphasize that an effective system exists to guide meta-analysis and that rigorously conducted, high-quality systematic reviews and meta-analyses are an indispensable tool in evidence synthesis despite their limitations. —William T. Cefalu, MD Editor in Chief, Diabetes Care PMID:24065844

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.

A Combination Histochemical and Autoradiographic Method for Analysis of Enzymatic and Proliferative Responses to Immunoreactive Osteoinducer

DTIC Science & Technology

1988-01-15

DNA replication and alkaline phosphate activity in the responding cells was shown to result in effective differential labeling of these features in mildly fixed tissue sections. Application of this method with monoclonal antibodies specific for induction-associated determinants and with modifications to permit ultrastructural analyses may provide important information relevant to the mechanism of matrix-induced bone formation. Keywords: Osteogenic implants; Immunohistochemistry;

A Data Analysis Center for Electromagnetic and Hadronic Interaction

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

Briscoe, William John; Strakovsky, Igor I.; Workman, Ronald L.

2015-05-31

The GW Data Analysis Center (DAC) has made significant progress in its program to enhance and expand the partial-wave and multipole analyses of fundamental reactions, while maintaining and expanding each associated database. These efforts provide guidance to national and international experimental and theoretical efforts, and are an important link between theory and experiment. Our principal goals are focused on baryon and meson physics programs and related topics.

Application of ion chromatography in pharmaceutical and drug analysis.

PubMed

Jenke, Dennis

2011-08-01

Ion chromatography (IC) has developed and matured into an important analytical methodology in a number of diverse applications and industries, including pharmaceuticals. This manuscript provides a review of IC applications for the determinations of active and inactive ingredients, excipients, degradation products, and impurities relevant to pharmaceutical analyses and thus serves as a resource for investigators looking for insights into the use of the IC methodology in this field of application.

Heterogeniety and Heterarchy: How far can network analyses in Earth and space sciences?

NASA Astrophysics Data System (ADS)

Prabhu, A.; Fox, P. A.; Eleish, A.; Li, C.; Pan, F.; Zhong, H.

2017-12-01

The vast majority of explorations of Earth systems are limited in their ability to effectively explore the most important (often most difficult) problems because they are forced to interconnect at the data-element, or syntactic, level rather than at a higher scientific, or conceptual/ semantic, level. Recent successes in the application of complex network theory and algorithms to minerology, fossils and proteins over billions of years of Earth's history, raise expectations that more general graph-based approaches offer the opportunity for new discoveries = needles instead of haystacks. In the past 10 years in the natural sciences there has substantial progress in providing both specialists and non-specialists the ability to describe in machine readable form, geophysical quantities and relations among them in meaningful and natural ways, effectively breaking the prior syntax barrier. The corresponding open-world semantics and reasoning provide higher-level interconnections. That is, semantics provided around the data structures, using open-source tools, allow for discovery at the knowledge level. This presentation will cover the fundamentals of data-rich network analyses for geosciences, provide illustrative examples in mineral evolution and offer future paths for consideration.

Population genomics provide insights into the evolution and adaptation of the eastern honey bee (Apis cerana).

PubMed

Chen, Chao; Wang, Huihua; Liu, Zhiguang; Chen, Xiao; Tang, Jiao; Meng, Fanming; Shi, Wei

2018-06-20

The mechanisms by which organisms adapt to variable environments are a fundamental question in evolutionary biology and are important to protect important species in response to a changing climate. An interesting candidate to study this question is the honey bee Apis cerana, a keystone pollinator with a wide distribution throughout a large variety of climates, that exhibits rapid dispersal. Here, we re-sequenced the genome of 180 A. cerana individuals from eighteen populations throughout China. Using a population genomics approach, we observed considerable genetic variation in A. cerana. Patterns of genetic differentiation indicate high divergence at the subspecies level, and physical barriers rather than distance are the driving force for population divergence. Estimations of divergence time suggested that the main branches diverged between 300 and 500 ka. Analyses of the population history revealed a substantial influence of the Earth's climate on the effective population size of A. cerana, as increased population sizes were observed during warmer periods. Further analyses identified candidate genes under natural selection that are potentially related to honey bee cognition, temperature adaptation, and olfactory. Based on our results, A. cerana may have great potential in response to climate change. Our study provides fundamental knowledge of the evolution and adaptation of A. cerana.

Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: A case study in Tibetan Schizothoracine fish

PubMed Central

Tian, Fei; Zhao, Kai

2017-01-01

Environmental acclimation is important episode in wildlife occupation of the high-altitude Tibetan Plateau (TP). Transcriptome-wide studies on thermal acclimation mechanism in fish species are rarely revealed in Tibetan Plateau fish at high altitude. Thus, we used mRNA and miRNA transcriptome sequencing to investigate regulation of thermal acclimation in larval Tibetan naked carp, Gymnocypris przewalskii. We first remodeled the regulation network of mRNA and miRNA in thermal acclimation, and then identified differential expression of miRNAs and target mRNAs enriched in metabolic and digestive pathways. Interestingly, we identified two candidate genes contributed to normal skeletal development. The altered expression of these gene groups could potentially be associated with the developmental issues of deformity and induced larval death. Our results have three important implications: first, these findings provide strong evidences to support our hypothesis that G. przewalskii possess ability to build heat-tolerance against the controversial issue. Second, this study shows that transcriptional and post-transcriptional regulations are extensively involved in thermal acclimation. Third, the integrated mRNA and microRNA transcriptome analyses provide a large number of valuable genetic resources for future studies on environmental stress response in G. przewalskii and as a case study in Tibetan Schizothoracine fish. PMID:29045433

Stratospheric Analysis and Forecasting in the Northern Winter of 1999/2000: The NASA DAO's GEOS-3 System

NASA Technical Reports Server (NTRS)

Pawson, Steven; Lamich, David; Ledvina, Andrea; Lucchesi, Robert; Owens, Tommy; Newman, Paul A.; Atlas, Robert (Technical Monitor)

2002-01-01

An evaluation is presented of the performance in the northern winter 1999/2000 of the GEOS-3 troposphere-stratosphere data assimilation system (DAS). The impacts of the two main input data types are assessed: upper-air soundings (sondes) provide wind and temperature information and satellite-based (Tiros Operational Vertical Sounders: TOVS) give estimates of the thermal structure. It is shown that in the low stratosphere (300-70hPa) the analyses are generally slightly warmer than the sonde data, but colder than the TOVS data; this relationship reverses between 70 and 10 hPa. There are geographical biases, related to the spatial and temporal coverage of the observation types and to the statistical weights assigned to them in the DAS. Forecasts show a tendency to reduce zonal asymmetries in the atmospheric flow and to suppress stratospheric temperature minima. In the DAS, the analysis increments compensate for this, but it leads to important biases in the multi-day forecasts. The analysis increments are as large as the diabatic forcing in the lower polar stratosphere, indicating a substantial model bias. The results provide important insights into the roles of different data types and the circulation model in producing accurate analyses for studies of polar chemistry and physical processes.

Detailed thermodynamic analyses of high-speed compressible turbulence

NASA Astrophysics Data System (ADS)

Towery, Colin; Darragh, Ryan; Poludnenko, Alexei; Hamlington, Peter

2016-11-01

Interactions between high-speed turbulence and flames (or chemical reactions) are important in the dynamics and description of many different combustion phenomena, including autoignition and deflagration-to-detonation transition. The probability of these phenomena to occur depends on the magnitude and spectral content of turbulence fluctuations, which can impact a wide range of science and engineering problems, from the hypersonic scramjet engine to the onset of Type Ia supernovae. In this talk, we present results from new direct numerical simulations (DNS) of homogeneous isotropic turbulence with turbulence Mach numbers ranging from 0 . 05 to 1 . 0 and Taylor-scale Reynolds numbers as high as 700. A set of detailed analyses are described in both Eulerian and Lagrangian reference frames in order to assess coherent (structural) and incoherent (stochastic) thermodynamic flow features. These analyses provide direct insights into the thermodynamics of strongly compressible turbulence. Furthermore, presented results provide a non-reacting baseline for future studies of turbulence-chemistry interactions in DNS with complex chemistry mechanisms. This work was supported by the Air Force Office of Scientific Research (AFOSR) under Award No. FA9550-14-1-0273, and the Department of Defense (DoD) High Performance Computing Modernization Program (HPCMP) under a Frontier project award.

Incorporating nonlinearity into mediation analyses.

PubMed

Knafl, George J; Knafl, Kathleen A; Grey, Margaret; Dixon, Jane; Deatrick, Janet A; Gallo, Agatha M

2017-03-21

Mediation is an important issue considered in the behavioral, medical, and social sciences. It addresses situations where the effect of a predictor variable X on an outcome variable Y is explained to some extent by an intervening, mediator variable M. Methods for addressing mediation have been available for some time. While these methods continue to undergo refinement, the relationships underlying mediation are commonly treated as linear in the outcome Y, the predictor X, and the mediator M. These relationships, however, can be nonlinear. Methods are needed for assessing when mediation relationships can be treated as linear and for estimating them when they are nonlinear. Existing adaptive regression methods based on fractional polynomials are extended here to address nonlinearity in mediation relationships, but assuming those relationships are monotonic as would be consistent with theories about directionality of such relationships. Example monotonic mediation analyses are provided assessing linear and monotonic mediation of the effect of family functioning (X) on a child's adaptation (Y) to a chronic condition by the difficulty (M) for the family in managing the child's condition. Example moderated monotonic mediation and simulation analyses are also presented. Adaptive methods provide an effective way to incorporate possibly nonlinear monotonicity into mediation relationships.

Building integrated business environments: analysing open-source ESB

NASA Astrophysics Data System (ADS)

Martínez-Carreras, M. A.; García Jimenez, F. J.; Gómez Skarmeta, A. F.

2015-05-01

Integration and interoperability are two concepts that have gained significant prominence in the business field, providing tools which enable enterprise application integration (EAI). In this sense, enterprise service bus (ESB) has played a crucial role as the underpinning technology for creating integrated environments in which companies may connect all their legacy-applications. However, the potential of these technologies remains unknown and some important features are not used to develop suitable business environments. The aim of this paper is to describe and detail the elements for building the next generation of integrated business environments (IBE) and to analyse the features of ESBs as the core of this infrastructure. For this purpose, we evaluate how well-known open-source ESB products fulfil these needs. Moreover, we introduce a scenario in which the collaborative system 'Alfresco' is integrated in the business infrastructure. Finally, we provide a comparison of the different open-source ESBs available for IBE requirements. According to this study, Fuse ESB provides the best results, considering features such as support for a wide variety of standards and specifications, documentation and implementation, security, advanced business trends, ease of integration and performance.

Variability of Kelvin wave momentum flux from high-resolution radiosonde and radio occultation data

NASA Astrophysics Data System (ADS)

Sjoberg, J. P.; Zeng, Z.; Ho, S. P.; Birner, T.; Anthes, R. A.; Johnson, R. H.

2017-12-01

Direct measurement of momentum flux from Kelvin waves in the stratosphere remains challenging. Constraining this flux from observations is an important step towards constraining the flux from models. Here we present results from analyses using linear theory to estimate the Kelvin wave amplitudes and momentum fluxes from both high-resolution radiosondes and from radio occultation (RO) data. These radiosonde data are from a contiguous 11-year span of soundings performed at two Department of Energy Atmospheric Radiation Measurement sites, while the RO data span 14 years from multiple satellite missions. Daily time series of the flux from both sources are found to be in quantitative agreement with previous studies. Climatological analyses of these data reveal the expected seasonal cycle and variability associated with the quasi-biennial oscillation. Though both data sets provide measurements on distinct spatial and temporal scales, the estimated flux from each provides insight into separate but complimentary aspects of how the Kelvin waves affect the stratosphere. Namely, flux derived from radiosonde sites provide details on the regional Kelvin wave variability, while the flux from RO data are zonal mean estimates.

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

Sarrack, A.G.

The purpose of this report is to document fault tree analyses which have been completed for the Defense Waste Processing Facility (DWPF) safety analysis. Logic models for equipment failures and human error combinations that could lead to flammable gas explosions in various process tanks, or failure of critical support systems were developed for internal initiating events and for earthquakes. These fault trees provide frequency estimates for support systems failures and accidents that could lead to radioactive and hazardous chemical releases both on-site and off-site. Top event frequency results from these fault trees will be used in further APET analyses tomore » calculate accident risk associated with DWPF facility operations. This report lists and explains important underlying assumptions, provides references for failure data sources, and briefly describes the fault tree method used. Specific commitments from DWPF to provide new procedural/administrative controls or system design changes are listed in the ''Facility Commitments'' section. The purpose of the ''Assumptions'' section is to clarify the basis for fault tree modeling, and is not necessarily a list of items required to be protected by Technical Safety Requirements (TSRs).« less

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

PubMed Central

Paley, Suzanne M.; Krummenacker, Markus; Latendresse, Mario; Dale, Joseph M.; Lee, Thomas J.; Kaipa, Pallavi; Gilham, Fred; Spaulding, Aaron; Popescu, Liviu; Altman, Tomer; Paulsen, Ian; Keseler, Ingrid M.; Caspi, Ron

2010-01-01

Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry. PMID:19955237

Live Cell Imaging of Alphaherpes Virus Anterograde Transport and Spread

PubMed Central

Taylor, Matthew P.; Kratchmarov, Radomir; Enquist, Lynn W.

2013-01-01

Advances in live cell fluorescence microscopy techniques, as well as the construction of recombinant viral strains that express fluorescent fusion proteins have enabled real-time visualization of transport and spread of alphaherpes virus infection of neurons. The utility of novel fluorescent fusion proteins to viral membrane, tegument, and capsids, in conjunction with live cell imaging, identified viral particle assemblies undergoing transport within axons. Similar tools have been successfully employed for analyses of cell-cell spread of viral particles to quantify the number and diversity of virions transmitted between cells. Importantly, the techniques of live cell imaging of anterograde transport and spread produce a wealth of information including particle transport velocities, distributions of particles, and temporal analyses of protein localization. Alongside classical viral genetic techniques, these methodologies have provided critical insights into important mechanistic questions. In this article we describe in detail the imaging methods that were developed to answer basic questions of alphaherpes virus transport and spread. PMID:23978901

MEDUSA (Martian Environmental DUst Systematic Analyser) for the monitoring of the Martian atmospheric dust and water vapour

NASA Astrophysics Data System (ADS)

Colangeli, L.; Battaglia, R.; della Corte, V.; Esposito, F.; Ferrini, G.; Mazzotta Epifani, E.; Palomba, E.; Palumbo, P.; Panizza, A.; Rotundi, A.

2004-03-01

The knowledge of Martian airborne dust properties and about mechanisms of dust settling/raising to/from the surface are important to determine climate and surface evolution on Mars. Water is an important tracer of climatic changes on long time-scales and is strictly related to the presence of life forms. The study in situ of dust and water vapour properties and evolution in Martian atmosphere is useful to trace back the planet climate, also in function of life form development. This investigation is also appropriate in preparation to future manned exploration of the planet (in relation to hazardous conditions). In this work we discuss the concept of the MEDUSA (Martian Environmental Dust Analyser) experiment that is designed to provide data on grain size and mass distribution, number density, velocity and scattering properties and on water vapour concentration. The instrument is a multisensor system based on optical and impact detection of grains, coupled with cumulative deposition sensors.

On the uniqueness of the constrained space orbital variation (CSOV) technique

NASA Technical Reports Server (NTRS)

Bauschlicher, C. W., Jr.

1986-01-01

Several CSOV analyses are performed for the 1Sigma(+) state of NiCO, and it is shown that the importance of the CO sigma donation, Ni pi back donation, and interunit polarizations are virtually independent of the order of the CSOV steps, provided that the open-shell 3d sigma and 4s Ni orbitals are orthogonalized to the CO. This order of orthogonalization is consistent with the polarization of the Ni observed in the unconstrained SCF wavefunction. If instead the CO is orthogonalized to the open-shell Ni orbitals, the frozen orbital repulsion and entire CSOV analysis becomes unphysical. A comparison of the SCF and CAS SCF descriptions for the NiCO 1Sigma(+) state shows the importance of the s to d promotion and sd hybridization in reducing the repulsion and increasing the Ni to CO pi bonding. For LiF, CSOV analyses starting from both the neutral and ionic asymptotes show the bonding to be predominantly Li(+) - F(-). These examples show the uniqueness of the CSOV decomposition.

Rural Idaho family physicians' scope of practice.

PubMed

Baker, Ed; Schmitz, David; Epperly, Ted; Nukui, Ayaka; Miller, Carissa Moffat

2010-01-01

Scope of practice is an important factor in both training and recruiting rural family physicians. To assess rural Idaho family physicians' scope of practice and to examine variations in scope of practice across variables such as gender, age and employment status. A survey instrument was developed based on a literature review and was validated by physician educators, practicing family physicians and executives at the state hospital association. This survey was mailed to rural family physicians practicing in Idaho counties with populations of less than 50,000. Descriptive, bivariate and multivariate analyses were employed to describe and compare scope of practice patterns. Responses were obtained from 92 of 248 physicians (37.1% response rate). Idaho rural family physicians reported providing obstetrical services in the areas of prenatal care (57.6%), vaginal delivery (52.2%) and C-sections (37.0%); other operating room services (43.5%); esophagogastroduodenoscopy (EGD) or colonoscopy services (22.5%); emergency room coverage (48.9%); inpatient admissions (88.9%); mental health services (90.1%); nursing home services (88.0%); and supervision to midlevel care providers (72.5%). Bivariate analyses showed differences in scope of practice patterns across gender, age group and employment status. Binomial logistic regression models indicated that younger physicians were roughly 3 times more likely to provide prenatal care and perform vaginal deliveries than older physicians in rural areas. Idaho practicing rural family physicians report a broad scope of practice. Younger, employed and female rural family medicine physicians are important subgroups for further study.

University Students' Knowledge Structures and Informal Reasoning on the Use of Genetically Modified Foods: Multidimensional Analyses

NASA Astrophysics Data System (ADS)

Wu, Ying-Tien

2013-10-01

This study aims to provide insights into the role of learners' knowledge structures about a socio-scientific issue (SSI) in their informal reasoning on the issue. A total of 42 non-science major university students' knowledge structures and informal reasoning were assessed with multidimensional analyses. With both qualitative and quantitative analyses, this study revealed that those students with more extended and better-organized knowledge structures, as well as those who more frequently used higher-order information processing modes, were more oriented towards achieving a higher-level informal reasoning quality. The regression analyses further showed that the "richness" of the students' knowledge structures explained 25 % of the variation in their rebuttal construction, an important indicator of reasoning quality, indicating the significance of the role of students' sophisticated knowledge structure in SSI reasoning. Besides, this study also provides some initial evidence for the significant role of the "core" concept within one's knowledge structure in one's SSI reasoning. The findings in this study suggest that, in SSI-based instruction, science instructors should try to identify students' core concepts within their prior knowledge regarding the SSI, and then they should try to guide students to construct and structure relevant concepts or ideas regarding the SSI based on their core concepts. Thus, students could obtain extended and well-organized knowledge structures, which would then help them achieve better learning transfer in dealing with SSIs.

Analyses of pig genomes provide insight into porcine demography and evolution

PubMed Central

Groenen, Martien A. M.; Archibald, Alan L.; Uenishi, Hirohide; Tuggle, Christopher K.; Takeuchi, Yasuhiro; Rothschild, Max F.; Rogel-Gaillard, Claire; Park, Chankyu; Milan, Denis; Megens, Hendrik-Jan; Li, Shengting; Larkin, Denis M.; Kim, Heebal; Frantz, Laurent A. F.; Caccamo, Mario; Ahn, Hyeonju; Aken, Bronwen L.; Anselmo, Anna; Anthon, Christian; Auvil, Loretta; Badaoui, Bouabid; Beattie, Craig W.; Bendixen, Christian; Berman, Daniel; Blecha, Frank; Blomberg, Jonas; Bolund, Lars; Bosse, Mirte; Botti, Sara; Bujie, Zhan; Bystrom, Megan; Capitanu, Boris; Silva, Denise Carvalho; Chardon, Patrick; Chen, Celine; Cheng, Ryan; Choi, Sang-Haeng; Chow, William; Clark, Richard C.; Clee, Christopher; Crooijmans, Richard P. M. A.; Dawson, Harry D.; Dehais, Patrice; De Sapio, Fioravante; Dibbits, Bert; Drou, Nizar; Du, Zhi-Qiang; Eversole, Kellye; Fadista, João; Fairley, Susan; Faraut, Thomas; Faulkner, Geoffrey J.; Fowler, Katie E.; Fredholm, Merete; Fritz, Eric; Gilbert, James G. R.; Giuffra, Elisabetta; Gorodkin, Jan; Griffin, Darren K.; Harrow, Jennifer L.; Hayward, Alexander; Howe, Kerstin; Hu, Zhi-Liang; Humphray, Sean J.; Hunt, Toby; Hornshøj, Henrik; Jeon, Jin-Tae; Jern, Patric; Jones, Matthew; Jurka, Jerzy; Kanamori, Hiroyuki; Kapetanovic, Ronan; Kim, Jaebum; Kim, Jae-Hwan; Kim, Kyu-Won; Kim, Tae-Hun; Larson, Greger; Lee, Kyooyeol; Lee, Kyung-Tai; Leggett, Richard; Lewin, Harris A.; Li, Yingrui; Liu, Wansheng; Loveland, Jane E.; Lu, Yao; Lunney, Joan K.; Ma, Jian; Madsen, Ole; Mann, Katherine; Matthews, Lucy; McLaren, Stuart; Morozumi, Takeya; Murtaugh, Michael P.; Narayan, Jitendra; Nguyen, Dinh Truong; Ni, Peixiang; Oh, Song-Jung; Onteru, Suneel; Panitz, Frank; Park, Eung-Woo; Park, Hong-Seog; Pascal, Geraldine; Paudel, Yogesh; Perez-Enciso, Miguel; Ramirez-Gonzalez, Ricardo; Reecy, James M.; Zas, Sandra Rodriguez; Rohrer, Gary A.; Rund, Lauretta; Sang, Yongming; Schachtschneider, Kyle; Schraiber, Joshua G.; Schwartz, John; Scobie, Linda; Scott, Carol; Searle, Stephen; Servin, Bertrand; Southey, Bruce R.; Sperber, Goran; Stadler, Peter; Sweedler, Jonathan V.; Tafer, Hakim; Thomsen, Bo; Wali, Rashmi; Wang, Jian; Wang, Jun; White, Simon; Xu, Xun; Yerle, Martine; Zhang, Guojie; Zhang, Jianguo; Zhang, Jie; Zhao, Shuhong; Rogers, Jane; Churcher, Carol; Schook, Lawrence B.

2013-01-01

For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. PMID:23151582

Diet of bottlenose dolphins (Tursiops truncatus) from the Gulf of Cadiz: Insights from stomach content and stable isotope analyses.

PubMed

Giménez, Joan; Marçalo, Ana; Ramírez, Francisco; Verborgh, Philippe; Gauffier, Pauline; Esteban, Ruth; Nicolau, Lídia; González-Ortegón, Enrique; Baldó, Francisco; Vilas, César; Vingada, José; G Forero, Manuela; de Stephanis, Renaud

2017-01-01

The ecological role of species can vary among populations depending on local and regional differences in diet. This is particularly true for top predators such as the bottlenose dolphin (Tursiops truncatus), which exhibits a highly varied diet throughout its distribution range. Local dietary assessments are therefore critical to fully understand the role of this species within marine ecosystems, as well as its interaction with important ecosystem services such as fisheries. Here, we combined stomach content analyses (SCA) and stable isotope analyses (SIA) to describe bottlenose dolphins diet in the Gulf of Cadiz (North Atlantic Ocean). Prey items identified using SCA included European conger (Conger conger) and European hake (Merluccius merluccius) as the most important ingested prey. However, mass-balance isotopic mixing model (MixSIAR), using δ13C and δ15N, indicated that the assimilated diet consisted mainly on Sparidae species (e.g. seabream, Diplodus annularis and D. bellottii, rubberlip grunt, Plectorhinchus mediterraneus, and common pandora, Pagellus erythrinus) and a mixture of other species including European hake, mackerels (Scomber colias, S. japonicus and S. scombrus), European conger, red bandfish (Cepola macrophthalma) and European pilchard (Sardina pilchardus). These contrasting results highlight differences in the temporal and taxonomic resolution of each approach, but also point to potential differences between ingested (SCA) and assimilated (SIA) diets. Both approaches provide different insights, e.g. determination of consumed fish biomass for the management of fish stocks (SCA) or identification of important assimilated prey species to the consumer (SIA).

Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L.).

PubMed

Turktas, Mine; Inal, Behcet; Okay, Sezer; Erkilic, Emine Gulden; Dundar, Ekrem; Hernandez, Pilar; Dorado, Gabriel; Unver, Turgay

2013-01-01

The olive tree (Olea europaea L.) is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between "on year" and "off year" leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree.

Nutrition Metabolism Plays an Important Role in the Alternate Bearing of the Olive Tree (Olea europaea L.)

PubMed Central

Turktas, Mine; Inal, Behcet; Okay, Sezer; Erkilic, Emine Gulden; Dundar, Ekrem; Hernandez, Pilar; Dorado, Gabriel; Unver, Turgay

2013-01-01

The olive tree (Olea europaea L.) is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between ”on year” and “off year” leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree. PMID:23555820

Arboreality, terrestriality and bipedalism

PubMed Central

Crompton, Robin Huw; Sellers, William I.; Thorpe, Susannah K. S.

2010-01-01

The full publication of Ardipithecus ramidus has particular importance for the origins of hominin bipedality, and strengthens the growing case for an arboreal origin. Palaeontological techniques however inevitably concentrate on details of fragmentary postcranial bones and can benefit from a whole-animal perspective. This can be provided by field studies of locomotor behaviour, which provide a real-world perspective of adaptive context, against which conclusions drawn from palaeontology and comparative osteology may be assessed and honed. Increasingly sophisticated dynamic modelling techniques, validated against experimental data for living animals, offer a different perspective where evolutionary and virtual ablation experiments, impossible for living mammals, may be run in silico, and these can analyse not only the interactions and behaviour of rigid segments but increasingly the effects of compliance, which are of crucial importance in guiding the evolution of an arboreally derived lineage. PMID:20855304

The matching law: a tutorial for practitioners.

PubMed

Reed, Derek D; Kaplan, Brent A

2011-01-01

The application of the matching law has historically been limited to use as a quantitative measurement tool in the experimental analysis of behavior to describe temporally extended patterns of behavior-environment relations. In recent years, however, applications of the matching law have been translated to clinical settings and populations to gain a better understanding of how naturally-occurring events affect socially important behaviors. This tutorial provides a brief background of the conceptual foundations of matching, an overview of the various matching equations that have been used in research, and a description of how to interpret the data derived from these equations in the context of numerous examples of matching analyses conducted with socially important behavior. An appendix of resources is provided to direct readers to primary sources, as well as useful articles and books on the topic.

The Matching Law: A Tutorial for Practitioners

PubMed Central

Kaplan, Brent A

2011-01-01

The application of the matching law has historically been limited to use as a quantitative measurement tool in the experimental analysis of behavior to describe temporally extended patterns of behavior-environment relations. In recent years, however, applications of the matching law have been translated to clinical settings and populations to gain a better understanding of how naturally-occurring events affect socially important behaviors. This tutorial provides a brief background of the conceptual foundations of matching, an overview of the various matching equations that have been used in research, and a description of how to interpret the data derived from these equations in the context of numerous examples of matching analyses conducted with socially important behavior. An appendix of resources is provided to direct readers to primary sources, as well as useful articles and books on the topic. PMID:22649575

Practical Approaches for Detecting Selection in Microbial Genomes.

PubMed

Hedge, Jessica; Wilson, Daniel J

2016-02-01

Microbial genome evolution is shaped by a variety of selective pressures. Understanding how these processes occur can help to address important problems in microbiology by explaining observed differences in phenotypes, including virulence and resistance to antibiotics. Greater access to whole-genome sequencing provides microbiologists with the opportunity to perform large-scale analyses of selection in novel settings, such as within individual hosts. This tutorial aims to guide researchers through the fundamentals underpinning popular methods for measuring selection in pathogens. These methods are transferable to a wide variety of organisms, and the exercises provided are designed for researchers with any level of programming experience.

Evidence-based practice.

PubMed Central

McKibbon, K A

1998-01-01

Evidence-based practice (EBP) is spreading in popularity in many health care disciplines. One of its main features is the reliance on the partnership among hard scientific evidence, clinical expertise, and individual patient needs and choices. Librarians play an important role in the spread of EBP because of the importance of identifying and retrieving appropriate literature from various sources for use in making health care decisions. This article gives an overview of how to search for therapy, diagnosis, etiology, and prognosis both for original studies and secondary publications such as systematic reviews, meta-analyses, and clinical practice guidelines. Understanding how this research is done, how it is indexed, and how to retrieve the clinical evidence are an important set of skills that librarians can provide for clinicians interested in EBP. PMID:9681176

European policymaking on the tobacco advertising ban: the importance of escape routes.

PubMed

Adamini, Sandra; Versluis, Esther; Maarse, Hans

2011-01-01

This article analyses the European Union policymaking process regarding tobacco advertising. While others already highlighted the importance of intergovernmental bargaining between member states to explain the outcome of the tobacco advertising case, the main aim of this article is to identify the use of escape routes by the Commission, the European Parliament, the Council and interest groups that played an important role in overcoming the deadlock. When looking at the different institutions that structure policymaking, we argue that indeed focusing on escape routes provides a clear insight in the process and in what strategies were necessary to 'make Europe work'. In the end, it appears to be a combination of escape routes that resulted in the final decision.

Data collection of patient outcomes: one institution's experience.

PubMed

Whitaker, Thomas J; Mayo, Charles S; Ma, Daniel J; Haddock, Michael G; Miller, Robert C; Corbin, Kimberly S; Neben-Wittich, Michelle; Leenstra, James L; Laack, Nadia N; Fatyga, Mirek; Schild, Steven E; Vargas, Carlos E; Tzou, Katherine S; Hadley, Austin R; Buskirk, Steven J; Foote, Robert L

2018-03-01

Patient- and provider-reported outcomes are recognized as important in evaluating quality of care, guiding health care policy, comparative effectiveness research, and decision-making in radiation oncology. Combining patient and provider outcome data with a detailed description of disease and therapy is the basis for these analyses. We report on the combination of technical solutions and clinical process changes at our institution that were used in the collection and dissemination of this data. This initiative has resulted in the collection of treatment data for 23 541 patients, 20 465 patients with provider-based adverse event records, and patient-reported outcome surveys submitted by 5622 patients. All of the data is made accessible using a self-service web-based tool.

Blue Growth: the 2014 FAO State of the World Fisheries and Aquaculture

USGS Publications Warehouse

Moffitt, Christine M.; Cajas-Cano, Lubia

2014-01-01

The latest United Nations Food and Agriculture Organization report (FAO 2014) addresses the prospect of feeding a human population set to rise to 9.6 billion by 2050. Aquaculture products now provide approximately one-half of all food fish consumed, and fish also provide important food security and economic growth. In the FAO analyses, food fish included finfish, crustaceans, mollusks, amphibians, freshwater turtles, and other aquatic animals (such as sea cucumbers, sea urchins, sea squirts, and edible jellyfish) produced for human consumption. At the present time, food fish provides the world population of nearly 7.3 billion people with an average of one-fifth of total animal protein intake.

Environmental effects of interstate power trading on electricity consumption mixes.

PubMed

Marriott, Joe; Matthews, H Scott

2005-11-15

Although many studies of electricity generation use national or state average generation mix assumptions, in reality a great deal of electricity is transferred between states with very different mixes of fossil and renewable fuels, and using the average numbers could result in incorrect conclusions in these studies. We create electricity consumption profiles for each state and for key industry sectors in the U.S. based on existing state generation profiles, net state power imports, industry presence by state, and an optimization model to estimate interstate electricity trading. Using these "consumption mixes" can provide a more accurate assessment of electricity use in life-cycle analyses. We conclude that the published generation mixes for states that import power are misleading, since the power consumed in-state has a different makeup than the power that was generated. And, while most industry sectors have consumption mixes similar to the U.S. average, some of the most critical sectors of the economy--such as resource extraction and material processing sectors--are very different. This result does validate the average mix assumption made in many environmental assessments, but it is important to accurately quantify the generation methods for electricity used when doing life-cycle analyses.

Bumble bee colony dynamics: quantifying the importance of land use and floral resources for colony growth and queen production.

PubMed

Crone, Elizabeth E; Williams, Neal M

2016-04-01

Bumble bee (Bombus) species are ecologically and economically important pollinators, and many species are in decline. In this article, we develop a mechanistic model to analyse growth trajectories of Bombus vosnesenskii colonies in relation to floral resources and land use. Queen production increased with floral resources and was higher in semi-natural areas than on conventional farms. However, the most important parameter for queen production was the colony growth rate per flower, as opposed to the average number of available flowers. This result indicates the importance of understanding mechanisms of colony growth, in order to predict queen production and enhance bumble bee population viability. Our work highlights the importance of interpreting bumble bee conservation efforts in the context of overall population dynamics and provides a framework for doing so. © 2016 John Wiley & Sons Ltd/CNRS.

Review of LCA studies of solid waste management systems – Part II: Methodological guidance for a better practice

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

Laurent, Alexis, E-mail: alau@dtu.dk; Clavreul, Julie; Bernstad, Anna

Highlights: • We perform a critical review of 222 LCA studies of solid waste management systems. • We analyse the past LCA practice against the ISO standard and ILCD Handbook guidance. • Malpractices exist in many methodological aspects with large variations among studies. • Many of these aspects are important for the reliability of the results. • We provide detailed recommendations to practitioners of waste management LCAs. - Abstract: Life cycle assessment (LCA) is increasingly used in waste management to identify strategies that prevent or minimise negative impacts on ecosystems, human health or natural resources. However, the quality of themore » provided support to decision- and policy-makers is strongly dependent on a proper conduct of the LCA. How has LCA been applied until now? Are there any inconsistencies in the past practice? To answer these questions, we draw on a critical review of 222 published LCA studies of solid waste management systems. We analyse the past practice against the ISO standard requirements and the ILCD Handbook guidelines for each major step within the goal definition, scope definition, inventory analysis, impact assessment, and interpretation phases of the methodology. Results show that malpractices exist in several aspects of the LCA with large differences across studies. Examples are a frequent neglect of the goal definition, a frequent lack of transparency and precision in the definition of the scope of the study, e.g. an unclear delimitation of the system boundaries, a truncated impact coverage, difficulties in capturing influential local specificities such as representative waste compositions into the inventory, and a frequent lack of essential sensitivity and uncertainty analyses. Many of these aspects are important for the reliability of the results. For each of them, we therefore provide detailed recommendations to practitioners of waste management LCAs.« less

'This is my story, how I remember it': In-depth analysis of Dignity Therapy documents from a study of Dignity Therapy for people with early stage dementia.

PubMed

Johnston, Bridget; Lawton, Sally; Pringle, Jan

2017-07-01

Dementia is a progressive condition that impacts on individuals, families and care professionals. Maintaining quality of life through engagement with the person with dementia is an important part of their care. Dignity Therapy is an interactive, psychotherapeutic intervention that uses a trained dignity therapist to guide the person with dementia through an interview that then creates a written legacy called a generativity document. This can provide knowledge to inform care, as the condition progresses. Generativity documents were analysed using framework analysis. Main themes from the analysis were origin of values, essence and affirmation of self, forgiveness and resolution and existentialism/ meaning of life. These themes provide evidence of the type, scope and contribution that information generated from Dignity Therapy can make to the care and support of people with dementia. They provide information about the values, self-identity and the people and events that have been important to them and influenced their lives.

How to interpret a healthcare economic analysis.

PubMed

Brown, Melissa M; Brown, Gary C

2005-06-01

The purpose of the review is to present guidelines to help the clinician to interpret healthcare economic analyses and review pertinent recent analysis in the ophthalmic literature. There are four variants of healthcare economic analyses: (1) cost-minimization analysis; (2) cost-benefit analysis; (3) cost-effectiveness analysis and (4) cost-utility analysis. Cost-utility utility analysis has assumed an increasingly important role in healthcare, with increasing number of analyses occurring in the peer-reviewed ophthalmic literature. These include cost-utility analyses of cataract surgery in the first and second eyes, amblyopia treatment, and cost-utility analyses encompassing the vitreoretinal interventions of the following: (1) laser photocoagulation for exudative macular degeneration; (2) laser treatment for diabetic retinopathy; (3) laser photocoagulation for branch retinal vein obstruction; (4) diabetic vitrectomy; (5) treatment of proliferative retinopathy of prematurity and (6) treatment of retinal detachment associated with proliferative vitreoretinopathy. As an increasing number of cost-utility analyses become available they will provide the information system for the practice of value-based medicine, or medicine based upon the patient-perceived value conferred by interventions. Increasing numbers of cost-utility analysis in the ophthalmic literature suggest that ophthalmic interventions, including vitreoretinal interventions, are cost effective. Cost-utility analysis is a major tool in value-based medicine, the practice of medicine based upon the patient-perceived value conferred by healthcare interventions.

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.

GIS analysis of the siting criteria for the Mixed and Low-Level Waste Treatment Facility and the Idaho Waste Processing Facility

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

Hoskinson, R.L.

1994-01-01

This report summarizes a study conducted using the Arc/Info{reg_sign} geographic information system (GIS) to analyze the criteria used for site selection for the Mixed and Low-Level Waste Treatment Facility (MLLWTF) and the Idaho Waste Processing Facility (IWPF). The purpose of the analyses was to determine, based on predefined criteria, the areas on the INEL that best satisfied the criteria. The coverages used in this study were produced by importing the AutoCAD files that produced the maps for a pre site selection draft report into the GIS. The files were then converted to Arc/Info{reg_sign} GIS format. The initial analysis was mademore » by considering all of the criteria as having equal importance in determining the areas of the INEL that would best satisfy the requirements. Another analysis emphasized four of the criteria as ``must`` criteria which had to be satisfied. Additional analyses considered other criteria that were considered for, but not included in the predefined criteria. This GIS analysis of the siting criteria for the IWPF and MLLWTF provides a logical, repeatable, and defensible approach to the determination of candidate locations for the facilities. The results of the analyses support the location of the Candidate Locations.« less

Samples from Martian craters: Origin of the Martian soil by hydrothermal alteration of impact melt deposits and atmospheric interactions with ejecta during crater formation

NASA Technical Reports Server (NTRS)

Newsom, Horton E.

1988-01-01

The origin of the Martian soil is an important question for understanding weathering processes on the Martian surface, and also for understanding the global geochemistry of Mars. Chemical analyses of the soil will provide an opportunity to examine what may be a crustal average, as studies of loess on the Earth have demonstrated. In this regard the origin of the Martian soil is also important for understanding the chemical fractionations that have affected the composition of the soil. Several processes that are likely to contribute to the Martian soil are examined.

Approximate bandpass and frequency response models of the difference of Gaussian filter

NASA Astrophysics Data System (ADS)

Birch, Philip; Mitra, Bhargav; Bangalore, Nagachetan M.; Rehman, Saad; Young, Rupert; Chatwin, Chris

2010-12-01

The Difference of Gaussian (DOG) filter is widely used in optics and image processing as, among other things, an edge detection and correlation filter. It has important biological applications and appears to be part of the mammalian vision system. In this paper we analyse the filter and provide details of the full width half maximum, bandwidth and frequency response in order to aid the full characterisation of its performance.

The importance of social identities in the management of and recovery from 'Diabulimia': A qualitative exploration.

PubMed

Hastings, Amy; McNamara, Niamh; Allan, Jacqueline; Marriott, Mike

2016-12-01

A significant barrier to recovery for individuals with co-morbid eating disorders and type 1 diabetes is the way in which group members self-categorise. Nonetheless, identity issues are neglected during the recovery process. The aim of this paper is to explore how group memberships (and the associated identities) both contribute to and hinder recovery in this cohort. Transcripts from five online focus groups with 13 members of an online support group for individuals with 'Diabulimia' were thematically analysed. Findings suggested that those with whom one shares a recovery identity can be well placed to provide psychological resources necessary for successful recovery although such connections can be damaging if group norms are not managed. Members recognised that other important relationships (including family and friends and health professionals) are also key to recovery; these other group memberships (and the associated identities) can be facilitated through the recovery identity group membership, which allows for external validation of the recovery identity, provides encouragement to disclose the illness to supportive others, and provides information to facilitate positive service interactions. While clinical interventions typically focus on eliminating disordered behaviours, we suggest that these should also include strengthening important group memberships that promote recovery.

Lesbian and bisexual health care.

PubMed Central

Mathieson, C. M.

1998-01-01

OBJECTIVE: To explore lesbian and bisexual women's experiences with their family physicians to learn about barriers to care and about how physicians can provide supportive care. DESIGN: Qualitative study that was part of a larger study of lesbian and bisexual women's health care. SETTING: The province of Nova Scotia, both urban and rural counties. PARTICIPANTS: Ninety-eight self-identified lesbian or bisexual women who volunteered through snowball sampling. Women were interviewed by lesbian, bisexual, or heterosexual female interviewers. METHOD: Semistructured, audiotaped, face-to-face interviews, exploring questions about demographic information, sexual orientation, general health care patterns, preferences for health care providers, disclosure issues, health care information, access issues, and important health care services. Transcription of audiotapes of interviews was followed by content, thematic, and discourse analyses. Thematic analysis is reported in this paper. MAIN OUTCOME FINDINGS: Three themes important for family physicians emerged: the importance of being gay positive, barriers to care, and strategies for providing appropriate care. CONCLUSIONS: Family physicians are in a pivotal position to ensure supportive care for lesbian and bisexual women. Physicians need to recognize barriers to care and to use gay-positive strategies, paying attention to self-education, health history, and clinic environment. PMID:9721419

The Influence of Parental Communication and Perception of Peers on Adolescent Sexual Behavior.

PubMed

Sneed, Carl D; Tan, Huey Peing; Meyer, Jacob C

2015-08-01

The authors used the theory of planned behavior to examine the influence of parents and peers on early adolescent sexual attitudes, self-efficacy to limit sexual behavior, and behavioral intentions to have vaginal intercourse. Adolescents (N = 212) provided self-reports of their perception of parent and peer attitudes regarding sexual behavior. The authors used bivariate and regression analyses to examine the relation between parent and peer attitudes with adolescent sexual attitudes, self-efficacy to limit sexual behavior, and behavioral intentions to have vaginal intercourse. Although there were gender differences, the analyses revealed the importance of both parents and peers on adolescent sexual attitudes, self-efficacy to limit sexual behavior, and intentions to have vaginal sex in the next year.

The conscientious retiree: The relationship between conscientiousness, retirement, and volunteering

PubMed Central

Mike, Anissa; Jackson, Joshua J.; Oltmanns, Thomas F.

2015-01-01

The current study examined the relationship between conscientiousness, work status, and volunteering utilizing two large samples, the St. Louis Personality and Aging Network (SPAN) and the Health and Retirement Study (HRS). It was hypothesized that conscientious adults who were retired would be more likely to volunteer because, after retirement, they gain a substantial amount of free time, while losing an outlet for their industrious and achievement-striving tendencies. Cross-sectional and longitudinal analyses revealed that conscientious, retired individuals were more likely to volunteer than conscientious, working individuals. Further analyses revealed that facets of conscientiousness provide differential information from the general trait. These findings indicate that volunteering during retirement fills an important niche for high-striving, conscientious individuals. PMID:25843985

Traffic crash involvement: experiential driving knowledge and stressful contextual antecedents.

PubMed

Legree, Peter J; Heffner, Tonia S; Psotka, Joseph; Martin, Daniel E; Medsker, Gina J

2003-02-01

Researchers have rarely examined stressful environments and psychological characteristics as predictors of driving behavior in the same study. The authors hypothesized that (a) safer drivers more accurately assess physical and emotional traffic hazards and (b) stress and emotional states elevate crash risk. The hypotheses were evaluated with procedural and declarative tacit driving knowledge tests requiring assessment of emotional and contextual hazards and with accident reports describing crash antecedents, including stressful events and environmental conditions. Analyses identified separate driving knowledge factors corresponding to emotional and contextual hazards that were significantly related to the crash criteria. Accident report analyses show that stress significantly elevates at-fault crash risk. The results demonstrate the importance of experiential knowledge acquired without instruction (procedural or tacit knowledge) and provide safety recommendations.

Isolation of Chromoplasts and Suborganellar Compartments from Tomato and Bell Pepper Fruit.

PubMed

Barsan, Cristina; Kuntz, Marcel; Pech, Jean-Claude

2017-01-01

Tomato is a model for fruit development and ripening. The isolation of intact plastids from this organism is therefore important for metabolic and proteomic analyses. Pepper, a species from the same family, is also of interest since it allows isolation of intact chromoplasts in large amounts. Here, we provide a detailed protocol for the isolation of tomato plastids at three fruit developmental stages, namely, nascent chromoplasts from the mature green stage, chromoplasts from an intermediate stage, and fully differentiated red chromoplasts. The method relies on sucrose density gradient centrifugations. It yields high purity organelles suitable for proteome analyses. Enzymatic and microscopy assays are summarized to assess purity and intactness. A method is also described for subfractionation of pepper chromoplast lipoprotein structures.

Comparative analysis of package inserts of local and imported antihypertensive medications in Palestine.

PubMed

Qatmosh, Sandra A; Koni, Amer A; Qeeno, Baraa G; Arandy, Dina A; Abu-Hashia, Maysa W; Al-Hroub, Bahaa M; Zyoud, Sa'ed H

2017-09-25

Package inserts (PIs) as a reliable reference for patients and health care providers should provide accurate, complete and up-to-date information. The purpose of the current study is to assess and compare the PIs of antihypertensive agents locally produced in Palestine and their imported counterparts. Thirty-five PIs were assessed for the presence of 31 information statements using a scoring method. Word counting of 20 headings and subheadings was used to evaluate and compare local and imported PIs for information quantity. None of the analysed PIs fulfilled the criteria. All of them included the brand name, active ingredients, indications, directions for use, adverse drug reactions, drug-drug interactions, pregnancy and lactation considerations, and storage. Whereas none of them, either local or imported PIs, included the shelf life and instructions to convert tablets or capsules into liquid forms. Additionally, only one (5%) imported and no (0%) local PIs mentioned the duration of therapy. Moreover, 93.4% of local PIs were deficient in areas regarding the inactive ingredients and date of last revision, and 86.7% did not mention the drug dose and possibility of tablet splitting. Furthermore, the maximum dose was not indicated in 90% of imported and 86.7% of local PIs. In general, imported PIs contained more detailed information than their local counterparts, where the range of differences in medians between the local and imported PIs was from 1.5-fold for pregnancy considerations to >42.00-fold for the effect on the ability to drive and use machines. The findings of this study revealed the superiority of imported over local PIs in both quality and quantity of information provided. This emphasises the need for appropriate measures to be taken by the Ministry of Health and local manufacturers to ensure efficiency of local PIs in providing accurate, complete and up-to-date information.

Winter diets of immature green turtles (Chelonia mydas) on a northern feeding ground: integrating stomach contents and stable isotope analyses

USGS Publications Warehouse

Williams, Natalie C.; Bjorndal, Karen A.; Lamont, Margaret M.; Carthy, Raymond R.

2015-01-01

The foraging ecology and diet of the green turtle, Chelonia mydas, remain understudied, particularly in peripheral areas of its distribution. We assessed the diet of an aggregation of juvenile green turtles at the northern edge of its range during winter months using two approaches. Stomach content analyses provide a single time sample, and stable isotope analyses integrate diet over a several-month period. We evaluated diet consistency in prey choice over time by comparing the results of these two approaches. We examined stomach contents from 43 juvenile green turtles that died during cold stunning events in St. Joseph Bay, Florida, in 2008 and 2011. Stomach contents were evaluated for volume, dry mass, percent frequency of occurrence, and index of relative importance of individual diet items. Juvenile green turtles were omnivorous, feeding primarily on seagrasses and tunicates. Diet characterizations from stomach contents differed from those based on stable isotope analyses, indicating the turtles are not feeding consistently during winter months. Evaluation of diets during warm months is needed.

A novel approach for modelling vegetation distributions and analysing vegetation sensitivity through trait-climate relationships in China

PubMed Central

Yang, Yanzheng; Zhu, Qiuan; Peng, Changhui; Wang, Han; Xue, Wei; Lin, Guanghui; Wen, Zhongming; Chang, Jie; Wang, Meng; Liu, Guobin; Li, Shiqing

2016-01-01

Increasing evidence indicates that current dynamic global vegetation models (DGVMs) have suffered from insufficient realism and are difficult to improve, particularly because they are built on plant functional type (PFT) schemes. Therefore, new approaches, such as plant trait-based methods, are urgently needed to replace PFT schemes when predicting the distribution of vegetation and investigating vegetation sensitivity. As an important direction towards constructing next-generation DGVMs based on plant functional traits, we propose a novel approach for modelling vegetation distributions and analysing vegetation sensitivity through trait-climate relationships in China. The results demonstrated that a Gaussian mixture model (GMM) trained with a LMA-Nmass-LAI data combination yielded an accuracy of 72.82% in simulating vegetation distribution, providing more detailed parameter information regarding community structures and ecosystem functions. The new approach also performed well in analyses of vegetation sensitivity to different climatic scenarios. Although the trait-climate relationship is not the only candidate useful for predicting vegetation distributions and analysing climatic sensitivity, it sheds new light on the development of next-generation trait-based DGVMs. PMID:27052108

Analyses of Digman's child-personality data: derivation of Big-Five factor scores from each of six samples.

PubMed

Goldberg, L R

2001-10-01

One of the world's richest collections of teacher descriptions of elementary-school children was obtained by John M. Digman from 1959 to 1967 in schools on two Hawaiian islands. In six phases of data collection, 88 teachers described 2,572 of their students, using one of five different sets of personality variables. The present report provides findings from new analyses of these important data, which have never before been analyzed in a comprehensive manner. When factors developed from carefully selected markers of the Big-Five factor structure were compared to those based on the total set of variables in each sample, the congruence between both types of factors was quite high. Attempts to extend the structure to 6 and 7 factors revealed no other broad factors beyond the Big Five in any of the 6 samples. These robust findings provide significant new evidence for the structure of teacher-based assessments of child personality attributes.

Holarctic genetic structure and range dynamics in the woolly mammoth

PubMed Central

Palkopoulou, Eleftheria; Dalén, Love; Lister, Adrian M.; Vartanyan, Sergey; Sablin, Mikhail; Sher, Andrei; Edmark, Veronica Nyström; Brandström, Mikael D.; Germonpré, Mietje; Barnes, Ian; Thomas, Jessica A.

2013-01-01

Ancient DNA analyses have provided enhanced resolution of population histories in many Pleistocene taxa. However, most studies are spatially restricted, making inference of species-level biogeographic histories difficult. Here, we analyse mitochondrial DNA (mtDNA) variation in the woolly mammoth from across its Holarctic range to reconstruct its history over the last 200 thousand years (kyr). We identify a previously undocumented major mtDNA lineage in Europe, which was replaced by another major mtDNA lineage 32–34 kyr before present (BP). Coalescent simulations provide support for demographic expansions at approximately 121 kyr BP, suggesting that the previous interglacial was an important driver for demography and intraspecific genetic divergence. Furthermore, our results suggest an expansion into Eurasia from America around 66 kyr BP, coinciding with the first exposure of the Bering Land Bridge during the Late Pleistocene. Bayesian inference indicates Late Pleistocene demographic stability until 20–15 kyr BP, when a severe population size decline occurred. PMID:24026825

Sharing brain mapping statistical results with the neuroimaging data model

PubMed Central

Maumet, Camille; Auer, Tibor; Bowring, Alexander; Chen, Gang; Das, Samir; Flandin, Guillaume; Ghosh, Satrajit; Glatard, Tristan; Gorgolewski, Krzysztof J.; Helmer, Karl G.; Jenkinson, Mark; Keator, David B.; Nichols, B. Nolan; Poline, Jean-Baptiste; Reynolds, Richard; Sochat, Vanessa; Turner, Jessica; Nichols, Thomas E.

2016-01-01

Only a tiny fraction of the data and metadata produced by an fMRI study is finally conveyed to the community. This lack of transparency not only hinders the reproducibility of neuroimaging results but also impairs future meta-analyses. In this work we introduce NIDM-Results, a format specification providing a machine-readable description of neuroimaging statistical results along with key image data summarising the experiment. NIDM-Results provides a unified representation of mass univariate analyses including a level of detail consistent with available best practices. This standardized representation allows authors to relay methods and results in a platform-independent regularized format that is not tied to a particular neuroimaging software package. Tools are available to export NIDM-Result graphs and associated files from the widely used SPM and FSL software packages, and the NeuroVault repository can import NIDM-Results archives. The specification is publically available at: http://nidm.nidash.org/specs/nidm-results.html. PMID:27922621

Clinic Workload, the Quality of Staff Relationships and Diabetes Management in Community Health Centers Catering to Latino and Chinese Patients.

PubMed

Vargas Bustamante, Arturo; Martinez, Ana; Chen, Xiao; Rodriguez, Hector P

2017-06-01

We examine whether workplace climate-quality of staff relationships (QSR) and manageable clinic workload (MCW) are related to better patient care experiences and diabetes care in community health centers (CHCs) catering to Latino and Chinese patients. Patient experience surveys of adult patients with type 2 diabetes and workplace climate surveys of clinicians and staff from CHCs were included in an analytic sample. Comparisons of means analyses examine patient and provider characteristics. The associations of QSR, MCW and the diabetes care management were examined using regression analyses. Diabetes care process were more consistently provided in CHCs with high quality staff relations and more manageable clinic workload, but HbA1c, LDL cholesterol, and blood pressure outcomes were no different between clinics with high vs. low QSR and MCW. Focusing efforts on improvements in practice climate may lead to more consistent provision of important processes of diabetes care for these patients.

Analyses of historical and projected climates to support climate adaptation in the northern Rocky Mountains: Chapter 4

USGS Publications Warehouse

Gross, John E.; Tercek, Michael; Guay, Kevin; Chang, Tony; Talbert, Marian; Rodman, Ann; Thoma, David; Jantz, Patrick; Morisette, Jeffrey T.

2016-01-01

Most of the western United States is experiencing the effects of rapid and directional climate change (Garfin et al. 2013). These effects, along with forecasts of profound changes in the future, provide strong motivation for resource managers to learn about and prepare for future changes. Climate adaptation plans are based on an understanding of historic climate variation and their effects on ecosystems and on forecasts of future climate trends. Frameworks for climate adaptation thus universally identify the importance of a summary of historical, current, and projected climates (Glick, Stein, and Edelson 2011; Cross et al. 2013; Stein et al. 2014). Trends in physical climate variables are usually the basis for evaluating the exposure component in vulnerability assessments. Thus, this chapter focuses on step 2 of the Climate-Smart Conservation framework (chap. 2): vulnerability assessment. We present analyses of historical and current observations of temperature, precipitation, and other key climate measurements to provide context and a baseline for interpreting the ecological impacts of projected climate changes.

'Of course we are on Facebook': Use and non-use of social media among Swedish and Norwegian politicians.

PubMed

Larsson, Anders O; Kalsnes, Bente

2014-12-01

While plenty of research has provided important insights into the uses of the Internet by politicians during elections, a relatively scarce amount of work has looked into these uses outside of such parliamentary events. This article seeks to remedy this lack of research by presenting a study on the 'routine' uses of two of the currently most popular social media services - Facebook and Twitter. Focusing on politicians elected to the national parliaments of Norway and Sweden, the article employs novel methodologies for data collection and statistical analyses in order to provide an overarching, structural view of the day-to-day social media practices of Scandinavian politicians. Findings indicate that use levels are rather low for both services - the median amount of tweets sent and messages posted on Facebook is close to one per day. Further analyses reveal that the most active politicians could be labelled as 'underdogs', as they are more likely to be younger, in opposition and out of the political limelight.

Methods for Evaluating Practice Change Toward a Patient-Centered Medical Home

PubMed Central

Jaén, Carlos Roberto; Crabtree, Benjamin F.; Palmer, Raymond F.; Ferrer, Robert L.; Nutting, Paul A.; Miller, William L.; Stewart, Elizabeth E.; Wood, Robert; Davila, Marivel; Stange, Kurt C.

2010-01-01

PURPOSE Understanding the transformation of primary care practices to patient-centered medical homes (PCMHs) requires making sense of the change process, multilevel outcomes, and context. We describe the methods used to evaluate the country’s first national demonstration project of the PCMH concept, with an emphasis on the quantitative measures and lessons for multimethod evaluation approaches. METHODS The National Demonstration Project (NDP) was a group-randomized clinical trial of facilitated and self-directed implementation strategies for the PCMH. An independent evaluation team developed an integrated package of quantitative and qualitative methods to evaluate the process and outcomes of the NDP for practices and patients. Data were collected by an ethnographic analyst and a research nurse who visited each practice, and from multiple data sources including a medical record audit, patient and staff surveys, direct observation, interviews, and text review. Analyses aimed to provide real-time feedback to the NDP implementation team and lessons that would be transferable to the larger practice, policy, education, and research communities. RESULTS Real-time analyses and feedback appeared to be helpful to the facilitators. Medical record audits provided data on process-of-care outcomes. Patient surveys contributed important information about patient-rated primary care attributes and patient-centered outcomes. Clinician and staff surveys provided important practice experience and organizational data. Ethnographic observations supplied insights about the process of practice development. Most practices were not able to provide detailed financial information. CONCLUSIONS A multimethod approach is challenging, but feasible and vital to understanding the process and outcome of a practice development process. Additional longitudinal follow-up of NDP practices and their patients is needed. PMID:20530398

Guidance for deriving and presenting percentage study weights in meta-analysis of test accuracy studies.

PubMed

Burke, Danielle L; Ensor, Joie; Snell, Kym I E; van der Windt, Danielle; Riley, Richard D

2018-06-01

Percentage study weights in meta-analysis reveal the contribution of each study toward the overall summary results and are especially important when some studies are considered outliers or at high risk of bias. In meta-analyses of test accuracy reviews, such as a bivariate meta-analysis of sensitivity and specificity, the percentage study weights are not currently derived. Rather, the focus is on representing the precision of study estimates on receiver operating characteristic plots by scaling the points relative to the study sample size or to their standard error. In this article, we recommend that researchers should also provide the percentage study weights directly, and we propose a method to derive them based on a decomposition of Fisher information matrix. This method also generalises to a bivariate meta-regression so that percentage study weights can also be derived for estimates of study-level modifiers of test accuracy. Application is made to two meta-analyses examining test accuracy: one of ear temperature for diagnosis of fever in children and the other of positron emission tomography for diagnosis of Alzheimer's disease. These highlight that the percentage study weights provide important information that is otherwise hidden if the presentation only focuses on precision based on sample size or standard errors. Software code is provided for Stata, and we suggest that our proposed percentage weights should be routinely added on forest and receiver operating characteristic plots for sensitivity and specificity, to provide transparency of the contribution of each study toward the results. This has implications for the PRISMA-diagnostic test accuracy guidelines that are currently being produced. Copyright © 2017 John Wiley & Sons, Ltd.

Cognitive Neuropsychology Has Been, Is, And Will Be Significant To Aphasiology

PubMed Central

Laine, Matti; Martin, Nadine

2012-01-01

Background In recent years, some critical voices have been raised in regard to the significance of cognitive neuropsychology (CNP) to the study of brain and mind. Given the central role of language disorders in CNP research, it is time to consider the relevance of this research approach in aphasiology. Aims We analyze the main points of criticism raised against the CNP research approach, evaluate the significance of this approach to the study of acquired language disorders, and make some suggestions concerning further development of the field. Main Contribution The main points of criticism against CNP (reliance on single-case studies; single-minded hunt for dissociations; emptiness of theorizing) have been important long-term concerns but do not take into account the fact that during its history of circa four decades, the CNP approach has diversified. There are thus CNP studies that rely on case series analyses, focus on error analyses rather than mere dissociations, or employ computational modeling rather than the “boxes-and-arrows” models of the mental architecture. The CNP approach to cognition and its disorders is thus applicable to different research questions and theoretical stances, providing experimental rigor to single-case patient studies. With regard to clinical applications in aphasia diagnostics and treatment, the CNP approach provides a richer view on the strengths and weaknesses of a patient’s cognitive-linguistic abilities. Conclusions We believe that CNP case studies continue to be an important source of information for generating hypotheses and providing converging evidence for research on the mind and on the brain. There is however a need for further research development especially in computational modeling of language processes, their impairments, and recovery. This research is expected to provide further benefit to clinical diagnostics and treatment of aphasia. PMID:23280004

Health care use amongst online buyers of medications and vitamins.

PubMed

Desai, Karishma; Chewning, Betty; Mott, David

2015-01-01

With increased use of the internet, more people access medications and health supplements online. However little is known about factors associated with using online buying. Given the variable quality of online pharmacies, an important question is whether online consumers also have health care providers with whom they discuss internet information and decisions. To help address these gaps this study used the Andersen Model to explore (1) the characteristics of internet buyers of medicines and/vitamins, (2) the association between health care use and buying medicines and/vitamins online drawing on the Andersen health care utilization framework, and (3) factors predicting discussion of internet information with health providers. The National Cancer Institute's Health Information National Trends Survey (HINTS) 2007 was analyzed to study online medication buying among a national sample of internet users (N = 5074). The Andersen Model of health care utilization guided the study's variable selection and analyses. Buying online and talking about online information are the two main outcome variables. Separate multivariate logistic regression analyses identified factors associated with online buying and factors predicting discussions with providers about online information. In 2007, 14.5% (n = 871) of internet users bought a medication or vitamin online. About 85% of online buyers had a regular provider, but only 39% talked to the provider about online information even though most (93.7%) visited the provider ≥1 times/year. Multivariate analyses found internet health product consumers were more likely to be over 50 years old, have insurance and discuss the internet with their provider than non-internet health product consumers. Moreover, discussion of internet information was more likely if consumers had a regular provider and perceived their communication to be at least fair or good in general. There is a clear association of online buying with age, frequency of visits and discussing online information with a provider. Although most online buyers visited a provider in the prior year, only a minority discussed the internet with them. This suggests a missed opportunity for providers to help patients navigate internet buying, particularly if they are a patient's regular provider and the patient perceives their communication as good. Published by Elsevier Inc.

Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae

PubMed Central

2012-01-01

Background Staphylococcus belongs to the Gram-positive low G + C content group of the Firmicutes division of bacteria. Staphylococcus aureus is an important human and veterinary pathogen that causes a broad spectrum of diseases, and has developed important multidrug resistant forms such as methicillin-resistant S. aureus (MRSA). Staphylococcus simiae was isolated from South American squirrel monkeys in 2000, and is a coagulase-negative bacterium, closely related, and possibly the sister group, to S. aureus. Comparative genomic analyses of closely related bacteria with different phenotypes can provide information relevant to understanding adaptation to host environment and mechanisms of pathogenicity. Results We determined a Roche/454 draft genome sequence for S. simiae and included it in comparative genomic analyses with 11 other Staphylococcus species including S. aureus. A genome based phylogeny of the genus confirms that S. simiae is the sister group to S. aureus and indicates that the most basal Staphylococcus lineage is Staphylococcus pseudintermedius, followed by Staphylococcus carnosus. Given the primary niche of these two latter taxa, compared to the other species in the genus, this phylogeny suggests that human adaptation evolved after the split of S. carnosus. The two coagulase-positive species (S. aureus and S. pseudintermedius) are not phylogenetically closest but share many virulence factors exclusively, suggesting that these genes were acquired by horizontal transfer. Enrichment in genes related to mobile elements such as prophage in S. aureus relative to S. simiae suggests that pathogenesis in the S. aureus group has developed by gene gain through horizontal transfer, after the split of S. aureus and S. simiae from their common ancestor. Conclusions Comparative genomic analyses across 12 Staphylococcus species provide hypotheses about lineages in which human adaptation has taken place and contributions of horizontal transfer in pathogenesis. PMID:22272658

Analysis of patients' narratives posted on social media websites on benfluorex's (Mediator® ) withdrawal in France.

PubMed

Abou Taam, M; Rossard, C; Cantaloube, L; Bouscaren, N; Roche, G; Pochard, L; Montastruc, F; Herxheimer, A; Montastruc, J L; Bagheri, H

2014-02-01

Websites and discussion lists on health issues are among the most popular resources on the Web. Use experience reported on social media websites may provide useful information on drugs and their adverse reactions (ADRs). Clear communication on the benefit/harm balance of drugs is important to inform proper use of drugs. Some data have shown that communication (advisories or warnings) is difficult. This study aimed to explore the Internet as a source of data on patients' perception of risk associated with benfluorex and the impact of wider media coverage. Three French websites were selected: Doctissimo, Atoute.org considered the best-known and visited website in France for health questions and Vivelesrondes (Long live the Tubbies) for overweight people. Three periods were chosen: (1) before November 2009 (i.e. before benfluorex withdrawal), (2) between November 2009 and November 2010 (when the risk of valvulopathy with benfluorex appeared in social media) and (3) after November 2010. Two hundred twenty initial postings were analysed. These lead to 660 secondary postings which were analysed separately. In period 1, 114 initial postings were analysed, mostly concerning efficacy of the drug (72%). In period 2, 42 initial postings were analysed involving mainly ADRs or warnings (73%). In period 3, 64 initial postings were analysed; most frequent expressing anger directed at the healthcare system (58%) and anxiety about cardiovascular ADRs (30%). Online consumer postings showed that there were drastic changes in consumers' perceptions following media coverage. This study suggests that analysis of website data can inform on drug ADRs. Social media are important for communicating information on drug ADRs and for assessing consumer behaviour and their risk perception. © 2013 John Wiley & Sons Ltd.

Gemas: issues from the comparison of aqua regia and X-ray fluorescence results

NASA Astrophysics Data System (ADS)

Dinelli, Enrico; Birke, Manfred; Reimann, Clemens; Demetriades, Alecos; DeVivo, Benedetto; Flight, Dee; Ladenberger, Anna; Albanese, Stefano; Cicchella, Domenico; Lima, Annamaria

2014-05-01

The comparison of analytical results from aqua regia (AR) and X-ray fluorescence spectroscopy (XRF) can provide information on soil processes controlling the element distribution. The GEMAS (GEochemical Mapping of Agricultural and grazing land Soils) agricultural soil database is used for this comparison. Analyses for the same suite of elements and parameters were carried out in the same laboratory under strict quality control procedures. Sample preparation has been conducted at the laboratory of the The comparison of analytical results from aqua regia (AR) and X-ray fluorescence spectroscopy (XRF) can provide information on soil processes controlling the element distribution in soil. The GEMAS (GEochemical Mapping of Agricultural and grazing land Soils) agricultural soil database, consisting of 2 x ca. 2100 samples spread evenly over 33 European countries, is used for this comparison. Analyses for the same suite of elements and parameters were carried out in the same laboratory under strict quality control procedures. Sample preparation has been conducted at the laboratory of the Geological Survey of the Slovak Republic, AR analyses were carried out at ACME Labs, and XRF analyses at the Federal Institute for Geosciences and Natural Resources, Germany Element recovery by AR is very different, ranging from <1% (e.g. Na, Zr) to > 80% (e.g. Mn, P, Co). Recovery is controlled by mineralogy of the parent material, but geographic and climatic factors and the weathering history of the soils are also important. Nonetheless, even the very low recovery elements show wide ranges of variation and spatial patterns that are affected by other factors than soil parent material. For many elements soil pH have a clear influence on AR extractability: under acidic soil conditions almost all elements tend to be leached and their extractability is generally low. It progressively increases with increasing pH and is highest in the pH range 7-8. Critical is the clay content of the soil that almost for all elements correspond to higher extractability with increasing clay abundance. Also other factors such as organic matter content of soil, Fe and Mn occurrence are important for certain elements or in selected areas. This work illustrates that there are significant differences in the extractability of elements from soils and addresses important influencing factors related to soil properties, geology, climate.

Barriers and facilitators to integrating care: experiences from the English Integrated Care Pilots

PubMed Central

Ling, Tom; Brereton, Laura; Conklin, Annalijn; Newbould, Jennifer; Roland, Martin

2012-01-01

Background: In 2008, the English Department of Health appointed 16 ‘Integrated Care Pilots’ which used a range of approaches to provide better integrated care. We report qualitative analyses from a three-year multi-method evaluation to identify barriers and facilitators to successful integration of care. Theory and methods: Data were analysed from transcripts of 213 in-depth staff interviews, and from semi-structured questionnaires (the ‘Living Document’) completed by staff in pilot sites at six points over a two-year period. Emerging findings were therefore built from ‘bottom up’ and grounded in the data. However, we were then interested in how these findings compared and contrasted with more generic analyses. Therefore after our analyses were complete we then systematically compared and contrasted the findings with the analysis of barriers and facilitators to quality improvement identified in a systematic review by Kaplan et al. (2010) and the analysis of more micro-level shapers of behaviour found in Normalisation Process Theory (May et al. 2007). Neither of these approaches claims to be full blown theories but both claim to provide mid-range theoretical arguments which may be used to structure existing data and which can be undercut or reinforced by new data. Results and discussion: Many barriers and facilitators to integrating care are those of any large-scale organisational change. These include issues relating to leadership, organisational culture, information technology, physician involvement, and availability of resources. However, activities which appear particularly important for delivering integrated care include personal relationships between leaders in different organisations, the scale of planned activities, governance and finance arrangements, support for staff in new roles, and organisational and staff stability. We illustrate our analyses with a ‘routemap’ which identifies questions that providers may wish to consider when planning interventions to improve the integration of care. PMID:23593044

Application of Sigma Metrics and Performance Comparison Between Two Biochemistry Analyser and a Blood Gas Analyser for the Determination of Electrolytes.

PubMed

Ustundag-Budak, Yasemin; Huysal, Kagan

2017-02-01

Electrolytes have a narrow range of biological variation and small changes are clinically significant. It is important to select the best method for clinical decision making and patient monitoring in the emergency room. The sigma metrics model provides an objective method to evaluate the performance of a method. To calculate sigma metrics for electrolytes measured with one arterial blood gas analyser including two auto-analysers that use different technologies. To identify the best approach for electrolyte monitoring in an emergency setting and the context of routine emergency room workflow. The Coefficient of Variation (CV) was determined from Internal Quality Control (IQC). Data was measured from July 2015 to January 2016 for all three analysers. The records of KBUD external quality data (Association of Clinical Biochemists, Istanbul, Turkey) for both Mindray BS-2000M analyser (Mindray, Shenzhen, China) and Architect C16000 (Abbott Diagnostics, Abbott Park, IL) and MLE clinical laboratory evaluation program (Washington, DC, USA) for Radiometer ABL 700 (Radiometer Trading, Copenhagen, Denmark) during the study period were used to determine the bias. The calculated average sigma values for sodium (-1.1), potassium (3.3), and chloride (0.06) were with the Radiometer ABL700. All calculated sigma values were better than the auto-analysers. The sigma values obtained from all analysers suggest that running more controls and increasing the calibration frequency for electrolytes is necessary for quality assurance.

Structural, functional and immunogenic insights on Cu,Zn superoxide dismutase pathogenic virulence factors from Neisseria meningitidis and Brucella abortus

DOE PAGES

Pratt, Ashley J.; DiDonato, Michael; Shin, David S.; ...

2015-10-12

Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen, general pathogenicity factors and therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomicmore » details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes and suggest general targets for anti-bacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against reactive oxygen insults, Cu,Zn superoxide dismutases (SODs) aid survival of many bacteria within their hosts. Despite the ubiquity and conservation of these key enzymes, notable species-specific differences relevant to pathogenesis remain undefined. To probe mechanisms that govern the functioning of Neisseria meningitidis and Brucella abortus SODs, we used X-ray structures, enzymology, modeling and murine infection experiments. We identified virulence determinants common to both homologs, assembly differences and a unique metal reservoir within meningococcal SOD that stabilizes the enzyme and may provide a safeguard against copper toxicity. The insights reported here provide a rationale and basis for SOD-specific drugs and extension of immunogen design to target two important pathogens that continue to pose global health threats.« less

Structural, Functional, and Immunogenic Insights on Cu,Zn Superoxide Dismutase Pathogenic Virulence Factors from Neisseria meningitidis and Brucella abortus

PubMed Central

Pratt, Ashley J.; DiDonato, Michael; Shin, David S.; Cabelli, Diane E.; Bruns, Cami K.; Belzer, Carol A.; Gorringe, Andrew R.; Langford, Paul R.; Tabatabai, Louisa B.; Kroll, J. Simon; Tainer, John A.

2015-01-01

ABSTRACT Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen and general pathogenicity factors and are therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomic details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and of SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly, and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes, and suggest general targets for antibacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors of or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against reactive oxygen insults, SODs aid survival of many bacteria within their hosts. Despite the ubiquity and conservation of these key enzymes, notable species-specific differences relevant to pathogenesis remain undefined. To probe mechanisms that govern the functioning of Neisseria meningitidis and Brucella abortus SODs, we used X-ray structures, enzymology, modeling, and murine infection experiments. We identified virulence determinants common to the two homologs, assembly differences, and a unique metal reservoir within meningococcal SOD that stabilizes the enzyme and may provide a safeguard against copper toxicity. The insights reported here provide a rationale and a basis for SOD-specific drug design and an extension of immunogen design to target two important pathogens that continue to pose global health threats. PMID:26459556

Structural, functional and immunogenic insights on Cu,Zn superoxide dismutase pathogenic virulence factors from Neisseria meningitidis and Brucella abortus

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

Pratt, Ashley J.; DiDonato, Michael; Shin, David S.

Bacterial pathogens Neisseria meningitidis and Brucella abortus pose threats to human and animal health worldwide, causing meningococcal disease and brucellosis, respectively. Mortality from acute N. meningitidis infections remains high despite antibiotics, and brucellosis presents alimentary and health consequences. Superoxide dismutases are master regulators of reactive oxygen, general pathogenicity factors and therefore therapeutic targets. Cu,Zn superoxide dismutases (SODs) localized to the periplasm promote survival by detoxifying superoxide radicals generated by major host antimicrobial immune responses. We discovered that passive immunization with an antibody directed at N. meningitidis SOD (NmSOD) was protective in a mouse infection model. To define the relevant atomicmore » details and solution assembly states of this important virulence factor, we report high-resolution and X-ray scattering analyses of NmSOD and SOD from B. abortus (BaSOD). The NmSOD structures revealed an auxiliary tetrahedral Cu-binding site bridging the dimer interface; mutational analyses suggested that this metal site contributes to protein stability, with implications for bacterial defense mechanisms. Biochemical and structural analyses informed us about electrostatic substrate guidance, dimer assembly and an exposed C-terminal epitope in the NmSOD dimer. In contrast, the monomeric BaSOD structure provided insights for extending immunogenic peptide epitopes derived from the protein. These collective results reveal unique contributions of SOD to pathogenic virulence, refine predictive motifs for distinguishing SOD classes and suggest general targets for anti-bacterial immune responses. The identified functional contributions, motifs, and targets distinguishing bacterial and eukaryotic SOD assemblies presented here provide a foundation for efforts to develop SOD-specific inhibitors or vaccines against these harmful pathogens. IMPORTANCE By protecting microbes against reactive oxygen insults, Cu,Zn superoxide dismutases (SODs) aid survival of many bacteria within their hosts. Despite the ubiquity and conservation of these key enzymes, notable species-specific differences relevant to pathogenesis remain undefined. To probe mechanisms that govern the functioning of Neisseria meningitidis and Brucella abortus SODs, we used X-ray structures, enzymology, modeling and murine infection experiments. We identified virulence determinants common to both homologs, assembly differences and a unique metal reservoir within meningococcal SOD that stabilizes the enzyme and may provide a safeguard against copper toxicity. The insights reported here provide a rationale and basis for SOD-specific drugs and extension of immunogen design to target two important pathogens that continue to pose global health threats.« less

Choice is good, but relevance is excellent: autonomy-enhancing and suppressing teacher behaviours predicting students' engagement in schoolwork.

PubMed

Assor, Avi; Kaplan, Haya; Roth, Guy

2002-06-01

This article examines two questions concerning teacher-behaviours that are characterised in Self-Determination Theory (Ryan & Deci, 2000) as autonomy-supportive or suppressive: (1) Can children differentiate among various types of autonomy-enhancing and suppressing teacher behaviours? (2) Which of those types of behaviour are particularly important in predicting feelings toward and engagement in schoolwork? It was hypothesised that teacher behaviours that help students to understand the relevance of schoolwork for their personal interests and goals are particularly important predictors of engagement in schoolwork. Israeli students in grades 3-5 (N = 498) and in grades 6-8 (N = 364) completed questionnaires assessing the variables of interest. Smallest Space Analyses indicated that both children and early adolescents can differentiate among three types of autonomy enhancing teacher behaviours - fostering relevance, allowing criticism, and providing choice - and three types of autonomy suppressing teacher behaviours - suppressing criticism, intruding, and forcing unmeaningful acts. Regression analyses supported the hypothesis concerning the importance of teacher behaviours that clarify the personal relevance of schoolwork. Among the autonomy-suppressing behaviours, 'Criticism-suppression' was the best predictor of feelings and engagement. The findings underscore the active and empathic nature of teachers' role in supporting students' autonomy, and suggest that autonomy-support is important not only for early adolescents but also for children. Discussion of potential determinants of the relative importance of various autonomy-affecting teacher actions suggests that provision of choice should not always be viewed as a major indicator of autonomy support.

An investigation of social media data during a product recall scandal

NASA Astrophysics Data System (ADS)

Tse, Ying Kei; Loh, Hanlin; Ding, Juling; Zhang, Minhao

2018-07-01

As social media has become an important part of modern daily life, users often share product opinions online and these tend to spike when large companies undergo crises. This paper investigates customer online responses to a large company crisis by uncovering hidden insights in social media comments and presents a framework for handling social media data and crisis management. Analysis of textual Facebook data from users responding to the 2013 horsemeat scandal is presented. In this study, we used a novel comprehensive data analysis framework alongside a text-mining framework to objectively classify and understand customer perceptions during this horsemeat scandal. This framework provides an effective approach for investigating customer perception during a company crisis and measures the effectiveness of crisis management practices which the company has adopted. Our analyses show that social media can provide important insights into customer behaviour during crisis communications.

Measuring patients' experiences with rheumatic care: the consumer quality index rheumatoid arthritis.

PubMed

Zuidgeest, Marloes; Sixma, Herman; Rademakers, Jany

2009-12-01

Rheumatologists and other caregivers can learn from patients’ experiences with the quality of care that can be measured with the CQ-index Rheumatoid Arthritis (CQ-index RA) survey. Patients with RA (n = 590) received this survey were they rated their actual experiences and what they find important in rheumatic healthcare. Descriptive analyses and psychometric methods were used to test the reliability. The response rate was 69%. The items in the pilot instrument could be grouped into 10 scales (α ranged from 0.77 to 0.94). The most important quality aspects according to patients concerned the alertness when prescribing medication. Providing patients with information on a special website of the hospital about RA was the highest quality improvement aspect. The results of this study show that the CQ-index RA is a reliable instrument for quality assessment from the patients’ perspective. The instrument provides rheumatologists and other caregivers with feedback for service improvement initiatives.

Seeking support: An interpretative phenomenological analysis of an Internet message board for people with Complex Regional Pain Syndrome.

PubMed

Rodham, Karen; McCabe, Candy; Blake, David

2009-07-01

In this article, we report on the findings of a qualitative inquiry into how an online message board for people who have Complex Regional Pain Syndrome (CRPS) was used by its members. All messages (and responses) posted on the CRPS message board over a 4-month period were collected retrospectively. The data were analysed using the method of Interpretative Phenomenological Analysis. Members used the message board to seek (and provide) support to those with CRPS, and also to express their emotions, feelings and experiences linked to their condition. The message board provided an important source of support for a patient group that can otherwise become isolated as a result of their mobility problems. Furthermore, the analysis revealed the unrealistic hopes that patients can hold concerning the anticipated outcomes of their treatment. This is an important issue for healthcare professionals to explicitly address when interacting with the patient group.

Identification and functional expression of the Arabidopsis thaliana vacuolar glucose transporter 1 and its role in seed germination and flowering.

PubMed

Aluri, Sirisha; Büttner, Michael

2007-02-13

Sugar compartmentation into vacuoles of higher plants is a very important physiological process, providing extra space for transient and long-term sugar storage and contributing to the osmoregulation of cell turgor and shape. Despite the long-standing knowledge of this subcellular sugar partitioning, the proteins responsible for these transport steps have remained unknown. We have identified a gene family in Arabidopsis consisting of three members homologous to known sugar transporters. One member of this family, Arabidopsis thaliana vacuolar glucose transporter 1 (AtVGT1), was localized to the vacuolar membrane. Moreover, we provide evidence for transport activity of a tonoplast sugar transporter based on its functional expression in bakers' yeast and uptake studies in isolated yeast vacuoles. Analyses of Atvgt1 mutant lines indicate an important function of this vacuolar glucose transporter during developmental processes like seed germination and flowering.

[Serological and clinical proof of freedom from Equine Infectious Anemia (EIA) in imported and domestic horses in Switzerland].

PubMed

Kaiser, A; Meier, H P; Doherr, M G; Perler, L; Zanoni, R; Gerber, V

2009-04-01

Since 1991, no cases of Equine Infectious Anemia (EIA) have been reported in Switzerland. Risk factors for introduction of the virus into Switzerland are still present or have even increased as frequent inapparent infections, large numbers of imported horses, (since 2003) absence of compulsory testing prior to importation, EIA cases in surrounding Europe, possible illegal importation of horses, frequent short-term stays, poor knowledge of the disease among horse owners and even veterinarians. The aim of this study was to provide evidence of freedom from EIA in imported and domestic horses in Switzerland. The serum samples from 434 horses imported since 2003 as well as from 232 domestic horses fifteen years of age or older (since older horses have naturally had a longer time of being exposed to the risk of infection) were analysed using a commercially available ELISA test. All samples were seronegative, indicating that the maximum possible prevalence that could have been missed with this sample was 0.5% (95% confidence).

The Control Attitudes Scale-Revised: psychometric evaluation in three groups of patients with cardiac illness.

PubMed

Moser, Debra K; Riegel, Barbara; McKinley, Sharon; Doering, Lynn V; Meischke, Hendrika; Heo, Seongkum; Lennie, Terry A; Dracup, Kathleen

2009-01-01

Perceived control is a construct with important theoretical and clinical implications for healthcare providers, yet practical application of the construct in research and clinical practice awaits development of an easily administered instrument to measure perceived control with evidence of reliability and validity. To test the psychometric properties of the Control Attitudes Scale-Revised (CAS-R) using a sample of 3,396 individuals with coronary heart disease, 513 patients with acute myocardial infarction, and 146 patients with heart failure. Analyses were done separately in each patient group. Reliability was assessed using Cronbach's alpha to determine internal consistency, and item homogeneity was assessed using item-total and interitem correlations. Validity was examined using principal component analysis and testing hypotheses about known associations. Cronbach's alpha values for the CAS-R in patients with coronary heart disease, acute myocardial infarction, and heart failure were all greater than .70. Item-total and interitem correlation coefficients for all items were acceptable in the groups. In factor analyses, the same single factor was extracted in all groups, and all items were loaded moderately or strongly to the factor in each group. As hypothesized in the final construct validity test, in all groups, patients with higher levels of perceived control had less depression and less anxiety compared with those of patients who had lower levels of perceived control. This study provides evidence of the reliability and validity of the 8-item CAS-R as a measure of perceived control in patients with cardiac illness and provides important insight into a key patient construct.

Data collection of patient outcomes: one institution’s experience

PubMed Central

Whitaker, Thomas J; Mayo, Charles S; Ma, Daniel J; Haddock, Michael G; Miller, Robert C; Corbin, Kimberly S; Neben-Wittich, Michelle; Leenstra, James L; Laack, Nadia N; Fatyga, Mirek; Schild, Steven E; Vargas, Carlos E; Tzou, Katherine S; Hadley, Austin R; Buskirk, Steven J; Foote, Robert L

2018-01-01

Abstract Patient- and provider-reported outcomes are recognized as important in evaluating quality of care, guiding health care policy, comparative effectiveness research, and decision-making in radiation oncology. Combining patient and provider outcome data with a detailed description of disease and therapy is the basis for these analyses. We report on the combination of technical solutions and clinical process changes at our institution that were used in the collection and dissemination of this data. This initiative has resulted in the collection of treatment data for 23 541 patients, 20 465 patients with provider-based adverse event records, and patient-reported outcome surveys submitted by 5622 patients. All of the data is made accessible using a self-service web-based tool. PMID:29538757

The Southern California Twin Register at the University of Southern California: III

PubMed Central

Baker, Laura A.; Tuvblad, Catherine; Wang, Pan; Gomez, Karina; Bezdjian, Serena; Niv, Sharon; Raine, Adrian

2013-01-01

The Southern California Twin Register at the University of Southern California (USC) was initiated in 1984 and continues to provide an important resource for studies investigating genetic and environmental influences on human behavior. This article provides an update on the current register and its potential for future twin studies using recruitment through school district databases and voter records. An overview is also provided for an ongoing longitudinal twin study investigating the development of externalizing psychopathology from childhood to young adulthood, the USC Study of Risk Factors for Antisocial Behavior. Characteristics of the twins and their families are presented, including recruitment and participation rates, as well as attrition analyses and a summary of key findings to date. PMID:23394193

Modelling Levels of Collaboration Among Health and Social Care Professionals in the Management of a Mental Health Plan.

PubMed

Luzi, Daniela; Pecoraro, Fabrizio; Tamburis, Oscar

2018-01-01

Professional collaboration among health and social care providers is considered an essential pattern to improve the integration of care. This is particularly important considering the planning activities for children with complex conditions. In this paper the level of collaboration among professionals in the development and implementation of the personalized plan in the mental health domain is analysed across 30 EU/EEA countries within the MOCHA project.

Study design and hierarchy of evidence for surgical decision making.

PubMed

Sprague, Sheila; McKay, Paula; Thoma, Achilleas

2008-04-01

This article provides a historical overview of the hierarchy of evidence for surgical decision making and discusses key study designs in the hierarchy of evidence. This encompasses meta-analyses, randomized controlled trials, and observational studies, including cohort and case-controlled studies, case series and case reports, and basic science studies. This article also reviews the principles and importance of evidence-based plastic surgery and describes several systems to rate the strength of the scientific evidence.

Forest Species Identification with High Spectral Resolution Data

NASA Technical Reports Server (NTRS)

Olson, C. E., Jr.; Zhu, Z.

1985-01-01

Data collected over the Sleeping Bear Sand Dunes Test Site and the Saginaw Forest Test Site (Michigan) with the JPL Airborne Imaging Spectrometer and the Collins' Airborne Spectroradiometer are being used for forest species identification. The linear discriminant function has provided higher identification accuracies than have principal components analyses. Highest identification accuracies are obtained in the 450 to 520 nm spectral region. Spectral bands near 1,300, 1,685 and 2,220 nm appear to be important, also.

Diet of bottlenose dolphins (Tursiops truncatus) from the Gulf of Cadiz: Insights from stomach content and stable isotope analyses

PubMed Central

Marçalo, Ana; Ramírez, Francisco; Verborgh, Philippe; Gauffier, Pauline; Esteban, Ruth; Nicolau, Lídia; González-Ortegón, Enrique; Baldó, Francisco; Vilas, César; Vingada, José; G. Forero, Manuela; de Stephanis, Renaud

2017-01-01

The ecological role of species can vary among populations depending on local and regional differences in diet. This is particularly true for top predators such as the bottlenose dolphin (Tursiops truncatus), which exhibits a highly varied diet throughout its distribution range. Local dietary assessments are therefore critical to fully understand the role of this species within marine ecosystems, as well as its interaction with important ecosystem services such as fisheries. Here, we combined stomach content analyses (SCA) and stable isotope analyses (SIA) to describe bottlenose dolphins diet in the Gulf of Cadiz (North Atlantic Ocean). Prey items identified using SCA included European conger (Conger conger) and European hake (Merluccius merluccius) as the most important ingested prey. However, mass-balance isotopic mixing model (MixSIAR), using δ13C and δ15N, indicated that the assimilated diet consisted mainly on Sparidae species (e.g. seabream, Diplodus annularis and D. bellottii, rubberlip grunt, Plectorhinchus mediterraneus, and common pandora, Pagellus erythrinus) and a mixture of other species including European hake, mackerels (Scomber colias, S. japonicus and S. scombrus), European conger, red bandfish (Cepola macrophthalma) and European pilchard (Sardina pilchardus). These contrasting results highlight differences in the temporal and taxonomic resolution of each approach, but also point to potential differences between ingested (SCA) and assimilated (SIA) diets. Both approaches provide different insights, e.g. determination of consumed fish biomass for the management of fish stocks (SCA) or identification of important assimilated prey species to the consumer (SIA). PMID:28898268

West Nile Virus lineage-2 in Culex specimens from Iran.

PubMed

Shahhosseini, Nariman; Chinikar, Sadegh; Moosa-Kazemi, Seyed Hassan; Sedaghat, Mohammad Mehdi; Kayedi, Mohammad Hassan; Lühken, Renke; Schmidt-Chanasit, Jonas

2017-10-01

Screening of mosquitoes for viruses is an important forecasting tool for emerging and re-emerging arboviruses. Iran has been known to harbour medically important arboviruses such as West Nile virus (WNV) and dengue virus (DENV) based on seroepidemiological data. However, there are no data about the potential mosquito vectors for arboviruses in Iran. This study was performed to provide mosquito and arbovirus data from Iran. A total of 32 317 mosquitos were collected at 16 sites in five provinces of Iran in 2015 and 2016. RT-PCR for detection of flaviviruses was performed. The PCR amplicons were sequenced, and 109 WNV sequences, including one obtained in this study, were used for phylogenetic analyses. The 32 317 mosquito specimens belonging to 25 species were morphologically distinguished and distributed into 1222 pools. Culex pipiens s.l. comprised 56.429%. One mosquito pool (0.08%), containing 46 unfed Cx. pipiens pipiens form pipiens (Cpp) captured in August 2015, was positive for flavivirus RNA. Subsequent sequencing and phylogenetic analyses revealed that the detected Iranian WNV strain belongs to lineage 2 and clusters with a strain recently detected in humans. No flaviviruses other than WNV were detected in the mosquito pools. Cpp could be a vector for WNV in Iran. Our findings indicate recent circulation of WNV lineage-2 strain in Iran and provide a solid base for more targeted arbovirus surveillance programs. © 2017 John Wiley & Sons Ltd.

The Functional Basis of Wing Patterning in Heliconius Butterflies: The Molecules Behind Mimicry

PubMed Central

Kronforst, Marcus R.; Papa, Riccardo

2015-01-01

Wing-pattern mimicry in butterflies has provided an important example of adaptation since Charles Darwin and Alfred Russell Wallace proposed evolution by natural selection >150 years ago. The neotropical butterfly genus Heliconius played a central role in the development of mimicry theory and has since been studied extensively in the context of ecology and population biology, behavior, and mimicry genetics. Heliconius species are notable for their diverse color patterns, and previous crossing experiments revealed that much of this variation is controlled by a small number of large-effect, Mendelian switch loci. Recent comparative analyses have shown that the same switch loci control wing-pattern diversity throughout the genus, and a number of these have now been positionally cloned. Using a combination of comparative genetic mapping, association tests, and gene expression analyses, variation in red wing patterning throughout Heliconius has been traced back to the action of the transcription factor optix. Similarly, the signaling ligand WntA has been shown to control variation in melanin patterning across Heliconius and other butterflies. Our understanding of the molecular basis of Heliconius mimicry is now providing important insights into a variety of additional evolutionary phenomena, including the origin of supergenes, the interplay between constraint and evolvability, the genetic basis of convergence, the potential for introgression to facilitate adaptation, the mechanisms of hybrid speciation in animals, and the process of ecological speciation. PMID:25953905

The Evolution of Ebola virus: Insights from the 2013–2016 Epidemic

PubMed Central

Holmes, Edward C.; Dudas, Gytis; Rambaut, Andrew; Andersen, Kristian G.

2017-01-01

Preface The 2013–2016 epidemic of Ebola virus disease in West Africa was of unprecedented magnitude and changed our perspective on this lethal but sporadically emerging virus. This outbreak also marked the beginning of large-scale real-time molecular epidemiology. Herein, we show how evolutionary analyses of Ebola virus genome sequences provided key insights into virus origins, evolution, and spread during the epidemic. We provide basic scientists, epidemiologists, medical practitioners, and other outbreak responders with an enhanced understanding of the utility and limitations of pathogen genomic sequencing. This will be crucially important in our attempts to track and control future infectious disease outbreaks. PMID:27734858

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

PubMed Central

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

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.

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.

Gait Analysis Methods for Rodent Models of Arthritic Disorders: Reviews and Recommendations

PubMed Central

Lakes, Emily H.; Allen, Kyle D.

2016-01-01

Gait analysis is a useful tool to understand behavioral changes in preclinical arthritis models. While observational scoring and spatiotemporal gait parameters are the most widely performed gait analyses in rodents, commercially available systems can now provide quantitative assessments of spatiotemporal patterns. However, inconsistencies remain between testing platforms, and laboratories often select different gait pattern descriptors to report in the literature. Rodent gait can also be described through kinetic and kinematic analyses, but systems to analyze rodent kinetics and kinematics are typically custom made and often require sensitive, custom equipment. While the use of rodent gait analysis rapidly expands, it is important to remember that, while rodent gait analysis is a relatively modern behavioral assay, the study of quadrupedal gait is not new. Nearly all gait parameters are correlated, and a collection of gait parameters is needed to understand a compensatory gait pattern used by the animal. As such, a change in a single gait parameter is unlikely to tell the full biomechanical story; and to effectively use gait analysis, one must consider how multiple different parameters contribute to an altered gait pattern. The goal of this article is to review rodent gait analysis techniques and provide recommendations on how to use these technologies in rodent arthritis models, including discussions on the strengths and limitations of observational scoring, spatiotemporal, kinetic, and kinematic measures. Recognizing rodent gait analysis is an evolving tool, we also provide technical recommendations we hope will improve the utility of these analyses in the future. PMID:26995111

Step-by-step guideline for disease-specific costing studies in low- and middle-income countries: a mixed methodology

PubMed Central

Hendriks, Marleen E.; Kundu, Piyali; Boers, Alexander C.; Bolarinwa, Oladimeji A.; te Pas, Mark J.; Akande, Tanimola M.; Agbede, Kayode; Gomez, Gabriella B.; Redekop, William K.; Schultsz, Constance; Tan, Siok Swan

2014-01-01

Background Disease-specific costing studies can be used as input into cost-effectiveness analyses and provide important information for efficient resource allocation. However, limited data availability and limited expertise constrain such studies in low- and middle-income countries (LMICs). Objective To describe a step-by-step guideline for conducting disease-specific costing studies in LMICs where data availability is limited and to illustrate how the guideline was applied in a costing study of cardiovascular disease prevention care in rural Nigeria. Design The step-by-step guideline provides practical recommendations on methods and data requirements for six sequential steps: 1) definition of the study perspective, 2) characterization of the unit of analysis, 3) identification of cost items, 4) measurement of cost items, 5) valuation of cost items, and 6) uncertainty analyses. Results We discuss the necessary tradeoffs between the accuracy of estimates and data availability constraints at each step and illustrate how a mixed methodology of accurate bottom-up micro-costing and more feasible approaches can be used to make optimal use of all available data. An illustrative example from Nigeria is provided. Conclusions An innovative, user-friendly guideline for disease-specific costing in LMICs is presented, using a mixed methodology to account for limited data availability. The illustrative example showed that the step-by-step guideline can be used by healthcare professionals in LMICs to conduct feasible and accurate disease-specific cost analyses. PMID:24685170

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.

Transparency in practice: Evidence from 'verification analyses' issued by the Polish Agency for Health Technology Assessment in 2012-2015.

PubMed

Ozierański, Piotr; Löblová, Olga; Nicholls, Natalia; Csanádi, Marcell; Kaló, Zoltán; McKee, Martin; King, Lawrence

2018-01-08

Transparency is recognised to be a key underpinning of the work of health technology assessment (HTA) agencies, yet it has only recently become a subject of systematic inquiry. We contribute to this research field by considering the Polish Agency for Health Technology Assessment (AHTAPol). We situate the AHTAPol in a broader context by comparing it with the National Institute for Health and Care Excellence (NICE) in England. To this end, we analyse all 332 assessment reports, called verification analyses, that the AHTAPol issued from 2012 to 2015, and a stratified sample of 22 Evidence Review Group reports published by NICE in the same period. Overall, by increasingly presenting its key conclusions in assessment reports, the AHTAPol has reached the transparency standards set out by NICE in transparency of HTA outputs. The AHTAPol is more transparent than NICE in certain aspects of the HTA process, such as providing rationales for redacting assessment reports and providing summaries of expert opinions. Nevertheless, it is less transparent in other areas of the HTA process, such as including information on expert conflicts of interest. Our findings have important implications for understanding HTA in Poland and more broadly. We use them to formulate recommendations for policymakers.

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

Multi-Dimensional Prioritization of Dental Caries Candidate Genes and Its Enriched Dense Network Modules

PubMed Central

Wang, Quan; Jia, Peilin; Cuenco, Karen T.; Feingold, Eleanor; Marazita, Mary L.; Wang, Lily; Zhao, Zhongming

2013-01-01

A number of genetic studies have suggested numerous susceptibility genes for dental caries over the past decade with few definite conclusions. The rapid accumulation of relevant information, along with the complex architecture of the disease, provides a challenging but also unique opportunity to review and integrate the heterogeneous data for follow-up validation and exploration. In this study, we collected and curated candidate genes from four major categories: association studies, linkage scans, gene expression analyses, and literature mining. Candidate genes were prioritized according to the magnitude of evidence related to dental caries. We then searched for dense modules enriched with the prioritized candidate genes through their protein-protein interactions (PPIs). We identified 23 modules comprising of 53 genes. Functional analyses of these 53 genes revealed three major clusters: cytokine network relevant genes, matrix metalloproteinases (MMPs) family, and transforming growth factor-beta (TGF-β) family, all of which have been previously implicated to play important roles in tooth development and carious lesions. Through our extensive data collection and an integrative application of gene prioritization and PPI network analyses, we built a dental caries-specific sub-network for the first time. Our study provided insights into the molecular mechanisms underlying dental caries. The framework we proposed in this work can be applied to other complex diseases. PMID:24146904

Functional Organization of the Action Observation Network in Autism: A Graph Theory Approach.

PubMed

Alaerts, Kaat; Geerlings, Franca; Herremans, Lynn; Swinnen, Stephan P; Verhoeven, Judith; Sunaert, Stefan; Wenderoth, Nicole

2015-01-01

The ability to recognize, understand and interpret other's actions and emotions has been linked to the mirror system or action-observation-network (AON). Although variations in these abilities are prevalent in the neuro-typical population, persons diagnosed with autism spectrum disorders (ASD) have deficits in the social domain and exhibit alterations in this neural network. Here, we examined functional network properties of the AON using graph theory measures and region-to-region functional connectivity analyses of resting-state fMRI-data from adolescents and young adults with ASD and typical controls (TC). Overall, our graph theory analyses provided convergent evidence that the network integrity of the AON is altered in ASD, and that reductions in network efficiency relate to reductions in overall network density (i.e., decreased overall connection strength). Compared to TC, individuals with ASD showed significant reductions in network efficiency and increased shortest path lengths and centrality. Importantly, when adjusting for overall differences in network density between ASD and TC groups, participants with ASD continued to display reductions in network integrity, suggesting that also network-level organizational properties of the AON are altered in ASD. While differences in empirical connectivity contributed to reductions in network integrity, graph theoretical analyses provided indications that also changes in the high-level network organization reduced integrity of the AON.

O-6 Optical Property Degradation of the Hubble Space Telescope's Wide Field Camera-2 Pick Off Mirror

NASA Technical Reports Server (NTRS)

McNamara, Karen M.; Hughes, D. W.; Lauer, H. V.; Burkett, P. J.; Reed, B. B.

2011-01-01

Degradation in the performance of optical components can be greatly affected by exposure to the space environment. Many factors can contribute to such degradation including surface contaminants; outgassing; vacuum, UV, and atomic oxygen exposure; temperature cycling; or combinations of parameters. In-situ observations give important clues to degradation processes, but there are relatively few opportunities to correlate those observations with post-flight ground analyses. The return of instruments from the Hubble Space Telescope (HST) after its final servicing mission in May 2009 provided such an opportunity. Among the instruments returned from HST was the Wide-Field Planetary Camera-2 (WFPC-2), which had been exposed to the space environment for 16 years. This work focuses on the identifying the sources of degradation in the performance of the Pick-off mirror (POM) from WFPC-2. Techniques including surface reflectivity measurements, spectroscopic ellipsometry, FTIR (and ATR-FTIR) analyses, SEM/EDS, X-ray photoelectron spectroscopy (XPS) with and without ion milling, and wet and dry physical surface sampling were performed. Destructive and contact analyses took place only after completion of the non-destructive measurements. Spectroscopic ellipsometry was then repeated to determine the extent of contaminant removal by the destructive techniques, providing insight into the nature and extent of polymerization of the contaminant layer.

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.

QPF verification using different radar-based analyses: a case study

NASA Astrophysics Data System (ADS)

Moré, J.; Sairouni, A.; Rigo, T.; Bravo, M.; Mercader, J.

2009-09-01

Verification of QPF in NWP models has been always challenging not only for knowing what scores are better to quantify a particular skill of a model but also for choosing the more appropriate methodology when comparing forecasts with observations. On the one hand, an objective verification technique can provide conclusions that are not in agreement with those ones obtained by the "eyeball" method. Consequently, QPF can provide valuable information to forecasters in spite of having poor scores. On the other hand, there are difficulties in knowing the "truth" so different results can be achieved depending on the procedures used to obtain the precipitation analysis. The aim of this study is to show the importance of combining different precipitation analyses and verification methodologies to obtain a better knowledge of the skills of a forecasting system. In particular, a short range precipitation forecasting system based on MM5 at 12 km coupled with LAPS is studied in a local convective precipitation event that took place in NE Iberian Peninsula on October 3rd 2008. For this purpose, a variety of verification methods (dichotomous, recalibration and object oriented methods) are used to verify this case study. At the same time, different precipitation analyses are used in the verification process obtained by interpolating radar data using different techniques.

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.

Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon.

PubMed

Sibout, Richard; Proost, Sebastian; Hansen, Bjoern Oest; Vaid, Neha; Giorgi, Federico M; Ho-Yue-Kuang, Severine; Legée, Frédéric; Cézart, Laurent; Bouchabké-Coussa, Oumaya; Soulhat, Camille; Provart, Nicholas; Pasha, Asher; Le Bris, Philippe; Roujol, David; Hofte, Herman; Jamet, Elisabeth; Lapierre, Catherine; Persson, Staffan; Mutwil, Marek

2017-08-01

While Brachypodium distachyon (Brachypodium) is an emerging model for grasses, no expression atlas or gene coexpression network is available. Such tools are of high importance to provide insights into the function of Brachypodium genes. We present a detailed Brachypodium expression atlas, capturing gene expression in its major organs at different developmental stages. The data were integrated into a large-scale coexpression database ( www.gene2function.de), enabling identification of duplicated pathways and conserved processes across 10 plant species, thus allowing genome-wide inference of gene function. We highlight the importance of the atlas and the platform through the identification of duplicated cell wall modules, and show that a lignin biosynthesis module is conserved across angiosperms. We identified and functionally characterised a putative ferulate 5-hydroxylase gene through overexpression of it in Brachypodium, which resulted in an increase in lignin syringyl units and reduced lignin content of mature stems, and led to improved saccharification of the stem biomass. Our Brachypodium expression atlas thus provides a powerful resource to reveal functionally related genes, which may advance our understanding of important biological processes in grasses. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

75 FR 52302 - Notice of Availability of Pest Risk Analyses for the Importation of Fresh Celery, Arugula, and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-25

... Inspection Service [Docket No. APHIS-2010-0074] Notice of Availability of Pest Risk Analyses for the... spinach from Colombia. We are making these pest risk analyses available to the public for review and..., based on the findings of a pest- risk analysis, can be safely imported subject to one or more of the...

The Global/Local Nexus in Comparative Policy Studies: Analysing the Triple Bonus System in Mongolia over Time

ERIC Educational Resources Information Center

Steiner-Khamsi, Gita

2012-01-01

The article analyses a phenomenon that has accompanied teacher salary reform in Mongolia: the import of two global education policies that were nearly identical to the already existing local bonus system ("olympiads"). To make sense of an import that appears superfluous, the author analyses the reception and translation of the triple…

Characterizing Flexible and Instrinsically Unstructured Biological Macromolecules by SAS using the Porod-Debye Law

PubMed Central

Rambo, Robert P.; Tainer, John A.

2011-01-01

Unstructured proteins, RNA or DNA components provide functionally important flexibility that is key to many macromolecular assemblies throughout cell biology. As objective, quantitative experimental measures of flexibility and disorder in solution are limited, small angle scattering (SAS), and in particular small angle X-ray scattering (SAXS), provides a critical technology to assess macromolecular flexibility as well as shape and assembly. Here, we consider the Porod-Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. We show that the Porod-Debye region fundamentally describes the nature of the scattering intensity decay, which captures information needed for distinguishing between folded and flexible particles. Particularly for comparative SAS experiments, application of the law, as described here, can distinguish between discrete conformational changes and localized flexibility relevant to molecular recognition and interaction networks. This approach aids insightful analyses of fully and partly flexible macromolecules that is more robust and conclusive than traditional Kratky analyses. Furthermore, we demonstrate for prototypic SAXS data that the ability to calculate particle density by the Porod-Debye criteria, as shown here, provides an objective quality assurance parameter that may prove of general use for SAXS modeling and validation. PMID:21509745

Exploring the potential uses of value-added metrics in the context of postgraduate medical education.

PubMed

Gregory, Simon; Patterson, Fiona; Baron, Helen; Knight, Alec; Walsh, Kieran; Irish, Bill; Thomas, Sally

2016-10-01

Increasing pressure is being placed on external accountability and cost efficiency in medical education and training internationally. We present an illustrative data analysis of the value-added of postgraduate medical education. We analysed historical selection (entry) and licensure (exit) examination results for trainees sitting the UK Membership of the Royal College of General Practitioners (MRCGP) licensing examination (N = 2291). Selection data comprised: a clinical problem solving test (CPST); a situational judgement test (SJT); and a selection centre (SC). Exit data was an applied knowledge test (AKT) from MRCGP. Ordinary least squares (OLS) regression analyses were used to model differences in attainment in the AKT based on performance at selection (the value-added score). Results were aggregated to the regional level for comparisons. We discovered significant differences in the value-added score between regional training providers. Whilst three training providers confer significant value-added, one training provider was significantly lower than would be predicted based on the attainment of trainees at selection. Value-added analysis in postgraduate medical education potentially offers useful information, although the methodology is complex, controversial, and has significant limitations. Developing models further could offer important insights to support continuous improvement in medical education in future.

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

PubMed Central

Paila, Umadevi; Chapman, Brad A.; Kirchner, Rory; Quinlan, Aaron R.

2013-01-01

Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics. PMID:23874191

Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification.

PubMed

Gupta, Radhey S

2016-07-01

Analyses of genome sequences, by some approaches, suggest that the widespread occurrence of horizontal gene transfers (HGTs) in prokaryotes disguises their evolutionary relationships and have led to questioning of the Darwinian model of evolution for prokaryotes. These inferences are critically examined in the light of comparative genome analysis, characteristic synapomorphies, phylogenetic trees and Darwin's views on examining evolutionary relationships. Genome sequences are enabling discovery of numerous molecular markers (synapomorphies) such as conserved signature indels (CSIs) and conserved signature proteins (CSPs), which are distinctive characteristics of different prokaryotic taxa. Based on these molecular markers, exhibiting high degree of specificity and predictive ability, numerous prokaryotic taxa of different ranks, currently identified based on the 16S rRNA gene trees, can now be reliably demarcated in molecular terms. Within all studied groups, multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs. These results strongly support Darwin's views on evolution and classification and supplement the current phylogenetic framework based on 16S rRNA in important respects. The identified molecular markers provide important means for developing novel diagnostics, therapeutics and for functional studies providing important insights regarding prokaryotic taxa. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular recognition of PTS-1 cargo proteins by Pex5p: implications for protein mistargeting in primary hyperoxaluria.

PubMed

Mesa-Torres, Noel; Tomic, Nenad; Albert, Armando; Salido, Eduardo; Pey, Angel L

2015-02-13

Peroxisomal biogenesis and function critically depends on the import of cytosolic proteins carrying a PTS1 sequence into this organelle upon interaction with the peroxin Pex5p. Recent structural studies have provided important insights into the molecular recognition of cargo proteins by Pex5p. Peroxisomal import is a key feature in the pathogenesis of primary hyperoxaluria type 1 (PH1), where alanine:glyoxylate aminotransferase (AGT) undergoes mitochondrial mistargeting in about a third of patients. Here, we study the molecular recognition of PTS1 cargo proteins by Pex5p using oligopeptides and AGT variants bearing different natural PTS1 sequences, and employing an array of biophysical, computational and cell biology techniques. Changes in affinity for Pex5p (spanning over 3-4 orders of magnitude) reflect different thermodynamic signatures, but overall bury similar amounts of molecular surface. Structure/energetic analyses provide information on the contribution of ancillary regions and the conformational changes induced in Pex5p and the PTS1 cargo upon complex formation. Pex5p stability in vitro is enhanced upon cargo binding according to their binding affinities. Moreover, we provide evidence that the rational modulation of the AGT: Pex5p binding affinity might be useful tools to investigate mistargeting and misfolding in PH1 by pulling the folding equilibria towards the native and peroxisomal import competent state.

Global malaria connectivity through air travel.

PubMed

Huang, Zhuojie; Tatem, Andrew J

2013-08-02

Air travel has expanded at an unprecedented rate and continues to do so. Its effects have been seen on malaria in rates of imported cases, local outbreaks in non-endemic areas and the global spread of drug resistance. With elimination and global eradication back on the agenda, changing levels and compositions of imported malaria in malaria-free countries, and the threat of artemisinin resistance spreading from Southeast Asia, there is a need to better understand how the modern flow of air passengers connects each Plasmodium falciparum- and Plasmodium vivax-endemic region to the rest of the world. Recently constructed global P. falciparum and P.vivax malaria risk maps, along with data on flight schedules and modelled passenger flows across the air network, were combined to describe and quantify global malaria connectivity through air travel. Network analysis approaches were then utilized to describe and quantify the patterns that exist in passenger flows weighted by malaria prevalence. Finally, the connectivity within and to the Southeast Asia region where the threat of imported artemisinin resistance arising is highest, was examined to highlight risk routes for its spread. The analyses demonstrate the substantial connectivity that now exists between and from malaria-endemic regions through air travel. While the air network provides connections to previously isolated malarious regions, it is clear that great variations exist, with significant regional communities of airports connected by higher rates of flow standing out. The structures of these communities are often not geographically coherent, with historical, economic and cultural ties evident, and variations between P. falciparum and P. vivax clear. Moreover, results highlight how well connected the malaria-endemic areas of Africa are now to Southeast Asia, illustrating the many possible routes that artemisinin-resistant strains could take. The continuing growth in air travel is playing an important role in the global epidemiology of malaria, with the endemic world becoming increasingly connected to both malaria-free areas and other endemic regions. The research presented here provides an initial effort to quantify and analyse the connectivity that exists across the malaria-endemic world through air travel, and provide a basic assessment of the risks it results in for movement of infections.

Global malaria connectivity through air travel

PubMed Central

2013-01-01

Background Air travel has expanded at an unprecedented rate and continues to do so. Its effects have been seen on malaria in rates of imported cases, local outbreaks in non-endemic areas and the global spread of drug resistance. With elimination and global eradication back on the agenda, changing levels and compositions of imported malaria in malaria-free countries, and the threat of artemisinin resistance spreading from Southeast Asia, there is a need to better understand how the modern flow of air passengers connects each Plasmodium falciparum- and Plasmodium vivax-endemic region to the rest of the world. Methods Recently constructed global P. falciparum and P.vivax malaria risk maps, along with data on flight schedules and modelled passenger flows across the air network, were combined to describe and quantify global malaria connectivity through air travel. Network analysis approaches were then utilized to describe and quantify the patterns that exist in passenger flows weighted by malaria prevalence. Finally, the connectivity within and to the Southeast Asia region where the threat of imported artemisinin resistance arising is highest, was examined to highlight risk routes for its spread. Results The analyses demonstrate the substantial connectivity that now exists between and from malaria-endemic regions through air travel. While the air network provides connections to previously isolated malarious regions, it is clear that great variations exist, with significant regional communities of airports connected by higher rates of flow standing out. The structures of these communities are often not geographically coherent, with historical, economic and cultural ties evident, and variations between P. falciparum and P. vivax clear. Moreover, results highlight how well connected the malaria-endemic areas of Africa are now to Southeast Asia, illustrating the many possible routes that artemisinin-resistant strains could take. Discussion The continuing growth in air travel is playing an important role in the global epidemiology of malaria, with the endemic world becoming increasingly connected to both malaria-free areas and other endemic regions. The research presented here provides an initial effort to quantify and analyse the connectivity that exists across the malaria-endemic world through air travel, and provide a basic assessment of the risks it results in for movement of infections. PMID:23914776

Perturbation analyses of intermolecular interactions

NASA Astrophysics Data System (ADS)

Koyama, Yohei M.; Kobayashi, Tetsuya J.; Ueda, Hiroki R.

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Perturbation analyses of intermolecular interactions.

PubMed

Koyama, Yohei M; Kobayashi, Tetsuya J; Ueda, Hiroki R

2011-08-01

Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect the function by changing the conformational fluctuations. However, it is difficult to systematically understand the role of environmental molecules because intermolecular interactions related to the conformational fluctuations are complicated. To identify important intermolecular interactions with regard to the conformational fluctuations, we develop herein (i) distance-independent and (ii) distance-dependent perturbation analyses of the intermolecular interactions. We show that these perturbation analyses can be realized by performing (i) a principal component analysis using conditional expectations of truncated and shifted intermolecular potential energy terms and (ii) a functional principal component analysis using products of intermolecular forces and conditional cumulative densities. We refer to these analyses as intermolecular perturbation analysis (IPA) and distance-dependent intermolecular perturbation analysis (DIPA), respectively. For comparison of the IPA and the DIPA, we apply them to the alanine dipeptide isomerization in explicit water. Although the first IPA principal components discriminate two states (the α state and PPII (polyproline II) + β states) for larger cutoff length, the separation between the PPII state and the β state is unclear in the second IPA principal components. On the other hand, in the large cutoff value, DIPA eigenvalues converge faster than that for IPA and the top two DIPA principal components clearly identify the three states. By using the DIPA biplot, the contributions of the dipeptide-water interactions to each state are analyzed systematically. Since the DIPA improves the state identification and the convergence rate with retaining distance information, we conclude that the DIPA is a more practical method compared with the IPA. To test the feasibility of the DIPA for larger molecules, we apply the DIPA to the ten-residue chignolin folding in explicit water. The top three principal components identify the four states (native state, two misfolded states, and unfolded state) and their corresponding eigenfunctions identify important chignolin-water interactions to each state. Thus, the DIPA provides the practical method to identify conformational states and their corresponding important intermolecular interactions with distance information.

Form and function of damselfish skulls: rapid and repeated evolution into a limited number of trophic niches.

PubMed

Cooper, W James; Westneat, Mark W

2009-01-30

Damselfishes (Perciformes, Pomacentridae) are a major component of coral reef communities, and the functional diversity of their trophic anatomy is an important constituent of the ecological morphology of these systems. Using shape analyses, biomechanical modelling, and phylogenetically based comparative methods, we examined the anatomy of damselfish feeding among all genera and trophic groups. Coordinate based shape analyses of anatomical landmarks were used to describe patterns of morphological diversity and determine positions of functional groups in a skull morphospace. These landmarks define the lever and linkage structures of the damselfish feeding system, and biomechanical analyses of this data were performed using the software program JawsModel4 in order to calculate the simple mechanical advantage (MA) employed by different skull elements during feeding, and to compute kinematic transmission coefficients (KT) that describe the efficiency with which angular motion is transferred through the complex linkages of damselfish skulls. Our results indicate that pomacentrid planktivores are significantly different from other damselfishes, that biting MA values and protrusion KT ratios are correlated with pomacentrid trophic groups more tightly than KT scores associated with maxillary rotation and gape angle, and that the MAs employed by their three biting muscles have evolved independently. Most of the biomechanical parameters examined have experienced low levels of phylogenetic constraint, which suggests that they have evolved quickly. Joint morphological and biomechanical analyses of the same anatomical data provided two reciprocally illuminating arrays of information. Both analyses showed that the evolution of planktivory has involved important changes in pomacentrid functional morphology, and that the mechanics of upper jaw kinesis have been of great importance to the evolution of damselfish feeding. Our data support a tight and biomechanically defined link between structure and the functional ecology of fish skulls, and indicate that certain mechanisms for transmitting motion through their jaw linkages may require particular anatomical configurations, a conclusion that contravenes the concept of "many-to-one mapping" for fish jaw mechanics. Damselfish trophic evolution is characterized by rapid and repeated shifts between a small number of eco-morphological states, an evolutionary pattern that we describe as reticulate adaptive radiation.

Designing drugs on the internet? Free web tools and services supporting medicinal chemistry.

PubMed

Ertl, Peter; Jelfs, Stephen

2007-01-01

The drug discovery process is supported by a multitude of freely available tools on the Internet. This paper summarizes some of the databases and tools that are of particular interest to medicinal chemistry. These include numerous data collections that provide access to valuable chemical data resources, allowing complex queries of compound structures, associated physicochemical properties and biological activities to be performed and, in many cases, providing links to commercial chemical suppliers. Further applications are available for searching protein-ligand complexes and identifying important binding interactions that occur. This is particularly useful for understanding the molecular recognition of ligands in the lead optimization process. The Internet also provides access to databases detailing metabolic pathways and transformations which can provide insight into disease mechanism, identify new targets entities or the potential off-target effects of a drug candidate. Furthermore, sophisticated online cheminformatics tools are available for processing chemical structures, predicting properties, and generating 2D or 3D structure representations--often required prior to more advanced analyses. The Internet provides a wealth of valuable resources that, if fully exploited, can greatly benefit the drug discovery community. In this paper, we provide an overview of some of the more important of these and, in particular, the freely accessible resources that are currently available.

Status of VICTORIA: NRC peer review and recent code applications

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

Bixler, N.E.; Schaperow, J.H.

1997-12-01

VICTORIA is a mechanistic computer code designed to analyze fission product behavior within a nuclear reactor coolant system (RCS) during a severe accident. It provides detailed predictions of the release of radioactive and nonradioactive materials from the reactor core and transport and deposition of these materials within the RCS. A summary of the results and recommendations of an independent peer review of VICTORIA by the US Nuclear Regulatory Commission (NRC) is presented, along with recent applications of the code. The latter include analyses of a temperature-induced steam generator tube rupture sequence and post-test analyses of the Phebus FPT-1 test. Themore » next planned Phebus test, FTP-4, will focus on fission product releases from a rubble bed, especially those of the less-volatile elements, and on the speciation of the released elements. Pretest analyses using VICTORIA to estimate the magnitude and timing of releases are presented. The predicted release of uranium is a matter of particular importance because of concern about filter plugging during the test.« less

Comparative Genomics of Erwinia amylovora and Related Erwinia Species—What do We Learn?

PubMed Central

Zhao, Youfu; Qi, Mingsheng

2011-01-01

Erwinia amylovora, the causal agent of fire blight disease of apples and pears, is one of the most important plant bacterial pathogens with worldwide economic significance. Recent reports on the complete or draft genome sequences of four species in the genus Erwinia, including E. amylovora, E. pyrifoliae, E. tasmaniensis, and E. billingiae, have provided us near complete genetic information about this pathogen and its closely-related species. This review describes in silico subtractive hybridization-based comparative genomic analyses of eight genomes currently available, and highlights what we have learned from these comparative analyses, as well as genetic and functional genomic studies. Sequence analyses reinforce the assumption that E. amylovora is a relatively homogeneous species and support the current classification scheme of E. amylovora and its related species. The potential evolutionary origin of these Erwinia species is also proposed. The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized. Future research directions are also suggested. PMID:24710213

Differential protein folding and chemical changes in lung tissues exposed to asbestos or particulates

PubMed Central

Pascolo, Lorella; Borelli, Violetta; Canzonieri, Vincenzo; Gianoncelli, Alessandra; Birarda, Giovanni; Bedolla, Diana E.; Salomé, Murielle; Vaccari, Lisa; Calligaro, Carla; Cotte, Marine; Hesse, Bernhard; Luisi, Fernando; Zabucchi, Giuliano; Melato, Mauro; Rizzardi, Clara

2015-01-01

Environmental and occupational inhalants may induce a large number of pulmonary diseases, with asbestos exposure being the most risky. The mechanisms are clearly related to chemical composition and physical and surface properties of materials. A combination of X-ray fluorescence (μXRF) and Fourier Transform InfraRed (μFTIR) microscopy was used to chemically characterize and compare asbestos bodies versus environmental particulates (anthracosis) in lung tissues from asbestos exposed and control patients. μXRF analyses revealed heterogeneously aggregated particles in the anthracotic structures, containing mainly Si, K, Al and Fe. Both asbestos and particulates alter lung iron homeostasis, with a more marked effect in asbestos exposure. μFTIR analyses revealed abundant proteins on asbestos bodies but not on anthracotic particles. Most importantly, the analyses demonstrated that the asbestos coating proteins contain high levels of β-sheet structures. The occurrence of conformational changes in the proteic component of the asbestos coating provides new insights into long-term asbestos effects. PMID:26159651

NEXT Ion Thruster Performance Dispersion Analyses

NASA Technical Reports Server (NTRS)

Soulas, George C.; Patterson, Michael J.

2008-01-01

The NEXT ion thruster is a low specific mass, high performance thruster with a nominal throttling range of 0.5 to 7 kW. Numerous engineering model and one prototype model thrusters have been manufactured and tested. Of significant importance to propulsion system performance is thruster-to-thruster performance dispersions. This type of information can provide a bandwidth of expected performance variations both on a thruster and a component level. Knowledge of these dispersions can be used to more conservatively predict thruster service life capability and thruster performance for mission planning, facilitate future thruster performance comparisons, and verify power processor capabilities are compatible with the thruster design. This study compiles the test results of five engineering model thrusters and one flight-like thruster to determine unit-to-unit dispersions in thruster performance. Component level performance dispersion analyses will include discharge chamber voltages, currents, and losses; accelerator currents, electron backstreaming limits, and perveance limits; and neutralizer keeper and coupling voltages and the spot-to-plume mode transition flow rates. Thruster level performance dispersion analyses will include thrust efficiency.

Analysis of the influence of the milling machine throw-out plate surfacing and structure design on throwing material

NASA Astrophysics Data System (ADS)

Fang, Yuanbin; Sha, Hongwei; Yu, Yunmin; Chen, Bing

2018-03-01

Material composition, hardness and wear properties of the throw-out plate improved are analysed on a road milling machine. At the same time, analyse the tissue and performance of Fe based alloy named Fe60 cladding layer using the plasma surfacing method. And the original and improved throw-out plates are analysed throwing material effect by the dynamic analysis. Then the throw-out plate samples are verified. The results show that Fe60 powder is selected as surface strengthening material. By the improved structure, the hardness of the throw-out plate increases from 14.6HRC to 57.5HRC, and the wear resistance increases from 0.452g-1 to 16.393g-1. At the same time, it increases from 3263 to 3433 to fall into the collecting material number of milling machine. It provides important guidance for structure design and process design of the milling machine throw-out plate.

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development.

PubMed

Yao, Zizhen; Mich, John K; Ku, Sherman; Menon, Vilas; Krostag, Anne-Rachel; Martinez, Refugio A; Furchtgott, Leon; Mulholland, Heather; Bort, Susan; Fuqua, Margaret A; Gregor, Ben W; Hodge, Rebecca D; Jayabalu, Anu; May, Ryan C; Melton, Samuel; Nelson, Angelique M; Ngo, N Kiet; Shapovalova, Nadiya V; Shehata, Soraya I; Smith, Michael W; Tait, Leah J; Thompson, Carol L; Thomsen, Elliot R; Ye, Chaoyang; Glass, Ian A; Kaykas, Ajamete; Yao, Shuyuan; Phillips, John W; Grimley, Joshua S; Levi, Boaz P; Wang, Yanling; Ramanathan, Sharad

2017-01-05

During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development. Bayesian analyses inferred a unified cell-type lineage tree that bifurcates between cortical and mid/hindbrain cell types. Two methods of clonal analyses confirmed these findings and further revealed the importance of Wnt/β-catenin signaling in controlling this lineage decision. Together, these findings provide a rich transcriptome-based lineage map for studying human brain development and modeling developmental disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

NEK1 variants confer susceptibility to amyotrophic lateral sclerosis

PubMed Central

Kenna, Kevin P; van Doormaal, Perry T C; Dekker, Annelot M; Ticozzi, Nicola; Kenna, Brendan J; Diekstra, Frank P; van Rheenen, Wouter; van Eijk, Kristel R; Jones, Ashley R; Keagle, Pamela; Shatunov, Aleksey; Sproviero, William; Smith, Bradley N; van Es, Michael A; Topp, Simon D; Kenna, Aoife; Miller, Jack W; Fallini, Claudia; Tiloca, Cinzia; McLaughlin, Russell L; Vance, Caroline; Troakes, Claire; Colombrita, Claudia; Mora, Gabriele; Calvo, Andrea; Verde, Federico; Al-Sarraj, Safa; King, Andrew; Calini, Daniela; de Belleroche, Jacqueline; Baas, Frank; van der Kooi, Anneke J; de Visser, Marianne; Asbroek, Anneloor L M A ten; Sapp, Peter C; McKenna-Yasek, Diane; Polak, Meraida; Asress, Seneshaw; Muñoz-Blanco, José Luis; Strom, Tim M; Meitinger, Thomas; Morrison, Karen E; Lauria, Giuseppe; Williams, Kelly L; Leigh, P Nigel; Nicholson, Garth A; Blair, Ian P; Leblond, Claire S; Dion, Patrick A; Rouleau, Guy A; Pall, Hardev; Shaw, Pamela J; Turner, Martin R; Talbot, Kevin; Taroni, Franco; Boylan, Kevin B; Van Blitterswijk, Marka; Rademakers, Rosa; Esteban-Pérez, Jesús; García-Redondo, Alberto; Van Damme, Phillip; Robberecht, Wim; Chio, Adriano; Gellera, Cinzia; Drepper, Carsten; Sendtner, Michael; Ratti, Antonia; Glass, Jonathan D; Mora, Jesús S; Basak, Nazli A; Hardiman, Orla; Ludolph, Albert C; Andersen, Peter M; Weishaupt, Jochen H; Brown, Robert H; Al-Chalabi, Ammar; Silani, Vincenzo; Shaw, Christopher E; van den Berg, Leonard H; Veldink, Jan H; Landers, John E

2017-01-01

To identify genetic factors contributing to amyotrophic lateral sclerosis (ALS), we conducted whole-exome analyses of 1,022 index familial ALS (FALS) cases and 7,315 controls. In a new screening strategy, we performed gene-burden analyses trained with established ALS genes and identified a significant association between loss-of-function (LOF) NEK1 variants and FALS risk. Independently, autozygosity mapping for an isolated community in the Netherlands identified a NEK1 p.Arg261His variant as a candidate risk factor. Replication analyses of sporadic ALS (SALS) cases and independent control cohorts confirmed significant disease association for both p.Arg261His (10,589 samples analyzed) and NEK1 LOF variants (3,362 samples analyzed). In total, we observed NEK1 risk variants in nearly 3% of ALS cases. NEK1 has been linked to several cellular functions, including cilia formation, DNA-damage response, microtubule stability, neuronal morphology and axonal polarity. Our results provide new and important insights into ALS etiopathogenesis and genetic etiology. PMID:27455347

Radiocarbon analysis of halophilic microbial lipids from an Australian salt lake

NASA Astrophysics Data System (ADS)

Bray, P. Sargent; Jones, Claudia M.; Fallon, Stewart J.; Brocks, Jochen J.; George, Simon C.

2012-01-01

Assigning accurate dates to hypersaline sediments opens important terrestrial records of local and regional paleoecologies and paleoclimatology. However, as of yet no conventional method of dating hypersaline systems has been widely adopted. Biomarker, mineralogical, and radiocarbon analyses of sediments and organic extracts from a shallow (13 cm) core from a hypersaline playa, Lake Tyrrell, southeastern Australia, produce a coherent age-depth curve beginning with modern microbial mats and extending to ~ 7500 cal yr BP. These analyses are furthermore used to identify and constrain the timing of the most recent change in hydrological regime at Lake Tyrrell, a shift from a clay deposit to the precipitation of evaporitic sands occurring at some time between ~ 4500 and 7000 yr. These analyses show the potential for widespread dating of hypersaline systems integrating the biomarker approach, reinforce the value of the radiocarbon content of biomarkers in understanding the flow of carbon in modern ecologies, and validate the temporal dimension of data provided by biomarkers when dating late Quaternary sediments.

The near real time Forensic Disaster Analysis of the central European flood in June 2013 - A graphical representation of the main results

NASA Astrophysics Data System (ADS)

Schröter, Kai; Elmer, Florian; Trieselmann, Werner; Kreibich, Heidi; Kunz, Michael; Khazai, Bijan; Dransch, Doris; Wenzel, Friedemann; Zschau, Jochen; Merz, Bruno; Mühr, Bernhard; Kunz-Plapp, Tina; Möhrle, Stella; Bessel, Tina; Fohringer, Joachim

2014-05-01

The Central European flood of June 2013 is one of the most severe flood events that have occurred in Central Europe in the past decades. All major German river basins were affected (Rhine, Danube, and Elbe as well as the smaller Weser catchment).In terms of spatial extent and event magnitude, it was the most severe event at least since 1950. Within the current research focus on near real time forensic disaster analysis, the Center for Disaster Management and Risk Reduction Technology (CEDIM) assessed and analysed the multiple facets of the flood event from the beginning. The aim is to describe the on-going event, analyse the event sources, link the physical characteristics to the impact and consequences of the event and to understand the root causes that turn the physical event into a disaster (or prevent it from becoming disastrous). For the near real time component of this research, tools for rapid assessment and concise presentation of analysis results are essential. This contribution provides a graphical summary of the results of the CEDIM-FDA analyses on the June 2013 flood. It demonstrates the potential of visual representations for improving the communication and hence usability of findings in a rapid, intelligible and expressive way as a valuable supplement to usual event reporting. It is based on analyses of the hydrometeorological sources, the flood pathways (from satellite imagery, data extraction from social media), the resilience of the affected regions, and causal loss analysis. The prototypical representation of the FDA-results for the June 2013 flood provides an important step in the development of graphical event templates for the visualisation of forensic disaster analyses. These are intended to become a standard component of future CEDIM-FDA event activities.

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

Comparative Pathogenomics Reveals Horizontally Acquired Novel Virulence Genes in Fungi Infecting Cereal Hosts

PubMed Central

Gardiner, Donald M.; McDonald, Megan C.; Covarelli, Lorenzo; Solomon, Peter S.; Rusu, Anca G.; Marshall, Mhairi; Kazan, Kemal; Chakraborty, Sukumar; McDonald, Bruce A.; Manners, John M.

2012-01-01

Comparative analyses of pathogen genomes provide new insights into how pathogens have evolved common and divergent virulence strategies to invade related plant species. Fusarium crown and root rots are important diseases of wheat and barley world-wide. In Australia, these diseases are primarily caused by the fungal pathogen Fusarium pseudograminearum. Comparative genomic analyses showed that the F. pseudograminearum genome encodes proteins that are present in other fungal pathogens of cereals but absent in non-cereal pathogens. In some cases, these cereal pathogen specific genes were also found in bacteria associated with plants. Phylogenetic analysis of selected F. pseudograminearum genes supported the hypothesis of horizontal gene transfer into diverse cereal pathogens. Two horizontally acquired genes with no previously known role in fungal pathogenesis were studied functionally via gene knockout methods and shown to significantly affect virulence of F. pseudograminearum on the cereal hosts wheat and barley. Our results indicate using comparative genomics to identify genes specific to pathogens of related hosts reveals novel virulence genes and illustrates the importance of horizontal gene transfer in the evolution of plant infecting fungal pathogens. PMID:23028337

Re-assessing the relationship between sporozoite dose and incubation period in Plasmodium vivax malaria: a systematic re-analysis.

PubMed

Lover, Andrew A; Coker, Richard J

2014-05-01

Infections with the malaria parasite Plasmodium vivax are noteworthy for potentially very long incubation periods (6-9 months), which present a major barrier to disease elimination. Increased sporozoite challenge has been reported to be associated with both shorter incubation and pre-patent periods in a range of human challenge studies. However, this evidence base has scant empirical foundation, as these historical analyses were limited by available analytic methods, and provides no quantitative estimates of effect size. Following a comprehensive literature search, we re-analysed all identified studies using survival and/or logistic models plus contingency tables. We have found very weak evidence for dose-dependence at entomologically plausible inocula levels. These results strongly suggest that sporozoite dosage is not an important driver of long-latency. Evidence presented suggests that parasite strain and vector species have quantitatively greater impacts, and the potential existence of a dose threshold for human dose-response to sporozoites. Greater consideration of the complex interplay between these aspects of vectors and parasites are important for human challenge experiments, vaccine trials, and epidemiology towards global malaria elimination.

Clumped isotope calibration data for lacustrine carbonates: A progress report

NASA Astrophysics Data System (ADS)

Tripati, A.

2015-12-01

Our capacity to understand Earth's environmental history is highly dependent on the accuracy of reconstructions of past climates. Lake sediments provide important archives of terrestrial climate change, and represent an important tool for reconstructing paleohydrology, paleoclimate, paleoenvironment, and paleoaltimetry. Unfortunately, while multiple methods for constraining marine temperature exist, quantitative terrestrial proxies are scarcer - tree rings, speleothems, and leaf margin analyses have all been used with varying degrees of accuracy. Clumped isotope thermometry has the potential to be a useful instrument for determining terrestrial climates: multiple studies have shown the fraction of 13C—18O bonds in carbonates is inversely related to the temperature at which the rocks formed. We have been measuring the abundance of 13C18O16O in the CO2 produced by the dissolution of carbonate minerals in phosphoric acid in modern lake samples and comparing results to independently known estimates of lake water temperature. Here we discuss an extensive calibration dataset comprised of 132 analyses of 97 samples from 44 localities, including microbialites, tufas, and micrites endogenic carbonates, freshwater gastropods, bivalves, microbialites, and ooids.

A multidisciplinary selection model for youth soccer: the Ghent Youth Soccer Project

PubMed Central

Vaeyens, R; Malina, R M; Janssens, M; Van Renterghem, B; Bourgois, J; Vrijens, J; Philippaerts, R M

2006-01-01

Objectives To determine the relationships between physical and performance characteristics and level of skill in youth soccer players aged 12–16 years. Methods Anthropometry, maturity status, functional and sport‐specific parameters were assessed in elite, sub‐elite, and non‐elite youth players in four age groups: U13 (n = 117), U14 (n = 136), U15 (n = 138) and U16 (n = 99). Results Multivariate analyses of covariance by age group with maturity status as the covariate showed that elite players scored better than the non‐elite players on strength, flexibility, speed, aerobic endurance, anaerobic capacity and several technical skills (p<0.05). Stepwise discriminant analyses showed that running speed and technical skills were the most important characteristics in U13 and U14 players, while cardiorespiratory endurance was more important in U15 and U16 players. The results suggest that discriminating characteristics change with competitive age levels. Conclusions Characteristics that discriminate youth soccer players vary by age group. Talent identification models should thus be dynamic and provide opportunities for changing parameters in a long‐term developmental context. PMID:16980535

Factors predicting work outcome in Japanese patients with schizophrenia: role of multiple functioning levels.

PubMed

Sumiyoshi, Chika; Harvey, Philip D; Takaki, Manabu; Okahisa, Yuko; Sato, Taku; Sora, Ichiro; Nuechterlein, Keith H; Subotnik, Kenneth L; Sumiyoshi, Tomiki

2015-09-01

Functional outcomes in individuals with schizophrenia suggest recovery of cognitive, everyday, and social functioning. Specifically improvement of work status is considered to be most important for their independent living and self-efficacy. The main purposes of the present study were 1) to identify which outcome factors predict occupational functioning, quantified as work hours, and 2) to provide cut-offs on the scales for those factors to attain better work status. Forty-five Japanese patients with schizophrenia and 111 healthy controls entered the study. Cognition, capacity for everyday activities, and social functioning were assessed by the Japanese versions of the MATRICS Cognitive Consensus Battery (MCCB), the UCSD Performance-based Skills Assessment-Brief (UPSA-B), and the Social Functioning Scale Individuals' version modified for the MATRICS-PASS (Modified SFS for PASS), respectively. Potential factors for work outcome were estimated by multiple linear regression analyses (predicting work hours directly) and a multiple logistic regression analyses (predicting dichotomized work status based on work hours). ROC curve analyses were performed to determine cut-off points for differentiating between the better- and poor work status. The results showed that a cognitive component, comprising visual/verbal learning and emotional management, and a social functioning component, comprising independent living and vocational functioning, were potential factors for predicting work hours/status. Cut-off points obtained in ROC analyses indicated that 60-70% achievements on the measures of those factors were expected to maintain the better work status. Our findings suggest that improvement on specific aspects of cognitive and social functioning are important for work outcome in patients with schizophrenia.

Assessing vaccination as a control strategy in an ongoing epidemic: Bovine tuberculosis in African buffalo

USGS Publications Warehouse

Cross, P.C.; Getz, W.M.

2006-01-01

Bovine tuberculosis (BTB) is an exotic disease invading the buffalo population (Syncerus caffer) of the Kruger National Park (KNP), South Africa. We used a sex and age-structured epidemiological model to assess the effectiveness of a vaccination program and define important research directions. The model allows for dispersal between a focal herd and background population and was parameterized with a combination of published data and analyses of over 130 radio-collared buffalo in the central region of the KNP. Radio-tracking data indicated that all sex and age categories move between mixed herds, and males over 8 years old had higher mortality and dispersal rates than any other sex or age category. In part due to the high dispersal rates of buffalo, sensitivity analyses indicate that disease prevalence in the background population accounts for the most variability in the BTB prevalence and quasi-eradication within the focal herd. Vaccination rate and the transmission coefficient were the second and third most important parameters of the sensitivity analyses. Further analyses of the model without dispersal suggest that the amount of vaccination necessary for quasi-eradication (i.e. prevalence 70% of the calf population would have to be vaccinated every year to reduce the prevalence to less than 1%. If the half-life of the vaccine is less than 5 years, even vaccinating every calf for 50 years may not eradicate BTB. Thus, although vaccination provides a means of controlling BTB prevalence it should be combined with other control measures if eradication is the objective.

Determinants of RNA binding and translational repression by the Bicaudal-C regulatory protein.

PubMed

Zhang, Yan; Park, Sookhee; Blaser, Susanne; Sheets, Michael D

2014-03-14

Bicaudal-C (Bic-C) RNA binding proteins function as important translational repressors in multiple biological contexts within metazoans. However, their RNA binding sites are unknown. We recently demonstrated that Bic-C functions in spatially regulated translational repression of the xCR1 mRNA during Xenopus development. This repression contributes to normal development by confining the xCR1 protein, a regulator of key signaling pathways, to specific cells of the embryo. In this report, we combined biochemical approaches with in vivo mRNA reporter assays to define the minimal Bic-C target site within the xCR1 mRNA. This 32-nucleotide Bic-C target site is predicted to fold into a stem-loop secondary structure. Mutational analyses provided evidence that this stem-loop structure is important for Bic-C binding. The Bic-C target site was sufficient for Bic-C mediated repression in vivo. Thus, we describe the first RNA binding site for a Bic-C protein. This identification provides an important step toward understanding the mechanisms by which evolutionarily conserved Bic-C proteins control cellular function in metazoans.

The use of meta-analysis or research synthesis to combine driving simulation or naturalistic study results on driver distraction.

PubMed

Caird, Jeff K; Johnston, Katherine A; Willness, Chelsea R; Asbridge, Mark

2014-06-01

Three important and inter-related topics are addressed in this paper. First, the importance of meta-analysis and research synthesis methods to combine studies on traffic safety, in general, and on driver distraction, in particular, is briefly reviewed. Second, naturalistic, epidemiologic, and driving simulation studies on driver distraction are used to illustrate convergent and divergent results that have accumulated thus far in this domain of research. In particular, mobile phone conversation, passenger presence, and text messaging naturalistic studies use meta-analyses and research syntheses to illustrate important patterns of results that are in need of more in-depth study. Third, a number of driver distraction study limitations such as poorly defined dependent variables, lack of methodological detail, and omission of statistical information prevent the integration of many studies into meta-analyses. In addition, the overall quality of road safety studies suffers from these same limitations and suggestions for improvement are made to guide researchers and reviewers. Practical Applications. The use of research synthesis and meta-analysis provide comprehensive estimates of the impact of distractions on driving performance, which can be used to guide public policy and future research. Copyright © 2014 National Safety Council and Elsevier Ltd. All rights reserved.

Analysing the usage and evidencing the importance of fast chargers for the adoption of battery electric vehicles

DOE PAGES

Neaimeh, Myriam; Salisbury, Shawn D.; Hill, Graeme A.; ...

2017-06-27

An appropriate charging infrastructure is one of the key aspects needed to support the mass adoption of battery electric vehicles (BEVs), and it is suggested that publically available fast chargers could play a key role in this infrastructure. As fast charging is a relatively new technology, very little research is conducted on the topic using real world datasets, and it is of utmost importance to measure actual usage of this technology and provide evidence on its importance to properly inform infrastructure planning. 90,000 fast charge events collected from the first large-scale roll-outs and evaluation projects of fast charging infrastructure inmore » the UK and the US and 12,700 driving days collected from 35 BEVs in the UK were analysed. Using multiple regression analysis, we examined the relationship between daily driving distance and standard and fast charging and demonstrated that fast chargers are more influential. Fast chargers enabled using BEVs on journeys above their single-charge range that would have been impractical using standard chargers. Fast chargers could help overcome perceived and actual range barriers, making BEVs more attractive to future users. At current BEV market share, there is a vital need for policy support to accelerate the development of fast charge networks.« less

Analysing the usage and evidencing the importance of fast chargers for the adoption of battery electric vehicles

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

Neaimeh, Myriam; Salisbury, Shawn D.; Hill, Graeme A.

An appropriate charging infrastructure is one of the key aspects needed to support the mass adoption of battery electric vehicles (BEVs), and it is suggested that publically available fast chargers could play a key role in this infrastructure. As fast charging is a relatively new technology, very little research is conducted on the topic using real world datasets, and it is of utmost importance to measure actual usage of this technology and provide evidence on its importance to properly inform infrastructure planning. 90,000 fast charge events collected from the first large-scale roll-outs and evaluation projects of fast charging infrastructure inmore » the UK and the US and 12,700 driving days collected from 35 BEVs in the UK were analysed. Using multiple regression analysis, we examined the relationship between daily driving distance and standard and fast charging and demonstrated that fast chargers are more influential. Fast chargers enabled using BEVs on journeys above their single-charge range that would have been impractical using standard chargers. Fast chargers could help overcome perceived and actual range barriers, making BEVs more attractive to future users. At current BEV market share, there is a vital need for policy support to accelerate the development of fast charge networks.« less

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

Datta, Kaustuv; Neder, Reinhard B.; Chen, Jun

Revelation of unequivocal structural information at the atomic level for complex systems is uniquely important for deeper and generic understanding of the structure property connections and a key challenge in materials science. Here in this paper we report an experimental study of the local structure by applying total elastic scattering and Raman scattering analyses to an important non-relaxor ferroelectric solid solution exhibiting the so-called composition-induced morphotropic phase boundary (MPB), where concomitant enhancement of physical properties have been detected. The powerful combination of static and dynamic structural probes enabled us to derive direct correspondence between the atomic-level structural correlations and reportedmore » properties. The atomic pair distribution functions obtained from the neutron total scattering experiments were analysed through big-box atom-modelling implementing reverse Monte Carlo method, from which distributions of magnitudes and directions of off-centred cationic displacements were extracted. We found that an enhanced randomness of the displacement-directions for all ferroelectrically active cations combined with a strong dynamical coupling between the A- and B-site cations of the perovskite structure, can explain the abrupt amplification of piezoelectric response of the system near MPB. Finally, altogether this provides a more fundamental basis in inferring structure-property connections in similar systems including important implications in designing novel and bespoke materials.« less

Operationalizing System Importance Measures for Assessing System of System Resilience

NASA Astrophysics Data System (ADS)

Chandrahasa, Rakshit

In recent times, there has been a shift in focus from component level to system level analysis and an increasing effort to understand and design resilience into the system. Several efforts have been carried out in creating metrics to analyse resilience. Understanding and implementing system resilience in complex System of Systems will help us in building safer and resilient systems. System Importance Measures (SIMs) was formulated to analyse System of System resilience and help in designing a resilient SoS. Here, we operationalize these System Importance Measures for designing a resilient SoS. We first look at the existing methodology to improve the visual representation of system resilience and its usability. We demonstrate this using our first case study with a Naval warfare SoS. We incorporate probability into the SIM formulation. We expand the existing SIMs to quantify the effects of disruptions and mitigation likelihoods. We built a second case study based on Air transportation networks and demonstrated our expanded metrics in both the case studies. SIM based analysis of SoS resilience provides us with two different analysis of resilience, with and without probability. Having an outlook on how the resilience changes with a probability of disruptions can aid the designer making informed choices on design changes and help in creating a resilient SoS.

Environmental effects of interstate power trading on electricity consumption mixes

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

Joe Marriott; H. Scott Matthews

2005-11-15

Although many studies of electricity generation use national or state average generation mix assumptions, in reality a great deal of electricity is transferred between states with very different mixes of fossil and renewable fuels, and using the average numbers could result in incorrect conclusions in these studies. The authors create electricity consumption profiles for each state and for key industry sectors in the U.S. based on existing state generation profiles, net state power imports, industry presence by state, and an optimization model to estimate interstate electricity trading. Using these 'consumption mixes' can provide a more accurate assessment of electricity usemore » in life-cycle analyses. It is concluded that the published generation mixes for states that import power are misleading, since the power consumed in-state has a different makeup than the power that was generated. And, while most industry sectors have consumption mixes similar to the U.S. average, some of the most critical sectors of the economy - such as resource extraction and material processing sectors - are very different. This result does validate the average mix assumption made in many environmental assessments, but it is important to accurately quantify the generation methods for electricity used when doing life-cycle analyses. 16 refs., 7 figs., 2 tabs.« less

Understanding differences in access to water fountains and sugar-sweetened beverages in children׳s environments: a pilot study in high and low deprivation neighbourhoods.

PubMed

Pearson, Amber L; de Latour, Phillip; Kemp, Gabrielle; Findlay, Nohoana; Halim, Angela; Atkinson, Nicola; Chong, Mark; Cameron, Rose; Brown, Courtney; Kim, Grace; Campbell, Paul; Hills, Toby; Jayawant, Aditya; Chae, Matthew; Bhagavan, Chiranth; French, Claire; Jenkin, Gabrielle; Smith, Moira; Signal, Louise

2014-11-01

Access to water fountains and sugar-sweetened beverages (SSBs) in children׳s environments may impact on child obesity and may vary with neighbourhood deprivation. Our pilot analyses of access to water fountains and SSBs in Wellington, New Zealand revealed that water fountain access was high in school environments and low in recreational environments. There were also differences in water fountain and SSB access points by neighbourhood deprivation. The methods piloted in this study could be translated in a larger study, more capable of detecting significant differences in access and allowing for more sophisticated analyses. Such future studies may provide important evidence for the improvement of children׳s health and well-being. Copyright © 2014 Elsevier Ltd. All rights reserved.

Patient-provider discussions about lung cancer screening pre- and post-guidelines: Health Information National Trends Survey (HINTS).

PubMed

Carter-Harris, Lisa; Tan, Andy S L; Salloum, Ramzi G; Young-Wolff, Kelly C

2016-11-01

In 2013, the USPSTF issued a Grade B recommendation that long-term current and former smokers receive lung cancer screening. Shared decision-making is important for individuals considering screening, and patient-provider discussions an essential component of the process. We examined prevalence and predictors of lung cancer screening discussions pre- and post-USPSTF guidelines. Data were obtained from two cycles of the Health Information National Trends Survey (2012; 2014). The analyzed sample comprised screening-eligible current and former smokers with no personal history of lung cancer (n=746 in 2012; n=795 in 2014). Descriptive and multiple logistic regression analyses were conducted; patient-reported discussion about lung cancer screening with provider was the outcome of interest. Contrary to expectations, patient-provider discussions about lung cancer screening were more prevalent pre-guideline, but overall patient-provider discussions were low in both years (17% in 2012; 10% in 2014). Current smokers were more likely to have had a discussion than former smokers. Significant predictors of patient-provider discussions included family history of cancer and having healthcare coverage. The prevalence of patient-provider discussions about lung cancer screening is suboptimal. There is a critical need for patient and provider education about shared decision-making and its importance in cancer screening decisions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

76 FR 4278 - Notice of Availability of Pest Risk Analyses for the Importation of Fresh Edible Flowers of Izote...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-25

... inflorescences of chufle, and fresh leaves of chipilin from El Salvador. Based on those analyses, we believe that... of chipilin from El Salvador. We are making the pest risk analyses available to the public for review... request from the Government of El Salvador to allow the importation of edible fresh flowers of izote...

From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

PubMed Central

2014-01-01

Background Next-generation sequencing has provided a wealth of plastid genome sequence data from an increasingly diverse set of green plants (Viridiplantae). Although these data have helped resolve the phylogeny of numerous clades (e.g., green algae, angiosperms, and gymnosperms), their utility for inferring relationships across all green plants is uncertain. Viridiplantae originated 700-1500 million years ago and may comprise as many as 500,000 species. This clade represents a major source of photosynthetic carbon and contains an immense diversity of life forms, including some of the smallest and largest eukaryotes. Here we explore the limits and challenges of inferring a comprehensive green plant phylogeny from available complete or nearly complete plastid genome sequence data. Results We assembled protein-coding sequence data for 78 genes from 360 diverse green plant taxa with complete or nearly complete plastid genome sequences available from GenBank. Phylogenetic analyses of the plastid data recovered well-supported backbone relationships and strong support for relationships that were not observed in previous analyses of major subclades within Viridiplantae. However, there also is evidence of systematic error in some analyses. In several instances we obtained strongly supported but conflicting topologies from analyses of nucleotides versus amino acid characters, and the considerable variation in GC content among lineages and within single genomes affected the phylogenetic placement of several taxa. Conclusions Analyses of the plastid sequence data recovered a strongly supported framework of relationships for green plants. This framework includes: i) the placement of Zygnematophyceace as sister to land plants (Embryophyta), ii) a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo sister to remaining extant gymnosperms and with gnetophytes (Gnetophyta) sister to non-Pinaceae conifers (Gnecup trees), and iii) within the monilophyte clade (Monilophyta), Equisetales + Psilotales are sister to Marattiales + leptosporangiate ferns. Our analyses also highlight the challenges of using plastid genome sequences in deep-level phylogenomic analyses, and we provide suggestions for future analyses that will likely incorporate plastid genome sequence data for thousands of species. We particularly emphasize the importance of exploring the effects of different partitioning and character coding strategies. PMID:24533922

Quality care for persons experiencing dementia: the significance of relational ethics.

PubMed

Sellevold, Gerd S; Egede-Nissen, Veslemøy; Jakobsen, Rita; Sørlie, Venke

2013-05-01

The degree of success in creating quality care for people suffering from dementia is limited despite extensive research. This article describes healthcare providers' experience with the ethical challenges and possibilities in the relationship with patients suffering from dementia and its impact on quality care. The material is based on qualitative, in-depth individual narrative interviews with 12 professional healthcare providers from two different nursing homes. The transcribed interview texts were subjected to a phenomenological-hermeneutical interpretation. To provide quality care to patients with dementia, the healthcare providers emphasized the importance of sensing and understanding the patients' emotional and bodily expressions through sentient attentiveness and recognition of the patient as a person. They also described reciprocity of expressions in the relationship where the patient recognized them both as persons and healthcare providers. The analyses of the findings are, inter alia, discussed in light of Løgstrup's relational philosophy of ethics.

Patient and healthcare perspectives on the importance and efficacy of addressing spiritual issues within an interdisciplinary bone marrow transplant clinic: a qualitative study

PubMed Central

Sinclair, Shane; McConnell, Shelagh; Raffin Bouchal, Shelley; Ager, Naree; Booker, Reanne; Enns, Bert; Fung, Tak

2015-01-01

Objectives The purpose of this study was to use a qualitative approach to better understand the importance and efficacy of addressing spiritual issues within an interdisciplinary bone marrow transplant clinic from the perspectives of patients and healthcare providers. Setting Participants were recruited from the bone marrow transplant clinic of a large urban outpatient cancer care centre in western Canada. Participants: Focus groups were conducted with patients (n=7) and healthcare providers (n=9) to explore the importance of addressing spiritual issues across the treatment trajectory and to identify factors associated with effectively addressing these needs. Results Data were analysed using the qualitative approach of latent content analysis. Addressing spiritual issues was understood by patients and healthcare providers, as a core, yet under addressed, component of comprehensive care. Both sets of participants felt that addressing basic spiritual issues was the responsibility of all members of the interdisciplinary team, while recognising the need for specialised and embedded support from a spiritual care professional. While healthcare providers felt that the impact of the illness and treatment had a negative effect on patients’ spiritual well-being, patients felt the opposite. Skills, challenges, key time points and clinical indicators associated with addressing spiritual issues were identified. Conclusions Despite a number of conceptual and clinical challenges associated with addressing spiritual issues patients and their healthcare providers emphasised the importance of an integrated approach whereby basic spiritual issues are addressed by members of the interdisciplinary team and by an embedded spiritual care professional, who in addition also provides specialised support. The identification of clinical issues associated with addressing spiritual needs provides healthcare providers with clinical guidance on how to better integrate this aspect of care into their clinical practice, while also identifying acute incidences when a more targeted and specialised approach may be of benefit. PMID:26614623

The self-perceived knowledge, skills and attitudes of Australian practice nurses in providing nutrition care to patients with chronic disease.

PubMed

Martin, Louise; Leveritt, Michael D; Desbrow, Ben; Ball, Lauren E

2014-04-01

Nutrition is important for the management of chronic diseases. While practice nurses have numerous roles in primary care, the expectations on practice nurses to provide nutrition care for chronic disease management are increasing. The self-perceived knowledge, skills and attitudes of practice nurses in providing nutrition care has not been widely investigated. The aim of the present study was to investigate the perceptions of Australian practice nurses on the provision of nutrition care for chronic disease management, including specific nutrition-related activities. A cross-sectional online survey was completed by 181 Australian practice nurses in 2013. Descriptive analyses were conducted on each survey item. The survey sample was tested for representation of the Australian practice nurse workforce, and associations between respondents' demographic characteristics and responses to survey items were explored. Almost all practice nurses (89%) felt it was important to address diet whenever they cared for a patient. Over half of practice nurses (61%) were unsure if their practices were effective in increasing patients' compliance with nutritional recommendations. Nearly all practice nurses (98%) perceived further education on nutrition would assist them in their role. Practice nurses perceive they have an important role and favourable attitudes towards providing nutrition care; however, further training and education to enhance their self-perceived effectiveness is warranted. Future research should clarify whether an increase in nutrition-focused training results in improved effectiveness of nutrition care provided by practice nurses in terms of patient health outcomes.

In silico analysis of the fucosylation-associated genome of the human blood fluke Schistosoma mansoni: cloning and characterization of the enzymes involved in GDP-L-fucose synthesis and Golgi import

PubMed Central

2013-01-01

Background Carbohydrate structures of surface-expressed and secreted/excreted glycoconjugates of the human blood fluke Schistosoma mansoni are key determinants that mediate host-parasite interactions in both snail and mammalian hosts. Fucose is a major constituent of these immunologically important glycans, and recent studies have sought to characterize fucosylation-associated enzymes, including the Golgi-localized fucosyltransferases that catalyze the transfer of L-fucose from a GDP-L-fucose donor to an oligosaccharide acceptor. Importantly, GDP-L-fucose is the only nucleotide-sugar donor used by fucosyltransferases and its availability represents a bottleneck in fucosyl-glycotope expression. Methods A homology-based genome-wide bioinformatics approach was used to identify and molecularly characterize the enzymes that contribute to GDP-L-fucose synthesis and Golgi import in S. mansoni. Putative functions were further investigated through molecular phylogenetic and immunocytochemical analyses. Results We identified homologs of GDP-D-mannose-4,6-dehydratase (GMD) and GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase (GMER), which constitute a de novo pathway for GDP-L-fucose synthesis, in addition to a GDP-L-fucose transporter (GFT) that putatively imports cytosolic GDP-L-fucose into the Golgi. In silico primary sequence analyses identified characteristic Rossman loop and short-chain dehydrogenase/reductase motifs in GMD and GMER as well as 10 transmembrane domains in GFT. All genes are alternatively spliced, generating variants of unknown function. Observed quantitative differences in steady-state transcript levels between miracidia and primary sporocysts may contribute to differential glycotope expression in early larval development. Additionally, analyses of protein expression suggest the occurrence of cytosolic GMD and GMER in the ciliated epidermal plates and tegument of miracidia and primary sporocysts, respectively, which is consistent with previous localization of highly fucosylated glycotopes. Conclusions This study is the first to identify and characterize three key genes that are putatively involved in the synthesis and Golgi import of GDP-L-fucose in S. mansoni and provides fundamental information regarding their genomic organization, genetic variation, molecular phylogenetics, and developmental expression in intramolluscan larval stages. PMID:23835114

In silico analysis of the fucosylation-associated genome of the human blood fluke Schistosoma mansoni: cloning and characterization of the enzymes involved in GDP-L-fucose synthesis and Golgi import.

PubMed

Peterson, Nathan A; Anderson, Tavis K; Wu, Xiao-Jun; Yoshino, Timothy P

2013-07-09

Carbohydrate structures of surface-expressed and secreted/excreted glycoconjugates of the human blood fluke Schistosoma mansoni are key determinants that mediate host-parasite interactions in both snail and mammalian hosts. Fucose is a major constituent of these immunologically important glycans, and recent studies have sought to characterize fucosylation-associated enzymes, including the Golgi-localized fucosyltransferases that catalyze the transfer of L-fucose from a GDP-L-fucose donor to an oligosaccharide acceptor. Importantly, GDP-L-fucose is the only nucleotide-sugar donor used by fucosyltransferases and its availability represents a bottleneck in fucosyl-glycotope expression. A homology-based genome-wide bioinformatics approach was used to identify and molecularly characterize the enzymes that contribute to GDP-L-fucose synthesis and Golgi import in S. mansoni. Putative functions were further investigated through molecular phylogenetic and immunocytochemical analyses. We identified homologs of GDP-D-mannose-4,6-dehydratase (GMD) and GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase (GMER), which constitute a de novo pathway for GDP-L-fucose synthesis, in addition to a GDP-L-fucose transporter (GFT) that putatively imports cytosolic GDP-L-fucose into the Golgi. In silico primary sequence analyses identified characteristic Rossman loop and short-chain dehydrogenase/reductase motifs in GMD and GMER as well as 10 transmembrane domains in GFT. All genes are alternatively spliced, generating variants of unknown function. Observed quantitative differences in steady-state transcript levels between miracidia and primary sporocysts may contribute to differential glycotope expression in early larval development. Additionally, analyses of protein expression suggest the occurrence of cytosolic GMD and GMER in the ciliated epidermal plates and tegument of miracidia and primary sporocysts, respectively, which is consistent with previous localization of highly fucosylated glycotopes. This study is the first to identify and characterize three key genes that are putatively involved in the synthesis and Golgi import of GDP-L-fucose in S. mansoni and provides fundamental information regarding their genomic organization, genetic variation, molecular phylogenetics, and developmental expression in intramolluscan larval stages.

Social Network Analysis and Nutritional Behavior: An Integrated Modeling Approach

PubMed Central

Senior, Alistair M.; Lihoreau, Mathieu; Buhl, Jerome; Raubenheimer, David; Simpson, Stephen J.

2016-01-01

Animals have evolved complex foraging strategies to obtain a nutritionally balanced diet and associated fitness benefits. Recent research combining state-space models of nutritional geometry with agent-based models (ABMs), show how nutrient targeted foraging behavior can also influence animal social interactions, ultimately affecting collective dynamics and group structures. Here we demonstrate how social network analyses can be integrated into such a modeling framework and provide a practical analytical tool to compare experimental results with theory. We illustrate our approach by examining the case of nutritionally mediated dominance hierarchies. First we show how nutritionally explicit ABMs that simulate the emergence of dominance hierarchies can be used to generate social networks. Importantly the structural properties of our simulated networks bear similarities to dominance networks of real animals (where conflicts are not always directly related to nutrition). Finally, we demonstrate how metrics from social network analyses can be used to predict the fitness of agents in these simulated competitive environments. Our results highlight the potential importance of nutritional mechanisms in shaping dominance interactions in a wide range of social and ecological contexts. Nutrition likely influences social interactions in many species, and yet a theoretical framework for exploring these effects is currently lacking. Combining social network analyses with computational models from nutritional ecology may bridge this divide, representing a pragmatic approach for generating theoretical predictions for nutritional experiments. PMID:26858671

Oral health in children in Denmark under different public dental health care schemes.

PubMed

Christensen, L B; Petersen, P E; Hede, B

2010-06-01

To describe and analyse oral health of children and adolescents under two types of dental health care schemes under the Public Dental Health Service in Denmark, and to analyse possible influence of socio-economic and socio-cultural factors. Data on children's oral health status was obtained from public oral health registers and were pooled with data from questionnaires sent to parents of the children and adolescents. The study comprised individuals aged 5, 12 and 15, in total 2168 persons, randomly drawn from four municipalities with dental care provided by salaried dentists in public dental clinics and three municipalities with dental care provided by dentists in private practice. 70% of the parents completed a questionnaire including questions on socio-economic and socio-cultural background, lifestyle-related factors, self assessment of parents' oral- and general health. After the data were merged, the final study population represented 60% of the original target population. The mean caries experience (DMFS+dmfs) was 2.2 and further analysis of caries experience in each age group showed no variations in relation to type of provider of dental care. However, multiple dummy regression analyses demonstrated that low education, poor general health, foreign citizenship and smoking habits of the parents were important determinants for high level of caries in their children. Occurrence of dental caries as well as changes over time in levels of dental caries of Danish children did not vary by scheme of Public Dental Health Service, i.e. whether dental health care was provided by public employed dentists or by private practitioners. However, social inequalities still relate to caries experience in children and adolescents. Adjustment of preventive oral health activities strategy seems to be needed.

Predictors of scoring at least 600 on COMLEX-USA Level 1: successful preparation strategies.

PubMed

Vora, Aditya; Maltezos, Nathan; Alfonzo, Lauren; Hernandez, Nilda; Calix, Erica; Fernandez, M Isabel

2013-02-01

Comprehensive Osteopathic Medical Licensing Examination-USA (COMLEX-USA) Level 1 scores are an important criterion used by residency directors to make residency placement decisions. To explore the association between scoring at least 600 on COMLEX-USA Level 1 and grade point average (GPA), scores on the Medical College Admission Test (MCAT), and different test preparation strategies. Third-year osteopathic medical students at Nova Southeastern University were invited to complete a self-administered survey regarding their COMLEX-USA preparation strategies and to provide consent for the researchers to access their preclinical GPA and their MCAT and COMLEX-USA scores. Descriptive analyses were conducted to understand examination preparation procedures and resources used, and bivariate analyses were conducted to identify the statisically significant predictors of scoring 600 or higher. Two separate logistic regressions were also run. The first included all of the statisically significant factors that emerged from the bivariate analyses, and the second examined which candidate predictors remained statistically significant once the effects of GPA and MCAT scores were removed. One hundred twenty-two students completed the survey, and 113 (93%) provided informed consent to access their preclinical GPA and their MCAT and COMLEX-USA scores. In the first regression, scoring 600 or higher was associated with a higher GPA (P<.02), a higher MCAT score (P<.05), earlier preparation initiation (P<.05), and not ranking the Comprehensive Osteopathic Medical Self-Assessment Examination (COMSAE) as the most helpful practice examination (P<.04). In the second regression, scoring 600 or higher was associated with earlier initiation of examination preparation (P<.01) and not ranking COMBANK (question bank for COMLEX-USA) as the most helpful question bank (P<.03). Among the different examination preparation methods, the specific resources ranked as most helpful were First Aid for the USMLE (United States Medical Licensing Examination) (review book), the COMSAE (practice examination); COMBANK (question bank); and Kaplan USMLE (lecture videos). Preclinical GPA and MCAT scores continue to be important predictors of scoring at least 600 on COMLEX-USA Level 1. However, the findings underscore the importance of maintaining a high GPA during the first 2 years of medical school and initiating COMLEX-USA preparation early.

Ozone process insights from field experiments - part I: overview

NASA Astrophysics Data System (ADS)

Hidy, G. M.

This paper gives an overview of selected approaches recently adopted to analyze observations from field experiments that characterize the tropospheric physics and chemistry of ozone and related oxidation products. Analysis of ambient oxidant and precursor concentration measurements, combined with meteorological observations, has provided important information about tropospheric processes. Projection of the response of tropospheric ozone concentrations to changes in precursor emissions is achieved through emissions based air quality models (AQMs). These models integrate several "process" elements from source emissions to meteorological and chemical phenomena. Through field campaigns, new knowledge has become available which has enabled workers to better understand the strengths and weaknesses of AQMs and their components. Examples of insightful results include: (a) reconciliation of ambient concentrations of speciated volatile organic compounds (VOCs) with estimates from emissions models, and inventories, (b) verification of chemical mechanisms for ozone formation from its precursors using approximations applicable in different chemical regimes, (c) inference of regimes of sensitivity in ozone concentration to changes in VOC and NO x precursors from ozone management practices, (d) conceptualization of important air mass transport and mixing processes on different spatial and temporal scales that affect ozone and precursor concentrations distributions, and (e) application of the analysis of spatial and temporal variance to infer the origins of chemical product transport, and precursor distributions. Studies from the first category have been used to improve emissions models substantially over previous forms. The remainder of the analyses has yielded valuable insight into the chemical and meteorological mechanisms at work on different spatial and temporal scales. The methods have provided an observationally based framework for effective choices to improve ozone management, notably in terms of NO x or VOC sensitive regimes. Investigation of meteorological processes relevant to ozone accumulation has illustrated the importance of accounting for both transport winds and the day-night vertical structure of the atmosphere in AQM analyses. Finally, variance analyses of O 3 concentrations with other aerometric parameters offer significant opportunities to use semi-empirically air monitoring data as a means determining space and time scales of O 3 variance, and detecting precursor emissions source-ozone receptor relationships.

The Experimental Design Assistant.

PubMed

Percie du Sert, Nathalie; Bamsey, Ian; Bate, Simon T; Berdoy, Manuel; Clark, Robin A; Cuthill, Innes; Fry, Derek; Karp, Natasha A; Macleod, Malcolm; Moon, Lawrence; Stanford, S Clare; Lings, Brian

2017-09-01

Addressing the common problems that researchers encounter when designing and analysing animal experiments will improve the reliability of in vivo research. In this article, the Experimental Design Assistant (EDA) is introduced. The EDA is a web-based tool that guides the in vivo researcher through the experimental design and analysis process, providing automated feedback on the proposed design and generating a graphical summary that aids communication with colleagues, funders, regulatory authorities, and the wider scientific community. It will have an important role in addressing causes of irreproducibility.

Validation of an In Vitro Bioaccessibility Test Method for Estimation of Bioavailability of Arsenic from Soil and Sediment

DTIC Science & Technology

2012-12-01

calibrated using a certified mineral or pure metal standard and counting times are chosen to provide 3-sigma detection limits of between 100-200 ppm...also submit “blind” duplicates for analyses. The precision of the data generated by the “EMPA point count ” will be evaluated by calculating RPD values...important to consider the variation in results among all samples studied for a particular media, since the overall particle count is very large. Data

The Experimental Design Assistant

PubMed Central

Bamsey, Ian; Bate, Simon T.; Berdoy, Manuel; Clark, Robin A.; Cuthill, Innes; Fry, Derek; Karp, Natasha A.; Macleod, Malcolm; Moon, Lawrence; Stanford, S. Clare; Lings, Brian

2017-01-01

Addressing the common problems that researchers encounter when designing and analysing animal experiments will improve the reliability of in vivo research. In this article, the Experimental Design Assistant (EDA) is introduced. The EDA is a web-based tool that guides the in vivo researcher through the experimental design and analysis process, providing automated feedback on the proposed design and generating a graphical summary that aids communication with colleagues, funders, regulatory authorities, and the wider scientific community. It will have an important role in addressing causes of irreproducibility. PMID:28957312

Sex as a Biological Variable: Who, What, When, Why, and How.

PubMed

Bale, Tracy L; Epperson, C Neill

2017-01-01

The inclusion of sex as a biological variable in research is absolutely essential for improving our understanding of disease mechanisms contributing to risk and resilience. Studies focusing on examining sex differences have demonstrated across many levels of analyses and stages of brain development and maturation that males and females can differ significantly. This review will discuss examples of animal models and clinical studies to provide guidance and reference for the inclusion of sex as an important biological variable relevant to a Neuropsychopharmacology audience.

Studies of yeast cell oxygenation and energetics by laser fluorometry of reduced nicotinamide adenine dinucleotide

NASA Astrophysics Data System (ADS)

Pan, Fu-shih; Chen, Stephen; Mintzer, Robert A.; Chen, Chin-Tu; Schumacker, Paul

1991-03-01

It is of fundamental importance for biological scientists to assess cellular energetics. Under aerobic conditions, the tricarboxylic acid cycle (TCA cycle) is coupled with the mitochondrial electron cascade pathway to provide the cell with energy. The nicotinamide adenine dinucleotide-conjugated pair (NAD and NADH) is the coenzyme in numerous important biomedical reactions which include several important dehydrogenase reactions in the TCA cycle. Based on Le Chatelier's principle, NADH will accumulate when this energy production mechanism is impaired. The relative amounts of NAD and NADH in a cell are defined as the redox state of the cell (Williamson et.al. 1967) which provides a valuable index of cellular energetics. The sum of the amounts of NAD and NADH in a cell may be assumed to be constant during a finite time; therefore, a reliable means of measuring the NADH concentration would provide us with a useful indicator of tissue viability. Traditionally, the quantities of NADH and NAD may be measured by chemical assay methods. We can avoid these tediois analyses by exploiting the significant difference between the ultraviolet absorption spectra of this redox pair. However, because of the opacity of biological samples and the interference of other biochemicals that also absorb ultraviolet radiation, measurement of NADH and NAD+ concentrations in vivo by absorption spectroscopy is not feasible.

Needs and care of older people living at home in Iceland.

PubMed

Sigurdardottir, Sigurveig H; Sundstrom, Gerdt; Malmberg, Bo; Bravell, Marie Ernsth

2012-02-01

The Icelandic old-age care system is universal and the official goal is to support older people live independently for as long as possible. The aim of this study is to analyse living conditions and use of formal and informal care of older people in Iceland. The results are based on the new study ICEOLD, a telephone survey which included questions on social network, health, activities of daily living, and received support from the community and/or from relatives, neighbours, and friends. Almost half of the sample (47%) receives some kind of care, with 27% of them receiving only informal care, which is understood to mean that informal care is of great importance and families are the main providers of help. For hypothetical future long-term care, older people wish to be cared for in their homes, but those already in need of assistance prefer to be cared for in institutions. Caring relatives are the main providers of support to older people in their homes and it is important to provide them with suitable formal support when the care responsibility increases. As the care system in Iceland is now under reconstruction, the important contribution of informal carers must be recognised and taken into account when planning the care of older people.

Multicentre, Prospective Observational Study of Pegfilgrastim Primary Prophylaxis in Patients at High Risk of Febrile Neutropenia in Poland: PROFIL Study

PubMed Central

Jurczak, Wojciech; Kalinka-Warzocha, Ewa; Chmielowska, Ewa; Duchnowska, Renata; Wojciechowska-Lampka, Elzbieta

2015-01-01

Aim of the study PROFIL was a prospective observational study conducted to investigate physicians’ evaluation of febrile neutropenia (FN) risk and reasons for giving pegfilgrastim primary prophylaxis (PP) in routine clinical practice in Poland. Material and methods Adult cancer patients treated with chemotherapy (CT), assessed by investigators as having high overall FN risk, and who received pegfilgrastim in cycle 1 were enrolled between 03/2009 and 09/2010. Investigators assessed FN risk of the CT regimen, individual risk factors, and overall FN risk, and were asked to provide the most important reasons for providing pegfilgrastim PP. Investigator-assessed CT FN risk was compared with guideline classification. Results Data were analysed from 1006 breast, ovarian, and lung cancer, and non-Hodgkin (NHL) and Hodgkin lymphoma (HL) patients. The most important reasons for using pegfilgrastim PP were high CT FN risk and advanced disease; these were consistent across tumour types and treatment intent. The investigators generally assessed high CT FN risk in agreement with guideline classification. Febrile neutropenia occurred in 4% of patients, most commonly in HL, NHL, and patients with advanced disease. Conclusions High CT FN risk and advanced stage of disease were found to be the most important reasons for providing pegfilgrastim PP by physicians in Poland. PMID:26557762

Temperature threshold models for benthic macroinvertebrates in Idaho wadeable streams and neighboring ecoregions.

PubMed

Richards, David C; Lester, Gary; Pfeiffer, John; Pappani, Jason

2018-02-07

Water temperatures are warming throughout the world including the Pacific Northwest, USA. Benthic macroinvertebrates are one of the most important and widely used indicators of freshwater impairment; however, their response to increased water temperatures and their use for monitoring water temperature impairment has been hindered by lack of knowledge of temperature occurrences, threshold change points, or indicator taxa. We present new analysis of a large macroinvertebrate database provided by Idaho Department of Environmental Quality from wadeable streams in Idaho that is to be used in conjunction with our previous analyses. This new analysis provides threshold change points for over 400 taxa along an increasing temperature gradient and provides a list of statistically important indicator taxa. The macroinvertebrate assemblage temperature change point for the taxa that decreased with increased temperatures was determined to be about 20.5 °C and for the taxa assemblage that increased with increased temperatures was about 11.5 °C. Results of this new analysis combined with our previous analysis will also be useful for others in neighboring regions where these taxa occur.

Electron donor concentrations in sediments and sediment properties at the agricultural chemicals team research site near New Providence, Iowa, 2006-07

USGS Publications Warehouse

Maharjan, Bijesh; Korom, Scott F.; Smith, Erik A.

2013-01-01

The concentrations of electron donors in aquifer sediments are important to the understanding of the fate and transport of redox-sensitive constituents in groundwater, such as nitrate. For a study by the U.S. Geological Survey National Water-Quality Assessment Program, 50 sediment samples were collected from below the water table from 11 boreholes at the U.S. Geological Survey Agricultural Chemicals Team research site near New Providence, Iowa, during 2006-07. All samples were analyzed for gravel, sand (coarse, medium, and fine), silt, clay, Munsell soil color, inorganic carbon content, and for the following electron donors: organic carbon, ferrous iron, and inorganic sulfide. A subset of 14 sediment samples also was analyzed for organic sulfur, but all of these samples had concentrations less than the method detection limit; therefore, the presence of this potential electron donor was not considered further. X-ray diffraction analyses provided important semi-quantitative information of well-crystallized dominant minerals within the sediments that might be contributing electron donors.

Clustered multistate models with observation level random effects, mover-stayer effects and dynamic covariates: modelling transition intensities and sojourn times in a study of psoriatic arthritis.

PubMed

Yiu, Sean; Farewell, Vernon T; Tom, Brian D M

2018-02-01

In psoriatic arthritis, it is important to understand the joint activity (represented by swelling and pain) and damage processes because both are related to severe physical disability. The paper aims to provide a comprehensive investigation into both processes occurring over time, in particular their relationship, by specifying a joint multistate model at the individual hand joint level, which also accounts for many of their important features. As there are multiple hand joints, such an analysis will be based on the use of clustered multistate models. Here we consider an observation level random-effects structure with dynamic covariates and allow for the possibility that a subpopulation of patients is at minimal risk of damage. Such an analysis is found to provide further understanding of the activity-damage relationship beyond that provided by previous analyses. Consideration is also given to the modelling of mean sojourn times and jump probabilities. In particular, a novel model parameterization which allows easily interpretable covariate effects to act on these quantities is proposed.

Evidence-based practice implementation: the impact of public versus private sector organization type on organizational support, provider attitudes, and adoption of evidence-based practice.

PubMed

Aarons, Gregory A; Sommerfeld, David H; Walrath-Greene, Christine M

2009-12-31

The goal of this study is to extend research on evidence-based practice (EBP) implementation by examining the impact of organizational type (public versus private) and organizational support for EBP on provider attitudes toward EBP and EBP use. Both organization theory and theory of innovation uptake and individual adoption of EBP guide the approach and analyses in this study. We anticipated that private sector organizations would provide greater levels of organizational support for EBPs leading to more positive provider attitudes towards EBPs and EBP use. We also expected attitudes toward EBPs to mediate the association of organizational support and EBP use. Participants were mental health service providers from 17 communities in 16 states in the United States (n = 170). Path analyses were conducted to compare three theoretical models of the impact of organization type on organizational support for EBP and of organizational support on provider attitudes toward EBP and EBP use. Consistent with our predictions, private agencies provided greater support for EBP implementation, and staff working for private agencies reported more positive attitudes toward adopting EBPs. Organizational support for EBP partially mediated the association of organization type on provider attitudes toward EBP. Organizational support was significantly positively associated with attitudes toward EBP and EBP use in practice. This study offers further support for the importance of organizational context as an influence on organizational support for EBP and provider attitudes toward adopting EBP. The study demonstrates the role organizational support in provider use of EBP in practice. This study also suggests that organizational support for innovation is a malleable factor in supporting use of EBP. Greater attention should be paid to organizational influences that can facilitate the dissemination and implementation of EBPs in community settings.

A morphologic characterisation of the 1963 Vajont Slide, Italy, using long-range terrestrial photogrammetry

NASA Astrophysics Data System (ADS)

Wolter, Andrea; Stead, Doug; Clague, John J.

2014-02-01

The 1963 Vajont Slide in northeast Italy is an important engineering and geological event. Although the landslide has been extensively studied, new insights can be derived by applying modern techniques such as remote sensing and numerical modelling. This paper presents the first digital terrestrial photogrammetric analyses of the failure scar, landslide deposits, and the area surrounding the failure, with a focus on the scar. We processed photogrammetric models to produce discontinuity stereonets, residual maps and profiles, and slope and aspect maps, all of which provide information on the failure scar morphology. Our analyses enabled the creation of a preliminary semi-quantitative morphologic classification of the Vajont failure scar based on the large-scale tectonic folds and step-paths that define it. The analyses and morphologic classification have implications for the kinematics, dynamics, and mechanism of the slide. Metre- and decametre-scale features affected the initiation, direction, and displacement rate of sliding. The most complexly folded and stepped areas occur close to the intersection of orthogonal synclinal features related to the Dinaric and Neoalpine deformation events. Our analyses also highlight, for the first time, the evolution of the Vajont failure scar from 1963 to the present.

Preservation of pathological tissue specimens by freeze-drying for immunohistochemical staining and various molecular biological analyses.

PubMed

Matsuo, S; Sugiyama, T; Okuyama, T; Yoshikawa, K; Honda, K; Takahashi, R; Maeda, S

1999-05-01

Conditions of preserving DNA, RNA and protein in pathological specimens are of great importance as degradation of such macromolecules would critically affect results of molecular biological analysis. The feasibility of freeze-drying as a means of preserving pathological tissue samples for molecular analysis has previously been shown. In the present study, further tests on long-term storage conditions and analyses of freeze-dried samples by polymerase chain reaction (PCR), reverse transcriptase (RT)-PCR, western blotting and immunohistochemistry are reported. Rat chromosomal DNA of freeze-dried samples stored for 4 years showed slight degradation while RNA degradation was more prominently seen at an earlier stage of storage. However, these 4 year DNA and RNA samples were still able to serve as a template for some PCR and RT-PCR analyses, respectively. Overexpression of c-erbB-2 and p53 protein was demonstrated by western blotting and immunohistochemical staining using freeze-dried human breast cancer tissues. Although macromolecules in freeze-dried samples degrade to some extent during the preservation period, they should still be of value for certain molecular biological analyses and morphological examination; hence, providing more convenient and inexpensive ways of pathological tissue storage.

Analysis of swimming performance: perceptions and practices of US-based swimming coaches.

PubMed

Mooney, Robert; Corley, Gavin; Godfrey, Alan; Osborough, Conor; Newell, John; Quinlan, Leo Richard; ÓLaighin, Gearóid

2016-01-01

In elite swimming, a broad range of methods are used to assess performance, inform coaching practices and monitor athletic progression. The aim of this paper was to examine the performance analysis practices of swimming coaches and to explore the reasons behind the decisions that coaches take when analysing performance. Survey data were analysed from 298 Level 3 competitive swimming coaches (245 male, 53 female) based in the United States. Results were compiled to provide a generalised picture of practices and perceptions and to examine key emerging themes. It was found that a disparity exists between the importance swim coaches place on biomechanical analysis of swimming performance and the types of analyses that are actually conducted. Video-based methods are most frequently employed, with over 70% of coaches using these methods at least monthly, with analyses being mainly qualitative in nature rather than quantitative. Barriers to the more widespread use of quantitative biomechanical analysis in elite swimming environments were explored. Constraints include time, cost and availability of resources, but other factors such as sources of information on swimming performance and analysis and control over service provision are also discussed, with particular emphasis on video-based methods and emerging sensor-based technologies.

Partner aggression and problem drinking across the lifespan: how much do they decline?

PubMed

O'Leary, K Daniel; Woodin, Erica M

2005-11-01

Cross-sectional analyses from nationally-representative samples demonstrate significant age-related trends in partner aggression and problem drinking. Both behaviors are most prevalent in the early to mid-twenties and increasingly less common thereafter. Aggregate associations based on percentage of individuals displaying the behavior in each age range are dramatically stronger than those found when correlating individuals' ages and behavior. Multilevel modeling demonstrates that group-level effects do not mask associations found at the level of the individual for either problem drinking or partner aggression. An analysis of recent abstracts from psychology journals showed that issues of aggregate and individual data are rarely if ever discussed, and even well-known statistics books in psychology rarely discuss such issues. The interpretation of aggregate data will become increasing important as psychologists themselves, and in collaboration with epidemiologists and sociologists, have access to large data sets that allow for data aggregation. Both aggregate and individual analyses are valid, although they provide answers to different questions. Individual analyses are necessary for predicting individual behavior; aggregate analyses are useful in policy planning for large scale prevention and intervention. Strengths and limitations of cross-sectional community samples and aggregate data are also discussed.

Predictors of physicians' stress related to information systems: a nine-year follow-up survey study.

PubMed

Heponiemi, Tarja; Hyppönen, Hannele; Kujala, Sari; Aalto, Anna-Mari; Vehko, Tuulikki; Vänskä, Jukka; Elovainio, Marko

2018-04-13

Among the important stress factors for physicians nowadays are poorly functioning, time consuming and inadequate information systems. The present study examined the predictors of physicians' stress related to information systems (SRIS) among Finnish physicians. The examined predictors were cognitive workload, staffing problems, time pressure, problems in teamwork and job satisfaction, adjusted for baseline levels of SRIS, age, gender and employment sector. The study has a follow-up design with two survey data collection waves, one in 2006 and one in 2015, based on a random sample of Finnish physicians was used. The present study used a sample that included 1109 physicians (61.9% women; mean age in 2015 was 54.5; range 34-72) who provided data on the SRIS in both waves. The effects of a) predictor variable levels in 2006 on SRIS in 2015 and b) the change in the predictor variables from 2006 to 2015 on SRIS in 2015 were analysed with linear regression analyses. Regression analyses showed that the higher level of cognitive workload in 2006 significantly predicted higher level of SRIS in 2015 (β = 0.08). The reciprocity of this association was tested with cross-lagged structural equation model analyses which showed that the direction of the association was from cognitive workload to SRIS, not from SRIS to cognitive workload. Moreover, increases in time pressure (β = 0.16) and problems in teamwork (β = 0.10) were associated with higher levels of SRIS in 2015, whereas job satisfaction increase was associated with lower SRIS (β = - 0.06). According to our results, physicians' cognitive workload may have long-lasting negative ramifications in regard to how stressful physicians experience their health information systems to be. Thus, organisations should pay attention to physicians workload if they wish physicians to master all the systems they need to use. It is also important to provide physicians with enough time and collegial support in their system-related problems, and in learning new systems and system updates.

Effects of dam construction and increasing pollutants on the ecohydrological evolution of a shallow freshwater lake in the Yangtze floodplain.

PubMed

Zeng, Linghan; McGowan, Suzanne; Cao, Yanmin; Chen, Xu

2018-04-15

Large river-floodplain systems which provide a variety of societal, economic and biological benefits are undergoing extensive and intensive human disturbance. However, floodplain lakes responses to multiple stressors are poorly understood. The Yangtze River and its floodplain which provide water and food resources for more than 300 million people are an important region in China. Hydrological regulation as well as socio-economic development have brought profound negative influence on this ecologically important area. To improve understanding of decadal-scale responses of floodplain lakes to multiple stressors, lake sediment proxies including particle size, geochemical elements, diatoms and chironomids were analysed in a lead-210 dated core from Futou Lake. The analyses show that dams constructed in 1935 and the early 1970s stabilized hydrological conditions in Futou Lake and impeded the interaction with the Yangtze River, resulting in a decrease in major elements (e.g., Mg, Al, Fe) transported into the lake and an increase of macrophyte-related chironomids (C. sylvestris-type, P. penicillatus-type and Paratanytarsus sp.). After the late 1990s, further decreases in major elements and increases in median grain size are attributed to the erosion of the Yangtze riverbed and declining supply of major elements-enriched sediments from the upper Yangtze caused by the impoundment of the Three Gorges Dam. Chironomid and diatom assemblages indicate that hydrological stabilization caused by dam constructions stimulated the growth of macrophytes, which may be important in buffering against an ecosystem state change towards a phytoplankton-dominated and turbid state with ongoing eutrophication. However, a recent increase in Zn, TP and the emergence of eutrophic diatom and chironomid species indicate initial signs of water quality deterioration which may be related to the combined effects of hydrological stabilization and aquaculture. Over all, the sediment record from Futou Lake emphasizes the importance of interactions between hydrological change and pollutant loads in determining floodplain lake ecosystem state. Copyright © 2017 Elsevier B.V. All rights reserved.

Getting the most out of parasitic helminth transcriptomes using HelmDB: implications for biology and biotechnology.

PubMed

Mangiola, Stefano; Young, Neil D; Korhonen, Pasi; Mondal, Alinda; Scheerlinck, Jean-Pierre; Sternberg, Paul W; Cantacessi, Cinzia; Hall, Ross S; Jex, Aaron R; Gasser, Robin B

2013-12-01

Compounded by a massive global food shortage, many parasitic diseases have a devastating, long-term impact on animal and human health and welfare worldwide. Parasitic helminths (worms) affect the health of billions of animals. Unlocking the systems biology of these neglected pathogens will underpin the design of new and improved interventions against them. Currently, the functional annotation of genomic and transcriptomic sequence data for socio-economically important parasitic worms relies almost exclusively on comparative bioinformatic analyses using model organism- and other databases. However, many genes and gene products of parasitic helminths (often >50%) cannot be annotated using this approach, because they are specific to parasites and/or do not have identifiable homologs in other organisms for which sequence data are available. This inability to fully annotate transcriptomes and predicted proteomes is a major challenge and constrains our understanding of the biology of parasites, interactions with their hosts and of parasitism and the pathogenesis of disease on a molecular level. In the present article, we compiled transcriptomic data sets of key, socioeconomically important parasitic helminths, and constructed and validated a curated database, called HelmDB (www.helmdb.org). We demonstrate how this database can be used effectively for the improvement of functional annotation by employing data integration and clustering. Importantly, HelmDB provides a practical and user-friendly toolkit for sequence browsing and comparative analyses among divergent helminth groups (including nematodes and trematodes), and should be readily adaptable and applicable to a wide range of other organisms. This web-based, integrative database should assist 'systems biology' studies of parasitic helminths, and the discovery and prioritization of novel drug and vaccine targets. This focus provides a pathway toward developing new and improved approaches for the treatment and control of parasitic diseases, with the potential for important biotechnological outcomes. Copyright © 2012 Elsevier Inc. All rights reserved.

Formalizing the definition of meta-analysis in Molecular Ecology.

PubMed

ArchMiller, Althea A; Bauer, Eric F; Koch, Rebecca E; Wijayawardena, Bhagya K; Anil, Ammu; Kottwitz, Jack J; Munsterman, Amelia S; Wilson, Alan E

2015-08-01

Meta-analysis, the statistical synthesis of pertinent literature to develop evidence-based conclusions, is relatively new to the field of molecular ecology, with the first meta-analysis published in the journal Molecular Ecology in 2003 (Slate & Phua 2003). The goal of this article is to formalize the definition of meta-analysis for the authors, editors, reviewers and readers of Molecular Ecology by completing a review of the meta-analyses previously published in this journal. We also provide a brief overview of the many components required for meta-analysis with a more specific discussion of the issues related to the field of molecular ecology, including the use and statistical considerations of Wright's FST and its related analogues as effect sizes in meta-analysis. We performed a literature review to identify articles published as 'meta-analyses' in Molecular Ecology, which were then evaluated by at least two reviewers. We specifically targeted Molecular Ecology publications because as a flagship journal in this field, meta-analyses published in Molecular Ecology have the potential to set the standard for meta-analyses in other journals. We found that while many of these reviewed articles were strong meta-analyses, others failed to follow standard meta-analytical techniques. One of these unsatisfactory meta-analyses was in fact a secondary analysis. Other studies attempted meta-analyses but lacked the fundamental statistics that are considered necessary for an effective and powerful meta-analysis. By drawing attention to the inconsistency of studies labelled as meta-analyses, we emphasize the importance of understanding the components of traditional meta-analyses to fully embrace the strengths of quantitative data synthesis in the field of molecular ecology. © 2015 John Wiley & Sons Ltd.

Mandatory HIV testing in China: the perception of health-care providers.

PubMed

Li, Li; Wu, Zunyou; Wu, Sheng; Lee, Sung-Jae; Rotheram-Borus, Mary Jane; Detels, Roger; Jia, Manhong; Sun, Stephanie

2007-07-01

Health-care providers in China are facing an exponential increase in HIV testing and HIV-positive patients. A total of 1101 service providers were recruited to examine attitudes toward people living with HIV/AIDS (PLWHA) in China. Logistic regression models were used to assess factors associated with providers' attitudes toward mandatory HIV testing. Providers were most likely to endorse mandatory HIV testing for patients with high-risk behaviour and for all patients before surgery. Over 43% of providers endorsed mandatory testing for anyone admitted to hospital. Controlling for demographics, multivariate analyses indicated that providers with higher perceived risk of HIV infection at work, higher general prejudicial attitudes toward PLWHA, and previous contact with HIV patients were more likely to endorse mandatory HIV testing for anyone admitted to hospital. Results underscore the importance of implementing universal precautions in health-care settings and call attention to social and ethical issues associated with HIV/AIDS control and treatment in China.

Provider Expectations for Recovery Scale: Refining a measure of provider attitudes

PubMed Central

Salyers, Michelle P.; Brennan, Madeline; Kean, Jacob

2014-01-01

Objective The purpose of this study was to refine and test the psychometric properties of a scale to measure provider attitudes about recovery. Methods This was a secondary data analysis that combined survey data from 1,128 mental health providers from 3 state hospitals, 6 community mental health centers, and 1 VA Medical Center. Rasch analyses were used to examine item-level functioning to reduce the scale to a briefer, unidimensional construct. Convergent validity was assessed through correlations with related measures. Results The Provider Expectations for Recovery scale had strong internal consistency, was related to education and setting in expected ways, and was associated with lower levels of burnout and higher levels of job satisfaction. Conclusions and Implications for Practice A 10-item scale of Provider Expectations for Recovery appears to be a useful tool to measure an important construct in recovery-oriented care. The process of refining the measure also highlights potential factors in how providers view recovery. PMID:23834613

Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes.

PubMed

You, Xinxin; Bian, Chao; Zan, Qijie; Xu, Xun; Liu, Xin; Chen, Jieming; Wang, Jintu; Qiu, Ying; Li, Wujiao; Zhang, Xinhui; Sun, Ying; Chen, Shixi; Hong, Wanshu; Li, Yuxiang; Cheng, Shifeng; Fan, Guangyi; Shi, Chengcheng; Liang, Jie; Tom Tang, Y; Yang, Chengye; Ruan, Zhiqiang; Bai, Jie; Peng, Chao; Mu, Qian; Lu, Jun; Fan, Mingjun; Yang, Shuang; Huang, Zhiyong; Jiang, Xuanting; Fang, Xiaodong; Zhang, Guojie; Zhang, Yong; Polgar, Gianluca; Yu, Hui; Li, Jia; Liu, Zhongjian; Zhang, Guoqiang; Ravi, Vydianathan; Coon, Steven L; Wang, Jian; Yang, Huanming; Venkatesh, Byrappa; Wang, Jun; Shi, Qiong

2014-12-02

Mudskippers are amphibious fishes that have developed morphological and physiological adaptations to match their unique lifestyles. Here we perform whole-genome sequencing of four representative mudskippers to elucidate the molecular mechanisms underlying these adaptations. We discover an expansion of innate immune system genes in the mudskippers that may provide defence against terrestrial pathogens. Several genes of the ammonia excretion pathway in the gills have experienced positive selection, suggesting their important roles in mudskippers' tolerance to environmental ammonia. Some vision-related genes are differentially lost or mutated, illustrating genomic changes associated with aerial vision. Transcriptomic analyses of mudskippers exposed to air highlight regulatory pathways that are up- or down-regulated in response to hypoxia. The present study provides a valuable resource for understanding the molecular mechanisms underlying water-to-land transition of vertebrates.

Reporting Standards for Research in Psychology

PubMed Central

2010-01-01

In anticipation of the impending revision of the Publication Manual of the American Psychological Association, APA’s Publications and Communications Board formed the Working Group on Journal Article Reporting Standards (JARS) and charged it to provide the board with background and recommendations on information that should be included in manuscripts submitted to APA journals that report (a) new data collections and (b) meta-analyses. The JARS Group reviewed efforts in related fields to develop standards and sought input from other knowledgeable groups. The resulting recommendations contain (a) standards for all journal articles, (b) more specific standards for reports of studies with experimental manipulations or evaluations of interventions using research designs involving random or nonrandom assignment, and (c) standards for articles reporting meta-analyses. The JARS Group anticipated that standards for reporting other research designs (e.g., observational studies, longitudinal studies) would emerge over time. This report also (a) examines societal developments that have encouraged researchers to provide more details when reporting their studies, (b) notes important differences between requirements, standards, and recommendations for reporting, and (c) examines benefits and obstacles to the development and implementation of reporting standards. PMID:19086746

The present and future of microplastic pollution in the marine environment.

PubMed

Ivar do Sul, Juliana A; Costa, Monica F

2014-02-01

Recently, research examining the occurrence of microplastics in the marine environment has substantially increased. Field and laboratory work regularly provide new evidence on the fate of microplastic debris. This debris has been observed within every marine habitat. In this study, at least 101 peer-reviewed papers investigating microplastic pollution were critically analysed (Supplementary material). Microplastics are commonly studied in relation to (1) plankton samples, (2) sandy and muddy sediments, (3) vertebrate and invertebrate ingestion, and (4) chemical pollutant interactions. All of the marine organism groups are at an eminent risk of interacting with microplastics according to the available literature. Dozens of works on other relevant issues (i.e., polymer decay at sea, new sampling and laboratory methods, emerging sources, externalities) were also analysed and discussed. This paper provides the first in-depth exploration of the effects of microplastics on the marine environment and biota. The number of scientific publications will increase in response to present and projected plastic uses and discard patterns. Therefore, new themes and important approaches for future work are proposed. Copyright © 2013 Elsevier Ltd. All rights reserved.

Germany wide seasonal flood risk analysis for agricultural crops

NASA Astrophysics Data System (ADS)

Klaus, Stefan; Kreibich, Heidi; Kuhlmann, Bernd; Merz, Bruno; Schröter, Kai

2016-04-01

In recent years, large-scale flood risk analysis and mapping has gained attention. Regional to national risk assessments are needed, for example, for national risk policy developments, for large-scale disaster management planning and in the (re-)insurance industry. Despite increasing requests for comprehensive risk assessments some sectors have not received much scientific attention, one of these is the agricultural sector. In contrast to other sectors, agricultural crop losses depend strongly on the season. Also flood probability shows seasonal variation. Thus, the temporal superposition of high flood susceptibility of crops and high flood probability plays an important role for agricultural flood risk. To investigate this interrelation and provide a large-scale overview of agricultural flood risk in Germany, an agricultural crop loss model is used for crop susceptibility analyses and Germany wide seasonal flood-frequency analyses are undertaken to derive seasonal flood patterns. As a result, a Germany wide map of agricultural flood risk is shown as well as the crop type most at risk in a specific region. The risk maps may provide guidance for federal state-wide coordinated designation of retention areas.

‘Of course we are on Facebook’: Use and non-use of social media among Swedish and Norwegian politicians

PubMed Central

Kalsnes, Bente

2014-01-01

While plenty of research has provided important insights into the uses of the Internet by politicians during elections, a relatively scarce amount of work has looked into these uses outside of such parliamentary events. This article seeks to remedy this lack of research by presenting a study on the ‘routine’ uses of two of the currently most popular social media services – Facebook and Twitter. Focusing on politicians elected to the national parliaments of Norway and Sweden, the article employs novel methodologies for data collection and statistical analyses in order to provide an overarching, structural view of the day-to-day social media practices of Scandinavian politicians. Findings indicate that use levels are rather low for both services – the median amount of tweets sent and messages posted on Facebook is close to one per day. Further analyses reveal that the most active politicians could be labelled as ‘underdogs’, as they are more likely to be younger, in opposition and out of the political limelight. PMID:28596632

Current Progress in Tonoplast Proteomics Reveals Insights into the Function of the Large Central Vacuole

PubMed Central

Trentmann, Oliver; Haferkamp, Ilka

2013-01-01

Vacuoles of plants fulfill various biologically important functions, like turgor generation and maintenance, detoxification, solute sequestration, or protein storage. Different types of plant vacuoles (lytic versus protein storage) are characterized by different functional properties apparently caused by a different composition/abundance and regulation of transport proteins in the surrounding membrane, the tonoplast. Proteome analyses allow the identification of vacuolar proteins and provide an informative basis for assigning observed transport processes to specific carriers or channels. This review summarizes techniques required for vacuolar proteome analyses, like e.g., isolation of the large central vacuole or tonoplast membrane purification. Moreover, an overview about diverse published vacuolar proteome studies is provided. It becomes evident that qualitative proteomes from different plant species represent just the tip of the iceberg. During the past few years, mass spectrometry achieved immense improvement concerning its accuracy, sensitivity, and application. As a consequence, modern tonoplast proteome approaches are suited for detecting alterations in membrane protein abundance in response to changing environmental/physiological conditions and help to clarify the regulation of tonoplast transport processes. PMID:23459586

Geological sampling data and benthic biota classification: Buzzards Bay and Vineyard Sound, Massachusetts

USGS Publications Warehouse

Ackerman, Seth D.; Pappal, Adrienne L.; Huntley, Emily C.; Blackwood, Dann S.; Schwab, William C.

2015-01-01

Sea-floor sample collection is an important component of a statewide cooperative mapping effort between the U.S. Geological Survey (USGS) and the Massachusetts Office of Coastal Zone Management (CZM). Sediment grab samples, bottom photographs, and video transects were collected within Vineyard Sound and Buzzards Bay in 2010 aboard the research vesselConnecticut. This report contains sample data and related information, including analyses of surficial-sediment grab samples, locations and images of sea-floor photography, survey lines along which sea-floor video was collected, and a classification of benthic biota observed in sea-floor photographs and based on the Coastal and Marine Ecological Classification Standard (CMECS). These sample data and analyses information are used to verify interpretations of geophysical data and are an essential part of geologic maps of the sea floor. These data also provide a valuable inventory of benthic habitat and resources. Geographic information system (GIS) data, maps, and interpretations, produced through the USGS and CZM mapping cooperative, are intended to aid efforts to manage coastal and marine resources and to provide baseline information for research focused on coastal evolution and environmental change.

Materials Informatics: Statistical Modeling in Material Science.

PubMed

Yosipof, Abraham; Shimanovich, Klimentiy; Senderowitz, Hanoch

2016-12-01

Material informatics is engaged with the application of informatic principles to materials science in order to assist in the discovery and development of new materials. Central to the field is the application of data mining techniques and in particular machine learning approaches, often referred to as Quantitative Structure Activity Relationship (QSAR) modeling, to derive predictive models for a variety of materials-related "activities". Such models can accelerate the development of new materials with favorable properties and provide insight into the factors governing these properties. Here we provide a comparison between medicinal chemistry/drug design and materials-related QSAR modeling and highlight the importance of developing new, materials-specific descriptors. We survey some of the most recent QSAR models developed in materials science with focus on energetic materials and on solar cells. Finally we present new examples of material-informatic analyses of solar cells libraries produced from metal oxides using combinatorial material synthesis. Different analyses lead to interesting physical insights as well as to the design of new cells with potentially improved photovoltaic parameters. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantification of the Early Small-Scale Fishery in the North-Eastern Baltic Sea in the Late 17th Century

PubMed Central

Verliin, Aare; Ojaveer, Henn; Kaju, Katre; Tammiksaar, Erki

2013-01-01

Historical perspectives on fisheries and related human behaviour provide valuable information on fishery resources and their exploitation, helping to more appropriately set management targets and determine relevant reference levels. In this study we analyse historical fisheries and fish trade at the north-eastern Baltic Sea coast in the late 17th century. Local consumption and export together amounted to the annual removal of about 200 tonnes of fish from the nearby sea and freshwater bodies. The fishery was very diverse and exploited altogether one cyclostome and 17 fish species with over 90% of the catch being consumed locally. The exported fish consisted almost entirely of high-valued species with Stockholm (Sweden) being the most important export destination. Due to rich political history and natural features of the region, we suggest that the documented evidence of this small-scale fishery should be considered as the first quantitative summary of exploitation of aquatic living resources in the region and can provide a background for future analyses. PMID:23861914

Application of multivariate statistical techniques in microbial ecology.

PubMed

Paliy, O; Shankar, V

2016-03-01

Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large-scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure. © 2016 John Wiley & Sons Ltd.

Monitoring chicken flock behaviour provides early warning of infection by human pathogen Campylobacter

PubMed Central

Colles, Frances M.; Cain, Russell J.; Nickson, Thomas; Smith, Adrian L.; Roberts, Stephen J.; Maiden, Martin C. J.; Lunn, Daniel; Dawkins, Marian Stamp

2016-01-01

Campylobacter is the commonest bacterial cause of gastrointestinal infection in humans, and chicken meat is the major source of infection throughout the world. Strict and expensive on-farm biosecurity measures have been largely unsuccessful in controlling infection and are hampered by the time needed to analyse faecal samples, with the result that Campylobacter status is often known only after a flock has been processed. Our data demonstrate an alternative approach that monitors the behaviour of live chickens with cameras and analyses the ‘optical flow’ patterns made by flock movements. Campylobacter-free chicken flocks have higher mean and lower kurtosis of optical flow than those testing positive for Campylobacter by microbiological methods. We show that by monitoring behaviour in this way, flocks likely to become positive can be identified within the first 7–10 days of life, much earlier than conventional on-farm microbiological methods. This early warning has the potential to lead to a more targeted approach to Campylobacter control and also provides new insights into possible sources of infection that could transform the control of this globally important food-borne pathogen. PMID:26740618

Analysing data from patient-reported outcome and quality of life endpoints for cancer clinical trials: a start in setting international standards.

PubMed

Bottomley, Andrew; Pe, Madeline; Sloan, Jeff; Basch, Ethan; Bonnetain, Franck; Calvert, Melanie; Campbell, Alicyn; Cleeland, Charles; Cocks, Kim; Collette, Laurence; Dueck, Amylou C; Devlin, Nancy; Flechtner, Hans-Henning; Gotay, Carolyn; Greimel, Eva; Griebsch, Ingolf; Groenvold, Mogens; Hamel, Jean-Francois; King, Madeleine; Kluetz, Paul G; Koller, Michael; Malone, Daniel C; Martinelli, Francesca; Mitchell, Sandra A; Moinpour, Carol M; Musoro, Jammbe; O'Connor, Daniel; Oliver, Kathy; Piault-Louis, Elisabeth; Piccart, Martine; Pimentel, Francisco L; Quinten, Chantal; Reijneveld, Jaap C; Schürmann, Christoph; Smith, Ashley Wilder; Soltys, Katherine M; Taphoorn, Martin J B; Velikova, Galina; Coens, Corneel

2016-11-01

Measures of health-related quality of life (HRQOL) and other patient-reported outcomes generate important data in cancer randomised trials to assist in assessing the risks and benefits of cancer therapies and fostering patient-centred cancer care. However, the various ways these measures are analysed and interpreted make it difficult to compare results across trials, and hinders the application of research findings to inform publications, product labelling, clinical guidelines, and health policy. To address these problems, the Setting International Standards in Analyzing Patient-Reported Outcomes and Quality of Life Endpoints Data (SISAQOL) initiative has been established. This consortium, directed by the European Organisation for Research and Treatment of Cancer (EORTC), was convened to provide recommendations on how to standardise the analysis of HRQOL and other patient-reported outcomes data in cancer randomised trials. This Personal View discusses the reasons why this project was initiated, the rationale for the planned work, and the expected benefits to cancer research, patient and provider decision making, care delivery, and policy making. Copyright © 2016 Elsevier Ltd. All rights reserved.

Complete sequences of organelle genomes from the medicinal plant Rhazya stricta (Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids.

PubMed

Park, Seongjun; Ruhlman, Tracey A; Sabir, Jamal S M; Mutwakil, Mohammed H Z; Baeshen, Mohammed N; Sabir, Meshaal J; Baeshen, Nabih A; Jansen, Robert K

2014-05-28

Rhazya stricta is native to arid regions in South Asia and the Middle East and is used extensively in folk medicine to treat a wide range of diseases. In addition to generating genomic resources for this medicinally important plant, analyses of the complete plastid and mitochondrial genomes and a nuclear transcriptome from Rhazya provide insights into inter-compartmental transfers between genomes and the patterns of evolution among eight asterid mitochondrial genomes. The 154,841 bp plastid genome is highly conserved with gene content and order identical to the ancestral organization of angiosperms. The 548,608 bp mitochondrial genome exhibits a number of phenomena including the presence of recombinogenic repeats that generate a multipartite organization, transferred DNA from the plastid and nuclear genomes, and bidirectional DNA transfers between the mitochondrion and the nucleus. The mitochondrial genes sdh3 and rps14 have been transferred to the nucleus and have acquired targeting presequences. In the case of rps14, two copies are present in the nucleus; only one has a mitochondrial targeting presequence and may be functional. Phylogenetic analyses of both nuclear and mitochondrial copies of rps14 across angiosperms suggests Rhazya has experienced a single transfer of this gene to the nucleus, followed by a duplication event. Furthermore, the phylogenetic distribution of gene losses and the high level of sequence divergence in targeting presequences suggest multiple, independent transfers of both sdh3 and rps14 across asterids. Comparative analyses of mitochondrial genomes of eight sequenced asterids indicates a complicated evolutionary history in this large angiosperm clade with considerable diversity in genome organization and size, repeat, gene and intron content, and amount of foreign DNA from the plastid and nuclear genomes. Organelle genomes of Rhazya stricta provide valuable information for improving the understanding of mitochondrial genome evolution among angiosperms. The genomic data have enabled a rigorous examination of the gene transfer events. Rhazya is unique among the eight sequenced asterids in the types of events that have shaped the evolution of its mitochondrial genome. Furthermore, the organelle genomes of R. stricta provide valuable genomic resources for utilizing this important medicinal plant in biotechnology applications.

Development of a Global Wetland Sustainability Index for comprehensive land use planning

NASA Astrophysics Data System (ADS)

Schleupner, C.; Schneider, U. A.; Havlik, P.; Stacke, T.

2012-04-01

Allocation of nature reserves for conservation of ecosystem functions and services is a multi-dimensional task. Conservation programs act from local to regional or national scales, and some efforts involve entire continents. Globally, several international environmental agreements have been established which include conservation issues. Examples are the Convention on Biological Diversity, the Convention on Migratory Species of Wild Animals, the UN Framework Convention on Climate Change, and the Ramsar Convention on Wetlands. A common aim of most initiatives is the protection and restoration of valuable natural sites by providing a functional network of sites. The planning of protected habitat networks to safeguard global biodiversity requires substantial knowledge on exposure, services, and functions of ecosystems. Further, the complex spatial relationships between humans and the environment under consideration of costs and land use competition have to be determined. Often such analyses are hindered by lack of data. We developed a global index that ranks sites for wetland protection according to its wetland quantity, wetland quality and pressure upon the wetland sites. Each of the three parts is based on several spatial-ecological datasets that contain important information for the adequate assessment of spatial economic and ecologic interdependencies. Applying cluster analyses and ecological decision trees the data are combined and results are translated to the final index and expressed per simulation unit for integration into the Global Biomass Optimization Model GLOBIOM. This global recursive dynamic partial equilibrium model integrates the agricultural, bio energy and forestry sectors with the aim to provide policy analyses on global issues concerning land use competition between the major land-based production sectors. Results not only show the most vulnerable wetland areas to nature loss and the most valuable wetland areas for biodiversity protection under certain land use scenarios. Moreover, costs of protection are estimated and the results give recommendations for action by illustrating wetland conservation areas in need for conservation. Often wetlands provide numerous ecosystem services to society, such as water retention, flood control, water purification, to name only a few. The sustainable conservation of wetland sites, especially in highly human dominated landscapes, is therefore an important global but still underestimated objective.

Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae

PubMed Central

Aguilar, María; Lado, Carlos

2012-01-01

Habitat availability and environmental preferences of species are among the most important factors in determining the success of dispersal processes and therefore in shaping the distribution of protists. We explored the differences in fundamental niches and potential distributions of an ecological guild of slime moulds—protosteloid amoebae—in the Iberian Peninsula. A large set of samples collected in a north-east to south-west transect of approximately 1000 km along the peninsula was used to test the hypothesis that, together with the existence of suitable microhabitats, climate conditions may determine the probability of survival of species. Although protosteloid amoebae share similar morphologies and life history strategies, canonical correspondence analyses showed that they have varied ecological optima, and that climate conditions have an important effect in niche differentiation. Maxent environmental niche models provided consistent predictions of the probability of presence of the species based on climate data, and they were used to generate maps of potential distribution in an ‘everything is everywhere' scenario. The most important climatic factors were, in both analyses, variables that measure changes in conditions throughout the year, confirming that the alternation of fruiting bodies, cysts and amoeboid stages in the life cycles of protosteloid amoebae constitutes an advantage for surviving in a changing environment. Microhabitat affinity seems to be influenced by climatic conditions, which suggests that the micro-environment may vary at a local scale and change together with the external climate at a larger scale. PMID:22402402

Ecological niche models reveal the importance of climate variability for the biogeography of protosteloid amoebae.

PubMed

Aguilar, María; Lado, Carlos

2012-08-01

Habitat availability and environmental preferences of species are among the most important factors in determining the success of dispersal processes and therefore in shaping the distribution of protists. We explored the differences in fundamental niches and potential distributions of an ecological guild of slime moulds-protosteloid amoebae-in the Iberian Peninsula. A large set of samples collected in a north-east to south-west transect of approximately 1000 km along the peninsula was used to test the hypothesis that, together with the existence of suitable microhabitats, climate conditions may determine the probability of survival of species. Although protosteloid amoebae share similar morphologies and life history strategies, canonical correspondence analyses showed that they have varied ecological optima, and that climate conditions have an important effect in niche differentiation. Maxent environmental niche models provided consistent predictions of the probability of presence of the species based on climate data, and they were used to generate maps of potential distribution in an 'everything is everywhere' scenario. The most important climatic factors were, in both analyses, variables that measure changes in conditions throughout the year, confirming that the alternation of fruiting bodies, cysts and amoeboid stages in the life cycles of protosteloid amoebae constitutes an advantage for surviving in a changing environment. Microhabitat affinity seems to be influenced by climatic conditions, which suggests that the micro-environment may vary at a local scale and change together with the external climate at a larger scale.

Convergent integration of animal model and human studies of bipolar disorder (manic-depressive illness).

PubMed

Le-Niculescu, Helen; Patel, Sagar D; Niculescu, Alexander B

2010-10-01

Animal models and human studies of bipolar disorder and other psychiatric disorders are becoming increasingly integrated, prompted by recent successes. Particularly for genomics, the convergence and integration of data across species, experimental modalities and technical platforms is providing a fit-to-disease way of extracting reproducible and biologically important signal, in sharp contrast to the fit-to-cohort effect, disappointing findings to date, and limited reproducibility of human genetic analyses alone. Such work in psychiatry can provide an example of how to address other genetically complex disorders, and in turn will benefit by incorporating concepts from other areas, such as cancer biology and diabetes. Copyright © 2010. Published by Elsevier Ltd.

A Brief Taxometrics Primer

PubMed Central

Beauchaine, Theodore P.

2009-01-01

Taxometric procedures provide an empirical means of determining which psychiatric disorders are typologically distinct from normal behavioral functioning. Although most disorders reflect extremes along continuously distributed behavioral traits, identifying those that are discrete has important implications for accurate diagnosis, effective treatment, early identification of risk, and improved understanding of etiology. This article provides (a) brief descriptions of the conceptual bases of several taxometric procedures, (b) example analyses using simulated data, and (c) strategies for avoiding common pitfalls that are often observed in taxometrics research. To date, most taxometrics studies have appeared in the adult psychopathology literature. It is hoped that this primer will encourage interested readers to extend taxometrics research to child and adolescent populations. PMID:18088222

Conservation paleobiology: putting the dead to work.

PubMed

Dietl, Gregory P; Flessa, Karl W

2011-01-01

Geohistorical data and analyses are playing an increasingly important role in conservation biology practice and policy. In this review, we discuss examples of how the near-time and deep-time fossil record can be used to understand the ecological and evolutionary responses of species to changes in their environment. We show that beyond providing crucial baseline data, the conservation paleobiology perspective helps us to identify which species will be most vulnerable and what kinds of responses will be most common. We stress that inclusion of geohistorical data in our decision-making process provides a more scientifically robust basis for conservation policies than those dependent on short-term observations alone. © 2010 Elsevier Ltd. All rights reserved.

Do polymorphisms of 5,10-methylenetetrahydrofolate reductase (MTHFR) gene affect the risk of childhood acute lymphoblastic leukemia?

PubMed

Pereira, Tiago Veiga; Rudnicki, Martina; Pereira, Alexandre Costa; Pombo-de-Oliveira, Maria S; Franco, Rendrik França

2006-01-01

Meta-analysis has become an important statistical tool in genetic association studies, since it may provide more powerful and precise estimates. However, meta-analytic studies are prone to several potential biases not only because the preferential publication of "positive'' studies but also due to difficulties in obtaining all relevant information during the study selection process. In this letter, we point out major problems in meta-analysis that may lead to biased conclusions, illustrating an empirical example of two recent meta-analyses on the relation between MTHFR polymorphisms and risk of acute lymphoblastic leukemia that, despite the similarity in statistical methods and period of study selection, provided partially conflicting results.

Potential distribution dataset of honeybees in Indian Ocean Islands: Case study of Zanzibar Island.

PubMed

Mwalusepo, Sizah; Muli, Eliud; Nkoba, Kiatoko; Nguku, Everlyn; Kilonzo, Joseph; Abdel-Rahman, Elfatih M; Landmann, Tobias; Fakih, Asha; Raina, Suresh

2017-10-01

Honeybees ( Apis mellifera ) are principal insect pollinators, whose worldwide distribution and abundance is known to largely depend on climatic conditions. However, the presence records dataset on potential distribution of honeybees in Indian Ocean Islands remain less documented. Presence records in shape format and probability of occurrence of honeybees with different temperature change scenarios is provided in this article across Zanzibar Island. Maximum entropy (Maxent) package was used to analyse the potential distribution of honeybees. The dataset provides information on the current and future distribution of the honey bees in Zanzibar Island. The dataset is of great importance for improving stakeholders understanding of the role of temperature change on the spatial distribution of honeybees.

Impact of immersion oils and mounting media on the confocal imaging of dendritic spines

PubMed Central

Peterson, Brittni M.; Mermelstein, Paul G.; Meisel, Robert L.

2015-01-01

Background Structural plasticity, such as changes in dendritic spine morphology and density, reflect changes in synaptic connectivity and circuitry. Procedural variables used in different methods for labeling dendritic spines have been quantitatively evaluated for their impact on the ability to resolve individual spines in confocal microscopic analyses. In contrast, there have been discussions, though no quantitative analyses, of the potential effects of choosing specific mounting media and immersion oils on dendritic spine resolution. New Method Here we provide quantitative data measuring the impact of these variables on resolving dendritic spines in 3D confocal analyses. Medium spiny neurons from the rat striatum and nucleus accumbens are used as examples. Results Both choice of mounting media and immersion oil affected the visualization of dendritic spines, with choosing the appropriate immersion oil as being more imperative. These biologic data are supported by quantitative measures of the 3D diffraction pattern (i.e. point spread function) of a point source of light under the same mounting medium and immersion oil combinations. Comparison with Existing Method Although not a new method, this manuscript provides quantitative data demonstrating that different mounting media and immersion oils can impact the ability to resolve dendritic spines. These findings highlight the importance of reporting which mounting medium and immersion oil are used in preparations for confocal analyses, especially when comparing published results from different laboratories. Conclusion Collectively, these data suggest that choosing the appropriate immersion oil and mounting media is critical for obtaining the best resolution, and consequently more accurate measures of dendritic spine densities. PMID:25601477

Impact of immersion oils and mounting media on the confocal imaging of dendritic spines.

PubMed

Peterson, Brittni M; Mermelstein, Paul G; Meisel, Robert L

2015-03-15

Structural plasticity, such as changes in dendritic spine morphology and density, reflect changes in synaptic connectivity and circuitry. Procedural variables used in different methods for labeling dendritic spines have been quantitatively evaluated for their impact on the ability to resolve individual spines in confocal microscopic analyses. In contrast, there have been discussions, though no quantitative analyses, of the potential effects of choosing specific mounting media and immersion oils on dendritic spine resolution. Here we provide quantitative data measuring the impact of these variables on resolving dendritic spines in 3D confocal analyses. Medium spiny neurons from the rat striatum and nucleus accumbens are used as examples. Both choice of mounting media and immersion oil affected the visualization of dendritic spines, with choosing the appropriate immersion oil as being more imperative. These biologic data are supported by quantitative measures of the 3D diffraction pattern (i.e. point spread function) of a point source of light under the same mounting medium and immersion oil combinations. Although not a new method, this manuscript provides quantitative data demonstrating that different mounting media and immersion oils can impact the ability to resolve dendritic spines. These findings highlight the importance of reporting which mounting medium and immersion oil are used in preparations for confocal analyses, especially when comparing published results from different laboratories. Collectively, these data suggest that choosing the appropriate immersion oil and mounting media is critical for obtaining the best resolution, and consequently more accurate measures of dendritic spine densities. Copyright © 2015 Elsevier B.V. All rights reserved.

Factors associated with seasonal influenza vaccination in pregnant women.

PubMed

Henninger, Michelle L; Irving, Stephanie A; Thompson, Mark; Avalos, Lyndsay Ammon; Ball, Sarah W; Shifflett, Pat; Naleway, Allison L

2015-05-01

This observational study followed a cohort of pregnant women during the 2010-2011 influenza season to determine factors associated with vaccination. Participants were 1105 pregnant women who completed a survey assessing health beliefs related to vaccination upon enrollment and were then followed to determine vaccination status by the end of the 2010-2011 influenza season. We conducted univariate and multivariate analyses to explore factors associated with vaccination status and a factor analysis of survey items to identify health beliefs associated with vaccination. Sixty-three percent (n=701) of the participants were vaccinated. In the univariate analyses, multiple factors were associated with vaccination status, including maternal age, race, marital status, educational level, and gravidity. Factor analysis identified two health belief factors associated with vaccination: participant's positive views (factor 1) and negative views (factor 2) of influenza vaccination. In a multivariate logistic regression model, factor 1 was associated with increased likelihood of vaccination (adjusted odds ratio [aOR]=2.18; 95% confidence interval [CI]=1.72-2.78), whereas factor 2 was associated with decreased likelihood of vaccination (aOR=0.36; 95% CI=0.28-0.46). After controlling for the two health belief factors in multivariate analyses, demographic factors significant in univariate analyses were no longer significant. Women who received a provider recommendation were about three times more likely to be vaccinated (aOR=3.14; 95% CI=1.99-4.96). Pregnant women's health beliefs about vaccination appear to be more important than demographic and maternal factors previously associated with vaccination status. Provider recommendation remains one of the most critical factors influencing vaccination during pregnancy.

Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana

PubMed Central

Henríquez-Valencia, Carlos; Arenas-M, Anita; Medina, Joaquín; Canales, Javier

2018-01-01

Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants. PMID:29692794

Integrative Transcriptomic Analysis Uncovers Novel Gene Modules That Underlie the Sulfate Response in Arabidopsis thaliana.

PubMed

Henríquez-Valencia, Carlos; Arenas-M, Anita; Medina, Joaquín; Canales, Javier

2018-01-01

Sulfur is an essential nutrient for plant growth and development. Sulfur is a constituent of proteins, the plasma membrane and cell walls, among other important cellular components. To obtain new insights into the gene regulatory networks underlying the sulfate response, we performed an integrative meta-analysis of transcriptomic data from five different sulfate experiments available in public databases. This bioinformatic approach allowed us to identify a robust set of genes whose expression depends only on sulfate availability, indicating that those genes play an important role in the sulfate response. In relation to sulfate metabolism, the biological function of approximately 45% of these genes is currently unknown. Moreover, we found several consistent Gene Ontology terms related to biological processes that have not been extensively studied in the context of the sulfate response; these processes include cell wall organization, carbohydrate metabolism, nitrogen compound transport, and the regulation of proteolysis. Gene co-expression network analyses revealed relationships between the sulfate-responsive genes that were distributed among seven function-specific co-expression modules. The most connected genes in the sulfate co-expression network belong to a module related to the carbon response, suggesting that this biological function plays an important role in the control of the sulfate response. Temporal analyses of the network suggest that sulfate starvation generates a biphasic response, which involves that major changes in gene expression occur during both the early and late responses. Network analyses predicted that the sulfate response is regulated by a limited number of transcription factors, including MYBs, bZIPs, and NF-YAs. In conclusion, our analysis identified new candidate genes and provided new hypotheses to advance our understanding of the transcriptional regulation of sulfate metabolism in plants.

GPU based framework for geospatial analyses

NASA Astrophysics Data System (ADS)

Cosmin Sandric, Ionut; Ionita, Cristian; Dardala, Marian; Furtuna, Titus

2017-04-01

Parallel processing on multiple CPU cores is already used at large scale in geocomputing, but parallel processing on graphics cards is just at the beginning. Being able to use an simple laptop with a dedicated graphics card for advanced and very fast geocomputation is an advantage that each scientist wants to have. The necessity to have high speed computation in geosciences has increased in the last 10 years, mostly due to the increase in the available datasets. These datasets are becoming more and more detailed and hence they require more space to store and more time to process. Distributed computation on multicore CPU's and GPU's plays an important role by processing one by one small parts from these big datasets. These way of computations allows to speed up the process, because instead of using just one process for each dataset, the user can use all the cores from a CPU or up to hundreds of cores from GPU The framework provide to the end user a standalone tools for morphometry analyses at multiscale level. An important part of the framework is dedicated to uncertainty propagation in geospatial analyses. The uncertainty may come from the data collection or may be induced by the model or may have an infinite sources. These uncertainties plays important roles when a spatial delineation of the phenomena is modelled. Uncertainty propagation is implemented inside the GPU framework using Monte Carlo simulations. The GPU framework with the standalone tools proved to be a reliable tool for modelling complex natural phenomena The framework is based on NVidia Cuda technology and is written in C++ programming language. The code source will be available on github at https://github.com/sandricionut/GeoRsGPU Acknowledgement: GPU framework for geospatial analysis, Young Researchers Grant (ICUB-University of Bucharest) 2016, director Ionut Sandric

Drivers of wetland conversion: a global meta-analysis.

PubMed

van Asselen, Sanneke; Verburg, Peter H; Vermaat, Jan E; Janse, Jan H

2013-01-01

Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability), mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors) are also identified as important causes of various types of land change (e.g., deforestation, desertification). Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have determined historic conversions.

Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments

PubMed Central

Klatt, Christian G.; Inskeep, William P.; Herrgard, Markus J.; Jay, Zackary J.; Rusch, Douglas B.;  Tringe, Susannah G.; Niki Parenteau, M.; Ward, David M.; Boomer, Sarah M.; Bryant, Donald A.;  Miller, Scott R.

2013-01-01

Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average ∼53 Mbp/site) were subjected to multiple taxonomic, phylogenetic, and functional analyses. All methods, including G + C content distribution, MEGAN analyses, and oligonucleotide frequency-based clustering, provided strong support for the dominant community members present in each site. Cyanobacteria were only observed in non-sulfidic sites; de novo assemblies were obtained for Synechococcus-like populations at Chocolate Pots (CP_7) and Fischerella-like populations at White Creek (WC_6). Chloroflexi-like sequences (esp. Roseiflexus and/or Chloroflexus spp.) were observed in all six samples and contained genes involved in bacteriochlorophyll biosynthesis and the 3-hydroxypropionate carbon fixation pathway. Other major sequence assemblies were obtained for a Chlorobiales population from CP_7 (proposed family Thermochlorobacteriaceae), and an anoxygenic, sulfur-oxidizing Thermochromatium-like (Gamma-proteobacteria) population from Bath Lake Vista Annex (BLVA_20). Additional sequence coverage is necessary to establish more complete assemblies of other novel bacteria in these sites (e.g., Bacteroidetes and Firmicutes); however, current assemblies suggested that several of these organisms play important roles in heterotrophic and fermentative metabolisms. Definitive linkages were established between several of the dominant phylotypes present in these habitats and important functional processes such as photosynthesis, carbon fixation, sulfur oxidation, and fermentation. PMID:23761787

Drivers of Wetland Conversion: a Global Meta-Analysis

PubMed Central

van Asselen, Sanneke; Verburg, Peter H.; Vermaat, Jan E.; Janse, Jan H.

2013-01-01

Meta-analysis of case studies has become an important tool for synthesizing case study findings in land change. Meta-analyses of deforestation, urbanization, desertification and change in shifting cultivation systems have been published. This present study adds to this literature, with an analysis of the proximate causes and underlying forces of wetland conversion at a global scale using two complementary approaches of systematic review. Firstly, a meta-analysis of 105 case-study papers describing wetland conversion was performed, showing that different combinations of multiple-factor proximate causes, and underlying forces, drive wetland conversion. Agricultural development has been the main proximate cause of wetland conversion, and economic growth and population density are the most frequently identified underlying forces. Secondly, to add a more quantitative component to the study, a logistic meta-regression analysis was performed to estimate the likelihood of wetland conversion worldwide, using globally-consistent biophysical and socioeconomic location factor maps. Significant factors explaining wetland conversion, in order of importance, are market influence, total wetland area (lower conversion probability), mean annual temperature and cropland or built-up area. The regression analyses results support the outcomes of the meta-analysis of the processes of conversion mentioned in the individual case studies. In other meta-analyses of land change, similar factors (e.g., agricultural development, population growth, market/economic factors) are also identified as important causes of various types of land change (e.g., deforestation, desertification). Meta-analysis helps to identify commonalities across the various local case studies and identify which variables may lead to individual cases to behave differently. The meta-regression provides maps indicating the likelihood of wetland conversion worldwide based on the location factors that have determined historic conversions. PMID:24282580

Protein kinases responsible for the phosphorylation of the nuclear egress core complex of human cytomegalovirus.

PubMed

Sonntag, Eric; Milbradt, Jens; Svrlanska, Adriana; Strojan, Hanife; Häge, Sigrun; Kraut, Alexandra; Hesse, Anne-Marie; Amin, Bushra; Sonnewald, Uwe; Couté, Yohann; Marschall, Manfred

2017-10-01

Nuclear egress of herpesvirus capsids is mediated by a multi-component nuclear egress complex (NEC) assembled by a heterodimer of two essential viral core egress proteins. In the case of human cytomegalovirus (HCMV), this core NEC is defined by the interaction between the membrane-anchored pUL50 and its nuclear cofactor, pUL53. NEC protein phosphorylation is considered to be an important regulatory step, so this study focused on the respective role of viral and cellular protein kinases. Multiply phosphorylated pUL50 varieties were detected by Western blot and Phos-tag analyses as resulting from both viral and cellular kinase activities. In vitro kinase analyses demonstrated that pUL50 is a substrate of both PKCα and CDK1, while pUL53 can also be moderately phosphorylated by CDK1. The use of kinase inhibitors further illustrated the importance of distinct kinases for core NEC phosphorylation. Importantly, mass spectrometry-based proteomic analyses identified five major and nine minor sites of pUL50 phosphorylation. The functional relevance of core NEC phosphorylation was confirmed by various experimental settings, including kinase knock-down/knock-out and confocal imaging, in which it was found that (i) HCMV core NEC proteins are not phosphorylated solely by viral pUL97, but also by cellular kinases; (ii) both PKC and CDK1 phosphorylation are detectable for pUL50; (iii) no impact of PKC phosphorylation on NEC functionality has been identified so far; (iv) nonetheless, CDK1-specific phosphorylation appears to be required for functional core NEC interaction. In summary, our findings provide the first evidence that the HCMV core NEC is phosphorylated by cellular kinases, and that the complex pattern of NEC phosphorylation has functional relevance.

Gains in efficiency and scientific potential of continental climate reconstruction provided by the LRC LacCore Facility, University of Minnesota

NASA Astrophysics Data System (ADS)

Noren, A.; Brady, K.; Myrbo, A.; Ito, E.

2007-12-01

Lacustrine sediment cores comprise an integral archive for the determination of continental paleoclimate, for their potentially high temporal resolution and for their ability to resolve spatial variability in climate across vast sections of the globe. Researchers studying these archives now have a large, nationally-funded, public facility dedicated to the support of their efforts. The LRC LacCore Facility, funded by NSF and the University of Minnesota, provides free or low-cost assistance to any portion of research projects, depending on the specific needs of the project. A large collection of field equipment (site survey equipment, coring devices, boats/platforms, water sampling devices) for nearly any lacustrine setting is available for rental, and Livingstone-type corers and drive rods may be purchased. LacCore staff can accompany field expeditions to operate these devices and curate samples, or provide training prior to device rental. The Facility maintains strong connections to experienced shipping agents and customs brokers, which vastly improves transport and importation of samples. In the lab, high-end instrumentation (e.g., multisensor loggers, high-resolution digital linescan cameras) provides a baseline of fundamental analyses before any sample material is consumed. LacCore staff provide support and training in lithological description, including smear-slide, XRD, and SEM analyses. The LRC botanical macrofossil reference collection is a valuable resource for both core description and detailed macrofossil analysis. Dedicated equipment and space for various subsample analyses streamlines these endeavors; subsamples for several analyses may be submitted for preparation or analysis by Facility technicians for a fee (e.g., carbon and sulfur coulometry, grain size, pollen sample preparation and analysis, charcoal, biogenic silica, LOI, freeze drying). The National Lacustrine Core Repository now curates ~9km of sediment cores from expeditions around the world, and stores metadata and analytical data for all cores processed at the facility. Any researcher may submit sample requests for material in archived cores. Supplies for field (e.g., polycarbonate pipe, endcaps), lab (e.g., sample containers, pollen sample spike), and curation (e.g., D-tubes) are sold at cost. In collaboration with facility users, staff continually develop new equipment, supplies, and procedures as needed in order to provide the best and most comprehensive set of services to the research community.

A systematic review of dosing frequency with bone-targeted agents for patients with bone metastases from breast cancer

PubMed Central

Hutton, Brian; Addison, Christina L.; Campbell, Kaitryn; Fergusson, Dean; Mazarello, Sasha; Clemons, Mark

2013-01-01

Background Bone-targeted agents are usually administered to breast cancer patients with bone metastases every 3–4 weeks. Less frequent (‘de-escalated’) treatment may provide similar benefits with improved safety and reduced cost. Methods To systematically review randomised trials comparing de-escalated treatment with bone-targeted agents (i.e. every 12–16 weeks) to standard treatment (i.e. every 3–4 weeks), a formal systematic review of the literature was performed. Two individuals independently screened citations and full text articles. Random effects meta-analyses of clinically important outcomes were planned provided homogeneous studies were identified. Results Five relevant studies (n=1287 patients) were identified. Sample size ranged from 38 to 425. Information on outcomes including occurrence of SREs, bone pain, urinary N-telopeptide concentrations, serum C-telopeptide concentrations, pain medication use and safety outcomes was not consistently available. Two trials were non-inferiority studies, two dose-response evaluations and one was a pilot study. Bone-targeted agents use varied between studies, as did duration of prior therapy. Patient populations were considered heterogeneous in several ways, and thus no meta-analyses were performed. Observations from the included studies suggest there is potential that 3 month de-escalated treatment may provide similar benefits compared to 3–4 weekly treatment and that lower doses of zoledronic acid and denosumab might be equally effective. Conclusions Studies comparing standard and de-escalated treatment with bone-targeted agents in breast cancer are rare. The benefits of standard treatment compared to de-escalated therapy on important clinical outcomes remain unclear. Future pragmatic studies must be conducted to determine the merits of this approach. PMID:26909282

Informing subjects of epidemiologic study results. Children's Cancer Group.

PubMed

Bunin, G R; Kazak, A E; Mitelman, O

1996-04-01

To assess the feasibility and process of providing feedback to parents regarding the results of epidemiologic research, in particular to look at the importance and clarity of the information provided, parental reactions to the results, and utilization of the data provided. Parents who participated in an epidemiologic study of pediatric brain tumors (patient and control mothers) were sent a letter summarizing the results of the study and the Parent Study Results Survey to complete and return. The final sample used for analyses was 109 (patient) and 90 (control) mothers. Analyses were conducted to determine differences between patient and control mothers and differences among subsets defined by educational level and vital status of the patient. Mothers rated the importance and clarity of the information very highly, although patient mothers were more likely than control mothers to want more information and a telephone contact. Patient and control mothers were similar in reported sadness, anxiety, and being overwhelmed, but patient mothers felt less satisfied and relieved. Patient mothers expressed feeling more guilt nad anger than control mothers, although even the levels among the patient mothers were only moderate. Close to half of all mothers commented on the inconclusiveness of the study results. Nearly all mothers indicated they would suggest that other parents participate in epidemiologic research. It is valuable to many parents that they receive information about results of research in which they have participated. We found little evidence of strong negative effects to a detailed feedback letter. We recommend that evaluative data be used to guide the process of informing research participants about study results and that investigators consider making feedback letters a standard part of research protocols.

The Economic Impact of Biosimilars on Chronic Immune-Mediated Inflammatory Diseases.

PubMed

Pentek, Marta; Zrubka, Zsombor; Gulacsi, Laszlo

2017-01-01

Biological drugs represent highly effective but costly treatments for chronic immunemediated inflammatory diseases posing substantial burden on health care budgets. Introduction of biosimilars since 2013 has brought forward the potential of market competition, and as a societal benefit, the hope of increased access at a lower cost. We aim to provide a descriptive review on economic aspects and market changes related to the introduction of biosimilar drugs. Our focus is on chronic immune-mediated inflammatory conditions in rheumatology, gastroenterology and dermatology. Based on available literature data, we discuss the determinants of access to biological treatment, summarize the available health economic evidences with special focus on cost-utility and budget impact analyses. Market penetration of biosimilars and their overall impact on biological markets are analyzed. Biosimilar markets are country specific due to differences in the regulatory and reimbursement systems. Cost-utility analyses suggest, that given the lower price of biosimilars, formerly established biological treatment sequence practices and the eligibility criteria for biological treatment deserve reconsideration. Budget impact analyses forecasted significant budget savings in various diagnoses and countries, providing opportunity for the treatment of more patients. Biosimilars may contribute to better patient-access and provide savings to governments. To increase their acceptability, further clinical evidences and real world experiences are needed, as well as education of physicians and patients. The high biosimilar penetration rates in Norway, Denmark and Poland suggest that policies which support interchanging from the reference product may be important drivers of biosimilar uptake. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

SZDB: A Database for Schizophrenia Genetic Research

PubMed Central

Wu, Yong; Yao, Yong-Gang

2017-01-01

Abstract Schizophrenia (SZ) is a debilitating brain disorder with a complex genetic architecture. Genetic studies, especially recent genome-wide association studies (GWAS), have identified multiple variants (loci) conferring risk to SZ. However, how to efficiently extract meaningful biological information from bulk genetic findings of SZ remains a major challenge. There is a pressing need to integrate multiple layers of data from various sources, eg, genetic findings from GWAS, copy number variations (CNVs), association and linkage studies, gene expression, protein–protein interaction (PPI), co-expression, expression quantitative trait loci (eQTL), and Encyclopedia of DNA Elements (ENCODE) data, to provide a comprehensive resource to facilitate the translation of genetic findings into SZ molecular diagnosis and mechanism study. Here we developed the SZDB database (http://www.szdb.org/), a comprehensive resource for SZ research. SZ genetic data, gene expression data, network-based data, brain eQTL data, and SNP function annotation information were systematically extracted, curated and deposited in SZDB. In-depth analyses and systematic integration were performed to identify top prioritized SZ genes and enriched pathways. Multiple types of data from various layers of SZ research were systematically integrated and deposited in SZDB. In-depth data analyses and integration identified top prioritized SZ genes and enriched pathways. We further showed that genes implicated in SZ are highly co-expressed in human brain and proteins encoded by the prioritized SZ risk genes are significantly interacted. The user-friendly SZDB provides high-confidence candidate variants and genes for further functional characterization. More important, SZDB provides convenient online tools for data search and browse, data integration, and customized data analyses. PMID:27451428

Coals of Hungary

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

Landis, E.R.; Rohrbacher, T.J.; Gluskoter, H.

1999-07-01

As part of the activities conducted under the U.S. Hungarian Science and Technology Fund, a total of 39 samples from five coal mines in Hungary were selected for standard coal analyses and major, minor and trace elements analysis. The mine areas sampled were selected to provide a spectrum of coal quality information for comparison with other coal areas in central Europe and worldwide. All of the areas are of major importance in the energy budget of Hungary. The five sample sites contain coal in rocks of Jurassic, Cretaceous, Eocene, Miocene, and Pliocene age. The coals, from four underground and onemore » surface mine, range in rank from high volatile bituminous to lignite B. Most of the coal produced from the mines sampled is used to generate electricity. Some of the power plants that utilize the coals also provide heat for domestic and process usage. The standard coal analysis program is based on tests performed in accordance with standards of the American Society for Testing and Materials (ASTM). Proximate and ultimate analyses were supplemented by determinations of the heating value, equilibrium moisture, forms of sulfur, free-swelling index, ash fusion temperatures (both reducing and oxidizing), apparent specific gravity and Hardgrove Grindability index. The major, minor and trace element analyses were performed in accordance with standardized procedures of the U.S. Geological Survey. The analytical results will be available in the International Coal Quality Data Base of the USGS. The results of the program provide data for comparison with test data from Europe and information of value to potential investors or cooperators in the coal industry of Hungary and Central Europe.« less

StreptoBase: An Oral Streptococcus mitis Group Genomic Resource and Analysis Platform.

PubMed

Zheng, Wenning; Tan, Tze King; Paterson, Ian C; Mutha, Naresh V R; Siow, Cheuk Chuen; Tan, Shi Yang; Old, Lesley A; Jakubovics, Nicholas S; Choo, Siew Woh

2016-01-01

The oral streptococci are spherical Gram-positive bacteria categorized under the phylum Firmicutes which are among the most common causative agents of bacterial infective endocarditis (IE) and are also important agents in septicaemia in neutropenic patients. The Streptococcus mitis group is comprised of 13 species including some of the most common human oral colonizers such as S. mitis, S. oralis, S. sanguinis and S. gordonii as well as species such as S. tigurinus, S. oligofermentans and S. australis that have only recently been classified and are poorly understood at present. We present StreptoBase, which provides a specialized free resource focusing on the genomic analyses of oral species from the mitis group. It currently hosts 104 S. mitis group genomes including 27 novel mitis group strains that we sequenced using the high throughput Illumina HiSeq technology platform, and provides a comprehensive set of genome sequences for analyses, particularly comparative analyses and visualization of both cross-species and cross-strain characteristics of S. mitis group bacteria. StreptoBase incorporates sophisticated in-house designed bioinformatics web tools such as Pairwise Genome Comparison (PGC) tool and Pathogenomic Profiling Tool (PathoProT), which facilitate comparative pathogenomics analysis of Streptococcus strains. Examples are provided to demonstrate how StreptoBase can be employed to compare genome structure of different S. mitis group bacteria and putative virulence genes profile across multiple streptococcal strains. In conclusion, StreptoBase offers access to a range of streptococci genomic resources as well as analysis tools and will be an invaluable platform to accelerate research in streptococci. Database URL: http://streptococcus.um.edu.my.

Analysing water use patterns for demand management: the case of the city of Masvingo, Zimbabwe

NASA Astrophysics Data System (ADS)

Dube, Emmanuel; van der Zaag, Pieter

Water use in urban centres is dynamic, fluctuates, differs between high and low-income users, and tends to increase over time. Supply infrastructure can often hardly keep pace with increased water consumption. Given (a) the high cost of infrastructure development, (b) the recent emphasis on demand management, and (c) the social obligation to provide water services to the poor, urban water providers are faced with an important choice: whether to go the demand management route, or to continue constructing new infrastructure. This paper sheds light on some of the possibilities and constraints of both choices by providing a case study of the city of Masvingo in Zimbabwe. The paper analyses water use patterns in this city with a population of 70,000, located in a drought prone region of average rainfall of 600 mm/a. Water consumption has reached the limits of the water supply capacity. The paper first looks at the long-term water use pattern of the city as a whole and the factors that have caused the observed pattern using multiple linear regression. The paper then analyses the patterns of water use of rich and poor households, and attempts to assess the (im)possibilities of influencing these by means of an appropriate tariff structure. In projecting future demand, the paper then considers a number of interventions that could influence demand, which include leakage control, pressure management, awareness campaigns, free technical advice to water users, as well as a new tariff structure. It also discusses when new supply infrastructure should be available, depending on the various demand management measures taken.

Examining associations between sexual behaviours and quality of life in older adults.

PubMed

Flynn, Taylor-Jane; Gow, Alan J

2015-09-01

while sexual behaviours are potentially important for quality of life in older adults, they are under-researched. The current study examined associations between frequency and importance of sexual behaviours and quality of life in older adults. one hundred and thirty-three participants (mean 74 years, SD = 7.1) provided information about the frequency with which they participated in six sexual behaviours and the perceived importance of these: touching/holding hands, embracing/hugging, kissing, mutual stroking, masturbating and intercourse. Participants also completed the WHO Quality of Life scale, providing an overall quality of life score, in addition to the domains of physical health, psychological health, social relationships and environment. Participants provided information on their marital status, living arrangements and self-reported health. both the frequency and importance of sexual behaviours were moderately positively correlated with quality of life (r = 0.52 and 0.47, respectively, both P < 0.001). In separate regression analyses, the frequency of sexual behaviours was a significant predictor of quality of life in the social relationships domain (β = 0.225, P < 0.05), and the importance of sexual behaviours was associated with the psychological domain (β = 0.151, P < 0.05), independent of the presence of a spouse/partner and self-reported health. with ageing trends, a broader understanding of the factors that influence quality of life in older adults is increasingly important. The current findings suggest that aspects of sexual behaviour and quality of life were positively associated. Researchers are encouraged to consider aspects of sex and sexuality when exploring determinants of well-being in later life. © The Author 2015. Published by Oxford University Press on behalf of the British Geriatrics Society. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Reconstitution of Homomeric GluA2flop Receptors in Supported Lipid Membranes

PubMed Central

Baranovic, Jelena; Ramanujan, Chandra S.; Kasai, Nahoko; Midgett, Charles R.; Madden, Dean R.; Torimitsu, Keiichi; Ryan, John F.

2013-01-01

AMPA receptors (AMPARs) are glutamate-gated ion channels ubiquitous in the vertebrate central nervous system, where they mediate fast excitatory neurotransmission and act as molecular determinants of memory formation and learning. Together with detailed analyses of individual AMPAR domains, structural studies of full-length AMPARs by electron microscopy and x-ray crystallography have provided important insights into channel assembly and function. However, the correlation between the structure and functional states of the channel remains ambiguous particularly because these functional states can be assessed only with the receptor bound within an intact lipid bilayer. To provide a basis for investigating AMPAR structure in a membrane environment, we developed an optimized reconstitution protocol using a receptor whose structure has previously been characterized by electron microscopy. Single-channel recordings of reconstituted homomeric GluA2flop receptors recapitulate key electrophysiological parameters of the channels expressed in native cellular membranes. Atomic force microscopy studies of the reconstituted samples provide high-resolution images of membrane-embedded full-length AMPARs at densities comparable to those in postsynaptic membranes. The data demonstrate the effect of protein density on conformational flexibility and dimensions of the receptors and provide the first structural characterization of functional membrane-embedded AMPARs, thus laying the foundation for correlated structure-function analyses of the predominant mediators of excitatory synaptic signals in the brain. PMID:23382380

Application of proteomics to ecology and population biology.

PubMed

Karr, T L

2008-02-01

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

Using Wavelets to Evaluate Persistence of High Frequency Hydrologic and Hydrochemistry Signals

NASA Astrophysics Data System (ADS)

Koirala, S. R.; Gentry, R. W.

2009-12-01

In the area of sustainability science, it is becoming increasingly important to understand the basal condition of a natural system, and its long-term behavior. Research is needed to better understand the temporal scaling of hydrochemistry in streams and watersheds and its relationship to the hydrologic factors that influence its behavior. Persistence of dissolved chemicals in streams has been demonstrated to be linked to certain hydrologic processes, such as interactions between hydrologic units and storage in surface or sub-surface systems. In this study, wavelet analyses provided a novel theoretical basis for insights into long-term hydrochemistry behavior in an east Tennessee watershed. Temporal analyses were conducted on weekly time series data of hydrochemistry (nitrate, chloride, sulfate and calcium concentrations) collected from November 1995 to December 2005 at the West Fork of Walker Branch in Oak Ridge, Tennessee. Hydrochemistry plays an important role in ecosystem services, particularly nitrate, and in general the signal responses can be complex. The signals in this study were modeled using a wavelet approach as a mechanism for evaluating short-and long term temporal effects. The Walker Branch conceptual hydrology model is augmented by these results that show characteristic periodicities or structures for flowpath lengths in the vadose zone (< 20 week period), saturated zone (20 to 50 week period) and bedrock zone (> 50 week period) with implications for hydrochemistry within the watershed. In general, time series signals of watershed hydrochemistry may provide clues as to broad environmental, ecological and economic impacts at the basin scale.

Ecological structure and function in a restored versus natural salt marsh

PubMed Central

Rezek, Ryan J.; Lebreton, Benoit; Sterba-Boatwright, Blair

2017-01-01

Habitat reconstruction is commonly employed to restore degraded estuarine habitats and lost ecological functions. In this study, we use a combination of stable isotope analyses and macrofauna community analysis to compare the ecological structure and function between a recently constructed Spartina alterniflora salt marsh and a natural reference habitat over a 2-year period. The restored marsh was successful in providing habitat for economically and ecologically important macrofauna taxa; supporting similar or greater density, biomass, and species richness to the natural reference during all but one sampling period. Stable isotope analyses revealed that communities from the natural and the restored marshes relied on a similar diversity of food resources and that decapods had similar trophic levels. However, some generalist consumers (Palaemonetes spp. and Penaeus aztecus) were more 13C-enriched in the natural marsh, indicating a greater use of macrophyte derived organic matter relative to restored marsh counterparts. This difference was attributed to the higher quantities of macrophyte detritus and organic carbon in natural marsh sediments. Reduced marsh flooding frequency was associated with a reduction in macrofaunal biomass and decapod trophic levels. The restored marsh edge occurred at lower elevations than natural marsh edge, apparently due to reduced fetch and wind-wave exposure provided by the protective berm structures. The lower elevation of the restored marsh edge mitigated negative impacts in sampling periods with low tidal elevations that affected the natural marsh. The results of this study highlight the importance of considering sediment characteristics and elevation in salt marsh constructions. PMID:29261795

The Reanalysis for Stratospheric Trace-gas Studies

NASA Technical Reports Server (NTRS)

Pawson, Steven; Li, Shuhua

2002-01-01

In order to re-examine trace gas transport in the middle atmosphere for the period May 1991 until April 1995, a "reanalysis" is being performed using an up-to-date version of the DAO's "GEOS" assimilation system. The Reanalysis for Stratospheric Trace-gas Studies (ReSTS) is intended to provide state-of-the-art estimates of the atmosphere during a period when the Upper Atmospheric Research Satellite provided a high density of trace-gas observations, and when the aerosol loading from the eruption of Mount Pinatubo contaminated the lower stratosphere, at the same time performing a natural tracer transport experiment. This study will present the first results from ReSTS, focussing on the improvements over the meteorological analyses produced by the then-operational GEOS-1 data assimilation system; emphasis will be placed on the improved representations of physical processes between GEOS-1 and the current GEOS-4 systems, highlighting the transport properties of the datasets. Alongside the production of a comprehensive atmospheric dataset, important components of ReSTS include performing sensitivity studies to the formulation of the assimilation system (including the representation of physical processes in the GCM, such as feedbacks between ozone/aerosols and meteorology) and to the inclusion of additional data types (including limb-sounding temperature data alongside the TOVS observations). Impacts of some of these factors on the analyzed meteorology and transport will be discussed. Of particular interest are attempts to determine the relative importance of various steps in the assimilation process to the quality of the final analyses.

Risk assessment for produced water discharges to Louisiana open bays. Final report

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

Meinhold, A.F.; DePhillips, M.P.; Holtzman, S.

1996-03-22

The US Department of Energy (USDOE) has a program of research in the environmental aspects of oil and gas extraction. This sampling project will characterize the environmental impacts associated with the discharge of naturally occurring radioactive materials (NORM), metals and organics in produced water. This report is part of a series of studies of the health and ecological risks from discharges of produced water to the Gulf of Mexico, supported by the USDOE. These assessments are being coordinated with the field study, using the collected data to perform human health and ecological risk assessments. These assessments will provide input tomore » regulators in the development of guidelines and permits, and to industry in the development and use of appropriate discharge practices. The initial human health and ecological risk assessments consist of conservative screening analyses meant to identify potentially important contaminants, and to eliminate others from further consideration. More quantitative assessments were done for contaminants identified, in the screening analysis, as being of potential concern. Section 2 gives an overview of human health and ecological risk assessment to help put the analyses presented here in perspective. Section 3 provides the hazard assessment portion of the risk assessment, and identifies the important receptors and pathways of concern. Section 3 also outlines the approach taken to the risk assessments presented in the rest of the report. The remaining sections (4 through 9) present the human health and ecological risk assessments for discharges of produced water to open bays in Louisiana.« less

Time-frequency analysis of GPR data to investigate the damage of monumental buildings

NASA Astrophysics Data System (ADS)

Leucci, Giovanni; Masini, Nicola; Persico, Raffaele

2012-08-01

The presence of particular microclimatic conditions inside monumental buildings is responsible for bio-deterioration processes. In many cases, efflorescence and moulds are visible on the facades of several monuments of historical importance. In many other cases, the effects of decay processes are not visible, thus making difficult the diagnosis and the consequent setup of effective rehabilitation and preservation interventions, especially in the presence of a complex geometry and/or a large variability of construction materials. In such cases, a valuable contribution could be provided by geophysical methods (such as electrical resistivity, electromagnetic conductivity, ground-penetrating radar (GPR), etc), which have been proved to be successful tools for sub-surface investigation and characterization of historical buildings. In old monumental buildings, the masonry structures frequently exhibit cracks, voids, detachments and high moisture contrasts that can give rise to reflection events in radar signals. However, the complexity of the geometry and the structural heterogeneity that characterize these old structures often make the GPR results difficult to analyse and interpret. In particular, the spatial variation in GPR signal attenuation can provide important information about the electrical properties of the investigated materials that, in turn, can be used to assess the physical parameters associated with damage. In this paper, we propose an approach that analyses the data in the form of ‘frequency maps’ to evidence absorption losses probably linked to higher moisture content. Two real case histories back up the proposed method.

Fast gravitational wave radiometry using data folding

NASA Astrophysics Data System (ADS)

Ain, Anirban; Dalvi, Prathamesh; Mitra, Sanjit

2015-07-01

Gravitational waves (GWs) from the early universe and unresolved astrophysical sources are expected to create a stochastic GW background (SGWB). The GW radiometer algorithm is well suited to probe such a background using data from ground-based laser interferometric detectors. Radiometer analysis can be performed in different bases, e.g., isotropic, pixel or spherical harmonic. Each of these analyses possesses a common temporal symmetry which we exploit here to fold the whole data set for every detector pair, typically a few hundred to a thousand days of data, to only one sidereal day, without any compromise in precision. We develop the algebra and a software pipeline needed to fold data, accounting for the effect of overlapping windows and nonstationary noise. We implement this on LIGO's fifth science run data and validate it by performing a standard anisotropic SGWB search on both folded and unfolded data. Folded data not only leads to orders of magnitude reduction in computation cost, but it results in a conveniently small data volume of few gigabytes, making it possible to perform an actual analysis on a personal computer, as well as easy movement of data. A few important analyses, yet unaccomplished due to computational limitations, will now become feasible. Folded data, being independent of the radiometer basis, will also be useful in reducing processing redundancies in multiple searches and provide a common ground for mutual consistency checks. Most importantly, folded data will allow vast amount of experimentation with existing searches and provide substantial help in developing new strategies to find unknown sources.

Ecological structure and function in a restored versus natural salt marsh.

PubMed

Rezek, Ryan J; Lebreton, Benoit; Sterba-Boatwright, Blair; Beseres Pollack, Jennifer

2017-01-01

Habitat reconstruction is commonly employed to restore degraded estuarine habitats and lost ecological functions. In this study, we use a combination of stable isotope analyses and macrofauna community analysis to compare the ecological structure and function between a recently constructed Spartina alterniflora salt marsh and a natural reference habitat over a 2-year period. The restored marsh was successful in providing habitat for economically and ecologically important macrofauna taxa; supporting similar or greater density, biomass, and species richness to the natural reference during all but one sampling period. Stable isotope analyses revealed that communities from the natural and the restored marshes relied on a similar diversity of food resources and that decapods had similar trophic levels. However, some generalist consumers (Palaemonetes spp. and Penaeus aztecus) were more 13C-enriched in the natural marsh, indicating a greater use of macrophyte derived organic matter relative to restored marsh counterparts. This difference was attributed to the higher quantities of macrophyte detritus and organic carbon in natural marsh sediments. Reduced marsh flooding frequency was associated with a reduction in macrofaunal biomass and decapod trophic levels. The restored marsh edge occurred at lower elevations than natural marsh edge, apparently due to reduced fetch and wind-wave exposure provided by the protective berm structures. The lower elevation of the restored marsh edge mitigated negative impacts in sampling periods with low tidal elevations that affected the natural marsh. The results of this study highlight the importance of considering sediment characteristics and elevation in salt marsh constructions.

Holistic stakeholder-oriented and case study-based risk analysis

NASA Astrophysics Data System (ADS)

Heisterkamp, Tobias

2013-04-01

Case studies of storm events in the Berlin conurbation demonstrate the chance of a holistic approach and its potential data sources. Data sets of population, but also data provided by insurance and transport companies, and operating data provided by fire brigades, are used. Various indicators for risk analysis are constructed to identify hot spots. These hot spots can be shortcomings or critical aspects in structure, communication, the warning chain, or even in the structure of potentially affected stakeholders or in the civil protection system itself. Due to increasing complexity of interactions and interdependencies in or between societies and nature, it is important to choose a holistic approach. For risk analyses like the storms in Berlin, it captures many important factors with their effects. For risk analyses, it is important to take potential users into concern: The analysis gets important due to its use later on. In addition to a theoretical background, a focus on the application should be set from the beginning on. To get usable results, it is helpful to complement the theoretical meta-level by a stakeholder-oriented level. An iterative investigation and combination of different layers for the risk analysis explores important influencing factors and allows a tailoring of results to different stakeholder groups. Layers are indicators, gained from data sets like losses from insurance data. Tailoring is important, because of different requirements e.g. by technical or medical assistance. Stakeholders' feedback in the iterative investigation also shows structural limitations for later applications, like special laws the fire brigades have to deal with. Additionally, using actors' perspectives offers the chance to convince practitioners of taking part in the analysis. Their participation is an essential component in applied science. They are important data suppliers, whose goodwill is needed to ensure good results. Based on their experience, they can also help by evaluating the results and their correspondence to reality continuously. Using case studies can help to identify important stakeholders, notably potential affected groups. To cover essential interests of all important stakeholders, a wide range of vulnerabilities, regarding physical and social aspects, and including their resiliences, has to be assessed. The case studies of storm events offer a solid base for investigations, no matter which method is used. They expose shortcomings like gaps in the warning chain or misunderstandings in warning communication. Case studies of extreme events are very interesting for many stakeholders, insurances or fire brigades use them in their daily work. Thus a case study-based approach is a further chance to integrated practitioners into the analysis process and to get results, which they easily understand and which they can transfer into application. There could a second advantage in taking many data sets into account: Each data set like the meteorological observations of wind gust speeds has inherent shortcomings like limited expressiveness, significance or especially uncertainties. Using various approaches could frame the final result and prevent expanding biases or misinterpretations. Altogether, this work stresses the role of transdisciplinary holistic approaches in vulnerability assessments for risk analyses.

The development and validation of the Incivility from Customers Scale.

PubMed

Wilson, Nicole L; Holmvall, Camilla M

2013-07-01

Scant research has examined customers as sources of workplace incivility, despite evidence suggesting that mistreatment is more common from organizational outsiders, including customers, than from organizational members (Grandey, Kern, & Frone, 2007; Schat & Kelloway, 2005). As an important step in extending the literature on customer incivility, we conducted two studies to develop and validate a measure of this construct. Study 1 used focus groups of retail and restaurant employees (n = 30) to elicit a list of uncivil customer behaviors, based on which we wrote initial scale items. Study 2 used a correlational survey design (n = 439) to pare down the number of scale items to 10 and to garner reliability and validity evidence for the scale. Exploratory and confirmatory factor analyses show that the scale is unidimensional and distinguishable from measures of the related, but distinct, constructs of interpersonal justice and psychological aggression from customers. Reliability analyses show that the scale is internally consistent. Significant correlations between the scale and individuals' job satisfaction, turnover intentions, and general and job-specific psychological strain provide evidence of criterion-related validity. Hierarchical regression analyses show that the scale significantly predicts three of four organizational and personal strain outcomes over and above a workplace incivility measure adapted for customer incivility, providing some evidence of incremental validity. Limitations and future research directions are discussed. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Defining functional biomes and monitoring their change globally.

PubMed

Higgins, Steven I; Buitenwerf, Robert; Moncrieff, Glenn R

2016-11-01

Biomes are important constructs for organizing understanding of how the worlds' major terrestrial ecosystems differ from one another and for monitoring change in these ecosystems. Yet existing biome classification schemes have been criticized for being overly subjective and for explicitly or implicitly invoking climate. We propose a new biome map and classification scheme that uses information on (i) an index of vegetation productivity, (ii) whether the minimum of vegetation activity is in the driest or coldest part of the year, and (iii) vegetation height. Although biomes produced on the basis of this classification show a strong spatial coherence, they show little congruence with existing biome classification schemes. Our biome map provides an alternative classification scheme for comparing the biogeochemical rates of terrestrial ecosystems. We use this new biome classification scheme to analyse the patterns of biome change observed over recent decades. Overall, 13% to 14% of analysed pixels shifted in biome state over the 30-year study period. A wide range of biome transitions were observed. For example, biomes with tall vegetation and minimum vegetation activity in the cold season shifted to higher productivity biome states. Biomes with short vegetation and low seasonality shifted to seasonally moisture-limited biome states. Our findings and method provide a new source of data for rigorously monitoring global vegetation change, analysing drivers of vegetation change and for benchmarking models of terrestrial ecosystem function. © 2016 John Wiley & Sons Ltd.

Comparisons of RELAP5-3D Analyses to Experimental Data from the Natural Convection Shutdown Heat Removal Test Facility

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

Bucknor, Matthew; Hu, Rui; Lisowski, Darius

2016-04-17

The Reactor Cavity Cooling System (RCCS) is an important passive safety system being incorporated into the overall safety strategy for high temperature advanced reactor concepts such as the High Temperature Gas- Cooled Reactors (HTGR). The Natural Convection Shutdown Heat Removal Test Facility (NSTF) at Argonne National Laboratory (Argonne) reflects a 1/2-scale model of the primary features of one conceptual air-cooled RCCS design. The project conducts ex-vessel, passive heat removal experiments in support of Department of Energy Office of Nuclear Energy’s Advanced Reactor Technology (ART) program, while also generating data for code validation purposes. While experiments are being conducted at themore » NSTF to evaluate the feasibility of the passive RCCS, parallel modeling and simulation efforts are ongoing to support the design, fabrication, and operation of these natural convection systems. Both system-level and high fidelity computational fluid dynamics (CFD) analyses were performed to gain a complete understanding of the complex flow and heat transfer phenomena in natural convection systems. This paper provides a summary of the RELAP5-3D NSTF model development efforts and provides comparisons between simulation results and experimental data from the NSTF. Overall, the simulation results compared favorably to the experimental data, however, further analyses need to be conducted to investigate any identified differences.« less

The Second International Piping Integrity Research Group (IPIRG-2) program. Final report, October 1991--April 1996

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

Hopper, A.; Wilowski, G.; Scott, P.

1997-03-01

The IPIRG-2 program was an international group program managed by the US NRC and funded by organizations from 15 nations. The emphasis of the IPIRG-2 program was the development of data to verify fracture analyses for cracked pipes and fittings subjected to dynamic/cyclic load histories typical of seismic events. The scope included: (1) the study of more complex dynamic/cyclic load histories, i.e., multi-frequency, variable amplitude, simulated seismic excitations, than those considered in the IPIRG-1 program, (2) crack sizes more typical of those considered in Leak-Before-Break (LBB) and in-service flaw evaluations, (3) through-wall-cracked pipe experiments which can be used to validatemore » LBB-type fracture analyses, (4) cracks in and around pipe fittings, such as elbows, and (5) laboratory specimen and separate effect pipe experiments to provide better insight into the effects of dynamic and cyclic load histories. Also undertaken were an uncertainty analysis to identify the issues most important for LBB or in-service flaw evaluations, updating computer codes and databases, the development and conduct of a series of round-robin analyses, and analyst`s group meetings to provide a forum for nuclear piping experts from around the world to exchange information on the subject of pipe fracture technology. 17 refs., 104 figs., 41 tabs.« less

Shrinkage regression-based methods for microarray missing value imputation.

PubMed

Wang, Hsiuying; Chiu, Chia-Chun; Wu, Yi-Ching; Wu, Wei-Sheng

2013-01-01

Missing values commonly occur in the microarray data, which usually contain more than 5% missing values with up to 90% of genes affected. Inaccurate missing value estimation results in reducing the power of downstream microarray data analyses. Many types of methods have been developed to estimate missing values. Among them, the regression-based methods are very popular and have been shown to perform better than the other types of methods in many testing microarray datasets. To further improve the performances of the regression-based methods, we propose shrinkage regression-based methods. Our methods take the advantage of the correlation structure in the microarray data and select similar genes for the target gene by Pearson correlation coefficients. Besides, our methods incorporate the least squares principle, utilize a shrinkage estimation approach to adjust the coefficients of the regression model, and then use the new coefficients to estimate missing values. Simulation results show that the proposed methods provide more accurate missing value estimation in six testing microarray datasets than the existing regression-based methods do. Imputation of missing values is a very important aspect of microarray data analyses because most of the downstream analyses require a complete dataset. Therefore, exploring accurate and efficient methods for estimating missing values has become an essential issue. Since our proposed shrinkage regression-based methods can provide accurate missing value estimation, they are competitive alternatives to the existing regression-based methods.

Functional Organization of the Action Observation Network in Autism: A Graph Theory Approach

PubMed Central

Alaerts, Kaat; Geerlings, Franca; Herremans, Lynn; Swinnen, Stephan P.; Verhoeven, Judith; Sunaert, Stefan; Wenderoth, Nicole

2015-01-01

Background The ability to recognize, understand and interpret other’s actions and emotions has been linked to the mirror system or action-observation-network (AON). Although variations in these abilities are prevalent in the neuro-typical population, persons diagnosed with autism spectrum disorders (ASD) have deficits in the social domain and exhibit alterations in this neural network. Method Here, we examined functional network properties of the AON using graph theory measures and region-to-region functional connectivity analyses of resting-state fMRI-data from adolescents and young adults with ASD and typical controls (TC). Results Overall, our graph theory analyses provided convergent evidence that the network integrity of the AON is altered in ASD, and that reductions in network efficiency relate to reductions in overall network density (i.e., decreased overall connection strength). Compared to TC, individuals with ASD showed significant reductions in network efficiency and increased shortest path lengths and centrality. Importantly, when adjusting for overall differences in network density between ASD and TC groups, participants with ASD continued to display reductions in network integrity, suggesting that also network-level organizational properties of the AON are altered in ASD. Conclusion While differences in empirical connectivity contributed to reductions in network integrity, graph theoretical analyses provided indications that also changes in the high-level network organization reduced integrity of the AON. PMID:26317222

Transoceanic Dispersal and Plate Tectonics Shaped Global Cockroach Distributions: Evidence from Mitochondrial Phylogenomics.

PubMed

Bourguignon, Thomas; Tang, Qian; Ho, Simon Y W; Juna, Frantisek; Wang, Zongqing; Arab, Daej A; Cameron, Stephen L; Walker, James; Rentz, David; Evans, Theodore A; Lo, Nathan

2018-04-01

Following the acceptance of plate tectonics theory in the latter half of the 20th century, vicariance became the dominant explanation for the distributions of many plant and animal groups. In recent years, however, molecular-clock analyses have challenged a number of well-accepted hypotheses of vicariance. As a widespread group of insects with a fossil record dating back 300 My, cockroaches provide an ideal model for testing hypotheses of vicariance through plate tectonics versus transoceanic dispersal. However, their evolutionary history remains poorly understood, in part due to unresolved relationships among the nine recognized families. Here, we present a phylogenetic estimate of all extant cockroach families, as well as a timescale for their evolution, based on the complete mitochondrial genomes of 119 cockroach species. Divergence dating analyses indicated that the last common ancestor of all extant cockroaches appeared ∼235 Ma, ∼95 My prior to the appearance of fossils that can be assigned to extant families, and before the breakup of Pangaea began. We reconstructed the geographic ranges of ancestral cockroaches and found tentative support for vicariance through plate tectonics within and between several major lineages. We also found evidence of transoceanic dispersal in lineages found across the Australian, Indo-Malayan, African, and Madagascan regions. Our analyses provide evidence that both vicariance and dispersal have played important roles in shaping the distribution and diversity of these insects.

Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data.

PubMed

Racle, Julien; de Jonge, Kaat; Baumgaertner, Petra; Speiser, Daniel E; Gfeller, David

2017-11-13

Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type-specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research (http://epic.gfellerlab.org).

Calculation of flow about posts and powerhead model

NASA Technical Reports Server (NTRS)

1988-01-01

A large number of computational fluid mechanics (CFD) problems were investigated. The primary studies include: the analysis of the turnaround duct/hot gas manifold/transfer tubes (fuel side) of the Space Shuttle Main Engine (SSME); the analysis of the LOX-T manifold (oxidizer side) of the SSME; the analysis of hydrogen accumulation in the Vandeburg flame trench; and modification of the Intel/VT241 systems to accommodate the EADS and PLOT 3D. Some of the analyses were exploratory in nature, using the CONTINUSYS code to provide preliminary information to enhance understanding of the problem, while in other the primary thrust was to acquire design information. In all cases the ability to predict information rapidly in these very complex analyses is seen to be an important demonstration of the power and utility of this mature predictive capability.

Analyses of 476 MHz and 952 MHz Crab Cavities for JLAB Electron Ion Collider

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

Park, HyeKyoung; Castilla, Alejandro; Delayen, Jean R.

2016-05-01

The Center for Accelerator Science at Old Dominion University has designed, fabricated and successfully tested a crab cavity for Electron Ion Collider at Jefferson Lab (JLEIC) [1]. This proof-of-principle cavity was based on the earlier MEIC design which used 748.5 MHz RF system. The updated JLEIC (called MEIC earlier) design [2] utilizes the components from PEP-II. It results in the change on the bunch repetition rate of stored beam to 476.3 MHz. The ion ring collider will eventually require 952.6 MHz crab cavities. This paper will present the analyses of crab cavities of both 476 MHz and 952 MHz options.more » It compares advantages and disadvantages of the options which provide the JLEIC design team important technical information for a system down selection.« less

A photoelectron spectroscopic investigation of vinyl fluoride (C2H3F): the HeI, threshold and CIS photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Locht, R.; Leyh, B.; Dehareng, D.; Hottmann, K.; Baumgärtel, H.

2010-01-01

The threshold photoelectron spectrum (TPES) and the constant ion state (CIS) spectra of the individual ionic states of C2H3F have been recorded using synchrotron radiation. For comparison a well-resolved HeI photoelectron spectrum (HeI-PES) has also been measured and analysed in detail. The TPES has been measured between 9.5 eV and 35 eV photon energy. Numerous vibrational structures, reported for the first time, observed in the ground state and the six excited states of the cation are analysed. Quantum chemical calculations have been performed and provide strong support to the assignments. State-selected CIS spectra highlighted the major importance of autoionization for the production of almost all ionized states of C2H3F observed in this work.

A virtue ethics approach to moral dilemmas in medicine

PubMed Central

Gardiner, P

2003-01-01

Most moral dilemmas in medicine are analysed using the four principles with some consideration of consequentialism but these frameworks have limitations. It is not always clear how to judge which consequences are best. When principles conflict it is not always easy to decide which should dominate. They also do not take account of the importance of the emotional element of human experience. Virtue ethics is a framework that focuses on the character of the moral agent rather than the rightness of an action. In considering the relationships, emotional sensitivities, and motivations that are unique to human society it provides a fuller ethical analysis and encourages more flexible and creative solutions than principlism or consequentialism alone. Two different moral dilemmas are analysed using virtue ethics in order to illustrate how it can enhance our approach to ethics in medicine. PMID:14519840

A virtue ethics approach to moral dilemmas in medicine.

PubMed

Gardiner, P

2003-10-01

Most moral dilemmas in medicine are analysed using the four principles with some consideration of consequentialism but these frameworks have limitations. It is not always clear how to judge which consequences are best. When principles conflict it is not always easy to decide which should dominate. They also do not take account of the importance of the emotional element of human experience. Virtue ethics is a framework that focuses on the character of the moral agent rather than the rightness of an action. In considering the relationships, emotional sensitivities, and motivations that are unique to human society it provides a fuller ethical analysis and encourages more flexible and creative solutions than principlism or consequentialism alone. Two different moral dilemmas are analysed using virtue ethics in order to illustrate how it can enhance our approach to ethics in medicine.

Reducing Missed Laboratory Results: Defining Temporal Responsibility, Generating User Interfaces for Test Process Tracking, and Retrospective Analyses to Identify Problems

PubMed Central

Tarkan, Sureyya; Plaisant, Catherine; Shneiderman, Ben; Hettinger, A. Zachary

2011-01-01

Researchers have conducted numerous case studies reporting the details on how laboratory test results of patients were missed by the ordering medical providers. Given the importance of timely test results in an outpatient setting, there is limited discussion of electronic versions of test result management tools to help clinicians and medical staff with this complex process. This paper presents three ideas to reduce missed results with a system that facilitates tracking laboratory tests from order to completion as well as during follow-up: (1) define a workflow management model that clarifies responsible agents and associated time frame, (2) generate a user interface for tracking that could eventually be integrated into current electronic health record (EHR) systems, (3) help identify common problems in past orders through retrospective analyses. PMID:22195201

Antibacterial properties of grapefruit seed extract against Paenibacillus larvae subsp. larvae.

PubMed

Semprini, P; Langella, V; Pasini, B; Falda, M T; Calvarese, S

2004-01-01

Twenty-one samples of grapefruit seed extract (GSE) either from marketed products or provided by an apiculturist were analysed to verify their inhibition activity, in particular against Paenibacillus larvae subsp. larvae, responsible for American foulbrood. The bactericide capacity of GSE has been measured in Bacillus subtilis BGA, Bacillus cereus 11778, Bacillus cereus K250 and Micrococcus luteus 9341a; these bacteria are normally used in the laboratory to study inhibitors. The results showed that not all GSE have the same inhibitory activity and two of those analysed do not inhibit the five bacteria used. Considering that 19 samples inhibited American foulbrood bacillus, the authors conclude that the use of a natural product (such as GSE) to control this important disease of bees, can be used as a substitute for chemotherapeutic products, after appropriate expedients.

Sinbase: an integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

PubMed

Wang, Linhai; Yu, Jingyin; Li, Donghua; Zhang, Xiurong

2015-01-01

Sesame (Sesamum indicum L.) is an ancient and important oilseed crop grown widely in tropical and subtropical areas. It belongs to the gigantic order Lamiales, which includes many well-known or economically important species, such as olive (Olea europaea), leonurus (Leonurus japonicus) and lavender (Lavandula spica), many of which have important pharmacological properties. Despite their importance, genetic and genomic analyses on these species have been insufficient due to a lack of reference genome information. The now available S. indicum genome will provide an unprecedented opportunity for studying both S. indicum genetic traits and comparative genomics. To deliver S. indicum genomic information to the worldwide research community, we designed Sinbase, a web-based database with comprehensive sesame genomic, genetic and comparative genomic information. Sinbase includes sequences of assembled sesame pseudomolecular chromosomes, protein-coding genes (27,148), transposable elements (372,167) and non-coding RNAs (1,748). In particular, Sinbase provides unique and valuable information on colinear regions with various plant genomes, including Arabidopsis thaliana, Glycine max, Vitis vinifera and Solanum lycopersicum. Sinbase also provides a useful search function and data mining tools, including a keyword search and local BLAST service. Sinbase will be updated regularly with new features, improvements to genome annotation and new genomic sequences, and is freely accessible at http://ocri-genomics.org/Sinbase/. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Immune cell functions in iron overload.

PubMed Central

de Sousa, M

1989-01-01

A number of studies done in the last 10 years demonstrate the importance of iron in regulating the expression of T lymphoid cell surface markers, in influencing the expansion of different T cell subsets and in affecting different immune cell functions in vitro. It has been argued that some of the results obtained could be explained by the formation of iron polymers in the experimental conditions used in vitro (Soyano Fernandez & Romano, 1985). In this review the results of studies of immunological function in clinical situations of iron overload are analysed. From this analysis, it is concluded that the majority of the observations made in vitro have a counterpart in vivo, thus providing additional compelling evidence for the importance of iron as an immunoregulator. PMID:2649280

Developing a Multi-Dimensional Early Elementary Mathematics Screener and Diagnostic Tool: The Primary Mathematics Assessment.

PubMed

Brendefur, Jonathan L; Johnson, Evelyn S; Thiede, Keith W; Strother, Sam; Severson, Herb H

2018-01-01

There is a critical need to identify primary level students experiencing difficulties in mathematics to provide immediate and targeted instruction that remediates their deficits. However, most early math screening instruments focus only on the concept of number, resulting in inadequate and incomplete information for teachers to design intervention efforts. We propose a mathematics assessment that screens and provides diagnostic information in six domains that are important to building a strong foundation in mathematics. This article describes the conceptual framework and psychometric qualities of a web-based assessment tool, the Primary Math Assessment (PMA). The PMA includes a screener to identify students at risk for poor math outcomes and a diagnostic tool to provide a more in-depth profile of children's specific strengths and weaknesses in mathematics. The PMA allows teachers and school personnel to make better instructional decisions by providing more targeted analyses.

Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.

PubMed

Burki, Fabien; Kudryavtsev, Alexander; Matz, Mikhail V; Aglyamova, Galina V; Bulman, Simon; Fiers, Mark; Keeling, Patrick J; Pawlowski, Jan

2010-12-02

Recent phylogenomic analyses have revolutionized our view of eukaryote evolution by revealing unexpected relationships between and within the eukaryotic supergroups. However, for several groups of uncultivable protists, only the ribosomal RNA genes and a handful of proteins are available, often leading to unresolved evolutionary relationships. A striking example concerns the supergroup Rhizaria, which comprises several groups of uncultivable free-living protists such as radiolarians, foraminiferans and gromiids, as well as the parasitic plasmodiophorids and haplosporids. Thus far, the relationships within this supergroup have been inferred almost exclusively from rRNA, actin, and polyubiquitin genes, and remain poorly resolved. To address this, we have generated large Expressed Sequence Tag (EST) datasets for 5 species of Rhizaria belonging to 3 important groups: Acantharea (Astrolonche sp., Phyllostaurus sp.), Phytomyxea (Spongospora subterranea, Plasmodiophora brassicae) and Gromiida (Gromia sphaerica). 167 genes were selected for phylogenetic analyses based on the representation of at least one rhizarian species for each gene. Concatenation of these genes produced a supermatrix composed of 36,735 amino acid positions, including 10 rhizarians, 9 stramenopiles, and 9 alveolates. Phylogenomic analyses of this large dataset revealed a strongly supported clade grouping Foraminifera and Acantharea. The position of this clade within Rhizaria was sensitive to the method employed and the taxon sampling: Maximum Likelihood (ML) and Bayesian analyses using empirical model of evolution favoured an early divergence, whereas the CAT model and ML analyses with fast-evolving sites or the foraminiferan species Reticulomyxa filosa removed suggested a derived position, closely related to Gromia and Phytomyxea. In contrast to what has been previously reported, our analyses also uncovered the presence of the rhizarian-specific polyubiquitin insertion in Acantharea. Finally, this work reveals another possible rhizarian signature in the 60S ribosomal protein L10a. Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.

Brettanomyces bruxellensis evolution and volatile phenols production in red wines during storage in bottles.

PubMed

Coulon, J; Perello, M C; Lonvaud-Funel, A; de Revel, G; Renouf, V

2010-04-01

The presence of Brettanomyces bruxellensis is an important issue during winemaking because of its volatile phenols production capacities. The aim of this study is to provide information on the ability of residual B. bruxellensis populations to multiply and spoil finished wines during storage in bottles. Several finished wines were studied. Brettanomyces bruxellensis populations were monitored during two and a half months, and volatile phenols as well as chemical parameters regularly determined. Variable growth and volatile phenols synthesis capacities were evidenced, in particularly when cells are in a noncultivable state. In addition, the volatile phenol production was clearly shown to be a two-step procedure that could strongly be correlated to the physiological state of the yeast population. This study underlines the importance of minimizing B. bruxellensis populations at the end of wine ageing to reduce volatile phenols production risk once the wine in bottle. Moreover, the physiological state of the yeast seems to have an important impact on ethyl-phenols production, hence demonstrating the importance of taking into account this parameter when analysing wine spoilage risks. Little data exist about the survival of B. bruxellensis once the wine in bottle. This study provides information on the alteration risks encountered during wine storage in bottle and reveals the importance of carrying on further studies to increase the knowledge on B. bruxellensis physiology.

Assessing vaccination as a control strategy in an ongoing epidemic: Bovine tuberculosis in African buffalo

USGS Publications Warehouse

Cross, Paul C.; Getz, W.M.

2006-01-01

Bovine tuberculosis (BTB) is an exotic disease invading the buffalo population (Syncerus caffer) of the Kruger National Park (KNP), South Africa. We used a sex and age-structured epidemiological model to assess the effectiveness of a vaccination program and define important research directions. The model allows for dispersal between a focal herd and background population and was parameterized with a combination of published data and analyses of over 130 radio-collared buffalo in the central region of the KNP. Radio-tracking data indicated that all sex and age categories move between mixed herds, and males over 8 years old had higher mortality and dispersal rates than any other sex or age category. In part due to the high dispersal rates of buffalo, sensitivity analyses indicate that disease prevalence in the background population accounts for the most variability in the BTB prevalence and quasi-eradication within the focal herd. Vaccination rate and the transmission coefficient were the second and third most important parameters of the sensitivity analyses. Further analyses of the model without dispersal suggest that the amount of vaccination necessary for quasi-eradication (i.e. prevalence < 5%) depends upon the duration that a vaccine grants protection. Vaccination programs are more efficient (i.e. fewer wasted doses) when they focus on younger individuals. However, even with a lifelong vaccine and a closed population, the model suggests that >70% of the calf population would have to be vaccinated every year to reduce the prevalence to less than 1%. If the half-life of the vaccine is less than 5 years, even vaccinating every calf for 50 years may not eradicate BTB. Thus, although vaccination provides a means of controlling BTB prevalence it should be combined with other control measures if eradication is the objective.

Grey literature in meta-analyses.

PubMed

Conn, Vicki S; Valentine, Jeffrey C; Cooper, Harris M; Rantz, Marilyn J

2003-01-01

In meta-analysis, researchers combine the results of individual studies to arrive at cumulative conclusions. Meta-analysts sometimes include "grey literature" in their evidential base, which includes unpublished studies and studies published outside widely available journals. Because grey literature is a source of data that might not employ peer review, critics have questioned the validity of its data and the results of meta-analyses that include it. To examine evidence regarding whether grey literature should be included in meta-analyses and strategies to manage grey literature in quantitative synthesis. This article reviews evidence on whether the results of studies published in peer-reviewed journals are representative of results from broader samplings of research on a topic as a rationale for inclusion of grey literature. Strategies to enhance access to grey literature are addressed. The most consistent and robust difference between published and grey literature is that published research is more likely to contain results that are statistically significant. Effect size estimates of published research are about one-third larger than those of unpublished studies. Unfunded and small sample studies are less likely to be published. Yet, importantly, methodological rigor does not differ between published and grey literature. Meta-analyses that exclude grey literature likely (a) over-represent studies with statistically significant findings, (b) inflate effect size estimates, and (c) provide less precise effect size estimates than meta-analyses including grey literature. Meta-analyses should include grey literature to fully reflect the existing evidential base and should assess the impact of methodological variations through moderator analysis.

Mass extinction in tetraodontiform fishes linked to the Palaeocene-Eocene thermal maximum.

PubMed

Arcila, Dahiana; Tyler, James C

2017-11-15

Integrative evolutionary analyses based upon fossil and extant species provide a powerful approach for understanding past diversification events and for assessing the tempo of evolution across the Tree of Life. Herein, we demonstrate the importance of integrating fossil and extant species for inferring patterns of lineage diversification that would otherwise be masked in analyses that examine only one source of evidence. We infer the phylogeny and macroevolutionary history of the Tetraodontiformes (triggerfishes, pufferfishes and allies), a group with one of the most extensive fossil records among fishes. Our analyses combine molecular and morphological data, based on an expanded matrix that adds newly coded fossil species and character states. Beyond confidently resolving the relationships and divergence times of tetraodontiforms, our diversification analyses detect a major mass-extinction event during the Palaeocene-Eocene Thermal Maximum (PETM), followed by a marked increase in speciation rates. This pattern is consistently obtained when fossil and extant species are integrated, whereas examination of the fossil occurrences alone failed to detect major diversification changes during the PETM. When taking into account non-homogeneous models, our analyses also detect a rapid lineage diversification increase in one of the groups (tetraodontoids) during the middle Miocene, which is considered a key period in the evolution of reef fishes associated with trophic changes and ecological opportunity. In summary, our analyses show distinct diversification dynamics estimated from phylogenies and the fossil record, suggesting that different episodes shaped the evolution of tetraodontiforms during the Cenozoic. © 2017 The Author(s).

Written plans: an overlooked mechanism to develop recovery-oriented primary care for depression?

PubMed

Palmer, Victoria J; Johnson, Caroline L; Furler, John S; Densley, Konstancja; Potiriadis, Maria; Gunn, Jane M

2014-01-01

There is a global shift to foster patient-centred and recovery-oriented mental health services. This has resulted from the expansion of how the concept of recovery is understood in mental health literature and practice. Recovery is now more than a return to function or reduction in symptoms; it is a subjective, individualised and multi-faceted experience. To date there has not been investigation of how recovery-oriented services can be translated and implemented into the primary mental health care system. This paper presents the results of a survey from a prospective cohort of primary care patients with probable depression about the importance of written plans to recover. The benefits of having a written plan to recover from depression, as outlined by the participants, were analysed using Leximancer software. The findings provide insights into how written plans may be an important mechanism for implementing a recovery-oriented primary mental health care system. We conclude that the benefits of a written plan provide insight into how patients conceptualise recovery.

Commentary: On the Importance of Early Life Cognitive Abilities in Shaping Later Life Outcomes.

PubMed

Hofer, Scott M; Clouston, Sean

2014-01-01

Early life cognitive ability is likely to be dynamically related to life course factors including educational attainment, occupational outcomes, health behaviors, activities, health, and subsequent cognitive health. Disentangling the selective and causal processes contributing to cognitive functioning across the lifespan is challenging and requires long-term investments in longitudinal data. We discuss results from several analyses using data from the Individual Development and Adaptation longitudinal research program (Bergman, 2000; Magnusson, 1988) that provide fresh insights into the relation of early life cognition, particularly high levels of cognitive capabilities, to educational achievement, emotional adjustment, and career success. These papers and the longitudinal data provide a remarkable window into the development and impacts of cognition, and high cognitive functioning, on a variety of important life outcomes that we hope will continue to inform us about additional outcomes in middle life, transition to retirement, and cognition and health in later years and to robustly examine how the early years matter across the whole lifespan.

Processing and analysis of cardiac optical mapping data obtained with potentiometric dyes

PubMed Central

Laughner, Jacob I.; Ng, Fu Siong; Sulkin, Matthew S.; Arthur, R. Martin

2012-01-01

Optical mapping has become an increasingly important tool to study cardiac electrophysiology in the past 20 years. Multiple methods are used to process and analyze cardiac optical mapping data, and no consensus currently exists regarding the optimum methods. The specific methods chosen to process optical mapping data are important because inappropriate data processing can affect the content of the data and thus alter the conclusions of the studies. Details of the different steps in processing optical imaging data, including image segmentation, spatial filtering, temporal filtering, and baseline drift removal, are provided in this review. We also provide descriptions of the common analyses performed on data obtained from cardiac optical imaging, including activation mapping, action potential duration mapping, repolarization mapping, conduction velocity measurements, and optical action potential upstroke analysis. Optical mapping is often used to study complex arrhythmias, and we also discuss dominant frequency analysis and phase mapping techniques used for the analysis of cardiac fibrillation. PMID:22821993

Data from the US and UK cystic fibrosis registries support disease modification by CFTR modulation with ivacaftor.

PubMed

Bessonova, Leona; Volkova, Nataliya; Higgins, Mark; Bengtsson, Leif; Tian, Simon; Simard, Christopher; Konstan, Michael W; Sawicki, Gregory S; Sewall, Ase; Nyangoma, Stephen; Elbert, Alexander; Marshall, Bruce C; Bilton, Diana

2018-05-10

Ivacaftor is the first cystic fibrosis transmembrane conductance regulator (CFTR) modulator demonstrating clinical benefit in patients with cystic fibrosis (CF). As ivacaftor is intended for chronic, lifelong use, understanding long-term effects is important for patients and healthcare providers. This ongoing, observational, postapproval safety study evaluates clinical outcomes and disease progression in ivacaftor-treated patients using data from the US and the UK CF registries following commercial availability. Annual analyses compare ivacaftor-treated and untreated matched comparator patients for: risks of death, transplantation, hospitalisation, pulmonary exacerbation; prevalence of CF-related complications and microorganisms and lung function changes in a subset of patients who initiated ivacaftor in the first year of commercial availability. Results from the 2014 analyses (2 and 3 years following commercial availability in the UK and USA, respectively) are presented here. Analyses included 1256 ivacaftor-treated and 6200 comparator patients from the USA and 411 ivacaftor-treated and 2069 comparator patients from the UK. No new safety concerns were identified based on the evaluation of clinical outcomes included in the analyses. As part of safety evaluations, ivacaftor-treated US patients were observed to have significantly lower risks of death (0.6% vs 1.6%, p=0.0110), transplantation (0.2% vs 1.1%, p=0.0017), hospitalisation (27.5% vs 43.1%, p<0.0001) and pulmonary exacerbation (27.8% vs 43.3%, p<0.0001) relative to comparators; trends were similar in the UK. In both registries, ivacaftor-treated patients had a lower prevalence of CF-related complications and select microorganisms and had better preserved lung function. While general limitations of observational research apply, analyses revealed favourable results for clinically important outcomes among ivacaftor-treated patients, adding to the growing body of literature supporting disease modification by CFTR modulation with ivacaftor. EUPAS4270. © 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.

Online sperm donors: the impact of family, friends, personality and risk perception on behaviour.

PubMed

Whyte, Stephen; Savage, David A; Torgler, Benno

2017-12-01

As informal sperm donation becomes more prevalent worldwide, understanding donor psychology and interactions is critical in providing effective policy, equitable legislative frameworks and frontline health support to an ever-growing number of global participants. We analyse data of informal sperm donors who were members of the connection website PrideAngel to identify the role and effect of several factors, e.g. kinship, social networks, personality, and risk perception, on behaviour. A key strength of the study is the ability to analyse various factors, such as the level and history of informal donation, risk concerns, number of women to whom donations are informally made and the number of offspring. Our results indicate donors who have also been active in formal clinical settings (compared with those who exclusively donate informally), donate to more women in the informal market and realise more offspring. Donor's sexual orientation also affects activity. From a personality perspective, conscientiousness provides comparative advantage. It is possible this characteristic provides positive externalities, as more conscientious men may be more efficient or organised in a market that requires increased cooperation and communication. The importance of kin and social networks seems to affect frequency of donation only, possibly representing a time constraint (or opportunity cost). Copyright © 2017 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

NG6: Integrated next generation sequencing storage and processing environment.

PubMed

Mariette, Jérôme; Escudié, Frédéric; Allias, Nicolas; Salin, Gérald; Noirot, Céline; Thomas, Sylvain; Klopp, Christophe

2012-09-09

Next generation sequencing platforms are now well implanted in sequencing centres and some laboratories. Upcoming smaller scale machines such as the 454 junior from Roche or the MiSeq from Illumina will increase the number of laboratories hosting a sequencer. In such a context, it is important to provide these teams with an easily manageable environment to store and process the produced reads. We describe a user-friendly information system able to manage large sets of sequencing data. It includes, on one hand, a workflow environment already containing pipelines adapted to different input formats (sff, fasta, fastq and qseq), different sequencers (Roche 454, Illumina HiSeq) and various analyses (quality control, assembly, alignment, diversity studies,…) and, on the other hand, a secured web site giving access to the results. The connected user will be able to download raw and processed data and browse through the analysis result statistics. The provided workflows can easily be modified or extended and new ones can be added. Ergatis is used as a workflow building, running and monitoring system. The analyses can be run locally or in a cluster environment using Sun Grid Engine. NG6 is a complete information system designed to answer the needs of a sequencing platform. It provides a user-friendly interface to process, store and download high-throughput sequencing data.

Within-individual versus between-individual predictors of antisocial behaviour: A longitudinal study of young people in Victoria, Australia

PubMed Central

Hemphill, Sheryl A; Heerde, Jessica A; Herrenkohl, Todd I; Farrington, David P

2016-01-01

In an influential 2002 paper, Farrington and colleagues argued that to understand ‘causes’ of delinquency, within-individual analyses of longitudinal data are required (compared to the vast majority of analyses that have focused on between-individual differences). The current paper aimed to complete similar analyses to those conducted by Farrington and colleagues by focusing on the developmental correlates and risk factors for antisocial behaviour and by comparing within-individual and between-individual predictors of antisocial behaviour using data from the youngest Victorian cohort of the International Youth Development Study, a state-wide representative sample of 927 students from Victoria, Australia. Data analysed in the current paper are from participants in Year 6 (age 11–12 years) in 2003 to Year 11 (age 16–17 years) in 2008 (N = 791; 85% retention) with data collected almost annually. Participants completed a self-report survey of risk and protective factors and antisocial behaviour. Complete data were available for 563 participants. The results of this study showed all but one of the forward- (family conflict) and backward-lagged (low attachment to parents) correlations were statistically significant for the within-individual analyses compared with all analyses being statistically significant for the between-individual analyses. In general, between-individual correlations were greater in magnitude than within-individual correlations. Given that forward-lagged within-individual correlations provide more salient measures of causes of delinquency, it is important that longitudinal studies with multi-wave data analyse and report their data using both between-individual and within-individual correlations to inform current prevention and early intervention programs seeking to reduce rates of antisocial behaviour. PMID:28123186

Evaluation of family-centred practices in the early intervention programmes for infants and young children in Singapore with Measure of Processes of Care for Service Providers and Measure of Beliefs about Participation in Family-Centred Service.

PubMed

Tang, H N; Chong, W H; Goh, W; Chan, W P; Choo, S

2012-01-01

The primary purpose of this study was to report on an evaluation of the perceptions and beliefs of service providers towards family-centred practices in 11 early intervention programmes for infants and young children in Singapore. The Measure of Processes of Care for Service Providers (MPOC-SP) and Measure of Beliefs about Participation in Family-Centred Service (MBP-FCS) were administered to 213 service providers made up of teachers, therapists, psychologists and social workers providing centre-based therapy to children with special needs who were below the age of 6 years. Exploratory factor analyses were performed with both scales. Nineteen of the 27 MPOC-SP items were retained and supported the original four-factor structure model. The exploratory factor analyses on MBP-FCS provided a less satisfactory outcome. Fourteen of the 28 items were retained and these loaded onto four factors. The two factors relating to Beliefs about benefits of FCS and Beliefs about the absence of negative outcomes from FCS failed to emerge as separate factors. Further multiple regressions indicated that more direct work with families and positive self-efficacy in implementing FCS contributed significantly to explaining service providers' positive perception towards family-centred practice in service delivery. This is the first time MPOC-SP and MBP-FCS were administered to a population in an Asian context. While MBP-FCS would benefit from further development work on its construct, MPOC-SP offered important insights into service providers' perspectives about family-centred practices that would have useful implications for professional and service development. © 2011 Blackwell Publishing Ltd.

Quantifying cross-border movements and migrations for guiding the strategic planning of malaria control and elimination

PubMed Central

2014-01-01

Background Identifying human and malaria parasite movements is important for control planning across all transmission intensities. Imported infections can reintroduce infections into areas previously free of infection, maintain ‘hotspots’ of transmission and import drug resistant strains, challenging national control programmes at a variety of temporal and spatial scales. Recent analyses based on mobile phone usage data have provided valuable insights into population and likely parasite movements within countries, but these data are restricted to sub-national analyses, leaving important cross-border movements neglected. Methods National census data were used to analyse and model cross-border migration and movement, using East Africa as an example. ‘Hotspots’ of origin-specific immigrants from neighbouring countries were identified for Kenya, Tanzania and Uganda. Populations of origin-specific migrants were compared to distance from origin country borders and population size at destination, and regression models were developed to quantify and compare differences in migration patterns. Migration data were then combined with existing spatially-referenced malaria data to compare the relative propensity for cross-border malaria movement in the region. Results The spatial patterns and processes for immigration were different between each origin and destination country pair. Hotspots of immigration, for example, were concentrated close to origin country borders for most immigrants to Tanzania, but for Kenya, a similar pattern was only seen for Tanzanian and Ugandan immigrants. Regression model fits also differed between specific migrant groups, with some migration patterns more dependent on population size at destination and distance travelled than others. With these differences between immigration patterns and processes, and heterogeneous transmission risk in East Africa and the surrounding region, propensities to import malaria infections also likely show substantial variations. Conclusion This was a first attempt to quantify and model cross-border movements relevant to malaria transmission and control. With national census available worldwide, this approach can be translated to construct a cross-border human and malaria movement evidence base for other malaria endemic countries. The outcomes of this study will feed into wider efforts to quantify and model human and malaria movements in endemic regions to facilitate improved intervention planning, resource allocation and collaborative policy decisions. PMID:24886389

tRNAs promote nuclear import of HIV-1 intracellular reverse transcription complexes.

PubMed

Zaitseva, Lyubov; Myers, Richard; Fassati, Ariberto

2006-10-01

Infection of non-dividing cells is a biological property of HIV-1 crucial for virus transmission and AIDS pathogenesis. This property depends on nuclear import of the intracellular reverse transcription and pre-integration complexes (RTCs/PICs). To identify cellular factors involved in nuclear import of HIV-1 RTCs, cytosolic extracts were fractionated by chromatography and import activity examined by the nuclear import assay. A near-homogeneous fraction was obtained, which was active in inducing nuclear import of purified and labeled RTCs. The active fraction contained tRNAs, mostly with defective 3' CCA ends. Such tRNAs promoted HIV-1 RTC nuclear import when synthesized in vitro. Active tRNAs were incorporated into and recovered from virus particles. Mutational analyses indicated that the anticodon loop mediated binding to the viral complex whereas the T-arm may interact with cellular factors involved in nuclear import. These tRNA species efficiently accumulated into the nucleus on their own in a energy- and temperature-dependent way. An HIV-1 mutant containing MLV gag did not incorporate tRNA species capable of inducing HIV-1 RTC nuclear import and failed to infect cell cycle-arrested cells. Here we provide evidence that at least some tRNA species can be imported into the nucleus of human cells and promote HIV-1 nuclear import.

Static and Motion-Based Visual Features Used by Airport Tower Controllers: Some Implications for the Design of Remote or Virtual Towers

NASA Technical Reports Server (NTRS)

Ellis, Stephen R.; Liston, Dorion B.

2011-01-01

Visual motion and other visual cues are used by tower controllers to provide important support for their control tasks at and near airports. These cues are particularly important for anticipated separation. Some of them, which we call visual features, have been identified from structured interviews and discussions with 24 active air traffic controllers or supervisors. The visual information that these features provide has been analyzed with respect to possible ways it could be presented at a remote tower that does not allow a direct view of the airport. Two types of remote towers are possible. One could be based on a plan-view, map-like computer-generated display of the airport and its immediate surroundings. An alternative would present a composite perspective view of the airport and its surroundings, possibly provided by an array of radially mounted cameras positioned at the airport in lieu of a tower. An initial more detailed analyses of one of the specific landing cues identified by the controllers, landing deceleration, is provided as a basis for evaluating how controllers might detect and use it. Understanding other such cues will help identify the information that may be degraded or lost in a remote or virtual tower not located at the airport. Some initial suggestions how some of the lost visual information may be presented in displays are mentioned. Many of the cues considered involve visual motion, though some important static cues are also discussed.

Does the Component Processes Task Assess Text-Based Inferences Important for Reading Comprehension? A Path Analysis in Primary School Children

PubMed Central

Wassenburg, Stephanie I.; de Koning, Björn B.; de Vries, Meinou H.; van der Schoot, Menno

2016-01-01

Using a component processes task (CPT) that differentiates between higher-level cognitive processes of reading comprehension provides important advantages over commonly used general reading comprehension assessments. The present study contributes to further development of the CPT by evaluating the relative contributions of its components (text memory, text inferencing, and knowledge integration) and working memory to general reading comprehension within a single study using path analyses. Participants were 173 third- and fourth-grade children. As hypothesized, knowledge integration was the only component of the CPT that directly contributed to reading comprehension, indicating that the text-inferencing component did not assess inferential processes related to reading comprehension. Working memory was a significant predictor of reading comprehension over and above the component processes. Future research should focus on finding ways to ensure that the text-inferencing component taps into processes important for reading comprehension. PMID:27378989

76 FR 45232 - Marine Mammals; File No. 16443

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-28

..., import, export, possession, and analyses of bones of sperm (Physeter macrocephalus) and minke... of a lander on which the whale bones have been placed on the bottom of the Weddell Sea, Antarctica by foreign researchers and under other authorizations. Bones would be imported into the U.S. for analyses. No...

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines.

PubMed

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan; Lee, Jun-Heon

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13-0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24-0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens.

Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.

PubMed

Choi, Jung-Woo; Liao, Xiaoping; Stothard, Paul; Chung, Won-Hyong; Jeon, Heoyn-Jeong; Miller, Stephen P; Choi, So-Young; Lee, Jeong-Koo; Yang, Bokyoung; Lee, Kyung-Tai; Han, Kwang-Jin; Kim, Hyeong-Cheol; Jeong, Dongkee; Oh, Jae-Don; Kim, Namshin; Kim, Tae-Hun; Lee, Hak-Kyo; Lee, Sung-Jin

2014-01-01

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea--Hanwoo, Jeju Heugu, and Korean Holstein--using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions-deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.

Ancient gene transfer from algae to animals: Mechanisms and evolutionary significance

PubMed Central

2012-01-01

Background Horizontal gene transfer (HGT) is traditionally considered to be rare in multicellular eukaryotes such as animals. Recently, many genes of miscellaneous algal origins were discovered in choanoflagellates. Considering that choanoflagellates are the existing closest relatives of animals, we speculated that ancient HGT might have occurred in the unicellular ancestor of animals and affected the long-term evolution of animals. Results Through genome screening, phylogenetic and domain analyses, we identified 14 gene families, including 92 genes, in the tunicate Ciona intestinalis that are likely derived from miscellaneous photosynthetic eukaryotes. Almost all of these gene families are distributed in diverse animals, suggesting that they were mostly acquired by the common ancestor of animals. Their miscellaneous origins also suggest that these genes are not derived from a particular algal endosymbiont. In addition, most genes identified in our analyses are functionally related to molecule transport, cellular regulation and methylation signaling, suggesting that the acquisition of these genes might have facilitated the intercellular communication in the ancestral animal. Conclusions Our findings provide additional evidence that algal genes in aplastidic eukaryotes are not exclusively derived from historical plastids and thus important for interpreting the evolution of eukaryotic photosynthesis. Most importantly, our data represent the first evidence that more anciently acquired genes might exist in animals and that ancient HGT events have played an important role in animal evolution. PMID:22690978

Detecting pyrethroid resistance in predatory mites inhabiting soil and litter: an in vitro test.

PubMed

El Adouzi, Marine; Bonato, Olivier; Roy, Lise

2017-06-01

While resistance against insecticides is widely known in pest arthropods, it remains poorly known in non-target arthropods of the same agrosystems. This may be of crucial importance in the context of organic pest management or integrated pest management. First, stopping of pesticide pressure during farm conversion may lead to important rearrangements of non-target communities due to fitness cost of resistance in populations of some species. Second, resistant biological agents may be useful to farms with low synthetic pesticide use. Communities of mesostigmatid mites, encompassing numerous predatory species, are supposed to be involved in important ecological processes in both crop soils and animal litter/manure. Here we provide a tarsal contact method for assessing resistance in different populations from various species of mesostigmatid mites. Analyses of data from repeated tests on three populations from different mesostigmatid families proved the method to be robust and able to generate consistent and reliable mortality percentages according to insecticide concentration. Our bioassay system allows for both one-shot estimate of pyrethroid sensitivity in mite populations and estimation of how it changes over time, making possible survival analyses and assessment of recovery from knockdown. The rating system retained makes it possible to score response to insecticides in a consistent and standard way in species from different mesostigmatid families. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Estimation of linkage disequilibrium and analysis of genetic diversity in Korean chicken lines

PubMed Central

Seo, Dongwon; Lee, Doo Ho; Choi, Nuri; Sudrajad, Pita; Lee, Seung-Hwan

2018-01-01

The development of genetic markers for animal breeding is an effective strategy to reduce the time and cost required to improve economically important traits. To implement genomic selection in the multibreed chicken population of Korea, an understanding of the linkage disequilibrium (LD) status of the target population is essential. In this study, we performed population genetic analyses to investigate LD decay, the effective population size, and breed diversity using 600K high-density single nucleotide polymorphism genotypes of 189 native chickens in 14 lines (including Korean native chicken, imported and adapted purebred and commercial chickens). The results indicated that commercial native chickens have less calculated LD (average, r2 = 0.13–0.26) and purebred native chickens have more calculated LD (average, r2 = 0.24–0.37) across the entire genome. The effective population sizes of the examined lines showed patterns opposite to those of population LD. The phylogeny and admixture analyses showed that commercial and purebred chickens were well distinguished, except for Rhode Island Red (RIR) purebred lines of NC (NIAS_RIR_C) and ND (NIAS_RIR_D). These lines are difficult to distinguish clearly because they originated from the same respective breeds. The results of this study may provide important information for the development of genetic markers that can be used in breeding to improve the economic traits of native chickens. PMID:29425208

Whole-Genome Analyses of Korean Native and Holstein Cattle Breeds by Massively Parallel Sequencing

PubMed Central

Stothard, Paul; Chung, Won-Hyong; Jeon, Heoyn-Jeong; Miller, Stephen P.; Choi, So-Young; Lee, Jeong-Koo; Yang, Bokyoung; Lee, Kyung-Tai; Han, Kwang-Jin; Kim, Hyeong-Cheol; Jeong, Dongkee; Oh, Jae-Don; Kim, Namshin; Kim, Tae-Hun; Lee, Hak-Kyo; Lee, Sung-Jin

2014-01-01

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea—Hanwoo, Jeju Heugu, and Korean Holstein—using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions–deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding. PMID:24992012

Survey of primary care providers' knowledge of screening for, diagnosing and managing prediabetes.

PubMed

Tseng, Eva; Greer, Raquel C; O'Rourke, Paul; Yeh, Hsin-Chieh; McGuire, Maura M; Clark, Jeanne M; Maruthur, Nisa M

2017-11-01

Prediabetes affects 86 million US adults, but primary care providers' (PCPs') knowledge, practices, attitudes and beliefs toward prediabetes are unclear. Assess PCPs' (1) knowledge of risk factors that should prompt prediabetes screening, laboratory criteria for diagnosing prediabetes and guidelines for management of prediabetes; (2) management practices around prediabetes; (3) attitudes and beliefs about prediabetes. Self-administered written survey of PCPs. One hundred forty of 155 PCPs (90%) attending an annual provider retreat for academically affiliated multispecialty practices in the mid-Atlantic region. Descriptive analyses of survey questions on knowledge, management, and attitudes and beliefs related to prediabetes. Multivariate logistic regression was used to determine the association between provider characteristics (gender, race/ethnicity, years since training, specialty and provider type) and knowledge, management, and attitudes and beliefs about prediabetes. Six percent of PCPs correctly identified all of the risk factors that should prompt prediabetes screening. Only 17% of PCPs correctly identified the laboratory parameters for diagnosing prediabetes based on both fasting glucose and hemoglobin A1c. Nearly 90% of PCPs reported close follow-up (within 6 months) of patients with prediabetes. Few PCPs (11%) selected referral to a behavioral weight loss program as the recommended initial management approach to prediabetes. PCPs agreed that patient-related factors are important barriers to lifestyle change and metformin use. Provider characteristics were generally not associated with knowledge, management, attitudes and beliefs about prediabetes in multivariate analyses. Addressing gaps in knowledge and the underutilization of behavioral weight loss programs in prediabetes are two essential areas where PCPs could take a lead in curbing the diabetes epidemic.

New, previously unreported correlations between latent Toxoplasma gondii infection and excessive ethanol consumption.

PubMed

Samojłowicz, Dorota; Borowska-Solonynko, Aleksandra; Kruczyk, Marcin

2017-11-01

A number of world literature reports indicate that a latent Toxoplasma gondii infection leads to development of central nervous system disorders, which in turn may lead to altered behavior in the affected individuals. T. gondii infection has been observed to play the greatest role in drivers, suicides, and psychiatric patients. Studies conducted for this manuscript involve a different, never before really reported correlation between latent T. gondii infection and ethanol abuse. A total of 538 decedents with a known cause of death were included in the study. These individuals were divided into three groups: the risky behavior group, inconclusively risky behavior group, and control group. The criterion for this division was the likely effect of the individual's behavior on the mechanism and cause of his/her death. The material used for analyses were blood samples collected during routine medico-legal examinations in these cases. The blood samples were used to measure anti-T. gondii IgG antibodies with an enzyme-linked immunosorbent assay (ELISA). Moreover, the following data were recorded for each decedent: sex, age, circumstances of death, cause of death, time from death to autopsy, and (if provided) substance abuse status (alcohol, illicit drugs). In those cases where blood alcohol level or toxicology tests were requested by the Prosecutor's Office, their results were also included in our analysis. Test results demonstrated a strong correlation between latent T. gondii infection and engaging in risky behaviors leading to death. Moreover, analyses demonstrated a positive correlation between the presence of anti-T. gondii IgG antibodies and psychoactive substance (especially ethanol) abuse, however, the causal relationship remains unclear. Due to the fact that alcohol abuse constitutes a significant social problem, searching for eliminable risk factors for addiction is extremely important. Our analyses provided new important information on the possible effects of latent T. gondii infection in humans. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Review of the Primary National Ambient Air Quality Standards ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) is conducting a review of the air quality criteria and the primary (health-based) national ambient air quality standards (NAAQS) for nitrogen dioxide (NO2). The major phases of the process for reviewing NAAQS include the following: (1) planning, (2) science assessment, (3) risk and exposure assessment, and (4) policy assessment. As an initial step in the risk and exposure assessment phase, EPA staff has considered the extent to which updated quantitative analyses of NO2 exposures and/or NO2-attributable health risks are warranted in the current review, based on the available scientific evidence and technical information. These considerations focus on the degree to which important uncertainties identified in quantitative analyses from the last review have been addressed by newly available evidence, tools, or information. The purpose of the REA planning document is to present staff's considerations and preliminary conclusions regarding potential updated quantitative analyses in the current review of the primary NO2 NAAQS. Provide opportunity for CASAC feedback on EPA's plans for the risk and exposure assessment for the Nitrogen Oxides NAAQS review

[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.

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.

Whole genome sequencing data and de novo draft assemblies for 66 teleost species

PubMed Central

Malmstrøm, Martin; Matschiner, Michael; Tørresen, Ole K.; Jakobsen, Kjetill S.; Jentoft, Sissel

2017-01-01

Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9–39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context. We further present a nuclear marker set used for phylogenetic inference and evaluate each gene tree in relation to the species tree to test for homogeneity in the phylogenetic signal. Collectively, these analyses illustrate the robustness of this highly diverse data set and enable extensive reuse of the selected phylogenetic markers and the genomic data in general. This data set covers all major teleost lineages and provides unprecedented opportunities for comparative studies of teleosts. PMID:28094797

Trade-off between taxon diversity and functional diversity in European lake ecosystems.

PubMed

Grossmann, Lars; Beisser, Daniela; Bock, Christina; Chatzinotas, Antonis; Jensen, Manfred; Preisfeld, Angelika; Psenner, Roland; Rahmann, Sven; Wodniok, Sabina; Boenigk, Jens

2016-12-01

Inferring ecosystem functioning and ecosystem services through inspections of the species inventory is a major aspect of ecological field studies. Ecosystem functions are often stable despite considerable species turnover. Using metatranscriptome analyses, we analyse a thus-far unparalleled freshwater data set which comprises 21 mainland European freshwater lakes from the Sierra Nevada (Spain) to the Carpathian Mountains (Romania) and from northern Germany to the Apennines (Italy) and covers an altitudinal range from 38 m above sea level (a.s.l) to 3110 m a.s.l. The dominant taxa were Chlorophyta and streptophytic algae, Ciliophora, Bacillariophyta and Chrysophyta. Metatranscriptomics provided insights into differences in community composition and into functional diversity via the relative share of taxa to the overall read abundance of distinct functional genes on the ecosystem level. The dominant metabolic pathways in terms of the fraction of expressed sequences in the cDNA libraries were affiliated with primary metabolism, specifically oxidative phosphorylation, photosynthesis and the TCA cycle. Our analyses indicate that community composition is a good first proxy for the analysis of ecosystem functions. However, differential gene regulation modifies the relative importance of taxa in distinct pathways. Whereas taxon composition varies considerably between lakes, the relative importance of distinct metabolic pathways is much more stable, indicating that ecosystem functioning is buffered against shifts in community composition through a functional redundancy of taxa. © 2016 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Evaluating species-specific changes in hydrologic regimes: an iterative approach for salmonids in the Greater Yellowstone Area (USA)

USGS Publications Warehouse

Al-Chokhachy, Robert K.; Sepulveda, Adam; Ray, Andrew M.; Thoma, David P.; Tercek, Michael T.

2017-01-01

Despite the importance of hydrologic regimes to the phenology, demography, and abundance of fishes such as salmonids, there have been surprisingly few syntheses that holistically assess regional, species-specific trends in hydrologic regimes within a framework of climate change. Here, we consider hydrologic regimes within the Greater Yellowstone Area in the Rocky Mountains of western North America to evaluate changes in hydrologic metrics anticipated to affect salmonids, a group of fishes with high regional ecological and socioeconomic value. Our analyses assessed trends across different sites and time periods (1930–, 1950–, and 1970–2015) as means to evaluate spatial and temporal shifts. Consistent patterns emerged from our analyses indicating substantial shifts to (1) earlier peak discharge events; (2) reductions of summer minimum streamflows; (3) declines in the duration of river ice; and (4) decreases in total volume of water. We found accelerated trends in hydrologic change for the 1970–2015 period, with an average peak discharge 7.5 days earlier, 27.5% decline in summer minimum streamflows, and a 15.6% decline in the annual total volume of water (1 October–September 30) across sites. We did observe considerable variability in magnitude of change across sites, suggesting different levels of vulnerability to a changing climate. Our analyses provide an iterative means for assessing climate predictions and an important step in identifying the climate resilience of landscapes.

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups".

PubMed

Hampl, Vladimir; Hug, Laura; Leigh, Jessica W; Dacks, Joel B; Lang, B Franz; Simpson, Alastair G B; Roger, Andrew J

2009-03-10

Nearly all of eukaryotic diversity has been classified into 6 suprakingdom-level groups (supergroups) based on molecular and morphological/cell-biological evidence; these are Opisthokonta, Amoebozoa, Archaeplastida, Rhizaria, Chromalveolata, and Excavata. However, molecular phylogeny has not provided clear evidence that either Chromalveolata or Excavata is monophyletic, nor has it resolved the relationships among the supergroups. To establish the affinities of Excavata, which contains parasites of global importance and organisms regarded previously as primitive eukaryotes, we conducted a phylogenomic analysis of a dataset of 143 proteins and 48 taxa, including 19 excavates. Previous phylogenomic studies have not included all major subgroups of Excavata, and thus have not definitively addressed their interrelationships. The enigmatic flagellate Andalucia is sister to typical jakobids. Jakobids (including Andalucia), Euglenozoa and Heterolobosea form a major clade that we name Discoba. Analyses of the complete dataset group Discoba with the mitochondrion-lacking excavates or "metamonads" (diplomonads, parabasalids, and Preaxostyla), but not with the final excavate group, Malawimonas. This separation likely results from a long-branch attraction artifact. Gradual removal of rapidly-evolving taxa from the dataset leads to moderate bootstrap support (69%) for the monophyly of all Excavata, and 90% support once all metamonads are removed. Most importantly, Excavata robustly emerges between unikonts (Amoebozoa + Opisthokonta) and "megagrouping" of Archaeplastida, Rhizaria, and chromalveolates. Our analyses indicate that Excavata forms a monophyletic suprakingdom-level group that is one of the 3 primary divisions within eukaryotes, along with unikonts and a megagroup of Archaeplastida, Rhizaria, and the chromalveolate lineages.

Longitudinal Evaluation of the Importance of Homework Assignment Completion for the Academic Performance of Middle School Students with ADHD

PubMed Central

Langberg, Joshua M.; Dvorsky, Melissa R.; Molitor, Stephen J.; Bourchtein, Elizaveta; Eddy, Laura D.; Smith, Zoe; Schultz, Brandon K.; Evans, Steven W.

2016-01-01

The primary goal of this study was to longitudinally evaluate the homework assignment completion patterns of middle school age adolescents with ADHD, their associations with academic performance, and malleable predictors of homework assignment completion. Analyses were conducted on a sample of 104 middle school students comprehensively diagnosed with ADHD and followed for 18 months. Multiple teachers for each student provided information about the percentage of homework assignments turned in at five separate timepoints and school grades were collected quarterly. Results showed that agreement between teachers with respect to students’ assignment completion was high, with an intraclass correlation of .879 at baseline. Students with ADHD were turning in an average of 12% fewer assignments each academic quarter in comparison to teacher-reported classroom averages. Regression analyses revealed a robust association between the percentage of assignments turned in at baseline and school grades 18 months later, even after controlling for baseline grades, achievement (reading and math), intelligence, family income, and race. Cross-lag analyses demonstrated that the association between assignment completion and grades was reciprocal, with assignment completion negatively impacting grades and low grades in turn being associated with decreased future homework completion. Parent ratings of homework materials management abilities at baseline significantly predicted the percentage of assignments turned in as reported by teachers 18 months later. These findings demonstrate that homework assignment completion problems are persistent across time and an important intervention target for adolescents with ADHD. PMID:26931065

Comparative systems biology across an evolutionary gradient within the Shewanella genus.

PubMed

Konstantinidis, Konstantinos T; Serres, Margrethe H; Romine, Margaret F; Rodrigues, Jorge L M; Auchtung, Jennifer; McCue, Lee-Ann; Lipton, Mary S; Obraztsova, Anna; Giometti, Carol S; Nealson, Kenneth H; Fredrickson, James K; Tiedje, James M

2009-09-15

To what extent genotypic differences translate to phenotypic variation remains a poorly understood issue of paramount importance for several cornerstone concepts of microbiology including the species definition. Here, we take advantage of the completed genomic sequences, expressed proteomic profiles, and physiological studies of 10 closely related Shewanella strains and species to provide quantitative insights into this issue. Our analyses revealed that, despite extensive horizontal gene transfer within these genomes, the genotypic and phenotypic similarities among the organisms were generally predictable from their evolutionary relatedness. The power of the predictions depended on the degree of ecological specialization of the organisms evaluated. Using the gradient of evolutionary relatedness formed by these genomes, we were able to partly isolate the effect of ecology from that of evolutionary divergence and to rank the different cellular functions in terms of their rates of evolution. Our ranking also revealed that whole-cell protein expression differences among these organisms, when the organisms were grown under identical conditions, were relatively larger than differences at the genome level, suggesting that similarity in gene regulation and expression should constitute another important parameter for (new) species description. Collectively, our results provide important new information toward beginning a systems-level understanding of bacterial species and genera.

Network meta-analysis in health psychology and behavioural medicine: a primer.

PubMed

Molloy, G J; Noone, C; Caldwell, D; Welton, N J; Newell, J

2018-04-05

Progress in the science and practice of health psychology depends on the systematic synthesis of quantitative psychological evidence. Meta-analyses of experimental studies have led to important advances in understanding health-related behaviour change interventions. Fundamental questions regarding such interventions have been systematically investigated through synthesising relevant experimental evidence using standard pairwise meta-analytic procedures that provide reliable estimates of the magnitude, homogeneity and potential biases in effects observed. However, these syntheses only provide information about whether particular types of interventions work better than a control condition or specific alternative approaches. To increase the impact of health psychology on health-related policy-making, evidence regarding the comparative efficacy of all relevant intervention approaches - which may include biomedical approaches - is necessary. With the development of network meta-analysis (NMA), such evidence can be synthesised, even when direct head-to-head trials do not exist. However, care must be taken in its application to ensure reliable estimates of the effect sizes between interventions are revealed. This review paper describes the potential importance of NMA to health psychology, how the technique works and important considerations for its appropriate application within health psychology.

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement.

PubMed

Duan, Naibin; Bai, Yang; Sun, Honghe; Wang, Nan; Ma, Yumin; Li, Mingjun; Wang, Xin; Jiao, Chen; Legall, Noah; Mao, Linyong; Wan, Sibao; Wang, Kun; He, Tianming; Feng, Shouqian; Zhang, Zongying; Mao, Zhiquan; Shen, Xiang; Chen, Xiaoliu; Jiang, Yuanmao; Wu, Shujing; Yin, Chengmiao; Ge, Shunfeng; Yang, Long; Jiang, Shenghui; Xu, Haifeng; Liu, Jingxuan; Wang, Deyun; Qu, Changzhi; Wang, Yicheng; Zuo, Weifang; Xiang, Li; Liu, Chang; Zhang, Daoyuan; Gao, Yuan; Xu, Yimin; Xu, Kenong; Chao, Thomas; Fazio, Gennaro; Shu, Huairui; Zhong, Gan-Yuan; Cheng, Lailiang; Fei, Zhangjun; Chen, Xuesen

2017-08-15

Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.Apple is one of the most important fruit crops. Here, the authors perform deep genome resequencing of 117 diverse accessions and reveal comprehensive models of apple origin, speciation, domestication, and fruit size evolution as well as candidate genes associated with important agronomic traits.

Association of Membrane Rafts and Postsynaptic Density: Proteomics, Biochemical, and Ultrastructural Analyses

PubMed Central

Suzuki, Tatsuo; Zhang, Jingping; Miyazawa, Shoko; Liu, Qian; Farzan, Michael R.; Yao, Wei-Dong

2011-01-01

Postsynaptic membrane rafts are believed to play important roles in synaptic signaling, plasticity, and maintenance. However, their molecular identities remain elusive. Further, how they interact with the well-established signaling specialization, the postsynaptic density (PSD), is poorly understood. We previously detected a number of conventional PSD proteins in detergent-resistant membranes (DRMs). Here, we have performed LC-MS/MS (liquid chromatography coupled with tandem mass spectrometry) analyses on postsynaptic membrane rafts and PSDs. Our comparative analysis identified an extensive overlap of protein components in the two structures. This overlapping could be explained, at least partly, by a physical association of the two structures. Meanwhile, a significant number of proteins displayed biased distributions to either rafts or PSDs, suggesting distinct roles for the two postsynaptic specializations. Using biochemical and electron microscopic methods, we directly detected membrane raft-PSD complexes. In vitro reconstitution experiments indicated that the formation of raft-PSD complexes was not due to the artificial reconstruction of once-solubilized membrane components and PSD structures, supporting that these complexes occurred in vivo. Taking together, our results provide evidence that postsynaptic membrane rafts and PSDs may be physically associated. Such association could be important in postsynaptic signal integration, synaptic function, and maintenance. PMID:21797867

Barriers and Strategies in Guideline Implementation—A Scoping Review

PubMed Central

Fischer, Florian; Lange, Kerstin; Klose, Kristina; Greiner, Wolfgang; Kraemer, Alexander

2016-01-01

Research indicates that clinical guidelines are often not applied. The success of their implementation depends on the consideration of a variety of barriers and the use of adequate strategies to overcome them. Therefore, this scoping review aims to describe and categorize the most important barriers to guideline implementation. Furthermore, it provides an overview of different kinds of suitable strategies that are tailored to overcome these barriers. The search algorithm led to the identification of 1659 articles in PubMed. Overall, 69 articles were included in the data synthesis. The content of these articles was analysed by using a qualitative synthesis approach, to extract the most important information on barriers and strategies. The barriers to guideline implementation can be differentiated into personal factors, guideline-related factors, and external factors. The scoping review revealed the following aspects as central elements of successful strategies for guideline implementation: dissemination, education and training, social interaction, decision support systems and standing orders. Available evidence indicates that a structured implementation can improve adherence to guidelines. Therefore, the barriers to guideline implementation and adherence need to be analysed in advance so that strategies that are tailored to the specific setting and target groups can be developed. PMID:27417624

Health economic studies: an introduction to cost-benefit, cost-effectiveness, and cost-utility analyses.

PubMed

Angevine, Peter D; Berven, Sigurd

2014-10-15

Narrative overview. To provide clinicians with a basic understanding of economic studies, including cost-benefit, cost-effectiveness, and cost-utility analyses. As decisions regarding public health policy, insurance reimbursement, and patient care incorporate factors other than traditional outcomes such as satisfaction or symptom resolution, health economic studies are increasingly prominent in the literature. This trend will likely continue, and it is therefore important for clinicians to have a fundamental understanding of the common types of economic studies and be able to read them critically. In this brief article, the basic concepts of economic studies and the differences between cost-benefit, cost-effectiveness, and cost-utility studies are discussed. An overview of the field of health economic analysis is presented. Cost-benefit, cost-effectiveness, and cost-utility studies all integrate cost and outcome data into a decision analysis model. These different types of studies are distinguished mainly by the way in which outcomes are valued. Obtaining accurate cost data is often difficult and can limit the generalizability of a study. With a basic understanding of health economic analysis, clinicians can be informed consumers of these important studies.

A profile of students receiving counselling services at a university in post-apartheid South Africa.

PubMed

Bowman, Brett; Payne, Jarrod

2011-12-01

The purpose of this study was to describe a profile of students seeking counselling at a racially diverse university in post-apartheid South Africa as a means to demonstrate the importance of routinely collecting and analysing student counselling data at university-based centres across the country. Student data were extracted from the only two counselling centres based at the University of the Witwatersrand in Johannesburg that provided services to 831 students during 2008. The 26 243 students that did not seek counselling during this period formed the comparison group. These data were analysed using logistic regression. Black, female and students within the 21-25 year age category were more likely to receive counselling, and presenting problems varied by population group. Given the country's past and continued levels of social asymmetry, we argue that the development of standardised university-based reporting systems able to describe the characteristics and presenting problems of students seeking counselling across South African universities should be prioritised by its higher education sector. Timely access to information of this kind is crucial to the generation of evidence-based mental health interventions in a population that is especially important to the country's development vision.

Analysis of grain characters in temperate grasses reveals distinctive patterns of endosperm organization associated with grain shape

PubMed Central

Drea, Sinéad

2012-01-01

Members of the core pooids represent the most important crops in temperate zones including wheat, barley, and oats. Their importance as crops is largely due to the grain, particularly the storage capabilities of the endosperm. In this study, a comprehensive survey of grain morphology and endosperm organization in representatives of wild and cultivated species throughout the core pooids was performed. As sister to the core pooid tribes Poeae, Aveneae, Triticeae, and Bromeae within the Pooideae subfamily, Brachypodium provides a taxonomically relevant reference point. Using macroscopic, histological, and molecular analyses distinct patterns of grain tissue organization in these species, focusing on the peripheral and modified aleurone, are described. The results indicate that aleurone organization is correlated with conventional grain quality characters such as grain shape and starch content. In addition to morphological and organizational variation, expression patterns of candidate gene markers underpinning this variation were examined. Features commonly associated with grains are largely defined by analyses on lineages within the Triticeae and knowledge of grain structure may be skewed as a result of the focus on wheat and barley. Specifically, the data suggest that the modified aleurone is largely restricted to species in the Triticeae tribe. PMID:23081982

Dehydration-induced WRKY genes from tobacco and soybean respond to jasmonic acid treatments in BY-2 cell culture.

PubMed

Rabara, Roel C; Tripathi, Prateek; Lin, Jun; Rushton, Paul J

2013-02-15

Drought is one of the important environmental factors affecting crop production worldwide and therefore understanding the molecular response of plant to stress is an important step in crop improvement. WRKY transcription factors are one of the 10 largest transcription factor families across the green lineage. In this study, highly upregulated dehydration-induced WRKY and enzyme-coding genes from tobacco and soybean were selected from microarray data for promoter analyses. Putative stress-related cis-regulatory elements such as TGACG motif, ABRE-like elements; W and G-like sequences were identified by an in silico analyses of promoter region of the selected genes. GFP quantification of transgenic BY-2 cell culture showed these promoters direct higher expression in-response to 100 μM JA treatment compared to 100 μM ABA, 10% PEG and 85 mM NaCl treatments. Thus promoter activity upon JA treatment and enrichment of MeJA-responsive elements in the promoter of the selected genes provides insights for these genes to be jasmonic acid responsive with potential of mediating cross-talk during dehydration responses. Copyright © 2013 Elsevier Inc. All rights reserved.

The Health Impact of Intensive and Nonintensive Grandchild Care in Europe: New Evidence From SHARE

PubMed Central

Glaser, Karen; Tinker, Anthea

2016-01-01

Objectives: Grandparents are an important source of childcare. However, caring for grandchildren may affect grandparents’ health in both positive and negative ways. Our study examines the association between grandparental childcare and grandparents’ health at 2- and 4-year follow-up. Method: Our study is based on grandparents aged 50 and older from Waves 1–4 of the Survey of Health, Ageing and Retirement in Europe (SHARE). Using multivariate analyses, we investigated associations between intensive and nonintensive grandparental childcare at Wave 2 and subsequent health (self-rated health, depressive symptoms, and disability) controlling for covariates and health at baseline. Associations between changes over time in grandparental childcare and health at follow-up were also explored. Multiple imputation techniques and sensitivity analyses were undertaken to investigate possible biases arising from sample attrition. Results: Grandparents looking after grandchildren, whether intensively or nonintensively, experienced some health benefits. Associations strengthened when attrition was accounted for, particularly if it is assumed that those who dropped out of the study were in poor health. Discussion: Our results show better health among grandparents who provided grandchild care in the European countries studied. These results are important given the widespread provision of grandchild care in Europe. PMID:26315046

Social affiliation in same-class and cross-class interactions.

PubMed

Côté, Stéphane; Kraus, Michael W; Carpenter, Nichelle C; Piff, Paul K; Beermann, Ursula; Keltner, Dacher

2017-02-01

Historically high levels of economic inequality likely have important consequences for relationships between people of the same and different social class backgrounds. Here, we test the prediction that social affiliation among same-class partners is stronger at the extremes of the class spectrum, given that these groups are highly distinctive and most separated from others by institutional and economic forces. An internal meta-analysis of 4 studies (N = 723) provided support for this hypothesis. Participant and partner social class were interactively, rather than additively, associated with social affiliation, indexed by affiliative behaviors and emotions during structured laboratory interactions and in daily life. Further, response surface analyses revealed that paired upper or lower class partners generally affiliated more than average-class pairs. Analyses with separate class indices suggested that these patterns are driven more by parental income and subjective social class than by parental education. The findings illuminate the dynamics of same- and cross-class interactions, revealing that not all same-class interactions feature the same degree of affiliation. They also reveal the importance of studying social class from an intergroup perspective. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The structure of social exchange in self-help support groups: development of a measure.

PubMed

Brown, Louis D; Tang, Xiaohui; Hollman, Ruth L

2014-03-01

Self-help support groups are indigenous community resources designed to help people manage a variety of personal challenges, from alcohol abuse to xeroderma pigmentosum. The social exchanges that occur during group meetings are central to understanding how people benefit from participation. This paper examines the different types of social exchange behaviors that occur during meetings, using two studies to develop empirically distinct scales that reliably measure theoretically important types of exchange. Resource theory informed the initial measurement development efforts. Exploratory factor analyses from the first study led to revisions in the factor structure of the social exchange scales. The revised measure captured the exchange of emotional support, experiential information, humor, unwanted behaviors, and exchanges outside meetings. Confirmatory factor analyses from a follow-up study with a different sample of self-help support groups provided good model fit, suggesting the revised structure accurately represented the data. Further, the scales demonstrated good convergent and discriminant validity with related constructs. Future research can use the scales to identify aspects of social exchange that are most important in improving health outcomes among self-help support group participants. Groups can use the scales in practice to celebrate strengths and address weaknesses in their social exchange dynamics.