Science.gov

Sample records for identify potential indicators

  1. Identifying Student Potential for ICT Entrepreneurship Using Myers-Briggs Personality Type Indicators

    ERIC Educational Resources Information Center

    Johnston, Kevin A.; Andersen, Barry K.; Davidge-Pitts, Jennifer; Ostensen-Saunders, Mark

    2009-01-01

    Literature relating to personality and entrepreneurship has focused primarily on personality characteristics of traditional entrepreneurs. The focus of this study was on personality characteristics and temperaments of potential Information and Communication Technology (ICT) entrepreneurs. The main objective of the study was to evaluate the

  2. Identifying Student Potential for ICT Entrepreneurship Using Myers-Briggs Personality Type Indicators

    ERIC Educational Resources Information Center

    Johnston, Kevin A.; Andersen, Barry K.; Davidge-Pitts, Jennifer; Ostensen-Saunders, Mark

    2009-01-01

    Literature relating to personality and entrepreneurship has focused primarily on personality characteristics of traditional entrepreneurs. The focus of this study was on personality characteristics and temperaments of potential Information and Communication Technology (ICT) entrepreneurs. The main objective of the study was to evaluate the…

  3. Identifying potential academic leaders

    PubMed Central

    White, David; Krueger, Paul; Meaney, Christopher; Antao, Viola; Kim, Florence; Kwong, Jeffrey C.

    2016-01-01

    Objective To identify variables associated with willingness to undertake leadership roles among academic family medicine faculty. Design Web-based survey. Bivariate and multivariable analyses (logistic regression) were used to identify variables associated with willingness to undertake leadership roles. Setting Department of Family and Community Medicine at the University of Toronto in Ontario. Participants A total of 687 faculty members. Main outcome measures Variables related to respondents’ willingness to take on various academic leadership roles. Results Of all 1029 faculty members invited to participate in the survey, 687 (66.8%) members responded. Of the respondents, 596 (86.8%) indicated their level of willingness to take on various academic leadership roles. Multivariable analysis revealed that the predictors associated with willingness to take on leadership roles were as follows: pursuit of professional development opportunities (odds ratio [OR] 3.79, 95% CI 2.29 to 6.27); currently holding at least 1 leadership role (OR 5.37, 95% CI 3.38 to 8.53); a history of leadership training (OR 1.86, 95% CI 1.25 to 2.78); the perception that mentorship is important for one’s current role (OR 2.25, 95% CI 1.40 to 3.60); and younger age (OR 0.97, 95% CI 0.95 to 0.99). Conclusion Willingness to undertake new or additional leadership roles was associated with 2 variables related to leadership experiences, 2 variables related to perceptions of mentorship and professional development, and 1 demographic variable (younger age). Interventions that support opportunities in these areas might expand the pool and strengthen the academic leadership potential of faculty members.

  4. Identifying Novel Drug Indications through Automated Reasoning

    PubMed Central

    Tari, Luis; Vo, Nguyen; Liang, Shanshan; Patel, Jagruti; Baral, Chitta; Cai, James

    2012-01-01

    Background With the large amount of pharmacological and biological knowledge available in literature, finding novel drug indications for existing drugs using in silico approaches has become increasingly feasible. Typical literature-based approaches generate new hypotheses in the form of protein-protein interactions networks by means of linking concepts based on their cooccurrences within abstracts. However, this kind of approaches tends to generate too many hypotheses, and identifying new drug indications from large networks can be a time-consuming process. Methodology In this work, we developed a method that acquires the necessary facts from literature and knowledge bases, and identifies new drug indications through automated reasoning. This is achieved by encoding the molecular effects caused by drug-target interactions and links to various diseases and drug mechanism as domain knowledge in AnsProlog, a declarative language that is useful for automated reasoning, including reasoning with incomplete information. Unlike other literature-based approaches, our approach is more fine-grained, especially in identifying indirect relationships for drug indications. Conclusion/Significance To evaluate the capability of our approach in inferring novel drug indications, we applied our method to 943 drugs from DrugBank and asked if any of these drugs have potential anti-cancer activities based on information on their targets and molecular interaction types alone. A total of 507 drugs were found to have the potential to be used for cancer treatments. Among the potential anti-cancer drugs, 67 out of 81 drugs (a recall of 82.7%) are indeed known cancer drugs. In addition, 144 out of 289 drugs (a recall of 49.8%) are non-cancer drugs that are currently tested in clinical trials for cancer treatments. These results suggest that our method is able to infer drug indications (original or alternative) based on their molecular targets and interactions alone and has the potential to discover novel drug indications for existing drugs. PMID:22911721

  5. Direct and indirect indicators to identify potential leakage of contaminants associated with unconventional oil and gas development based on conceptual geochemical and isotopic monitoring approaches

    NASA Astrophysics Data System (ADS)

    Humez, P.; Mayer, B.; Negrel, P. J.; Lions, J.; Lagneau, V.; Kloppmann, W.; Ing, J.; Becker, V.; Nightingale, M.

    2014-12-01

    The extraction of tightly bound natural gas and oil raises environmental concerns regarding shallow drinking water resources. These concerns include impacts of migration of contaminants through induced and natural fractures, drilling imperfections, wastewater discharge and accidental spills. Improved understanding of the fate and transport of contaminants through long-term monitoring, and sharing of data between industry, regulators and researchers will help to effectively manage risks for shallow water resources associated with the unconventional gas and oil industry. Based on the North-American experiences related to unconventional oil and gas resources and monitoring approaches developed in the Carbon Capture and Storage (CCS) context, we suggest conceptual models for monitoring the potential contamination of shallow aquifers overlying production zones. The strength of sensitive geochemical tracers is demonstrated based on conceptual approaches (e.g. diffusion model) and field and tracer studies (e.g. geochemical and isotopic monitoring) with three objectives: 1) characterize subsurface derived contaminants as direct geochemical and isotopic indicators; 2) assess geochemical processes enhanced by the fluid intrusion; 3) understand parameters and processes which could impact or alter the geochemical and isotopic signatures of the contaminants (e.g. microbial oxidation, migration or transport processes etc.) to determine indirect indicators of potential contaminant leakage. This comprehensive geochemical and isotope approach using direct and indirect indicators with the analyses of major and minor ions, trace elements, and δ11B, δ7Li, δ34SSO4, δ18OSO4, 87Sr/86Sr, δ18OH2O, and δ2HH2O values in the CO2FIELDLAB project (Humez et al., 2014) allowed discriminating reactive mechanisms from non-reactive mixing processes associated with gas leakage within a shallow aquifer. These and other results indicate that this conceptual approach is promising for monitoring strategies related to unconventional oil and gas resources. Humez et al., 2014. Chem. Geol., 368, 11-30.

  6. Identifying Potential Dropouts. ERIC Digest.

    ERIC Educational Resources Information Center

    Gaustad, Joan

    An overview of issues and problems in identifying and predicting dropouts is presented in this Digest. The topics discussed are as follows: factors associated with dropping out; defining and calculating dropouts; problems in prediction; the usefulness of current prediction models; and suggestions for improving prediction. The recommendation is

  7. Biotechnological valorization potential indicator for lignocellulosic materials.

    PubMed

    Duarte, Luís C; Esteves, Maria P; Carvalheiro, Florbela; Gírio, Francisco M

    2007-12-01

    This report introduces the biotechnological valorization potential indicator (BVPI) concept, a metric to measure the degree of suitability of lignocellulosic materials to be used as feedstock in a biorefinery framework. This indicator groups the impact of the main factors influencing upgrade-ability, both the biological/chemical nature of the materials, and the economical, technological and geographical factors. The BVPI was applied to the identification of the most relevant opportunities and constraints pertaining to the lignocellulosic by-products from the Portuguese agro-industrial cluster. Several by-products were identified with a high valorization potential, e.g., rice husks, brewery's spent grain, tomato pomace, carob pulp, de-alcoholized grape bagasse, and extracted olive bagasse, that would greatly benefit from the further development of specific biotechnology processes, specifically concerning the upgrade of their hemicellulosic fraction. PMID:18061896

  8. Identifying Potential Test Item Misalignment Using Student Verbal Reports

    ERIC Educational Resources Information Center

    Leighton, Jacqueline P.; Gokiert, Rebecca J.

    2008-01-01

    The purpose of the present investigation was to identify the relationship among different indicators of uncertainty that lead to potential item misalignment. The item-based indicators included ratings of ambiguity and cognitive complexity. The student-based indicators included (a) frequency of cognitive monitoring per item, (b) levels of…

  9. Identifying node role in social network based on multiple indicators.

    PubMed

    Huang, Shaobin; Lv, Tianyang; Zhang, Xizhe; Yang, Yange; Zheng, Weimin; Wen, Chao

    2014-01-01

    It is a classic topic of social network analysis to evaluate the importance of nodes and identify the node that takes on the role of core or bridge in a network. Because a single indicator is not sufficient to analyze multiple characteristics of a node, it is a natural solution to apply multiple indicators that should be selected carefully. An intuitive idea is to select some indicators with weak correlations to efficiently assess different characteristics of a node. However, this paper shows that it is much better to select the indicators with strong correlations. Because indicator correlation is based on the statistical analysis of a large number of nodes, the particularity of an important node will be outlined if its indicator relationship doesn't comply with the statistical correlation. Therefore, the paper selects the multiple indicators including degree, ego-betweenness centrality and eigenvector centrality to evaluate the importance and the role of a node. The importance of a node is equal to the normalized sum of its three indicators. A candidate for core or bridge is selected from the great degree nodes or the nodes with great ego-betweenness centrality respectively. Then, the role of a candidate is determined according to the difference between its indicators' relationship with the statistical correlation of the overall network. Based on 18 real networks and 3 kinds of model networks, the experimental results show that the proposed methods perform quite well in evaluating the importance of nodes and in identifying the node role. PMID:25089823

  10. Identifying Node Role in Social Network Based on Multiple Indicators

    PubMed Central

    Huang, Shaobin; Lv, Tianyang; Zhang, Xizhe; Yang, Yange; Zheng, Weimin; Wen, Chao

    2014-01-01

    It is a classic topic of social network analysis to evaluate the importance of nodes and identify the node that takes on the role of core or bridge in a network. Because a single indicator is not sufficient to analyze multiple characteristics of a node, it is a natural solution to apply multiple indicators that should be selected carefully. An intuitive idea is to select some indicators with weak correlations to efficiently assess different characteristics of a node. However, this paper shows that it is much better to select the indicators with strong correlations. Because indicator correlation is based on the statistical analysis of a large number of nodes, the particularity of an important node will be outlined if its indicator relationship doesn't comply with the statistical correlation. Therefore, the paper selects the multiple indicators including degree, ego-betweenness centrality and eigenvector centrality to evaluate the importance and the role of a node. The importance of a node is equal to the normalized sum of its three indicators. A candidate for core or bridge is selected from the great degree nodes or the nodes with great ego-betweenness centrality respectively. Then, the role of a candidate is determined according to the difference between its indicators' relationship with the statistical correlation of the overall network. Based on 18 real networks and 3 kinds of model networks, the experimental results show that the proposed methods perform quite well in evaluating the importance of nodes and in identifying the node role. PMID:25089823

  11. Identifying Indicators Related to Constructs for Engineering Design Outcome

    ERIC Educational Resources Information Center

    Wilhelmsen, Cheryl A.; Dixon, Raymond A.

    2016-01-01

    This study ranked constructs articulated by Childress and Rhodes (2008) and identified the key indicators for each construct as a starting point to explore what should be included on an instrument to measure the engineering design process and outcomes of students in high schools that use the PLTW and EbDTM curricula in Idaho. A case-study design…

  12. Identifying and Nurturing Potential Academic Leaders

    ERIC Educational Resources Information Center

    Hoppe, Sherry L.

    2003-01-01

    With a move away from rotational chairs and a reluctance to tackle the conflicting responsibilities inherent in the lower levels of academic leadership, how can those at the top of the pipeline identify faculty who have the ability and desire to move through the ranks? What characteristics will increase the probability of willingness, commitment,…

  13. Life Potential as a Basic Demographic Indicator

    ERIC Educational Resources Information Center

    Goerlich, Francisco J.; Soler, Angel

    2013-01-01

    This paper proposes an indicator that integrates life expectancy with the demographic structure of the population for a given society. By doing this, we have a simple indicator of mortality and aging combined, which could be very useful for developed societies. As is widely known, life expectancy at birth is independent of the demographic…

  14. Life Potential as a Basic Demographic Indicator

    ERIC Educational Resources Information Center

    Goerlich, Francisco J.; Soler, Angel

    2013-01-01

    This paper proposes an indicator that integrates life expectancy with the demographic structure of the population for a given society. By doing this, we have a simple indicator of mortality and aging combined, which could be very useful for developed societies. As is widely known, life expectancy at birth is independent of the demographic

  15. Identifying mechanistic indicators of childhood asthma from blood gene expression

    EPA Science Inventory

    Asthmatic individuals have been identified as a susceptible subpopulation for air pollutants. However, asthma represents a syndrome with multiple probable etiologies, and the identification of these asthma endotypes is critical to accurately define the most susceptible subpopula...

  16. [Evoked potentials. Indications and diagnostic significance].

    PubMed

    Riffel, B; Stöhr, M; Reich, H; Delcker, A

    1986-07-15

    Visual, auditory and somatosensory evoked potentials are useful in the detection and localization of demyelinating lesions, which mainly cause a slowing of conduction and therefore a latency increase in the evoked potential. Primarily amplitude reductions or loss of the response are seen in partial or complete impulse conduction blocks due to a tumor e.g. Acoustic nerve tumors can be detected by AEP, orbit tumors or processes of the chiasm by VEP and spinal cord tumors by SEP. The use of evoked potentials for the evaluation of ophthalmologic disorders, for audiometry in children and for monitoring head-injured patients with coma have become a valuable aid to the physician too. PMID:3765650

  17. Anthropometric Indices in Adults: Which Is the Best Indicator to Identify Alanine Aminotransferase Levels?

    PubMed Central

    Chen, Shuang; Guo, Xiaofan; Yu, Shasha; Zhou, Ying; Li, Zhao; Sun, Yingxian

    2016-01-01

    Background: To evaluate the correlations between serum alanine aminotransferase (ALT) levels and anthropometric indices including body mass index (BMI), waist circumference (WC), hip circumference (HC), waist-to-height ratio (WHtR), waist-to-hip ratio (WHR), and a new body index, the A Body Shape Index (ABSI) in Chinese adults. Methods: A multicenter, cross-sectional study was conducted in rural areas of China in 2012–2013, and 11,331 adults were included in our final analysis. Results: BMI, WC, HC, WHtR, WHR and ABSI were significantly positively correlated with ALT levels. Spearman rank test showed that WHtR (r = 0.346 for men, r = 0.282 for women, both p < 0.001) had the highest correlation coefficient for ALT level, whereas ABSI showed the lowest, and the correlation coefficient of each measure was higher in men than that in women. Comparing the lowest with the highest quintile of each anthropometric measure, the multivariate logistic model presented that WHtR had the superiority of identifying the presence of elevated ALT (OR 4.38; 95% CI 3.15–6.08 for men, OR 4.29; 95% CI 2.91–6.33 for women, both p < 0.001), and the ABSI was the poorest predictor in men (OR 2.51; 95% CI 1.93–3.27, p < 0.001). No association was observed for ABSI in women. Conclusions: Our results indicated that BMI, WC, HC, WHtR and WHR were able to determine elevated ALT presence, while ABSI was not capable. WHtR and to some extent BMI were the best body indices, for predicting the ALT levels in this population. Nevertheless, the predictive ability of ABSI as a novel body index was not superior compared to established anthropometric indices. PMID:26901214

  18. Identifying indicators through modified Delphi technique in polytechnics system

    NASA Astrophysics Data System (ADS)

    Nashir, Irdayanti Mat; Mustapha, Ramlee; Yusoff, Abdullah

    2015-02-01

    This study aims to examine how the panel has been selected as experts in assessing indicators of innovative instructional leadership (IIL) administrator in polytechnics based on 222 items were obtained through previous studies. A total of eleven people were selected as the expert panels in a study where expert selection criteria based on their background in the leadership. Experts were interviewed separately. Interviews were carried out for a half hour in their offices. The data obtained were analyzed using Atlas Ti. Overall findings indicate experts agree that a total of 188 items and 14 indicators should be maintained in this innovative instructional leadership instruments and next by using Modified Delphi Technique. The instrument will then be analyzed to obtain findings on the perception of lecturers on every administrator innovative instructional leadership in their respective polytechnics.

  19. Identifying Value Indicators and Social Capital in Community Health Partnerships

    ERIC Educational Resources Information Center

    Hausman, Alice J.; Becker, Julie; Brawer, Rickie

    2005-01-01

    Increasingly, public health practice is turning to the application of community collaborative models to improve population health status. Despite the growth of these activities, however, evaluations of the national demonstrations have indicated that community health partnerships fail to achieve measurable results and struggle to maintain integrity…

  20. Accomplishing structural change: identifying intermediate indicators of success.

    PubMed

    Miller, Robin Lin; Reed, Sarah J; Francisco, Vincent

    2013-03-01

    Coalitions are routinely employed across the United States as a method of mobilizing communities to improve local conditions that impact on citizens' well-being. Success in achieving specific objectives for environmental or structural community change may not quickly translate into improved population outcomes in the community, posing a dilemma for coalitions that pursue changes that focus on altering community conditions. Considerable effort by communities to plan for and pursue structural change objectives, without evidence of logical and appropriate intermediate markers of success could lead to wasted effort. Yet, the current literature provides little guidance on how coalitions might select intermediate indicators of achievement to judge their progress and the utility of their effort. The current paper explores the strengths and weaknesses of various indicators of intermediate success in creating structural changes among a sample of 13 coalitions organized to prevent exposure to HIV among high-risk adolescents in their local communities. PMID:22875684

  1. Chrysophyte cysts as potential environmental indicators.

    USGS Publications Warehouse

    Adam, D.P.; Mahood, A.D.

    1981-01-01

    Many chrysophyte algae produce morphologically distinctive, siliceous, microscopic cysts during a resting stage of their life cycles; these cysts are often preserved in sediments. Scanning electron microscopy and Nomarski optics permit much more detailed observation of these cysts than was heretofore possible. Many cyst types are found only in specific habitats, such as montane lakes, wet meadows, ephemeral ponds, and Sphagnum bogs. In the samples studied, cysts seem to be most common in fluctuating fresh-water habitats of low to moderate pH and some winter freezing. Chrysophyte cysts have the potential to be a useful tool for modern environmental assessments and paleoecological studies of Cenozoic fresh-water lacustrine deposits. -from Authors

  2. Amu-Daria liquids potential indicated

    SciTech Connect

    O'Connor, R.B. Jr. ); Sonnenberg, S.

    1991-06-03

    The Amu-Daria basin is a large, primarily gas producing basin located in the Soviet Republics of Turkmen and Uzbek and in Afghanistan. It covers an area roughly three fourths that of Texas and has estimated gas reserves on a scale of several hundred trillion cubic feet. Of these, somewhat less that 50% have been produced, proven, or indicated as probable by drilling. The basin is of current interest because roughly 66,000 sq km of exploration and producing rights in its lightly explored southern part will be put up for foreign competitive bidding by the Turkmen government later this year. The purpose of this article is to present growing evidence that significant new oil and condensate reserves, in addition to large new gas reserves, are likely to be found in the subsalt carbonate reef complexes of Upper Jurassic age in the deeper part of the basin. In fact, there is a very real possibility, that a good portion of these reserves may be found in fields of giant or even supergiant size.

  3. Indicators of ecosystem function identify alternate states in the sagebrush steppe.

    PubMed

    Kachergis, Emily; Rocca, Monique E; Fernandez-Gimenez, Maria E

    2011-10-01

    Models of ecosystem change that incorporate nonlinear dynamics and thresholds, such as state-and-transition models (STMs), are increasingly popular tools for land management decision-making. However, few models are based on systematic collection and documentation of ecological data, and of these, most rely solely on structural indicators (species composition) to identify states and transitions. As STMs are adopted as an assessment framework throughout the United States, finding effective and efficient ways to create data-driven models that integrate ecosystem function and structure is vital. This study aims to (1) evaluate the utility of functional indicators (indicators of rangeland health, IRH) as proxies for more difficult ecosystem function measurements and (2) create a data-driven STM for the sagebrush steppe of Colorado, USA, that incorporates both ecosystem structure and function. We sampled soils, plant communities, and IRH at 41 plots with similar clayey soils but different site histories to identify potential states and infer the effects of management practices and disturbances on transitions. We found that many IRH were correlated with quantitative measures of functional indicators, suggesting that the IRH can be used to approximate ecosystem function. In addition to a reference state that functions as expected for this soil type, we identified four biotically and functionally distinct potential states, consistent with the theoretical concept of alternate states. Three potential states were related to management practices (chemical and mechanical shrub treatments and seeding history) while one was related only to ecosystem processes (erosion). IRH and potential states were also related to environmental variation (slope, soil texture), suggesting that there are environmental factors within areas with similar soils that affect ecosystem dynamics and should be noted within STMs. Our approach generated an objective, data-driven model of ecosystem dynamics for rangeland management. Our findings suggest that the IRH approximate ecosystem processes and can distinguish between alternate states and communities and identify transitions when building data-driven STMs. Functional indicators are a simple, efficient way to create data-driven models that are consistent with alternate state theory. Managers can use them to improve current model-building methods and thus apply state-and-transition models more broadly for land management decision-making. PMID:22073659

  4. Using SCOPE to identify potential regulatory motifs in coregulated genes.

    PubMed

    Martyanov, Viktor; Gross, Robert H

    2011-01-01

    SCOPE is an ensemble motif finder that uses three component algorithms in parallel to identify potential regulatory motifs by over-representation and motif position preference. Each component algorithm is optimized to find a different kind of motif. By taking the best of these three approaches, SCOPE performs better than any single algorithm, even in the presence of noisy data. In this article, we utilize a web version of SCOPE to examine genes that are involved in telomere maintenance. SCOPE has been incorporated into at least two other motif finding programs and has been used in other studies. The three algorithms that comprise SCOPE are BEAM, which finds non-degenerate motifs (ACCGGT), PRISM, which finds degenerate motifs (ASCGWT), and SPACER, which finds longer bipartite motifs (ACCnnnnnnnnGGT). These three algorithms have been optimized to find their corresponding type of motif. Together, they allow SCOPE to perform extremely well. Once a gene set has been analyzed and candidate motifs identified, SCOPE can look for other genes that contain the motif which, when added to the original set, will improve the motif score. This can occur through over-representation or motif position preference. Working with partial gene sets that have biologically verified transcription factor binding sites, SCOPE was able to identify most of the rest of the genes also regulated by the given transcription factor. Output from SCOPE shows candidate motifs, their significance, and other information both as a table and as a graphical motif map. FAQs and video tutorials are available at the SCOPE web site which also includes a "Sample Search" button that allows the user to perform a trial run. Scope has a very friendly user interface that enables novice users to access the algorithm's full power without having to become an expert in the bioinformatics of motif finding. As input, SCOPE can take a list of genes, or FASTA sequences. These can be entered in browser text fields, or read from a file. The output from SCOPE contains a list of all identified motifs with their scores, number of occurrences, fraction of genes containing the motif, and the algorithm used to identify the motif. For each motif, result details include a consensus representation of the motif, a sequence logo, a position weight matrix, and a list of instances for every motif occurrence (with exact positions and "strand" indicated). Results are returned in a browser window and also optionally by email. Previous papers describe the SCOPE algorithms in detail. PMID:21673638

  5. Identifying potential kidney donors using social networking web sites.

    PubMed

    Chang, Alexander; Anderson, Emily E; Turner, Hang T; Shoham, David; Hou, Susan H; Grams, Morgan

    2013-01-01

    Social networking sites like Facebook may be a powerful tool for increasing rates of live kidney donation. They allow for wide dissemination of information and discussion and could lessen anxiety associated with a face-to-face request for donation. However, sparse data exist on the use of social media for this purpose. We searched Facebook, the most popular social networking site, for publicly available English-language pages seeking kidney donors for a specific individual, abstracting information on the potential recipient, characteristics of the page itself, and whether potential donors were tested. In the 91 pages meeting inclusion criteria, the mean age of potential recipients was 37 (range: 2-69); 88% were US residents. Other posted information included the individual's photograph (76%), blood type (64%), cause of kidney disease (43%), and location (71%). Thirty-two percent of pages reported having potential donors tested, and 10% reported receiving a live-donor kidney transplant. Those reporting donor testing shared more potential recipient characteristics, provided more information about transplantation, and had higher page traffic. Facebook is already being used to identify potential kidney donors. Future studies should focus on how to safely, ethically, and effectively use social networking sites to inform potential donors and potentially expand live kidney donation. PMID:23600791

  6. Collaboration Indices for Monitoring Potential Problems in Online Small Groups

    ERIC Educational Resources Information Center

    Jahng, Namsook

    2013-01-01

    The purpose of this study is to test the validity and reliability of three collaboration indices ("quantity", "equality", "and shareness") proposed by Jahng et al. (2010). The present study repeated the quantitative assessment of Jahng et al., and performed a further qualitative analysis to identify possible factors that might be associated with…

  7. COLIPHAGES AS POTENTIAL VIRAL INDICATORS OF FECAL POLLUTION

    EPA Science Inventory

    Friedman, Stephanie D. In press. Coliphages as Potential Viral Indicators of Fecal Pollution (Abstract). To be presented at the SWS/GERS Fall Joint Society Meeting: Communication and Collaboration: Coastal Systems of the Gulf of Mexico and Southeastern United States, 6-9 October ...

  8. A comparison of five anthropometric indices for identifying factors of malnutrition.

    PubMed

    Bairagi, R

    1987-08-01

    Five anthropometric indices--weight-for-age, height-for-age, weight-for-height, weight velocity, and height velocity--are compared for identifying factors of nutritional status of children. Data come from Matlab, the field station of the International Centre for Diarrhoeal Disease Research, Bangladesh. Weights and heights on approximately 1,400 children aged 12-60 months were taken 11 times at two-month intervals. Dwelling floor space, a proxy for socioeconomic status, is considered a long-term factor; the 1974-1975 Bangladesh famine, a medium-term factor; and season, a short-term factor of nutritional status. The figures of the indices by socioeconomic status at different times show their power to identify the factors visually; the regression analyses test statistical significance of the factors; and the standardized regression coefficients provide relative power of the indices to identify the factors. Weight-for-age and height-for-age appear best for identifying long- and medium-term factors; weight velocity, for identifying short-term factors. Weight-for-height is third in identifying long- and medium-term factors, second for identifying short-term factors. Height velocity identifies short-term factors only. The effect of short-term factors on height velocity appears approximately four months later than it appears on weight velocity. This study clarifies why certain indices do not predict mortality in this study population and others. PMID:3605054

  9. Identifying psychophysiological indices of expert vs. novice performance in deadly force judgment and decision making

    PubMed Central

    Johnson, Robin R.; Stone, Bradly T.; Miranda, Carrie M.; Vila, Bryan; James, Lois; James, Stephen M.; Rubio, Roberto F.; Berka, Chris

    2014-01-01

    Objective: To demonstrate that psychophysiology may have applications for objective assessment of expertise development in deadly force judgment and decision making (DFJDM). Background: Modern training techniques focus on improving decision-making skills with participative assessment between trainees and subject matter experts primarily through subjective observation. Objective metrics need to be developed. The current proof of concept study explored the potential for psychophysiological metrics in deadly force judgment contexts. Method: Twenty-four participants (novice, expert) were recruited. All wore a wireless Electroencephalography (EEG) device to collect psychophysiological data during high-fidelity simulated deadly force judgment and decision-making simulations using a modified Glock firearm. Participants were exposed to 27 video scenarios, one-third of which would have justified use of deadly force. Pass/fail was determined by whether the participant used deadly force appropriately. Results: Experts had a significantly higher pass rate compared to novices (p < 0.05). Multiple metrics were shown to distinguish novices from experts. Hierarchical regression analyses indicate that psychophysiological variables are able to explain 72% of the variability in expert performance, but only 37% in novices. Discriminant function analysis (DFA) using psychophysiological metrics was able to discern between experts and novices with 72.6% accuracy. Conclusion: While limited due to small sample size, the results suggest that psychophysiology may be developed for use as an objective measure of expertise in DFDJM. Specifically, discriminant function measures may have the potential to objectively identify expert skill acquisition. Application: Psychophysiological metrics may create a performance model with the potential to optimize simulator-based DFJDM training. These performance models could be used for trainee feedback, and/or by the instructor to assess performance objectively. PMID:25100966

  10. Costa Rican data synthesis indicates oil, gas potential

    SciTech Connect

    Barrientos, J.; Bottazzi, G.; Fernandez, A.; Barboza, G.

    1997-05-12

    The hydrocarbon exploration data base in Costa Rica, gathered through various recent periods, indicates promising hydrocarbon potential in the country. During 1980--94, Recope SA, the state petroleum company, performed a series of studies to evaluate the petroleum potential in the whole Costa Rican territory. As a first step, the information compiled during previous studies was re-evaluated, and later new information was collected with the aid of foreign governments and cooperating institutions. A new exploratory era began with the Costa Rican Congress` approval in 1994 of the Hydrocarbon Law, which allows private companies to participate in hydrocarbon exploration and exploitation. This article brings together some highlights about Costa Rica oil potential and gives basic information on future hydrocarbon exploration and development under the regulation of the new Hydrocarbon Law.

  11. Identifying potential cancer driver genes by genomic data integration

    NASA Astrophysics Data System (ADS)

    Chen, Yong; Hao, Jingjing; Jiang, Wei; He, Tong; Zhang, Xuegong; Jiang, Tao; Jiang, Rui

    2013-12-01

    Cancer is a genomic disease associated with a plethora of gene mutations resulting in a loss of control over vital cellular functions. Among these mutated genes, driver genes are defined as being causally linked to oncogenesis, while passenger genes are thought to be irrelevant for cancer development. With increasing numbers of large-scale genomic datasets available, integrating these genomic data to identify driver genes from aberration regions of cancer genomes becomes an important goal of cancer genome analysis and investigations into mechanisms responsible for cancer development. A computational method, MAXDRIVER, is proposed here to identify potential driver genes on the basis of copy number aberration (CNA) regions of cancer genomes, by integrating publicly available human genomic data. MAXDRIVER employs several optimization strategies to construct a heterogeneous network, by means of combining a fused gene functional similarity network, gene-disease associations and a disease phenotypic similarity network. MAXDRIVER was validated to effectively recall known associations among genes and cancers. Previously identified as well as novel driver genes were detected by scanning CNAs of breast cancer, melanoma and liver carcinoma. Three predicted driver genes (CDKN2A, AKT1, RNF139) were found common in these three cancers by comparative analysis.

  12. Identifying potential programs and platforms to deliver multiple micronutrient interventions.

    PubMed

    Olney, Deanna K; Rawat, Rahul; Ruel, Marie T

    2012-01-01

    This article reviews the potential of four broad types of platforms, health, agriculture, market-based, and social protection programs, to deliver multiple micronutrient (MMN) interventions (supplementation, fortification, and dietary modification). We assessed the platforms' potential based on seven performance criteria related to programs within these platforms: 1) targeting, 2) efficacy of interventions, 3) quality of implementation, 4) utilization, 5) impact, 6) coverage, and 7) sustainability. We highlight one type of program per platform to illustrate strengths and weaknesses for delivering MMN interventions, identify critical knowledge gaps, and highlight what is needed to increase effectiveness for delivering MMN interventions. We found that all four platforms have the potential to effectively deliver MMN interventions if the following key program elements are addressed: 1) strong behavior change communication strategies to increase demand and proper utilization of services/products; 2) supply side interventions to ensure consistent availability of high quality interventions, products, and well-trained staff; 3) rigorous evaluations of effectiveness, quality of delivery, and impact pathways to generate best practices for replication and scale-up; and 4) timely dissemination of evaluation results to ensure use by program implementers and policy makers. The diversification of delivery platforms, which simultaneously addresses multiple determinants of MMN deficiencies and expands coverage, is needed to accelerate progress in reducing MMN deficiencies. PMID:22131548

  13. Newer Approaches to Identify Potential Untoward Effects in Functional Foods.

    PubMed

    Marone, Palma Ann; Birkenbach, Victoria L; Hayes, A Wallace

    2016-03-01

    Globalization has greatly accelerated the numbers and variety of food and beverage products available worldwide. The exchange among greater numbers of countries, manufacturers, and products in the United States and worldwide has necessitated enhanced quality measures for nutritional products for larger populations increasingly reliant on functionality. These functional foods, those that provide benefit beyond basic nutrition, are increasingly being used for their potential to alleviate food insufficiency while enhancing quality and longevity of life. In the United States alone, a steady import increase of greater than 15% per year or 24 million shipments, over 70% products of which are food related, is regulated under the Food and Drug Administration (FDA). This unparalleled growth has resulted in the need for faster, cheaper, and better safety and efficacy screening methods in the form of harmonized guidelines and recommendations for product standardization. In an effort to meet this need, the in vitro toxicology testing market has similarly grown with an anticipatory 15% increase between 2010 and 2015 of US$1.3 to US$2.7 billion. Although traditionally occupying a small fraction of the market behind pharmaceuticals and cosmetic/household products, the scope of functional food testing, including additives/supplements, ingredients, residues, contact/processing, and contaminants, is potentially expansive. Similarly, as functional food testing has progressed, so has the need to identify potential adverse factors that threaten the safety and quality of these products. PMID:26657815

  14. Potentials for Soil Enzyme as Indicators of Ecological Management

    NASA Technical Reports Server (NTRS)

    Senwo, Z. N.; Manu, A.; Coleman, T. L.

    1997-01-01

    Activity measurements of selected soil enzymes (cellulase, glucosidase, amidohydrolase, phosphatase, arylsulfatase) involved in carbon, nitrogen, phosphorus, and sulfur cycling in the biosphere, hold potential as early and sensitive indicators of soil ecological stress and restoration, These measurements are advantageous because the procedures are simple, rapid, and reproducible over time. Enzyme activities are sensitive to short-term changes in soil and kind-use management. Enzyme activities have also been observed to be closely related to soil organic matter proposed as an index of soil quality.

  15. Potential anti-cancer drugs commonly used for other indications.

    PubMed

    Hanusova, Veronika; Skalova, Lenka; Kralova, Vera; Matouskova, Petra

    2015-01-01

    An increasing resistance of mammalian tumor cells to chemotherapy along with the severe side effects of commonly used cytostatics has raised the urgency in the search for new anti-cancer agents. Several drugs originally approved for indications other than cancer treatment have recently been found to have a cytostatic effect on cancer cells. These drugs could be expediently repurposed as anti-cancer agents, since they have already been tested for toxicity in humans and animals. The groups of newly recognized potential cytostatics discussed in this review include benzimidazole anthelmintics (albendazole, mebendazole, flubendazole), anti-hypertensive drugs (doxazosin, propranolol), psychopharmaceuticals (chlorpromazine, clomipramine) and antidiabetic drugs (metformin, pioglitazone). All these drugs have a definite potential to be used especially in combinations with other cytostatics; the chemotherapy targeting of multiple sites now represents a promising approach in cancer treatment. The present review summarizes recent information about the anti-cancer effects of selected drugs commonly used for other medical indications. Our aim is not to collect all the reported results, but to present an overview of various possibilities. Advantages, disadvantages and further perspectives regarding individual drugs are discussed and evaluated. PMID:25544649

  16. Scavenging Rate Ecoassay: A Potential Indicator of Estuary Condition

    PubMed Central

    Porter, Augustine G.; Scanes, Peter R.

    2015-01-01

    Monitoring of estuary condition is essential due to the highly productive and often intensely impacted nature of these ecosystems. Assessment of the physico-chemical condition of estuaries is expensive and difficult due to naturally fluctuating water quality and biota. Assessing the vigour of ecosystem processes is an alternative method with potential to overcome much of the variability associated with physico-chemical measures. Indicators of estuary condition should have small spatial and temporal variability, have a predictable response to perturbation and be ecologically relevant. Here, we present tests of the first criterion, the spatio-temporal variability of a potential ecoassay measuring the rate of scavenging in estuaries. We hypothesised that the proposed scavenging ecoassay would not vary significantly among A) sites in an estuary, B) trips separated by weeks, or C) days in a trip. Because not all habitats are present in all estuaries, this test was undertaken in two habitats. When conducted over bare substrate there were occasional significant differences, but no discernible patterns, within levels of the experiment. When conducted over vegetated substrate, days within a trip did not vary significantly, but later trips experienced greater scavenging. This scavenging ecoassay shows potential as a tool for assessing the condition of estuarine ecosystems, and further exploration of this protocol is warranted by implementation in estuaries across a gradient of anthropogenic stress. PMID:26024225

  17. Sorption behavior of potential organic wastewater indicators with soils.

    PubMed

    Yu, Liang; Fink, Guido; Wintgens, Thomas; Melin, Thomas; Ternes, Thomas A

    2009-03-01

    Soil-aquifer treatment is a wastewater treatment and reclamation option to facilitate beneficial water reuse. The fate of wastewater originated micropollutants in the soil-aquifer system is important to understand. In the study the sorption behavior of potential wastewater indicators such as two antiepileptic drugs (carbamazepine, primidone), one sulfonamide (sulfamethoxazole), and one corrosion inhibitor (benzotriazole) were determined with three natural soils (Lufa 2.2, Euro Soil 5, and Wulpen sand) that differed in pH, organic carbon content and particle size distribution. As aqueous phase a 0.01M CaCl(2) solution as well as the effluent of a municipal wastewater treatment plant was used. Affinities of all analytes to the soil increased from Wulpen sand, over Lufa 2.2 to Euro Soil 5, indicating that the organic carbon contents might be crucial for sorption. Isotherms were well described by the Freundlich model. Sorption was mainly close to linear (n=0.93-1.07) for most target compounds and soils. Desorption gave rise to a small hysteresis only for Euro Soil 5 which was likely artificial, due to slow desorption kinetics beyond 24h used in the experiment. All sorption studies confirmed that Carbamazepine, Benzotriazole and Primidone are appropriate to be used as wastewater indicator substances based on their low sorption affinity to soils, while the suitability of Sulfamethoxazole is limited due to the formation of non-extractable residues, especially at lower pH values. PMID:19095277

  18. Redox potential: An indicator of site productivity in forest management

    NASA Astrophysics Data System (ADS)

    Sajedi, Toktam; Prescott, Cindy; Lavkulich, Les

    2010-05-01

    Redox potential (Eh) is an integrated soil measurement that reflects several environmental conditions in the soil associated with aeration, moisture and carbon (organic matter) dynamics. Its measurement can be related to water table fluctuations, precipitation and landscape gradients, organic matter decomposition rates, nutrient dynamics, biological diversity and plant species distribution. Redox is an excellent indicator of soil biological processes, as it is largely a reflection of microbial activities which to a large extent govern carbon dynamics and nutrient cycling. Redox thus serves as an ecological indicator of site productivity at the ecosystem scale and may be used for management purposes as its magnitude can be altered by activities such as harvesting and drainage. A threshold value of 300 mv has been documented as the critical value below which anaerobic conditions in the soil develop. However, redox measurements and its impacts on ecosystem processes such as nutrient cycling and productivity, especially in forest ecosystems, have not received the attention that this "master" variable deserves, On northern Vancouver Island, Canada, regenerating stands of western redcedar-western hemlock (CH) sites exhibit symptoms of nutrient deficiencies and slow growth, but this phenomenon does not occur on adjacent western hemlock- amabalis fir (HA) sites. We tested the hypothesis that differences in nutrient supply and distribution of plant species was caused by differences in moisture regime and redox potential. Redox potential, pH, soil aeration depth (steel rods), organic matter thickness, bulk density, soil carbon store, plant species distribution and richness were measured at five old-growth and five 10-year-old cutover blocks. Results of investigations confirmed that CH forests were wetter, had redox values lower than the critical 300mv and a shallower aerated zone, compared with adjacent regenerating HA sites. Fifty percent of the CH plots had redox values less than +300 mv in the forest floor; whereas only 15 percent of the HA plots had such low values. Composition of the forest understory species was related to soil moisture/aeration. Soil aeration was the most important soil variable influencing plant species composition, explaining 25% of the plant community variability. Eh was always greater than +300 mv in the mineral soil of old growth HA forests but below +300 mv in HA clearcuts, suggesting paludification; however it was below or at this threshold in both CH forests and clearcuts. The reduction in measured redox without a noticeable change in the watertable in HA sites suggests that harvesting HA forests shifts the ecosystem towards more anaerobic conditions more similar to CH sites. In a complimentary study, the significance of redox was assessed in a cedar swamp cutover by exploring the relationships between soil redox potential and tree growth, and mineralization of C and soil C store along a gradient of moisture caused by drainage. Drainage improved aeration in the rooting zone, expressed as redox, and above- and below ground C storage; however C mineralization measured as CO2 evolution was not affected. Tree growth was positively correlated with redox potential. Our results indicate that drainage could be a useful silvicultural practice for improving the productivity of these ecosystems and that it may be possible to improve tree growth without stimulating loss of soil C. This requires that drainage improve aeration in the rooting zone while maintaining redox levels of less than +300 mV in the bulk soil, indicating that redox measurements should be incorporated into silviculture interventions to improve productivity of these forests.

  19. A Method to Identify Estuarine Macroinvertebrate Pollution Indicator Species in the Virginian Biogeogarphic Province

    EPA Science Inventory

    Macroinvertebrates are commonly used as biomonitors to detect pollution impacts in estuaries. The goal of this research was to identify estuarine benthic invertebrates that could be used as indicator species to detect presence or absence of pollution in the Virginian Biogeograph...

  20. The value of anthropometric indices for identifying women with features of metabolic syndrome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    BMI is a widely used anthropometric measure for identifying CVD and metabolic syndrome (MetS) risk. Two new anthropometric indices are A Body Shape Index (ABSI) and Body Roundness Index (BRI) that may provide better correlations to features of MetS. Methods: Subject data were obtained from 91 over...

  1. Biologically controlled minerals as potential indicators of life

    NASA Technical Reports Server (NTRS)

    Schwartz, D. E.; Mancinelli, R. L.; Kaneshiro, E.

    1991-01-01

    Minerals can be produced and deposited either by abiotic or biologic means. Regardless of their origin, mineral crystals reflect the environment conditions (e.g., temperature, pressure, chemical composition, and redox potential) present during crystal formation. Biologically-produced mineral crystals are grown or reworked under the control of their host organism and reflect an environment different from the abiotic environment. In addition, minerals of either biologic or abiotic origin have great longevities. For these reasons, biologically produced minerals have been proposed as biomarkers. Biomarkers are key morphological, chemical, and isotopic signatures of living systems that can be used to determine if life processes have occurred. Studies of biologically controlled minerals produced by the protist, Paramecium tetraurelia, were initiated since techniques have already been developed to culture them and isolate their crystalline material, and methods are already in place to analyze this material. Two direct crystalline phases were identified. One phase, whose chemical composition is high in Mg, was identified as struvite. The second phase, whose chemical composition is high in Ca, has not been previously found occurring naturally and may be considered a newly discovered material. Analyses are underway to determine the characteristics of these minerals in order to compare them with characteristics of these minerals in order to compare them with characteristics of minerals formed abiotically, but with the same chemical composition.

  2. Female lions can identify potentially infanticidal males from their roars.

    PubMed

    McComb, K; Pusey, A; Packer, C; Grinnell, J

    1993-04-22

    Despite evidence from several bird, fish and mammal species that listeners can discriminate between the vocalizations of familiar and unfamiliar adult conspecifics, direct links between discriminatory abilities and fitness benefits have been difficult to identify. In free-ranging populations of African lions (Panthera leo), females with cubs face a substantial threat from one particular category of unfamiliar individuals: infanticidal males. Here we use playback experiments to demonstrate that females with cubs can distinguish immediately between roars from their own resident males (the fathers of the cubs) and those from unfamiliar, potentially infanticidal males. Although they remain relaxed when played roars from resident males, they immediately become agitated on hearing unfamiliar males and retreat rapidly with their cubs if the latter have reached about 4.5 months of age. These responses are not simply a function of the roarers being unfamiliar, for when played the roars of unfamiliar females, females with cubs consistently approach the loudspeaker. Furthermore, females often move toward the cubs in response to playbacks of unfamiliar males but not in response to playbacks of unfamiliar females or resident males. Our results suggest how females with cubs might, by quickly detecting and categorizing unfamiliar intruders within their territory, protect their cubs from infanticidal males and expel intruding females. Distinguishing between individuals on the basis of their vocal characteristics could therefore confer direct fitness benefits on discriminating lionesses. PMID:8389047

  3. Comparing the Ability of Anthropometric Indicators in Identifying Metabolic Syndrome in HIV Patients

    PubMed Central

    Beraldo, Rebeca Antunes; Meliscki, Gabriela Cristina; Silva, Bruna Ramos; Navarro, Anderson Marliere; Bollela, Valdes Roberto; Schmidt, André; Foss-Freitas, Maria Cristina

    2016-01-01

    Background Highly active antiretroviral therapy (HAART) can cause side effects in HIV patients, as the metabolic syndrome. Early identification of risk for development of cardiovascular diseases using available reliable and practical methods is fundamental. On this basis, the aim of this study was to compare the effectiveness of anthropometric indicators to identify metabolic syndrome in HIV patients on HAART. Methods It is a cross-sectional study. A number of 280 stable HIV patients were studied. It measured weight, height, waist circumference (WC), hip circumference (HP), thigh circumference (TC) and calculated body mass index (BMI), body adiposity index (BAI), waist to hip ratio (WHR) and waist to thigh ratio (WTR). There was also a performance of biochemical tests of lipid profile and fasting glucose. Systemic blood pressure was measured. The criteria proposed by the National Cholesterol Education Program III (NCEP-ATP III) to metabolic syndrome classification was used. Individuals were divided in groups with or without metabolic alterations and their anthropometric indicators were compared. Receiver operating characteristic (ROC) curves were designed for each anthropometric indicator using the metabolic syndrome classification to identify sensitivity and specificity. Results WC was a good tool to identify each metabolic disorder separately: total cholesterol (only females, p<0.05), triglycerides (only males, p<0.001), HDL cholesterol (p<0.05), LDL cholesterol (p<005) and fasting glycemic (p<005). WC also showed the best performance to identify metabolic syndrome in both genders (areas under the curve (AUCs): 0.79 and 0.76 for male and female, respectively), while BAI proved to be an inadequate indicator (AUCs: 0.63 and 0.67 for males and females), respectively, in this population. Conclusions The central adiposity measure (WC) had the best performance to identify metabolic syndrome, and it is a convenient, cheap and reliable tool that can be used in clinical practice routinely to prevent cardiovascular complications in HIV patients. PMID:26919174

  4. Potential theory, path integrals and the Laplacian of the indicator

    NASA Astrophysics Data System (ADS)

    Lange, Rutger-Jan

    2012-11-01

    This paper links the field of potential theory i.e. the Dirichlet and Neumann problems for the heat and Laplace equation to that of the Feynman path integral, by postulating the following seemingly ill-defined potential: V(x):=? {{?^2}}/2nabla_x^2{1_{{xin D}}} where the volatility is the reciprocal of the mass (i.e. m = 1/ ? 2) and ? = 1. The Laplacian of the indicator can be interpreted using the theory of distributions: it is the d-dimensional analogue of the Dirac ?'-function, which can formally be defined as partial_x^2{1_{x>0 }} . We show, first, that the path integral's perturbation series (or Born series) matches the classical single and double boundary layer series of potential theory, thereby connecting two hitherto unrelated fields. Second, we show that the perturbation series is valid for all domains D that allow Green's theorem (i.e. with a finite number of corners, edges and cusps), thereby expanding the classical applicability of boundary layers. Third, we show that the minus (plus) in the potential holds for the Dirichlet (Neumann) boundary condition; showing for the first time a particularly close connection between these two classical problems. Fourth, we demonstrate that the perturbation series of the path integral converges as follows:

    mode of convergence absorbed propagator reflected propagator convex domain alternating monotone concave domain monotone alternating
    We also discuss the third boundary problem (which poses Robin boundary conditions) and discuss an extension to moving domains.

  5. Identifying Quality Indicators Used by Patients to Choose Secondary Health Care Providers: A Mixed Methods Approach

    PubMed Central

    Zaman, Saman Sara; Kahlon, Gurnaaz Kaur; Naik, Aditi; Jessel, Amar Singh; Nanavati, Niraj; Shah, Akash; Cox, Benita; Darzi, Ara

    2015-01-01

    Background Patients in health systems across the world can now choose between different health care providers. Patients are increasingly using websites and apps to compare the quality of health care services available in order to make a choice of provider. In keeping with many patient-facing platforms, most services currently providing comparative information on different providers do not take account of end-user requirements or the available evidence base. Objective To investigate what factors were considered most important when choosing nonemergency secondary health care providers in the United Kingdom with the purpose of translating these insights into a ratings platform delivered through a consumer mHealth app. Methods A mixed methods approach was used to identify key indicators incorporating a literature review to identify and categorize existing quality indicators, a questionnaire survey to formulate a ranked list of performance indicators, and focus groups to explore rationales behind the rankings. Findings from qualitative and quantitative methodologies were mapped onto each other under the four categories identified by the literature review. Results Quality indicators were divided into four categories. Hospital access was the least important category. The mean differences between the other three categories hospital statistics, hospital staff, and hospital facilities, were not statistically significant. Staff competence was the most important indicator in the hospital staff category; cleanliness and up-to-date facilities were equally important in hospital facilities; ease of travel to the hospital was found to be most important in hospital access. All quality indicators within the hospital statistics category were equally important. Focus groups elaborated that users find it difficult to judge staff competence despite its importance. Conclusions A mixed methods approach is presented, which supported a patient-centered development and evaluation of a hospital ratings mobile app. Where possible, mHealth developers should use systematic research methods in order to more closely meet the needs of the end user and add credibility to their platform. PMID:26048441

  6. GIS-BASED SPATIAL INDICES FOR IDENTIFICATION OF POTENTIAL NUTRIENT EXPORT AT WATERSHED SCALE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spatial indices for identifying potential pollution resulting from manure spread on agricultural lands were developed for evaluating lands in support of decision and policy-making. An existing nutrient delivery ratio was modified by calculating actual distance that water would have to travel to reac...

  7. Productivity, Fluency, and Grammaticality Measures from Narratives: Potential Indicators of Language Proficiency?

    ERIC Educational Resources Information Center

    Tilstra, Janet; McMaster, Kristen

    2007-01-01

    The purpose of this study was to identify potential general outcome indicators (GOIs) of language proficiency. Brief narratives were elicited from 45 kindergarten, first-grade, and third-grade children using single-picture scenes and a standardized protocol. Measures of language productivity, verbal fluency, and grammaticality were examined for…

  8. Kernel density surface modelling as a means to identify significant concentrations of vulnerable marine ecosystem indicators.

    PubMed

    Kenchington, Ellen; Murillo, Francisco Javier; Lirette, Camille; Sacau, Mar; Koen-Alonso, Mariano; Kenny, Andrew; Ollerhead, Neil; Wareham, Vonda; Beazley, Lindsay

    2014-01-01

    The United Nations General Assembly Resolution 61/105, concerning sustainable fisheries in the marine ecosystem, calls for the protection of vulnerable marine ecosystems (VME) from destructive fishing practices. Subsequently, the Food and Agriculture Organization (FAO) produced guidelines for identification of VME indicator species/taxa to assist in the implementation of the resolution, but recommended the development of case-specific operational definitions for their application. We applied kernel density estimation (KDE) to research vessel trawl survey data from inside the fishing footprint of the Northwest Atlantic Fisheries Organization (NAFO) Regulatory Area in the high seas of the northwest Atlantic to create biomass density surfaces for four VME indicator taxa: large-sized sponges, sea pens, small and large gorgonian corals. These VME indicator taxa were identified previously by NAFO using the fragility, life history characteristics and structural complexity criteria presented by FAO, along with an evaluation of their recovery trajectories. KDE, a non-parametric neighbour-based smoothing function, has been used previously in ecology to identify hotspots, that is, areas of relatively high biomass/abundance. We present a novel approach of examining relative changes in area under polygons created from encircling successive biomass categories on the KDE surface to identify "significant concentrations" of biomass, which we equate to VMEs. This allows identification of the VMEs from the broader distribution of the species in the study area. We provide independent assessments of the VMEs so identified using underwater images, benthic sampling with other gear types (dredges, cores), and/or published species distribution models of probability of occurrence, as available. For each VME indicator taxon we provide a brief review of their ecological function which will be important in future assessments of significant adverse impact on these habitats here and elsewhere. PMID:25289667

  9. Kernel Density Surface Modelling as a Means to Identify Significant Concentrations of Vulnerable Marine Ecosystem Indicators

    PubMed Central

    Kenchington, Ellen; Murillo, Francisco Javier; Lirette, Camille; Sacau, Mar; Koen-Alonso, Mariano; Kenny, Andrew; Ollerhead, Neil; Wareham, Vonda; Beazley, Lindsay

    2014-01-01

    The United Nations General Assembly Resolution 61/105, concerning sustainable fisheries in the marine ecosystem, calls for the protection of vulnerable marine ecosystems (VME) from destructive fishing practices. Subsequently, the Food and Agriculture Organization (FAO) produced guidelines for identification of VME indicator species/taxa to assist in the implementation of the resolution, but recommended the development of case-specific operational definitions for their application. We applied kernel density estimation (KDE) to research vessel trawl survey data from inside the fishing footprint of the Northwest Atlantic Fisheries Organization (NAFO) Regulatory Area in the high seas of the northwest Atlantic to create biomass density surfaces for four VME indicator taxa: large-sized sponges, sea pens, small and large gorgonian corals. These VME indicator taxa were identified previously by NAFO using the fragility, life history characteristics and structural complexity criteria presented by FAO, along with an evaluation of their recovery trajectories. KDE, a non-parametric neighbour-based smoothing function, has been used previously in ecology to identify hotspots, that is, areas of relatively high biomass/abundance. We present a novel approach of examining relative changes in area under polygons created from encircling successive biomass categories on the KDE surface to identify “significant concentrations” of biomass, which we equate to VMEs. This allows identification of the VMEs from the broader distribution of the species in the study area. We provide independent assessments of the VMEs so identified using underwater images, benthic sampling with other gear types (dredges, cores), and/or published species distribution models of probability of occurrence, as available. For each VME indicator taxon we provide a brief review of their ecological function which will be important in future assessments of significant adverse impact on these habitats here and elsewhere. PMID:25289667

  10. Sigma-2 Receptor as Potential Indicator of Stem Cell Differentiation

    PubMed Central

    Haller, Jodi L.; Panyutin, Irina; Chaudhry, Aneeka; Zeng, Chenbo; Mach, Robert H.; Frank, Joseph A.

    2011-01-01

    Purpose The sigma-2 (σ2) receptor is a potential biomarker of proliferative status of solid tumors. Specific synthetic probes using N-substituted-9-azabicyclo[3.3.1]nonan-3α-yl carbamate analogs have been designed and implemented for experimental cancer diagnosis and therapy. Procedures We employed the fluorescently-labeled σ2 receptor probe, SW120, to evaluate σ2 receptor expression in human stem cells (SC), including: bone marrow stromal (BMSC), neural progenitor (NPC), amniotic fluid (AFSC), hematopoetic (HSC) and embryonic stem cells (ESC). We concurrently evaluated the intensity of SW120 and 5-ethynyl-2′-deoxyuridine (EdU) relative to passage number and multipotency. Results We substantiated significantly higher σ2 receptor density among proliferating SC relative to lineage-restricted cell types. Additionally, cellular internalization of the σ2 receptor in SC was consistent with receptor-mediated endocytosis and confocal microscopy indicated SW120 specific co-localization with a fluorescent marker of lysosomes in all SC imaged. Conclusion These results suggest that σ2 receptors may serve to monitor stem cell differentiation in future experimental studies. PMID:21614680

  11. Identifying and Quantifying Heterogeneity in High Content Analysis: Application of Heterogeneity Indices to Drug Discovery

    PubMed Central

    Gough, Albert H.; Chen, Ning; Shun, Tong Ying; Lezon, Timothy R.; Boltz, Robert C.; Reese, Celeste E.; Wagner, Jacob; Vernetti, Lawrence A.; Grandis, Jennifer R.; Lee, Adrian V.; Stern, Andrew M.; Schurdak, Mark E.; Taylor, D. Lansing

    2014-01-01

    One of the greatest challenges in biomedical research, drug discovery and diagnostics is understanding how seemingly identical cells can respond differently to perturbagens including drugs for disease treatment. Although heterogeneity has become an accepted characteristic of a population of cells, in drug discovery it is not routinely evaluated or reported. The standard practice for cell-based, high content assays has been to assume a normal distribution and to report a well-to-well average value with a standard deviation. To address this important issue we sought to define a method that could be readily implemented to identify, quantify and characterize heterogeneity in cellular and small organism assays to guide decisions during drug discovery and experimental cell/tissue profiling. Our study revealed that heterogeneity can be effectively identified and quantified with three indices that indicate diversity, non-normality and percent outliers. The indices were evaluated using the induction and inhibition of STAT3 activation in five cell lines where the systems response including sample preparation and instrument performance were well characterized and controlled. These heterogeneity indices provide a standardized method that can easily be integrated into small and large scale screening or profiling projects to guide interpretation of the biology, as well as the development of therapeutics and diagnostics. Understanding the heterogeneity in the response to perturbagens will become a critical factor in designing strategies for the development of therapeutics including targeted polypharmacology. PMID:25036749

  12. Evaluating the Usefulness of High-Temporal Resolution Vegetation Indices to Identify Crop Types

    NASA Astrophysics Data System (ADS)

    Hilbert, K.; Lewis, D.; O'Hara, C. G.

    2006-12-01

    The National Aeronautical and Space Agency (NASA) and the United States Department of Agriculture (USDA) jointly sponsored research covering the 2004 to 2006 South American crop seasons that focused on developing methods for the USDA's Foreign Agricultural Service's (FAS) Production Estimates and Crop Assessment Division (PECAD) to identify crop types using MODIS-derived, hyper-temporal Normalized Difference Vegetation Index (NDVI) images. NDVI images were composited in 8 day intervals from daily NDVI images and aggregated to create a hyper-termporal NDVI layerstack. This NDVI layerstack was used as input to image classification algorithms. Research results indicated that creating high-temporal resolution Normalized Difference Vegetation Index (NDVI) composites from NASA's MODerate Resolution Imaging Spectroradiometer (MODIS) data products provides useful input to crop type classifications as well as potential useful input for regional crop productivity modeling efforts. A current NASA-sponsored Rapid Prototyping Capability (RPC) experiment will assess the utility of simulated future Visible Infrared Imager / Radiometer Suite (VIIRS) imagery for conducting NDVI-derived land cover and specific crop type classifications. In the experiment, methods will be considered to refine current MODIS data streams, reduce the noise content of the MODIS, and utilize the MODIS data as an input to the VIIRS simulation process. The effort also is being conducted in concert with an ISS project that will further evaluate, verify and validate the usefulness of specific data products to provide remote sensing-derived input for the Sinclair Model a semi-mechanistic model for estimating crop yield. The study area encompasses a large portion of the Pampas region of Argentina--a major world producer of crops such as corn, soybeans, and wheat which makes it a competitor to the US. ITD partnered with researchers at the Center for Surveying Agricultural and Natural Resources (CREAN) of the National University of Cordoba, Argentina, and CREAN personnel collected and continue to collect field-level, GIS-based in situ information. Current efforts involve both developing and optimizing software tools for the necessary data processing. The software includes the Time Series Product Tool (TSPT), Leica's ERDAS Imagine, and Mississippi State University's Temporal Map Algebra computational tools.

  13. Identifying the Potentially Successful Among Marginal College Entrants. Final Report.

    ERIC Educational Resources Information Center

    Beach, Leslie R.

    This is an exploratory effort to determine factors available at the time of application for admission, which will better identify who among marginal applicants are most likely to succeed in college. Some 19 marginal applicants to Hope College were studied in terms of admissions data, their performance in the specially designed summer trial

  14. Potential Utility of Actuarial Methods for Identifying Specific Learning Disabilities

    ERIC Educational Resources Information Center

    Benson, Nicholas; Newman, Isadore

    2010-01-01

    This article describes how actuarial methods can supplant discrepancy models and augment problem solving and Response to Intervention (RTI) efforts by guiding the process of identifying specific learning disabilities (SLD). Actuarial methods use routinized selection and execution of formulas derived from empirically established relationships to…

  15. Potential indicators of final ecosystem services in wetlands

    EPA Science Inventory

    Numerous and inconsistent lists of wetland ecosystem services exist because services are identified using ambiguous definitions or categorization schemes based around divergent or ambiguous objectives. A consistent and scientific approach would provide clarity and provide greater...

  16. IDENTIFYING POTENTIAL SOURCES OF BACKGROUND CONTAMINATION IN RT-PCR

    EPA Science Inventory

    Extraction of nucleic acids from low biomass samples, such as drinking water, is particularly sensitive to potential background contamination because the contaminating material is minimally diluted by the sample. The presence of bacterial DNA in Taq DNA polymerase is wel...

  17. Spontaneous Swallowing Frequency [Has Potential to] Identify Dysphagia in Acute Stroke

    PubMed Central

    Carnaby, Giselle D; Sia, Isaac; Khanna, Anna; Waters, Michael

    2014-01-01

    Background and Purpose Spontaneous swallowing frequency has been described as an index of dysphagia in various health conditions. This study evaluated the potential of spontaneous swallow frequency analysis as a screening protocol for dysphagia in acute stroke. Methods In a cohort of 63 acute stroke cases swallow frequency rates (swallows per minute: SPM) were compared to stroke and swallow severity indices, age, time from stroke to assessment, and consciousness level. Mean differences in SPM were compared between patients with vs. without clinically significant dysphagia. ROC analysis was used to identify the optimal threshold in SPM which was compared to a validated clinical dysphagia examination for identification of dysphagia cases. Time series analysis was employed to identify the minimally adequate time period to complete spontaneous swallow frequency analysis. Results SPM correlated significantly with stroke and swallow severity indices but not with age, time from stroke onset, or consciousness level. Patients with dysphagia demonstrated significantly lower SPM rates. SPM differed by dysphagia severity. ROC analysis yielded a threshold of SPM ≤ 0.40 which identified dysphagia (per the criterion referent) with 0.96 sensitivity, 0.68 specificity, and 0.96 negative predictive value. Time series analysis indicated that a 5 to 10 minute sampling window was sufficient to calculate spontaneous swallow frequency to identify dysphagia cases in acute stroke. Conclusions Spontaneous swallowing frequency presents high potential to screen for dysphagia in acute stroke without the need for trained, available personnel. PMID:24149008

  18. MODELING POTENTIAL PATHOGEN INFECTED WATERS UTILIZING LANDSCAPE INDICES

    EPA Science Inventory

    The federal Clean Water Act (CWA) requires states, territories and tribal lands to assess their waters on a biennial schedule and identify, list and prioritize impaired waters not meeting water quality standards. Once a water body is listed, the state is required to develop Tota...

  19. Identifying improvement potentials in cement production with life cycle assessment.

    PubMed

    Boesch, Michael Elias; Hellweg, Stefanie

    2010-12-01

    Cement production is an environmentally relevant process responsible for 5% of total anthropogenic carbon dioxide emissions and 7% of industrial fuel use. In this study, life cycle assessment is used to evaluate improvement potentials in the cement production process in Europe and the USA. With a current fuel substitution rate of 18% in Europe and 11% in the USA, both regions have a substantial potential to reduce greenhouse gas emissions and save virgin resources by further increasing the coprocessing of waste fuels. Upgrading production technology would be particularly effective in the USA where many kiln systems with very low energy efficiency are still in operation. Using best available technology and a thermal substitution rate of 50% for fuels, greenhouse gas emissions could be reduced by 9% for Europe and 18% for the USA per tonne of cement. Since clinker production is the dominant pollution producing step in cement production, the substitution of clinker with mineral components such as ground granulated blast furnace slag or fly ash is an efficient measure to reduce the environmental impact. Blended cements exhibit substantially lower environmental footprints than Portland cement, even if the substitutes feature lower grindability and require additional drying and large transport distances. The highest savings in CO(2) emissions and resource consumption are achieved with a combination of measures in clinker production and cement blending. PMID:21047057

  20. AN INDICATOR OF POTENTIAL STREAM WOOD CONTRIBUTION FOR RIPARIAN FORESTS

    EPA Science Inventory

    In northwestern Oregon a key function of riparian forests is to provide wood to the stream network. This function is a prominent feature of Federal and State forest practices in the region. Thus, defining indicators which are associated with this function are important for desi...

  1. Seagrass epiphytes: useful indicator, potential biological criterion, or forlorn hope?

    EPA Science Inventory

    Epiphytes on seagrasses have been studied for more than 50 years, and proposed as an indicator of anthropogenic nutrient enrichment for over 30 years. Epiphytes have been correlated with seagrass declines, causally related to nutrient additions in both field and mesocosm experim...

  2. Nationwide Benthic Macroinvertebrate Assemblage Multimetric Indices: Identifying Inconsistencies and Limitations in Reporting Stream Impairment Status, USA

    NASA Astrophysics Data System (ADS)

    Lau, J. K.; Lauer, T. E.

    2015-07-01

    The objective of this study was to identify the current status of stream water-quality assessment and reporting methods for four states in the Ohio River basin (Indiana, Ohio, Tennessee, and Virginia), as required by the 305(b) section of the United States (US) Clean Water Act. Specifically, we clarified the discrepancies that exist among stream-impairment status classified by benthic macroinvertebrate multimetric indices (MMIs) and depicted using Geographic Information Systems shapefiles. In addition, we provided guidance in solving some of the comparability problems that arise when developing state-specific MMIs and depicting stream-impairment status using Geographic Information Systems technology. The MMI variation among states and differences in shapefile formats resulted in a nationwide dataset, which cannot be directly compared. Incorporating the changes suggested in this study allow for a uniform assessment and reporting method nationwide. Successful implementation of these changes would strengthen the US Environmental Protection Agency efforts to identify impaired streams and sources of those impairments without the limitations of state-by-state .developed assessment methods.

  3. Nationwide benthic macroinvertebrate assemblage multimetric indices: identifying inconsistencies and limitations in reporting stream impairment status, USA.

    PubMed

    Lau, J K; Lauer, T E

    2015-07-01

    The objective of this study was to identify the current status of stream water-quality assessment and reporting methods for four states in the Ohio River basin (Indiana, Ohio, Tennessee, and Virginia), as required by the 305(b) section of the United States (US) Clean Water Act. Specifically, we clarified the discrepancies that exist among stream-impairment status classified by benthic macroinvertebrate multimetric indices (MMIs) and depicted using Geographic Information Systems shapefiles. In addition, we provided guidance in solving some of the comparability problems that arise when developing state-specific MMIs and depicting stream-impairment status using Geographic Information Systems technology. The MMI variation among states and differences in shapefile formats resulted in a nationwide dataset, which cannot be directly compared. Incorporating the changes suggested in this study allow for a uniform assessment and reporting method nationwide. Successful implementation of these changes would strengthen the US Environmental Protection Agency efforts to identify impaired streams and sources of those impairments without the limitations of state-by-state .developed assessment methods. PMID:25832346

  4. Identifying Key Indicators for Adaptive Management of the Metropolitan Water District Integrated Resource Plan

    NASA Astrophysics Data System (ADS)

    Lempert, R.; Fischbach, J.; Groves, D. G.; Bloom, E.; Goshi, B.; Nevills, J.

    2011-12-01

    The Metropolitan Water District of Southern California's 2010 Integrated Resource Plan Update (IRP) describes a resource investment strategy that would meet projected demand under a range of anticipated climate and demographic conditions through 2035. The IRP also identifies that alternative or additional investments may have to be considered in order to address uncertainty over the next 25 years and posits that an adaptive management strategy is needed to decide when to make these investments. Current water planning methodologies do not, however, offer means to operationalize such an adaptive management strategy, in particular by offering Metropolitan guidance as to the conditions that ought to signal the need to make additional investments as key trends unfold over time. This talk will describe a novel application of robust decision making (RDM) methods to help Metropolitan identify such key indicators- that is the trends the agency should monitor and threshold values for those trends that suggest a need to make additional investments. We ran Metropolitan's water resource planning models in over 1000 cases to explore the performance of the IRP in a wide range of future conditions due uncertainties in future demand, climate, ground water management, and timeliness of project implementation. Cluster-finding "scenario discovery" algorithms applied to the resulting database of simulation model results identifies the key combination of future conditions - the boundaries of the coping range -- associated with success and failure of the IRP. This analysis will not only help Metropolitan implement the adaptive management aspect of its IRP, it provides a widely applicable new approach for making water management plans more cognizant and responsive to a wide range of uncertainties.

  5. Immunohistochemical analysis of RTKs expression identified HER3 as a prognostic indicator of gastric cancer

    PubMed Central

    Ema, Akira; Yamashita, Keishi; Ushiku, Hideki; Kojo, Ken; Minatani, Naoko; Kikuchi, Mariko; Mieno, Hiroaki; Moriya, Hiromitsu; Hosoda, Kei; Katada, Natsuya; Kikuchi, Shiro; Watanabe, Masahiko

    2014-01-01

    Standard treatment in Japan for the 13th Japanese Gastric Cancer Association stage II/III advanced gastric cancer is postoperative adjuvant S-1 administration after curative surgery. High expression of receptor type tyrosine kinases (RTKs) has repeatedly represented poor prognosis for cancers. However it has not been demonstrated whether RTKs have prognostic relevance for stage II/III gastric cancer with standard treatment. Tumor tissues were obtained from 167 stage II/III advanced gastric cancer patients who underwent curative surgery and received postoperative S-1 chemotherapy from 2000 to 2010. Expression of the RTKs including EGFR, HER2, HER3, IGF-1R, and EphA2 was analyzed using immunohistochemistry (IHC). Analysis using a multivariate proportional hazard model identified the most significant RTKs that represented independent prognostic relevance. When tumor HER3 expression was classified into IHC 1+/2+ (n = 98) and IHC 0 (n = 69), the cumulative 5-year Relapse Free Survival (5y-RFS) was 56.5 and 82.9%, respectively (P = 0.0034). Significant prognostic relevance was similarly confirmed for IGF-1R (P = 0.014), and EGFR (P = 0.030), but not for EphA2 or HER2 expression. Intriguingly, HER3 expression was closely correlated with IGF-1R (P < 0.0001, R = 0.41), and EphA2 (P < 0.0001, R = 0.34) expression. Multivariate proportional hazard model analysis identified HER3 (IHC 1+/2+) (HR; 1.53, 95% CI, 1.112.16, P = 0.0078) as the sole RTK that was a poor prognostic factor independent of stage. Of the 53 patients who recurred, 40 patients (75.5%) were HER3-positive. Thus, of the RTKs studied, HER3 was the only RTK identified as an independent prognostic indicator of stage II/III advanced gastric cancer with standard treatment. PMID:25455899

  6. Coupling groundwater modeling and biological indicators for identifying river/aquifer exchanges.

    PubMed

    Graillot, Didier; Paran, Frédéric; Bornette, Gudrun; Marmonier, Pierre; Piscart, Christophe; Cadilhac, Laurent

    2014-01-01

    Future climate changes and the resulting modifications in anthropogenic activities will alter the interactions between rivers and groundwater. The quantification of these hydraulic interactions is absolutely necessary for achieving sustainable water use and requires accurate analytical methodologies. This report proposes an interdisciplinary approach to the quantitative and qualitative characterization of hydraulic interactions between rivers and shallow aquifers, wherein it outlines the advantages of coupling groundwater modeling with biological markers. As a first step, we built independent diagnostic maps of hydrological exchanges at the sector scale on the basis of hydrogeological modeling and biological indicators. In a second step, these maps were compared to provide a quantitative and qualitative understanding of exchanges between groundwater and surface water. This comparison significantly improved the calibration of groundwater models through a better assessment of boundary zones. Our approach enabled us to identify the conditions under which it could be possible to use biological indicators instead of a large set of piezometric measures. The integration of such combined tools in a future decision support system will assist governmental authorities in proposing appropriate long-term water policies for the preservation of groundwater resources, such as for supplying potable water and/or mitigating pollution risks. PMID:24567877

  7. Polymorphisms in canine platelet glycoproteins identify potential platelet antigens.

    PubMed

    Callan, Mary Beth; Werner, Petra; Mason, Nicola J; Meny, Geralyn M; Raducha, Michael G; Henthorn, Paula S

    2013-08-01

    Human alloimmune thrombocytopenic conditions caused by exposure to a platelet-specific alloantigen include neonatal alloimmune thrombocytopenia, posttransfusion purpura, and platelet transfusion refractoriness. More than 30 platelet-specific alloantigens have been defined in the human platelet antigen (HPA) system; however, there is no previous information on canine platelet-specific alloantigens. Using the HPA system as a model, we evaluated the canine ITGB3, ITGA2B, and GP1BB genes encoding GPIIIa (β3), GPIIb (αIIb), and GPIbβ, respectively, which account for 21 of 27 HPA, to determine whether amino acid polymorphisms are present in the orthologous canine genes. A secondary objective was to perform a pilot study to assess possible association between specific alleles of these proteins and a diagnosis of idiopathic thrombocytopenic purpura (ITP) in dogs. By using genomic DNA from dogs of various breeds with and without ITP, sequencing of PCR products encompassing all coding regions and exon-intron boundaries for these 3 genes revealed 4 single-nucleotide polymorphisms in ITGA2B resulting in amino acid polymorphisms in the canine genome, 3 previously reported and 1 newly identified (Gly[GGG]/Arg[AGG] at amino acid position 576 of ITGA2B. Of 16 possible ITGA2B protein alleles resulting from unique combinations of the 4 polymorphic amino acids, 5 different protein isoforms were present in homozygous dogs and explain all of the genotype combinations in heterozygous dogs. There was no amino acid polymorphism or protein isoform that was specific for a particular breed or for the diagnosis of ITP. PMID:24209971

  8. A potential individual cell malignancy indicator: focal length

    NASA Astrophysics Data System (ADS)

    Wang, Weina; Lear, Kevin L.

    2011-03-01

    The label-free technique of optofluidic intracavity spectroscopy (OFIS) utilizes the optical transmission spectrum of a cell in a microfluidic Fabry-Pérot (F-P) cavity to distinguish cells from cancerous cell lines and baseline normal blood cells. The classification between canine hemangiosarcoma (HSA) cancer cells and monocytes in canine normal peripheral blood mononuclear cells (PBMCs) had been demonstrated with 95% sensitivity and 98% specificity. Now with a new optical model that treats the cell settled at the bottom of the cavity as a thin lens, the focal length of cells was extracted and used as an individual cell malignancy indicator.

  9. Using a geographic information system to identify areas with potential for off-target pesticide exposure.

    PubMed

    Pfleeger, Thomas G; Olszyk, David; Burdick, Connie A; King, George; Kern, Jeffrey; Fletcher, John

    2006-08-01

    In many countries, numerous tests are required as part of the risk assessment process before chemical registration to protect human health and the environment from unintended effects of chemical releases. Most of these tests are not based on ecological or environmental relevance but, rather, on consistent performance in the laboratory. A conceptual approach based on Geographic Information System (GIS) technology has been developed to identify areas that are vulnerable to nontarget chemical exposure. This GIS-based approach uses wind speed, frequency of those winds, pesticide application rates, and spatial location of agricultural crops to identify areas with the highest potential for pesticide exposure. A test scenario based on an incident in Idaho (USA) was used to identify the relative magnitude of risk from off-target movement of herbicides to plants in the conterminous United States. This analysis indicated that the western portion of the Corn Belt, the central California valley, southeastern Washington, the Willamette Valley of Oregon, and agricultural areas bordering the Great Lakes are among those areas in the United States that appear to have the greatest potential for off-target movement of herbicides via drift. Agricultural areas, such as the Mississippi River Valley and the southeastern United States, appears to have less potential, possibly due to lower average wind speeds. Ecological risk assessments developed for pesticide registration would be improved by using response data from species common to high-risk areas instead of extrapolating test data from species unrelated to those areas with the highest potential for exposure. PMID:16916045

  10. Geochemical Indicators and Diatoms Identify the Inundation Limit of the 2010 Maule Tsunami

    NASA Astrophysics Data System (ADS)

    Chague-Goff, C.; Goff, J. R.; Wong, H. K.; Cisternas, M.

    2013-05-01

    It has long been known that tsunamis inundate further than the limit of the sand deposit they leave behind, and that relying on the extent of the sandy sedimentary evidence is likely to result in an under-estimation of event magnitude and risk. However, the question remains about how to identify the real limit of tsunami inundation, particularly several months or more after the event. Here we report on a study carried out at a site on the Pacific coast of Chile south of Constitución in August 2010, nearly 6 months after the Mw 8.8 Maule tsunami. Eight pits were dug along a 480 m long shore-perpendicular transect, incorporating the area covered by tsunami sediment, a zone covered by a discontinuous and decomposing debris scatter up to the point of maximum inundation, and an area further landward from this point. The tsunami sand deposit extended from ~160 to 260 m inland and ranged in thickness from 22 to less than 1 cm at the limit of sediment deposition. It consisted of dark, generally well-sorted, coarse to medium sand. Logs, pumice and various organic debris were found up to a limit of tsunami inundation (380 m inland - confirmed by a local eye witness). New grass growth also covered the tsunami deposit and the field further inland. While the chemical composition of the tsunami deposit differed to that of the underlying soil, indicators of saltwater inundation were low in the sandy units, reflecting downward leaching and dilution by rainfall in the porous material in the 6 months since the tsunami. Concentrations of saltwater indicators (e.g. chloride, sulphate, bromide) were however elevated in the area covered by scattered debris up to the limit of tsunami inundation, suggesting preferential retention in organic-rich material. Marine and brackish-marine diatoms were found both in the sandy units and beyond, at the surface of the grass field, and occurred in higher concentrations than in the underlying soil. Both diatom assemblages and geochemical marine proxies are indicative of tsunami inundation well beyond the sediment limit. While sea spray and associated wind cannot be totally excluded as the source of soluble salts and wind-blown diatoms, chloride concentrations do not decrease landward within the area of tsunami inundation. A decrease in chloride would have been expected if it was solely due to sea spray. While further research is required to allow us to distinguish the effects of marine inundation from sea spray, the use of geochemical proxies and diatoms provides a means to identify the limit of tsunami inundation beyond the limit of sand deposition, and as previous studies have shown, even after debris marking it have decayed. This is of importance for tsunami risk assessment and mitigation.

  11. Self-Selection Patterns of College Roommates as Identified by the Myers-Briggs Type Indicator.

    ERIC Educational Resources Information Center

    Anchors, W. Scott; Hale, John, Jr.

    1985-01-01

    Investigated patterns and processes by which students (N=422) made unassisted roommate pairings within residence halls using the Myers-Briggs Type Indicator. Results indicated introverts, intuitives, feelers, and perceivers each tended to self-select. (BL)

  12. Characterization of potential mineralization in Afghanistan: four permissive areas identified using imaging spectroscopy data

    USGS Publications Warehouse

    King, Trude V.V.; Berger, Byron R.; Johnson, Michaela R.

    2014-01-01

    As part of the U.S. Geological Survey and Department of Defense Task Force for Business and Stability Operations natural resources revitalization activities in Afghanistan, four permissive areas for mineralization, Bamyan 1, Farah 1, Ghazni 1, and Ghazni 2, have been identified using imaging spectroscopy data. To support economic development, the areas of potential mineralization were selected on the occurrence of selected mineral assemblages mapped using the HyMap™ data (kaolinite, jarosite, hydrated silica, chlorite, epidote, iron-bearing carbonate, buddingtonite, dickite, and alunite) that may be indicative of past mineralization processes in areas with limited or no previous mineral resource studies. Approximately 30 sites were initially determined to be candidates for areas of potential mineralization. Additional criteria and material used to refine the selection and prioritization process included existing geologic maps, Landsat Thematic Mapper data, and published literature. The HyMapTM data were interpreted in the context of the regional geologic and tectonic setting and used the presence of alteration mineral assemblages to identify areas with the potential for undiscovered mineral resources. Further field-sampling, mapping, and supporting geochemical analyses are necessary to fully substantiate and verify the specific deposit types in the four areas of potential mineralization.

  13. Research Questions to Identify Ecological Indicators Most Useful for Linking Ecosystems and Human Wellbeing

    EPA Science Inventory

    Background/Question/Methods While the desirability of ecological indicators that foster social science interpretation and use as well as public comprehension is well established, guidelines for developing indicators that meet these needs are not as well developed. In the past f...

  14. Identifying malaria vector breeding habitats with remote sensing data and terrain-based landscape indices in Zambia

    PubMed Central

    2010-01-01

    Background Malaria, caused by the parasite Plasmodium falciparum, is a significant source of morbidity and mortality in southern Zambia. In the Mapanza Chiefdom, where transmission is seasonal, Anopheles arabiensis is the dominant malaria vector. The ability to predict larval habitats can help focus control measures. Methods A survey was conducted in March-April 2007, at the end of the rainy season, to identify and map locations of water pooling and the occurrence anopheline larval habitats; this was repeated in October 2007 at the end of the dry season and in March-April 2008 during the next rainy season. Logistic regression and generalized linear mixed modeling were applied to assess the predictive value of terrain-based landscape indices along with LandSat imagery to identify aquatic habitats and, especially, those with anopheline mosquito larvae. Results Approximately two hundred aquatic habitat sites were identified with 69 percent positive for anopheline mosquitoes. Nine species of anopheline mosquitoes were identified, of which, 19% were An. arabiensis. Terrain-based landscape indices combined with LandSat predicted sites with water, sites with anopheline mosquitoes and sites specifically with An. arabiensis. These models were especially successful at ruling out potential locations, but had limited ability in predicting which anopheline species inhabited aquatic sites. Terrain indices derived from 90 meter Shuttle Radar Topography Mission (SRTM) digital elevation data (DEM) were better at predicting water drainage patterns and characterizing the landscape than those derived from 30 m Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) DEM. Conclusions The low number of aquatic habitats available and the ability to locate the limited number of aquatic habitat locations for surveillance, especially those containing anopheline larvae, suggest that larval control maybe a cost-effective control measure in the fight against malaria in Zambia and other regions with seasonal transmission. This work shows that, in areas of seasonal malaria transmission, incorporating terrain-based landscape models to the planning stages of vector control allows for the exclusion of significant portions of landscape that would be unsuitable for water to accumulate and for mosquito larvae occupation. With increasing free availability of satellite imagery such as SRTM and LandSat, the development of satellite imagery-based prediction models is becoming more accessible to vector management coordinators. PMID:21050496

  15. Cluster analysis for identifying sub-groups and selecting potential discriminatory variables in human encephalitis

    PubMed Central

    2010-01-01

    Background Encephalitis is an acute clinical syndrome of the central nervous system (CNS), often associated with fatal outcome or permanent damage, including cognitive and behavioural impairment, affective disorders and epileptic seizures. Infection of the central nervous system is considered to be a major cause of encephalitis and more than 100 different pathogens have been recognized as causative agents. However, a large proportion of cases have unknown disease etiology. Methods We perform hierarchical cluster analysis on a multicenter England encephalitis data set with the aim of identifying sub-groups in human encephalitis. We use the simple matching similarity measure which is appropriate for binary data sets and performed variable selection using cluster heatmaps. We also use heatmaps to visually assess underlying patterns in the data, identify the main clinical and laboratory features and identify potential risk factors associated with encephalitis. Results Our results identified fever, personality and behavioural change, headache and lethargy as the main characteristics of encephalitis. Diagnostic variables such as brain scan and measurements from cerebrospinal fluids are also identified as main indicators of encephalitis. Our analysis revealed six major clusters in the England encephalitis data set. However, marked within-cluster heterogeneity is observed in some of the big clusters indicating possible sub-groups. Overall, the results show that patients are clustered according to symptom and diagnostic variables rather than causal agents. Exposure variables such as recent infection, sick person contact and animal contact have been identified as potential risk factors. Conclusions It is in general assumed and is a common practice to group encephalitis cases according to disease etiology. However, our results indicate that patients are clustered with respect to mainly symptom and diagnostic variables rather than causal agents. These similarities and/or differences with respect to symptom and diagnostic measurements might be attributed to host factors. The idea that characteristics of the host may be more important than the pathogen is also consistent with the observation that for some causes, such as herpes simplex virus (HSV), encephalitis is a rare outcome of a common infection. PMID:21192831

  16. Establishing and testing the "reuse potential" indicator for managing wastes as resources.

    PubMed

    Park, Joo Young; Chertow, Marian R

    2014-05-01

    This study advances contemporary ideas promoting the importance of managing wastes as resources such as closed-loop or circular material economies, and sustainable materials management by reinforcing the notion of a resource-based paradigm rather than a waste-based one. It features the creation of a quantitative tool, the "reuse potential indicator" to specify how "resource-like" versus how "waste-like" specific materials are on a continuum. Even with increasing attention to waste reuse and resource conservation, constant changes in product composition and complexity have left material managers without adequate guidance to make decisions about what is technically feasible to recover from the discard stream even before markets can be considered. The reuse potential indicator is developed to aid management decision-making about waste based not on perception but more objectively on the technical ability of the materials to be reused in commerce. This new indicator is based on the extent of technological innovation and commercial application of actual reuse approaches identified and cataloged. Coal combustion by-products (CCBs) provide the test case for calculating the reuse potential indicator. While CCBs are often perceived as wastes and then isolated in landfills or surface impoundments, there is also a century-long history in the industry of developing technologies to reuse CCBs. The recent statistics show that most CCBs generated in Europe and Japan are reused (90-95%), but only 40-45% of CCBs are used in the United States. According to the reuse potential calculation, however, CCBs in the United States have high technical reusability. Of the four CCBs examined under three different regulatory schemes, reuse potential for boiler slag and flue-gas desulfurization gypsum maintains a value greater than 0.8 on a 0-1 scale, indicating they are at least 80% resource-like. Under current regulation in the United States, both fly ash and bottom ash are 80-90% resource-like. Very strict regulation would remove many reuse options decreasing potential for these two CCBs to 30% resource-like. A more holistic view of waste and broad application of the new indicator would make clear what technologies are available and assist public and private decision makers in setting quantitative material reuse targets from a new knowledge base that reinforces a resource-based paradigm. PMID:24594758

  17. Gangs in Our Schools: Identifying Gang Indicators in Our School Population

    ERIC Educational Resources Information Center

    Struyk, Ruth

    2006-01-01

    Although teachers used to teach in the communities where they resided, they now commute to schools in other districts. For teachers who teach in districts that are culturally or ethnically different than their own, it may be a new experience of which to become aware or identify issues such as dealing with gang behavior. For other teachers, there

  18. Gangs in Our Schools: Identifying Gang Indicators in Our School Population

    ERIC Educational Resources Information Center

    Struyk, Ruth

    2006-01-01

    Although teachers used to teach in the communities where they resided, they now commute to schools in other districts. For teachers who teach in districts that are culturally or ethnically different than their own, it may be a new experience of which to become aware or identify issues such as dealing with gang behavior. For other teachers, there…

  19. Identifying Early Numeracy Indicators for Kindergarten and First-Grade Students

    ERIC Educational Resources Information Center

    Lembke, Erica; Foegen, Anne

    2009-01-01

    Recent studies have documented positive effects for early intervention in improving the mathematics performance of low-achieving children. Consequently, educators need technically sound mathematics screening measures to identify children at risk and then intervene to improve achievement. In this article, we describe preliminary technical adequacy…

  20. Using patient safety indicators to estimate the impact of potential adverse events on outcomes.

    PubMed

    Rivard, Peter E; Luther, Stephen L; Christiansen, Cindy L; Shibei Zhao; Loveland, Susan; Elixhauser, Anne; Romano, Patrick S; Rosen, Amy K

    2008-02-01

    The authors estimated the impact of potentially preventable patient safety events, identified by Agency for Healthcare Research and Quality (AHRQ) Patient Safety Indicators (PSIs), on patient outcomes: mortality, length of stay (LOS), and cost. The PSIs were applied to all acute inpatient hospitalizations at Veterans Health Administration (VA) facilities in fiscal 2001. Two methods-regression analysis and multivariable case matching- were used independently to control for patient and facility characteristics while predicting the effect of the PSI on each outcome. The authors found statistically significant (p < .0001) excess mortality, LOS, and cost in all groups with PSIs. The magnitude of the excess varied considerably across the PSIs. These VA findings are similar to those from a previously published study of nonfederal hospitals, despite differences between VA and non-VA systems. This study contributes to the literature measuring outcomes of medical errors and provides evidence that AHRQ PSIs may be useful indicators for comparison across delivery systems. PMID:18184870

  1. Identifying Important Career Indicators of Undergraduate Geoscience Students Upon Completion of Their Degree

    NASA Astrophysics Data System (ADS)

    Wilson, C. E.; Keane, C. M.; Houlton, H. R.

    2012-12-01

    The American Geosciences Institute (AGI) decided to create the National Geoscience Student Exit Survey in order to identify the initial pathways into the workforce for these graduating students, as well as assess their preparedness for entering the workforce upon graduation. The creation of this survey stemmed from a combination of experiences with the AGI/AGU Survey of Doctorates and discussions at the following Science Education Research Center (SERC) workshops: "Developing Pathways to Strong Programs for the Future", "Strengthening Your Geoscience Program", and "Assessing Geoscience Programs". These events identified distinct gaps in understanding the experiences and perspectives of geoscience students during one of their most profound professional transitions. Therefore, the idea for the survey arose as a way to evaluate how the discipline is preparing and educating students, as well as identifying the students' desired career paths. The discussions at the workshops solidified the need for this survey and created the initial framework for the first pilot of the survey. The purpose of this assessment tool is to evaluate student preparedness for entering the geosciences workforce; identify student decision points for entering geosciences fields and remaining in the geosciences workforce; identify geosciences fields that students pursue in undergraduate and graduate school; collect information on students' expected career trajectories and geosciences professions; identify geosciences career sectors that are hiring new graduates; collect information about salary projections; overall effectiveness of geosciences departments regionally and nationally; demonstrate the value of geosciences degrees to future students, the institutions, and employers; and establish a benchmark to perform longitudinal studies of geosciences graduates to understand their career pathways and impacts of their educational experiences on these decisions. AGI's Student Exit Survey went through a second pilot testing with Spring 2012 graduates from 45 departments across the United States. These graduating students from undergraduate and graduate programs answered questions about their earth science education experiences at the high school, community college, and university levels; their quantitative skills; their research and internship experiences and their immediate plans after graduation. Out of the 294 complete responses to the survey, 233 were from undergraduate students. This presentation will focus on the responses of these undergraduate students. AGI hopes to fully deploy this survey broadly to geosciences departments across the country in Spring 2013. AGI will also begin longitudinally participants from the previous Exit Survey efforts in order to understand their progression through their chosen career paths.

  2. Identifying potential recommendation domains for conservation agriculture in Ethiopia, Kenya, and Malawi.

    PubMed

    Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

    2015-02-01

    Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (?1 km(2)) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5% of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21% of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries. PMID:25331642

  3. Identifying Potential Recommendation Domains for Conservation Agriculture in Ethiopia, Kenya, and Malawi

    NASA Astrophysics Data System (ADS)

    Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

    2015-02-01

    Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (≈1 km2) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5 % of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21 % of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries.

  4. A methodological approach to identify external factors for indicator-based risk adjustment illustrated by a cataract surgery register

    PubMed Central

    2014-01-01

    Background Risk adjustment is crucial for comparison of outcome in medical care. Knowledge of the external factors that impact measured outcome but that cannot be influenced by the physician is a prerequisite for this adjustment. To date, a universal and reproducible method for identification of the relevant external factors has not been published. The selection of external factors in current quality assurance programmes is mainly based on expert opinion. We propose and demonstrate a methodology for identification of external factors requiring risk adjustment of outcome indicators and we apply it to a cataract surgery register. Methods Defined test criteria to determine the relevance for risk adjustment are clinical relevance and statistical significance. Clinical relevance of the association is presumed when observed success rates of the indicator in the presence and absence of the external factor exceed a pre-specified range of 10%. Statistical significance of the association between the external factor and outcome indicators is assessed by univariate stratification and multivariate logistic regression adjustment. The cataract surgery register was set up as part of a German multi-centre register trial for out-patient cataract surgery in three high-volume surgical sites. A total of 14,924 patient follow-ups have been documented since 2005. Eight external factors potentially relevant for risk adjustment were related to the outcome indicators refractive accuracy and visual rehabilitation 25 weeks after surgery. Results The clinical relevance criterion confirmed 2 (refractive accuracy) and 5 (visual rehabilitation) external factors. The significance criterion was verified in two ways. Univariate and multivariate analyses revealed almost identical external factors: 4 were related to refractive accuracy and 7 (6) to visual rehabilitation. Two (refractive accuracy) and 5 (visual rehabilitation) factors conformed to both criteria and were therefore relevant for risk adjustment. Conclusion In a practical application, the proposed method to identify relevant external factors for risk adjustment for comparison of outcome in healthcare proved to be feasible and comprehensive. The method can also be adapted to other quality assurance programmes. However, the cut-off score for clinical relevance needs to be individually assessed when applying the proposed method to other indications or indicators. PMID:24965949

  5. Non-linear models based on simple topological indices to identify RNase III protein members.

    PubMed

    Agüero-Chapin, Guillermin; de la Riva, Gustavo A; Molina-Ruiz, Reinaldo; Sánchez-Rodríguez, Aminael; Pérez-Machado, Gisselle; Vasconcelos, Vítor; Antunes, Agostinho

    2011-03-21

    Alignment-free classifiers are especially useful in the functional classification of protein classes with variable homology and different domain structures. Thus, the Topological Indices to BioPolymers (TI2BioP) methodology (Agüero-Chapin et al., 2010) inspired in both the TOPS-MODE and the MARCH-INSIDE methodologies allows the calculation of simple topological indices (TIs) as alignment-free classifiers. These indices were derived from the clustering of the amino acids into four classes of hydrophobicity and polarity revealing higher sequence-order information beyond the amino acid composition level. The predictability power of such TIs was evaluated for the first time on the RNase III family, due to the high diversity of its members (primary sequence and domain organization). Three non-linear models were developed for RNase III class prediction: Decision Tree Model (DTM), Artificial Neural Networks (ANN)-model and Hidden Markov Model (HMM). The first two are alignment-free approaches, using TIs as input predictors. Their performances were compared with a non-classical HMM, modified according to our amino acid clustering strategy. The alignment-free models showed similar performances on the training and the test sets reaching values above 90% in the overall classification. The non-classical HMM showed the highest rate in the classification with values above 95% in training and 100% in test. Although the higher accuracy of the HMM, the DTM showed simplicity for the RNase III classification with low computational cost. Such simplicity was evaluated in respect to HMM and ANN models for the functional annotation of a new bacterial RNase III class member, isolated and annotated by our group. PMID:21192951

  6. A Program Evaluation Model: Using Bloom's Taxonomy to Identify Outcome Indicators in Outcomes-Based Program Evaluations

    ERIC Educational Resources Information Center

    McNeil, Rita C.

    2011-01-01

    Outcomes-based program evaluation is a systematic approach to identifying outcome indicators and measuring results against those indicators. One dimension of program evaluation is assessing the level of learner acquisition to determine if learning objectives were achieved as intended. The purpose of the proposed model is to use Bloom's Taxonomy to…

  7. Novel high-throughput screen against Candida albicans identifies antifungal potentiators and agents effective against biofilms

    PubMed Central

    LaFleur, Michael D.; Lucumi, Edinson; Napper, Andrew D.; Diamond, Scott L.; Lewis, Kim

    2011-01-01

    Objectives Microbial adhesion and biofilms have important implications for human health and disease. Candida albicans is an opportunistic pathogen which forms drug-resistant biofilms that contribute to the recalcitrance of disease. We have developed a high-throughput screen for potentiators of clotrimazole, a common therapy for Candida infections, including vaginitis and thrush. The screen was performed against C. albicans biofilms grown in microtitre plates in order to target the most resilient forms of the pathogen. Methods Biofilm growth, in individual wells of 384-well plates, was measured using the metabolic indicator alamarBlue® and found to be very consistent and reproducible. This assay was used to test the effect of more than 120 000 small molecule compounds from the NIH Molecular Libraries Small Molecule Repository, and compounds that enhanced the activity of clotrimazole or acted on the biofilms alone were identified as hits. Results Nineteen compounds (0.016% hit rate) were identified and found to cause more than 30% metabolic inhibition of biofilms compared with clotrimazole alone, which had a modest effect on biofilm viability at the concentration tested. Hits were confirmed for activity against biofilms with dose–response measurements. Several compounds had increased activity in combination with clotrimazole, including a 1,3-benzothiazole scaffold that exhibited a >100-fold improvement against biofilms of three separate C. albicans isolates. Cytotoxicity experiments using human fibroblasts confirmed the presence of lead molecules with favourable antifungal activity relative to cytotoxicity. Conclusions We have validated a novel approach to identify antifungal potentiators and completed a high-throughput screen to identify small molecules with activity against C. albicans biofilms. These small molecules may specifically target the biofilm and make currently available antifungals more effective. PMID:21393183

  8. Microtubule inhibitors: structure-activity analyses suggest rational models to identify potentially active compounds.

    PubMed Central

    Callahan, H L; Kelley, C; Pereira, T; Grogl, M

    1996-01-01

    Trifluralin, a dinitroaniline microtubule inhibitor currently in use as an herbicide, has been shown to inhibit the proliferation of Plasmodium falciparum, Trypanosoma brucei, and several species of Leishmania, in vitro. As a topical formulation, trifluralin is also effective in vivo (in BALB/c mice) against Leishmania major and Leishmania mexicana. Although trifluralin and other dinitroaniline herbicides show significant activity as antiparasitic compounds, disputed indications of potential carcinogenicity will probably limit advanced development of these substances. However, researchers have suggested that the activity of trifluralin is due to an impurity or contaminant, not to trifluralin itself. We have pursued this lead and identified the structure of the active impurity. This compound, chloralin, is 100 times more active than trifluralin. On the basis of its structure, we developed a rational structure-activity model for chloralin. Using this model, we have successfully predicted and tested active analogs in a Leishmania promastigote assay; thus, we have identified the putative mechanism of action of this class of drugs in Leishmania species. Potentially, this will allow the design of noncarcinogenic, active drugs. PMID:8849257

  9. MicroRNA screening identifies circulating microRNAs as potential biomarkers for osteosarcoma

    PubMed Central

    LI, HUI; ZHANG, KUN; LIU, LI-HONG; OUYANG, YURONG; GUO, HONG-BIN; ZHANG, HANCHONG; BU, JIE; XIAO, TAO

    2015-01-01

    MicroRNAs (miRNAs) are a family of small non-protein coding RNAs, which regulate the expression of a wide variety of genes at the post-transcriptional level to control numerous biological and pathological processes. Various circulating miRNAs have been identified as potential diagnostic and prognostic biomarkers in multiple types of cancer and disease. The aim of the present study was to identify potential miRNA biomarkers for the early diagnosis and relapse prediction of osteosarcoma (OS). miRNA profiling was performed on serum from patients with osteosarcoma and healthy controls. All putative miRNAs were verified by reverse transcription-quantitative polymerase chain reaction analysis of 20 pre-therapeutic OS patients and 20 healthy individuals. The expression of miR-106a-5p, miR16-5p, miR-20a-5p, miR-425-5p, miR451a, miR-25-3p and miR139-5p was demonstrated to be downregulated in the serum of OS patients when compared with that of the healthy controls. Receiver-operating characteristic curve analyses indicated that these 7 miRNAs may be used as diagnostic biomarkers with the ability to discriminate between the healthy cohort and patients with OS. These results provide novel insights into the use of miRNAs in early blood screening for OS. PMID:26622728

  10. Chemical and structural indicators for large redox potentials in Fe-based positive electrode materials.

    PubMed

    Melot, Brent C; Scanlon, David O; Reynaud, Marine; Rousse, Gwenaëlle; Chotard, Jean-Noël; Henry, Marc; Tarascon, Jean-Marie

    2014-07-23

    Li-ion batteries have enabled a revolution in the way portable consumer-electronics are powered and will play an important role as large-scale electrochemical storage applications like electric vehicles and grid-storage are developed. The ability to identify and design promising new positive insertion electrodes will be vital in continuing to push Li-ion technology to its fullest potential. Utilizing a combination of computational tools and structural analysis, we report new indicators which will facilitate the recognition of phases with the desired redox potential. Most importantly of these, we find there is a strong correlation between the presence of Li ions sitting in close-proximity to the redox center of polyanionic phases and the open circuit voltage in Fe-based cathodes. This common structural feature suggests that the bonding associated with Li may have a secondary inductive effect which increases the ionic character of Fe bonds beyond what is typically expected based purely on arguments of electronegativity associated with the polyanionic group. This correlation is supported by ab initio calculations which show the Bader charge increases (reflecting an increased ionicity) in a nearly linear fashion with the experimental cell potentials. These features are demonstrated to be consistent across a wide variety of compositions and structures and should help to facilitate the design of new, high-potential, and environmentally sustainable insertion electrodes. PMID:24588538

  11. Metabolomics studies identify novel diagnostic and prognostic indicators in patients with alcoholic hepatitis

    PubMed Central

    Ascha, Mona; Wang, Zeneng; Ascha, Mustafa S; Dweik, Raed; Zein, Nizar N; Grove, David; Brown, J Mark; Marshall, Stephanie; Lopez, Rocio; Hanouneh, Ibrahim A

    2016-01-01

    AIM: To identify plasma analytes using metabolomics that correlate with the diagnosis and severity of liver disease in patients with alcoholic hepatitis (AH). METHODS: We prospectively recruited patients with cirrhosis from AH (n = 23) and those with cirrhosis with acute decompensation (AD) from etiologies other than alcohol (n = 25). We used mass spectrometry to identify 29 metabolic compounds in plasma samples from fasted subjects. A receiver operating characteristics analysis was performed to assess the utility of biomarkers in distinguishing acute AH from alcoholic cirrhosis. Logistic regression analysis was performed to build a predictive model for AH based on clinical characteristics. A survival analysis was used to construct Kaplan Meier curves evaluating transplant-free survival. RESULTS: A comparison of model for end-stage liver disease (MELD)-adjusted metabolomics levels between cirrhosis patients who had AD or AH showed that patients with AH had significantly higher levels of betaine, and lower creatinine, phenylalanine, homocitrulline, citrulline, tyrosine, octenoyl-carnitine, and symmetric dimethylarginine. When considering combined levels, betaine and citrulline were highly accurate predictors for differentiation between AH and AD (area under receiver operating characteristics curve = 0.84). The plasma levels of carnitine [0.54 (0.18, 0.91); P = 0.005], homocitrulline [0.66 (0.34, 0.99); P < 0.001] and pentanoyl-carnitine [0.53 (0.16, 0.90); P = 0.007] correlated with MELD scores in patients diagnosed with AH. Increased levels of many biomarkers (carnitine P = 0.005, butyrobetaine P = 0.32, homocitrulline P = 0.002, leucine P = 0.027, valine P = 0.024, phenylalanine P = 0.037, tyrosine P = 0.012, acetyl-carnitine P = 0.006, propionyl-carnitine P = 0.03, butyryl-carnitine P = 0.03, trimethyl-lisine P = 0.034, pentanoyl-carnitine P = 0.03, hexanoyl-carnitine P = 0.026) were associated with increased mortality in patients with AH. CONCLUSION: Metabolomics plasma analyte levels might be used to diagnose of AH or help predict patient prognoses. PMID:27057307

  12. EVOKED POTENTIALS AS INDICES OF ADAPTATION IN THE SOMATOSENSORY SYSTEM IN HUMANS: A REVIEW AND PROSPECTUS

    EPA Science Inventory

    Population-level behavior of large neural aggregates can be efficiently monitored by corresponding population-level indices such as somatosensory evoked potentials (SEPs). The literature reviewed clearly indicates that SEPs undergo systematic and often marked changes under condit...

  13. Field-directed assembly of nanowires: identifying directors, disruptors and indices to maximize the device yield

    NASA Astrophysics Data System (ADS)

    Sam, Mahshid; Moghimian, Nima; Bhiladvala, Rustom B.

    2015-12-01

    Individually-addressable nano-electro-mechanical (NEMS) devices have been used to demonstrate sensitive mass detection to the single-proton level, as well as neutral-particle mass spectrometry. The cost of individually securing or patterning such devices is proportional to their number or the chip area covered. This limits statistical support for new research, as well as paths to the commercial availability of extraordinarily sensitive instruments. Field-directed assembly of synthesized nanowires addresses this problem and shows potential for low-cost, large-area coverage with NEMS devices. For positive dielectrophoresis (pDEP) as the main assembly director, the space of field, geometric and material parameters is large, with combinations that can serve either as directors or disruptors for directed assembly. We seek parameter values to obtain the best yield, by introducing a rational framework to reduce trial-and-error. We show that sorting the disruptors by severity and eliminating those weakly coupled to the director, allows reduction of the parameter space. The remaining disruptors are then represented compactly by dimensionless parameters. In the example protocol chosen, a single dimensionless parameter, the yield index, allows minimization of disruptors by the choice of frequency. Following this, the voltage may be selected to maximize the yield. Using this framework, we obtained 94% pre-clamped and 88% post-clamped yield over 57000 nanowire sites. Organizing the parameter space using a director-disruptor framework, with economy introduced by non-dimensional parameters, provides a path to controllably decrease the effort and cost of manufacturing nanoscale devices. This should help in the commercialization of individually addressable nanodevices.Individually-addressable nano-electro-mechanical (NEMS) devices have been used to demonstrate sensitive mass detection to the single-proton level, as well as neutral-particle mass spectrometry. The cost of individually securing or patterning such devices is proportional to their number or the chip area covered. This limits statistical support for new research, as well as paths to the commercial availability of extraordinarily sensitive instruments. Field-directed assembly of synthesized nanowires addresses this problem and shows potential for low-cost, large-area coverage with NEMS devices. For positive dielectrophoresis (pDEP) as the main assembly director, the space of field, geometric and material parameters is large, with combinations that can serve either as directors or disruptors for directed assembly. We seek parameter values to obtain the best yield, by introducing a rational framework to reduce trial-and-error. We show that sorting the disruptors by severity and eliminating those weakly coupled to the director, allows reduction of the parameter space. The remaining disruptors are then represented compactly by dimensionless parameters. In the example protocol chosen, a single dimensionless parameter, the yield index, allows minimization of disruptors by the choice of frequency. Following this, the voltage may be selected to maximize the yield. Using this framework, we obtained 94% pre-clamped and 88% post-clamped yield over 57000 nanowire sites. Organizing the parameter space using a director-disruptor framework, with economy introduced by non-dimensional parameters, provides a path to controllably decrease the effort and cost of manufacturing nanoscale devices. This should help in the commercialization of individually addressable nanodevices. Electronic supplementary information (ESI) available: This section includes micrographs of high yield pre- and post-clamped nanowires. See DOI: 10.1039/C5NR06763D

  14. Identifying Potential Areas for Siting Interim Nuclear Waste Facilities Using Map Algebra and Optimization Approaches

    SciTech Connect

    Omitaomu, Olufemi A; Liu, Cheng; Cetiner, Sacit M; Belles, Randy; Mays, Gary T; Tuttle, Mark A

    2013-01-01

    The renewed interest in siting new nuclear power plants in the United States has brought to the center stage, the need to site interim facilities for long-term management of spent nuclear fuel (SNF). In this paper, a two-stage approach for identifying potential areas for siting interim SNF facilities is presented. In the first stage, the land area is discretized into grids of uniform size (e.g., 100m x 100m grids). For the continental United States, this process resulted in a data matrix of about 700 million cells. Each cell of the matrix is then characterized as a binary decision variable to indicate whether an exclusion criterion is satisfied or not. A binary data matrix is created for each of the 25 siting criteria considered in this study. Using map algebra approach, cells that satisfy all criteria are clustered and regarded as potential siting areas. In the second stage, an optimization problem is formulated as a p-median problem on a rail network such that the sum of the shortest distance between nuclear power plants with SNF and the potential storage sites from the first stage is minimized. The implications of obtained results for energy policies are presented and discussed.

  15. Heart Rate Variability as an Alternative Indicator for Identifying Cardiac Iron Status in Non-Transfusion Dependent Thalassemia Patients

    PubMed Central

    Wijarnpreecha, Karn; Siri-Angkul, Natthaphat; Shinlapawittayatorn, Krekwit; Charoenkwan, Pimlak; Silvilairat, Suchaya; Siwasomboon, Chate; Visarutratna, Pannee; Srichairatanakool, Somdet; Tantiworawit, Adisak; Phrommintikul, Arintaya; Chattipakorn, Siriporn C.; Chattipakorn, Nipon

    2015-01-01

    Background Iron-overload cardiomyopathy is a major cause of death in thalassemia patients due to the lack of an early detection strategy. Although cardiac magnetic resonance (CMR) T2* is used for early detection of cardiac iron accumulation, its availability is limited. Heart rate variability (HRV) has been used to evaluate cardiac autonomic function and found to be depressed in thalassemia. However, its direct correlation with cardiac iron accumulation has never been investigated. We investigated whether HRV can be used as an alternative indicator for early identification of cardiac iron deposition in thalassemia patients. Methods Ninety-nine non-transfusion dependent thalassemia patients (23.00 (17.00, 32.75) years, 35 male) were enrolled. The correlation between HRV recorded using 24-hour Holter monitoring and non-transferrin bound iron (NTBI), hemoglobin (Hb), serum ferritin, LV ejection fraction (LVEF), and CMR-T2* were determined. Results The median NTBI value was 3.15 (1.11, 6.59) μM. Both time and frequency domains of HRV showed a significant correlation with the NTBI level, supporting HRV as a marker of iron overload. Moreover, the LF/HF ratio showed a significant correlation with CMR-T2* with the receiver operating characteristic (ROC) curve of 0.684±0.063, suggesting that it could represent the cardiac iron deposit in thalassemia patients. HRV was also significantly correlated with serum ferritin and Hb. Conclusions This novel finding regarding the correlation between HRV and CMR-T2* indicates that HRV could be a potential marker in identifying early cardiac iron deposition prior to the development of LV dysfunction, and may be used as an alternative to CMR-T2* for screening cardiac iron status in thalassemia patients. PMID:26083259

  16. Using a watershed-centric approach to identify potentially impacted beaches

    EPA Science Inventory

    Beaches can be affected by a variety of contaminants. Of particular concern are beaches impacted by human fecal contamination and urban runoff. This poster demonstrates a methodology to identify potentially impacted beaches using Geographic Information Systems (GIS). Since h...

  17. Docking and virtual screening to identify PKC agonists: potentials in anticancer therapeutics.

    PubMed

    Jain, Anish; Trivedi, Vishal

    2014-03-01

    Protein kinase C (PKC) is down-stream to most of the G-protein coupled receptor or tyrosine kinase receptors mediated signaling events from the cell surface. PKC C1 domain has a hydrophobic region with a polar groove to facilitate 1,2-diacyl-glycerol (DAG) binding or other agonist molecule for PKC activation. Post activation, a partial or complete blocking of hydrophilic groove makes the DAG binding site completely hydrophobic and facilitates easier penetration of the PKC into the membrane. Phorbol ester, a strong PKC agonist, uses this mechanism to induce tumor formation. A total of 300 heterocyclic compounds with 70% similarity to phorbol 12-myristate 13-acetate (PMA) were selected, and virtual docking was performed with PKC-α as target. An initial screening indicated that most of the molecules fit well into the C1 domain and had better binding energy than PMA. Further analysis in a PMA competition experiment identified five molecules, Zc 67913417, Zc 68601770, Zc 25726447, Zc 35376386 and Zc 49785214 as potent PKC agonists. In addition, as these compounds showed better binding than PMA, more interaction with PKC residues (hydrogen bonding and hydrophobic), and the top five hit molecules was potent enough to abolish carcinogenic effects of PMA. Searching the top heterocyclic compounds into the drug database gave a number of approved drugs. Testing two candidate drugs, nandrolone decanoate and budesonide, reduced cellular viability of HT1080 in a dose-dependent manner with an IC50 values of 96.8 nM and 200nM respectively. An in silico toxicity analysis indicated that top hit molecules are non-toxic, non-mutagenic in cellular and bacterial system, and have no tumorigenic potentials in a single cell or animal model. Hence, a virtual screening, agonist competition assay, and in silico toxicity assessment allowed us to identify five new PKC agonist molecules for future drug discovery against cancer. PMID:24138399

  18. Analysis of the Methods Used for Identifying Potential School Dropouts. Final Report.

    ERIC Educational Resources Information Center

    Neyman, C. A., Jr.

    This final report analyzes the research methods used in the identification of potential dropouts. This program was administered under Title I (ESEA, 1965) in the District of Columbia (see also ED 049 319). Three forms were used in the evaluation of Title I students identified as potential dropouts during the school year 1967-68: (1) Student…

  19. The Efficacy of a Head Start Educational Program for Parents Identified as Potential Child Abusers.

    ERIC Educational Resources Information Center

    Stanberry, Anne M.

    This paper describes a study conducted to determine if parents' enrollment in a Head Start Resource Center for Parents and Children reduced the parents' potential for child abuse. Subjects were 17 mothers who were enrolled in the Resource Center, had a child from 2 to 4 years old, and were identified as potential child abusers. The Resource…

  20. Evaluation of indicated suicide risk prevention approaches for potential high school dropouts.

    PubMed Central

    Thompson, E A; Eggert, L L; Randell, B P; Pike, K C

    2001-01-01

    OBJECTIVES: This study evaluated the efficacy of 2 indicated preventive interventions, postintervention and at 9-month follow-up. METHODS: Drawn from a pool of potential high school dropouts, 460 youths were identified as being at risk for suicide and participated in 1 of 3 conditions randomly assigned by school: (1) Counselors CARE (C-CARE) (n = 150), a brief one-to-one assessment and crisis intervention; (2) Coping and Support Training (CAST) (n = 155), a small-group skills-building and social support intervention delivered with C-CARE; and (3) usual-care control (n = 155). Survey instruments were administered pre-intervention, following C-CARE (4 weeks), following CAST (10 weeks), and at a 9-month follow-up. RESULTS: Growth curve analyses showed significant rates of decline in attitude toward suicide and suicidal ideation associated with the experimental interventions. C-CARE and CAST, compared with usual care, also were effective in reducing depression and hopelessness. Among females, reductions in anxiety and anger were greater in response to the experimental programs. CAST was most effective in enhancing and sustaining personal control and problem-solving coping for males and females. CONCLUSIONS: School-based, indicated prevention approaches are feasible and effective for reducing suicidal behaviors and related emotional distress and for enhancing protective factors. PMID:11344882

  1. Land surface temperature as potential indicator of burn severity in forest Mediterranean ecosystems

    NASA Astrophysics Data System (ADS)

    Quintano, C.; Fernández-Manso, A.; Calvo, L.; Marcos, E.; Valbuena, L.

    2015-04-01

    Forest fires are one of the most important causes of environmental alteration in Mediterranean countries. Discrimination of different degrees of burn severity is critical for improving management of fire-affected areas. This paper aims to evaluate the usefulness of land surface temperature (LST) as potential indicator of burn severity. We used a large convention-dominated wildfire, which occurred on 19-21 September, 2012 in Northwestern Spain. From this area, a 1-year series of six LST images were generated from Landsat 7 Enhanced Thematic Mapper (ETM+) data using a single channel algorithm. Further, the Composite Burn Index (CBI) was measured in 111 field plots to identify the burn severity level (low, moderate, and high). Evaluation of the potential relationship between post-fire LST and ground measured CBI was performed by both correlation analysis and regression models. Correlation coefficients were higher in the immediate post-fire LST images, but decreased during the fall of 2012 and increased again with a second maximum value in summer, 2013. A linear regression model between post-fire LST and CBI allowed us to represent spatially predicted CBI (R-squaredadj > 85%). After performing an analysis of variance (ANOVA) between post-fire LST and CBI, a Fisher's least significant difference test determined that two burn severity levels (low-moderate and high) could be statistically distinguished. The identification of such burn severity levels is sufficient and useful to forest managers. We conclude that summer post-fire LST from moderate resolution satellite data may be considered as a valuable indicator of burn severity for large fires in Mediterranean forest ecosytems.

  2. A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

    PubMed

    Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

    2015-02-01

    The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. PMID:25399920

  3. Surveillance methods for identifying, characterizing, and monitoring tobacco products: potential reduced exposure products as an example

    PubMed Central

    O’Connor, Richard J.; Cummings, K. Michael; Rees, Vaughan W.; Connolly, Gregory N.; Norton, Kaila J.; Sweanor, David; Parascandola, Mark; Hatsukami, Dorothy K.; Shields, Peter G.

    2015-01-01

    Tobacco products are widely sold and marketed, yet integrated data systems for identifying, tracking, and characterizing products are lacking. Tobacco manufacturers recently have developed potential reduction exposure products (PREPs) with implied or explicit health claims. Currently, a systematic approach for identifying, defining, and evaluating PREPs sold at the local, state or national levels in the US has not been developed. Identifying, characterizing, and monitoring new tobacco products could be greatly enhanced with a responsive surveillance system. This paper critically reviews available surveillance data sources for identifying and tracking tobacco products, including PREPs, evaluating strengths and weaknesses of potential data sources in light of their reliability and validity. Absent regulations mandating disclosure of product-specific information, it is likely that public health officials will need to rely on a variety of imperfect data sources to help identify, characterize, and monitor tobacco products, including PREPs. PMID:19959680

  4. POTENTIAL USE OF ALGAE AS INDICATORS OF HYDROLOGIC PERMANENCE IN HEADWATER STREAMS: INITIAL DATA EXPLORATION

    EPA Science Inventory

    Periphyton from headwater intermittent streams was sampled in order to evaluate the potential use of algal assemblages as indicators of flow permanence. Streams from four forests near Cincinnati, Ohio were classified according to hydrologic permanence as ephemeral, intermittent ...

  5. The stingless bee species, Scaptotrigona aff. depilis, as a potential indicator of environmental pesticide contamination.

    PubMed

    de Souza Rosa, Annelise; I'Anson Price, Robbie; Ferreira Caliman, Maria Juliana; Pereira Queiroz, Elisa; Blochtein, Betina; Sílvia Soares Pires, Carmen; Imperatriz-Fonseca, Vera Lucia

    2015-08-01

    Neonicotinoids have the potential to enter the diet of pollinators that collect resources from contaminated plants. The species Scaptotrigona aff. depilis (Moure, 1942) can be a useful indicator of the prevalence of these chemicals in the environment. Using high-performance liquid chromatography-mass spectrometry, the authors devised a protocol for neonicotinoid residue extraction and detected the presence of neonicotinoids in the bee bodies. Thus, the authors consider this species to be a potential indicator of environmental contamination. PMID:26190578

  6. Release of genetically engineered insects: a framework to identify potential ecological effects

    PubMed Central

    David, Aaron S; Kaser, Joe M; Morey, Amy C; Roth, Alexander M; Andow, David A

    2013-01-01

    Genetically engineered (GE) insects have the potential to radically change pest management worldwide. With recent approvals of GE insect releases, there is a need for a synthesized framework to evaluate their potential ecological and evolutionary effects. The effects may occur in two phases: a transitory phase when the focal population changes in density, and a steady state phase when it reaches a new, constant density. We review potential effects of a rapid change in insect density related to population outbreaks, biological control, invasive species, and other GE organisms to identify a comprehensive list of potential ecological and evolutionary effects of GE insect releases. We apply this framework to the Anopheles gambiae mosquito – a malaria vector being engineered to suppress the wild mosquito population – to identify effects that may occur during the transitory and steady state phases after release. Our methodology reveals many potential effects in each phase, perhaps most notably those dealing with immunity in the transitory phase, and with pathogen and vector evolution in the steady state phase. Importantly, this framework identifies knowledge gaps in mosquito ecology. Identifying effects in the transitory and steady state phases allows more rigorous identification of the potential ecological effects of GE insect release. PMID:24198955

  7. Transcriptome Profiling of Peripheral Blood Cells Identifies Potential Biomarkers for Doxorubicin Cardiotoxicity in a Rat Model

    PubMed Central

    Todorova, Valentina K.; Beggs, Marjorie L.; Delongchamp, Robert R.; Dhakal, Ishwori; Makhoul, Issam; Wei, Jeanne Y.; Klimberg, V. Suzanne

    2012-01-01

    Aims Doxorubicin (DOX), a widely used anticancer agent, can cause an unpredictable cardiac toxicity which remains a major limitation in cancer chemotherapy. There is a need for noninvasive, sensitive and specific biomarkers which will allow identifying patients at risk for DOX-induced cardiotoxicity to prevent permanent cardiac damage. The aim of this study was to investigate whether the expression of specific genes in the peripheral blood can be used as surrogate marker(s) for DOX-induced cardiotoxicity. Methods/Results Rats were treated with a single dose of DOX similar to one single dose that is often administered in humans. The cardiac and peripheral blood mononuclear cells (PBMCs) genome-wide expression profiling were examined using Illumina microarrays. The results showed 4,409 differentially regulated genes (DRG) in the hearts and 4,120 DRG in PBMC. Of these 2411 genes were similarly DRG (SDRG) in both the heart and PBMC. Pathway analysis of the three datasets of DRG using Gene Ontology (GO) enrichment analysis and Ingenuity Pathways Analysis (IPA) showed that most of the genes in these datasets fell into pathways related to oxidative stress response and protein ubiquination. IPA search for potential eligible biomarkers for cardiovascular disease within the SDRG list revealed 188 molecules. Conclusions We report the first in-depth comparison of DOX-induced global gene expression profiles of hearts and PBMCs. The high similarity between the gene expression profiles of the heart and PBMC induced by DOX indicates that the PBMC transcriptome may serve as a surrogate marker of DOX-induced cardiotoxicity. Future directions of this research will include analysis of PBMC expression profiles of cancer patients treated with DOX-based chemotherapy to identify the cardiotoxicity risk, predict DOX-treatment response and ultimately to allow individualized anti-cancer therapy. PMID:23209553

  8. Enterococcus phages as potential tool for identifying sewage inputs in the Great Lakes region

    USGS Publications Warehouse

    K.Vijayavel; K.Vijayavel; Byappanahalli, Muruleedhara N.; J. Ebdon; J. Ebdon; H. Taylor; H. Taylor; Whitman, Richard L.; D.R. Kashian; D.R. Kashian

    2014-01-01

    Bacteriophages are viruses living in bacteria that can be used as a tool to detect fecal contamination in surface waters around the world. However, the lack of a universal host strain makes them unsuitable for tracking fecal sources. We evaluated the suitability of two newly isolated Enterococcus host strains (ENT-49 and ENT-55) capable for identifying sewage contamination in impacted waters by targeting phages specific to these hosts. Both host strains were isolated from wastewater samples and identified as E. faecium by 16S rRNA gene sequencing. Occurrence of Enterococcus phages was evaluated in sewage samples (n = 15) from five wastewater treatment plants and in fecal samples from twenty-two species of wild and domesticated animals (individual samples; n = 22). Levels of Enterococcus phages, F + coliphages, Escherichia coli and enterococci were examined from four rivers, four beaches, and three harbors. Enterococcus phages enumeration was at similar levels (Mean = 6.72 Log PFU/100 mL) to F + coliphages in all wastewater samples, but were absent from all non-human fecal sources tested. The phages infecting Enterococcus spp. and F + coliphages were not detected in the river samples (detection threshold < 10 PFU/100 mL), but were present in the beach and harbor samples (range = 1.83 to 2.86 Log PFU/100 mL). Slightly higher concentrations (range = 3.22 to 3.69 Log MPN/100 mL) of E. coli and enterococci when compared to F + coliphages and Enterococcus phages, were observed in the river, beach and harbor samples. Our findings suggest that the bacteriophages associated with these particular Enterococcus host strains offer potentially sensitive and human-source specific indicators of enteric pathogen risk.

  9. Multiplatform molecular profiling identifies potentially targetable biomarkers in malignant phyllodes tumors of the breast

    PubMed Central

    Gatalica, Zoran; Vranic, Semir; Ghazalpour, Anatole; Xiu, Joanne; Ocal, Idris Tolgay; McGill, John; Bender, Ryan P.; Discianno, Erin; Schlum, Aaron; Sanati, Souzan; Palazzo, Juan; Reddy, Sandeep; Pockaj, Barbara

    2016-01-01

    Malignant phyllodes tumor is a rare breast malignancy with sarcomatous overgrowth and with limited effective treatment options for recurrent and metastatic cases. Recent clinical trials indicated a potential for anti-angiogenic, anti-EGFR and immunotherapeutic approaches for patients with sarcomas, which led us to investigate these and other targetable pathways in malignant phyllodes tumor of the breast. Thirty-six malignant phyllodes tumors (including 8 metastatic tumors with two cases having matched primary and metastatic tumors) were profiled using gene sequencing, gene copy number analysis, whole genome expression, and protein expression. Whole genome expression analysis demonstrated consistent over-expression of genes involved in angiogenesis including VEGFA, Angiopoietin-2, VCAM1, PDGFRA, and PTTG1. EGFR protein overexpression was observed in 26/27 (96%) of cases with amplification of the EGFR gene in 8/24 (33%) cases. Two EGFR mutations were identified including EGFRvIII and a presumed pathogenic V774M mutation, respectively. The most common pathogenic mutations included TP53 (50%) and PIK3CA (15%). Cases with matched primary and metastatic tumors harbored identical mutations in both sites (PIK3CA/KRAS and RB1 gene mutations, respectively). Tumor expression of PD-L1 immunoregulatory protein was observed in 3/22 (14%) of cases. Overexpression of molecular biomarkers of increased angiogenesis, EGFR and immune checkpoints provides novel targeted therapy options in malignant phyllodes tumors of the breast. PMID:26625196

  10. Analytical approaches to identify potential migrants in polyester-polyurethane can coatings.

    PubMed

    Louise Bradley, Emma; Driffield, Malcolm; Guthrie, James; Harmer, Nick; Thomas Oldring, Peter Kenneth; Castle, Laurence

    2009-12-01

    The safety of a polyester-polyurethane can coating has been assessed using a suite of complementary analytical methods to identify and estimate the concentrations of potential chemical migrants. The polyester was based on phthalic acids and aliphatic diols. The polyisocyanate cross-linking agent was 1-isocyanato-3-isocyanatomethyl-3,5,5-trimethyl cyclohexane homopolymer (IPDI) blocked with methylethylketone oxime (MEKO) to make a one-part formulation. The overall migrate, obtained using solvent extraction of cured films, comprised almost completely of 12 cyclic and one linear polyester oligomer up to molecular weight 800 and containing up to six monomer units. These 13 oligomers covered a total of 28 isomeric forms. Other minor components detected were plasticisers and surfactants as well as impurities present in the starting materials. There was no detectable residue of either the blocked isocyanate (<0.01 microg/dm(2)) used as the starting substance or the unblocked isocyanate (<0.02 microg/dm(2)). The level of extractable IPDI was used as an indicator of the completeness of cure in experimental coatings. These studies revealed that there was an influence of time, temperature and catalyst content. Polymerisation was also influenced by the additives used and by the ageing of the wet coating formulation over several months. These studies allow parameters to be specified to ensure that commercial production coatings receive a full cure giving low migration characteristics. PMID:19787516

  11. Multiplatform molecular profiling identifies potentially targetable biomarkers in malignant phyllodes tumors of the breast.

    PubMed

    Gatalica, Zoran; Vranic, Semir; Ghazalpour, Anatole; Xiu, Joanne; Ocal, Idris Tolgay; McGill, John; Bender, Ryan P; Discianno, Erin; Schlum, Aaron; Sanati, Souzan; Palazzo, Juan; Reddy, Sandeep; Pockaj, Barbara

    2016-01-12

    Malignant phyllodes tumor is a rare breast malignancy with sarcomatous overgrowth and with limited effective treatment options for recurrent and metastatic cases. Recent clinical trials indicated a potential for anti-angiogenic, anti-EGFR and immunotherapeutic approaches for patients with sarcomas, which led us to investigate these and other targetable pathways in malignant phyllodes tumor of the breast. Thirty-six malignant phyllodes tumors (including 8 metastatic tumors with two cases having matched primary and metastatic tumors) were profiled using gene sequencing, gene copy number analysis, whole genome expression, and protein expression. Whole genome expression analysis demonstrated consistent over-expression of genes involved in angiogenesis including VEGFA, Angiopoietin-2, VCAM1, PDGFRA, and PTTG1. EGFR protein overexpression was observed in 26/27 (96%) of cases with amplification of the EGFR gene in 8/24 (33%) cases. Two EGFR mutations were identified including EGFRvIII and a presumed pathogenic V774M mutation, respectively. The most common pathogenic mutations included TP53 (50%) and PIK3CA (15%). Cases with matched primary and metastatic tumors harbored identical mutations in both sites (PIK3CA/KRAS and RB1 gene mutations, respectively). Tumor expression of PD-L1 immunoregulatory protein was observed in 3/22 (14%) of cases. Overexpression of molecular biomarkers of increased angiogenesis, EGFR and immune checkpoints provides novel targeted therapy options in malignant phyllodes tumors of the breast. PMID:26625196

  12. Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon “Candidatus Nitrosotalea devanaterra”

    PubMed Central

    Sayavedra-Soto, Luis A.; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y.; Prosser, James I.; Nicol, Graeme W.

    2016-01-01

    Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer “Candidatus Nitrosotalea devanaterra” provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of “Ca. Nitrosotalea devanaterra” reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that “Ca. Nitrosotalea devanaterra” contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography–mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of “Ca. Nitrosotalea devanaterra” were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. PMID:26896134

  13. Identifying Potential Mechanisms Enabling Acidophily in the Ammonia-Oxidizing Archaeon "Candidatus Nitrosotalea devanaterra".

    PubMed

    Lehtovirta-Morley, Laura E; Sayavedra-Soto, Luis A; Gallois, Nicolas; Schouten, Stefan; Stein, Lisa Y; Prosser, James I; Nicol, Graeme W

    2016-05-01

    Ammonia oxidation is the first and rate-limiting step in nitrification and is dominated by two distinct groups of microorganisms in soil: ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). AOA are often more abundant than AOB and dominate activity in acid soils. The mechanism of ammonia oxidation under acidic conditions has been a long-standing paradox. While high rates of ammonia oxidation are frequently measured in acid soils, cultivated ammonia oxidizers grew only at near-neutral pH when grown in standard laboratory culture. Although a number of mechanisms have been demonstrated to enable neutrophilic AOB growth at low pH in the laboratory, these have not been demonstrated in soil, and the recent cultivation of the obligately acidophilic ammonia oxidizer "CandidatusNitrosotalea devanaterra" provides a more parsimonious explanation for the observed high rates of activity. Analysis of the sequenced genome, transcriptional activity, and lipid content of "Ca Nitrosotalea devanaterra" reveals that previously proposed mechanisms used by AOB for growth at low pH are not essential for archaeal ammonia oxidation in acidic environments. Instead, the genome indicates that "Ca Nitrosotalea devanaterra" contains genes encoding both a predicted high-affinity substrate acquisition system and potential pH homeostasis mechanisms absent in neutrophilic AOA. Analysis of mRNA revealed that candidate genes encoding the proposed homeostasis mechanisms were all expressed during acidophilic growth, and lipid profiling by high-performance liquid chromatography-mass spectrometry (HPLC-MS) demonstrated that the membrane lipids of "Ca Nitrosotalea devanaterra" were not dominated by crenarchaeol, as found in neutrophilic AOA. This study for the first time describes a genome of an obligately acidophilic ammonia oxidizer and identifies potential mechanisms enabling this unique phenotype for future biochemical characterization. PMID:26896134

  14. Potential Biomarkers of Fatigue Identified by Plasma Metabolome Analysis in Rats

    PubMed Central

    Kume, Satoshi; Yamato, Masanori; Tamura, Yasuhisa; Jin, Guanghua; Nakano, Masayuki; Miyashige, Yukiharu; Eguchi, Asami; Ogata, Yoshiyuki; Goda, Nobuhito; Iwai, Kazuhiro; Yamano, Emi; Watanabe, Yasuyoshi; Soga, Tomoyoshi; Kataoka, Yosky

    2015-01-01

    In the present study, prior to the establishment of a method for the clinical diagnosis of chronic fatigue in humans, we validated the utility of plasma metabolomic analysis in a rat model of fatigue using capillary electrophoresis-mass spectrometry (CE-MS). In order to obtain a fatigued animal group, rats were placed in a cage filled with water to a height of 2.2 cm for 5 days. A food-restricted group, in which rats were limited to 10 g/d of food (around 50% of the control group), was also assessed. The food-restricted group exhibited weight reduction similar to that of the fatigued group. CE-MS measurements were performed to evaluate the profile of food intake-dependent metabolic changes, as well as the profile in fatigue loading, resulting in the identification of 48 metabolites in plasma. Multivariate analyses using hierarchical clustering and principal component analysis revealed that the plasma metabolome in the fatigued group showed clear differences from those in the control and food-restricted groups. In the fatigued group, we found distinctive changes in metabolites related to branched-chain amino acid metabolism, urea cycle, and proline metabolism. Specifically, the fatigued group exhibited significant increases in valine, leucine, isoleucine, and 2-oxoisopentanoate, and significant decreases in citrulline and hydroxyproline compared with the control and food-restricted groups. Plasma levels of total nitric oxide were increased in the fatigued group, indicating systemic oxidative stress. Further, plasma metabolites involved in the citrate cycle, such as cis-aconitate and isocitrate, were reduced in the fatigued group. The levels of ATP were significantly decreased in the liver and skeletal muscle, indicative of a deterioration in energy metabolism in these organs. Thus, this comprehensive metabolic analysis furthered our understanding of the pathophysiology of fatigue, and identified potential diagnostic biomarkers based on fatigue pathophysiology. PMID:25793974

  15. Morbidity and Risk of Subsequent Diagnosis of HIV: A Population Based Case Control Study Identifying Indicator Diseases for HIV Infection

    PubMed Central

    Søgaard, Ole S.; Lohse, Nicolai; Østergaard, Lars; Kronborg, Gitte; Røge, Birgit; Gerstoft, Jan; Sørensen, Henrik T.; Obel, Niels

    2012-01-01

    Background Early identification of persons with undiagnosed HIV infection is an important health care issue. We examined associations between diseases diagnosed in hospitals and risk of subsequent HIV diagnosis. Methods In this population-based case control study, cases were persons with incident HIV infection diagnosed in Denmark between 1 January 1995 and 1 June 2008. Risk-set sampling was used to identify 19 age- and gender-matched population controls for each HIV case, using the HIV diagnosis date as the index date for both cases and controls. Prior hospital diagnoses obtained from Danish medical databases were first categorized into 22 major disease categories (excluding AIDS-defining diseases except tuberculosis) and then subdivided into 161 subcategories, allowing us to examine specific diseases as potential HIV indicators by conditional logistic regression. Results The study included 2,036 HIV cases and 35,718 controls. Persons with the following disease categories had a high risk of HIV diagnosis during the subsequent 5-year period: sexually transmitted infections and viral hepatitis (adjusted odds ratio [aOR] = 12.3, 95% CI: 9.60–15.7), hematological diseases (aOR = 4.28, 3.13–5.85), lower respiratory tract infections (aOR = 3.98, 3.14–5.04)), CNS infections (aOR = 3.44, 1.74–6.80), skin infections (aOR = 3.05, 2.47–3.75), other infections (aOR = 4.64, 3.89–5.54), and substance abuse (aOR = 2.60, 2.06–3.29). Several specific diseases were associated with aORs >20 including syphilis, hepatitis A, non “A” viral hepatitis, herpes zoster, candida infection, endocarditis, thrombocytopenia, and opioid abuse. Conclusions Targeted testing for HIV in patients diagnosed with diseases associated with HIV may lead to earlier treatment and thereby reduced morbidity, mortality and HIV transmission. PMID:22403672

  16. Robust global identifiability theory using potentials--Application to compartmental models.

    PubMed

    Wongvanich, N; Hann, C E; Sirisena, H R

    2015-04-01

    This paper presents a global practical identifiability theory for analyzing and identifying linear and nonlinear compartmental models. The compartmental system is prolonged onto the potential jet space to formulate a set of input-output equations that are integrals in terms of the measured data, which allows for robust identification of parameters without requiring any simulation of the model differential equations. Two classes of linear and non-linear compartmental models are considered. The theory is first applied to analyze the linear nitrous oxide (N2O) uptake model. The fitting accuracy of the identified models from differential jet space and potential jet space identifiability theories is compared with a realistic noise level of 3% which is derived from sensor noise data in the literature. The potential jet space approach gave a match that was well within the coefficient of variation. The differential jet space formulation was unstable and not suitable for parameter identification. The proposed theory is then applied to a nonlinear immunological model for mastitis in cows. In addition, the model formulation is extended to include an iterative method which allows initial conditions to be accurately identified. With up to 10% noise, the potential jet space theory predicts the normalized population concentration infected with pathogens, to within 9% of the true curve. PMID:25660327

  17. Water Mites (Acari: Hydrachnida) of Ozark Streams - Abundance, Species Richness, and Potential as Environmental Indicators

    NASA Astrophysics Data System (ADS)

    Radwell, A. J.; Brown, A. V.

    2005-05-01

    Because water mites are tightly linked to other stream metazoans through parasitism and predation, they are potentially effective indicators of environmental quality. Meiofauna (80 μm to 1 mm) were sampled from headwater riffles of 11 Ozark streams to determine relative abundance and densities of major meiofauna taxa. Water mites comprised 15.3% of the organisms collected exceeded only by chironomids (50.2%) and oligochaetes (17.8%), and mean water mite density among the 11 streams was 265 organisms per liter. The two streams that differed the most in environmental quality were sampled using techniques suitable for identification of species. An estimated 32 species from 20 genera and 13 families were found in the least disturbed stream; an estimated 19 species from 13 genera and 8 families were found in the most disturbed stream. This preliminary finding supports the notion that water mite species richness declines in response to environmental disturbance. Many species could only be identified as morphospecies of particular genera, but the ongoing taxonomic revision of Hydrachnida is expected to provide needed information. A collaborative effort between those interested in taxonomy/systematics of water mites and ecologists interested in the significance of water mites in aquatic communities could prove mutually beneficial.

  18. Bivalves as indicators of environmental variation and potential anthropogenic impacts in the southern Barents Sea.

    PubMed

    Carroll, Michael L; Johnson, Beverly J; Henkes, Gregory A; McMahon, Kelton W; Voronkov, Andrey; Ambrose, William G; Denisenko, Stanislav G

    2009-01-01

    Identifying patterns and drivers of natural variability in populations is necessary to gauge potential effects of climatic change and the expected increases in commercial activities in the Arctic on communities and ecosystems. We analyzed growth rates and shell geochemistry of the circumpolar Greenland smooth cockle, Serripes groenlandicus, from the southern Barents Sea over almost 70 years between 1882 and 1968. The datasets were calibrated via annually-deposited growth lines, and growth, stable isotope (delta(18)O, delta(13)C), and trace elemental (Mg, Sr, Ba, Mn) patterns were linked to environmental variations on weekly to decadal scales. Standardized growth indices revealed an oscillatory growth pattern with a multi-year periodicity, which was inversely related to the North Atlantic Oscillation Index (NAO), and positively related to local river discharge. Up to 60% of the annual variability in Ba/Ca could be explained by variations in river discharge at the site closest to the rivers, but the relationship disappeared at a more distant location. Patterns of delta(18)O, delta(13)C, and Sr/Ca together provide evidence that bivalve growth ceases at elevated temperatures during the fall and recommences at the coldest temperatures in the early spring, with the implication that food, rather than temperature, is the primary driver of bivalve growth. The multi-proxy approach of combining the annually integrated information from the growth results and higher resolution geochemical results yielded a robust interpretation of biophysical coupling in the region over temporal and spatial scales. We thus demonstrate that sclerochronological proxies can be useful retrospective analytical tools for establishing a baseline of ecosystem variability in assessing potential combined impacts of climatic change and increasing commercial activities on Arctic communities. PMID:19394657

  19. Bivalves as indicators of environmental variation and potential anthropogenic impacts in the southern Barents Sea

    PubMed Central

    Carroll, Michael L.; Johnson, Beverly J.; Henkes, Gregory A.; McMahon, Kelton W.; Voronkov, Andrey; Ambrose, William G.; Denisenko, Stanislav G.

    2009-01-01

    Identifying patterns and drivers of natural variability in populations is necessary to gauge potential effects of climatic change and the expected increases in commercial activities in the Arctic on communities and ecosystems. We analyzed growth rates and shell geochemistry of the circumpolar Greenland smooth cockle, Serripes groenlandicus, from the southern Barents Sea over almost 70 years between 1882 and 1968. The datasets were calibrated via annually-deposited growth lines, and growth, stable isotope (δ18O, δ13C), and trace elemental (Mg, Sr, Ba, Mn) patterns were linked to environmental variations on weekly to decadal scales. Standardized growth indices revealed an oscillatory growth pattern with a multi-year periodicity, which was inversely related to the North Atlantic Oscillation Index (NAO), and positively related to local river discharge. Up to 60% of the annual variability in the Ba/Ca could be explained by variations in river discharge at the site closest to the rivers, but the relationship disappeared at a more distant location. Patterns of δ18O, δ13C, and Sr/Ca together provide evidence that bivalve growth ceases at elevated temperatures during the fall and recommences at the coldest temperatures in the early spring, with the implication that food, rather than temperature, is the primary driver of bivalve growth. The multi-proxy approach of combining the annually integrated information from the growth results and higher resolution geochemical results yielded a robust interpretation of biophysical coupling in the region over temporal and spatial scales. We thus demonstrate that sclerochronological proxies can be useful retrospective analytical tools for establishing a baseline of ecosystem variability in assessing potential combined impacts of climatic change and increasing commercial activities on Arctic communities. PMID:19394657

  20. Development of evidence-based Australian medication-related indicators of potentially preventable hospitalisations: a modified RAND appropriateness method

    PubMed Central

    Caughey, Gillian E; Kalisch Ellett, Lisa M; Wong, Te Ying

    2014-01-01

    Objective Indicators of potentially preventable hospitalisations have been adopted internationally as a measure of health system performance; however, few assess appropriate processes of care around medication use, that if followed may prevent hospitalisation. The aim of this study was to develop and validate evidence-based medication-related indicators of potentially preventable hospitalisations. Setting Australian primary healthcare. Participants Medical specialists, general practitioners and pharmacists. A modified RAND appropriateness method was used for the development of medication-related indicators of potentially preventable hospitalisations, which included a literature review, assessment of the strength of the supporting evidence base, an initial face and content validity by an expert panel, followed by an independent assessment of indicators by an expert clinical panel across various disciplines, using an online survey. Primary outcome measure Analysis of ratings was performed on the four key elements of preventability; the medication-related problem must be recognisable, the adverse outcomes foreseeable and the causes and outcomes identifiable and controllable. Results A total of 48 potential indicators across all major disease groupings were developed based on level III evidence or greater, that were independently assessed by 78 expert clinicians (22.1% response rate). The expert panel considered 29 of these (60.4%) sufficiently valid. Of these, 21 (72.4%) were based on level I evidence. Conclusions This study provides a set of face and content validated indicators of medication-related potentially preventable hospitalisations, linking suboptimal processes of care and medication use with subsequent hospitalisation. Further analysis is required to establish operational validity in a population-based sample, using an administrative health database. Implementation of these indicators within routine monitoring of healthcare systems will highlight those conditions where hospitalisations could potentially be avoided through improved medication management. PMID:24776711

  1. Leadership Succession in New South Wales Catholic Schools: Identifying Potential Principals.

    ERIC Educational Resources Information Center

    Dorman, Jeffrey P.; D'Arbon, Tony

    2003-01-01

    Reports on research conducted on leadership succession in New South Wales Catholic schools in order to identify potential principals using data collected from middle and senior management staff (n=943). Explains that short-term targeting of this population may be helpful, but impediments to leadership succession need to be addressed. (CMK)

  2. A spatial modeling approach to identify potential butternut restoration sites in Mammoth Cave National Park

    USGS Publications Warehouse

    Thompson, L.M.; Van Manen, F.T.; Schlarbaum, S.E.; DePoy, M.

    2006-01-01

    Incorporation of disease resistance is nearly complete for several important North American hardwood species threatened by exotic fungal diseases. The next important step toward species restoration would be to develop reliable tools to delineate ideal restoration sites on a landscape scale. We integrated spatial modeling and remote sensing techniques to delineate potential restoration sites for Butternut (Juglans cinerea L.) trees, a hardwood species being decimated by an exotic fungus, in Mammoth Cave National Park (MCNP), Kentucky. We first developed a multivariate habitat model to determine optimum Butternut habitats within MCNP. Habitat characteristics of 54 known Butternut locations were used in combination with eight topographic and land use data layers to calculate an index of habitat suitability based on Mahalanobis distance (D2). We used a bootstrapping technique to test the reliability of model predictions. Based on a threshold value for the D2 statistic, 75.9% of the Butternut locations were correctly classified, indicating that the habitat model performed well. Because Butternut seedlings require extensive amounts of sunlight to become established, we used canopy cover data to refine our delineation of favorable areas for Butternut restoration. Areas with the most favorable conditions to establish Butternut seedlings were limited to 291.6 ha. Our study provides a useful reference on the amount and location of favorable Butternut habitat in MCNP and can be used to identify priority areas for future Butternut restoration. Given the availability of relevant habitat layers and accurate location records, our approach can be applied to other tree species and areas. ?? 2006 Society for Ecological Restoration International.

  3. Evaluating potential indicators of ecosystem processes across local gradients in a temperate grassland

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Science-based information is needed to identify indicators of ecosystem services that may then be used to monitor natural resources and quantify effects of management. Here our aim was to perform a local gradient study to elucidate correlative associations between vegetation and multiple soil prope...

  4. Anthropometric indices to identify metabolic syndrome and hypertriglyceridemic waist phenotype: a comparison between the three stages of adolescence

    PubMed Central

    Pereira, Patrícia Feliciano; de Faria, Franciane Rocha; de Faria, Eliane Rodrigues; Hermsdorff, Helen Hermana Miranda; Peluzio, Maria do Carmo Gouveia; Franceschini, Sylvia do Carmo Castro; Priore, Silvia Eloiza

    2015-01-01

    OBJECTIVE: To determine the prevalence of metabolic syndrome (MS) and the hypertriglyceridemic waist phenotype (HW) in a representative adolescent sample; as well as to establish which anthropometric indicator better identifies MS and HW, according to gender and adolescent age. METHODS: This cross sectional study had the participation of 800 adolescents (414 girls) from 10-19 years old. Anthropometric indicators (body mass index, waist perimeter, waist/stature ratio, waist/hip ratio, and central/peripheral skinfolds) were determined by standard protocols. For diagnosis of MS, the criteria proposed by de Ferranti et al. (2004) were used. HW was defined by the simultaneous presence of increased waist perimeter (>75th percentile for age and sex) and high triglycerides (>100 mg/dL). The ability of anthropometric indicators was evaluated by Receiver Operating Characteristic curve. RESULTS: The prevalence of MS was identical to HW (6.4%), without differences between genders and the adolescence phases. The waist perimeter showed higher area under the curve for the diagnosis of MS, except for boys with 17-19 years old, for whom the waist/stature ratio exhibited better performance. For diagnosing HW, waist perimeter also showed higher area under the curve, except for boys in initial and final phases, in which the waist/stature ratio obtained larger area under the curve. The central/peripheral skinfolds had the lowest area under the curve for the presence of both MS and HW phenotype. CONCLUSIONS: The waist perimeter and the waist/stature showed a better performance to identify MS and HW in both genders and in all three phases of adolescence. PMID:25913494

  5. Riverine threat indices to assess watershed condition and identify primary management capacity of agriculture natural resource management agencies.

    PubMed

    Fore, Jeffrey D; Sowa, Scott P; Galat, David L; Annis, Gust M; Diamond, David D; Rewa, Charles

    2014-03-01

    Managers can improve conservation of lotic systems over large geographies if they have tools to assess total watershed conditions for individual stream segments and can identify segments where conservation practices are most likely to be successful (i.e., primary management capacity). The goal of this research was to develop a suite of threat indices to help agriculture resource management agencies select and prioritize watersheds across Missouri River basin in which to implement agriculture conservation practices. We quantified watershed percentages or densities of 17 threat metrics that represent major sources of ecological stress to stream communities into five threat indices: agriculture, urban, point-source pollution, infrastructure, and all non-agriculture threats. We identified stream segments where agriculture management agencies had primary management capacity. Agriculture watershed condition differed by ecoregion and considerable local variation was observed among stream segments in ecoregions of high agriculture threats. Stream segments with high non-agriculture threats were most concentrated near urban areas, but showed high local variability. 60 % of stream segments in the basin were classified as under U.S. Department of Agriculture's Natural Resources Conservation Service (NRCS) primary management capacity and most segments were in regions of high agricultural threats. NRCS primary management capacity was locally variable which highlights the importance of assessing total watershed condition for multiple threats. Our threat indices can be used by agriculture resource management agencies to prioritize conservation actions and investments based on: (a) relative severity of all threats, (b) relative severity of agricultural threats, and (c) and degree of primary management capacity. PMID:24390081

  6. Riverine Threat Indices to Assess Watershed Condition and Identify Primary Management Capacity of Agriculture Natural Resource Management Agencies

    NASA Astrophysics Data System (ADS)

    Fore, Jeffrey D.; Sowa, Scott P.; Galat, David L.; Annis, Gust M.; Diamond, David D.; Rewa, Charles

    2014-03-01

    Managers can improve conservation of lotic systems over large geographies if they have tools to assess total watershed conditions for individual stream segments and can identify segments where conservation practices are most likely to be successful (i.e., primary management capacity). The goal of this research was to develop a suite of threat indices to help agriculture resource management agencies select and prioritize watersheds across Missouri River basin in which to implement agriculture conservation practices. We quantified watershed percentages or densities of 17 threat metrics that represent major sources of ecological stress to stream communities into five threat indices: agriculture, urban, point-source pollution, infrastructure, and all non-agriculture threats. We identified stream segments where agriculture management agencies had primary management capacity. Agriculture watershed condition differed by ecoregion and considerable local variation was observed among stream segments in ecoregions of high agriculture threats. Stream segments with high non-agriculture threats were most concentrated near urban areas, but showed high local variability. 60 % of stream segments in the basin were classified as under U.S. Department of Agriculture's Natural Resources Conservation Service (NRCS) primary management capacity and most segments were in regions of high agricultural threats. NRCS primary management capacity was locally variable which highlights the importance of assessing total watershed condition for multiple threats. Our threat indices can be used by agriculture resource management agencies to prioritize conservation actions and investments based on: (a) relative severity of all threats, (b) relative severity of agricultural threats, and (c) and degree of primary management capacity.

  7. Event-related potential indices of congruency sequence effects without feature integration or contingency learning confounds.

    PubMed

    Larson, Michael J; Clayson, Peter E; Kirwan, C Brock; Weissman, Daniel H

    2016-06-01

    The congruency effect in Stroop-like tasks (i.e., increased response time and reduced accuracy in incongruent relative to congruent trials) is often smaller when the previous trial was incongruent as compared to congruent. This congruency sequence effect (CSE) is thought to reflect cognitive control processes that shift attention to the target and/or modulate the response engendered by the distracter differently after incongruent relative to congruent trials. The neural signatures of CSEs are therefore usually attributed to cognitive control processes that minimize distraction from irrelevant stimuli. However, CSEs in previous functional neuroimaging studies were ubiquitously confounded with feature integration and/or contingency learning processes. We therefore investigated whether a neural CSE can be observed without such confounds in a group of healthy young adults (n = 56). To this end, we combined a prime-probe task that lacks such confounds with high-density ERPs to identify, for the first time, the neural time course of confound-minimized CSEs. Replicating recent behavioral findings, we observed strong CSEs in this task for mean response time and mean accuracy. Critically, conceptually replicating prior ERP results from confounded tasks, we also observed a CSE in both the parietal conflict slow potential (conflict SP) and the frontomedial N450. These findings indicate for the first time that neural CSEs as indexed by ERPs can be observed without the typical confounds. More broadly, the present study provides a confound-minimized protocol that will help future researchers to better isolate the neural bases of control processes that minimize distraction from irrelevant stimuli. PMID:26854028

  8. Potentially mineralizable nitrogen as a soil health indicator in a Long-Term Agroecosystem Research site

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Potentially mineralizable nitrogen (PMN) has demonstrated utility as a valuable soil health indicator. However, the relationship between the total PMN pool and nitrogen mineralization rates has not been well described. A better understanding of PMN dynamics in agroecosystems is essential for optimiz...

  9. Scientific Research in the Kingdom of Saudi Arabia: Potential for Excellence and Indicators of Underdevelopment

    ERIC Educational Resources Information Center

    Alshayea, Ali

    2013-01-01

    This study analyzes the status of scientific research and development efforts in the Kingdom of Saudi Arabia, and then sheds lights on the potential for excellence in this area in terms of organization and structure, financing and partnership, and human resources. Accordingly, the study reviews both achievements and indicators of underdevelopment…

  10. Mitochondrial NAD(P)H In vivo: Identifying Natural Indicators of Oxidative Phosphorylation in the 31P Magnetic Resonance Spectrum

    PubMed Central

    Conley, Kevin E.; Ali, Amir S.; Flores, Brandon; Jubrias, Sharon A.; Shankland, Eric G.

    2016-01-01

    Natural indicators provide intrinsic probes of metabolism, biogenesis and oxidative protection. Nicotinamide adenine dinucleotide metabolites (NAD(P)) are one class of indicators that have roles as co-factors in oxidative phosphorylation, glycolysis, and anti-oxidant protection, as well as signaling in the mitochondrial biogenesis pathway. These many roles are made possible by the distinct redox states (NAD(P)+ and NAD(P)H), which are compartmentalized between cytosol and mitochondria. Here we provide evidence for detection of NAD(P)+ and NAD(P)H in separate mitochondrial and cytosol pools in vivo in human tissue by phosphorus magnetic resonance spectroscopy (31P MRS). These NAD(P) pools are identified by chemical standards (NAD+, NADP+, and NADH) and by physiological tests. A unique resonance reflecting mitochondrial NAD(P)H is revealed by the changes elicited by elevation of mitochondrial oxidation. The decline of NAD(P)H with oxidation is matched by a stoichiometric rise in the NAD(P)+ peak. This unique resonance also provides a measure of the improvement in mitochondrial oxidation that parallels the greater phosphorylation found after exercise training in these elderly subjects. The implication is that the dynamics of the mitochondrial NAD(P)H peak provides an intrinsic probe of the reversal of mitochondrial dysfunction in elderly muscle. Thus, non-invasive detection of NAD(P)+ and NAD(P)H in cytosol vs. mitochondria yields natural indicators of redox compartmentalization and sensitive intrinsic probes of the improvement of mitochondrial function with an intervention in human tissues in vivo. These natural indicators hold the promise of providing mechanistic insight into metabolism and mitochondrial function in vivo in a range of tissues in health, disease and with treatment. PMID:27065875

  11. Structured methods for identifying and correcting potential human errors in aviation operations

    SciTech Connect

    Nelson, W.R.

    1997-10-01

    Human errors have been identified as the source of approximately 60% of the incidents and accidents that occur in commercial aviation. It can be assumed that a very large number of human errors occur in aviation operations, even though in most cases the redundancies and diversities built into the design of aircraft systems prevent the errors from leading to serious consequences. In addition, when it is acknowledged that many system failures have their roots in human errors that occur in the design phase, it becomes apparent that the identification and elimination of potential human errors could significantly decrease the risks of aviation operations. This will become even more critical during the design of advanced automation-based aircraft systems as well as next-generation systems for air traffic management. Structured methods to identify and correct potential human errors in aviation operations have been developed and are currently undergoing testing at the Idaho National Engineering and Environmental Laboratory (INEEL).

  12. Automated system for identifying potential dosage problems at a large university hospital.

    PubMed

    McMullin, S T; Reichley, R M; Kahn, M G; Dunagan, W C; Bailey, T C

    1997-03-01

    A hospital's experience with an automated system for screening drug orders for potential dosage problems is described. DoseChecker was developed by the hospital pharmacy department in collaboration with a local university. Pharmacy, laboratory, and patient demographic data are transferred nightly from the hospital's mainframe system to a database server; DoseChecker uses these data and user-defined rules to (1) identify patients receiving any of 35 targeted medications, (2) evaluate the appropriateness of current dosages, and (3) generate alerts for patients potentially needing dosage adjustments. The alert reports are distributed to satellite pharmacists, who evaluate each patient's condition and make recommendations to physicians as needed. One of the system's primary purposes is to calculate creatinine clearance and verify that dosages are properly adjusted for renal function. Between May and October 1995, the system electronically screened 28,528 drug orders and detected potential dosage problems in 2859 (10%). The system recommended a lower daily dose in 1992 cases (70%) and a higher daily dose in 867 (30%). Pharmacists contacted physicians concerning 1163 (41%) of the 2859 alerts; in 868 cases (75%), the physicians agreed to adjust the dosage. The most common dosage problem identified was failure to adjust dosages on the basis of declining renal function. An automated system provided an efficient method of identifying inappropriate dosages at a large university hospital. PMID:9066863

  13. Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis

    NASA Technical Reports Server (NTRS)

    Singer, M. S.; Oliveira, L.; Vriend, G.; Shepherd, G. M.

    1995-01-01

    A family of G-protein-coupled receptors is believed to mediate the recognition of odor molecules. In order to identify potential ligand-binding residues, we have applied correlated mutation analysis to receptor sequences from the rat. This method identifies pairs of sequence positions where residues remain conserved or mutate in tandem, thereby suggesting structural or functional importance. The analysis supported molecular modeling studies in suggesting several residues in positions that were consistent with ligand-binding function. Two of these positions, dominated by histidine residues, may play important roles in ligand binding and could confer broad specificity to mammalian odor receptors. The presence of positive (overdominant) selection at some of the identified positions provides additional evidence for roles in ligand binding. Higher-order groups of correlated residues were also observed. Each group may interact with an individual ligand determinant, and combinations of these groups may provide a multi-dimensional mechanism for receptor diversity.

  14. Body Mass Index Is Better than Other Anthropometric Indices for Identifying Dyslipidemia in Chinese Children with Obesity

    PubMed Central

    Jing, Jin; Ma, Jun; Chen, Yajun; Li, Xiuhong; Yang, Wenhan; Guo, Li; Jin, Yu

    2016-01-01

    Background Body mass index (BMI), waist circumference (WC), and waist-to-hip ratio (WHR) are used in screening and predicting obesity in adults. However, the best identifier of metabolic complications in children with obesity remains unclear. This study evaluated lipid profile distribution and investigated the best anthropometric parameter in association with lipid disorders in children with obesity. Methods A total of 2243 school children aged 7–17 years were enrolled in Guangzhou, China, in 2014. The anthropometric indices and lipid profiles were measured. Dyslipidemia was defined according to the US Guidelines for Cardiovascular Health and Risk Reduction in Children and Adolescents. The association between anthropometry (BMI, WC, and WHR) and lipid profile values was examined using chi-square analysis and discriminant function analysis. Information about demography, physical activity, and dietary intake was provided by the participant children and their parents. Results Children aged 10–14 and 15–17 years old generally had higher triglyceride values but lower median concentration of total cholesterol, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol compared with children aged 7–9 years old (all P < 0.001). These lipid parameters fluctuated in children aged 10–14 years old. The combination of age groups, BMI, WC and WHR achieved 65.1% accuracy in determining dyslipidemic disorders. BMI correctly identified 77% of the total dyslipidemic disorders in obese children, which was higher than that by WHR (70.8%) (P< 0.05). Conclusion The distribution of lipid profiles in Chinese children differed between younger and older age groups, and the tendency of these lipid levels remarkably fluctuated during 10 to 14 years old. BMI had better practical utility in identifying dyslipidemia among school-aged children with obesity compared with other anthropometric measures. PMID:26963377

  15. Manual and automated methods for identifying potentially preventable readmissions: a comparison in a large healthcare system

    PubMed Central

    2014-01-01

    Background Identification of potentially preventable readmissions is typically accomplished through manual review or automated classification. Little is known about the concordance of these methods. Methods We manually reviewed 459 30-day, all-cause readmissions at 18 Kaiser Permanente Northern California hospitals, determining potential preventability through a four-step manual review process that included a chart review tool, interviews with patients, their families, and treating providers, and nurse reviewer and physician evaluation of findings and determination of preventability on a five-point scale. We reassessed the same readmissions with 3 M’s Potentially Preventable Readmission (PPR) software. We examined between-method agreement and the specificity and sensitivity of the PPR software using manual review as the reference. Results Automated classification and manual review respectively identified 78% (358) and 47% (227) of readmissions as potentially preventable. Overall, the methods agreed about the preventability of 56% (258) of readmissions. Using manual review as the reference, the sensitivity of PPR was 85% and specificity was 28%. Conclusions Concordance between methods was not high enough to replace manual review with automated classification as the primary method of identifying preventable 30-day, all-cause readmission for quality improvement purposes. PMID:24708889

  16. Strengths and weaknesses of sea ice as a potential early indicator of climate change

    SciTech Connect

    Parkinson, C.L.

    1992-03-01

    Sea ice is examined for its potential as an early indicator of climate change by considering how well it satisfies four criteria listed as desired characteristics for potential early indicators. Results of numerical modeling studies in the 1970s and 1980s suggested that sea ice satisfies the first characteristic, that the variable be expected to exhibit a large climate signal, very well; but these results have recently been updated in a way that decreases the success of sea ice in satisfying this particular property. Sea ice satisfies the second characteristic, that it be routinely measurable on a global basis, exceptionally well through satellite passive-microwave observations, and at the moment this is the core of its strength as a potential early indicator. However, the absence of a solid pre-satellite database considerably hinders how well sea ice satisfies the third characteristic, that it have low enough and known natural variability to allow a climate signal to be distinguished from the background noise, and how well it can be known to satisfy the final characteristic, that changes in it should not significantly lag changes in other climate variables. The conclusion reached is that although changes in the sea ice cover, when analyzed in conjunction with changes in other variables, will provide important information on climate change, sea ice is unlikely any time in the near future to be a definitive early indicator of climate change when considered by itself.

  17. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

    SciTech Connect

    Schulze, Kornelius; Imbeaud, Sandrine; Letouz, Eric; Alexandrov, Ludmil B.; Calderaro, Julien; Rebouissou, Sandra; Couchy, Gabrielle; Meiller, Clment; Shinde, Jayendra; Soysouvanh, Frederic; Calatayud, Anna-Line; Pinyol, Roser; Pelletier, Laura; Balabaud, Charles; Laurent, Alexis; Blanc, Jean-Frederic; Mazzaferro, Vincenzo; Calvo, Fabien; Villanueva, Augusto; Nault, Jean-Charles; Bioulac-Sage, Paulette; Stratton, Michael R.; Llovet, Josep M.; Zucman-Rossi, Jessica

    2015-03-30

    Our genomic analyses promise to improve tumor characterization to optimize personalized treatment for patients with hepatocellular carcinoma (HCC). Exome sequencing analysis of 243 liver tumors identified mutational signatures associated with specific risk factors, mainly combined alcohol and tobacco consumption and exposure to aflatoxin B1. We identified 161 putative driver genes associated with 11 recurrently altered pathways. Associations of mutations defined 3 groups of genes related to risk factors and centered on CTNNB1 (alcohol), TP53 (hepatitis B virus, HBV) and AXIN1. These analyses according to tumor stage progression identified TERT promoter mutation as an early event, whereasFGF3, FGF4, FGF19 or CCND1 amplification and TP53 and CDKN2A alterations appeared at more advanced stages in aggressive tumors. In 28% of the tumors, we identified genetic alterations potentially targetable by US Food and Drug Administration (FDA)approved drugs. Finally, we identified risk factorspecific mutational signatures and defined the extensive landscape of altered genes and pathways in HCC, which will be useful to design clinical trials for targeted therapy.

  18. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

    DOE PAGESBeta

    Schulze, Kornelius; Imbeaud, Sandrine; Letouzé, Eric; Alexandrov, Ludmil B.; Calderaro, Julien; Rebouissou, Sandra; Couchy, Gabrielle; Meiller, Clément; Shinde, Jayendra; Soysouvanh, Frederic; et al

    2015-03-30

    Our genomic analyses promise to improve tumor characterization to optimize personalized treatment for patients with hepatocellular carcinoma (HCC). Exome sequencing analysis of 243 liver tumors identified mutational signatures associated with specific risk factors, mainly combined alcohol and tobacco consumption and exposure to aflatoxin B1. We identified 161 putative driver genes associated with 11 recurrently altered pathways. Associations of mutations defined 3 groups of genes related to risk factors and centered on CTNNB1 (alcohol), TP53 (hepatitis B virus, HBV) and AXIN1. These analyses according to tumor stage progression identified TERT promoter mutation as an early event, whereasFGF3, FGF4, FGF19 or CCND1more » amplification and TP53 and CDKN2A alterations appeared at more advanced stages in aggressive tumors. In 28% of the tumors, we identified genetic alterations potentially targetable by US Food and Drug Administration (FDA)–approved drugs. Finally, we identified risk factor–specific mutational signatures and defined the extensive landscape of altered genes and pathways in HCC, which will be useful to design clinical trials for targeted therapy.« less

  19. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

    SciTech Connect

    Schulze, Kornelius; Imbeaud, Sandrine; Letouzé, Eric; Alexandrov, Ludmil B.; Calderaro, Julien; Rebouissou, Sandra; Couchy, Gabrielle; Meiller, Clément; Shinde, Jayendra; Soysouvanh, Frederic; Calatayud, Anna-Line; Pinyol, Roser; Pelletier, Laura; Balabaud, Charles; Laurent, Alexis; Blanc, Jean-Frederic; Mazzaferro, Vincenzo; Calvo, Fabien; Villanueva, Augusto; Nault, Jean-Charles; Bioulac-Sage, Paulette; Stratton, Michael R.; Llovet, Josep M.; Zucman-Rossi, Jessica

    2015-03-30

    Our genomic analyses promise to improve tumor characterization to optimize personalized treatment for patients with hepatocellular carcinoma (HCC). Exome sequencing analysis of 243 liver tumors identified mutational signatures associated with specific risk factors, mainly combined alcohol and tobacco consumption and exposure to aflatoxin B1. We identified 161 putative driver genes associated with 11 recurrently altered pathways. Associations of mutations defined 3 groups of genes related to risk factors and centered on CTNNB1 (alcohol), TP53 (hepatitis B virus, HBV) and AXIN1. These analyses according to tumor stage progression identified TERT promoter mutation as an early event, whereasFGF3, FGF4, FGF19 or CCND1 amplification and TP53 and CDKN2A alterations appeared at more advanced stages in aggressive tumors. In 28% of the tumors, we identified genetic alterations potentially targetable by US Food and Drug Administration (FDA)–approved drugs. Finally, we identified risk factor–specific mutational signatures and defined the extensive landscape of altered genes and pathways in HCC, which will be useful to design clinical trials for targeted therapy.

  20. Potential for diamond in kimberlites from Michigan and Montana as indicated by garnet xenocryst compositions

    USGS Publications Warehouse

    McGee, E.S.

    1988-01-01

    The Williams kimberlite in north-central Montana and the Lake Ellen kimberlite in northern Michigan contain diagnostic xenoliths and xenocrysts which indicate that diamonds may be present. To date, however, no diamonds have been reported from either locality. In this study, particular compositions of garnet xenocrysts which are associated with diamond elsewhere were sought as an indication of the potential for diamond in the Williams and Lake Ellen kimberlites. For this study, garnets were carefully selected for purple color in order to increase the chance of finding the subcalcic chrome-rich compositions that are associated with the presence of diamond. -Author

  1. The potential for research-based information in public health: Identifying unrecognised information needs

    PubMed Central

    Forsetlund, Louise; Bjrndal, Arild

    2001-01-01

    Objective To explore whether there is a potential for greater use of research-based information in public health practice in a local setting. Secondly, if research-based information is relevant, to explore the extent to which this generates questioning behaviour. Design Qualitative study using focus group discussions, observation and interviews. Setting Public health practices in Norway. Participants 52 public health practitioners. Results In general, the public health practitioners had a positive attitude towards research-based information, but believed that they had few cases requiring this type of information. They did say, however, that there might be a potential for greater use. During five focus groups and six observation days we identified 28 questions/cases where it would have been appropriate to seek out research evidence according to our definition. Three of the public health practitioners identified three of these 28 cases as questions for which research-based information could have been relevant. This gap is interpreted as representing unrecognised information needs. Conclusions There is an unrealised potential in public health practice for more frequent and extensive use of research-based information. The practitioners did not appear to reflect on the need for scientific information when faced with new cases and few questions of this type were generated. PMID:11208260

  2. Using Helicopter Electromagnetic Surveys to Identify Potential Hazards at Mine Waste Impoundments

    SciTech Connect

    Hammack, R.W.

    2008-01-01

    In July 2003, helicopter electromagnetic surveys were conducted at 14 coal waste impoundments in southern West Virginia. The purpose of the surveys was to detect conditions that could lead to impoundment failure either by structural failure of the embankment or by the flooding of adjacent or underlying mine works. Specifically, the surveys attempted to: 1) identify saturated zones within the mine waste, 2) delineate filtrate flow paths through the embankment or into adjacent strata and receiving streams, and 3) identify flooded mine workings underlying or adjacent to the waste impoundment. Data from the helicopter surveys were processed to generate conductivity/depth images. Conductivity/depth images were then spatially linked to georeferenced air photos or topographic maps for interpretation. Conductivity/depth images were found to provide a snapshot of the hydrologic conditions that exist within the impoundment. This information can be used to predict potential areas of failure within the embankment because of its ability to image the phreatic zone. Also, the electromagnetic survey can identify areas of unconsolidated slurry in the decant basin and beneath the embankment. Although shallow, flooded mineworks beneath the impoundment were identified by this survey, it cannot be assumed that electromagnetic surveys can detect all underlying mines. A preliminary evaluation of the data implies that helicopter electromagnetic surveys can provide a better understanding of the phreatic zone than the piezometer arrays that are typically used.

  3. Identifying a potential receptor for the antibacterial peptide of sponge Axinella donnani endosymbiont.

    PubMed

    Vimala, A; Ramakrishnan, C; Gromiha, M Michael

    2015-07-25

    Marine sponges and their associated bacteria are rich sources of novel secondary metabolites with therapeutic usefulness. In our earlier work, we have identified a novel antibacterial peptide from the marine sponge Axinella donnani endosymbiotic bacteria. In this work, we have carried out a comparative genomic analysis and identified a set of 60 proteins as probable receptor which is common in all the strains. The analysis on binding substrate showed that β barrel assembly machinery (BamA) of the outer membrane protein 85 (omp85) superfamily is a potential receptor protein for the antibacterial peptide. It plays a central role in OMP biogenesis, especially in cell viability. Further, the triplet and quartet motifs RGF and YGDG, respectively in L6 loop are conserved over all the strains and these conserved residues interact with antibacterial peptide to inhibit the BamA function, which is essential for OMP biogenesis. PMID:25939848

  4. The Potential for Spatial Distribution Indices to Signal Thresholds in Marine Fish Biomass

    PubMed Central

    Reuchlin-Hugenholtz, Emilie

    2015-01-01

    The frequently observed positive relationship between fish population abundance and spatial distribution suggests that changes in distribution can be indicative of trends in abundance. If contractions in spatial distribution precede declines in spawning stock biomass (SSB), spatial distribution reference points could complement the SSB reference points that are commonly used in marine conservation biology and fisheries management. When relevant spatial distribution information is integrated into fisheries management and recovery plans, risks and uncertainties associated with a plan based solely on the SSB criterion would be reduced. To assess the added value of spatial distribution data, we examine the relationship between SSB and four metrics of spatial distribution intended to reflect changes in population range, concentration, and density for 10 demersal populations (9 species) inhabiting the Scotian Shelf, Northwest Atlantic. Our primary purpose is to assess their potential to serve as indices of SSB, using fisheries independent survey data. We find that metrics of density offer the best correlate of spawner biomass. A decline in the frequency of encountering high density areas is associated with, and in a few cases preceded by, rapid declines in SSB in 6 of 10 populations. Density-based indices have considerable potential to serve both as an indicator of SSB and as spatially based reference points in fisheries management. PMID:25789624

  5. Genetic studies of plasma analytes identify novel potential biomarkers for several complex traits

    PubMed Central

    Deming, Yuetiva; Xia, Jian; Cai, Yefei; Lord, Jenny; Del-Aguila, Jorge L.; Fernandez, Maria Victoria; Carrell, David; Black, Kathleen; Budde, John; Ma, ShengMei; Saef, Benjamin; Howells, Bill; Bertelsen, Sarah; Bailey, Matthew; Ridge, Perry G.; Hefti, Franz; Fillit, Howard; Zimmerman, Earl A.; Celmins, Dzintra; Brown, Alice D.; Carrillo, Maria; Fleisher, Adam; Reeder, Stephanie; Trncic, Nadira; Burke, Anna; Tariot, Pierre; Reiman, Eric M.; Chen, Kewei; Sabbagh, Marwan N.; Beiden, Christine M.; Jacobson, Sandra A.; Sirrel, Sherye A.; Doody, Rachelle S.; Villanueva-Meyer, Javier; Chowdhury, Munir; Rountree, Susan; Dang, Mimi; Kowall, Neil; Killiany, Ronald; Budson, Andrew E.; Norbash, Alexander; Johnson, Patricia Lynn; Green, Robert C.; Marshall, Gad; Johnson, Keith A.; Sperling, Reisa A.; Snyder, Peter; Salloway, Stephen; Malloy, Paul; Correia, Stephen; Bernick, Charles; Munic, Donna; Stern, Yaakov; Honig, Lawrence S.; Bell, Karen L.; Relkin, Norman; Chaing, Gloria; Ravdin, Lisa; Paul, Steven; Flashman, Laura A.; Seltzer, Marc; Hynes, Mary L.; Santulli, Robert B.; Bates, Vernice; Capote, Horacio; Rainka, Michelle; Friedl, Karl; Murali Doraiswamy, P.; Petrella, Jeffrey R.; Borges-Neto, Salvador; James, Olga; Wong, Terence; Coleman, Edward; Schwartz, Adam; Cellar, Janet S.; Levey, Allan L.; Lah, James J.; Behan, Kelly; Scott Turner, Raymond; Johnson, Kathleen; Reynolds, Brigid; Pearlson, Godfrey D.; Blank, Karen; Anderson, Karen; Obisesan, Thomas O.; Wolday, Saba; Allard, Joanne; Lerner, Alan; Ogrocki, Paula; Tatsuoka, Curtis; Fatica, Parianne; Farlow, Martin R.; Saykin, Andrew J.; Foroud, Tatiana M.; Shen, Li; Faber, Kelly; Kim, Sungeun; Nho, Kwangsik; Marie Hake, Ann; Matthews, Brandy R.; Brosch, Jared R.; Herring, Scott; Hunt, Cynthia; Albert, Marilyn; Onyike, Chiadi; D’Agostino, Daniel; Kielb, Stephanie; Graff-Radford, Neill R; Parfitt, Francine; Kendall, Tracy; Johnson, Heather; Petersen, Ronald; Jack, Clifford R.; Bernstein, Matthew; Borowski, Bret; Gunter, Jeff; Senjem, Matt; Vemuri, Prashanthi; Jones, David; Kantarci, Kejal; Ward, Chad; Mason, Sara S.; Albers, Colleen S.; Knopman, David; Johnson, Kris; Chertkow, Howard; Hosein, Chris; Mintzer, Jacob; Spicer, Kenneth; Bachman, David; Grossman, Hillel; Mitsis, Effie; Pomara, Nunzio; Hernando, Raymundo; Sarrael, Antero; Potter, William; Buckholtz, Neil; Hsiao, John; Kittur, Smita; Galvin, James E.; Cerbone, Brittany; Michel, Christina A.; Pogorelec, Dana M.; Rusinek, Henry; de Leon, Mony J; Glodzik, Lidia; De Santi, Susan; Johnson, Nancy; Chuang-Kuo; Kerwin, Diana; Bonakdarpour, Borna; Weintraub, Sandra; Grafman, Jordan; Lipowski, Kristine; Mesulam, Marek-Marsel; Scharre, Douglas W.; Kataki, Maria; Adeli, Anahita; Kaye, Jeffrey; Quinn, Joseph; Silbert, Lisa; Lind, Betty; Carter, Raina; Dolen, Sara; Borrie, Michael; Lee, T-Y; Bartha, Rob; Martinez, Walter; Villena, Teresa; Sadowsky, Carl; Khachaturian, Zaven; Ott, Brian R.; Querfurth, Henry; Tremont, Geoffrey; Frank, Richard; Fleischman, Debra; Arfanakis, Konstantinos; Shah, Raj C.; deToledo-Morrell, Leyla; Sorensen, Greg; Finger, Elizabeth; Pasternack, Stephen; Rachinsky, Irina; Drost, Dick; Rogers, John; Kertesz, Andrew; Furst, Ansgar J.; Chad, Stevan; Yesavage, Jerome; Taylor, Joy L.; Lane, Barton; Rosen, Allyson; Tinklenberg, Jared; Black, Sandra; Stefanovic, Bojana; Caldwell, Curtis; Robin Hsiung, Ging-Yuek; Mudge, Benita; Assaly, Michele; Fox, Nick; Schultz, Susan K.; Boles Ponto, Laura L.; Shim, Hyungsub; Ekstam Smith, Karen; Burns, Jeffrey M.; Swerdlow, Russell H.; Brooks, William M.; Marson, Daniel; Griffith, Randall; Clark, David; Geldmacher, David; Brockington, John; Roberson, Erik; Natelson Love, Marissa; DeCarli, Charles; Carmichael, Owen; Olichney, John; Maillard, Pauline; Fletcher, Evan; Nguyen, Dana; Preda, Andrian; Potkin, Steven; Mulnard, Ruth A.; Thai, Gaby; McAdams-Ortiz, Catherine; Landau, Susan; Jagust, William; Apostolova, Liana; Tingus, Kathleen; Woo, Ellen; Silverman, Daniel H.S.; Lu, Po H.; Bartzokis, George; Thompson, Paul; Donohue, Michael; Thomas, Ronald G.; Walter, Sarah; Gessert, Devon; Brewer, James; Vanderswag, Helen; Sather, Tamie; Jiminez, Gus; Balasubramanian, Archana B.; Mason, Jennifer; Sim, Iris; Aisen, Paul; Davis, Melissa; Morrison, Rosemary; Harvey, Danielle; Thal, Lean; Beckett, Laurel; Neylan, Thomas; Finley, Shannon; Weiner, Michael W.; Hayes, Jacqueline; Rosen, Howard J.; Miller, Bruce L.; Perry, David; Massoglia, Dino; Brawman-Mentzer, Olga; Schuff, Norbert; Smith, Charles D.; Hardy, Peter; Sinha, Partha; Oates, Elizabeth; Conrad, Gary; Koeppe, Robert A.; Lord, Joanne L.; Heidebrink, Judith L.; Arnold, Steven E.; Karlawish, Jason H.; Wolk, David; Clark, Christopher M.; Trojanowki, John Q.; Shaw, Leslie M.; Lee, Virginia; Korecka, Magdalena; Figurski, Michal; Toga, Arthur W.; Crawford, Karen; Neu, Scott; Schneider, Lon S.; Pawluczyk, Sonia; Beccera, Mauricio; Teodoro, Liberty; Spann, Bryan M.; Womack, Kyle; Mathews, Dana; Quiceno, Mary; Foster, Norm; Montine, Tom; Fruehling, J. Jay; Harding, Sandra; Johnson, Sterling; Asthana, Sanjay; Carlsson, Cynthia M.; Petrie, Eric C.; Peskind, Elaine; Li, Gail; Porsteinsson, Anton P.; Goldstein, Bonnie S.; Martin, Kim; Makino, Kelly M.; Ismail, M. Saleem; Brand, Connie; Smith, Amanda; Ashok Raj, Balebail; Fargher, Kristin; Kuller, Lew; Mathis, Chet; Ann Oakley, Mary; Lopez, Oscar L.; Simpson, Donna M.; Sink, Kaycee M.; Gordineer, Leslie; Williamson, Jeff D.; Garg, Pradeep; Watkins, Franklin; Cairns, Nigel J.; Raichle, Marc; Morris, John C.; Householder, Erin; Taylor-Reinwald, Lisa; Holtzman, David; Ances, Beau; Carroll, Maria; Creech, Mary L.; Franklin, Erin; Mintun, Mark A.; Schneider, Stacy; Oliver, Angela; Duara, Ranjan; Varon, Daniel; Greig, Maria T.; Roberts, Peggy; Varma, Pradeep; MacAvoy, Martha G.; Carson, Richard E.; van Dyck, Christopher H.; Davies, Peter; Holtzman, David; Morris, John C.; Bales, Kelly; Pickering, Eve H.; Lee, Jin-Moo; Heitsch, Laura; Kauwe, John; Goate, Alison; Piccio, Laura; Cruchaga, Carlos

    2016-01-01

    Genome-wide association studies of 146 plasma protein levels in 818 individuals revealed 56 genome-wide significant associations (28 novel) with 47 analytes. Loci associated with plasma levels of 39 proteins tested have been previously associated with various complex traits such as heart disease, inflammatory bowel disease, Type 2 diabetes, and multiple sclerosis. These data suggest that these plasma protein levels may constitute informative endophenotypes for these complex traits. We found three potential pleiotropic genes: ABO for plasma SELE and ACE levels, FUT2 for CA19-9 and CEA plasma levels, and APOE for ApoE and CRP levels. We also found multiple independent signals in loci associated with plasma levels of ApoH, CA19-9, FetuinA, IL6r, and LPa. Our study highlights the power of biological traits for genetic studies to identify genetic variants influencing clinically relevant traits, potential pleiotropic effects, and complex disease associations in the same locus.

  6. Development of biological indices for identifying and evaluating impacts of pollutants on freshwater ecosystems. Final report, June 1975-October 1980

    SciTech Connect

    Cairns, J. Jr.; Cherry, D.S.

    1980-09-30

    The ten Research Areas reported included: (1) the development of functional indices for identifying and evaluating impacts of pollutants on Aufwuchs communities, (2) relationship of protozoan colonization rates to the eutrophication process, (3) testing of methods to determine the functioning of zooplankton communities subjected to entrainment stress, (4) the use of the first steps of detritus processing (microbial decomposition) as a technique for assessing pollutional stress on aquatic communities in a river system, (5) relationship of protozoan invasion and extinction rate to the eutrophication process, (6) extension of present early colonization studies to the simultaneous evaluation of natural environmental parameters and power plant effluents and application of the early colonization approach to microbial communities in streams of the New River drainage, (7) testing of single species-community responses of protozoans from selected heavy metals, (8) the effects of selected power plant pollutants on grazer utilization of Aufwuchs, (9) investigation of bioconcentration and bioaccumulation mechanisms of the Asiatic clam (Corbicula fluminea) populations in field artificial streams and laboratory microcosms with reference to physical chemistry and diet alterations, and (10) investigation of the homeostatic regulation in bluegill sunfish following acute hypothermal shock and to other power plant related effluents.

  7. Clonal analyses and gene profiling identify genetic biomarkers of human brown and white preadipocyte thermogenic potential

    PubMed Central

    Xue, Ruidan; Lynes, Matthew D.; Dreyfuss, Jonathan M.; Shamsi, Farnaz; Schulz, Tim J.; Zhang, Hongbin; Huang, Tian Lian; Townsend, Kristy L.; Li, Yiming; Takahashi, Hirokazu; Weiner, Lauren S.; White, Andrew P.; Lynes, Maureen S.; Rubin, Lee L.; Goodyear, Laurie J.; Cypess, Aaron M.; Tseng, Yu-Hua

    2015-01-01

    Targeting brown adipose tissue (BAT) content or activity has therapeutic potential for treating obesity and the metabolic syndrome by increasing energy expenditure. Both inter- and intra-individual differences contribute to heterogeneity in human BAT and potentially to differential thermogenic capacity in human populations. Here, we demonstrated the generated clones of brown and white preadipocytes from human neck fat of four individuals and characterized their adipogenic differentiation and thermogenic function. Combining an uncoupling protein 1(UCP1) reporter system and expression profiling, we defined novel sets of gene signatures in human preadipocytes that could predict the thermogenic potential of the cells once they were maturated in culture. Knocking out the positive UCP1 regulators identified by this approach, PREX1 and EDNRB in brown preadipocytes using CRISPR/Cas9 markedly abolished the high level of UCP1 in brown adipocytes differentiated from the preadipocytes. Finally, we were able to prospectively isolate adipose progenitors with great thermogenic potential using cell surface marker CD29. These data provide new insights into the cellular heterogeneity in human fat and offer the identification of possible biomarkers of thermogenically competent preadipocytes. PMID:26076036

  8. Ability of Dental Students in Spain to Identify Potentially Malignant Disorders and Oral Cancer.

    PubMed

    Cerero-Lapiedra, Rocío; Esparza-Gómez, Germán C; Casado-de la Cruz, Laura; Domínguez-Gordillo, Adelaida A; Corral-Linaza, César; Seoane-Romero, Juan M

    2015-08-01

    The aim of this study was to assess the ability of students at the School of Dentistry, Complutense University of Madrid, Spain, to diagnose oral cancer and other potentially malignant disorders, as well as to compare their ability at different stages of the learning process and evaluate their knowledge retention. Students were surveyed after they had studied oral medicine and oral pathology at two time points: midway through and near the end of their studies. The survey consisted of questions about 40 photographs of benign oral lesions, malignant oral lesions, and potentially malignant disorders. The response rate for all groups was greater than 70%. The results showed that these students' overall success rate in differentiating benign from malignant lesions averaged 73.9%. When the distinction for potentially malignant disorders was included, their average overall success rate decreased to 42.8% (p<0.001). Furthermore, the students' average success rate was at its lowest at the end of the dental program (p<0.001). Results from this study suggest that, given these students' difficulties in identifying potentially malignant disorders, an increased emphasis on cancer education in the dental curriculum may be needed for future practitioners to master this ability. PMID:26246535

  9. Human enteric viruses--potential indicators for enhanced monitoring of recreational water quality.

    PubMed

    Updyke, Erin Allmann; Wang, Zi; Sun, Si; Connell, Christina; Kirs, Marek; Wong, Mayee; Lu, Yuanan

    2015-10-01

    Recreational waters contaminated with human fecal pollution are a public health concern, and ensuring the safety of recreational waters for public use is a priority of both the Environmental Protection Agency (EPA) and the Centers for Disease Control and Prevention (CDC). Current recreational water standards rely on fecal indicator bacteria (FIB) levels as indicators of human disease risk. However present evidence indicates that levels of FIB do not always correspond to the presence of other potentially harmful organisms, such as viruses. Thus, enteric viruses are currently tested as water quality indicators, but have yet to be successfully implemented in routine monitoring of water quality. This study utilized enteric viruses as possible alternative indicators of water quality to examine 18 different fresh and offshore recreational waters on O'ahu, Hawai'i, by using newly established laboratory techniques including highly optimized PCR, real time PCR, and viral infectivity assays. All sample sites were detected positive for human enteric viruses by PCR including enterovirus, norovirus genogroups I and II, and male specific FRNA coliphage. A six time-point seasonal study of enteric virus presence indicated significant variation in virus detection between the rainy and dry seasons. Quantitative PCR detected the presence of norovirus genogroup II at levels at which disease risk may occur, and there was no correlation found between enteric virus presence and FIB counts. Under the present laboratory conditions, no infectious viruses were detected from the samples PCR-positive for enteric viruses. These data emphasize both the need for additional indicators for improved monitoring of water quality, and the feasibility of using enteric viruses as these indicators. PMID:26494480

  10. Bacterial Targets as Potential Indicators of Diesel Fuel Toxicity in Subantarctic Soils

    PubMed Central

    van Dorst, Josie; Siciliano, Steven D.; Winsley, Tristrom; Snape, Ian

    2014-01-01

    Appropriate remediation targets or universal guidelines for polar regions do not currently exist, and a comprehensive understanding of the effects of diesel fuel on the natural microbial populations in polar and subpolar soils is lacking. Our aim was to investigate the response of the bacterial community to diesel fuel and to evaluate if these responses have the potential to be used as indicators of soil toxicity thresholds. We set up short- and long-exposure tests across a soil organic carbon gradient. Utilizing broad and targeted community indices, as well as functional genes involved in the nitrogen cycle, we investigated the bacterial community structure and its potential functioning in response to special Antarctic blend (SAB) diesel fuel. We found the primary effect of diesel fuel toxicity was a reduction in species richness, evenness, and phylogenetic diversity, with the resulting community heavily dominated by a few species, principally Pseudomonas. The decline in richness and phylogenetic diversity was linked to disruption of the nitrogen cycle, with species and functional genes involved in nitrification significantly reduced. Of the 11 targets we evaluated, we found the bacterial amoA gene indicative of potential ammonium oxidation, the most suitable indicator of toxicity. Dose-response modeling for this target generated an average effective concentration responsible for 20% change (EC20) of 155 mg kg−1, which is consistent with previous Macquarie Island ecotoxicology assays. Unlike traditional single-species tolerance testing, bacterial targets allowed us to simultaneously evaluate more than 1,700 species from 39 phyla, inclusive of rare, sensitive, and functionally relevant portions of the community. PMID:24771028

  11. Bacterial targets as potential indicators of diesel fuel toxicity in subantarctic soils.

    PubMed

    van Dorst, Josie; Siciliano, Steven D; Winsley, Tristrom; Snape, Ian; Ferrari, Belinda C

    2014-07-01

    Appropriate remediation targets or universal guidelines for polar regions do not currently exist, and a comprehensive understanding of the effects of diesel fuel on the natural microbial populations in polar and subpolar soils is lacking. Our aim was to investigate the response of the bacterial community to diesel fuel and to evaluate if these responses have the potential to be used as indicators of soil toxicity thresholds. We set up short- and long-exposure tests across a soil organic carbon gradient. Utilizing broad and targeted community indices, as well as functional genes involved in the nitrogen cycle, we investigated the bacterial community structure and its potential functioning in response to special Antarctic blend (SAB) diesel fuel. We found the primary effect of diesel fuel toxicity was a reduction in species richness, evenness, and phylogenetic diversity, with the resulting community heavily dominated by a few species, principally Pseudomonas. The decline in richness and phylogenetic diversity was linked to disruption of the nitrogen cycle, with species and functional genes involved in nitrification significantly reduced. Of the 11 targets we evaluated, we found the bacterial amoA gene indicative of potential ammonium oxidation, the most suitable indicator of toxicity. Dose-response modeling for this target generated an average effective concentration responsible for 20% change (EC20) of 155 mg kg(-1), which is consistent with previous Macquarie Island ecotoxicology assays. Unlike traditional single-species tolerance testing, bacterial targets allowed us to simultaneously evaluate more than 1,700 species from 39 phyla, inclusive of rare, sensitive, and functionally relevant portions of the community. PMID:24771028

  12. Transcript Profiling and RNA Interference as Tools to Identify Small Molecule Mechanisms and Therapeutic Potential

    PubMed Central

    Palchaudhuri, Rahul; Hergenrother, Paul J.

    2011-01-01

    Summary The identification of the mechanism-of-action and therapeutic potential of bioactive small molecules remain considerable challenges in the field of drug discovery and chemical biology. Apart from traditional target identification techniques, new tools have emerged that can significantly aid mechanism elucidation efforts. The development of pattern matching algorithms that compare transcription profile data to analogous data on compounds with known cellular targets allows for mechanistic insights without the need to synthesize chemically modified probes. In addition, such methods can be used to connect small molecules to particular disease states, thus aiding the rational identification of candidate therapeutics. Another method with considerable potential is whole-genome RNAi screening, a technique that can identify critical upstream proteins involved in a small molecules mechanism-of-action. Several proof-of-concept studies using compounds with known cellular targets suggest this tool will enable mechanistic characterization of bioactive small molecules with unknown mechanisms. This review highlights recent successes in using these pattern matching and chemical genetic tools, with the goal of uncovering small molecule mechanisms and identifying therapeutic candidates for disease treatment. PMID:21105689

  13. Energy-optimised pharmacophore approach to identify potential hotspots during inhibition of Class II HDAC isoforms.

    PubMed

    Ganai, Shabir Ahmad; Shanmugam, Karthi; Mahadevan, Vijayalakshmi

    2015-01-01

    Histone deacetylases (HDACs) are conjugated enzymes that modulate chromatin architecture by deacetylating lysine residues on the histone tails leading to transcriptional repression. Pharmacological interventions of these enzymes with small molecule inhibitors called Histone deacetylase inhibitors (HDACi) have shown enhanced acetylation of the genome and are hence emerging as potential targets at the clinic. Type-specific inhibition of Class II HDACs has shown enhanced therapeutic benefits against developmental and neurodegenerative disorders. However, the structural identity of class-specific isoforms limits the potential of their inhibitors in precise targeting of their enzymes. Diverse strategies have been implemented to recognise the features in HDAC enzymes which may help in identifying isoform specificity factors. This work attempts a computational approach that combines in silico docking and energy-optimised pharmacophore (E-pharmacophore) mapping of 18 known HDAC inhibitors and has identified structural variations that regulate their interactions against the six Class II HDAC enzymes considered for the study. This combined approach establishes that inhibitors possessing higher number of aromatic rings in different structural regions might function as potent inhibitors, while inhibitors with scarce ring structures might point to compromised potency. This would aid the rationale for chemical optimisation and design of isoform selective HDAC inhibitors with enhanced affinity and therapeutic efficiency. PMID:24460542

  14. Short communication: Noninvasive indicators to identify lactating dairy cows with a greater risk of subacute rumen acidosis.

    PubMed

    Gao, X; Oba, M

    2015-08-01

    The objective of the current study was to evaluate if milk urea nitrogen (MUN) and milk fat content could be used as the noninvasive indicator to identify cows with greater or lower risk of subacute ruminal acidosis (SARA). Our hypothesis was that cows with lower MUN and milk fat content would have greater risk of SARA, whereas cows with higher MUN and milk fat content would have lower risk of SARA. In the screening study, 35 late-lactating Holstein cows (DIM=250±71.1; BW=601±45.4kg) were fed a high-grain diet containing 35% forage and 65% concentrate mix ad libitum for 21 d. Concentration of MUN ranged from 5.7 to 13.9Mg/dL among the 35 cows, and the average milk fat content was 3.5%. Then, 5 cows with highest MUN concentrations with milk fat higher than 3.5% were selected as animals that presumably have low risk of SARA, and 5 cows with lowest MUN concentrations with milk fat less than 3.5% were selected as animals that presumably have high risk of SARA. These 10 animals were ruminally cannulated during the subsequent dry period. As 1 low-risk cow was culled due to fatty liver, 9 animals (DIM=122±33.2; BW=615±49.1kg) were used in the subsequent study in the following lactation. All cows were fed a high-grain diet consisting of 35% forage and 65% concentrate mix ad libitum for 21 d. Ruminal pH was measured every 30 s for 72 h. Minimum (5.75 vs. 5.30) and mean ruminal pH (6.35 vs. 6.04) was higher for low- compared with high-risk animals. In addition, duration of rumen pH below 5.8 was shorter in low-risk animals (52.5 vs. 395min/d). These results suggested that MUN and milk fat content in late-lactating cows fed a high-grain diet may be used to identify cows that have higher or lower risk of SARA. PMID:26026756

  15. Using Market Research to Characterize College Students and Identify Potential Targets for Influencing Health Behaviors

    PubMed Central

    Berg, Carla J.; Ling, Pamela M.; Guo, Hongfei; Windle, Michael; Thomas, Janet L.; Ahluwalia, Jasjit S.; An, Lawrence C.

    2013-01-01

    Marketing campaigns, such as those developed by the tobacco industry, are based on market research, which defines segments of a population by assessing psychographic characteristics (i.e., attitudes, interests). This study uses a similar approach to define market segments of college smokers, to examine differences in their health behaviors (smoking, drinking, binge drinking, exercise, diet), and to determine the validity of these segments. A total of 2,265 undergraduate students aged 18–25 years completed a 108-item online survey in fall 2008 assessing demographic, psychographic (i.e., attitudes, interests), and health-related variables. Among the 753 students reporting past 30-day smoking, cluster analysis was conducted using 21 psychographic questions and identified three market segments – Stoic Individualists, Responsible Traditionalists, and Thrill-Seeking Socializers. We found that segment membership was related to frequency of alcohol use, binge drinking, and limiting dietary fat. We then developed three messages targeting each segment and conducted message testing to validate the segments on a subset of 73 smokers representing each segment in spring 2009. As hypothesized, each segment indicated greater relevance and salience for their respective message. These findings indicate that identifying qualitatively different subgroups of young adults through market research may inform the development of engaging interventions and health campaigns targeting college students. PMID:25264429

  16. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets

    PubMed Central

    Alexandrov, Ludmil B; Calderaro, Julien; Rebouissou, Sandra; Couchy, Gabrielle; Meiller, Clément; Shinde, Jayendra; Soysouvanh, Frederic; Calatayud, Anna-Line; Pinyol, Roser; Pelletier, Laura; Balabaud, Charles; Laurent, Alexis; Blanc, Jean-Frederic; Mazzaferro, Vincenzo; Calvo, Fabien; Villanueva, Augusto; Nault, Jean-Charles; Bioulac-Sage, Paulette; Stratton, Michael R; Llovet, Josep M; Zucman-Rossi, Jessica

    2015-01-01

    Genomic analyses promise to improve tumor characterization in order to optimize personalized treatment for patients with hepatocellular carcinoma (HCC). Exome sequencing analysis of 243 liver tumors revealed mutational signatures associated with specific risk factors, mainly combined alcohol/tobacco consumption, and aflatoxin B1. We identified 161 putative driver genes associated with 11 recurrent pathways. Associations of mutations defined 3 groups of genes related to risk factors and centered on CTNNB1 (alcohol), TP53 (HBV), and AXIN1. Analyses according to tumor stage progression revealed TERT promoter mutation as an early event whereas FGF3, FGF4, FGF19/CCND1 amplification, TP53 and CDKN2A alterations, appeared at more advanced stages in aggressive tumors. In 28% of the tumors we identified genetic alterations potentially targetable by FDA-approved drugs. In conclusion, we identified risk factor-specific mutational signatures and defined the extensive landscape of altered genes and pathways in HCC which will be useful to design clinical trials for targeted therapy. PMID:25822088

  17. Potential of calcium isotopes to identify fractionations in vegetation: experimental approach

    NASA Astrophysics Data System (ADS)

    Cobert, F.; Schmitt, A.; Bourgade, P.; Stille, P.; Chabaux, F. J.; Badot, P.; Jaegler, T.

    2010-12-01

    This study aims to better understand the role of vegetation on the Ca cycle at the level of the critical zone of the Earth, in order to specify the mechanisms controlling the Ca absorption by plants at the rock/plant interface. To do this, we performed experiments using hydroponic plant cultures in a way that we could control the cooccuring geochemical and biological processes and determine the impact of the nutritive solution on the Ca cycle within plants. A dicotyledon and calcicole plant with rapid growth, the French bean (Phaseolus vulgaris L.), has been chosen to have access to one complete growth cycle. Several experiments have been conducted with two Ca concentrations, 5 (L) and 60 (H) ppm and two pH values (4 and 6) in the nutritive solution, for which the Ca concentration was maintained constant, so its Ca content is considered to be infinite. We determined Ca concentrations and isotopic ratios in the nutritive solution and in different organs (main roots, secondary roots, old and young stems, old and young leaves and fruits) at two different growth stages (10 days and 6 weeks). Our results show, in accord with previously published field studies, that the bean organs are all enriched in the light 40Ca isotope compared to the nutritive solution (e.g. Wigand et al., 2005; Page et al., 2008; Cenki-Tok et al., 2009; Holmden and Bélanger, 2010). We identify two fractionation levels. The first occurs during the uptake of the nutrient elements by the lateral roots. This implies that the main mechanisms of light isotope enrichments in the plant are due to electrochemical gradient transport processes taking place at this interface. The second fractionation can be observed within the plant itself and is due to the nature of the considered organ itself. Indeed structural reservoirs (primary roots, stem, reproductive organs) incorporate more the light 40Ca isotope compared to the transfer reservoirs (lateral roots, xylem sap, leaves). This could be linked to ion-exchange reactions with the pectins in the cell walls of the conducting xylem. However, we also observe that bean organs from L4 experiment growing in nutrient solutions with lower Ca concentrations and low pH behave slightly differently and show reduced Ca isotopic fractionations compared with beans from the other experiments. All these results indicate that there is no simple correlation between Ca isotopic variations, Ca content and pH of the nutrient solution, and that also biological effects have to be involved. The data confirm the potential of the Ca isotopic system for tracing biological fractionations in natural ecosystems. Wiegand et al., (2005). Geophys. Res. Lett., 32, L11404 Page et al., (2008). Biogeochemistry, 88, 1-13 Cenki-Tok et al,. (2009). Geochim. Cosmochim. Acta, 73, 2215-2228 Holmden and Bélanger(2010). Geochim. Cosmochim. Acta, 74, 995-1015

  18. Leveraging Concept-based Approaches to Identify Potential Phyto-therapies

    PubMed Central

    Sharma, Vivekanand; Sarkar, Indra Neil

    2013-01-01

    The potential of plant-based remedies has been documented in both traditional and contemporary biomedical literature. Such types of text sources may thus be sources from which one might identify potential plant-based therapies (“phyto-therapies”). Concept-based analytic approaches have been shown to uncover knowledge embedded within biomedical literature. However, to date there has been limited attention towards leveraging such techniques for the identification of potential phyto-therapies. This study presents concept-based analytic approaches for the retrieval and ranking of associations between plants and human diseases. Focusing on identification of phyto-therapies described in MEDLINE, both MeSH descriptors used for indexing and MetaMap inferred UMLS concepts are considered. Furthermore, the identification and ranking consider both direct (i.e., plant concepts directly correlated with disease concepts) and inferred (i.e., plant concepts associated with disease concepts based on shared signs and symptoms) relationships. Based on the two scoring methodologies used in this study, it was found that a vector space model approach outperformed probabilistic reliability based inferences. An evaluation of the approach is provided based on therapeutic interventions catalogued in both ClinicalTrials.gov and NDF-RT. The promising findings from this feasibility study highlight the challenges and applicability of concept-based analytic strategies for distilling phyto-therapeutic knowledge from text based knowledge sources like MEDLINE. PMID:23665360

  19. Identifying potential conflict associated with oil and gas exploration in Texas state coastal waters: A multicriteria spatial analysis.

    PubMed

    Brody, Samuel D; Grover, Himanshu; Bernhardt, Sarah; Tang, Zhenghong; Whitaker, Bianca; Spence, Colin

    2006-10-01

    Recent interest in expanding offshore oil production within waters of the United States has been met with opposition by groups concerned with recreational, environmental, and aesthetic values associated with the coastal zone. Although the proposition of new oil platforms off the coast has generated conflict over how coastal resources should be utilized, little research has been conducted on where these user conflicts might be most intense and which sites might be most suitable for locating oil production facilities in light of the multiple, and often times, competing interests. In this article, we develop a multiple-criteria spatial decision support tool that identifies the potential degree of conflict associated with oil and gas production activities for existing lease tracts in the coastal margin of Texas. We use geographic information systems to measure and map a range of potentially competing representative values impacted by establishing energy extraction infrastructure and then spatially identify which leased tracts are the least contentious sites for oil and gas production in Texas state waters. Visual and statistical results indicate that oil and gas lease blocks within the study area vary in their potential to generate conflict among multiple stakeholders. PMID:16933080

  20. Evaluating stakeholder participation in water management: intermediary outcomes as potential indicators for future resource management outcomes

    NASA Astrophysics Data System (ADS)

    Carr, Gemma; Bloeschl, Guenter; Loucks, Daniel Pete

    2013-04-01

    Evaluation of participation programmes, projects and activities is essential to identify whether stakeholder involvement has been successful in achieving its aims. Aims may include an improvement in water resource management such as enhanced ecological functioning, an improvement in human wellbeing and economic conditions, or overcoming a conflict between interest groups. Evaluating against "interest-based" resource management criteria requires that a desirable outcome can be identified, agreed upon and be measured at the time of evaluation. In many water management situations where collaborative approaches are applied, multiple interests and objectives are present, or stakeholders have not yet identified their own positions and priorities. Even if a resource management objective has been identified and strategy agreed upon, resource management changes tend to emerge over longer timescales and evaluation frequently takes place before they can be recognised. Evaluating against resource management criteria may lead evaluators to conclude that a programme has failed because it has not achieved a resource management objective at the time of evaluation. This presents a critical challenge to researchers assessing the effectiveness of stakeholder participation programmes. One strategy to overcome this is to conduct "goal-free" evaluation to identify what the programme is actually achieving. An evaluation framework that includes intermediary outcomes that are both tangible achievements such as innovation, creation of new organisations, and shared information and knowledge, as well as intangible achievements such as trust and network development can be applied to more broadly assess a programme's success. Analysis of case-studies in the published literature for which a resource management outcome has been achieved shows that intermediary outcomes frequently precede resource management outcomes. They seem to emerge over shorter timescales than resource management outcomes. Furthermore, failure to achieve intermediary outcomes correlates to failure to achieve resource management outcomes. Evaluating intermediary outcomes leads to both a broader assessment of a programme's achievements at the time of evaluation, and can indicate whether a programme will go on to achieve resource management objectives in the future.

  1. Event-related potential indices of workload in a single task paradigm

    NASA Technical Reports Server (NTRS)

    Horst, R. L.; Munson, R. C.; Ruchkin, D. S.

    1984-01-01

    Many previous studies of both behavioral and physiological correlates of cognitive workload have burdened subjects with a contrived secondary task in order to assess the workload of a primary task. The present study investigated event-related potential (ERP) indices of workload in a single task paradigm. Subjects monitored changing digital readouts for values that went 'out-of-bounds'. The amplitude of a long-latency positivity in the ERPs elicited by readout changes increased with the number of readouts being monitored. This effect of workload on ERPs is reported, along with plans for additional analyses to address theoretical implications.

  2. Gyrineum natator: a potential indicator of imposex along the Indian coast.

    PubMed

    Vishwakiran, Y; Anil, A C; Venkat, K; Sawant, S S

    2006-03-01

    Imposex related studies have used neogastropods as sentinel organism. In this effort, we elucidate the potential of a mesogastropod, Gyrineum natator, for imposex monitoring on the central west coast of India. Observations were made with specimens collected from Mumbai (three stations), Ratnagiri (two stations), Goa (one station) and Mangalore (one station). The analyzed populations at all four sites were affected by imposex. The six different stages of imposex in this organism are illustrated through schematic and scanning electron micrographs. In view of the anticipated ban on TBT based antifouling paints this baseline information can serve as an indicator for environmental monitoring in this region. PMID:16084567

  3. Potential Coastal Pumped Hydroelectric Energy Storage Locations Identified using GIS-based Topographic Analysis

    NASA Astrophysics Data System (ADS)

    Parsons, R.; Barnhart, C. J.; Benson, S. M.

    2013-12-01

    Large-scale electrical energy storage could accommodate variable, weather dependent energy resources such as wind and solar. Pumped hydroelectric energy storage (PHS) and compressed energy storage area (CAES) have life cycle energy and financial costs that are an order of magnitude lower than conventional electrochemical storage technologies. However PHS and CAES storage technologies require specific geologic conditions. Conventional PHS requires an upper and lower reservoir separated by at least 100 m of head, but no more than 10 km in horizontal distance. Conventional PHS also impacts fresh water supplies, riparian ecosystems, and hydrologic environments. A PHS facility that uses the ocean as the lower reservoir benefits from a smaller footprint, minimal freshwater impact, and the potential to be located near off shore wind resources and population centers. Although technologically nascent, today one coastal PHS facility exists. The storage potential for coastal PHS is unknown. Can coastal PHS play a significant role in augmenting future power grids with a high faction of renewable energy supply? In this study we employ GIS-based topographic analysis to quantify the coastal PHS potential of several geographic locations, including California, Chile and Peru. We developed automated techniques that seek local topographic minima in 90 m spatial resolution shuttle radar topography mission (SRTM) digital elevation models (DEM) that satisfy the following criteria conducive to PHS: within 10 km from the sea; minimum elevation 150 m; maximum elevation 1000 m. Preliminary results suggest the global potential for coastal PHS could be very significant. For example, in northern Chile we have identified over 60 locations that satisfy the above criteria. Two of these locations could store over 10 million cubic meters of water or several GWh of energy. We plan to report a global database of candidate coastal PHS locations and to estimate their energy storage capacity.

  4. The potential of trace fossils as tidal indicators in bays and estuaries

    NASA Astrophysics Data System (ADS)

    Gingras, Murray K.; MacEachern, James A.; Dashtgard, Shahin E.

    2012-11-01

    Ichnological datasets have been used to infer the presence of tidal processes primarily through the identification of trace-fossil assemblages characteristic of brackish-water settings. However, this limited means of (ichnologically) identifying tidal settings is unsatisfying and the establishment of ichnological-tidal relationships for the purpose of discerning tidal depositional processes is desirable. We suggest that several types of ichnological data can be used to identify tidal influence: (1) ichnological response to rhythmic sedimentation; (2) the presence of tubular tidalites (i.e. biogenic structures infilled by tidally derived sediments); (3) the identification of anisotropic resource exploitation associated with food-rich slack-tide laminations; (4) the identification of tidal-flat deposits through bioturbation intensity and ichnological composition; (5) the recognition of brackish-water trace fossils; and potentially (6) system-scale ichnological distributions (which are presently poorly understood). As with tidal sedimentary structures, the inference of tidal processes from biogenic sedimentary structures should depend on identifying as many of the above characteristics as possible.

  5. Positive selection moments identify potential functional residues in human olfactory receptors

    NASA Technical Reports Server (NTRS)

    Singer, M. S.; Weisinger-Lewin, Y.; Lancet, D.; Shepherd, G. M.

    1996-01-01

    Correlated mutation analysis and molecular models of olfactory receptors have provided evidence that residues in the transmembrane domains form a binding pocket for odor ligands. As an independent test of these results, we have calculated positive selection moments for the alpha-helical sixth transmembrane domain (TM6) of human olfactory receptors. The moments can be used to identify residues that have been preferentially affected by positive selection and are thus likely to interact with odor ligands. The results suggest that residue 622, which is commonly a serine or threonine, could form critical H-bonds. In some receptors a dual-serine subsite, formed by residues 622 and 625, could bind hydroxyl determinants on odor ligands. The potential importance of these residues is further supported by site-directed mutagenesis in the beta-adrenergic receptor. The findings should be of practical value for future physiological studies, binding assays, and site-directed mutagenesis.

  6. Exome Sequencing of Only Seven Qataris Identifies Potentially Deleterious Variants in the Qatari Population

    PubMed Central

    Rodriguez-Flores, Juan L.; Fuller, Jennifer; Hackett, Neil R.; Salit, Jacqueline; Malek, Joel A.; Al-Dous, Eman; Chouchane, Lotfi; Zirie, Mahmoud; Jayoussi, Amin; Mahmoud, Mai A.; Crystal, Ronald G.; Mezey, Jason G.

    2012-01-01

    The Qatari population, located at the Arabian migration crossroads of African and Eurasia, is comprised of Bedouin, Persian and African genetic subgroups. By deep exome sequencing of only 7 Qataris, including individuals in each subgroup, we identified 2,750 nonsynonymous SNPs predicted to be deleterious, many of which are linked to human health, or are in genes linked to human health. Many of these SNPs were at significantly elevated deleterious allele frequency in Qataris compared to other populations worldwide. Despite the small sample size, SNP allele frequency was highly correlated with a larger Qatari sample. Together, the data demonstrate that exome sequencing of only a small number of individuals can reveal genetic variations with potential health consequences in understudied populations. PMID:23139751

  7. Unusual phyletic distribution of peptidases as a tool for identifying potential drug targets

    PubMed Central

    Rawlings, Neil D.

    2006-01-01

    Eukaryote homologues of carboxypeptidases Taq have been discovered by Niemirowicz et al. in the protozoan Trypanosoma cruzi, the causative agent of Chagas' disease. This is surprising, because the peptidase family was thought to be restricted to bacteria and archaea. In this issue of the Biochemical Journal, the authors propose that the Trypanosoma carboxypeptidases are potential drug targets for treatment of the disease. The authors also propose that the presence of the genes in the zooflagellates can be explained by a horizontal transfer of an ancestral gene from a prokaryote. Because peptidases are popular drug targets, identifying parasite or pathogen peptidases that have no homologues in their hosts would be a method to select the most promising targets. To understand how unusual this phyletic distribution is among the 183 families of peptidases, several other examples of horizontal transfers are presented, as well as some unusual losses of peptidase genes. PMID:17173540

  8. An analytical approach to identifying potential use-related issues concerning a medical device under development.

    PubMed

    Gupta, Suresh P; Pidgeon, Andy

    2016-04-01

    Identifying potential use-related issues at the onset of the design process of a medical device can reduce use errors, enhance safety and improve usability of the product. Regulatory bodies such as the US Food and Drug Administration (FDA) suggest manufacturers should investigate use-related problems that have occurred in the past with devices that are similar to the one under development. Publically available device incident databases, such as the FDA's Manufacturer and User Facility Device Experience (MAUDE) database, are a good source of information. However, haphazard searches of these databases can be confounding and unproductive. This paper presents a systematic approach to conducting the database searches, analysing the data and reporting the findings in a meaningful way. The approach outlined in this paper is an extract of the methodology that has been effectively implemented in a number of medical products that are already on the market, in submission or under development. PMID:26795586

  9. A new simplex chemometric approach to identify olive oil blends with potentially high traceability.

    PubMed

    Semmar, N; Laroussi-Mezghani, S; Grati-Kamoun, N; Hammami, M; Artaud, J

    2016-10-01

    Olive oil blends (OOBs) are complex matrices combining different cultivars at variable proportions. Although qualitative determinations of OOBs have been subjected to several chemometric works, quantitative evaluations of their contents remain poorly developed because of traceability difficulties concerning co-occurring cultivars. Around this question, we recently published an original simplex approach helping to develop predictive models of the proportions of co-occurring cultivars from chemical profiles of resulting blends (Semmar & Artaud, 2015). Beyond predictive model construction and validation, this paper presents an extension based on prediction errors' analysis to statistically define the blends with the highest predictability among all the possible ones that can be made by mixing cultivars at different proportions. This provides an interesting way to identify a priori labeled commercial products with potentially high traceability taking into account the natural chemical variability of different constitutive cultivars. PMID:27132835

  10. Identifying At-Risk Employees: Modeling Psychosocial Precursors of Potential Insider Threats

    SciTech Connect

    Greitzer, Frank L.; Kangas, Lars J.; Noonan, Christine F.; Dalton, Angela C.; Hohimer, Ryan E.

    2012-01-04

    In many insider crimes, managers and other coworkers observed that the offenders had exhibited signs of stress, disgruntlement, or other issues, but no alarms were raised. Barriers to using such psychosocial indicators include the inability to recognize the signs and the failure to record the behaviors so that they can be assessed. A psychosocial model was developed to assess an employee's behavior associated with an increased risk of insider abuse. The model is based on case studies and research literature on factors/correlates associated with precursor behavioral manifestations of individuals committing insider crimes. To test the model's agreement with human resources and management professionals, we conducted an experiment with positive results. If implemented in an operational setting, the model would be part of a set of management tools for employee assessment to identify employees who pose a greater insider threat.

  11. Multi-trait BLUP model indicates sorghum hybrids with genetic potential for agronomic and nutritional traits.

    PubMed

    Almeida Filho, J E; Tardin, F D; Guimarães, J F R; Resende, M D V; Silva, F F; Simeone, M L; Menezes, C B; Queiroz, V A V

    2016-01-01

    The breeding of sorghum, Sorghum bicolor (L.) Moench, aimed at improving its nutritional quality, is of great interest, since it can be used as a highly nutritive alternative food source and can possibly be cultivated in regions with low rainfall. The objective of the present study was to evaluate the potential and genetic diversity of grain-sorghum hybrids for traits of agronomic and nutritional interest. To this end, the traits grain yield and flowering, and concentrations of protein, potassium, calcium, magnesium, sulfur, iron, manganese, and zinc in the grain were evaluated in 25 grain-sorghum hybrids, comprising 18 experimental hybrids of Embrapa Milho e Sorgo and seven commercial hybrids. The genetic potential was analyzed by a multi-trait best linear unbiased prediction (BLUP) model, and cluster analysis was accomplished by squared Mahalanobis distance using the predicted genotypic values. Hybrids 0306037 and 0306034 stood out in the agronomic evaluation. The hybrids with agronomic prominence, however, did not stand out for the traits related to the nutritional quality of the grain. Three clusters were formed from the dendrogram obtained with the unweighted pair group method with arithmetic mean method. From the results of the genotypic BLUP and the analysis of the dendrogram, hybrids 0577337, 0441347, 0307651, and 0306037 were identified as having the potential to establish a population that can aggregate alleles for all the evaluated traits of interest. PMID:26985915

  12. The Potential of Metatranscriptomics for Identifying Screening Targets for Bacterial Vaginosis

    PubMed Central

    Twin, Jimmy; Bradshaw, Catriona S.; Garland, Suzanne M.; Fairley, Christopher K.; Fethers, Katherine; Tabrizi, Sepehr N.

    2013-01-01

    Background The ribosomal RNA content of a sample collected from a woman with bacterial vaginosis (BV) was analysed to determine the active microbial community, and to identify potential targets for further screening. Methodology/Principal Findings The sample from the BV patient underwent total RNA extraction, followed by physical subtraction of human rRNA and whole transcriptome amplification. The metatranscriptome was sequenced using Roche 454 titanium chemistry. The bioinformatics pipeline MG-RAST and desktop DNA analysis platforms were utilised to analyse results. Bacteria of the genus Prevotella (predominately P. amnii) constituted 36% of the 16S rRNA reads, followed by Megasphaera (19%), Leptotrichia/Sneathia (8%) and Fusobacterium (8%). Comparison of the abundances of several bacteria to quantitative PCR (qPCR) screening of extracted DNA revealed comparable relative abundances. This suggests a correlation between what was present and transcriptionally active in this sample: however distinct differences were seen when compared to the microbiome determined by 16S rRNA gene amplicon sequencing. To assess the presence of P. amnii in a larger pool of samples, 90 sexually active women were screened using qPCR. This bacterium was found to be strongly associated with BV (P<0.001, OR 23.3 (95%CI:2.9–190.7)) among the 90 women. Conclusions/Significance This study highlighted the potential of metatranscriptomics as a tool for characterising metabolically active microbiota and identifying targets for further screening. Prevotella amnii was chosen as an example target, being the most metabolically active species present in the single patient with BV, and was found to be detected at a high concentration by qPCR in 31% of cohort with BV, with an association with both oral and penile-vaginal sex. PMID:24086764

  13. Analysis of Potential Deep-Seated Landslide in Hekeng Watershed by Environment Indices

    NASA Astrophysics Data System (ADS)

    Hsieh, C. J.; Chompuchan, C.

    2014-12-01

    Landslides are a major natural disaster in Taiwan relevant to the human life. After the catastrophic Xiaolin landslide during Typhoon Morakot in August 2009 caused around 400 casualties, the deep-seated landslide has become a serious issue. This study explored the potential deep-seated landslide in Hekeng watershed extracted from SPOT-5 imageries. The empirical topographic correction was applied to minimize effect of the mountain shaded area due to the difference of sun elevation and terrain angle. Consequently the multi-temporal environmental indices, i.e., modified Normalized Difference Vegetation Index (mNDVI) and modified Normalized Difference Water Index (mNDWI) were corrected. Seasonal vegetation cover and surface moisture change were analyzed incorporate with a slope which obtain from DEM data. The result showed that the distribution of potential deep-seated landslide vulnerable area mainly located at headstream watershed. It could be explained that the headstream watershed has less human interference, therefore the environmental indices interpreted those area as deep soil layer and dense vegetation coverage. However, the upstream canal could suffer from the long-term erosion and possibly cause slope toe collapse. In addition, the western watershed is the afforestation zone whereas the eastern watershed is natural forest zone with higher development ratio. The upslope forest management of eastern and western watershed should be discussed variously.

  14. A filtering strategy identifies FOXQ1 as a potential effector of lamin A dysfunction.

    PubMed

    Candelario, Jose; Chen, Leng-Ying; Marjoram, Paul; Reddy, Sita; Comai, Lucio

    2012-08-01

    Small increases in the expression of wild-type prelamin A are sufficient to recapitulate the reduced cell proliferation and altered nuclear membrane morphology observed in cells expressing progerin, the mutant lamin A associated with progeria. We hypothesized that the manifestation of these phenotypes in cells expressing elevated levels of wild-type prelamin A or progerin is caused by the same molecular effectors, which play a central role in the onset of the progeroid phenotype. To experimentally test this hypothesis, we compared the transcriptomes of isogenic diploid fibroblasts expressing progerin or elevated levels of wild-type prelamin A with that of wild-type fibroblasts. We subsequently used the reversion towards normal of two phenotypes, reduced cell growth and dismorphic nuclei, by treatment with farnesyltransferase inhibitor (FTI) or overexpression of ZMPSTE24, as a filtering strategy to identify genes linked to the onset of these two phenotypes. Through this analysis we identified the gene encoding for the transcription factor FOXQ1, as a gene whose expression is induced in both cells expressing progerin and elevated levels of wild-type prelamin A, and subsequently reduced in both cell types upon conditions that ameliorate the phenotypes. We overexpressed FOXQ1 in normal fibroblasts and demonstrated that increased levels of this factor lead to the development of both features that were used in the filtering strategy. These findings suggest a potential link between this transcription factor and cell dysfunction induced by altered prelamin A metabolism. PMID:22948034

  15. Using a neural network to identify potential HLA-DR1 binding sites within proteins.

    PubMed

    Bisset, L R; Fierz, W

    1993-03-01

    The presentation by antigen-presenting cells of immunodominant peptide segments in association with major histocompatibility complex (MHC) encoded proteins is fundamental to the efficacy of a specific immune response. One approach used to identify immunodominant segments within proteins has involved the development of predictive algorithms which utilize amino acid sequence data to identify structural characteristics or motifs associated with in vivo antigenicity. The parallel-computing technique termed 'neural networking' has recently been shown to be remarkably efficient at addressing the problem of pattern recognition and can be applied to predict protein secondary structure attributes directly from amino acid sequence data. In order to examine the potential of a neural network to generalize peptide structural features related to binding within class II MHC-encoded proteins, we have trained a neural network to determine whether or not any given amino acid of a protein is part of a peptide segment capable of binding to HLA-DR1. We report that a neural network trained on a data base consisting of peptide segments known to bind to HLA-DR1 is able to generalize features relating to HLA-DR1-binding capacity (r = 0.17 and p = 0.0001). PMID:8251191

  16. Gene Expression Analysis Identifies Potential Biomarkers of Neurofibromatosis Type 1 Including Adrenomedullin

    PubMed Central

    Hummel, Trent R.; Jessen, Walter J.; Miller, Shyra J.; Kluwe, Lan; Mautner, Victor F.; Wallace, Margaret R.; Lázaro, Conxi; Page, Grier P.; Worley, Paul F.; Aronow, Bruce J.; Schorry, Elizabeth K.; Ratner, Nancy

    2016-01-01

    Purpose Plexiform neurofibromas (pNF) are Schwann cell tumors found in a third of individuals with neurofibromatosis type 1 (NF1). pNF can undergo transformation to malignant peripheral nerve sheath tumors (MPNST). There are no identified serum biomarkers of pNF tumor burden or transformation to MPNST. Serum biomarkers would be useful to verify NF1 diagnosis, monitor tumor burden, and/or detect transformation. Experimental Design We used microarray gene expression analysis to define 92 genes that encode putative secreted proteins in neurofibroma Schwann cells, neurofibromas, and MPNST. We validated differential expression by quantitative reverse transcription-PCR, Western blotting, and ELISA assays in cell conditioned medium and control and NF1 patient sera. Results Of 13 candidate genes evaluated, only adrenomedullin (ADM) was confirmed as differentially expressed and elevated in serum of NF1 patients. ADM protein concentrati on was further elevated in serum of a small sampling of NF1 patients with MPNST. MPNST cell conditioned medium, containing ADM and hepatocyte growth factor, stimulated MPNST migration and endothelial cell proliferation. Conclusions Thus, microarray analysis identifies potential serum biomarkers for disease, and ADM is a serum biomarker of NF1. ADM serum levels do not seem to correlate with the presence of pNFs but may be a biomarker of transformation to MPNST. PMID:20739432

  17. GPR56 identifies primary human acute myeloid leukemia cells with high repopulating potential in vivo.

    PubMed

    Pabst, Caroline; Bergeron, Anne; Lavallée, Vincent-Philippe; Yeh, Jonathan; Gendron, Patrick; Norddahl, Gudmundur L; Krosl, Jana; Boivin, Isabel; Deneault, Eric; Simard, Jessica; Imren, Suzan; Boucher, Geneviève; Eppert, Kolja; Herold, Tobias; Bohlander, Stefan K; Humphries, Keith; Lemieux, Sébastien; Hébert, Josée; Sauvageau, Guy; Barabé, Frédéric

    2016-04-21

    Acute myeloid leukemia (AML) is a genetically heterogeneous hematologic malignancy, which is initiated and driven by a rare fraction of leukemia stem cells (LSCs). Despite the difficulties of identifying a common LSC phenotype, there is increasing evidence that high expression of stem cell gene signatures is associated with poor clinical outcome. Identification of functionally distinct subpopulations in this disease is therefore crucial to dissecting the molecular machinery underlying LSC self-renewal. Here, we combined next-generation sequencing technology with in vivo assessment of LSC frequencies and identified the adhesion G protein-coupled receptor 56 (GPR56) as a novel and stable marker for human LSCs for the majority of AML samples. High GPR56 expression was significantly associated with high-risk genetic subgroups and poor outcome. Analysis of GPR56 in combination with CD34 expression revealed engraftment potential of GPR56(+)cells in both the CD34(-)and CD34(+)fractions, thus defining a novel LSC compartment independent of the CD34(+)CD38(-)LSC phenotype. PMID:26834243

  18. Identifying potential misfit items in cognitive process of learning engineering mathematics based on Rasch model

    NASA Astrophysics Data System (ADS)

    Ataei, Sh; Mahmud, Z.; Khalid, M. N.

    2014-04-01

    The students learning outcomes clarify what students should know and be able to demonstrate after completing their course. So, one of the issues on the process of teaching and learning is how to assess students' learning. This paper describes an application of the dichotomous Rasch measurement model in measuring the cognitive process of engineering students' learning of mathematics. This study provides insights into the perspective of 54 engineering students' cognitive ability in learning Calculus III based on Bloom's Taxonomy on 31 items. The results denote that some of the examination questions are either too difficult or too easy for the majority of the students. This analysis yields FIT statistics which are able to identify if there is data departure from the Rasch theoretical model. The study has identified some potential misfit items based on the measurement of ZSTD where the removal misfit item was accomplished based on the MNSQ outfit of above 1.3 or less than 0.7 logit. Therefore, it is recommended that these items be reviewed or revised to better match the range of students' ability in the respective course.

  19. Subtype distribution of Blastocystis isolates identified in a Sydney population and pathogenic potential of Blastocystis.

    PubMed

    Roberts, T; Stark, D; Harkness, J; Ellis, J

    2013-03-01

    Blastocystis is one of the most common enteric parasites present in humans. There is still much uncertainty about the pathogenic potential of this parasite, and it was suggested that its pathogenicity could be subtype-related. This report aimed to study 98 Blastocystis isolates found in human stool specimens to identify the subtypes present and carry out phylogenetic analysis on these isolates. This study also aimed to show the relationship between subtype and symptoms. Five-hundred and thirteen stool samples were submitted to five different diagnostic techniques for the detection of Blastocystis. Polymerase chain reaction (PCR)-positive samples were then sequenced and the small subunit (SSU) rDNA sequences were aligned and submitted to phylogenetic analysis. Ninety-eight samples were positive by any of the diagnostic methods for Blastocystis and 96 were positive by PCR. There were seven different subtypes (1, 2, 3, 4, 6, 7 and 8) identified by PCR and sequencing. This is the first large-scale study to examine the occurrence of Blastocystis in Australia. This study reports the high incidence of subtype 3 (44%) in this population and discusses the emerging idea of subtype-dependent pathogenicity. PMID:22996007

  20. Network Analysis Identifies SOD2 mRNA as a Potential Biomarker for Parkinson's Disease

    PubMed Central

    Santiago, Jose A.; Scherzer, Clemens R.; Potashkin, Judith A.

    2014-01-01

    Increasing evidence indicates that Parkinson's disease (PD) and type 2 diabetes (T2DM) share dysregulated molecular networks. We identified 84 genes shared between PD and T2DM from curated disease-gene databases. Nitric oxide biosynthesis, lipid and carbohydrate metabolism, insulin secretion and inflammation were identified as common dysregulated pathways. A network prioritization approach was implemented to rank genes according to their distance to seed genes and their involvement in common biological pathways. Quantitative polymerase chain reaction assays revealed that a highly ranked gene, superoxide dismutase 2 (SOD2), is upregulated in PD patients compared to healthy controls in 192 whole blood samples from two independent clinical trials, the Harvard Biomarker Study (HBS) and the Diagnostic and Prognostic Biomarkers in Parkinson's disease (PROBE). The results from this study reinforce the idea that shared molecular networks between PD and T2DM provides an additional source of biologically meaningful biomarkers. Evaluation of this biomarker in de novo PD patients and in a larger prospective longitudinal study is warranted. PMID:25279756

  1. Omen: identifying potential spear-phishing targets before the email is sent.

    SciTech Connect

    Wendt, Jeremy Daniel

    2013-07-01

    We present the results of a two year project focused on a common social engineering attack method called %22spear phishing%22. In a spear phishing attack, the user receives an email with information specifically focused on the user. This email contains either a malware-laced attachment or a link to download the malware that has been disguised as a useful program. Spear phishing attacks have been one of the most effective avenues for attackers to gain initial entry into a target network. This project focused on a proactive approach to spear phishing. To create an effective, user-specific spear phishing email, the attacker must research the intended recipient. We believe that much of the information used by the attacker is provided by the target organization's own external website. Thus when researching potential targets, the attacker leaves signs of his research in the webserver's logs. We created tools and visualizations to improve cybersecurity analysts' abilities to quickly understand a visitor's visit patterns and interests. Given these suspicious visitors and log-parsing tools, analysts can more quickly identify truly suspicious visitors, search for potential spear-phishing targeted users, and improve security around those users before the spear phishing email is sent.

  2. A Quest to Identify Prostate Cancer Circulating Biomarkers with a Bench-to-Bedside Potential

    PubMed Central

    Batra, Jaspreet Singh; Girdhani, Swati

    2014-01-01

    Prostate cancer (PCA) is a major health concern in current times. Ever since prostate specific antigen (PSA) was introduced in clinical practice almost three decades ago, the diagnosis and management of PCA have been revolutionized. With time, concerns arose as to the inherent shortcomings of this biomarker and alternatives were actively sought. Over the past decade new PCA biomarkers have been identified in tissue, blood, urine, and other body fluids that offer improved specificity and supplement our knowledge of disease progression. This review focuses on superiority of circulating biomarkers over tissue biomarkers due to the advantages of being more readily accessible, minimally invasive (blood) or noninvasive (urine), accessible for sampling on regular intervals, and easily utilized for follow-up after surgery or other treatment modalities. Some of the circulating biomarkers like PCA3, IL-6, and TMPRSS2-ERG are now detectable by commercially available kits while others like microRNAs (miR-21, -221, -141) and exosomes hold potential to become available as multiplexed assays. In this paper, we will review some of these potential candidate circulating biomarkers that either individually or in combination, once validated with large-scale trials, may eventually get utilized clinically for improved diagnosis, risk stratification, and treatment. PMID:26317031

  3. Development of a Fire Risk Model to Identify Areas of Increased Potential for Fire Occurrences.

    PubMed

    Lehna, Carlee; Speller, Amanda; Hanchette, Carol; Fahey, Erin; Coty, Mary-Beth

    2016-01-01

    The purposes of this study were to use geographic information systems to create a cartographic risk model predicting areas of increased potential for fire occurrences and to validate the model. Seven literature-identified risk factors associated with burn injury were older than 65 years, non-white race, below high school education, low socioeconomic status, rented housing, year home built, and home value. Geographic information system methods were used in risk factor model development. Model validation occurred using residential county fire dispatch data and statistical analysis. Areas of high and severe risk were primarily located in the northwestern and central county regions. A strong correlation (r = .66) was found between risk model scores and fire incidence rates. Significant differences in mean fire rates by risk category (F (187,3) = 87.58, P < .0001) were found, with the exception of the low and medium risk categories. Fire incidence rates among census tracts showed positive spatial autocorrelation (Moran's I = 0.542, P < .0001) producing a map showing a significant cluster of high fire incidence in the northwestern region. The risk model has potential to lead to more targeted and effective fire prevention education programs. Such models would allow fire departments to focus limited resources in areas of highest fire risk. PMID:26284643

  4. Structured methods for identifying and correcting potential human errors in space operations.

    PubMed

    Nelson, W R; Haney, L N; Ostrom, L T; Richards, R E

    1998-01-01

    Human performance plays a significant role in the development and operation of any complex system, and human errors are significant contributors to degraded performance, incidents, and accidents for technologies as diverse as medical systems, commercial aircraft, offshore oil platforms, nuclear power plants, and space systems. To date, serious accidents attributed to human error have fortunately been rare in space operations. However, as flight rates go up and the duration of space missions increases, the accident rate could increase unless proactive action is taken to identity and correct potential human errors in space operations. The Idaho National Engineering and Environmental Laboratory (INEEL) has developed and applied structured methods of human error analysis to identify potential human errors, assess their effects on system performance, and develop strategies to prevent the errors or mitigate their consequences. These methods are being applied in NASA-sponsored programs to the domain of commercial aviation, focusing on airplane maintenance and air traffic management. The application of human error analysis to space operations could contribute to minimize the risks associated with human error in the design and operation of future space systems. PMID:11541925

  5. Discussion on pharmacogenetic interaction in G6PD deficiency and methods to identify potential hemolytic drugs.

    PubMed

    Manganelli, Genesia; Fico, Annalisa; Martini, Giuseppe; Filosa, Stefania

    2010-06-01

    Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common form of red blood cell enzymopathy. The disorder has reached polymorphic frequencies in different parts of the world due to the relative protection conferred against malaria. G6PD is a housekeeping X-linked gene encoding the first enzyme of the pentose phosphate pathway, an NADPH-producing dehydrogenase. Because erythrocytes do not generate NADPH in any other way than pentose phosphate pathway, they are more susceptible than any other cells to oxidative damages. G6PD deficiency is a prime example of a hemolytic anemia due to an interaction between an intracorpuscular cause and an extracorpuscular cause, because in the majority of cases an exogenous agent triggers hemolysis. Hemolysis, in fact, can be caused by exposure to oxidant agents. Although studies performed on epidemiology, genetics and molecular biology have broaden the information on G6pd deficiency, there are still no reliable and validated methods to test drug hemolytic potential in G6PD deficient patients. The review gives an overview of current knowledge on G6pd deficiency and on the methods that have been developed so far in order to identify drugs causing acute hemolytic anemia in G6pd deficiency. Moreover, we discuss the new potential preclinical strategies to assess, in vitro and in vivo, drug hemolytic risks. PMID:20350285

  6. CD133: a potential indicator for differentiation and prognosis of human cholangiocarcinoma

    PubMed Central

    2011-01-01

    Background CD133 is known to be a cancer stem cell (CSC) marker. However, recent studies have revealed that CD133 is not restricted to CSC but to be expressed not only in human normal tissues but also in some cancers and could serve as a prognostic factor for the patients. Nevertheless, the expression of CD133 in human cholangiocarcinoma (CC) is rare and our study is to detect the expression and explore the potential functions of CD133 in human CC. Methods Fifty-nine cases, comprised of 5 normal liver tissues and 54 consecutive CC specimens (21 well-differentiated, 12 moderately-differentiated and 21 poorly-differentiated), were included in the study. Immunohistochemical stainning with CD133 protein was carried out, and statistical analyses were performed. Results CD133 was found to express in all 5 normal livers and 40 out of 54 (74%) CC tissues with different subcellular localization. In the well, moderately and poorly differentiated cases, the numbers of CD133 positive cases were 19 (19 of 21, 90%), 10 (10 of 12, 83%) and 11 (11 of 21, 52%) respectively. Further statistical analyses indicated that the expression and different subcellular localization of CD133 were significantly correlated with the differentiation status of tumors (P = 0.004, P = 0.009). Among 23 patients followed up for survival, the median survival was 4 months for fourteen CD133 negative patients but 14 months for nine CD133 positive ones. In univariate survival analysis, CD133 negative expression correlated with poor prognosis while CD133 positive expression predicted a favorable outcome of CC patients (P = 0.001). Conclusions Our study demonstrates that CD133 expression correlates with the differentiation of CC and indicates that CD133 is a potential indicator for differentiation and prognosis of human CC. PMID:21798073

  7. Two mechanisms by which fluorescent oxonols indicate membrane potential in human red blood cells.

    PubMed Central

    Pratap, P R; Novak, T S; Freedman, J C

    1990-01-01

    Optical potentiometric indicators have been used to monitor the transmembrane electrical potential (Em) of many cells and organelles. A better understanding of the mechanisms of dye response is needed for the design of dyes with improved responses and for unambiguous interpretation of experimental results. This paper describes the responses to delta Em of 20 impermeant oxonols in human red blood cells. Most of the oxonols interacted with valinomycin, but not with gramicidin. The fluorescence of 15 oxonols decreased with hyperpolarization, consistent with an "on-off" mechanism, whereas five oxonols unexpectedly showed potential-dependent increases in fluorescence at less than 2 microM [dye]. Binding curves were determined for two dyes (WW781, negative response and RGA451, positive response) at 1 mM [K]o (membrane hyperpolarized with gramicidin) and at 90 mM [K]o (delta Em = 0 with gramicidin). Both dyes showed potential-dependent decreases in binding. Changes in the fluorescence of cell suspensions correlated with changes in [dye]bound for WW781, in accordance with the "on-off" mechanism, but not for RGA451. Large positive fluorescence changes (greater than 30%) dependent on Em were observed between 0.1 and 1.0 microM RGA451. A model is suggested in which RGA451 moves between two states of different quantum efficiencies within the membrane. PMID:1693090

  8. International comparison of cave radon concentrations identifying the potential alpha radiation risks to British cave users

    SciTech Connect

    Hyland, R.; Gunn, J.

    1994-08-01

    Elevated concentrations of {sup 222}Rn have been recorded in many limestone caves throughout the world. As prolonged exposure to high radon concentrations has been linked to cancer and tumors, particularly of the lung, a national survey of radon in British caves was undertaken. Passive radon detectors were exposed at 250 sites in 47 caves over four 7-d sampling periods. Mean concentrations ranging from 454-8,868 Bq m{sup {minus}3} were recorded. In one system, in the Peak District, radon concentrations of 155,000 Bq m{sup {minus}3} were recorded. The results indicate that the potential radiation dose from a single 4-h trip could exceed the national average annual background radiation dose (for the UK) from radon of 1.25 mSv. 18 refs., 3 tabs.

  9. International comparison of cave radon concentrations identifying the potential alpha radiation risks to British cave users.

    PubMed

    Hyland, R; Gunn, J

    1994-08-01

    Elevated concentrations of 222Rn have been recorded in many limestone caves throughout the world. As prolonged exposure to high radon concentrations has been linked to cancer and tumors, particularly of the lung (National Academy of Science 1988; Eatough and Henshaw 1990), a national survey of radon in British caves was undertaken. Passive radon detectors were exposed at 250 sites in 47 caves over four 7-d sampling periods. Mean concentrations ranging from 454-8,868 Bq m-3 were recorded. In one system, in the Peak District, radon concentrations of 155,000 Bq m-3 were recorded. The results indicate that the potential radiation dose from a single 4-h trip could exceed the national average annual background radiation dose (for the UK) from radon of 1.25 mSv. PMID:8026972

  10. Using event related potentials to identify a user's behavioural intention aroused by product form design.

    PubMed

    Ding, Yi; Guo, Fu; Zhang, Xuefeng; Qu, Qingxing; Liu, Weilin

    2016-07-01

    The capacity of product form to arouse user's behavioural intention plays a decisive role in further user experience, even in purchase decision, while traditional methods rarely give a fully understanding of user experience evoked by product form, especially the feeling of anticipated use of product. Behavioural intention aroused by product form designs has not yet been investigated electrophysiologically. Hence event related potentials (ERPs) were applied to explore the process of behavioural intention when users browsed different smart phone form designs with brand and price not taken into account for mainly studying the brain activity evoked by variety of product forms. Smart phone pictures with different anticipated user experience were displayed with equiprobability randomly. Participants were asked to click the left mouse button when certain picture gave them a feeling of behavioural intention to interact with. The brain signal of each participant was recorded by Curry 7.0. The results show that pictures with an ability to arouse participants' behavioural intention for further experience can evoke enhanced N300 and LPPs (late positive potentials) in central-parietal, parietal and occipital regions. The scalp topography shows that central-parietal, parietal and occipital regions are more activated. The results indicate that the discrepancy of ERPs can reflect the neural activities of behavioural intention formed or not. Moreover, amplitude of ERPs occurred in corresponding brain areas can be used to measure user experience. The exploring of neural correlated with behavioural intention provide an accurate measurement method of user's perception and help marketers to know which product can arouse users' behavioural intention, maybe taken as an evaluating indicator of product design. PMID:26995041

  11. Transcriptome analysis of Burkholderia pseudomallei T6SS identifies Hcp1 as a potential serodiagnostic marker.

    PubMed

    Chieng, Sylvia; Mohamed, Rahmah; Nathan, Sheila

    2015-02-01

    Burkholderia pseudomallei, the causative agent of melioidosis, is able to survive extreme environments and utilizes various virulence factors for survival and pathogenicity. To compete and survive within these different ecological niches, B. pseudomallei has evolved specialized pathways, including the Type VI secretion systems (T6SSs), that have a role in pathogenesis as well as interbacterial interactions. We examined the expression profile of B. pseudomallei T6SS six gene clusters during infection of U937 macrophage cells. T6SS-5 was robustly transcribed while the other five clusters were not significantly regulated proposing the utility of T6SS-5 as a potential biomarker of exposure to B. pseudomallei. Transcription of T6SS regulators VirAG and BprB was also not significant during infection when compared to bacteria grown in culture. Guided by these findings, three highly expressed T6SS genes, tssJ-4, hcp1 and tssE-5, were expressed as recombinant proteins and screened against melioidosis patient sera by western analysis and ELISA. Only Hcp1 was reactive by both types of analysis. The recombinant Hcp1 protein was further evaluated against a cohort of melioidosis patients (n = 32) and non-melioidosis individuals (n = 20) sera and the data clearly indicates a higher sensitivity (93.7%) and specificity (100%) for Hcp1 compared to bacterial lysate. The detection of anti-Hcp1 antibodies in patients' sera indicating the presence of B. pseudomallei highlights the potential of Hcp1 to be further developed as a serodiagnostic marker for melioidosis. PMID:25616255

  12. Measuring Quality in Higher Education: Can a Performance Indicator Approach Be Extended to Identifying the Quality of Students' Union Provision?

    ERIC Educational Resources Information Center

    Rodgers, Timothy

    2008-01-01

    The desire to enhance the quality of the services provided by higher education institutions in the UK has led to the development of a series of benchmarking performance indicators to aid the quality management process. This paper examines whether or not similar indicators could be developed for use as tools in the management of quality within…

  13. Expression Profiling Identifies Bezafibrate as Potential Therapeutic Drug for Lung Adenocarcinoma

    PubMed Central

    Liu, Xinyan; Yang, Xiaoqin; Chen, Xinmei; Zhang, Yantao; Pan, Xuebin; Wang, Guiping; Ye, Yun

    2015-01-01

    Drug-induced gene expression patterns that invert disease profiles have recently been illustrated to be a new strategy for drug-repositioning. In the present study, we validated this approach and focused on prediction of novel drugs for lung adenocarcinoma (AC), for which there is a pressing need to find novel therapeutic compounds. Firstly, connectivity map (CMap) analysis computationally predicted bezafibrate as a putative compound against lung AC. Then this hypothesis was verified by in vitro assays of anti-proliferation and cell cycle arrest. In silico docking evidence indicated that bezafibrate could target cyclin dependent kinase 2(CDK2), which regulates progression through the cell cycle. Furthermore, we found that bezafibrate can significantly down-regulate the expression of CDK2 mRNA and p-CDK2. Using a nude mice xenograft model, we also found that bezafibrate could inhibit tumor growth of lung AC in vivo. In conclusion, this study proposed bezafibrate as a potential therapeutic option for lung AC patients, illustrating the potential of in silico drug screening. PMID:26535062

  14. Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite.

    PubMed

    An, Dongshan; Dong, Xiaoli; An, Annie; Park, Hyung S; Strous, Marc; Voordouw, Gerrit

    2016-01-01

    Sodium bisulfite (SBS) is used as an oxygen scavenger to decrease corrosion in pipelines transporting brackish subsurface water used in the production of bitumen by steam-assisted gravity drainage. Sequencing 16S rRNA gene amplicons has indicated that SBS addition increased the fraction of the sulfate-reducing bacteria (SRB) Desulfomicrobium, as well as of Desulfocapsa, which can also grow by disproportionating sulfite into sulfide, sulfur, and sulfate. SRB use cathodic H2, formed by reduction of aqueous protons at the iron surface, or use low potential electrons from iron and aqueous protons directly for sulfate reduction. In order to reveal the effects of SBS treatment in more detail, metagenomic analysis was performed with pipe-associated solids (PAS) scraped from a pipe section upstream (PAS-616P) and downstream (PAS-821TP) of the SBS injection point. A major SBS-induced change in microbial community composition and in affiliated hynL genes for the large subunit of [NiFe] hydrogenase was the appearance of sulfur-metabolizing Epsilonproteobacteria of the genera Sulfuricurvum and Sulfurovum. These are chemolithotrophs, which oxidize sulfide or sulfur with O2 or reduce sulfur with H2. Because O2 was absent, this class likely catalyzed reduction of sulfur (S(0)) originating from the metabolism of bisulfite with cathodic H2 (or low potential electrons and aqueous protons) originating from the corrosion of steel (Fe(0)). Overall this accelerates reaction of of S(0) and Fe(0) to form FeS, making this class a potentially powerful contributor to microbial corrosion. The PAS-821TP metagenome also had increased fractions of Deltaproteobacteria including the SRB Desulfomicrobium and Desulfocapsa. Altogether, SBS increased the fraction of hydrogen-utilizing Delta- and Epsilonproteobacteria in brackish-water-transporting pipelines, potentially stimulating anaerobic pipeline corrosion if dosed in excess of the intended oxygen scavenger function. PMID:26858705

  15. Dipole potentials indicate restructuring of the membrane interface induced by gadolinium and beryllium ions

    NASA Technical Reports Server (NTRS)

    Ermakov, Y. A.; Averbakh, A. Z.; Yusipovich, A. I.; Sukharev, S.

    2001-01-01

    The dipole component of the membrane boundary potential, phi(d), is an integral parameter that may report on the conformational state of the lipid headgroups and their hydration. In this work, we describe an experimental approach to measurements of the dipole potential changes, Deltaphi(d), and apply it in studies of Be(2+) and Gd(3+) interactions with membranes composed of phosphatidylserine (PS), phosphatidylcholine (PC), and their mixtures. Deltaphi(d) is determined as the difference between the changes of the total boundary potential, phi(b), measured by the IFC method in planar lipid membranes and the surface potential, phi(s), determined from the electrophoretic mobility of liposomes. The Gouy-Chapman-Stern formalism, combined with the condition of mass balance, well describes the ion equilibria for these high-affinity cations. For the adsorption of Be(2+) and Gd(3+) to PC membranes, and of Mg(2+) to PS membranes, the values of Deltaphi(b) and Deltaphi(s) are the same, indicative of no change of phi(d). Binding of Gd(3+) to PS-containing membranes induces changes of phi(d) of opposite signs depending on the density of ionized PS headgroups in the bilayer. At low density, the induced Deltaphi(d) is negative (-30 mV), consistent with the effect of dehydration of the surface. At maximal density (pure PS, neutral pH), adsorption of Be(2+) or Gd(3+) induces an increase of phi(d) of 35 or 140 mV, respectively. The onset of the strong positive dipole effect on PS membranes with Gd(3+) is observed near the zero charge point and correlates with a six-fold increase of membrane tension. The observed phenomena may reflect concerted reorientation of dipole moments of PS headgroups as a result of ion adsorption and lipid condensation. Their possible implications to in-vivo effects of these high-affinity ions are discussed.

  16. Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite

    PubMed Central

    An, Dongshan; Dong, Xiaoli; An, Annie; Park, Hyung S.; Strous, Marc; Voordouw, Gerrit

    2016-01-01

    Sodium bisulfite (SBS) is used as an oxygen scavenger to decrease corrosion in pipelines transporting brackish subsurface water used in the production of bitumen by steam-assisted gravity drainage. Sequencing 16S rRNA gene amplicons has indicated that SBS addition increased the fraction of the sulfate-reducing bacteria (SRB) Desulfomicrobium, as well as of Desulfocapsa, which can also grow by disproportionating sulfite into sulfide, sulfur, and sulfate. SRB use cathodic H2, formed by reduction of aqueous protons at the iron surface, or use low potential electrons from iron and aqueous protons directly for sulfate reduction. In order to reveal the effects of SBS treatment in more detail, metagenomic analysis was performed with pipe-associated solids (PAS) scraped from a pipe section upstream (PAS-616P) and downstream (PAS-821TP) of the SBS injection point. A major SBS-induced change in microbial community composition and in affiliated hynL genes for the large subunit of [NiFe] hydrogenase was the appearance of sulfur-metabolizing Epsilonproteobacteria of the genera Sulfuricurvum and Sulfurovum. These are chemolithotrophs, which oxidize sulfide or sulfur with O2 or reduce sulfur with H2. Because O2 was absent, this class likely catalyzed reduction of sulfur (S0) originating from the metabolism of bisulfite with cathodic H2 (or low potential electrons and aqueous protons) originating from the corrosion of steel (Fe0). Overall this accelerates reaction of of S0 and Fe0 to form FeS, making this class a potentially powerful contributor to microbial corrosion. The PAS-821TP metagenome also had increased fractions of Deltaproteobacteria including the SRB Desulfomicrobium and Desulfocapsa. Altogether, SBS increased the fraction of hydrogen-utilizing Delta- and Epsilonproteobacteria in brackish-water-transporting pipelines, potentially stimulating anaerobic pipeline corrosion if dosed in excess of the intended oxygen scavenger function. PMID:26858705

  17. Identifying Key Issues and Potential Solutions for Integrated Arrival, Departure, Surface Operations by Surveying Stakeholder Preferences

    NASA Technical Reports Server (NTRS)

    Aponso, Bimal; Coppenbarger, Richard A.; Jung, Yoon; Quon, Leighton; Lohr, Gary; O’Connor, Neil; Engelland, Shawn

    2015-01-01

    NASA's Aeronautics Research Mission Directorate (ARMD) collaborates with the FAA and industry to provide concepts and technologies that enhance the transition to the next-generation air-traffic management system (NextGen). To facilitate this collaboration, ARMD has a series of Airspace Technology Demonstration (ATD) sub-projects that develop, demonstrate, and transitions NASA technologies and concepts for implementation in the National Airspace System (NAS). The second of these sub-projects, ATD-2, is focused on the potential benefits to NAS stakeholders of integrated arrival, departure, surface (IADS) operations. To determine the project objectives and assess the benefits of a potential solution, NASA surveyed NAS stakeholders to understand the existing issues in arrival, departure, and surface operations, and the perceived benefits of better integrating these operations. NASA surveyed a broad cross-section of stakeholders representing the airlines, airports, air-navigation service providers, and industry providers of NAS tools. The survey indicated that improving the predictability of flight times (schedules) could improve efficiency in arrival, departure, and surface operations. Stakeholders also mentioned the need for better strategic and tactical information on traffic constraints as well as better information sharing and a coupled collaborative planning process that allows stakeholders to coordinate IADS operations. To assess the impact of a potential solution, NASA sketched an initial departure scheduling concept and assessed its viability by surveying a select group of stakeholders for a second time. The objective of the departure scheduler was to enable flights to move continuously from gate to cruise with minimal interruption in a busy metroplex airspace environment using strategic and tactical scheduling enhanced by collaborative planning between airlines and service providers. The stakeholders agreed that this departure concept could improve schedule predictability and suggested several key attributes that were necessary to make the concept successful. The goals and objectives of the planned ATD-2 sub-project will incorporate the results of this stakeholder feedback.

  18. Identifying remote paleoclimate proxies with potential for inferring long-term hydroclimatic variability

    NASA Astrophysics Data System (ADS)

    Ho, M. W.; Verdon-Kidd, D. C.; Kiem, A.; Drysdale, R.

    2012-12-01

    Recent advances in the collection and analysis of paleoclimate information have allowed insights into historical environmental events and processes prior to the availability of instrumental records, enabling greater understanding of long-term environmental change and associated hydroclimatic risks. However, there is still currently a lack of paleoclimate information in many areas where such insights and long-term data are crucial (Gell et al., 2009). The Murray-Darling Basin (MDB), Australia's 'food bowl', is a prime example of this, where currently there is very limited in situ proxy data available. To date, only three studies have attempted to incorporate paleoclimate archives in the investigation of long-term hydroclimatic variability in the MDB (Gallant and Gergis, 2011, Verdon and Franks, 2007, McGowan et al., 2009). These studies utilized existing remote paleoclimate proxies of large-scale climate mechanisms (such as the El Niño/Southern Oscillation and the Interdecadal Pacific Oscillation) to infer MDB hydroclimatic variability, but there is a lack of studies that identify key land-based Australian regions that could be used to inform pre-instrumental MDB hydroclimatic reconstructions within the Common Era. This study identifies key locations where paleoclimate information that currently exists within Australia is most useful for expanding long-term knowledge of MDB hydroclimatology. Regions where the future collection and interpretation of as yet unrealized paleoclimate archives that are of greatest value are also identified. To pinpoint the crucial existing or potential paleoclimate proxy locations, rainfall relationships between the MDB and remote locations within Australia have been explored through correlations and principal component analysis (Jolliffe, 2002) using both the Australian High Quality gauged rainfall network (Lavery et al., 1997) and the Australian Water Availability Project interpolated gridded dataset (Jones et al., 2007). The rainfall-rainfall relationship fields were then overlain by locations of known proxy records in order to assess each record's contribution to the overall variability of MDB rainfall, as well as highlight regions where strong relationships exist and paleoclimate sources have yet to be explored. An objective analysis using optimal interpolation (Evans et al., 1998) is currently being investigated to identify the most strategic locations and quantify the benefit of obtaining and analyzing additional paleoclimate information. While this study focuses on the MDB and Australian paleoclimate archives, the techniques used could be applied to any region that currently lacks extensive instrumental records, paleoclimate proxy records or both. This would enable improved assessments of long-term interannual to multidecadal hydroclimatic risks.

  19. Potential for identifying abiotic chloroalkane degradation mechanisms using carbon isotopic fractionation.

    PubMed

    Vanstone, Nancy; Elsner, Martin; Lacrampe-Couloume, Georges; Mabury, Scott; Lollar, Barbara Sherwood

    2008-01-01

    Degradation of 1,1- and 1,2-dichloroethane (1,1-DCA, 1,2-DCA) and carbon tetrachloride (CCl4) on Zn0 was investigated using compound specific isotope analysis (CSIA) to measure isotopic fractionation factors for chloroalkane degradation by hydrogenolysis, by alpha-elimination, and by beta-elimination. Significant differences in enrichment factors (epsilon) and associated apparent kinetic isotope effects (AKIE) were measured for these different reaction pathways, suggesting that carbon isotope fractionation by beta-elimination is substantially larger than fractionation by hydrogenolysis or by alpha-elimination. Specifically, for 1,1-DCA, the isotopic composition of the reductive alpha-elimination product (ethane) and the hydrogenolysis product (chloroethane) were the same, indicating that cleavage of a single C-Cl bond was the rate-limiting step in both cases. In contrast, for 1,2-DCA, epsilon = epsilon(reactive position) = -29.7 +/- 1.5% per hundred, and the calculated AKIE (1.03) indicated that beta-elimination was likely concerted, possibly involving two C-Cl bonds simultaneously. Compared to 1,1-DCA hydrogenolysis, the AKIE of 1.01 for hydrogenolysis of CCl4 was much lower, indicating that, for this highly reactive organohalide, mass transfer to the surface was likely partially rate-limiting. These findings are a first step toward delineating the relative contribution of these competing pathways in other abiotic systems such as the degradation of chlorinated ethenes on zerovalent iron (ZVI), iron sulfide, pyrite, or magnetite, and, potentially, toward distinguishing between degradation of chlorinated ethenes by abiotic versus biotic processes. PMID:18350886

  20. Groundwater baseline sampling programs designed to identify potential leakage from unconventional gas plays in Alberta, Canada

    NASA Astrophysics Data System (ADS)

    Mayer, B.; Humez, P.; Ing, J.; Nightingale, M.

    2014-12-01

    With the rapid expansion of natural gas exploitation from unconventional reservoirs including coalbed methane and shale gas plays, there is significant public concern about potential future contamination of shallow potable groundwater with stray gases, formation waters or chemicals used during hydraulic fracturing. In order to enable a scientifically sound assessment of potential future deterioration of freshwater resources in shallow aquifers, it is essential to first establish and understand the current baseline of groundwater quality including its dissolved or free gases. Since 2006, we have conducted monitoring programs determining the chemical and isotopic compositions of water, its dissolved constituents, and of gases obtained from shallow groundwater and formation fluids collected from coalbed methane and shale gas plays in Western Canada. For groundwater samples, we placed special emphasis on determining the sources of dissolved and free gases using isotope techniques to assess whether gases produced from shale gas plays or potentially leaking from the intermediate zone are isotopically distinct from those in shallow aquifers. Methane and ethane in free gas samples obtained from shallow aquifers (n = 24) were found to have mean δ13C values of -72.4 ‰ and -50.2 ‰, respectively. These values are markedly different from the much higher δ13C values of methane and ethane in deeper portions of the Western Canadian Sedimentary Basin and in shale gas plays. Therefore, it appears highly feasible to identify potential gas leakage from unconventional gas plays provided that baseline data for shallow groundwater have been determined. Repeat baseline sampling of free gas from selected wells revealed a comparatively low variability of δ13C values of methane and ethane of usually < 2 ‰ over periods of several years, suggesting that it is not necessary to conduct baseline analyses more than three times. Also, δ13C values of methane in free gas samples and dissolved gas samples typically agreed within 1 ‰ suggesting that both sampling approaches are suitable for determining baseline carbon isotope ratios in case that methane occurs in shallow aquifers.

  1. University males' sexual interest in children: predicting potential indices of "pedophilia" in a nonforensic sample.

    PubMed

    Briere, J; Runtz, M

    1989-01-01

    A survey was administered to 193 male undergraduate students regarding their sexual interest in children, as well as their responses to a number of questions theoretically relevant to pedophilia. In total, 21% of subjects reported sexual attraction to some small children, 9% described sexual fantasies involving children, 5% admitted to having masturbated to such fantasies, and 7% indicated some likelihood of having sex with a child if they could avoid detection and punishment. These sexual interests were associated with negative early sexual experiences, masturbation to pornography, self-reported likelihood of raping a woman, frequent sex partners, sexual conflicts, and attitudes supportive of sexual dominance over women. The data did not, however, support clinical theories regarding sexual repression or impulse-control problems among potential pedophiles. PMID:2706562

  2. Long-term characterization of residential runoff and assessing potential surrogates of fecal indicator organisms.

    PubMed

    Reano, Dane C; Haver, Darren L; Oki, Lorence R; Yates, Marylynn V

    2015-05-01

    Investigations into the microbiological impacts of urban runoff on receiving water bodies, especially during storm conditions, have yielded general paradigms that influence runoff abatement and control management strategies. To determine whether these trends are present in other runoff sources, the physical, chemical, and microbiological components of residential runoff from eight neighborhoods in Northern and Southern California were characterized over the course of five years. Sampling occurred regularly and during storm events, resulting in 833 data sets. Analysis of runoff data assisted in characterizing residential runoff, elucidating differences between dry and storm conditions, and identifying surrogates capable of assessing microbiological quality. Results indicate that although microbial loading increases during storm events similar to urban runoff, annual microbial loading in these study sites principally occurs during dry conditions (24% storm, 76% dry). Generated artificial neural network and multiple linear regression models assessed surrogate performance by accurately predicting Escherichia coli concentrations from validation data sets (R(2) = 0.74 and 0.77, respectively), but required input from other fecal indicator organism (FIO) variables to maintain performance (R(2) = 0.27 and 0.18, respectively, without FIO). This long-term analysis of residential runoff highlights characteristics distinct from urban runoff and establishes necessary variables for determining microbiological quality, thus better informing future management strategies. PMID:25710901

  3. Fault locking near Istanbul: indication of earthquake potential from InSAR and GPS observations

    NASA Astrophysics Data System (ADS)

    Diao, Faqi; Walter, Thomas R.; Solaro, Giuseppe; Wang, Rongjiang; Bonano, Manuela; Manzo, Mariarosaria; Ergintav, Semih; Zheng, Yong; Xiong, Xiong; Lanari, Riccardo

    2016-04-01

    A sequence of large earthquakes occurred along the North Anatolian fault in the 20th century. These earthquakes, including the 1999 İzmit/Düzce earthquakes, generally propagated westward towards the Marmara Sea, defining the Main Marmara fault as a potential seismic gap. It is important to conduct a detailed assessment of the seismic hazards along the main Marmara fault because the megacity Istanbul lies only approximately 10 km north of the eastern segment of the Main Marmara fault, which is referred to as the Princes' Islands Fault segment (PIF). Here, we study the locking status of this fault segment to evaluate the seismic hazard potential. For the first time, combined ascending and descending Interferometric Synthetic Aperture Radar and Global Positioning System observations were used to investigate the crustal deformation associated with the PIF. After careful corrections of the estimated ground velocity, a deformation pattern relating to fault locking near the Princes' Islands was identified. The modeling results revealed that the slip rate and locking depth of the fault segment show a clear trade-off, which were estimated as 18.9 ± 7.2 mm yr-1 and 12.1 ± 7.0 km, respectively. With a moment accumulation rate of 1.7 ± 0.4 × 1017 Nm yr-1 (proportional to the product of slip rate and locking depth), our results imply a build-up of a geodetic moment on the PIF and therefore a potential for earthquake hazards in the vicinity of the Istanbul megacity.

  4. Fault locking near Istanbul: indication of earthquake potential from InSAR and GPS observations

    NASA Astrophysics Data System (ADS)

    Diao, Faqi; Walter, Thomas R.; Solaro, Giuseppe; Wang, Rongjiang; Bonano, Manuela; Manzo, Mariarosaria; Ergintav, Semih; Zheng, Yong; Xiong, Xiong; Lanari, Riccardo

    2016-02-01

    A sequence of large earthquakes occurred along the North Anatolian fault in the 20th century. These earthquakes, including the 1999 İzmit/Düzce earthquakes, generally propagated westward towards the Marmara Sea, defining the Main Marmara fault as a potential seismic gap. It is important to conduct a detailed assessment of the seismic hazards along the main Marmara fault because the megacity Istanbul lies only approximately 10 km north of the eastern segment of the Main Marmara fault, which is referred to as the Princes' Islands Fault segment (PIF). Here, we study the locking status of this fault segment to evaluate the seismic hazard potential. For the first time, combined ascending and descending Interferometric Synthetic Aperture Radar and Global Positioning System observations were used to investigate the crustal deformation associated with the PIF. After careful corrections of the estimated ground velocity, a deformation pattern relating to fault locking near the Princes' Islands was identified. The modeling results revealed that the slip rate and locking depth of the fault segment show a clear trade-off, which were estimated as 18.9 ± 7.2 mm/y and 12.1 ± 7.0 km, respectively. With a moment accumulation rate of 1.7 ± 0.4 × 1017 Nm/y (proportional to the product of slip rate and locking depth), our results imply a build-up of a geodetic moment on the PIF and therefore a potential for earthquake hazards in the vicinity of the Istanbul megacity.

  5. Cheap and Nasty? The Potential Perils of Using Management Costs to Identify Global Conservation Priorities

    PubMed Central

    McCreless, Erin; Visconti, Piero; Carwardine, Josie; Wilcox, Chris; Smith, Robert J.

    2013-01-01

    The financial cost of biodiversity conservation varies widely around the world and such costs should be considered when identifying countries to best focus conservation investments. Previous global prioritizations have been based on global models for protected area management costs, but this metric may be related to other factors that negatively influence the effectiveness and social impacts of conservation. Here we investigate such relationships and first show that countries with low predicted costs are less politically stable. Local support and capacity can mitigate the impacts of such instability, but we also found that these countries have less civil society involvement in conservation. Therefore, externally funded projects in these countries must rely on government agencies for implementation. This can be problematic, as our analyses show that governments in countries with low predicted costs score poorly on indices of corruption, bureaucratic quality and human rights. Taken together, our results demonstrate that using national-level estimates for protected area management costs to set global conservation priorities is simplistic, as projects in apparently low-cost countries are less likely to succeed and more likely to have negative impacts on people. We identify the need for an improved approach to develop global conservation cost metrics that better capture the true costs of avoiding or overcoming such problems. Critically, conservation scientists must engage with practitioners to better understand and implement context-specific solutions. This approach assumes that measures of conservation costs, like measures of conservation value, are organization specific, and would bring a much-needed focus on reducing the negative impacts of conservation to develop projects that benefit people and biodiversity. PMID:24260502

  6. Nucleolin identified by comparative mass‑spectra analysis is a potential marker for invasive progression of hepatocellular carcinoma.

    PubMed

    Qian, Bin; Yao, Yusheng; Liu, Yihong; Yan, Maolin; Huang, Ying; Chen, Yanqing

    2014-09-01

    At present, the diagnosis and prognosis of hepatocellular carcinoma (HCC) metastasis remains poor. Recently, a number of proteins associated with the metastasis and invasion of HCC were identified; however, the effective markers require further elucidation. In the current study, a nucleolin expression was observed in MHCC97L and HCCLM9 HCC cell lines, with low and high metastatic potentials respectively, using comparative proteomics. The data indicated that nucleolin expression in the nucleus was significantly higher in HCCLM9 cells, and it primarily influenced the migration of HCC cells in vitro. Thus, to the best of our knowledge this is the first study to hypothesize that nucleolin may be a novel marker for HCC invasive progression. PMID:24927373

  7. Antioxidant potential of a polyherbal antimalarial as an indicator of its therapeutic value.

    PubMed

    Arrey Tarkang, Protus; Nwachiban Atchan, Achille Parfait; Kuiate, Jules-Roger; Okalebo, Faith Apoelot; Guantai, Anastasia Nkatha; Agbor, Gabriel Agbor

    2013-01-01

    Nefang is a polyherbal product composed of Mangifera indica (bark and leaf), Psidium guajava, Carica papaya, Cymbopogon citratus, Citrus sinensis, and Ocimum gratissimum (leaves), used for the treatment of malaria. Compounds with antioxidant activity are believed to modulate plasmodial infection. Antioxidant activity of the constituent aqueous plants extracts, in vitro, was evaluated using the 2,2-diphenyl-1-picrylhydrazyl (DPPH), total phenolic content (TPC), and ferric reducing antioxidant power (FRAP) methods and, in vivo, Nefang (100 and 500 mg kg(-1)) activity was evaluated in carbon tetrachloride-induced oxidative stressed Wistar rats. Superoxide dismutase, catalase activities, and lipid peroxidation by the malondialdehyde and total proteins assays were carried out. P. guajava, M. indica leaf, and bark extracts had the highest antioxidant properties in all three assays, with no statistically significant difference. Rats treated with the carbon tetrachloride had a statistically significant decrease in levels of triglycerides, superoxide dismutase, and catalase (P < 0.05) and increase in malondialdehyde activity, total protein levels, and liver and renal function markers, whereas rats treated with Nefang showed increased levels in the former and dose-dependent decrease towards normal levels in the later. These results reveal the constituent plants of Nefang that contribute to its in vivo antioxidant potential. This activity is a good indication of the therapeutic potential of Nefang. PMID:24454347

  8. Comparative evaluation of potential indicators and temporal sampling protocols for monitoring genetic erosion

    PubMed Central

    Hoban, Sean; Arntzen, Jan A; Bruford, Michael W; Godoy, José A; Rus Hoelzel, A; Segelbacher, Gernot; Vilà, Carles; Bertorelle, Giorgio

    2014-01-01

    Genetic biodiversity contributes to individual fitness, species' evolutionary potential, and ecosystem stability. Temporal monitoring of the genetic status and trends of wild populations' genetic diversity can provide vital data to inform policy decisions and management actions. However, there is a lack of knowledge regarding which genetic metrics, temporal sampling protocols, and genetic markers are sufficiently sensitive and robust, on conservation-relevant timescales. Here, we tested six genetic metrics and various sampling protocols (number and arrangement of temporal samples) for monitoring genetic erosion following demographic decline. To do so, we utilized individual-based simulations featuring an array of different initial population sizes, types and severity of demographic decline, and DNA markers [single nucleotide polymorphisms (SNPs) and microsatellites] as well as decline followed by recovery. Number of alleles markedly outperformed other indicators across all situations. The type and severity of demographic decline strongly affected power, while the number and arrangement of temporal samples had small effect. Sampling 50 individuals at as few as two time points with 20 microsatellites performed well (good power), and could detect genetic erosion while 80–90% of diversity remained. This sampling and genotyping effort should often be affordable. Power increased substantially with more samples or markers, and we observe that power of 2500 SNPs was nearly equivalent to 250 microsatellites, a result of theoretical and practical interest. Our results suggest high potential for using historic collections in monitoring programs, and demonstrate the need to monitor genetic as well as other levels of biodiversity. PMID:25553062

  9. Potential for early warning of maalria in India using NOAA-AVHRR based vegetation health indices

    NASA Astrophysics Data System (ADS)

    Dhiman, R. C.; Kogan, Felix; Singh, Neeru; Singh, R. P.; Dash, A. P.

    Malaria is still a major public health problem in India with about 1 82 million cases annually and 1000 deaths As per World Health Organization WHO estimates about 1 3 million Disability Adjusted Life Years DALYs are lost annually due to malaria in India Central peninsular region of India is prone to malaria outbreaks Meteorological parameters changes in ecological conditions development of resistance in mosquito vectors development of resistance in Plasmodium falciparum parasite and lack of surveillance are the likely reasons of outbreaks Based on satellite data and climatic factors efforts have been made to develop Early Warning System EWS in Africa but there is no headway in this regard in India In order to find out the potential of NOAA satellite AVHRR derived Vegetation Condition Index VCI Temperature Condition Index TCI and a cumulative indicator Vegetation Health Index VHI were attempted to find out their potential for development of EWS Studies were initiated by analysing epidemiological data of malaria vis-a-vis VCI TCI and VHI from Bikaner and Jaisalmer districts of Rajasthan and Tumkur and Raichur districts of Karnataka Correlation coefficients between VCI and monthly malaria cases for epidemic years were computed Positive correlation 0 67 has been found with one-month lag between VCI and malaria incidence in respect of Tumkur while a negative correlation with TCI -0 45 is observed In Bikaner VCI is found to be negatively related -0 71 with malaria cases in epidemic year of 1994 Weekly

  10. National valuation of monarch butterflies indicates an untapped potential for incentive-based conservation

    USGS Publications Warehouse

    Diffendorfer, Jay E.; Loomis, John B.; Ries, Leslie; Oberhauser, Karen; Semmens, Darius; Semmens, Brice; Butterfield, Bruce; Bagstad, Ken; Goldstein, Josh; Wiederholt, Ruscena; Mattsson, Brady; Thogmartin, Wayne E.

    2013-01-01

    The annual migration of monarch butterflies (Danaus plexippus) has high cultural value and recent surveys indicate monarch populations are declining. Protecting migratory species is complex because they cross international borders and depend on multiple regions. Understanding how much, and where, humans place value on migratory species can facilitate market-based conservation approaches. We performed a contingent valuation study of monarchs to understand the potential for such approaches to fund monarch conservation. The survey asked U.S. respondents about the money they would spend, or have spent, growing monarch-friendly plants, and the amount they would donate to monarch conservation organizations. Combining planting payments and donations, the survey indicated U.S. households valued monarchs as a total one-time payment of $4.78–$6.64 billion, levels similar to many endangered vertebrate species. The financial contribution of even a small percentage of households through purchases or donations could generate new funding for monarch conservation through market-based approaches.

  11. Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance.

    PubMed

    Saunus, Jodi M; Quinn, Michael C J; Patch, Ann-Marie; Pearson, John V; Bailey, Peter J; Nones, Katia; McCart Reed, Amy E; Miller, David; Wilson, Peter J; Al-Ejeh, Fares; Mariasegaram, Mythily; Lau, Queenie; Withers, Teresa; Jeffree, Rosalind L; Reid, Lynne E; Da Silva, Leonard; Matsika, Admire; Niland, Colleen M; Cummings, Margaret C; Bruxner, Timothy J C; Christ, Angelika N; Harliwong, Ivon; Idrisoglu, Senel; Manning, Suzanne; Nourse, Craig; Nourbakhsh, Ehsan; Wani, Shivangi; Anderson, Matthew J; Fink, J Lynn; Holmes, Oliver; Kazakoff, Stephen; Leonard, Conrad; Newell, Felicity; Taylor, Darrin; Waddell, Nick; Wood, Scott; Xu, Qinying; Kassahn, Karin S; Narayanan, Vairavan; Taib, Nur Aishah; Teo, Soo-Hwang; Chow, Yock Ping; kConFab; Jat, Parmjit S; Brandner, Sebastian; Flanagan, Adrienne M; Khanna, Kum Kum; Chenevix-Trench, Georgia; Grimmond, Sean M; Simpson, Peter T; Waddell, Nicola; Lakhani, Sunil R

    2015-11-01

    Treatment options for patients with brain metastases (BMs) have limited efficacy and the mortality rate is virtually 100%. Targeted therapy is critically under-utilized, and our understanding of mechanisms underpinning metastatic outgrowth in the brain is limited. To address these deficiencies, we investigated the genomic and transcriptomic landscapes of 36 BMs from breast, lung, melanoma and oesophageal cancers, using DNA copy-number analysis and exome- and RNA-sequencing. The key findings were as follows. (a) Identification of novel candidates with possible roles in BM development, including the significantly mutated genes DSC2, ST7, PIK3R1 and SMC5, and the DNA repair, ERBB-HER signalling, axon guidance and protein kinase-A signalling pathways. (b) Mutational signature analysis was applied to successfully identify the primary cancer type for two BMs with unknown origins. (c) Actionable genomic alterations were identified in 31/36 BMs (86%); in one case we retrospectively identified ERBB2 amplification representing apparent HER2 status conversion, then confirmed progressive enrichment for HER2-positivity across four consecutive metastatic deposits by IHC and SISH, resulting in the deployment of HER2-targeted therapy for the patient. (d) In the ERBB/HER pathway, ERBB2 expression correlated with ERBB3 (r(2)  = 0.496; p < 0.0001) and HER3 and HER4 were frequently activated in an independent cohort of 167 archival BM from seven primary cancer types: 57.6% and 52.6% of cases were phospho-HER3(Y1222) or phospho-HER4(Y1162) membrane-positive, respectively. The HER3 ligands NRG1/2 were barely detectable by RNAseq, with NRG1 (8p12) genomic loss in 63.6% breast cancer-BMs, suggesting a microenvironmental source of ligand. In summary, this is the first study to characterize the genomic landscapes of BM. The data revealed novel candidates, potential clinical applications for genomic profiling of resectable BMs, and highlighted the possibility of therapeutically targeting HER3, which is broadly over-expressed and activated in BMs, independent of primary site and systemic therapy. PMID:26172396

  12. What data should we collect? A framework for identifying indicators of ecosystem contributions to human well being

    EPA Science Inventory

    Ecological data enable a range of policy relevant analyses; the right ecological data enable ecosystem analyses to be linked to human well being making them more relevant and useful. The challenge we address is how to identify the right data. Our approach, founded on the “final e...

  13. A study of the landslide potential along the mountain road using environmental indices

    NASA Astrophysics Data System (ADS)

    Lin, C. Y.

    2014-12-01

    Utilization of slope land in recent years is rapid as a result of the dense population and limit of land resources in Taiwan. Therefore, mountain road plays an essential role for the necessity of human life. However, landslide disaster resulting in road failure occurred frequently in Taiwan on the slope land due to earthquake and typhoon. Previous studies found that the extreme rainfall coupled with the property of fragile geology could cause landslide. Nevertheless, the landslide occurrence might be affected by the drainage of the road side ditches. Taiwan Highway No.21 in Chi-Shan watershed and the forest roads located in Xiao-Lin Village, which failure during the hit of Typhoon Morakot in 2009, were selected for exploring the potential of vulnerable to landslides. Topographic Wetness Index (TWI) and Road Curvature (RC) were extracted along the road to indicate the potential sites which are vulnerable to slope failure. The surface runoff diverted by the road side ditches could spoil the sites with high RC due to the straight movement characteristics of the diverted runoff and cause the downslope collapse. The sites with higher mean value and lower standard deviation of Normalized Difference Vegetation Index (NDVI) derived from the SPOT imagery taken in dry and/or rainy seasons could be implied as the vegetation stands showing highly buffer effects in environmental stress due to having deeper soil layer, and are hardly interfered by the drought. The stands located in such sites once collapsed are often resulting in huge volumes of debris. Drainage Density (DD) index could be applied as the degrees of geologic fragile in the slope land. A road across the sites with higher mean value and lower standard deviation of NDVI and/or higher DD should be paid more attention because of having highly vulnerable to deep seated landslide. This study is focusing on extracting and analyzing the environmental indices such as TWI, RC, NDVI and DD for exploring the slope stability along the mountain road. The results could be used as the references of related authorities for understanding the potential landslides along a road.

  14. Use of alternative assays to identify and prioritize organophosphorus flame retardants for potential developmental and neurotoxicity.

    PubMed

    Behl, Mamta; Hsieh, Jui-Hua; Shafer, Timothy J; Mundy, William R; Rice, Julie R; Boyd, Windy A; Freedman, Jonathan H; Hunter, E Sidney; Jarema, Kimberly A; Padilla, Stephanie; Tice, Raymond R

    2015-01-01

    Due to their toxicity and persistence in the environment, brominated flame retardants (BFRs) are being phased out of commercial use, leading to the increased use of alternative chemicals such as the organophosphorus flame retardants (OPFRs). There is, however, limited information on the potential health effects of OPFRs. Due to the structural similarity of the OPFRs to organophosphorus insecticides, there is concern regarding developmental toxicity and neurotoxicity. In response, we evaluated a set of OPFRs (triphenyl phosphate [TPHP]), isopropylated phenyl phosphate [IPP], 2-ethylhexyl diphenyl phosphate [EHDP], tert-butylated phenyl diphenyl phosphate [BPDP], trimethyl phenyl phosphate [TMPP], isodecyl diphenyl phosphate [IDDP], (tris(1,3-dichloroisopropyl) phosphate [TDCIPP], and tris(2-chloroethyl)phosphate [TCEP]) in a battery of cell-based in vitro assays and alternative model organisms and compared the results to those obtained for two classical BFRs (3,3',5,5'-tetrabromobisphenol A [TBBPA] and 2,2'4,4'-brominated diphenyl ether [BDE-47]). The assays used evaluated the effects of chemicals on the differentiation of mouse embryonic stem cells, the proliferation and growth of human neural stem cells, rat neuronal growth and network activity, and development of nematode (Caenorhabditis elegans) and zebrafish (Danio rerio). All assays were performed in a concentration-response format, allowing for the determination of the point of departure (POD: the lowest concentration where a chemically-induced response exceeds background noise). The majority of OPFRs (8/9) were active in multiple assays in the range of 1-10 μM, most of which had comparable activity to the BFRs TBBPA and BDE-47. TCEP was negative in all assays. The results indicate that the replacement OPFRs, with the exception of TCEP, showed comparable activity to the two BFRs in the assays tested. Based on these results, more comprehensive studies are warranted to further characterize the potential hazard of some of these OPFR compounds. PMID:26386178

  15. Potential High-Temperature Shape-Memory Alloys Identified in the Ti(Ni,Pt) System

    NASA Technical Reports Server (NTRS)

    Noebe, Ronald D.; Biles, Tiffany A.; Garg, Anita; Nathal, Michael V.

    2004-01-01

    "Shape memory" is a unique property of certain alloys that, when deformed (within certain strain limits) at low temperatures, will remember and recover to their original predeformed shape upon heating. It occurs when an alloy is deformed in the low-temperature martensitic phase and is then heated above its transformation temperature back to an austenitic state. As the material passes through this solid-state phase transformation on heating, it also recovers its original shape. This behavior is widely exploited, near room temperature, in commercially available NiTi alloys for connectors, couplings, valves, actuators, stents, and other medical and dental devices. In addition, there are limitless applications in the aerospace, automotive, chemical processing, and many other industries for materials that exhibit this type of shape-memory behavior at higher temperatures. But for high temperatures, there are currently no commercial shape-memory alloys. Although there are significant challenges to the development of high-temperature shape-memory alloys, at the NASA Glenn Research Center we have identified a series of alloy compositions in the Ti-Ni-Pt system that show great promise as potential high-temperature shape-memory materials.

  16. 2D-DIGE proteomic analysis identifies new potential therapeutic targets for adrenocortical carcinoma

    PubMed Central

    Armignacco, Roberta; Ercolino, Tonino; Canu, Letizia; Baroni, Gianna; Nesi, Gabriella; Galli, Andrea; Mannelli, Massimo; Luconi, Michaela

    2015-01-01

    Adrenocortical carcinoma (ACC) is a rare aggressive tumor with poor prognosis when metastatic at diagnosis. The tumor biology is still mostly unclear, justifying the limited specificity and efficacy of the anti-cancer drugs currently available. This study reports the first proteomic analysis of ACC by using two-dimensional-differential-in-gel-electrophoresis (2D-DIGE) to evaluate a differential protein expression profile between adrenocortical carcinoma and normal adrenal. Mass spectrometry, associated with 2D-DIGE analysis of carcinomas and normal adrenals, identified 22 proteins in 27 differentially expressed 2D spots, mostly overexpressed in ACC. Gene ontology analysis revealed that most of the proteins concurs towards a metabolic shift, called the Warburg effect, in adrenocortical cancer. The differential expression was validated by Western blot for Aldehyde-dehydrogenase-6-A1,Transferrin, Fascin-1,Lamin A/C,Adenylate-cyclase-associated-protein-1 and Ferredoxin-reductase. Moreover, immunohistochemistry performed on paraffin-embedded ACC and normal adrenal specimens confirmed marked positive staining for all 6 proteins diffusely expressed by neoplastic cells, compared with normal adrenal cortex. In conclusion, our preliminary findings reveal a different proteomic profile in adrenocortical carcinoma compared with normal adrenal cortex characterized by overexpression of mainly metabolic enzymes, thus suggesting the Warburg effect also occurs in ACC. These proteins may represent promising novel ACC biomarkers and potential therapeutic targets if validated in larger cohorts of patients. PMID:25691058

  17. Identifying populations potentially exposed to agricultural pesticides using remote sensing and a Geographic Information System

    USGS Publications Warehouse

    Ward, M.H.; Nuckols, J.R.; Weigel, S. J.; Cantor, K.P.; Miller, Roger S.

    2000-01-01

    Pesticides used in agriculture may cause adverse health effects among the population living near agricultural areas. However, identifying the populations most likely to be exposed is difficult. We conducted a feasibility study to determine whether satellite imagery could be used to reconstruct historical crop patterns. We used historical Farm Service Agency records as a source of ground reference data to classify a late summer 1984 satellite image into crop species in a three-county area in south central Nebraska. Residences from a population-based epidemiologic study of non-Hodgkin lymphoma were located on the crop maps using a geographic information system (GIS). Corn, soybeans, sorghum, and alfalfa were the major crops grown in the study area. Eighty-five percent of residences could be located, and of these 22% had one of the four major crops within 500 m of the residence, an intermediate distance for the range of drift effects from pesticides applied in agriculture. We determined the proximity of residences to specific crop species and calculated crop-specific probabilities of pesticide use based on available data. This feasibility study demonstrated that remote sensing data and historical records on crop location can be used to create historical crop maps. The crop pesticides that were likely to have been applied can be estimated when information about crop-specific pesticide use is available. Using a GIS, zones of potential exposure to agricultural pesticides and proximity measures can be determined for residences in a study.

  18. A multicenter photoprovocation study to identify potential biomarkers by global peptide profiling in cutaneous lupus erythematosus.

    PubMed

    Calderon, C; Zucht, H D; Kuhn, A; Wozniacka, A; Szepietowski, J C; Nyberg, F; Weichenthal, M; Piantone, A; Budde, P

    2015-11-01

    Cutaneous lupus erythematosus (CLE) is an inflammatory autoimmune skin disease in which abnormal photosensitivity is an important pathogenetic factor but is difficult to predict, creating a challenge in determining treatment efficacy. Although photosensitivity in CLE patients may change over time, photoprovocation testing with ultraviolet (UV) A and UVB irradiation can be a helpful tool to explore differences between responders and nonresponders during photoprovocation. To identify biomarkers that could substitute for the clinical endpoint lesion development, we performed a global peptidomics profiling analysis of CLE subjects in a controlled photoprovocation study. Plasma and skin biopsy samples were collected before and after UV-irradiation from 13 healthy volunteers and 47 CLE subjects. Twenty-two of the 47 CLE subjects developed skin lesions. The samples were analyzed using a label-free quantitative peptidomics workflow combined with univariate and multivariate statistical analyses. The primary finding was identification of a specific plasma peptide signature separating responders versus nonresponders at baseline. The peptide signature consisted of beta 2-microglobulin (B2MG), human beta-defensin-1, and peptides derived from CD99, polymeric immunoglobulin receptor, and immunoglobulin kappa light chains. In skin, elevated B2MG levels correlated with lesion formation. Our results show that the peptidome is a rich source of potential biomarkers for predicting photosensitivity in CLE. PMID:26206719

  19. Potential multidrug resistance gene POHL: an ecologically relevant indicator in marine sponges.

    PubMed

    Krasko, A; Kurelec, B; Batel, R; Müller, I M; Müller, W E

    2001-01-01

    Sponges are sessile filter feeders found in all aquatic habitats from the tropics to the arctic. Against potential environmental hazards, they are provided with efficient defense systems, e.g., protecting chaperones and/or the P-170/multidrug resistance pump system. Here we report on a further multidrug resistance pathway that is related to the pad one homologue (POH1) mechanism recently identified in humans. It is suggested that proteolysis is involved in the inactivation of xenobiotics by the POH1 system. Two cDNAs were cloned, one from the demosponge Geodia cydonium and a second from the hexactinellid sponge Aphrocallistes vastus. The cDNA from G. cydonium, termed GCPOHL, encodes a deduced polypeptide with a size of 34,591 Da and that from A. vastus, AVPOHL, a protein of a calculated M(r) of 34,282. The two sponge cDNAs are highly similar to each other as well as to the known sequences from fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae) and other Metazoa (from Schistosoma mansoni to humans). Under controlled laboratory conditions, the expression of the potential multidrug resistance gene POHL is, in G. cydonium, strongly upregulated in response to the toxins staurosporin (20 microM) or taxol (50 microM); the first detectable transcripts appear after 1 d and reach a maximum after 3 to 5 d of incubation. The relevance of the expression pattern of the G. cydonium gene POHL for the assessment of pollution in the field was determined at differently polluted sites in the area around Rovinj (Croatia; Mediterranean Sea, Adriatic Sea). The load of the selected sites was assessed by measuring the potency of XAD-7 concentrates of water samples taken from those places to induce the level of benzo[a]pyrene monooxygenase (BaPMO) in fish and to impair the multidrug resistance (MDR)/P-170 extrusion pump in clams. These field experiments revealed that the levels of inducible BaPMO activity in fish and of the MDR potential by the water concentrates are highly correlated with the level of expression of the potential multidrug resistance gene POHL in G. cydonium. This report demonstrates that the detoxification POH pathway, here mediated by the G. cydonium GCPOHL gene, is an additional marker for the assessment of the environmental load in a given marine area. PMID:11351409

  20. In Silico Screening Identifies a Novel Potential PARP1 Inhibitor Targeting Synthetic Lethality in Cancer Treatment.

    PubMed

    Li, Jian; Zhou, Nan; Cai, Peiling; Bao, Jinku

    2016-01-01

    Synthetic lethality describes situations in which defects in two different genes or pathways together result in cell death. This concept has been applied to drug development for cancer treatment, as represented by Poly (ADP-ribose) polymerase (PARPs) inhibitors. In the current study, we performed a computational screening to discover new PARP inhibitors. Among the 11,247 compounds analyzed, one natural product, ZINC67913374, stood out by its superior performance in the simulation analyses. Compared with the FDA approved PARP1 inhibitor, olaparib, our results demonstrated that the ZINC67913374 compound achieved a better grid score (-86.8) and amber score (-51.42). Molecular dynamics simulations suggested that the PARP1-ZINC67913374 complex was more stable than olaparib. The binding free energy for ZINC67913374 was -177.28 kJ/mol while that of olaparib was -159.16 kJ/mol. These results indicated ZINC67913374 bound to PARP1 with a higher affinity, which suggest ZINC67913374 has promising potential for cancer drug development. PMID:26907257

  1. The Potential Use of DNA Methylation Biomarkers to Identify Risk and Progression of Type 2 Diabetes

    PubMed Central

    Gillberg, Linn; Ling, Charlotte

    2015-01-01

    Type 2 diabetes mellitus (T2D) is a slowly progressive disease that can be postponed or even avoided through lifestyle changes. Recent data demonstrate highly significant correlations between DNA methylation and the most important risk factors of T2D, including age and body mass index, in blood and human tissues relevant to insulin resistance and T2D. Also, T2D patients and individuals with increased risk of the disease display differential DNA methylation profiles and plasticity compared to controls. Accordingly, the novel clues to DNA methylation fingerprints in blood and tissues with deteriorated metabolic capacity indicate that blood-borne epigenetic biomarkers of T2D progression might become a reality. This Review will address the most recent associations between DNA methylation and diabetes-related traits in human tissues and blood. The overall focus is on the potential of future epigenome-wide studies, carried out across tissues and populations with correlations to pre-diabetes and T2D risk factors, to build up a library of epigenetic markers of risk and early progression of T2D. These markers may, tentatively in combination with other predictors of T2D development, increase the possibility of individual-based lifestyle prevention of T2D and associated metabolic diseases. PMID:25870586

  2. In Silico Screening Identifies a Novel Potential PARP1 Inhibitor Targeting Synthetic Lethality in Cancer Treatment

    PubMed Central

    Li, Jian; Zhou, Nan; Cai, Peiling; Bao, Jinku

    2016-01-01

    Synthetic lethality describes situations in which defects in two different genes or pathways together result in cell death. This concept has been applied to drug development for cancer treatment, as represented by Poly (ADP-ribose) polymerase (PARPs) inhibitors. In the current study, we performed a computational screening to discover new PARP inhibitors. Among the 11,247 compounds analyzed, one natural product, ZINC67913374, stood out by its superior performance in the simulation analyses. Compared with the FDA approved PARP1 inhibitor, olaparib, our results demonstrated that the ZINC67913374 compound achieved a better grid score (−86.8) and amber score (−51.42). Molecular dynamics simulations suggested that the PARP1-ZINC67913374 complex was more stable than olaparib. The binding free energy for ZINC67913374 was −177.28 kJ/mol while that of olaparib was −159.16 kJ/mol. These results indicated ZINC67913374 bound to PARP1 with a higher affinity, which suggest ZINC67913374 has promising potential for cancer drug development. PMID:26907257

  3. Comparison of Sewage and Animal Fecal Microbiomes by Using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups

    PubMed Central

    Fisher, Jenny C.; Eren, A. Murat; Green, Hyatt C.; Shanks, Orin C.; Morrison, Hilary G.; Vineis, Joseph H.; Sogin, Mitchell L.

    2015-01-01

    Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but the gut microbiota of humans and other animals contain organisms from an array of other taxonomic groups that might provide indicators of fecal pollution sources. To discern between human and nonhuman fecal sources, we compared the V6 regions of the 16S rRNA genes detected in fecal samples from six animal hosts to those found in sewage (as a proxy for humans). We focused on 10 abundant genera and used oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically distinct organisms. Our analysis showed clear patterns of differential oligotype distributions between sewage and animal samples. Over 100 oligotypes of human origin occurred preferentially in sewage samples, and 99 human oligotypes were sewage specific. Sequences represented by the sewage-specific oligotypes can be used individually for development of PCR-based assays or together with the oligotypes preferentially associated with sewage to implement a signature-based approach. Analysis of sewage from Spain and Brazil showed that the sewage-specific oligotypes identified in U.S. sewage have the potential to be used as global alternative indicators of human fecal pollution. Environmental samples with evidence of prior human fecal contamination had consistent ratios of sewage signature oligotypes that corresponded to the trends observed for sewage. Our methodology represents a promising approach to identifying new bacterial taxa for MST applications and further highlights the potential of the family Lachnospiraceae to provide human-specific markers. In addition to source tracking applications, the patterns of the fine-scale population structure within fecal taxa suggest a fundamental relationship between bacteria and their hosts. PMID:26231648

  4. Evaluation of potential sources and transport mechanisms of fecal indicator bacteria to beach water, Murphy Park Beach, Door County, Wisconsin

    USGS Publications Warehouse

    Juckem, Paul F.; Corsi, Steven R.; McDermott, Colleen; Kleinheinz, Gregory; Fogarty, Lisa R.; Haack, Sheridan K.; Johnson, Heather E.

    2013-01-01

    Fecal Indicator Bacteria (FIB) concentrations in beach water have been used for many years as a criterion for closing beaches due to potential health concerns. Yet, current understanding of sources and transport mechanisms that drive FIB occurrence remains insufficient for accurate prediction of closures at many beaches. Murphy Park Beach, a relatively pristine beach on Green Bay in Door County, Wis., was selected for a study to evaluate FIB sources and transport mechanisms. Although the relatively pristine nature of the beach yielded no detection of pathogenic bacterial genes and relatively low FIB concentrations during the study period compared with other Great Lakes Beaches, its selection limited the number of confounding FIB sources and associated transport mechanisms. The primary sources of FIB appear to be internal to the beach rather than external sources such as rivers, storm sewer outfalls, and industrial discharges. Three potential FIB sources were identified: sand, swash-zone groundwater, and Cladophora mats. Modest correlations between FIB concentrations in these potential source reservoirs and FIB concentrations at the beach from the same day illustrate the importance of understanding transport mechanisms between FIB sources and the water column. One likely mechanism for transport and dispersion of FIB from sand and Cladophora sources appears to be agitation of Cladophora mats and erosion of beach sand due to storm activity, as inferred from storm indicators including turbidity, wave height, current speed, wind speed, sky visibility, 24-hour precipitation, and suspended particulate concentration. FIB concentrations in beach water had a statistically significant relation (p-value 0.05) with the magnitude of these storm indicators. In addition, transport of FIB in swash-zone groundwater into beach water appears to be driven by groundwater recharge associated with multiday precipitation and corresponding increased swash-zone groundwater discharge at the beach, as indicated by an increase in the specific conductance of beach water. Understanding the dynamics of FIB sources (sand, swash-zone groundwater, and Cladophora) and transport mechanisms (dispersion and erosion from storm energy, and swash-zone groundwater discharge) is important for improving predictions of potential health risks from FIB in beach water.

  5. A Genome-Wide Association Study Identifies Potential Susceptibility Loci for Hirschsprung Disease

    PubMed Central

    Kim, Jeong-Hyun; Cheong, Hyun Sub; Sul, Jae Hoon; Seo, Jeong-Meen; Kim, Dae-Yeon; Oh, Jung-Tak; Park, Kwi-Won; Kim, Hyun-Young; Jung, Soo-Min; Jung, Kyuwhan; Cho, Min Jeng; Bae, Joon Seol; Shin, Hyoung Doo

    2014-01-01

    Hirschsprung disease (HSCR) is a congenital and heterogeneous disorder characterized by the absence of intramural nervous plexuses along variable lengths of the hindgut. Although RET is a well-established risk factor, a recent genome-wide association study (GWAS) of HSCR has identified NRG1 as an additional susceptibility locus. To discover additional risk loci, we performed a GWAS of 123 sporadic HSCR patients and 432 unaffected controls using a large-scale platform with coverage of over 1 million polymorphic markers. The result was that our study replicated the findings of RET-CSGALNACT2-RASGEF1A genomic region (rawP = 5.69×10−19 before a Bonferroni correction; corrP = 4.31×10−13 after a Bonferroni correction) and NRG1 as susceptibility loci. In addition, this study identified SLC6A20 (adjP = 2.71×10−6), RORA (adjP = 1.26×10−5), and ABCC9 (adjP = 1.86×10−5) as new potential susceptibility loci under adjusting the already known loci on the RET-CSGALNACT2-RASGEF1A and NRG1 regions, although none of the SNPs in these genes passed the Bonferroni correction. In further subgroup analysis, the RET-CSGALNACT2-RASGEF1A genomic region was observed to have different significance levels among subgroups: short-segment (S-HSCR, corrP = 1.71×10−5), long-segment (L-HSCR, corrP = 6.66×10−4), and total colonic aganglionosis (TCA, corrP>0.05). This differential pattern in the significance level suggests that other genomic loci or mechanisms may affect the length of aganglionosis in HSCR subgroups during enteric nervous system (ENS) development. Although functional evaluations are needed, our findings might facilitate improved understanding of the mechanisms of HSCR pathogenesis. PMID:25310821

  6. Brain potential indices of novelty processing are associated with preference for amphetamine.

    PubMed

    Gabbay, Frances H; Duncan, Connie C; McDonald, Craig G

    2010-12-01

    A behavioral drug preference procedure was used to identify two groups of healthy individuals. One group preferred 10 mg of d-amphetamine over placebo (Choosers) and the other preferred placebo (Nonchoosers). In separate sessions, participants were administered placebo, 10, and 15 mg of d-amphetamine, and event-related brain potentials (ERPs) were recorded while participants performed two 3-stimulus oddball tasks. The effect of d-amphetamine on P3a, an ERP index of the orienting response, differed between groups: In Choosers, target stimuli elicited P3a after d-amphetamine but not after placebo; in Nonchoosers, the drug had no effect on P3a. Moreover, two group differences were evident after placebo and were unaffected by d-amphetamine. (1) N100 was larger in Nonchoosers than in Choosers, suggesting that Nonchoosers were more attentive than Choosers to the physical features of the stimuli. (2) The reorienting negativity (RON) elicited by targets in both tasks and by rare nontargets in a novelty oddball task (i.e., novel sounds) was larger in Nonchoosers than in Choosers. This suggests that Nonchoosers more effectively refocused attention on the task after distraction. It is hypothesized that these processing differences reflect a group difference in the balance between midbrain dopamine function and ascending cholinergic influences. The findings have implications for vulnerability to addiction and illustrate the promise of ERPs in parsing elemental phenotypes. PMID:21186922

  7. Marine bacterial succession as a potential indicator of postmortem submersion interval.

    PubMed

    Dickson, Gemma C; Poulter, Russell T M; Maas, Elizabeth W; Probert, P Keith; Kieser, Jules A

    2011-06-15

    The process of decomposition of bodies in the marine environment is poorly understood and almost nothing is currently known about the microorganisms involved. This study aimed to investigate the microbes involved in decomposition in the sea and to evaluate the potential use of marine bacterial succession for postmortem submersion interval (PMSI) estimation, for which there is currently no reliable method. Partial pig remains were completely submerged during autumn and winter and were regularly sampled to document marine bacterial colonisation and the changes in community composition over time. Five stages of decomposition were recognised, some of which exhibited characters specific for partial carrion. Marine bacteria rapidly colonised the submerged remains in a successional manner. Seasonal differences were observed for the rate of decomposition and also for several groups of colonising bacteria. Marine bacteria specific for particular PMSIs were identified. This study provides an insight into the involvement of saprophytic marine bacteria in the decomposition of mammalian remains in the sea and is the first to explore the use of marine bacterial colonisation and succession as a novel tool for PMSI estimation. We propose that with further study, marine bacterial succession will prove useful for determination of the length of time a body may have been immersed in a marine environment. PMID:21074955

  8. Altered cerebral response during cognitive control: a potential indicator of genetic liability for schizophrenia.

    PubMed

    Sambataro, Fabio; Mattay, Venkata S; Thurin, Kristina; Safrin, Martin; Rasetti, Roberta; Blasi, Giuseppe; Callicott, Joseph H; Weinberger, Daniel R

    2013-04-01

    Aberrant activity in brain regions underlying various aspects of executive cognition has been reported in patients with schizophrenia and in their healthy relatives, suggesting an association with genetic liability. The aim of this study was to investigate brain responses to selective aspects of cognitive control in unaffected siblings who are at increased genetic risk of schizophrenia. Altogether, 65 non-affected siblings, 70 patients with schizophrenia spectrum disorders, and 235 normal controls participated in this study. Blood-oxygen-level-dependent functional magnetic resonance imaging was conducted while participants performed a cognitive control task ('flanker task') to identify brain activity and connectivity associated with response inhibition and conflict monitoring, and suppression. Behaviorally, similar to patients with schizophrenia, siblings were less accurate when inhibiting prepotent responses relative to normal controls. During response inhibition, again similar to patients with schizophrenia, siblings showed decreased activity in the anterior cingulate (ACC), along with increased functional coupling with the dorsolateral prefrontal cortex (PFC) when compared to normal controls. Our findings show altered ACC activity and PFC connectivity in unaffected siblings and patients with schizophrenia during response inhibition. These results suggest that such changes in the neural activity underlying aspects of cognitive control may represent a potential intermediate phenotype for the investigation of the genetic basis of schizophrenia. PMID:23299932

  9. Altered Cerebral Response During Cognitive Control: A Potential Indicator of Genetic Liability for Schizophrenia

    PubMed Central

    Sambataro, Fabio; Mattay, Venkata S; Thurin, Kristina; Safrin, Martin; Rasetti, Roberta; Blasi, Giuseppe; Callicott, Joseph H; Weinberger, Daniel R

    2013-01-01

    Aberrant activity in brain regions underlying various aspects of executive cognition has been reported in patients with schizophrenia and in their healthy relatives, suggesting an association with genetic liability. The aim of this study was to investigate brain responses to selective aspects of cognitive control in unaffected siblings who are at increased genetic risk of schizophrenia. Altogether, 65 non-affected siblings, 70 patients with schizophrenia spectrum disorders, and 235 normal controls participated in this study. Blood-oxygen-Ievel-dependent functional magnetic resonance imaging was conducted while participants performed a cognitive control task (‘flanker task') to identify brain activity and connectivity associated with response inhibition and conflict monitoring, and suppression. Behaviorally, similar to patients with schizophrenia, siblings were less accurate when inhibiting prepotent responses relative to normal controls. During response inhibition, again similar to patients with schizophrenia, siblings showed decreased activity in the anterior cingulate (ACC), along with increased functional coupling with the dorsolateral prefrontal cortex (PFC) when compared to normal controls. Our findings show altered ACC activity and PFC connectivity in unaffected siblings and patients with schizophrenia during response inhibition. These results suggest that such changes in the neural activity underlying aspects of cognitive control may represent a potential intermediate phenotype for the investigation of the genetic basis of schizophrenia. PMID:23299932

  10. Multi-temporal terrestrial laser scanning for identifying rockslide modifications: potentialities and problems

    NASA Astrophysics Data System (ADS)

    Castagnetti, Cristina; Bertacchini, Eleonora; Capra, Alessandro; Rivola, Riccardo

    2013-04-01

    The heart of this research is to provide an efficient methodology for a reliable acquisition and interpretation of Terrestrial Laser Scanner (TLS) data in the application field of landslide monitoring. In particular, rockslides, which are characterized by vertical walls of rock and by a complex morphology, are of great concern in the study. In these cases the airborne laser scanning is not able to provide useful and reliable description and the terrestrial laser scanning might be the only possible choice to obtain a good and reliable description of the geomorphology or to identify the changes occurred over time. The last purpose is still a challenging task when long distances are involved because the accurate and punctual identification of displacements is not possible due to the laser beam divergence. The final purpose of the research is a proposal of a methodology which is based on TLS technology for identifying displacements and extracting geomorphological changes. The approach is clearly based on a multi-temporal analysis which is computed on several repetitions of TLS surveys performed on the area of interest. To achieve best results and optimize the processing strategy, different methods about point clouds alignment have been tested together with algorithms both for filtering and post-processing. The case study is the Collagna Landslide that is located in the North Appennines (Reggio Emilia, Italy) on the right flank of Biola torrent. The large scale composite landslide area is made both by a wide rock slide sector and a more limited earth slide sector that, after high precipitation rates, disrupted the National Road 63 in December 2008. An integrated monitoring system is installed since 2009 and comprises both point-based technologies such as extensometers, total station and global positioning system, and also area-based technologies such as airborne laser scanner, long-range TLS and ground-based radar. This choice allows to couple the advantages of both approaches. The research focuses on TLS surveys for trying to detect displacements which might be responsible for instability. Four point clouds acquired in the last two years allow to monitor the spatial displacements of the whole slope, especially focusing on the rockslide sector. It is worth to underline an important aspect which contributes to highlight the significance of the work: the mean scanning distance is about 1.3 km. Few examples exist in literature about the use of very long-range TLS for displacements investigation. By sequentially analyzing TLS surfaces, displacement maps have been obtained for the rockslide area. Confirmation have been achieved by comparing results with movements of reflectors sited on the entire slope and continuously measured by total station. Such validation strengthens the idea that TLS has serious potentialities to be successfully used for analyzing instability. Comparing surfaces is not easy at all, thus a discussion about the encountered problems will be taken into account: any significant detail about potentialities and difficulties of the alignment strategy and the processing procedure will be given together with details about the specific algorithm implemented for filtering displacements by taking into account actual geomorphological conditions.

  11. Indications for potential parent-of-origin effects within the FTO gene.

    PubMed

    Liu, Xuanshi; Hinney, Anke; Scholz, Markus; Scherag, André; Tönjes, Anke; Stumvoll, Michael; Stadler, Peter F; Hebebrand, Johannes; Böttcher, Yvonne

    2015-01-01

    Genome-Wide Association Studies (GWAS) were successfully applied to discover associations with obesity. However, the GWAS design is usually based on unrelated individuals and inheritance information on the parental origin of the alleles is missing. Taking into account parent-of-origin may provide further insights into the genetic mechanisms contributing to obesity. We hypothesized that there may be variants within the robustly replicated fat mass and obesity associated (FTO) gene that may confer different risk for obesity depending on transmission from mother or father. Genome-wide genotypes and pedigree information from the Sorbs population were used. Phased genotypes among 525 individuals were generated by AlphaImpute. Subsequently, 22 SNPs within FTO introns 1 to 3 were selected and parent-of-origin specific association analyses were performed using PLINK. Interestingly, we identified several SNPs conferring different genetic effects (P≤0.05) depending on parental origin--among them, rs1861868, rs1121980 and rs9939973 (all in intron 1). To confirm our findings, we investigated the selected variants in 705 German trios comprising an (extremely) obese child or adolescent and both parents. Again, we observed evidence for POE effects in intron 2 and 3 (P≤0.05) as indicated by the parental asymmetry test. Our results suggest that the obesity risk transmitted by several FTO variants may depend on the parental origin of the allele. Larger family-based studies are warranted to replicate our findings. PMID:25793382

  12. Generators of the brainstem auditory evoked potential in cat. III: Identified cell populations.

    PubMed

    Melcher, J R; Kiang, N Y

    1996-04-01

    This paper examines the relationship between different brainstem cell populations and the brainstem auditory evoked potential (BAEP). First, we present a mathematical model relating the BAEP to underlying cellular activity. Then, we identify specific cellular generators of the click-evoked BAEP in cats by combining model-derived insights with key experimental data. These data include (a) a correspondence between particular brainstem regions and specific extrema in the BAEP waveform, determined from lesion experiments, and (b) values for model parameters derived from published physiological and anatomical information. Ultimately, we conclude (with varying degrees of confidence) that: (1) the earliest extrema in the BAEP are generated by spiral ganglion cells, (2) P2 is mainly generated by cochlear nucleus (CN) globular cells, (3) P3 is partly generated by CN spherical cells and partly by cells receiving inputs from globular cells, (4) P4 is predominantly generated by medial superior olive (MSO) principal cells, which are driven by spherical cells, (5) the generators of P5 are driven by MSO principal cells, and (6) the BAEP, as a whole, is generated mainly by cells with characteristic frequencies above 2 kHz. Thus, the BAEP in cats mainly reflects cellular activity in two parallel pathways, one originating with globular cells and the other with spherical cells. Since the globular cell pathway is poorly represented in humans, we suggest that the human BAEP is largely generated by brainstem cells in the spherical cell pathway. Given our conclusions, it should now be possible to relate activity in specific cell populations to psychophysical performance since the BAEP can be recorded in behaving humans and animals. PMID:8735068

  13. Identifying populations potentially exposed to agricultural pesticides using remote sensing and a Geographic Information System.

    PubMed Central

    Ward, M H; Nuckols, J R; Weigel, S J; Maxwell, S K; Cantor, K P; Miller, R S

    2000-01-01

    Pesticides used in agriculture may cause adverse health effects among the population living near agricultural areas. However, identifying the populations most likely to be exposed is difficult. We conducted a feasibility study to determine whether satellite imagery could be used to reconstruct historical crop patterns. We used historical Farm Service Agency records as a source of ground reference data to classify a late summer 1984 satellite image into crop species in a three-county area in south central Nebraska. Residences from a population-based epidemiologic study of non-Hodgkin lymphoma were located on the crop maps using a geographic information system (GIS). Corn, soybeans, sorghum, and alfalfa were the major crops grown in the study area. Eighty-five percent of residences could be located, and of these 22% had one of the four major crops within 500 m of the residence, an intermediate distance for the range of drift effects from pesticides applied in agriculture. We determined the proximity of residences to specific crop species and calculated crop-specific probabilities of pesticide use based on available data. This feasibility study demonstrated that remote sensing data and historical records on crop location can be used to create historical crop maps. The crop pesticides that were likely to have been applied can be estimated when information about crop-specific pesticide use is available. Using a GIS, zones of potential exposure to agricultural pesticides and proximity measures can be determined for residences in a study. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:10622770

  14. Altered protein S-glutathionylation identifies a potential mechanism of resistance to acetaminophen-induced hepatotoxicity.

    PubMed

    McGarry, David J; Chakravarty, Probir; Wolf, C Roland; Henderson, Colin J

    2015-11-01

    Acetaminophen (APAP) is the most commonly used over-the-counter analgesic. However, hepatotoxicity induced by APAP is a major clinical issue, and the factors that define sensitivity to APAP remain unclear. We have previously demonstrated that mice nulled for glutathione S-transferase Pi (GSTP) are resistant to APAP-induced hepatotoxicity. This study aims to exploit this difference to delineate pathways of importance in APAP toxicity. We used mice nulled for GSTP and heme oxygenase-1 oxidative stress reporter mice, together with a novel nanoflow liquid chromatography-tandem mass spectrometry methodology to investigate the role of oxidative stress, cell signaling, and protein S-glutathionylation in APAP hepatotoxicity. We provide evidence that the sensitivity difference between wild-type and Gstp1/2(-/-) mice is unrelated to the ability of APAP to induce oxidative stress, despite observing significant increases in c-Jun N-terminal kinase and extracellular signal-regulated kinase phosphorylation in wild-type mice. The major difference in response to APAP was in the levels of protein S-glutathionylation: Gstp1/2(-/-) mice exhibited a significant increase in the number of S-glutathionylated proteins compared with wild-type animals. Remarkably, these S-glutathionylated proteins are involved in oxidative phosphorylation, respiratory complexes, drug metabolism, and mitochondrial apoptosis. Furthermore, we found that S-glutathionylation of the rate-limiting glutathione-synthesizing enzyme, glutamate cysteine ligase, was markedly increased in Gstp1/2(-/-) mice in response to APAP. The data demonstrate that S-glutathionylation provides an adaptive response to APAP and, as a consequence, suggest that this is an important determinant in APAP hepatotoxicity. This work identifies potential novel avenues associated with cell survival for the treatment of chemical-induced hepatotoxicity. PMID:26311813

  15. Altered Protein S-Glutathionylation Identifies a Potential Mechanism of Resistance to Acetaminophen-Induced Hepatotoxicity

    PubMed Central

    McGarry, David J.; Chakravarty, Probir; Wolf, C. Roland

    2015-01-01

    Acetaminophen (APAP) is the most commonly used over-the-counter analgesic. However, hepatotoxicity induced by APAP is a major clinical issue, and the factors that define sensitivity to APAP remain unclear. We have previously demonstrated that mice nulled for glutathione S-transferase Pi (GSTP) are resistant to APAP-induced hepatotoxicity. This study aims to exploit this difference to delineate pathways of importance in APAP toxicity. We used mice nulled for GSTP and heme oxygenase-1 oxidative stress reporter mice, together with a novel nanoflow liquid chromatography–tandem mass spectrometry methodology to investigate the role of oxidative stress, cell signaling, and protein S-glutathionylation in APAP hepatotoxicity. We provide evidence that the sensitivity difference between wild-type and Gstp1/2−/− mice is unrelated to the ability of APAP to induce oxidative stress, despite observing significant increases in c-Jun N-terminal kinase and extracellular signal-regulated kinase phosphorylation in wild-type mice. The major difference in response to APAP was in the levels of protein S-glutathionylation: Gstp1/2−/− mice exhibited a significant increase in the number of S-glutathionylated proteins compared with wild-type animals. Remarkably, these S-glutathionylated proteins are involved in oxidative phosphorylation, respiratory complexes, drug metabolism, and mitochondrial apoptosis. Furthermore, we found that S-glutathionylation of the rate-limiting glutathione-synthesizing enzyme, glutamate cysteine ligase, was markedly increased in Gstp1/2−/− mice in response to APAP. The data demonstrate that S-glutathionylation provides an adaptive response to APAP and, as a consequence, suggest that this is an important determinant in APAP hepatotoxicity. This work identifies potential novel avenues associated with cell survival for the treatment of chemical-induced hepatotoxicity. PMID:26311813

  16. Joint spatial modeling to identify shared patterns among chronic related potentially preventable hospitalizations

    PubMed Central

    2014-01-01

    Background Rates of Potentially Preventable Hospitalizations (PPH) are used to evaluate access of territorially delimited populations to high quality ambulatory care. A common geographic pattern of several PPH would reflect the performance of healthcare providers. This study is aimed at modeling jointly the geographical variation in six chronic PPH conditions in one Spanish Autonomous Community for describing common and discrepant patterns, and to assess the relative weight of the common pattern on each condition. Methods Data on the 39,970 PPH hospital admissions for diabetes short term complications, chronic obstructive pulmonary disease (COPD), congestive heart failure, dehydration, angina admission and adult asthma, between 2007 and 2009 were extracted from the Hospital Discharge Administrative Databases and assigned to one of the 240 Basic Health Zones. Rates and Standardized Hospitalization Ratios per geographic unit were estimated. The spatial analysis was carried out jointly for PPH conditions using Shared Component Models (SCM). Results The component shared by the six PPH conditions explained about the 36% of the variability of each PPH condition, ranging from the 25.9 for dehydration to 58.7 for COPD. The geographical pattern found in the latent common component identifies territorial clusters with particularly high risk. The specific risk pattern that each isolated PPH does not share with the common pattern for all six conditions show many non-significant areas for most PPH, but with some exceptions. Conclusions The geographical distribution of the risk of the PPH conditions is captured in a 36% by a unique latent pattern. The SCM modeling may be useful to evaluate healthcare system performance. PMID:24899214

  17. Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species

    PubMed Central

    2013-01-01

    Background Eucalyptus is one of the most important sources of industrial cellulose. Three species of this botanical group are intensively used in breeding programs: E. globulus, E. grandis and E. urophylla. E. globulus is adapted to subtropical/temperate areas and is considered a source of high-quality cellulose; E. grandis grows rapidly and is adapted to tropical/subtropical climates; and E. urophylla, though less productive, is considered a source of genes related to robustness. Wood, or secondary xylem, results from cambium vascular differentiation and is mostly composed of cellulose, lignin and hemicelluloses. In this study, the xylem transcriptomes of the three Eucalyptus species were investigated in order to provide insights on the particularities presented by each of these species. Results Data analysis showed that (1) most Eucalyptus genes are expressed in xylem; (2) most genes expressed in species-specific way constitutes genes with unknown functions and are interesting targets for future studies; (3) relevant differences were observed in the phenylpropanoid pathway: E. grandis xylem presents higher expression of genes involved in lignin formation whereas E. urophylla seems to deviates the pathway towards flavonoid formation; (4) stress-related genes are considerably more expressed in E. urophylla, suggesting that these genes may contribute to its robustness. Conclusions The comparison of these three transcriptomes indicates the molecular signatures underlying some of their distinct wood characteristics. This information may contribute to the understanding of xylogenesis, thus increasing the potential of genetic engineering approaches aiming at the improvement of Eucalyptus forest plantations productivity. PMID:23521840

  18. Functional bacteria as potential indicators of water quality in Three Gorges Reservoir, China.

    PubMed

    Wang, Hongyuan; Shen, Zhenyao; Niu, Junfeng; He, Ya; Hong, Qian; Wang, Ying

    2010-04-01

    The distributions of culturable bacteria and functional bacteria associated with nitrogen (N) or phosphorus (P) in the backwater areas of the Three Gorges Reservoir (TGR) were investigated. Results from seven locations in the TGR indicated that the abundance of total bacteria was high, with 8.12 x 10(6), 2.70 x 10(7), and 6.73 x 10(10) colony-forming units per milliliter or per gram dry weight in surface water, bottom water, and sediments, respectively. Aquatic environments with higher nutrient loadings possessed higher bacteria densities and lower bacteria community diversities. Eight kinds of functional bacteria ratios, including surface water to bottom water and ratios of water to sediments, were calculated, in which four kinds of functional bacteria, namely, nitrogen-fixing bacteria, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and organophosphate-solubilizing bacteria, displayed obvious differences in different locations. Based on the functional bacteria ratios of water to sediments, it was found that the obtained result of location grouping from cluster analysis was similar to that based on the community-level physiological profiles studies. The above results showed that the ratios of functional bacteria could distinguish the aquatic environments with different trophic conditions in the TGR. This demonstrated that the distribution ratios of functional bacteria in aquatic environments could work as potential bioindicators to reflect the trophic condition of the water. PMID:19333770

  19. MicroRNAs as prognostic indicators and therapeutic targets: potential effect on breast cancer management.

    PubMed

    Lowery, Aoife J; Miller, Nicola; McNeill, Roisin E; Kerin, Michael J

    2008-01-15

    The discovery of microRNAs (miRNA) as novel modulators of gene expression has resulted in a rapidly expanding repertoire of molecules in this family, as reflected in the concomitant expansion of scientific literature. MiRNAs are a category of naturally occurring RNA molecules that play important regulatory roles in plants and animals by targeting mRNAs for cleavage or translational repression. Characteristically, miRNAs are noncoding, single-stranded short (18-22 nucleotides) RNAs, features which possibly explain why they had not been intensively investigated until recently. Accumulating experimental evidence indicates that miRNAs play a pivotal role in many cellular functions via the regulation of gene expression. Furthermore, their dysregulation and/or mutation has been shown in carcinogenesis. We provide a brief review of miRNA biogenesis and discuss the technical challenges of modifying experimental techniques to facilitate the identification and characterization of these small RNAs. MiRNA function and their involvement in malignancy, particularly their putative role as oncogenes or tumor suppressors is also discussed, with a specific emphasis on breast cancer. Finally, we comment on the potential role of miRNAs in breast cancer management, particularly in improving current prognostic tools and achieving the goal of individualized cancer treatment. PMID:18223209

  20. Event-related potentials indicate context effect in reading ambiguous words.

    PubMed

    Kotchoubey, Boris; El-Khoury, Sylvain

    2014-10-29

    The aim of the study was a comparison of lexical and contextual factors in understanding ambiguous words in German. First, a sample of native speakers selected 56 words having maximally strong differences between a dominant and a subordinate meaning. After this, another sample from the same population was visually presented with sentences that activated dominant or subordinate meanings of the words and were accompanied by probes associated with dominant or subordinate meanings. This resulted in a crossed design with two factors: sentence dominant vs. sentence subordinate and probe dominant vs. probe subordinate. An analysis of event-related brain potentials revealed a large, long-lasting and highly-significant N400 wave whenever the meaning of the probe was incongruent with the meaning of the sentence and the lack of this wave whenever the two meanings were congruent. In the typical N400 space and time, the effect was independent of whether the lexical word meaning was dominant or subordinate. At other sites and times, however (e.g., at lateral frontal electrodes F7/F8, and after 700ms), the congruence effect was significant after dominant sentences only. The data indicate that lexical factors have a rather limited influence on the activation of a particular meaning of ambiguous words. A strong context can virtually override even a very strong difference in the preference for different meanings. PMID:25463139

  1. Potential regrowth and recolonization of salmonellae and indicators in biosolids and biosolid-amended soil.

    PubMed

    Zaleski, Kathleen J; Josephson, Karen L; Gerba, Charles P; Pepper, Ian L

    2005-07-01

    This study evaluated the potential for conversion of Class B to Class A biosolids with respect to salmonellae and fecal coliforms during solar drying in concrete lined drying beds. Anaerobically (8% solids) and aerobically (2% solids) digested Class B biosolids were pumped into field-scale drying beds, and microbial populations and environmental conditions were monitored. Numbers of fecal coliforms and salmonellae decreased as temperature and rate of desiccation increased. After 3 to 4 weeks, Class A requirements were achieved in both biosolids for the pathogens and the indicators. However, following rainfall events, significant increase in numbers was observed for both fecal coliforms and salmonellae. In laboratory studies, regrowth of fecal coliforms was observed in both biosolids and biosolid-amended soil, but the regrowth of salmonellae observed in the concrete-lined drying beds did not occur. These laboratory studies demonstrated that pathogens decreased in numbers when soil was amended with biosolids. Based on serotyping, the increased numbers of salmonellae seen in the concrete lined drying beds following rainfall events was most likely due to recolonization due to contamination from fecal matter introduced by animals and not from regrowth of salmonellae indigenous to biosolids. Overall, we conclude that the use of concrete-lined beds created a situation in which moisture added as rainfall accumulated in the beds, promoting the growth of fecal coliforms and salmonellae added from external sources. PMID:16000779

  2. On the use of the resting potential and level set methods for identifying ischemic heart disease: An inverse problem

    NASA Astrophysics Data System (ADS)

    Nielsen, Bjørn Fredrik; Lysaker, Marius; Tveito, Aslak

    2007-01-01

    The electrical activity in the heart is modeled by a complex, nonlinear, fully coupled system of differential equations. Several scientists have studied how this model, referred to as the bidomain model, can be modified to incorporate the effect of heart infarctions on simulated ECG (electrocardiogram) recordings. We are concerned with the associated inverse problem; how can we use ECG recordings and mathematical models to identify the position, size and shape of heart infarctions? Due to the extreme CPU efforts needed to solve the bidomain equations, this model, in its full complexity, is not well-suited for this kind of problems. In this paper we show how biological knowledge about the resting potential in the heart and level set techniques can be combined to derive a suitable stationary model, expressed in terms of an elliptic PDE, for such applications. This approach leads to a nonlinear ill-posed minimization problem, which we propose to regularize and solve with a simple iterative scheme. Finally, our theoretical findings are illuminated through a series of computer simulations for an experimental setup involving a realistic heart in torso geometry. More specifically, experiments with synthetic ECG recordings, produced by solving the bidomain model, indicate that our method manages to identify the physical characteristics of the ischemic region(s) in the heart. Furthermore, the ill-posed nature of this inverse problem is explored, i.e. several quantitative issues of our scheme are explored.

  3. Potential New Genes for Resistance to Mycosphaerella Graminicola Identified in Triticum Aestivum x Lophopyrum Elongatum Disomic Substitution Lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lophopyrum species carry many desirable agronomic traits, including disease resistance, which can be transferred to wheat by interspecific hybridizations. To identify potentially new genes for disease and insect resistance carried by individual Lophopyrum chromosomes, 19 of 21 possible wheat cultiv...

  4. Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems

    SciTech Connect

    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui; Lehman, R. Michael

    2015-06-09

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and Verrucomicrobia, and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors.

  5. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems

    PubMed Central

    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui

    2015-01-01

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and Verrucomicrobia, and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors. PMID:26057123

  6. Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems.

    PubMed

    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui

    2015-01-01

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that were correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and Verrucomicrobia, and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors. PMID:26057123

  7. Multi-analytical approach reveals potential microbial indicators in soil for sugarcane model systems

    DOE PAGESBeta

    Navarrete, Acacio Aparecido; Diniz, Tatiana Rosa; Braga, Lucas Palma Perez; Silva, Genivaldo Gueiros Zacarias; Franchini, Julio Cezar; Rossetto, Raffaella; Edwards, Robert Alan; Tsai, Siu Mui; Lehman, R. Michael

    2015-06-09

    This study focused on the effects of organic and inorganic amendments and straw retention on the microbial biomass (MB) and taxonomic groups of bacteria in sugarcane-cultivated soils in a greenhouse mesocosm experiment monitored for gas emissions and chemical factors. The experiment consisted of combinations of synthetic nitrogen (N), vinasse (V; a liquid waste from ethanol production), and sugarcane-straw blankets. Increases in CO2-C and N2O-N emissions were identified shortly after the addition of both N and V to the soils, thus increasing MB nitrogen (MB-N) and decreasing MB carbon (MB-C) in the N+V-amended soils and altering soil chemical factors that weremore » correlated with the MB. Across 57 soil metagenomic datasets, Actinobacteria (31.5%), Planctomycetes (12.3%), Deltaproteobacteria (12.3%), Alphaproteobacteria (12.0%) and Betaproteobacteria (11.1%) were the most dominant bacterial groups during the experiment. Differences in relative abundance of metagenomic sequences were mainly revealed for Acidobacteria, Actinobacteria, Gammaproteobacteria and Verrucomicrobia with regard to N+V fertilization and straw retention. Differential abundances in bacterial groups were confirmed using 16S rRNA gene-targeted phylum-specific primers for real-time PCR analysis in all soil samples, whose results were in accordance with sequence data, except for Gammaproteobacteria. Actinobacteria were more responsive to straw retention with Rubrobacterales, Bifidobacteriales and Actinomycetales related to the chemical factors of N+V-amended soils. Acidobacteria subgroup 7 and Opitutae, a verrucomicrobial class, were related to the chemical factors of soils without straw retention as a surface blanket. Taken together, the results showed that MB-C and MB-N responded to changes in soil chemical factors and CO2-C and N2O-N emissions, especially for N+V-amended soils. The results also indicated that several taxonomic groups of bacteria, such as Acidobacteria, Actinobacteria and Verrucomicrobia, and their subgroups acted as early-warning indicators of N+V amendments and straw retention in sugarcane-cultivated soils, which can alter the soil chemical factors.« less

  8. Seasonal variation of Fatty acids and stable carbon isotopes in sponges as indicators for nutrition: biomarkers in sponges identified.

    PubMed

    Koopmans, Marieke; van Rijswijk, Pieter; Boschker, Henricus T S; Marco, Houtekamer; Martens, Dirk; Wijffels, Rene H

    2015-02-01

    To get a better understanding of sponge feeding biology and efficiencies, the fatty acid (FA) composition and (13)C natural abundance of sponges and of suspended particulate matter (SPM) from surrounding seawater was studied in different seasons at three locations. Haliclona oculata and Haliclona xena from the Oosterschelde, the Netherlands, Halichondria panicea and H. xena from Lake Veere, the Netherlands, and Aplysina aerophoba and Dysidea avara from the Mediterranean, Spain, were studied. Several FA biomarkers for different algal groups, bacteria and sponge biomass were identified in all sponges. The FA concentration variation in sponges was related to changes in fatty acid concentration in SPM. Stable carbon isotopic ratios (δ(13)C) in sponge specific FAs showed very limited seasonal variation at all sites. Algal FAs in sponges were mainly acquired from the SPM through active filtration in all seasons. At the two sites in the Netherlands only in May (spring), the sponge specific FAs had similar δ(13)C ratios as algal FAs, suggesting that sponges were mainly growing during spring and probably summer. During autumn and winter, they were still actively filtering, but the food collected during this period had little effect on sponge δ(13)C values suggesting limited incorporation of filtered material into the sponge body. The sponge A. aerophoba relied mostly on the symbiotic bacteria. In conclusion, fatty acid composition in combination with stable carbon isotope analysis can be used to analyze the food source of sponges. PMID:25107690

  9. Use of medaka (Oryzias latipes) as a model teleost to identify reproductive endpoints indicative of exposure to endocrine disrupting chemicals

    SciTech Connect

    Papoulias, D.M.; Tillitt, D.; Jones, S.; Noltie, D.

    1995-12-31

    The purpose of this research is to identify effects of endocrine disrupting chemicals on the reproductive system of fish at various stages of sexual differentiation and development. The model teleost used was the d-rR strain of medaka (Oryzias latipes) which has a heritable sex-linked color gene. In medaka, sex differences are first detected at the cellular level at hatch. In males, the mitotic activity of the primordial germ cells (PGC) is arrested while the PGCs of the females continue to divide. The germ cells of the gonochoristic medaka have been demonstrated to be totipotent with respective to gonia production. Because endogenous sex steroid hormones are believed to regulate this early process of sexual differentiation, the authors have hypothesized that mitotic activity in males and females exposed to endocrine disrupting chemicals will be different than unexposed individuals. Results are presented for tests conducted by injecting medaka eggs within 36 hours post-hatch with 3 doses of 2,3,7,8-TCDD (nominally 2.3, 1.3, 0.2 pg/embryo), a known anti-estrogen, dissolved in triolein.

  10. Potential risk indicators of retained placenta and other diseases in multiparous cows.

    PubMed

    Qu, Y; Fadden, A N; Traber, M G; Bobe, G

    2014-07-01

    Retained placenta (RP), defined as fetal membranes not being expelled within 24 h after calving, is a costly disease in multiparous dairy cows that has been linked to immune suppression, infections, elevated lipid mobilization, and depleted status of antioxidants including α-tocopherol, and that increases the risk of other diseases (OD) in early lactation. Early detection of cows at increased risk of developing RP, OD, or both in early lactation could improve treatment success and result in improved milk production and reproductive performance. To identify risk indicators of RP, OD, or both, we used a nested case-control design and compared multiparous dairy cows that developed RP (n=32) with cows that remained healthy (H; n=32) or cows that developed OD (n=32) in early lactation. We compared peripartal body condition score (BCS) as well as serum concentrations of α-tocopherol, metabolites [β-hydroxybutyrate (BHBA), cholesterol, glucose, nonesterified fatty acids (NEFA), and urea N], haptoglobin, and macrominerals (i.e., calcium, magnesium, and phosphorus) on d -21, -14, -7, -3, -1, 0, 1, 3, 7, 14, 21, 28, 35, 42, and 49 postpartum. In addition, average serum concentrations were calculated for each cow for the last 3 wk prepartum, for 3 and 2 wk prepartum combined, for the last week prepartum, and for the morning after calving and compared between groups. The RP cows had lower BCS than the H or OD cows until 2 wk postpartum. During the prepartal periods, RP and OD cows had lower α-tocopherol concentrations (corrected or not for cholesterol concentration) and higher NEFA and BHBA concentrations than H cows. Thus, lower prepartal BCS could be an early predictor for RP risk, and lower α-tocopherol concentrations and higher NEFA and BHBA concentrations could be early predictors for disease. PMID:24792789

  11. Li zoning in zircon as a potential geospeedometer and peak temperature indicator

    NASA Astrophysics Data System (ADS)

    Trail, Dustin; Cherniak, Daniele J.; Watson, E. Bruce; Harrison, T. Mark; Weiss, Benjamin P.; Szumila, Ian

    2016-03-01

    Zircon Li concentrations and δ7Li values may potentially trace crustal recycling because continental and mantle-derived zircons yield distinct values. The usefulness of these differences may depend upon the retentivity of zircon to Li concentrations and isotopic ratios. Given the relatively high Li diffusivities measured by Cherniak and Watson (Contrib Mineral Petrol 160: 383-390, 2010), we sought to discover the scenarios under which Li mobility might be inhibited by charge-compensating cations. Toward this end, we conducted "in" diffusion experiments in which Li depth profiles of synthetic Lu-doped, P-doped, and undoped zircon were determined by nuclear reaction analysis. In separate experiments, Li was ion-implanted at depth within polished natural zircon slabs to form a Gaussian Li concentration profile. Diffusively relaxed concentration profiles were measured after heating the slabs to determine diffusivities. In all experiments, which ranged from 920 to 650 °C, calculated diffusivities are in agreement with a previously established Arrhenius relationship calibrated on trace-element-poor Mud Tank zircon. Our revised Arrhenius relationship that includes both datasets is: D_{Li} = 9.60 × 10^{ - 7} exp [ {{ - 278 ± 8{{kJ}/{mol}^{ - 1} }}{RT}} ]{m}^{ 2} {{s}}^{ - 1} We also observed that synthetic sector-zoned zircon exhibits near-step-function Li concentration profiles across sectors that correlate with changes in the rare earth element (REE) and P concentrations. This allowed us to examine how Li diffusion might couple with REE diffusion in a manner different than that described above. In particular, re-heating these grains revealed significant Li migration, but no detectable migration of the rare earth elements. Thus, unlike most elements in zircon which are not mobile at the micrometer scale under most time-temperature paths in the crust, Li zoning, relaxation of zoning, or lack of zoning altogether could be used to reveal time-temperature information. Discrete 10 μm concentration zones of Li within zircon may be partially preserved at 700 °C for tens to hundreds of years, and at 450 °C for millions of years. In this regard, Li zoning in zircon holds significant potential as a geospeedometer, and in some instances as a qualitative indicator of the maximum temperature experienced by the zircon.

  12. Using Smoke Injection in Drains to Identify Potential Preferential Pathways in a Drained Arable Field

    NASA Astrophysics Data System (ADS)

    Nielsen, M. H.; Petersen, C. T.; Hansen, S.

    2014-12-01

    Macropores forming a continuous pathway between the soil surface and subsurface drains favour the transport of many contaminants from agricultural fields to surface waters. The smoke injection method presented by Shipitalo and Gibbs (2000) used for demonstrating and quantifying such pathways has been further developed and used on a drained Danish sandy loam. In order to identify the preferential pathways to drains, smoke was injected in three 1.15 m deep tile drains (total drain length 93 m), and smoke emitting macropores (SEMP) at the soil surface were counted and characterized as producing either strong or weak plumes compared to reference plumes from 3 and 6 mm wide tubes. In the two situations investigated in the present study - an early spring and an autumn situation, smoke only penetrated the soil surface layer via earthworm burrows located in a 1.0 m wide belt directly above the drain lines. However, it is known from previous studies that desiccation fractures in a dry summer situation also can contribute to the smoke pattern. The distance between SEMP measured along the drain lines was on average 0.46 m whereas the average spacing between SEMP with strong plumes was 2.3 m. Ponded water was applied in 6 cm wide rings placed above 52 burrows including 17 reference burrows which did not emit smoke. Thirteen pathways in the soil were examined using dye tracer and profile excavation. SEMP with strong plumes marked the entrance of highly efficient transport pathways conducting surface applied water and dye tracer into the drain. However, no single burrow was traced all the way from the surface into the drain, the dye patterns branched off in a network of other macropores. Water infiltration rates were significantly higher (P < 0.05) in SEMP with strong plumes (average rate: 247 mL min-1 n = 19) compared to SEMP with weak plumes (average rate: 87 mL min-1 n = 16) and no plumes (average rate: 56 mL min-1 n = 17). The results suggest that the smoke injection method is useful for identification of potentially efficient pathways for surface applied contaminants to drains and surface waters, pathways being associated primarily with unevenly distributed SEMP producing strong smoke plumes.

  13. Epigenetic screen identifies genotype-specific promoter DNA methylation and oncogenic potential of CHRNB4.

    PubMed

    Scherf, D B; Sarkisyan, N; Jacobsson, H; Claus, R; Bermejo, J L; Peil, B; Gu, L; Muley, T; Meister, M; Dienemann, H; Plass, C; Risch, A

    2013-07-11

    Genome-wide association studies have highlighted three major lung cancer susceptibility regions at 15q25.1, 5p15.33 and 6p21.33. To gain insight into the possible mechanistic relevance of the genes in these regions, we investigated the regulation of candidate susceptibility gene expression by epigenetic alterations in healthy and lung tumor tissues. For genes up or downregulated in lung tumors, the influence of genetic variants on DNA methylation was investigated and in vitro studies were performed. We analyzed 394 CpG units within 19 CpG islands in the susceptibility regions in a screening set of 34 patients. Significant findings were validated in an independent patient set (n=50) with available DNA and RNA. The most consistent overall DNA methylation difference between tumor and adjacent normal tissue on 15q25 was tumor hypomethylation in the promoter region of CHRNB4 with a median difference of 8% (P<0.001), which resulted in overexpression of the transcript in tumors (P<0.001). Confirming previous studies, we also found hypermethylation in CHRNA3 and telomerase reverse transcriptase (TERT) with significant expression changes. Decitabine treatment of H1299 cells resulted in reduced methylation levels in gene promoters, elevated transcript levels of CHRNB4 and CHRNA3, and a slight downregulation of TERT demonstrating epigenetic regulation of lung cancer cells. Single-nucleotide polymorphisms rs421629 on 5p15.33 and rs1948, rs660652, rs8040868 and rs2036527 on 15q25.1, previously identified as lung cancer risk or nicotine-addiction modifiers, were associated with tumor DNA methylation levels in the promoters of TERT and CHRNB4 (P<0.001), respectively, in two independent sample sets (n=82; n=150). In addition, CHRNB4 knockdown in two different cell lines (A549 and H1299) resulted in reduced proliferation (PA549<0.05;PH1299<0.001) and propensity to form colonies in H1299 cells. These results suggest epigenetic deregulation of nicotinic acetylcholine receptor subunit (nAChR) genes which in the case of CHRNB4 is strongly associated with genetic lung cancer susceptibility variants and a functional impact on tumorigenic potential. PMID:22945651

  14. Epigenetic screen identifies genotype- specific promoter DNA methylation and oncogenic potential of CHRNB4

    PubMed Central

    Scherf, David B; Sarkisyan, Narek; Jacobsson, Hanna; Claus, Rainer; Bermejo, Justo L; Peil, Barbara; Gu, Lei; Muley, Thomas; Meister, Michael; Dienemann, Hendrik; Plass, Christoph; Risch, Angela

    2012-01-01

    Genome-wide association studies have highlighted three major lung cancer susceptibility regions at 15q25.1, 5p15.33 and 6p21.33. To gain insight into the possible mechanistic relevance of the genes in these regions, we investigated the regulation of candidate susceptibility gene expression by epigenetic alterations in healthy and lung tumor tissues. For genes up- or downregulated in lung tumors the influence of genetic variants on DNA methylation was investigated and in vitro studies were performed. We analyzed 394 CpG units within 19 CpG islands in the susceptibility regions in a screening set of 34 patients. Significant findings were validated in an independent patient set (n=50) with available DNA and RNA. The most consistent overall DNA methylation difference between tumor and adjacent normal tissue on 15q25 was tumor hypomethylation in the promoter region of CHRNB4 with a median difference of 8% (p<0.001) which resulted in overexpression of the transcript in tumors (p<0.001). Confirming previous studies we also found hypermethylation in CHRNA3 and TERT with significant expression changes. Decitabine treatment of H1299 cells resulted in reduced methylation levels in gene promoters, elevated transcript levels of CHRNB4 and CHRNA3 and a slight downregulation of TERT demonstrating epigenetic regulation of lung cancer cells. SNPs rs421629 on 5p15.33 and rs1948, rs660652, rs8040868 and rs2036527 on 15q25.1, previously identified as lung cancer risk or nicotine addiction modifiers were associated with tumor DNA methylation levels in the promoters of TERT and CHRNB4 (p<0.001) respectively in two independent sample sets (n=82; n=150). In addition, CHRNB4 knock down in two different cell lines (A549 and H1299) resulted in reduced proliferation (pA549<0.05;pH1299L<0.001) and propensity to form colonies in H1299 cells. These results suggest epigenetic deregulation of nicotinic acetylcholinereceptor subunit (nAChR) genes which in the case of CHRNB4 is strongly associated with genetic lung cancer susceptibility variants and a functional impact on tumorigenic potential. PMID:22945651

  15. Hyperuricaemia – A Potential Indicator to Diagnose the Risk of Essential Hypertension

    PubMed Central

    Kaur, Manjinder; Suhalka, M.L.; Sharma, Suman; Basu, Abhijit

    2016-01-01

    Introduction Hypertension has turned out to be the major cause of morbidity among the life style diseases. Studies in human and animal models have documented an independent association of hyperuricaemia with early hypertension. Hyperuricaemia is a modifiable and treatable risk factor, which might reduce the incidence of Essential Hypertension (EHT). Aim Hence, the present study was designed to find out the association between hyperuricaemia and EHT in the population of Southern Rajasthan as there is a dearth of literature on Indian scenario especially in Rajasthan. Materials and Methods A cross-sectional, case control study was carried out in the Department of Physiology among 125 subjects; aged 20-50 years of both sexes, which were chosen randomly from Medicine OPD and healthy volunteers. The subjects were broadly divided into two groups (A & B); group A comprised of newly diagnosed cases of EHT (n=75) and group B had healthy normotensive controls (n=50). S. Uric Acid (SUA), Serum creatinine and fasting blood glucose levels were estimated by using the respective kit methods on semi auto-analyser in both groups. S. creatinine and fasting blood glucose levels were estimated to exclude renal disorder and diabetes mellitus respectively. The data was analysed by student t-test, chi-square test and Odds Ratio. Results The mean SUA level in group A was significantly higher than group B (6.56 ± 0.76, 4.91 ± 0.97 mg/dl, p<0.001 respectively). 37.33% of patients had hyperuricaemia in group A as compared to 14% in group B (p<0.01, OR=3.66) indicating that a hyperuricaemic individual has 3.66 times more risk of developing EHT as compared to the one with lower value of SUA. Conclusion The mean SUA level and the frequency of hyperuricaemia was significantly higher in newly diagnosed cases of EHT as compared to healthy controls. Hence, SUA could be useful as a potential indicator for early risk detection of development of EHT. PMID:27134862

  16. Anthropogenic waste indicators (AWIs), particularly PAHs and LABs, in Malaysian sediments: Application of aquatic environment for identifying anthropogenic pollution.

    PubMed

    Masood, Najat; Zakaria, Mohamad Pauzi; Halimoon, Normala; Aris, Ahmad Zaharin; Magam, Sami M; Kannan, Narayanan; Mustafa, Shuhaimi; Ali, Masni Mohd; Keshavarzifard, Mehrzad; Vaezzadeh, Vahab; Alkhadher, Sadeq Abdullah Abdo; Al-Odaini, Najat Ahmed

    2016-01-15

    Polycyclic aromatic hydrocarbons (PAHs) and linear alkylbenzenes (LABs) were used as anthropogenic markers of organic chemical pollution of sediments in the Selangor River, Peninsular Malaysia. This study was conducted on sediment samples from the beginning of the estuary to the upstream river during dry and rainy seasons. The concentrations of ƩPAHs and ƩLABs ranged from 203 to 964 and from 23 to 113ngg(-1) dry weight (dw), respectively. In particular, the Selangor River was found to have higher sedimentary levels of PAHs and LABs during the wet season than in the dry season, which was primarily associated with the intensity of domestic wastewater discharge and high amounts of urban runoff washing the pollutants from the surrounding area. The concentrations of the toxic contaminants were determined according to the Sediment Quality Guidelines (SQGs). The PAH levels in the Selangor River did not exceed the SQGs, for example, the effects range low (ERL) value, indicating that they cannot exert adverse biological effects. PMID:26616745

  17. Quantitative Profiling Identifies Potential Regulatory Proteins Involved in Development from Dauer Stage to L4 Stage in Caenorhabditis elegans.

    PubMed

    Kim, Sunhee; Lee, Hyoung-Joo; Hahm, Jeong-Hoon; Jeong, Seul-Ki; Park, Don-Ha; Hancock, William S; Paik, Young-Ki

    2016-02-01

    When Caenorhabditis elegans encounters unfavorable growth conditions, it enters the dauer stage, an alternative L3 developmental period. A dauer larva resumes larval development to the normal L4 stage by uncharacterized postdauer reprogramming (PDR) when growth conditions become more favorable. During this transition period, certain heterochronic genes involved in controlling the proper sequence of developmental events are known to act, with their mutations suppressing the Muv (multivulva) phenotype in C. elegans. To identify the specific proteins in which the Muv phenotype is highly suppressed, quantitative proteomic analysis with iTRAQ labeling of samples obtained from worms at L1 + 30 h (for continuous development [CD]) and dauer recovery +3 h (for postdauer development [PD]) was carried out to detect changes in protein abundance in the CD and PD states of both N2 and lin-28(n719). Of the 1661 unique proteins identified with a < 1% false discovery rate at the peptide level, we selected 58 proteins exhibiting ≥2-fold up-regulation or ≥2-fold down-regulation in the PD state and analyzed the Gene Ontology terms. RNAi assays against 15 selected up-regulated genes showed that seven genes were predicted to be involved in higher Muv phenotype (p < 0.05) in lin-28(n791), which is not seen in N2. Specifically, two genes, K08H10.1 and W05H9.1, displayed not only the highest rate (%) of Muv phenotype in the RNAi assay but also the dauer-specific mRNA expression, indicating that these genes may be required for PDR, leading to the very early onset of dauer recovery. Thus, our proteomic approach identifies and quantitates the regulatory proteins potentially involved in PDR in C. elegans, which safeguards the overall lifecycle in response to environmental changes. PMID:26751275

  18. Cortical EEG oscillations and network connectivity as efficacy indices for assessing drugs with cognition enhancing potential.

    PubMed

    Ahnaou, A; Huysmans, H; Jacobs, T; Drinkenburg, W H I M

    2014-11-01

    Synchronization of electroencephalographic (EEG) oscillations represents a core mechanism for cortical and subcortical networks, and disturbance in neural synchrony underlies cognitive processing deficits in neurological and neuropsychiatric disorders. Here, we investigated the effects of cognition enhancers (donepezil, rivastigmine, tacrine, galantamine and memantine), which are approved for symptomatic treatment of dementia, on EEG oscillations and network connectivity in conscious rats chronically instrumented with epidural electrodes in different cortical areas. Next, EEG network indices of cognitive impairments with the muscarinic receptor antagonist scopolamine were modeled. Lastly, we examined the efficacy of cognition enhancers to normalize those aberrant oscillations. Cognition enhancers elicited systematic ("fingerprint") enhancement of cortical slow theta (4.5-6 Hz) and gamma (30.5-50 Hz) oscillations correlated with lower activity levels. Principal component analysis (PCA) revealed a compact cluster that corresponds to shared underlying mechanisms as compared to different drug classes. Functional network connectivity revealed consistent elevated coherent slow theta activity in parieto-occipital and between interhemispheric cortical areas. In rats instrumented with depth hippocampal CA1-CA3 electrodes, donepezil elicited similar oscillatory and coherent activities in cortico-hippocampal networks. When combined with scopolamine, the cognition enhancers attenuated the leftward shift in coherent slow delta activity. Such a consistent shift in EEG coherence into slow oscillations associated with altered slow theta and gamma oscillations may underlie cognitive deficits in scopolamine-treated animals, whereas enhanced coherent slow theta and gamma activity may be a relevant mechanism by which cognition enhancers exert their beneficial effect on plasticity and cognitive processes. The findings underscore that PCA and network connectivity are valuable tools to assess efficacy of novel therapeutic drugs with cognition enhancing potential. PMID:25181033

  19. Trehalose as an indicator of desiccation stress in Drosophila melanogaster larvae: A potential marker of anhydrobiosis

    SciTech Connect

    Thorat, Leena J.; Gaikwad, Sushama M.; Nath, Bimalendu B.

    2012-03-23

    Highlights: Black-Right-Pointing-Pointer First report confirming anhydrobiosis in Drosophila melanogaster larvae. Black-Right-Pointing-Pointer Trehalose synthesis and accumulation in larvae that hydrolyzed on rehydration. Black-Right-Pointing-Pointer Trehalose synthesis in concert with the enzymes involved in trehalose metabolism. Black-Right-Pointing-Pointer Inhibition of trehalose hydrolysis in presence of a specific trehalase inhibitor. Black-Right-Pointing-Pointer Trehalose proposed as a reliable marker for biomonitoring of climate change studies. -- Abstract: In the current scenario of global climate change, desiccation is considered as one of the major environmental stressors for the biota exposed to altered levels of ambient temperature and humidity. Drosophila melanogaster, a cosmopolitan terrestrial insect has been chosen as a humidity-sensitive bioindicator model for the present study since its habitat undergoes frequent stochastic and/or seasonally aggravated dehydration regimes. We report here for the first time the occurrence of anhydrobiosis in D. melanogaster larvae by subjecting them to desiccation stress under laboratory conditions. Larvae desiccated for ten hours at <5% relative humidity could enter anhydrobiosis and could revive upon rehydration followed by resumption of active metabolism. As revealed by FTIR and HPLC analyzes, our findings strongly indicated the synthesis and accumulation of trehalose in the desiccating larvae. Biochemical measurements pointed out the desiccation-responsive trehalose metabolic pathway that was found to be coordinated in concert with the enzymes trehalose 6-phosphate synthase and trehalase. Further, an inhibitor-based experimental approach using deoxynojirimycin, a specific trehalase inhibitor, demonstrated the pivotal role of trehalose in larval anhydrobiosis of D. melanogaster. We therefore propose trehalose as a potential marker for the assessment of anhydrobiosis in Drosophila. The present findings thus add to the growing list of novel biochemical markers in specific bioindicator organisms for fulfilling the urgent need of environmental biomonitoring of climate change.

  20. Looking at Dauphiné twins in vein quartz as a potential paleostress indicator

    NASA Astrophysics Data System (ADS)

    Sintubin, Manuel; Wenk, Hans-Rudolf

    2013-04-01

    Paleostress studies commonly call upon (1) a fault slip data inversion technique, (2) a calcite twin stress inversion technique, (3) recrystallized grain size piezometry for quartz, or (4) direct measurements of residual lattice strain. Recent advances in orientation imaging microscopy (OIM) using electron backscatter diffraction (EBSD) on a scanning electron microscope (SEM) have revealed that Dauphiné twinning is very common in quartz in naturally deformed quartz-bearing rocks in a wide range of tectonometamorphic conditions. It has long been known that mechanical Dauphiné twinning in quartz can be stress-induced. Based on the results of an extensive EBSD-OIM analysis on vein quartz, taken from well-studied early to late-orogenic veins in the High-Ardenne slate belt (Germany, Belgium), we explore the potential use of mechanical Dauphiné twins as a paleostress indicator, possibly completing our toolbox for reconstructing paleostresses in the Earth's crust. The vein quartz studied precipitated in low-grade tectonometamorphic conditions (~200-400°C), typical for the brittle-plastic transition zone at the base of the seismogenic crust (~7-15km). Quartz has only been weakly affected by low to moderate temperature (200 to 400°C) crystal-plastic deformation. The samples show grains with a high concentration of Dauphiné twin boundaries and others free of twin boundaries, thus being untwinned or completely twinned. This pattern depends on the crystallographic orientation. Twin boundaries are arrested by grain or subgrain boundaries, suggesting that Dauphiné twinning occurred on a pre-existing fabric that resulted from crystal-plastic deformation. An analysis of the orientation distribution of the rhombs in the twinned variant domains of individual quartz (sub-)grains reveals a particular preferred orientation of the poles to rhombs. We will discuss the possible significance of these observations with respect to paleostresses that may have caused the mechanical Dauphiné twinning.

  1. Use of AIRSAR to identify woody shrub invasion and other indicators of desertification in the Jornada LTER

    NASA Technical Reports Server (NTRS)

    Musick, H. Brad; Schaber, Gerald G.; Breed, Carol S.

    1995-01-01

    The replacement of semidesert grassland by woody shrubland is a widespread form of desertification. This change in physiognomy and species composition tends to sharply reduce the productivity of the land for grazing by domestic livestock, increase soil erosion and reduce soil fertility, and greatly alter many other aspects of ecosystem structure and functioning. Remote sensing methods are needed to assess and monitor shrubland encroachment. Detection of woody shrubs at low density would provide a particularly useful baseline on which to access changes, because an initially low shrub density often tends to increase even after cessation of the disturbance (e.g., overgrazing, drought, or fire suppression) responsible for triggering the initial stages of the invasion (Grover and Musick, 1990). Limited success has been achieved using optical remote sensing. In contrast to other forms of desertification, biomass does not consistently decrease with a shift from grassland to shrubland. Estimation of green vegetation amount (e.g., by NDVI) is thus of limited utility, unless the shrubs and herbaceous plants differ consistently in phenology and the area can be viewed during a season when only one of these is green. The objective of this study was to determine if the potential sensitivity of active microwave remote sensing to vegetation structure could be used to assess the degree of shrub invasion of grassland. Polarimetric Airborne Synthetic Aperture Radar (AIRSAR) data were acquired for a semiarid site containing varied mixtures of shrubs and herbaceous vegetation and compared with ground observations of vegetation type and other landsurface characteristics. In this preliminary report we examine the response of radar backscatter intensity to shrub density. The response of other multipolarization parameters will be examined in future work.

  2. Whole genome sequencing indicates Corynebacterium jeikeium comprises 4 separate genomospecies and identifies a dominant genomospecies among clinical isolates

    PubMed Central

    Salipante, Stephen J.; Sengupta, Dhruba J.; Cummings, Lisa A.; Robinson, Aaron; Kurosawa, Kyoko; Hoogestraat, Daniel R.; Cookson, Brad T.

    2014-01-01

    Corynebacterium jeikeium is an opportunistic pathogen which has been noted for significant genomic diversity. The population structure within this species remains poorly understood. Here we explore the relationships among fifteen clinical isolates of C. jeikeium (reference strains K411 and ATCC 43734, and 13 primary isolates collected over a period of 7 years) through genetic, genomic, and phenotypic studies. We report a high degree of divergence among strains based on 16S ribosomal RNA (rRNA) gene and rpoB gene sequence analysis, supporting the presence of genetically distinct subgroups. Whole genome sequencing indicates genomic-level dissimilarity among subgroups, which qualify as 4 separate and distinct Corynebacterium species based on an Average Nucleotide Identity (ANIb) threshold of < 95%. Functional distinctions in antibiotic susceptibilities and metabolic profiles characterize two of these genomospecies, allowing their differentiation from others through routine laboratory testing. The remaining genomospecies can be classified through a biphasic approach integrating phenotypic testing and rpoB gene sequencing. The genomospecies predominantly recovered from patient specimens does not include either of the existing C. jeikeium reference strains, implying that studies of this pathogen would benefit from examination of representatives from the primary disease-causing group. The clinically dominant genomospecies also has the smallest genome size and gene repertoire, suggesting the possibility of increased virulence relative to the other genomospecies. The ability to classify isolates to one of the four C. jeikeium genomospecies in a clinical context provides diagnostic information for tailoring antimicrobial therapy and may aid in identification of species-specific disease associations. PMID:25116839

  3. Quantification of Impervious Surfaces Along the Wasatch Front, Utah: AN Object-Based Image Analysis Approach to Identifying AN Indicator for Wetland Stress

    NASA Astrophysics Data System (ADS)

    Leydsman-McGinty, E. I.; Ramsey, R. D.; McGinty, C.

    2013-12-01

    The Remote Sensing/GIS Laboratory at Utah State University, in cooperation with the United States Environmental Protection Agency, is quantifying impervious surfaces for three watershed sub-basins in Utah. The primary objective of developing watershed-scale quantifications of impervious surfaces is to provide an indicator of potential impacts to wetlands that occur within the Wasatch Front and along the Great Salt Lake. A geospatial layer of impervious surfaces can assist state agencies involved with Utah's Wetlands Program Plan (WPP) in understanding the impacts of impervious surfaces on wetlands, as well as support them in carrying out goals and actions identified in the WPP. The three watershed sub-basins, Lower Bear-Malad, Lower Weber, and Jordan, span the highly urbanized Wasatch Front and are consistent with focal areas in need of wetland monitoring and assessment as identified in Utah's WPP. Geospatial layers of impervious surface currently exist in the form of national and regional land cover datasets; however, these datasets are too coarse to be utilized in fine-scale analyses. In addition, the pixel-based image processing techniques used to develop these coarse datasets have proven insufficient in smaller scale or detailed studies, particularly when applied to high-resolution satellite imagery or aerial photography. Therefore, object-based image analysis techniques are being implemented to develop the geospatial layer of impervious surfaces. Object-based image analysis techniques employ a combination of both geospatial and image processing methods to extract meaningful information from high-resolution imagery. Spectral, spatial, textural, and contextual information is used to group pixels into image objects and then subsequently used to develop rule sets for image classification. eCognition, an object-based image analysis software program, is being utilized in conjunction with one-meter resolution National Agriculture Imagery Program (NAIP) aerial photography from 2011.

  4. Identifying Potentially Hazardous Co-orbiting Material of Known NEOs Using Magnetic Signatures Produced in Destructive Collisions

    NASA Astrophysics Data System (ADS)

    Lai, Hairong; Russell, Christopher; Jia, Yingdong; Wei, Hanying; Connors, Martin

    2015-04-01

    It is estimated that over 99% of near-Earth objects (NEOs) with diameters of about tens of meters are undiscovered. However, simulations show that they result in the most damage per year. Many of these bodies, produced in non-destructive collisions with larger well-characterized NEOs, are co-orbiting with their parent objects. Thereafter, scattering will occur due to gravitational perturbations when the co-orbiters have close encounters to any planets. Such gravitational scattering may not affect the orbits of the parent body. Therefore "safe" NEOs which have negligible impact probability with the Earth may be accompanied by potentially hazardous co-orbiting material. Those co-orbitals do reveal their existence in collisions with meteoroids, which are numerous and can be as small as tens of centimeters in diameter. Clouds of fine dust/gas particles released in such collisions become charged after generation and interact coherently with the solar wind electromagnetically. The interplanetary magnetic field is then perturbed. The resultant structures have been called interplanetary field enhancements (IFEs). They are readily identified when they pass spacecraft equipped with magnetometers. Although the co-orbitals responsible for the IFEs were disrupted in collisions, they are valid samples of the remaining co-orbiting material. Therefore, we can use IFEs to identify the spatial and mass distribution of such co-orbitals. With statistical studies of IFE occurrence, we identified asteroid 2201 Oljato and asteroid 138175 to have such co-orbiting material. The mass of the co-orbitals can be inferred by combining the results from observations and MHD simulations. Multi-spacecraft simultaneous observations measure the dimensions of the magnetic perturbations and the forces lifting them away from the Sun, while multi-fluid simulations give the accelerations of the perturbations. In summary, our technique not only helps us to identify which NEOs are accompanied by hazardous co-orbitals, but also gives their mass distributions. Although our technique provides only the statistical properties, it indicates where high resolution optical surveys should be obtained in order to identify and track specific hazardous bodies.

  5. Identifying cold-water coral ecosystem by using benthic foraminiferal indicators: from active reefs to the geological record

    NASA Astrophysics Data System (ADS)

    Margreth, Stephan; Rüggeberg, Andres; Gennari, Giordana; Spezzaferri, Silvia

    2010-05-01

    Cold-water coral ecosystems dominated by the species Lophelia pertusa and Madrepora oculata, as well as cold-water coral carbonate mounds (fossils and/or active) occur worldwide and are especially developed along the European margin, from northern Norway to the Gulf of Cadiz and into the Alboran Sea. Their discovery is a major achievement of the last few decades and their widespread occurrence presents a challenge to understand their development, preservation and possible importance in the geologic record. On the Norwegian shelf active/living reefs are developed on elevated hard substrata. Along the Irish margin L. pertusa builds large fossil and/or active carbonate mounds. In the Gulf of Cadiz and in the Alboran Sea buried reefs and patch reefs are generally found in association with mud volcanoes. In modern oceans, they provide important ecological niches for the marine benthic fauna in the deep-sea. In comparison to the macrofauna the microfauna, particularly the foraminifera associated to these systems, are poorly known. We present here a detailed study based on quantitative analyses of benthic and planktonic foraminifera together with the statistical treatment of assemblage data collected along the Norwegian margin, in the Porcupine-Rockall region and in the Alboran Sea. The three regions were and/or are site of cold-water coral ecosystems settlements. Our study reveals that in the Porcupine/Rockall region benthic foraminiferal assemblages are strictly related to the distribution of facies. On the Norwegian margin, benthic foraminiferal habitats are weakly defined and grade one into the other preventing the sharp facies separation observed along the Irish margin (Margreth et al., 2009). In the Alboran Sea cold-water coral ecosystems and cold-water carbonate mounds are presently buried and corals are generally fragmented. However, benthic assemblages from coral-rich layers in the Alboran Sea and those from Porcupine/Rockall and Norway show remarkable similarities. In particular, epifaunal-attached species such as Discanomalina coronata, Cibicides refulgens, and Lobatula lobatula dominate the assemblages with D. coronata restricted to living cold-water coral reefs facies only and/or in co-occurrence with coral fragments. In conclusion, our data suggest that although cold-water coral ecosystems occur at different latitudes, the associated foraminiferal assemblages are consistent from Norway to the Western Mediterranean. Thus they can be used to identify these ecosystems even in the geologic record, when the corals are often strongly dissolved like in the Alboran Sea. References: Margreth, S., Rüggeberg, A. and Spezzaferri, S., 2009. Benthic foraminifera as bioindicator for cold-water coral reef ecosystems along the Irish margin. Deep Sea Res. Part I, 56: 2216-2234. This study is funded by the Swiss National Foundation Projects 200020-117928 and 200021-111694.

  6. Relevant magnetic and soil parameters as potential indicators of soil conservation status of Mediterranean agroecosystems

    NASA Astrophysics Data System (ADS)

    Quijano, Laura; Chaparro, Marcos A. E.; Marié, Débora C.; Gaspar, Leticia; Navas, Ana

    2014-09-01

    The main sources of magnetic minerals in soils unaffected by anthropogenic pollution are iron oxides and hydroxides derived from parent materials through soil formation processes. Soil magnetic minerals can be used as indicators of environmental factors including soil forming processes, degree of pedogenesis, weathering processes and biological activities. In this study measurements of magnetic susceptibility are used to detect the presence and the concentration of soil magnetic minerals in topsoil and bulk samples in a small cultivated field, which forms a hydrological unit that can be considered to be representative of the rainfed agroecosystems of Mediterranean mountain environments. Additional magnetic studies such as isothermal remanent magnetization (IRM), anhysteretic remanent magnetization (ARM) and thermomagnetic measurements are used to identify and characterize the magnetic mineralogy of soil minerals. The objectives were to analyse the spatial variability of the magnetic parameters to assess whether topographic factors, soil redistribution processes, and soil properties such as soil texture, organic matter and carbonate contents analysed in this study, are related to the spatial distribution pattern of magnetic properties. The medians of mass specific magnetic susceptibility at low frequency (χlf) were 36.0 and 31.1 × 10-8 m3 kg-1 in bulk and topsoil samples respectively. High correlation coefficients were found between the χlf in topsoil and bulk core samples (r = 0.951, p < 0.01). In addition, volumetric magnetic susceptibility was measured in situ in the field (κis) and values varied from 13.3 to 64.0 × 10-5 SI. High correlation coefficients were found between χlf in topsoil measured in the laboratory and volumetric magnetic susceptibility field measurements (r = 0.894, p < 0.01). The results obtained from magnetic studies such as IRM, ARM and thermomagnetic measurements show the presence of magnetite, which is the predominant magnetic carrier, and hematite. The predominance of superparamagnetic minerals in upper soil layers suggests enrichment in pedogenic minerals. The finer soil particles, the organic matter content and the magnetic susceptibility values are statistically correlated and their spatial variability is related to similar physical processes. Runoff redistributes soil components including magnetic minerals and exports fine particles out the field. This research contributed to further knowledge on the application of soil magnetic properties to derive useful information on soil processes in Mediterranean cultivated soils.

  7. Carbamazepine as indicator for potential short-term contamination of karst springs

    NASA Astrophysics Data System (ADS)

    Doummar, J.; Baierl, M.; Noedler, K.; Licha, T.; Sauter, M.; Geyer, T.

    2012-04-01

    Karst aquifers are complex systems which vulnerability is very difficult to assess mainly because of the duality of recharge processes and duality of flow. Recharge to a karst aquifer occurs as diffuse or concentrated (sinkholes and dolines). Moreover, karst aquifers are formed by an unsaturated zone comprising soil, epikarst and unsaturated rock matrix, and a saturated zone formed of highly permeable conduits and low permeability matrix storage. In the case of contamination of groundwater by wastewater effluent polluted water can be either transported rapidly and have short term major risk on spring water quality or infiltrate into fractured rock matrix and therefore have a long term effect on the water quality. In order to identify the risk of wastewater infiltrating into an aquifer, researches have focused to date on the identification of indicative wastewater markers. Carbamazepine (CBZ) was frequently detected in surface water as well as in effluents of sewage treatment plants, as less than 10% of carbamazepine are usually eliminated during sewage treatment. Moreover, CBZ is not attenuated in aquifers (Heberer, 2002), is unlikely degradable or adsorbed, and can be detected in groundwater (Clara et al., 2004). Therefore, CBZ is considered to be fairly persistent in groundwater (Tixier et al., 2003), and is consequently regarded as an effective wastewater marker. In this case study, the Jeita spring in Lebanon (spring discharge: 1-20 m3/s) was monitored and sampled for major ions and micro-pollutants following a combined precipitation/snowmelt events. A total of 28 samples (major ions and micro-pollutants) were taken over a total sampling time of 16 days at interval varying between 4 and 24 hours. Based on the variation with time of discharge and electrical conductivity (monitored every 20 minutes) as well as the concentrations of the major ions, a conceptual model showing the response of the aquifer compartments to the precipitation event was generated. A breakthrough curve of the persistent micro-pollutant carbamazepine shows that CBZ enters the aquifer system through rapid flow pathways, whereas it is heavily diluted with old CBZ free waters stored in the soil/ epikarst zone released as a response to the precipitation event. Furthermore, based on travel times estimated from artificial tracer tests, the distance to the contamination source was estimated and reveals to be relatively small.

  8. Wildlife Abundance and Diversity as Indicators of Tourism Potential in Northern Botswana.

    PubMed

    Winterbach, Christiaan W; Whitesell, Carolyn; Somers, Michael J

    2015-01-01

    Wildlife tourism can provide economic incentives for conservation. Due to the abundance of wildlife and the presence of charismatic species some areas are better suited to wildlife tourism. Our first objective was to develop criteria based on wildlife abundance and diversity to evaluate tourism potential in the Northern Conservation Zone of Botswana. Secondly we wanted to quantify and compare tourism experiences in areas with high and low tourism potential. We used aerial survey data to estimate wildlife biomass and diversity to determine tourism potential, while data from ground surveys quantified the tourist experience. Areas used for High Paying Low Volume tourism had significantly higher mean wildlife biomass and wildlife diversity than the areas avoided for this type of tourism. Only 22% of the Northern Conservation Zone has intermediate to high tourism potential. The areas with high tourism potential, as determined from the aerial survey data, provided tourists with significantly better wildlife sightings (ground surveys) than the low tourism potential areas. Even Low Paying tourism may not be economically viable in concessions that lack areas with intermediate to high tourism potential. The largest part of the Northern Conservation Zone has low tourism potential, but low tourism potential is not equal to low conservation value. Alternative conservation strategies should be developed to complement the economic incentive provided by wildlife-based tourism in Botswana. PMID:26308859

  9. Wildlife Abundance and Diversity as Indicators of Tourism Potential in Northern Botswana

    PubMed Central

    Winterbach, Christiaan W.; Whitesell, Carolyn; Somers, Michael J.

    2015-01-01

    Wildlife tourism can provide economic incentives for conservation. Due to the abundance of wildlife and the presence of charismatic species some areas are better suited to wildlife tourism. Our first objective was to develop criteria based on wildlife abundance and diversity to evaluate tourism potential in the Northern Conservation Zone of Botswana. Secondly we wanted to quantify and compare tourism experiences in areas with high and low tourism potential. We used aerial survey data to estimate wildlife biomass and diversity to determine tourism potential, while data from ground surveys quantified the tourist experience. Areas used for High Paying Low Volume tourism had significantly higher mean wildlife biomass and wildlife diversity than the areas avoided for this type of tourism. Only 22% of the Northern Conservation Zone has intermediate to high tourism potential. The areas with high tourism potential, as determined from the aerial survey data, provided tourists with significantly better wildlife sightings (ground surveys) than the low tourism potential areas. Even Low Paying tourism may not be economically viable in concessions that lack areas with intermediate to high tourism potential. The largest part of the Northern Conservation Zone has low tourism potential, but low tourism potential is not equal to low conservation value. Alternative conservation strategies should be developed to complement the economic incentive provided by wildlife-based tourism in Botswana. PMID:26308859

  10. 7 CFR 170.6 - How are potential market participants identified for the USDA Farmers Market?

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) MISCELLANEOUS MARKETING PRACTICES UNDER THE AGRICULTURAL MARKETING ACT OF 1946 USDA...? Potential market participants are recruited by AMS market management through local farm organizations in...

  11. 7 CFR 170.6 - How are potential market participants identified for the USDA Farmers Market?

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) MISCELLANEOUS MARKETING PRACTICES UNDER THE AGRICULTURAL MARKETING ACT OF 1946 USDA...? Potential market participants are recruited by AMS market management through local farm organizations in...

  12. 7 CFR 170.6 - How are potential market participants identified for the USDA Farmers Market?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) MISCELLANEOUS MARKETING PRACTICES UNDER THE AGRICULTURAL MARKETING ACT OF 1946 USDA...? Potential market participants are recruited by AMS market management through local farm organizations in...

  13. 7 CFR 170.6 - How are potential market participants identified for the USDA Farmers Market?

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) MISCELLANEOUS MARKETING PRACTICES UNDER THE AGRICULTURAL MARKETING ACT OF 1946 USDA...? Potential market participants are recruited by AMS market management through local farm organizations in...

  14. 7 CFR 170.6 - How are potential market participants identified for the USDA Farmers Market?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) MISCELLANEOUS MARKETING PRACTICES UNDER THE AGRICULTURAL MARKETING ACT OF 1946 USDA...? Potential market participants are recruited by AMS market management through local farm organizations in...

  15. Just the Right Mix: Identifying Potential Dropouts in Montgomery County Public Schools Using an Early Warning Indicators Approach

    ERIC Educational Resources Information Center

    West, Thomas C.

    2013-01-01

    Each school year, roughly a thousand students drop out of Montgomery County (Maryland) Public Schools (MCPS). However, unlike other large, urban school districts where students who drop out skip school and are suspended often (Balfanz & Byrnes, 2010), students who drop out of MCPS are present in school; they just are not doing well…

  16. Identifying High Potential Well Targets with 3D Seismic and Mineralogy

    SciTech Connect

    Mellors, R. J.

    2015-10-30

    Seismic reflection the primary tool used in petroleum exploration and production, but use in geothermal exploration is less standard, in part due to cost but also due to the challenges in identifying the highly-permeable zones essential for economic hydrothermal systems [e.g. Louie et al., 2011; Majer, 2003]. Newer technology, such as wireless sensors and low-cost high performance computing, has helped reduce the cost and effort needed to conduct 3D surveys. The second difficulty, identifying permeable zones, has been less tractable so far. Here we report on the use of seismic attributes from a 3D seismic survey to identify and map permeable zones in a hydrothermal area.

  17. Data in support of quantitative proteomics to identify potential virulence regulators in Paracoccidioides brasiliensis isolates.

    PubMed

    Tashima, Alexandre Keiji; Castilho, Daniele Gonçalves; Chaves, Alison Felipe Alencar; Xander, Patricia; Zelanis, André; Batista, Wagner Luiz

    2015-12-01

    Paracoccidioides genus are the etiologic agents of paracoccidioidomycosis (PCM), a systemic mycosis endemic in Latin America. Few virulence factors have been identified in these fungi. This paper describes support data from the quantitative proteomics of Paracoccidioides brasiliensis attenuated and virulent isolates [1]. The protein compositions of two isolates of the Pb18 strain showing distinct infection profiles were quantitatively assessed by stable isotopic dimethyl labeling and proteomic analysis. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with identifier PXD000804. PMID:26501084

  18. Data in support of quantitative proteomics to identify potential virulence regulators in Paracoccidioides brasiliensis isolates

    PubMed Central

    Tashima, Alexandre Keiji; Castilho, Daniele Gonçalves; Chaves, Alison Felipe Alencar; Xander, Patricia; Zelanis, André; Batista, Wagner Luiz

    2015-01-01

    Paracoccidioides genus are the etiologic agents of paracoccidioidomycosis (PCM), a systemic mycosis endemic in Latin America. Few virulence factors have been identified in these fungi. This paper describes support data from the quantitative proteomics of Paracoccidioides brasiliensis attenuated and virulent isolates [1]. The protein compositions of two isolates of the Pb18 strain showing distinct infection profiles were quantitatively assessed by stable isotopic dimethyl labeling and proteomic analysis. The mass spectrometry and the analysis dataset have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with identifier PXD000804. PMID:26501084

  19. Identifying Carcinogenic Potentials of Drinking Water Disinfection Byproducts using Normal Human Colonocyte Cultures

    EPA Science Inventory

    Epidemiological studies have linked the consumption of disinfected surface waters to an increased risk of colorectal cancer. Approximately 600 byproducts (DBPs) have been identified for the major disinfectants currently in use and represent less than half of the total organic car...

  20. Development of Normal Human Colonocyte Cultures to Identify a Carcinogenic Potential for Priority Disinfection Byproducts

    EPA Science Inventory

    Epidemiological studies have linked the consumption of disinfected surface waters to an increased risk of colorectal cancer. Of the approximately >600 disinfection byproducts (DBPs) identified, the US EPA regulates 11 DBPS for an increased risk of cancer. An in-depth mechanism-ba...

  1. Identifying chemical carcinogens and assessing potential risk in short-term bioassays using transgenic mouse models.

    PubMed Central

    Tennant, R W; French, J E; Spalding, J W

    1995-01-01

    Cancer is a worldwide public health concern. Identifying carcinogens and limiting their exposure is one approach to the problem of reducing risk. Currently, epidemiology and rodent bioassays are the means by which putative human carcinogens are identified. Both methods have intrinsic limitations: they are slow and expensive processes with many uncertainties. The development of methods to modify specific genes in the mammalian genome has provided promising new tools for identifying carcinogens and characterizing risk. Transgenic mice may provide advantages in shortening the time required for bioassays and improving the accuracy of carcinogen identification; transgenic mice might now be included in the testing armamentarium without abandoning the two-year bioassay, the current standard. We show that mutagenic carcinogens can be identified with increased sensitivity and specificity using hemizygous p53 mice in which one allele of the p53 gene has been inactivated. Furthermore, the TG.AC transgenic model, carrying a v-Ha-ras construct, has developed papillomas and malignant tumors in response to a number of mutagenic and nonmutagenic carcinogens and tumor promoters, but not to noncarcinogens. We present a decision-tree approach that permits, at modest extra cost, the testing of more chemicals with improved ability to extrapolate from rodents to humans. Images Figure 1. Figure 2. Figure 3. PMID:8529591

  2. Identifying Leadership Potential: The Process of Principals within a Charter School Network

    ERIC Educational Resources Information Center

    Waidelich, Lynn A.

    2012-01-01

    The importance of strong educational leadership for American K-12 schools cannot be overstated. As such, school districts need to actively recruit and develop leaders. One way to do so is for school officials to become more strategic in leadership identification and development. If contemporary leaders are strategic about whom they identify and…

  3. Developing Early Warning Systems to Identify Potential High School Dropouts. Issue Brief

    ERIC Educational Resources Information Center

    Heppen, Jessica B.; Therriault, Susan Bowles

    2008-01-01

    The high school dropout problem has been called a national crisis. Educators, researchers, and policymakers continue to work to identify effective dropout prevention approaches. One important element of such prevention efforts is the identification of students at highest risk for dropping out and then the targeting of resources to keep them in…

  4. Effects of some heavy metals on the action potentials of an identified Helix pomatia photosensitive neuron.

    PubMed

    Kartelija, Gordana; Radenović, Lidija; Todorović, Natasa; Nedeljković, Miodrag

    2005-06-01

    In the photosensitive MB neuron in the left parietal ganglion of Helix pomatia, the onset of light prolongs significantly (by about 40%) the duration of the action potential. The broadening of the action potential after the onset of light was found to be due to its calcium component and could not be induced after blocking Ca(2+) channels by Cd(2+) and Pb(2+) and in absence of Ca(2+) in medium. The blocking effect of both compounds was reversible. It was found that CdCl(2) exhibited a more intense blocking effect than PbCl(2). PMID:16154952

  5. Multidisciplinary approach to identify, characterize and minimize, potential health and environmental problems associated with chemically complex mixtures: a case study

    SciTech Connect

    Gray, R.H.

    1984-11-01

    Chemists, biologists, and ecologists at Battelle's Pacific Northwest Laboratories are developing a data-base to evaluate risk to man and the environment from large-scale deployment of various synfuel options. Since 1976, chemically complex materials produced by several coal liquefaction processes and under various stages of process design and operating conditions have been screened for potential health and environmental effects. Biologically active materials have been fractionated and rescreened. Chemical constitutents of biologically active fractions have been identified, and the environmental fate of problematic agents is currently being determined. Preliminary results had indicated that full-boiling-range coal-derived liquids were generally more active than shale oil and petroleum crudes in biological and ecological test systems. Several biologically active agents were identified, including primary aromatic amines (PAA), polynuclear aromatic hydrocarbons (PAH), and phenols. Although some components of coal-derived materials were taken up by biota and metabolized, hydrotreating, a refining or upgrading process, reduced PAA, PAH and phenol content, as well as mutagenicity, carcinogenicity and toxicity of coal liquids. Also, selective distillation restricted PAA and PAH content, as well as mutagenicity and carcinogenicity, to high-boiling-range coal liquids. The growing health and environmental data-base has provided input for assessment, and has been used by developers when selecting process modifications and product slates (marketable products that boil below 700/sup 0/F) that minimize risk to man and the environment. These data have also been used in developing occupational health and industrial hygiene practices, and may aid selection of control technologies. 18 references, 2 figures, 2 tables.

  6. Combined single channel and single molecule detection identifies subunit composition of STIM1-activated transient receptor potential canonical (TRPC) channels.

    PubMed

    Asanov, Alexander; Sampieri, Alicia; Moreno, Claudia; Pacheco, Jonathan; Salgado, Alfonso; Sherry, Ryan; Vaca, Luis

    2015-01-01

    Depletion of intracellular calcium ion stores initiates a rapid cascade of events culminating with the activation of the so-called Store-Operated Channels (SOC) at the plasma membrane. Calcium influx via SOC is essential in the initiation of calcium-dependent intracellular signaling and for the refilling of internal calcium stores, ensuring the regeneration of the signaling cascade. In spite of the significance of this evolutionary conserved mechanism, the molecular identity of SOC has been the center of a heated controversy spanning over the last 20 years. Initial studies positioned some members of the transient receptor potential canonical (TRPC) channel superfamily of channels (with the more robust evidence pointing to TRPC1) as a putative SOC. Recent evidence indicates that Stromal Interacting Molecule 1 (STIM1) activates some members from the TRPC family of channels. However, the exact subunit composition of TRPC channels remains undetermined to this date. To identify the subunit composition of STIM1-activated TRPC channels, we developed novel method, which combines single channel electrophysiological measurements based on the patch clamp technique with single molecule fluorescence imaging. We termed this method Single ion Channel Single Molecule Detection technique (SC-SMD). Using SC-SMD method, we have obtained direct evidence of the subunit composition of TRPC channels activated by STIM1. Furthermore, our electrophysiological-imaging SC-SMD method provides evidence at the molecular level of the mechanism by which STIM1 and calmodulin antagonize to modulate TRPC channel activity. PMID:25465892

  7. Identifying the Potential Organizational Impact of an Educational Peer Review Program

    ERIC Educational Resources Information Center

    Toth, Kate E.; McKey, Colleen A.

    2010-01-01

    The literature on educational peer review (EPR) has focused on evaluating EPR's impact on faculty and/or student learning outcomes; no literature exists on the potential organizational impact. A qualitative (case study) research design explored perceptions of 17 faculty and 10 administrators within a school of nursing in an Ontario university

  8. An Event-Related Potentials Study of Mental Rotation in Identifying Chemical Structural Formulas

    ERIC Educational Resources Information Center

    Huang, Chin-Fei; Liu, Chia-Ju

    2012-01-01

    The purpose of this study was to investigate how mental rotation strategies affect the identification of chemical structural formulas. This study conducted event-related potentials (ERPs) experiments. In addition to the data collected in the ERPs, a Chemical Structure Conceptual Questionnaire and interviews were also admin-istered for data…

  9. Utilization of solar energy in developing countries: Identifying some potential markets

    NASA Technical Reports Server (NTRS)

    Hein, G. F.; Siddiqi, T. A.

    1978-01-01

    The potential use of solar electricity generated from photovoltaic cells is examined for nineteen developing nations. Energy and economic profiles are summarized for each country. A comparison is made between the use of autogeneration and photovoltaics in a rural area of Haiti.

  10. Comparing OECD PISA Reading in English to Other Languages: Identifying Potential Sources of Non-Invariance

    ERIC Educational Resources Information Center

    Asil, Mustafa; Brown, Gavin T. L.

    2016-01-01

    The use of the Programme for International Student Assessment (PISA) across nations, cultures, and languages has been criticized. The key criticisms point to the linguistic and cultural biases potentially underlying the design of reading comprehension tests, raising doubts about the legitimacy of comparisons across economies. Our research focused…

  11. Cooperative Development of the Digital Library: Identifying and Working with Potential Partners.

    ERIC Educational Resources Information Center

    Poland, Jean

    In a university environment, the library can benefit from interest in the digital future on the part of other concerned groups. Computer science departments are natural partners in the development of digital libraries. Professional societies, for-profit companies, and foundations are also potential sources of support. Cornell University Library…

  12. Identifying the Potential Organizational Impact of an Educational Peer Review Program

    ERIC Educational Resources Information Center

    Toth, Kate E.; McKey, Colleen A.

    2010-01-01

    The literature on educational peer review (EPR) has focused on evaluating EPR's impact on faculty and/or student learning outcomes; no literature exists on the potential organizational impact. A qualitative (case study) research design explored perceptions of 17 faculty and 10 administrators within a school of nursing in an Ontario university…

  13. Identifying potential gas accumulation sites from Oligocene overpressure data in the Qiongdongnan basin, offshore South China

    SciTech Connect

    Liu Funing )

    1993-05-01

    Overpressure in Oligocene formations in southern Qiongdongnan basin, offshore China, can be determined either by actual measurements in wells or by calculations using data derived from well logs and seismic surveys. The overpressure is mainly the result of undercompaction of Oligocene rocks during rapid loading by Pliocene and Quaternary sedimentation and of the subsequent thermal expansion of fluids in the Oligocene strata. Every formation possesses its own normal compaction trend (plot of shale-interval acoustic transit times vs. depth). The actual fluid pressures and potential pressures can be computed by the equilibrium-depth method. This method must be corrected for the thermal expansion of fluid. The pressure corrections are based on shale-interval transit times from well logs, interval velocities interpreted from vertical seismic profile (VSP) surveys, and stacking velocity from sonic log data of nearby wells. Gas generated from source rocks is assumed to have moved vertically from strata of higher hydraulic pressure potential to those of lower potentials and to have moved laterally and accumulated within areas where the contour closures of a gas equipotential hydraulic-pressure surface (U curves) have lower values. In the study area, the vicinity of the Yacheng gas field, the potential maps (U, gas, and V, water, maps) and hydraulic head profiles can be plotted from values derived either from actual pressure measurements or from calculations. These maps and profiles show prospective areas of gas accumulation. 5 refs., 10 figs., 1 tab.

  14. A Comparison between Survey and Verbal Choice Methods of Identifying Potential Reinforcers among Employees

    ERIC Educational Resources Information Center

    Wilder, David A; Therrien, Kelly; Wine, Byron

    2006-01-01

    Two methods of assessing preference for stimuli (i.e., potential reinforcers) were compared for adult administrative assistant employees. During Phase 1, a survey method and a verbal choice method of assessing preference for 6 stimuli were administered. During Phase 2, a coupon system was used to determine which categories of stimuli actually…

  15. POTENTIAL USE OF BENTHIC ALGAE AS HYDROLOGIC INDICATORS FOR HEADWATER STREAMS: SOME DATA EXPLORATION

    EPA Science Inventory

    Benthic algae were sampled to determine the utility of algal communities as indicators of hydrologic regime as part of a national survey involving habitat measurements and community assessments. Streams from four forests near Cincinnati were classified according to hydrologic pe...

  16. White spots in pharmaceutical pipelines-EMA identifies potential areas of unmet medical needs.

    PubMed

    Papaluca, Marisa; Greco, Martina; Tognana, Enrico; Ehmann, Falk; Saint-Raymond, Agnès

    2015-05-01

    Unmet medical needs are a priority for organizations such as the WHO and major public-private initiatives, such as Innovative Medicines Initiative, were established to speed up the development of better and safer medicines for patients. To assist such projects, the EMA in its 'Road Map to 2015' considered the mapping of unmet medical needs as a priority. This study has identified medical conditions for which the EMA could not identify developments in the pharmaceutical pipelines, that is, 'white spots'. Our analysis was made using external data sources as well as mining data of the EMA. The main areas for white spots were oncology, infectious diseases and certain psychiatric conditions. According to our data and a review of literature, in a number of these white spots, diagnostic tools may even be missing. The identification of those conditions will benefit stakeholders, including regulators, research funding bodies and patients' organizations. PMID:25797498

  17. Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet Syndrome treatment

    PubMed Central

    Baraban, Scott C.; Dinday, Matthew T.; Hortopan, Gabriela A.

    2013-01-01

    Dravet syndrome (DS) is a catastrophic pediatric epilepsy with severe intellectual disability, impaired social development and persistent drug-resistant seizures. One of its primary monogenic causes are mutations in Nav1.1 (SCN1A), a voltage-gated sodium channel. Here we characterise zebrafish Nav1.1 (scn1Lab) mutants originally identified in a chemical mutagenesis screen. Mutants exhibit spontaneous abnormal electrographic activity, hyperactivity and convulsive behaviors. Although scn1Lab expression is reduced, microarray analysis is remarkable for the small fraction of differentially expressed genes (~3%) and lack of compensatory expression changes in other scn subunits. Ketogenic diet, diazepam, valproate, potassium bromide and stiripentol attenuate mutant seizure activity; seven other antiepileptic drugs have no effect. A phenotype-based screen of 320 compounds identifies a US Food and Drug Administration-approved compound (clemizole) that inhibits convulsive behaviors and electrographic seizures. This approach represents a new direction in modeling pediatric epilepsy and could be used to identify novel therapeutics for any monogenic epilepsy disorder. PMID:24002024

  18. Vibrational stark effects to identify ion pairing and determine reduction potentials in electrolyte-free environments

    SciTech Connect

    Mani, Tomoyasu; Grills, David C.; Miller, John R.

    2015-01-02

    A recently-developed instrument for time-resolved infrared detection following pulse radiolysis has been used to measure the ν(C≡N) IR band of the radical anion of a CN-substituted fluorene in tetrahydrofuran. Specific vibrational frequencies can exhibit distinct frequency shifts due to ion-pairing, which can be explained in the framework of the vibrational Stark effect. Measurements of the ratio of free ions and ion-pairs in different electrolyte concentrations allowed us to obtain an association constant and free energy change for ion-pairing. As a result, this new method has the potential to probe the geometry of ion-pairing and allows the reduction potentials of molecules to be determined in the absence of electrolyte in an environment of low dielectric constant.

  19. Vibrational stark effects to identify ion pairing and determine reduction potentials in electrolyte-free environments

    DOE PAGESBeta

    Mani, Tomoyasu; Grills, David C.; Miller, John R.

    2015-01-02

    A recently-developed instrument for time-resolved infrared detection following pulse radiolysis has been used to measure the ν(C≡N) IR band of the radical anion of a CN-substituted fluorene in tetrahydrofuran. Specific vibrational frequencies can exhibit distinct frequency shifts due to ion-pairing, which can be explained in the framework of the vibrational Stark effect. Measurements of the ratio of free ions and ion-pairs in different electrolyte concentrations allowed us to obtain an association constant and free energy change for ion-pairing. As a result, this new method has the potential to probe the geometry of ion-pairing and allows the reduction potentials of moleculesmore » to be determined in the absence of electrolyte in an environment of low dielectric constant.« less

  20. Identifying Potential Therapeutic Targets of Methicillin-resistant Staphylococcus aureus Through in Vivo Proteomic Analysis

    PubMed Central

    Diep, Binh An; Phung, Qui; Date, Shailesh; Arnott, David; Bakalarski, Corey; Xu, Min; Nakamura, Gerald; Swem, Danielle L.; Alexander, Mary Kate; Le, Hoan N.; Mai, Thuy T.; Tan, Man-Wah; Brown, Eric J.; Nishiyama, Mireille

    2014-01-01

    Background. Detailed knowledge on protein repertoire of a pathogen during host infection is needed for both developing a better understanding of the pathogenesis and defining potential therapeutic targets. Such data, however, have been missing for Staphylococcus aureus, a major human pathogen. Methods. We determined the surface proteome of methicillin-resistant S. aureus (MRSA) clone USA300 derived directly from murine systemic infection. Results. The majority of the in vivo-expressed surface-associated proteins were lipoproteins involved in nutrient acquisition, especially uptake of metal ions. Enzyme-linked immunosorbent assay (ELISA) of convalescent human serum samples revealed that proteins that were highly produced during murine experimental infection were also produced during natural human infection. We found that among the 7 highly abundant lipoproteins only MntC, which is the manganese-binding protein of the MntABC system, was essential for MRSA virulence during murine systemic infection. Moreover, we show that MntA and MntB are equally important for MRSA virulence. Conclusions. Besides providing experimental evidence that MntABC might be a potential therapeutic target for the development of antibiotics, our in vivo proteomics data will serve as a valuable basis for defining potential antigen combinations for multicomponent vaccines. PMID:24280367

  1. Database identifies FDA-approved drugs with potential to be repurposed for treatment of orphan diseases.

    TOXLINE Toxicology Bibliographic Information

    Xu K; Coté TR

    2011-07-01

    Facing substantial obstacles to developing new therapies for rare diseases, some sponsors are looking to 'repurpose' drugs already approved for other conditions and use those therapies to treat rare diseases. In an effort to facilitate such repurposing and speed the delivery of new therapies to people who need them, we have established a new resource, the Rare Disease Repurposing Database (RDRD). The advantages of repurposed compounds include their demonstrated efficacy (in some clinical contexts), their observed toxicity profiles and their clearly described manufacturing controls. To create the RDRD, we matched the US Food and Drug Administration (FDA) orphan designation database to FDA drug and biological product approval lists. The RDRD lists 236 products that have received orphan status designation--that is, were found to be 'promising' for the treatment of a rare disease--and though not yet approved for marketing for that rare disease, they are already approved for marketing to treat some other disease or condition. The RDRD contains three tables: Orphan-designated products with at least one marketing approval for a common disease indication (N = 109); orphan-designated products with at least one marketing approval for a rare disease indication (N = 76); and orphan-designated products with marketing approvals for both common and rare disease indications (N = 51). While the data included in the database is a re-configuration/cross-indexing of information already released by the FDA, it offers sponsors a new tool for finding special opportunities to develop niche therapies for rare disease patients.

  2. Exome sequencing identifies potential novel candidate genes in patients with unexplained colorectal adenomatous polyposis.

    PubMed

    Spier, Isabel; Kerick, Martin; Drichel, Dmitriy; Horpaopan, Sukanya; Altmüller, Janine; Laner, Andreas; Holzapfel, Stefanie; Peters, Sophia; Adam, Ronja; Zhao, Bixiao; Becker, Tim; Lifton, Richard P; Holinski-Feder, Elke; Perner, Sven; Thiele, Holger; Nöthen, Markus M; Hoffmann, Per; Timmermann, Bernd; Schweiger, Michal R; Aretz, Stefan

    2016-04-01

    In up to 30 % of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, and POLE or POLD1, causing Polymerase-Proofreading-associated polyposis can be identified, although a hereditary etiology is likely. To uncover new causative genes, exome sequencing was performed using DNA from leukocytes and a total of 12 colorectal adenomas from seven unrelated patients with unexplained sporadic adenomatous polyposis. For data analysis and variant filtering, an established bioinformatics pipeline including in-house tools was applied. Variants were filtered for rare truncating point mutations and copy-number variants assuming a dominant, recessive, or tumor suppressor model of inheritance. Subsequently, targeted sequence analysis of the most promising candidate genes was performed in a validation cohort of 191 unrelated patients. All relevant variants were validated by Sanger sequencing. The analysis of exome sequencing data resulted in the identification of rare loss-of-function germline mutations in three promising candidate genes (DSC2, PIEZO1, ZSWIM7). In the validation cohort, further variants predicted to be pathogenic were identified in DSC2 and PIEZO1. According to the somatic mutation spectra, the adenomas in this patient cohort follow the classical pathways of colorectal tumorigenesis. The present study identified three candidate genes which might represent rare causes for a predisposition to colorectal adenoma formation. Especially PIEZO1 (FAM38A) and ZSWIM7 (SWS1) warrant further exploration. To evaluate the clinical relevance of these genes, investigation of larger patient cohorts and functional studies are required. PMID:26780541

  3. Event-Related Potential Indicators of Text Integration across Sentence Boundaries

    ERIC Educational Resources Information Center

    Yang, Chin Lung; Perfetti, Charles A.; Schmalhofer, Franz

    2007-01-01

    An event-related potentials (ERPs) study examined word-to-text integration processes across sentence boundaries. In a two-sentence passage, the accessibility of a referent for the first content word of the second sentence (the target word) was varied by the wording of the first sentence in one of the following ways: lexically (explicitly using…

  4. Sorghum bioenergy cropping systems: production potential and early indications of soil benefits under limited water

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A two year field study was conducted to evaluate biofuel production potential of two forage sorghum cultivars differing in brown midrib trait under non-irrigated and deficit irrigation conditions in the semiarid Southern High Plains of the U.S. Cultivar SP1990 (non-bmr = conventional cell wall comp...

  5. Validation of Brain Event-Related Potentials as Indicators of Cognitive Styles, Abilities, and Aptitudes.

    ERIC Educational Resources Information Center

    Federico, Pat-Anthony; And Others

    Fifty Navy recruits were given 11 paper-and-pencil tests of cognitive styles, abilities, and aptitudes. Visual, auditory, and bimodal brain event-related potential (ERP) amplitudes were recorded from each of these subjects. Product-moment and canonical correlational analyses, as well as principal-factor analysis and varimax rotation, were…

  6. MACROCLIMATIC INDICES TO DEFINE POTENTIAL SOIL ORGANIC CARBON STORAGE WITH NO TILLAGE

    Technology Transfer Automated Retrieval System (TEKTRAN)

    No tillage has become an accepted cropping practice throughout the USA. Potential climate change has prompted great interest in conservation tillage as a practice to help sequester CO2 from the atmosphere into the soil. Numerous reports published in recent years about the effect of no tillage compar...

  7. Electrophysiological (Event-Related Potentials) Indices of Cognitive Processing in Autistic Learners.

    ERIC Educational Resources Information Center

    Shibley, Ralph, Jr.; And Others

    Event-related Potentials (ERPs) were recorded to both auditory and visual stimuli from the scalps of nine autistic males and nine normal controls (all Ss between 12 and 22 years of age) to examine the differences in information processing strategies. Ss were tested on three different tasks: an auditory missing stimulus paradigm, a visual color…

  8. Potential of infrared spectroscopy in combination with extended canonical variate analysis for identifying different paper types

    NASA Astrophysics Data System (ADS)

    Riba, Jordi-Roger; Canals, Trini; Cantero, Rosa; Iturriaga, Hortensia

    2011-02-01

    The increasing use of secondary fiber in papermaking has led to the production of paper containing a wide range of contaminants. Wastepaper mills need to develop quality control methods for evaluating the incoming wastepaper stock as well as testing the specifications of the final product. The goal of this work is to present a fast and successful methodology for identifying different paper types. In this way, undesirable paper types can be refused, thus improving the runnability of the paper machine and the quality of the paper manufactured. In this work we examine various types of paper using information obtained by an appropriate chemometric treatment of infrared spectral data. For this purpose, we studied a large number of paper sheets of three different types (namely coated, offset and cast-coated) supplied by several paper manufacturers. We recorded Fourier transform infrared (FTIR) spectra with the aid of an attenuated total reflectance (ATR) module and near-infrared (NIR) reflectance spectra by means of fiber optics. Both techniques proved expeditious and required no sample pretreatment. The primary objective of this work was to develop a methodology for the accurate identification of samples of different paper types. For this purpose, we used the chemometric discrimination technique extended canonical variate analysis (ECVA) in combination with the k nearest neighbor (kNN) method to classify samples in the prediction set. Use of the NIR and FTIR techniques under these conditions allowed paper types to be identified with 100% success in prediction samples.

  9. Sleep-related eye symptoms and their potential for identifying driver sleepiness.

    PubMed

    Filtness, Ashleigh J; Anund, Anna; Fors, Carina; Ahlström, Christer; Akerstedt, Torbjørn; Kecklund, Göran

    2014-10-01

    The majority of individuals appear to have insight into their own sleepiness, but there is some evidence that this does not hold true for all, for example treated patients with obstructive sleep apnoea. Identification of sleep-related symptoms may help drivers determine their sleepiness, eye symptoms in particular show promise. Sixteen participants completed four motorway drives on two separate occasions. Drives were completed during daytime and night-time in both a driving simulator and on the real road. Ten eye symptoms were rated at the end of each drive, and compared with driving performance and subjective and objective sleep metrics recorded during driving. 'Eye strain', 'difficulty focusing', 'heavy eyelids' and 'difficulty keeping the eyes open' were identified as the four key sleep-related eye symptoms. Drives resulting in these eye symptoms were more likely to have high subjective sleepiness and more line crossings than drives where similar eye discomfort was not reported. Furthermore, drivers having unintentional line crossings were likely to have 'heavy eyelids' and 'difficulty keeping the eyes open'. Results suggest that drivers struggling to identify sleepiness could be assisted with the advice 'stop driving if you feel sleepy and/or have heavy eyelids or difficulty keeping your eyes open'. PMID:24861146

  10. Combined expressional analysis, bioinformatics and targeted proteomics identify new potential therapeutic targets in glioblastoma stem cells

    PubMed Central

    Stangeland, Biljana; Mughal, Awais A.; Grieg, Zanina; Sandberg, Cecilie Jonsgar; Joel, Mrinal; Nygård, Ståle; Meling, Torstein; Murrell, Wayne; Vik Mo, Einar O.; Langmoen, Iver A.

    2015-01-01

    Glioblastoma (GBM) is both the most common and the most lethal primary brain tumor. It is thought that GBM stem cells (GSCs) are critically important in resistance to therapy. Therefore, there is a strong rationale to target these cells in order to develop new molecular therapies. To identify molecular targets in GSCs, we compared gene expression in GSCs to that in neural stem cells (NSCs) from the adult human brain, using microarrays. Bioinformatic filtering identified 20 genes (PBK/TOPK, CENPA, KIF15, DEPDC1, CDC6, DLG7/DLGAP5/HURP, KIF18A, EZH2, HMMR/RHAMM/CD168, NOL4, MPP6, MDM1, RAPGEF4, RHBDD1, FNDC3B, FILIP1L, MCC, ATXN7L4/ATXN7L1, P2RY5/LPAR6 and FAM118A) that were consistently expressed in GSC cultures and consistently not expressed in NSC cultures. The expression of these genes was confirmed in clinical samples (TCGA and REMBRANDT). The first nine genes were highly co-expressed in all GBM subtypes and were part of the same protein-protein interaction network. Furthermore, their combined up-regulation correlated negatively with patient survival in the mesenchymal GBM subtype. Using targeted proteomics and the COGNOSCENTE database we linked these genes to GBM signalling pathways. Nine genes: PBK, CENPA, KIF15, DEPDC1, CDC6, DLG7, KIF18A, EZH2 and HMMR should be further explored as targets for treatment of GBM. PMID:26295306

  11. Antibody microarray profiling of osteosarcoma cell serum for identifying potential biomarkers.

    PubMed

    Zhu, Zi-Qiang; Tang, Jin-Shan; Gang, Duan; Wang, Ming-Xing; Wang, Jian-Qiang; Lei, Zhou; Feng, Zhou; Fang, Ming-Liang; Yan, Lin

    2015-07-01

    The aim of the present study was to identify biomarkers in osteosarcoma (OS) cell serum by antibody microarray profiling, which may be used for OS diagnosis and therapy. An antibody microarray was used to detect the expression levels of cytokines in serum samples from 20 patients with OS and 20 healthy individuals. Significantly expressed cytokines in OS serum were selected when P<0.05 and fold change >2. An enzyme-linked immunosorbent assay (ELISA) was used to validate the antibody microarray results. Finally, classification accuracy was calculated by cluster analysis. Twenty one cytokines were significantly upregulated in OS cell serum samples compared with control samples. Expression of interleukin-6, monocyte chemoattractant protein-1, tumor growth factor-β, growth-related oncogene, hepatocyte growth factor, chemokine ligand 16, Endoglin, matrix metalloproteinase-9 and platelet-derived growth factor-AA was validated by ELISAs. OS serum samples and control samples were distinguished by significantly expressed cytokines with an accuracy of 95%. The results demonstrated that expressed cytokines identified by antibody microarray may be used as biomarkers for OS diagnosis and therapy. PMID:25815525

  12. Gremlin 1 Identifies a Skeletal Stem Cell with Bone, Cartilage, and Reticular Stromal Potential

    PubMed Central

    Worthley, Daniel L.; Churchill, Michael; Compton, Jocelyn T.; Tailor, Yagnesh; Rao, Meenakshi; Si, Yiling; Levin, Daniel; Schwartz, Matthew G.; Uygur, Aysu; Hayakawa, Yoku; Gross, Stefanie; Renz, Bernhard W.; Setlik, Wanda; Martinez, Ashley N.; Chen, Xiaowei; Nizami, Saqib; Lee, Heon Goo; Kang, H. Paco; Caldwell, Jon-Michael; Asfaha, Samuel; Westphalen, C. Benedikt; Graham, Trevor; Jin, Guangchun; Nagar, Karan; Wang, Hongshan; Kheirbek, Mazen A.; Kolhe, Alka; Carpenter, Jared; Glaire, Mark; Nair, Abhinav; Renders, Simon; Manieri, Nicholas; Muthupalani, Sureshkumar; Fox, James G.; Reichert, Maximilian; Giraud, Andrew S.; Schwabe, Robert F.; Pradere, Jean-Phillipe; Walton, Katherine; Prakash, Ajay; Gumucio, Deborah; Rustgi, Anil K.; Stappenbeck, Thaddeus S.; Friedman, Richard A.; Gershon, Michael D.; Sims, Peter; Grikscheit, Tracy; Lee, Francis Y.; Karsenty, Gerard; Mukherjee, Siddhartha; Wang, Timothy C.

    2014-01-01

    The stem cells that maintain and repair the postnatal skeleton remain undefined. One model suggests that perisinusoidal mesenchymal stem cells (MSCs) give rise to osteoblasts, chondrocytes, marrow stromal cells, and adipocytes, although the existence of these cells has not been proven through fate-mapping experiments. We demonstrate here that expression of the bone morphogenetic protein (BMP) antagonist gremlin 1 defines a population of osteochondroreticular (OCR) stem cells in the bone marrow. OCR stem cells self-renew and generate osteoblasts, chondrocytes, and reticular marrow stromal cells, but not adipocytes. OCR stem cells are concentrated within the metaphysis of long bones not in the perisinusoidal space and are needed for bone development, bone remodeling, and fracture repair. Grem1 expression also identifies intestinal reticular stem cells (iRSCs) that are cells of origin for the periepithelial intestinal mesenchymal sheath. Grem1 expression identifies distinct connective tissue stem cells in both the bone (OCR stem cells) and the intestine (iRSCs). PMID:25594183

  13. Assessing indices for predicting potential N mineralization in pedogenically distinct soils under different tillage management systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A reliable laboratory index of nitrogen availability would be useful for making N recommendations but no single approach has received broad acceptance across a wide range of soils. We compared several indices over a range of soil conditions to test the possibility of determining the best combination...

  14. Acoustic Noise Alters Selective Attention Processes as Indicated by Direct Current (DC) Brain Potential Changes

    PubMed Central

    Trimmel, Karin; Schätzer, Julia; Trimmel, Michael

    2014-01-01

    Acoustic environmental noise, even of low to moderate intensity, is known to adversely affect information processing in animals and humans via attention mechanisms. In particular, facilitation and inhibition of information processing are basic functions of selective attention. Such mechanisms can be investigated by analyzing brain potentials under conditions of externally directed attention (intake of environmental information) versus internally directed attention (rejection of environmental stimuli and focusing on memory/planning processes). This study investigated brain direct current (DC) potential shifts—which are discussed to represent different states of cortical activation—of tasks that require intake and rejection of environmental information under noise. It was hypothesized that without background noise rejection tasks would show more positive DC potential changes compared to intake tasks and that under noise both kinds of tasks would show positive DC shifts as an expression of cortical inhibition caused by noise. DC potential shifts during intake and rejection tasks were analyzed at 16 standard locations in 45 persons during irrelevant speech or white noise vs. control condition. Without noise, rejection tasks were associated with more positive DC potential changes compared to intake tasks. During background noise, however, this difference disappeared and both kinds of tasks led to positive DC shifts. Results suggest—besides some limitations—that noise modulates selective attention mechanisms by switching to an environmental information processing and noise rejection mode, which could represent a suggested “attention shift”. Implications for fMRI studies as well as for public health in learning and performance environments including susceptible persons are discussed. PMID:25264675

  15. Acoustic noise alters selective attention processes as indicated by direct current (DC) brain potential changes.

    PubMed

    Trimmel, Karin; Schätzer, Julia; Trimmel, Michael

    2014-01-01

    Acoustic environmental noise, even of low to moderate intensity, is known to adversely affect information processing in animals and humans via attention mechanisms. In particular, facilitation and inhibition of information processing are basic functions of selective attention. Such mechanisms can be investigated by analyzing brain potentials under conditions of externally directed attention (intake of environmental information) versus internally directed attention (rejection of environmental stimuli and focusing on memory/planning processes). This study investigated brain direct current (DC) potential shifts-which are discussed to represent different states of cortical activation-of tasks that require intake and rejection of environmental information under noise. It was hypothesized that without background noise rejection tasks would show more positive DC potential changes compared to intake tasks and that under noise both kinds of tasks would show positive DC shifts as an expression of cortical inhibition caused by noise. DC potential shifts during intake and rejection tasks were analyzed at 16 standard locations in 45 persons during irrelevant speech or white noise vs. control condition. Without noise, rejection tasks were associated with more positive DC potential changes compared to intake tasks. During background noise, however, this difference disappeared and both kinds of tasks led to positive DC shifts. Results suggest-besides some limitations-that noise modulates selective attention mechanisms by switching to an environmental information processing and noise rejection mode, which could represent a suggested "attention shift". Implications for fMRI studies as well as for public health in learning and performance environments including susceptible persons are discussed. PMID:25264675

  16. On the Potential of Surfers to Monitor Environmental Indicators in the Coastal Zone

    PubMed Central

    Brewin, Robert J. W.; de Mora, Lee; Jackson, Thomas; Brewin, Thomas G.; Shutler, Jamie

    2015-01-01

    The social and economic benefits of the coastal zone make it one of the most treasured environments on our planet. Yet it is vulnerable to increasing anthropogenic pressure and climate change. Coastal management aims to mitigate these pressures while augmenting the socio-economic benefits the coastal region has to offer. However, coastal management is challenged by inadequate sampling of key environmental indicators, partly due to issues relating to cost of data collection. Here, we investigate the use of recreational surfers as platforms to improve sampling coverage of environmental indicators in the coastal zone. We equipped a recreational surfer, based in the south west United Kingdom (UK), with a temperature sensor and Global Positioning System (GPS) device that they used when surfing for a period of one year (85 surfing sessions). The temperature sensor was used to derive estimates of sea-surface temperature (SST), an important environmental indicator, and the GPS device used to provide sample location and to extract information on surfer performance. SST data acquired by the surfer were compared with data from an oceanographic station in the south west UK and with satellite observations. Our results demonstrate: (i) high-quality SST data can be acquired by surfers using low cost sensors; and (ii) GPS data can provide information on surfing performance that may help motivate data collection by surfers. Using recent estimates of the UK surfing population, and frequency of surfer participation, we speculate around 40 million measurements on environmental indicators per year could be acquired at the UK coastline by surfers. This quantity of data is likely to enhance coastal monitoring and aid UK coastal management. Considering surfing is a world-wide sport, our results have global implications and the approach could be expanded to other popular marine recreational activities for coastal monitoring of environmental indicators. PMID:26154173

  17. On the Potential of Surfers to Monitor Environmental Indicators in the Coastal Zone.

    PubMed

    Brewin, Robert J W; de Mora, Lee; Jackson, Thomas; Brewin, Thomas G; Shutler, Jamie

    2015-01-01

    The social and economic benefits of the coastal zone make it one of the most treasured environments on our planet. Yet it is vulnerable to increasing anthropogenic pressure and climate change. Coastal management aims to mitigate these pressures while augmenting the socio-economic benefits the coastal region has to offer. However, coastal management is challenged by inadequate sampling of key environmental indicators, partly due to issues relating to cost of data collection. Here, we investigate the use of recreational surfers as platforms to improve sampling coverage of environmental indicators in the coastal zone. We equipped a recreational surfer, based in the south west United Kingdom (UK), with a temperature sensor and Global Positioning System (GPS) device that they used when surfing for a period of one year (85 surfing sessions). The temperature sensor was used to derive estimates of sea-surface temperature (SST), an important environmental indicator, and the GPS device used to provide sample location and to extract information on surfer performance. SST data acquired by the surfer were compared with data from an oceanographic station in the south west UK and with satellite observations. Our results demonstrate: (i) high-quality SST data can be acquired by surfers using low cost sensors; and (ii) GPS data can provide information on surfing performance that may help motivate data collection by surfers. Using recent estimates of the UK surfing population, and frequency of surfer participation, we speculate around 40 million measurements on environmental indicators per year could be acquired at the UK coastline by surfers. This quantity of data is likely to enhance coastal monitoring and aid UK coastal management. Considering surfing is a world-wide sport, our results have global implications and the approach could be expanded to other popular marine recreational activities for coastal monitoring of environmental indicators. PMID:26154173

  18. Carbohydrate Microarrays Identify Blood Group Precursor Cryptic Epitopes as Potential Immunological Targets of Breast Cancer

    PubMed Central

    Wang, Denong; Tang, Jin; Liu, Shaoyi; Huang, Jiaoti

    2015-01-01

    Using carbohydrate microarrays, we explored potential natural ligands of antitumor monoclonal antibody HAE3. This antibody was raised against a murine mammary tumor antigen but was found to cross-react with a number of human epithelial tumors in tissues. Our carbohydrate microarray analysis reveals that HAE3 is specific for an O-glycan cryptic epitope that is normally hidden in the cores of blood group substances. Using HAE3 to screen tumor cell surface markers by flow cytometry, we found that the HAE3 glycoepitope, gpHAE3, was highly expressed by a number of human breast cancer cell lines, including some triple-negative cancers that lack the estrogen, progesterone, and Her2/neu receptors. Taken together, we demonstrate that HAE3 recognizes a conserved cryptic glycoepitope of blood group precursors, which is nevertheless selectively expressed and surface-exposed in certain breast tumor cells. The potential of this class of O-glycan cryptic antigens in breast cancer subtyping and targeted immunotherapy warrants further investigation. PMID:26539555

  19. Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential

    PubMed Central

    Chauhan, Santosh; Ahmed, Zahra; Bradfute, Steven B.; Arko-Mensah, John; Mandell, Michael A.; Won Choi, Seong; Kimura, Tomonori; Blanchet, Fabien; Waller, Anna; Mudd, Michal H.; Jiang, Shanya; Sklar, Larry; Timmins, Graham S.; Maphis, Nicole; Bhaskar, Kiran; Piguet, Vincent; Deretic, Vojo

    2015-01-01

    Autophagy is a conserved homeostatic process active in all human cells and affecting a spectrum of diseases. Here we use a pharmaceutical screen to discover new mechanisms for activation of autophagy. We identify a subset of pharmaceuticals inducing autophagic flux with effects in diverse cellular systems modelling specific stages of several human diseases such as HIV transmission and hyperphosphorylated tau accumulation in Alzheimer's disease. One drug, flubendazole, is a potent inducer of autophagy initiation and flux by affecting acetylated and dynamic microtubules in a reciprocal way. Disruption of dynamic microtubules by flubendazole results in mTOR deactivation and dissociation from lysosomes leading to TFEB (transcription factor EB) nuclear translocation and activation of autophagy. By inducing microtubule acetylation, flubendazole activates JNK1 leading to Bcl-2 phosphorylation, causing release of Beclin1 from Bcl-2-Beclin1 complexes for autophagy induction, thus uncovering a new approach to inducing autophagic flux that may be applicable in disease treatment. PMID:26503418

  20. Melatonin identified in meats and other food stuffs: potentially nutritional impact.

    PubMed

    Tan, Dun-Xian; Zanghi, Brian M; Manchester, Lucien C; Reiter, Russel J

    2014-09-01

    Melatonin has been identified in primitive photosynthetic bacteria, fungi, plants, and animals including humans. Vegetables, fruits, cereals, wine, and beers all contain melatonin. However, the melatonin content in meats has not been reported previously. Here, for the first time, we report melatonin in meats, eggs, colostrum, and in other edible food products. The levels of melatonin measured by HPLC, in lamb, beef, pork, chicken, and fish, are comparable to other food stuffs (in the range of ng/g). These levels are significantly higher than melatonin concentrations in the blood of vertebrates. As melatonin is a potent antioxidant, its presence in the meat could contribute to shelf life duration as well as preserve their quality and taste. In addition, the consumption of these foods by humans or animals could have health benefits considering the important functions of melatonin as a potent free radical scavenger and antioxidant. PMID:24942090

  1. Potential tumor biomarkers identified in ovarian cyst fluid by quantitative proteomic analysis, iTRAQ

    PubMed Central

    2013-01-01

    Background Epithelial-derived ovarian adenocarcinoma (EOC) is the most deadly gynecologic tumor, and the principle cause of the poor survival rate is diagnosis at a late stage. Screening and diagnostic biomarkers with acceptable specificity and sensitivity are lacking. Ovarian cyst fluid should harbor early ovarian cancer biomarkers because of its closeness to the tumor. We investigated ovarian cyst fluid as a source for discovering biomarkers for use in the diagnosis of EOC. Results Using quantitative mass spectrometry, iTRAQ MS, we identified 837 proteins in cyst fluid from benign, EOC stage I, and EOC stage III. Only patients of serous histology were included in the study. Comparing the benign (n = 5) with the malignant (n = 10) group, 87 of the proteins were significantly (p < 0.05) differentially expressed. Two proteins, serum amyloid A-4 (SAA4) and astacin-like metalloendopeptidase (ASTL), were selected for verification of the iTRAQ method and external validation with immunoblot in a larger cohort with mixed histology, in plasma (n = 68), and cyst fluid (n = 68). The protein selections were based on either high significance and high fold change or abundant appearance and several peptide recognitions in the sample sets (p = 0.04, FC = 1.95) and (p < 0.001, FC = 8.48) for SAA4 and ASTL respectively. Both were found to be significantly expressed (p < 0.05), but the methods did not correlate concerning ASTL. Conclusions Fluid from ovarian cysts connected directly to the primary tumor harbor many possible new tumor-specific biomarkers. We have identified 87 differentially expressed proteins and validated two candidates to verify the iTRAQ method. However several of the proteins are of interest for validation in a larger setting. PMID:23557354

  2. Kinase analysis in alcoholic hepatitis identifies p90RSK as a potential mediator of liver fibrogenesis

    PubMed Central

    Morales-Ibanez, Oriol; Affò, Silvia; Rodrigo-Torres, Daniel; Blaya, Delia; Millán, Cristina; Coll, Mar; Perea, Luis; Odena, Gemma; Knorpp, Thomas; Templin, Markus F; Moreno, Montserrat; Altamirano, José; Miquel, Rosa; Arroyo, Vicente; Ginès, Pere; Caballería, Juan; Sancho-Bru, Pau; Bataller, Ramon

    2015-01-01

    Objective Alcoholic hepatitis (AH) is often associated with advanced fibrosis, which negatively impacts survival. We aimed at identifying kinases deregulated in livers from patients with AH and advanced fibrosis in order to discover novel molecular targets. Design Extensive phosphoprotein analysis by reverse phase protein microarrays was performed in AH (n=12) and normal human livers (n=7). Ribosomal S6 kinase (p90RSK) hepatic expression was assessed by qPCR, Western blot and immunohistochemistry. Kaempferol was used as a selective pharmacological inhibitor of the p90RSK pathway to assess the regulation of experimentally-induced liver fibrosis and injury, using in vivo and in vitro approaches. Results Proteomic analysis identified p90RSK as one of the most deregulated kinases in AH. Hepatic p90RSK gene and protein expression was also upregulated in livers with chronic liver disease. Immunohistochemistry studies showed increased p90RSK staining in areas of active fibrogenesis in cirrhotic livers. Therapeutic administration of kaempferol to carbon tetrachloride-treated mice resulted in decreased hepatic collagen deposition, and expression of profibrogenic and proinflammatory genes, compared to vehicle administration. In addition, kaempferol reduced the extent of hepatocellular injury and degree of apoptosis. In primary hepatic stellate cells, kaempferol and small interfering RNA decreased activation of p90RSK, which in turn regulated key profibrogenic actions. In primary hepatocytes, kaempferol attenuated proapoptotic signalling. Conclusions p90RSK is upregulated in patients with chronic liver disease and mediates liver fibrogenesis in vivo and in vitro. These results suggest that the p90RSK pathway could be a new therapeutic approach for liver diseases characterised by advanced fibrosis. PMID:25652085

  3. Genome-Wide Expression Profiles Identify Potential Targets for Gene by Environment Interactions in Asthma Severity

    PubMed Central

    Sordillo, Joanne E; Kelly, Roxanne; Bunyavanich, Supinda; McGeachie, Michael; Qiu, Weiliang; Croteau-Chonka, Damien C.; Soto-Quiros, Manuel; Avila, Lydiana; Celedón, Juan C.; Brehm, John M.; Weiss, Scott T; Gold, Diane R; Litonjua, Augusto A

    2015-01-01

    Background Gene by environment interaction (G × E) studies utilizing GWAS data are often underpowered after adjustment for multiple comparisons. Differential gene expression, in response to the exposure of interest, may capture the most biologically relevant genes at the genome-wide level. Methods We used differential genome-wide expression profiles from the Home Allergens and Asthma Birth cohort in response to Der f 1 allergen (sensitized vs. non-sensitized) to inform a G × E study of dust mite exposure and asthma severity. Polymorphisms in differentially expressed genes were identified in GWAS data from CAMP, a clinical trial in childhood asthmatics. Home dust mite allergen (< or ≥ 10µg/g dust) was assessed at baseline, and (≥ 1) severe asthma exacerbation (emergency room (ER) visit or hospitalization for asthma in the first trial year) served as the disease severity outcome. The Genetics of Asthma in Costa Rica (GACRS) study, and a Puerto Rico/Connecticut asthma cohortwere used for replication. Results IL-9, IL-5 and PRG2 expression was up-regulated in Der f 1 stimulated PBMCs from dust mite sensitized individuals (adj. p value <0.04). IL-9 polymorphisms (rs11741137, rs2069885, rs1859430) showed evidence for interaction with dust mite in CAMP (p=0.02 to 0.03), with replication in GACRS (p=0.04). Subjects with the dominant genotype for these IL-9 polymorphisms were more likely to report a severe asthma exacerbation if exposed to elevated dust mite. Conclusions Genome-wide differential gene expression in response to dust mite allergen identified IL-9, a biologically plausible gene target that may interact with environmental dust mite to increase severe asthma exacerbations in children. PMID:25913104

  4. Potential Desiccation Cracks on Mars as Indicators of Paleolacustrine Sites: Implications for Future Exploration

    NASA Astrophysics Data System (ADS)

    El Maarry, M. R.; Watters, W.; McKeown, N. K.; Carter, J.; Noe Dobrea, E.; Bishop, J. L.; Pommerol, A.; Thomas, N.

    2014-04-01

    The HiRISE instrument has aided in the identification of polygonal crack patterns in association with phyllosilicate-bearing terrains in low to mid-latitudes on Mars, which have been suggested to be potential desiccation cracks. In this study, we summarize and review the global observations of such polygonal patterns and assess their morphology, mineralogy, geologic setting and global distribution as well as their implications for future exploration.

  5. Event-related brain potentials as indices of mental workload and attentional allocation

    NASA Technical Reports Server (NTRS)

    Kramer, Arthur F.; Donchin, Emanuel; Wickens, Christopher D.

    1988-01-01

    Over the past decade considerable strides were made in explicating the antecedant conditions necessary for the elicitation, and the modulation of the amplitude and latency, of a number of components of the event-related brain potential (ERP). The focus of this report is on P300. The degree to which the psychophysiological measures contribute to issues in two real-world domains (communication devices for the motor impaired and the assessment of mental workload of aircraft pilots) are examined.

  6. Effect of cooking on meat proteins: mapping hydrothermal protein modification as a potential indicator of bioavailability.

    PubMed

    Deb-Choudhury, Santanu; Haines, Stephen; Harland, Duane; Clerens, Stefan; van Koten, Chikako; Dyer, Jolon

    2014-08-13

    Thermal treatment of meat proteins induces a range of observable and molecular-level changes. In order to understand and track these heat-induced modifications at the amino acid level, various analytical techniques were used. Changes were observed both in the soluble and in the insoluble fractions after hydrothermal treatment of minced beef samples. Redox proteomics clearly indicated increasing oxidative modification of proteins with increased heat exposure. Collagens in the soluble fraction and myosin in the insoluble fraction were found to be highly susceptible to such modifications. Maillard reaction products in the insoluble and pyrrolidone formation in the soluble fraction steadily increased with increased heat exposure. Fluorescence studies indicated a rapid increase in fluorescence with heat, suggesting the formation of advanced glycation end products. Overall these results provide a deeper understanding of the effect of cooking on meat proteins and the possible relationship to processing conditions in meat-derived food. PMID:25033321

  7. Risk-based surveillance of antimicrobial residues in pigs--identification of potential risk indicators.

    PubMed

    Alban, Lis; Pacheco, Goncalo; Petersen, Jesper Valentin

    2014-05-01

    Around 20,000 samples are analysed each year for the presence of antibacterial residues in Danish finisher pigs, and between zero and five samples are detected positive above the maximum residue level (MRL). The intention was to develop a risk-based surveillance programme involving fewer samples while ensuring equal sensitivity. Therefore, risk indicators were searched for. Data were obtained from the Danish slaughterhouse database covering the period from July 2010 to December 2012. Residues were found or suspected in 17 incidents. In nine of these, the farmer had called in to prevent the pigs from being slaughtered. Hence, eight suspect cases were found through the surveillance programme, and two of these were above MRL. For these eight case herds, the number of pigs slaughtered and the number in which each of the following lesions were found were included in a statistical analysis: chronic pleuritis, tail bite, chronic pericarditis, chronic pneumonia, chronic peritonitis, osteomyelitis, abscess in hindquarters, abscess in leg/toe and abscess in forequarters. Only chronic pleuritis was associated with the presence of residues. Next, data from all herds delivering pigs for slaughter to the same abattoir were included covering a 3-month period prior to the residue finding. The prevalence of chronic pleuritis was on average 1.7 times higher in the eight case herds compared to all other herds. In two herds, the prevalence was significantly higher (P≤0.05), and in one herd substantially higher, but only borderline significant (P=0.1). In the remaining herds, the prevalence did not differ from the other herds delivering pigs to the abattoir. This indicates that chronic pleuritis might be considered as a risk indicator for use in surveillance. Other risk indicators/factors - reported in the cases where the farmers called in - were inadequate marking of treated animals and incorrect use of medication dispensers. These factors are not suited for use in surveillance and should be dealt with otherwise. PMID:24582122

  8. A potential to monitor nutrients as an indicator of rangeland quality using space borne remote sensing

    NASA Astrophysics Data System (ADS)

    Ramoelo, A.; Cho, M. A.; Madonsela, S.; Mathieu, R.; van der Korchove, R.; Kaszta, Z.; Wolf, E.

    2014-02-01

    Global change consisting of land use and climate change could have huge impacts on food security and the health of various ecosystems. Leaf nitrogen (N) is one of the key factors limiting agricultural production and ecosystem functioning. Leaf N can be used as an indicator of rangeland quality which could provide information for the farmers, decision makers, land planners and managers. Leaf N plays a crucial role in understanding the feeding patterns and distribution of wildlife and livestock. Assessment of this vegetation parameter using conventional methods at landscape scale level is time consuming and tedious. Remote sensing provides a synoptic view of the landscape, which engenders an opportunity to assess leaf N over wider rangeland areas from protected to communal areas. Estimation of leaf N has been successful during peak productivity or high biomass and limited studies estimated leaf N in dry season. The objective of this study is to monitor leaf N as an indicator of rangeland quality using WorldView 2 satellite images in the north-eastern part of South Africa. Series of field work to collect samples for leaf N were undertaken in the beginning of May (end of wet season) and July (dry season). Several conventional and red edge based vegetation indices were computed. Simple regression was used to develop prediction model for leaf N. Using bootstrapping, indicator of precision and accuracy were analyzed to select a best model for the combined data sets (May and July). The may model for red edge based simple ratio explained over 90% of leaf N variations. The model developed from the combined data sets with normalized difference vegetation index explained 62% of leaf N variation, and this is a model used to estimate and map leaf N for two seasons. The study demonstrated that leaf N could be monitored using high spatial resolution with the red edge band capability.

  9. Web-based Tool Identifies and Quantifies Potential Cost Savings Measures at the Hanford Site

    SciTech Connect

    Renevitz, Marisa J.; Peschong, Jon C.; Charboneau, Briant L.; Simpson, Brett C.

    2014-01-09

    The Technical Improvement system is an approachable web-based tool that is available to Hanford DOE staff, site contractors, and general support service contractors as part of the baseline optimization effort underway at the Hanford Site. Finding and implementing technical improvements are a large part of DOE’s cost savings efforts. The Technical Improvement dashboard is a key tool for brainstorming and monitoring the progress of submitted baseline optimization and potential cost/schedule efficiencies. The dashboard is accessible to users over the Hanford Local Area Network (HLAN) and provides a highly visual and straightforward status to management on the ideas provided, alleviating the need for resource intensive weekly and monthly reviews.

  10. Screening of Transient Receptor Potential Canonical Channel Activators Identifies Novel Neurotrophic Piperazine Compounds.

    PubMed

    Sawamura, Seishiro; Hatano, Masahiko; Takada, Yoshinori; Hino, Kyosuke; Kawamura, Tetsuya; Tanikawa, Jun; Nakagawa, Hiroshi; Hase, Hideharu; Nakao, Akito; Hirano, Mitsuru; Rotrattanadumrong, Rachapun; Kiyonaka, Shigeki; Mori, Masayuki X; Nishida, Motohiro; Hu, Yaopeng; Inoue, Ryuji; Nagata, Ryu; Mori, Yasuo

    2016-03-01

    Transient receptor potential canonical (TRPC) proteins form Ca(2+)-permeable cation channels activated upon stimulation of metabotropic receptors coupled to phospholipase C. Among the TRPC subfamily, TRPC3 and TRPC6 channels activated directly by diacylglycerol (DAG) play important roles in brain-derived neurotrophic factor (BDNF) signaling, promoting neuronal development and survival. In various disease models, BDNF restores neurologic deficits, but its therapeutic potential is limited by its poor pharmacokinetic profile. Elucidation of a framework for designing small molecules, which elicit BDNF-like activity via TRPC3 and TRPC6, establishes a solid basis to overcome this limitation. We discovered, through library screening, a group of piperazine-derived compounds that activate DAG-activated TRPC3/TRPC6/TRPC7 channels. The compounds [4-(5-chloro-2-methylphenyl)piperazin-1-yl](3-fluorophenyl)methanone (PPZ1) and 2-[4-(2,3-dimethylphenyl)piperazin-1-yl]-N-(2-ethoxyphenyl)acetamide (PPZ2) activated, in a dose-dependent manner, recombinant TRPC3/TRPC6/TRPC7 channels, but not other TRPCs, in human embryonic kidney cells. PPZ2 activated native TRPC6-like channels in smooth muscle cells isolated from rabbit portal vein. Also, PPZ2 evoked cation currents and Ca(2+) influx in rat cultured central neurons. Strikingly, both compounds induced BDNF-like neurite growth and neuroprotection, which were abolished by a knockdown or inhibition of TRPC3/TRPC6/TRPC7 in cultured neurons. Inhibitors of Ca(2+) signaling pathways, except calcineurin, impaired neurite outgrowth promotion induced by PPZ compounds. PPZ2 increased activation of the Ca(2+)-dependent transcription factor, cAMP response element-binding protein. These findings suggest that Ca(2+) signaling mediated by activation of DAG-activated TRPC channels underlies neurotrophic effects of PPZ compounds. Thus, piperazine-derived activators of DAG-activated TRPC channels provide important insights for future development of a new class of synthetic neurotrophic drugs. PMID:26733543

  11. Assessment of the in vitro antimicrobial activity of Lactobacillus species for identifying new potential antibiotics.

    PubMed

    Dubourg, Grégory; Elsawi, Ziena; Raoult, Didier

    2015-11-01

    The bacteriocin-mediated antimicrobial properties of Lactobacillus spp. have been widely studied, leading to the use of these micro-organisms in the food industry as preservative agents against foodborne pathogens. In an era in which antibiotic resistance is becoming a public health issue, the antimicrobial activity of Lactobacillus spp. could be used for the discovery of new potential antibiotics. Thus, it is essential to have an accurate method of screening the production of antimicrobial agents by prokaryotes. Many in vitro assays have been published to date, largely concerning but not limited to Lactobacillus spp. However, these methods mainly use the spot-on-the-lawn method, which is prone to contamination during the overlay stage, with protocols using methanol vapours or the reverse side agar technique being applied to avoid such contamination. In this study, a method combining the spot-on-the-lawn and well diffusion methods was tested, permitting clear identification of inhibition zones from eight Lactobacillus spp. towards clinical isolates of 12 species (11 bacteria and 1 yeast) commonly found in human pathology. Lactobacillus plantarum CIP 106786 and Lactobacillus rhamnosus CSUR P567 exhibited the widest antimicrobial activity, whereas Lactobacillus acidophilus strain DSM 20079 was relatively inactive. In addition, the putative MIC(50) of L. rhamnosus against Proteus mirabilis was estimated at 1.1×10(9)CFU/mL using culture broth dilution. In conclusion, considering the increasing cultivable bacterial human repertoire, these findings open the way of an effective method to screen in vitro for the production of potential antimicrobial compounds. PMID:26163158

  12. USE OF qRTPCR TO IDENTIFY POTENTIAL BIOMARKERS OF BROMATE EXPOSURE IN F344 MALE RAT KIDNEYS

    EPA Science Inventory

    Potassium bromate (KBrO3) is a drinking water disinfection by-product that is nephrotoxic and carcinogenic. To identify potential biomarkers of carcinogenicity, male F344 rats were chronically exposed to a carcinogenic dose (400mg/l) of KBrO3 in their drinking water. Kidneys were...

  13. A NEW HIGH RESOLUTION MASS SPECTROMETRY TECHNIQUE FOR IDENTIFYING PHARMACEUTICALS AND POTENTIAL ENDOCRINE DISRUPTORS IN DRINKING WATER SOURCES

    EPA Science Inventory

    A New High Resolution Mass Spectrometry Technique for Identifying Pharmaceuticals and Potential Endocrine Disruptors in Drinking Water Sources

    Andrew H. Grange and G. Wayne Sovocool U.S.EPA, ORD, NERL, ESD, ECB, P.O. Box 93478, Las Vegas, NV 891933478

    Mass spectra...

  14. 49 CFR 192.917 - How does an operator identify potential threats to pipeline integrity and use the threat...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 3 2010-10-01 2010-10-01 false How does an operator identify potential threats to pipeline integrity and use the threat identification in its integrity program? 192.917 Section 192.917 Transportation Other Regulations Relating to Transportation (Continued) PIPELINE AND HAZARDOUS MATERIALS SAFETY ADMINISTRATION, DEPARTMENT...

  15. A Delphi exercise used to identify potential causes of variation in litter size of Ontario swine

    PubMed Central

    Dewey, Catherine E.; Martin, S. Wayne; Friendship, Robert M.; Kennedy, Brain

    1992-01-01

    Forty-eight people, considered to the swine experts, were asked to collaborate in a Delphi exercise to identify the factors which they believed affect litter size in Ontario swine. The panel included 16 animal scientists, 16 pork producers, and 16 veterinarians in swine practice. The ten factors with the highest ratings were parity of the sow, mycotoxins in the feed, infections with porcine parvovirus or Leptospira spp., breeding gilts on their second versus first observed estrus, the timing of breeding with respect to the onset of estrus, purebred versus crossbred sows, boar overuse (bred by a boar that was mated more than six times per week), pen versus hand mating, age of gilt when first bred, and body condition of the sow at the time of conception. The experts did not agree about the effect on litter size of the sow's previous lactation, factors ensuring adequate nutrient intake during lactation, health of the sow and the boar, breed of a purebred sow, or the ease of mating the sow. Key items in the use of the Delphi technique to arrive at a consensus are discussed. PMID:17423928

  16. Sca-1 Identifies a Distinct Androgen-Independent Murine Prostatic Luminal Cell Lineage with Bipotent Potential

    PubMed Central

    Kwon, Oh-Joon; Zhang, Li; Xin, Li

    2016-01-01

    Recent lineage tracing studies support the existence of prostate luminal progenitors that possess extensive regenerative capacity, but their identity remains unknown. We show that Sca-1 (Stem Cell Antigen-1) identifies a small population of murine prostate luminal cells that reside in the proximal prostatic ducts adjacent to the urethra. Sca-1+ luminal cells do not express Nkx3.1. They do not carry the secretory function, although they express the androgen receptor. These cells are enriched in the prostates of castrated mice. In the in vitro prostate organoid assay, a small fraction of the Sca-1+ luminal cells are capable of generating budding organoids that are morphologically distinct from those derived from other cell lineages. Histologically, this type of organoid is composed of multiple inner layers of luminal cells surrounded by multiple outer layers of basal cells. When passaged, these organoids retain their morphological and histological features. Finally, the Sca-1+ luminal cells are capable of forming small prostate glands containing both basal and luminal cells in an in vivo prostate regeneration assay. Collectively, our study establishes the androgen-independent and bipotent organoid-forming Sca-1+ luminal cells as a functionally distinct cellular entity. These cells may represent a putative luminal progenitor population and serve as a cellular origin for castration resistant prostate cancer. PMID:26418304

  17. Using self-organizing maps to identify potential halo white dwarfs.

    PubMed

    García-Berro, Enrique; Torres, Santiago; Isern, Jordi

    2003-01-01

    We present the results of an unsupervised classification of the disk and halo white dwarf populations in the solar neighborhood. The classification is done by merging the results of detailed Monte Carlo (MC) simulations, which reproduce very well the characteristics of the white dwarf populations in the solar neighborhood, with a catalogue of real stars. The resulting composite catalogue is analyzed using a competitive learning algorithm. In particular we have used the so-called self-organized map. The MC simulated stars are used as tracers and help in identifying the resulting clusters. The results of such an strategy turn out to be quite satisfactory, suggesting that this approach can provide an useful framework for analyzing large databases of white dwarfs with well determined kinematical, spatial and photometric properties once they become available in the next decade. Moreover, the results are of astrophysical interest as well, since a straightforward interpretation of several recent astronomical observations, like the detected microlensing events in the direction of the Magellanic Clouds, the possible detection of high proper motion white dwarfs in the Hubble Deep Field and the discovery of high velocity white dwarfs in the solar neighborhood, suggests that a fraction of the baryonic dark matter component of our galaxy could be in the form of old and dim halo white dwarfs. PMID:12672435

  18. Program development to identify and characterize potential emergency situations at a petroleum refinery and determination of industrial hygiene emergency responses

    SciTech Connect

    Oransky, J.J.; Delp, S.N.; Deppen, E.A.; Barrett, D.

    1995-12-31

    In the modern world the field of industrial hygiene continues to grow beyond the traditional definition of the profession. This case study documents the problem solving approach used to identify potential exposures and evaluate industrial hygiene preparedness to handle emergencies due to fire or major spill at a complex multi-process petroleum refinery. In the recent past an environmental engineer and industrial hygiene consulting firm was retained by a mature, multi-process petroleum refinery to assist in the program development to identify and characterize potential emergency situations due to a fire, major release, or spill. This study would assist the refinery in compliance with the process safety and emergency response standards and to protect refinery operations and fire fighting personnel by minimizing potential exposures and risk when responding to such a major incident.

  19. Onset Dynamics of Action Potentials in Rat Neocortical Neurons and Identified Snail Neurons: Quantification of the Difference

    PubMed Central

    Volgushev, Maxim; Malyshev, Aleksey; Balaban, Pavel; Chistiakova, Marina; Volgushev, Stanislav; Wolf, Fred

    2008-01-01

    The generation of action potentials (APs) is a key process in the operation of nerve cells and the communication between neurons. Action potentials in mammalian central neurons are characterized by an exceptionally fast onset dynamics, which differs from the typically slow and gradual onset dynamics seen in identified snail neurons. Here we describe a novel method of analysis which provides a quantitative measure of the onset dynamics of action potentials. This method captures the difference between the fast, step-like onset of APs in rat neocortical neurons and the gradual, exponential-like AP onset in identified snail neurons. The quantitative measure of the AP onset dynamics, provided by the method, allows us to perform quantitative analyses of factors influencing the dynamics. PMID:18398478

  20. Corning Inc.: Proposed Changes at Glass Plant Indicate $26 Million in Potential Savings

    SciTech Connect

    2004-01-01

    In 2000, the Corning glass plant in Greenville, Ohio, consumed almost 114 million kWh of electricity and nearly 308,000 MMBtu of natural gas in its glassmaking processes for a total cost of approximately $6.4 million. A plant-wide assessment indicated that improvement projects could save nearly $26 million and reduce natural gas use by 122,900 MMBtu per year, reduce electrical use by 72,300,000 kWh per year, and reduce CO2 emissions by 180 million pounds per year.

  1. Identifying the Potential for Robotics to Assist Older Adults in Different Living Environments

    PubMed Central

    Mitzner, Tracy L.; Chen, Tiffany L.; Kemp, Charles C.; Rogers, Wendy A.

    2014-01-01

    As the older adult population grows and becomes more diverse, so will their needs and preferences for living environments. Many adults over 65 years of age require some assistance [1, 2]; yet it is important for their feelings of well-being that the assistance not restrict their autonomy [3]. Not only is autonomy correlated with quality of life [4], autonomy enhancement may improve functionality [2, 5]. The goal of this paper is to provide guidance for the development of technology to enhance autonomy and quality of life for older adults. We explore the potential for robotics to meet these needs. We evaluated older adults' diverse living situations and the predictors of residential moves to higher levels of care in the United States. We also examined older adults' needs for assistance with activities of daily living (ADLs), instrumental activities of daily living (IADLs), and medical conditions when living independently or in a long-term care residence. By providing support for older adults, mobile manipulator robots may reduce need-driven, undesired moves from residences with lower levels of care (i.e., private homes, assisted living) to those with higher levels of care (i.e., skilled nursing). PMID:24729800

  2. Diversity and Biocatalytic Potential of Epoxide Hydrolases Identified by Genome Analysis†

    PubMed Central

    van Loo, Bert; Kingma, Jaap; Arand, Michael; Wubbolts, Marcel G.; Janssen, Dick B.

    2006-01-01

    Epoxide hydrolases play an important role in the biodegradation of organic compounds and are potentially useful in enantioselective biocatalysis. An analysis of various genomic databases revealed that about 20% of sequenced organisms contain one or more putative epoxide hydrolase genes. They were found in all domains of life, and many fungi and actinobacteria contain several putative epoxide hydrolase-encoding genes. Multiple sequence alignments of epoxide hydrolases with other known and putative α/β-hydrolase fold enzymes that possess a nucleophilic aspartate revealed that these enzymes can be classified into eight phylogenetic groups that all contain putative epoxide hydrolases. To determine their catalytic activities, 10 putative bacterial epoxide hydrolase genes and 2 known bacterial epoxide hydrolase genes were cloned and overexpressed in Escherichia coli. The production of active enzyme was strongly improved by fusion to the maltose binding protein (MalE), which prevented inclusion body formation and facilitated protein purification. Eight of the 12 fusion proteins were active toward one or more of the 21 epoxides that were tested, and they converted both terminal and nonterminal epoxides. Four of the new epoxide hydrolases showed an uncommon enantiopreference for meso-epoxides and/or terminal aromatic epoxides, which made them suitable for the production of enantiopure (S,S)-diols and (R)-epoxides. The results show that the expression of epoxide hydrolase genes that are detected by analyses of genomic databases is a useful strategy for obtaining new biocatalysts. PMID:16597997

  3. Development of a Novel Virtual Screening Cascade Protocol to Identify Potential Trypanothione Reductase Inhibitors

    PubMed Central

    2009-01-01

    The implementation of a novel sequential computational approach that can be used effectively for virtual screening and identification of prospective ligands that bind to trypanothione reductase (TryR) is reported. The multistep strategy combines a ligand-based virtual screening for building an enriched library of small molecules with a docking protocol (AutoDock, X-Score) for screening against the TryR target. Compounds were ranked by an exhaustive conformational consensus scoring approach that employs a rank-by-rank strategy by combining both scoring functions. Analysis of the predicted ligand?protein interactions highlights the role of bulky quaternary amine moieties for binding affinity. The scaffold hopping (SHOP) process derived from this computational approach allowed the identification of several chemotypes, not previously reported as antiprotozoal agents, which includes dibenzothiepine, dibenzooxathiepine, dibenzodithiepine, and polycyclic cationic structures like thiaazatetracyclo-nonadeca-hexaen-3-ium. Assays measuring the inhibiting effect of these compounds on T. cruzi and T. brucei TryR confirm their potential for further rational optimization. PMID:19296695

  4. Identifying at-risk employees: A behavioral model for predicting potential insider threats

    SciTech Connect

    Greitzer, Frank L.; Kangas, Lars J.; Noonan, Christine F.; Dalton, Angela C.

    2010-09-01

    A psychosocial model was developed to assess an employee’s behavior associated with an increased risk of insider abuse. The model is based on case studies and research literature on factors/correlates associated with precursor behavioral manifestations of individuals committing insider crimes. In many of these crimes, managers and other coworkers observed that the offenders had exhibited signs of stress, disgruntlement, or other issues, but no alarms were raised. Barriers to using such psychosocial indicators include the inability to recognize the signs and the failure to record the behaviors so that they could be assessed by a person experienced in psychosocial evaluations. We have developed a model using a Bayesian belief network with the help of human resources staff, experienced in evaluating behaviors in staff. We conducted an experiment to assess its agreement with human resources and management professionals, with positive results. If implemented in an operational setting, the model would be part of a set of management tools for employee assessment that can raise an alarm about employees who pose higher insider threat risks. In separate work, we combine this psychosocial model’s assessment with computer workstation behavior to raise the efficacy of recognizing an insider crime in the making.

  5. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution.

    PubMed

    Clarke, Thomas H; Garb, Jessica E; Hayashi, Cheryl Y; Arensburger, Peter; Ayoub, Nadia A

    2015-07-01

    The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). PMID:26058392

  6. Spider Transcriptomes Identify Ancient Large-Scale Gene Duplication Event Potentially Important in Silk Gland Evolution

    PubMed Central

    Clarke, Thomas H.; Garb, Jessica E.; Hayashi, Cheryl Y.; Arensburger, Peter; Ayoub, Nadia A.

    2015-01-01

    The evolution of specialized tissues with novel functions, such as the silk synthesizing glands in spiders, is likely an influential driver of adaptive success. Large-scale gene duplication events and subsequent paralog divergence are thought to be required for generating evolutionary novelty. Such an event has been proposed for spiders, but not tested. We de novo assembled transcriptomes from three cobweb weaving spider species. Based on phylogenetic analyses of gene families with representatives from each of the three species, we found numerous duplication events indicative of a whole genome or segmental duplication. We estimated the age of the gene duplications relative to several speciation events within spiders and arachnids and found that the duplications likely occurred after the divergence of scorpions (order Scorpionida) and spiders (order Araneae), but before the divergence of the spider suborders Mygalomorphae and Araneomorphae, near the evolutionary origin of spider silk glands. Transcripts that are expressed exclusively or primarily within black widow silk glands are more likely to have a paralog descended from the ancient duplication event and have elevated amino acid replacement rates compared with other transcripts. Thus, an ancient large-scale gene duplication event within the spider lineage was likely an important source of molecular novelty during the evolution of silk gland-specific expression. This duplication event may have provided genetic material for subsequent silk gland diversification in the true spiders (Araneomorphae). PMID:26058392

  7. Potential of a sequence-based antigenic distance measure to indicate equine influenza vaccine strain efficacy.

    PubMed

    Daly, Janet M; Elton, Debra

    2013-12-01

    The calculation of p(epitope) values, a sequence-based measure of antigenic distance between strains, was developed for human influenza. The potential to apply the p(epitope) value to equine influenza vaccine strain selection was assessed. There was a negative correlation between p(epitope) value and vaccine efficacy for pairs of vaccine and challenge strains used in cross-protection studies in ponies that just reached statistical significance (p=0.046) only if one pair of viruses was excluded from the analysis. Thus the p(epitope) value has potential to provide additional data to consider in the decision-making process for updating equine influenza vaccine strains. However, further work is required to define the epitopes of the equine H3N8 haemagglutinin protein recognised by equine antibodies, which could lead to refinement of the p(epitope) value calculation. Furthermore, other factors such as vaccine potency and virulence of circulating strains may also influence vaccine efficacy. PMID:23831320

  8. Brain potentials indicate the effect of other observers' emotions on perceptions of facial attractiveness.

    PubMed

    Huang, Yujing; Pan, Xuwei; Mo, Yan; Ma, Qingguo

    2016-03-23

    Perceptions of facial attractiveness are sensitive to emotional expression of the perceived face. However, little is known about whether the emotional expression on the face of another observer of the perceived face may have an effect on perceptions of facial attractiveness. The present study used event-related potential technique to examine social influence of the emotional expression on the face of another observer of the perceived face on perceptions of facial attractiveness. The experiment consisted of two phases. In the first phase, a neutral target face was paired with two images of individuals gazing at the target face with smiling, fearful or neutral expressions. In the second phase, participants were asked to judge the attractiveness of the target face. We found that a target face was more attractive when other observers positively gazing at the target face in contrast to the condition when other observers were negative. Additionally, the results of brain potentials showed that the visual positive component P3 with peak latency from 270 to 330ms was larger after participants observed the target face paired with smiling individuals than the target face paired with neutral individuals. These findings suggested that facial attractiveness of an individual may be influenced by the emotional expression on the face of another observer of the perceived face. PMID:26601630

  9. Reduced habituation of auditory evoked potentials indicate cortical hyper-excitability in Fragile X Syndrome.

    PubMed

    Ethridge, L E; White, S P; Mosconi, M W; Wang, J; Byerly, M J; Sweeney, J A

    2016-01-01

    Sensory hypersensitivities are common, clinically distressing features of Fragile X Syndrome (FXS). Preclinical evidence suggests this abnormality may result from synaptic hyper-excitability in sensory systems. This model predicts reduced sensory habituation to repeated stimulus presentation. Fourteen adolescents and adults with FXS and 15 age-matched controls participated in a modified auditory gating task using trains of 4 identical tones during dense array electroencephalography (EEG). Event-related potential and single trial time-frequency analyses revealed decreased habituation of the N1 event-related potential response in FXS, and increased gamma power coupled with decreases in gamma phase-locking during the early-stimulus registration period. EEG abnormalities in FXS were associated with parent reports of heightened sensory sensitivities and social communication deficits. Reduced habituation and altered gamma power and phase-locking to auditory cues demonstrated here in FXS patients parallels preclinical findings with Fmr1 KO mice. Thus, the EEG abnormalities seen in FXS patients support the model of neocortical hyper-excitability in FXS, and may provide useful translational biomarkers for evaluating novel treatment strategies targeting its neural substrate. PMID:27093069

  10. Reduced habituation of auditory evoked potentials indicate cortical hyper-excitability in Fragile X Syndrome

    PubMed Central

    Ethridge, L E; White, S P; Mosconi, M W; Wang, J; Byerly, M J; Sweeney, J A

    2016-01-01

    Sensory hypersensitivities are common, clinically distressing features of Fragile X Syndrome (FXS). Preclinical evidence suggests this abnormality may result from synaptic hyper-excitability in sensory systems. This model predicts reduced sensory habituation to repeated stimulus presentation. Fourteen adolescents and adults with FXS and 15 age-matched controls participated in a modified auditory gating task using trains of 4 identical tones during dense array electroencephalography (EEG). Event-related potential and single trial time–frequency analyses revealed decreased habituation of the N1 event-related potential response in FXS, and increased gamma power coupled with decreases in gamma phase-locking during the early-stimulus registration period. EEG abnormalities in FXS were associated with parent reports of heightened sensory sensitivities and social communication deficits. Reduced habituation and altered gamma power and phase-locking to auditory cues demonstrated here in FXS patients parallels preclinical findings with Fmr1 KO mice. Thus, the EEG abnormalities seen in FXS patients support the model of neocortical hyper-excitability in FXS, and may provide useful translational biomarkers for evaluating novel treatment strategies targeting its neural substrate. PMID:27093069

  11. Personality traits of endodontic residents indicate potential for becoming endodontic faculty.

    PubMed

    O'Neill, Paula N; Svec, Timothy A; Ludington, John R; Suchina, John A

    2007-04-01

    Dental schools across America are challenged by the shortage of qualified faculty to fill vacant positions. This project, conducted through survey methodology, focused on obtaining a basic understanding of the personality types that seek out and maintain positions as full-time endodontic educators and compared those educators with endodontic residents to define similarities and differences that could lead to strategies to recruit those residents into academic endodontic education to assist in alleviating the faculty shortage in dentistry. All full-time endodontic faculty and residents were invited to participate. The Myers Briggs type indicator form M was administered electronically to faculty and postgraduates/residents. A 38.8% faculty and 21.3% resident response rate was achieved. Survey results were analyzed by using description statistics and chi-square tests. Results of the study indicate that there are parallel personality preferences of residents and faculty resulting in recommendations of early identification of academic interest, structured mentoring, faculty development of residents, and the implementation of debt-reduction strategies to ease entry into academic dentistry. PMID:17368332

  12. Sedimentary ladderane core lipids as potential indicators of hypoxia in the East China Sea

    NASA Astrophysics Data System (ADS)

    Zhao, Zongshan; Cao, Yali; Li, Li; Song, Guodong; Yang, Hongmei; Liu, Sumei; Zhao, Meixun

    2013-01-01

    Anammox (anaerobic ammonium oxidation) is an important process in many suboxic to anoxic marine environments for converting fixed nitrogen to N2, and has a major impact on the marine nitrogen cycle. Ladderane core lipids have been utilized as an indicator of the contribution of anammox to the marine nitrogen cycles. However, such studies have not been reported for the China seas and little is known about the importance of anammox within the nitrogen cycle of these marginal seas. In the research reported here, the ladderane core lipid contents of 17 surface sediment samples from the East China Sea are reported, and their spatial distribution is investigated. C18 -[5]-ladderane FAME, C20-[5]-ladderane FAME and C20-[3]-ladderane FAME have all been detected, suggesting that the anammox bacteria are widely present within the study area. The total contents of the three ladderane lipids (ΣFAMEs) range from 24-355 ng/g (weight of dry sediments), with higher contents occurring in the Minzhe Mud Zone and broadly coincident with the spatial distribution of hypoxia. It is suggested that the sedimentary ladderane core lipids are mainly produced in the water column and their sedimentary contents can be used as indicators of water column hypoxia.

  13. Contrast-enhanced ultrasound in the biliary system: Potential uses and indications.

    PubMed

    Xu, Hui-Xiong

    2009-12-31

    Conventional ultrasound (US) is the first-line imaging investigation for biliary diseases. However, it is lack of the ability to depict the microcirculation of some lesions which may lead to failure in diagnosis for some biliary diseases. The use of contrast-enhanced US (CEUS) has reached the field of bile duct disease in recent years and promising results have been achieved. In this review, the methodology, image interpretation, enhancement pattern, clinical usefulness, and indications for CEUS in the biliary system are summarized. CEUS may be indicated in the biliary system under the following circumstances: (1) Where there is a need to make a characterization of intrahepatic cholangiocarcinoma (ICC); (2) For differentiation diagnosis between ICC and other tumors (i.e. hepatocellular carcinoma or liver metastasis) or infectious diseases; (3) For differentiation diagnosis between biliary cystadenoma and biliary cystadenocarcinoma; (4) To detect malignant change in Caroli's disease; (5) To depict the extent of Klatskin's tumor with greater clarity; (6) To make a distinction between gallbladder cholesterol polyp, adenoma and polypoid cancer; (7) To make a distinction between chronic cholecystitis with thickened wall and gallbladder cancer; (8) For differentiation diagnosis between motionless sludge and gallbladder cancer; (9) For differentiation diagnosis between common bile duct cancer and sludge or stone without acoustic shadowing; and (10) In patients who are suspected of having a drop of their percutaneous transhepatic cholangiodrainage tube, US contrast agent can be administered to through the tube detect the site of the tube. PMID:21160719

  14. DNA microarray analysis identifies CKS2 and LEPR as potential markers of meningioma recurrence.

    PubMed

    Menghi, Francesca; Orzan, Francesca N; Eoli, Marica; Farinotti, Mariangela; Maderna, Emanuela; Pisati, Federica; Bianchessi, Donatella; Valletta, Lorella; Lodrini, Sandro; Galli, Giuseppe; Anghileri, Elena; Pellegatta, Serena; Pollo, Bianca; Finocchiaro, Gaetano

    2011-01-01

    Meningiomas are the most frequent intracranial tumors. Surgery can be curative, but recurrences are possible. We performed gene expression analyses and loss of heterozygosity (LOH) studies looking for new markers predicting the recurrence risk. We analyzed expression profiles of 23 meningiomas (10 grade I, 10 grade II, and 3 grade III) and validated the data using quantitative polymerase chain reaction (qPCR). We performed LOH analysis on 40 meningiomas, investigating chromosomal regions on 1p, 9p, 10q, 14q, and 22q. We found 233 and 268 probe sets to be significantly down- and upregulated, respectively, in grade II or III meningiomas. Genes downregulated in high-grade meningiomas were overrepresented on chromosomes 1, 6, 9, 10, and 14. Based on functional enrichment analysis, we selected LIM domain and actin binding 1 (LIMA1), tissue inhibitor of metalloproteinases 3 (TIMP3), cyclin-dependent kinases regulatory subunit 2 (CKS2), leptin receptor (LEPR), and baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) for validation using qPCR and confirmed their differential expression in the two groups of tumors. We calculated ΔCt values of CKS2 and LEPR and found that their differential expression (C-L index) was significantly higher in grade I than in grade II or III meningiomas (p < .0001). Interestingly, the C-L index of nine grade I meningiomas from patients who relapsed in <5 years was significantly lower than in grade I meningiomas from patients who did not relapse. These findings indicate that the C-L index may be relevant to define the progression risk in meningioma patients, helping guide their clinical management. A prospective analysis on a larger number of cases is warranted. PMID:21948653

  15. COSMO-SkyMed potentiality to identify crop-specific behavior and monitor phenological parameters

    NASA Astrophysics Data System (ADS)

    Guarini, Rocchina; Segalini, Federica; Mastronardi, Giovanni; Notarnicola, Claudia; Vuolo, Francesco; Dini, Luigi

    2014-10-01

    This work aims at investigating the capability of COSMO-SkyMed® (CSK®) constellation of Synthetic Aperture Radar (SAR) system to monitor the Leaf Area Index (LAI) of different crops. The experiment was conducted in the Marchfeld Region, an agricultural Austrian area, and focused on five crop species: sugar beet, soybean, potato, pea and corn. A linear regression analysis was carried out to assess the sensitivity of CSK® backscattering coefficients to crops changes base on LAI values. CSK® backscattering coefficients were averaged at a field scale (<σ°dB>) and were compared to the DEIMOS-1 derived values of estimated LAI. LAI were as well averaged over the corresponding fields (). CSK® data acquired at three polarizations (HH, VV and VH), four incidence angles (23°, 33°, 40° and 57°) and at different pixel spacings (2.5 m and 10 m) were tested to assess whether spatial resolution may influence results at a field scale and to find the best combination of polarizations and CSK® acquisition beams which indicate the highest sensitivity to crop LAI values. The preliminary results show that sugar beet can be well monitored (r = 0.72 - 0.80) by CSK® by using any of the polarization acquisition modes, at moderate to shallow incidence angles (33° - 57°). Slightly weaker correlations were found, at VH polarization only, between CSK® < σ°dB> and for potato (r = 0.65), pea (r = 0.65) and soybean (r = -0.83). Shallower view incidence angles seem to be preferable to steep ones in most cases. CSK® backscattering coefficients were no sensitive at all to LAI changes for already developed corn fields.

  16. Brachial Arterial Temperature as an Indicator of Core Temperature: Proof of Concept and Potential Applications

    PubMed Central

    Pawley, Matthew D.M.; Martinsen, Paul; Mitchell, Simon J.; Cheeseman, James F.; Merry, Alan F.; Willcox, Timothy; Grieve, Robert; Nand, Parma; Davies, Elaine; Warman, Guy R.

    2013-01-01

    Abstract: There is potential for heat loss and hypothermia during anesthesia and also for hyperthermia if heat conservation and active warming measures are not accurately titrated. Accurate temperature monitoring is particularly important in procedures in which the patient is actively cooled and then rewarmed such as during cardiopulmonary bypass surgery (CPB). We simultaneously measured core, nasopharyngeal, and brachial artery temperatures to investigate the last named as a potential peripheral temperature monitoring site. Ten patients undergoing hypothermic CPB were instrumented for simultaneous monitoring of temperatures in the pulmonary artery (PA), aortic arterial inflow (AI), nasopharynx (NP), and brachial artery (BA). Core temperature was defined as PA temperature before and after CPB and the AI temperature during CPB. Mean deviations of BA and NP temperatures from core temperature were calculated for three steady-state periods (before, during, and after CPB). Mean deviation of BA and NP temperatures from AI temperature was also calculated during active rewarming. A total of 1862 measurements were obtained and logged from eight patients. Mean BA and NP deviations from core temperature across the steady-state periods (before, during, and after CBP) were, respectively: .23 ± .25, −.26 ± .3, and −.09 ± .05°C (BA), and .11 ± .19, −.1 ± .47, and −.04 ± .3°C (NP). During steadystate periods, there was no evidence of a difference between the mean BA and NP deviation. During active rewarming, the mean difference between the BA and AI temperatures was .14 ± .36°C. During this period, NP temperature lagged behind AI and BA temperatures by up to 41 minutes and was up to 5.3°C lower than BA (mean difference between BA and NP temperatures was 1.22 ± .58°C). The BA temperature is an adequate surrogate for core temperature. It also accurately tracks the changing AI temperature during rewarming and is therefore potentially useful in detecting a hyperthermic perfusate, which might cause cerebral hyperthermia. PMID:23930377

  17. A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes.

    PubMed

    Egelund, Jack; Skjøt, Michael; Geshi, Naomi; Ulvskov, Peter; Petersen, Bent Larsen

    2004-09-01

    Plant cell wall (CW) synthesizing enzymes can be divided into the glycan (i.e. cellulose and callose) synthases, which are multimembrane spanning proteins located at the plasma membrane, and the glycosyltransferases (GTs), which are Golgi localized single membrane spanning proteins, believed to participate in the synthesis of hemicellulose, pectin, mannans, and various glycoproteins. At the Carbohydrate-Active enZYmes (CAZy) database where e.g. glucoside hydrolases and GTs are classified into gene families primarily based on amino acid sequence similarities, 415 Arabidopsis GTs have been classified. Although much is known with regard to composition and fine structures of the plant CW, only a handful of CW biosynthetic GT genes-all classified in the CAZy system-have been characterized. In an effort to identify CW GTs that have not yet been classified in the CAZy database, a simple bioinformatics approach was adopted. First, the entire Arabidopsis proteome was run through the Transmembrane Hidden Markov Model 2.0 server and proteins containing one or, more rarely, two transmembrane domains within the N-terminal 150 amino acids were collected. Second, these sequences were submitted to the SUPERFAMILY prediction server, and sequences that were predicted to belong to the superfamilies NDP-sugartransferase, UDP-glycosyltransferase/glucogen-phosphorylase, carbohydrate-binding domain, Gal-binding domain, or Rossman fold were collected, yielding a total of 191 sequences. Fifty-two accessions already classified in CAZy were discarded. The resulting 139 sequences were then analyzed using the Three-Dimensional-Position-Specific Scoring Matrix and mGenTHREADER servers, and 27 sequences with similarity to either the GT-A or the GT-B fold were obtained. Proof of concept of the present approach has to some extent been provided by our recent demonstration that two members of this pool of 27 non-CAZy-classified putative GTs are xylosyltransferases involved in synthesis of pectin rhamnogalacturonan II (J. Egelund, B.L. Petersen, A. Faik, M.S. Motawia, C.E. Olsen, T. Ishii, H. Clausen, P. Ulvskov, and N. Geshi, unpublished data). PMID:15333752

  18. “What is this?” Gesture as a potential cue to identify referents in discourse

    PubMed Central

    So, Wing Chee; Lim, Jia Yi

    2010-01-01

    This study explores whether caregivers follow the discourse-pragmatic principle of information status of referents (given vs. new) in their gestures and how children respond to their caregivers’ gestures. Chinese and American caregivers were videotaped while interacting spontaneously with their children. Their speech and gestures were coded for referential expressions. Even though Chinese caregivers gestured more often than American caregivers, we found that both groups produced more gestures when asking their children to identify new referents than when asking their children to identify given referents. In addition, both groups of children were sensitive to the gestures accompanying new referents and using these gestures to identify the referents. Thus, we conclude that gesture serves as a potential cue for both caregivers and children to identify referents according to the discourse-pragmatic principle of information status. PMID:22505785

  19. Variations in Environmental Signals in Tree-Ring Indices in Trees with Different Growth Potential

    PubMed Central

    Hafner, Polona; Gričar, Jožica; Skudnik, Mitja; Levanič, Tom

    2015-01-01

    We analysed two groups of Quercus robur trees, growing at nearby plots with different micro-location condition (W-wet and D-dry) in the floodplain Krakovo forest, Slovenia. In the study we compared the growth response of two different tree groups to environmental variables, the potential signal stored in earlywood (EW) structure and the potential difference of the information stored in carbon isotope discrimination of EW and latewood (LW). For that purpose EW and LW widths and carbon isotope discrimination for the period 1970–2008 AD were measured. EW and LW widths were measured on stained microscopic slides and chronologies were standardised using the ARSTAN program. α-cellulose was extracted from pooled EW and LW samples and homogenized samples were further analysed using an elemental analyser and IRMS. We discovered that W oaks grew significantly better over the whole analysed period. The difference between D and W oaks was significant in all analysed variables with the exception of stable carbon isotope discrimination in latewood. In W oaks, latewood widths correlated with summer (June to August) climatic variables, while carbon isotope discrimination was more connected to River Krka flow during the summer. EW discrimination correlated with summer and autumn River Krka flow of the previous year, while latewood discrimination correlated with flow during the current year. In the case of D oaks, the environmental signal appears to be vague, probably due to less favourable growth conditions resulting in markedly reduced increments. Our study revealed important differences in responses to environmental factors between the two oak groups of different physiological conditions that are preconditioned by environmental stress. Environmental information stored in tree-ring features may vary, even within the same forest stand, and largely depends on the micro-environment. Our analysis confirmed our assumptions that separate EW and LW analysis of widths and carbon isotope discrimination provides complementary information in Q. robur dendroecology. PMID:26619344

  20. Hyperdensity of the Basilar Artery on Postmortem CT: A Potential Indicator for Basilar Artery Thrombosis.

    PubMed

    Garland, Jack; Tse, Rexson; Beh, Raymond J; Lyons, Timothy J; Cala, Allan D

    2016-06-01

    Basilar artery thrombosis constitutes 1% of all types of stroke, carries a mortality rate of up to 90%, and is one of the rarer causes of sudden death. It leads to brain stem ischemia and commonly presents with impaired consciousness, cranial nerve palsy, hemiplegia or quadriplegia, and sudden collapse. Clinically, the diagnosis of basilar artery thrombosis is made on clinical symptoms, along with a hyperdense basilar artery in antemortem computed tomography (CT) scan. To our knowledge, whether a hyperdense basilar artery indicates basilar artery thrombosis on postmortem CT scan is not documented in the literature. We present a case report of a 55-year-old man who on postmortem CT scan showed a hyperdense basilar artery and was subsequently confirmed to be a fatal basilar artery thrombosis. We suggest that a hyperdense basilar artery on postmortem CT should prompt the pathologist to consider basilar artery thrombosis. PMID:27049662

  1. Martian impact crater ejecta morphologies and their potential as indicators of subsurface volatile distribution

    NASA Technical Reports Server (NTRS)

    Barlow, Nadine G.

    1991-01-01

    Many martian impact craters ejecta morphologies suggestive of fluidization during ejecta emplacement. Impact into subsurface volatile reserviors (i.e., water, ice, CO2, etc.) is the mechanism favored by many scientists, although acceptance of this mechanism is not unanimous. In recent years, a number of studies were undertaken to better understand possible relationships between ejecta morphology and latitude, longitude, crater diameter, and terrain. These results suggest that subsurface volatiles do influence the formation of specific ejecta morphologies and may provide clues to the vertical and horizontal distribution of volatiles in more localized regions of Mars. The location of these volatile reservoirs will be important to humans exploring and settling Mars in the future. Qualitative descriptions of ejecta morphology and quantitative analyses of ejecta sinuosity and ejecta lobe areal extent from the basis of the studies. Ejecta morphology studies indicate that morphology is correlated with crater diameter and latitude, and, using depth-diameter relationships, these correlations strongly suggest that changes in morphology are related to transition among subsurface layers with varying amounts of volatiles. Ejecta sinuosity studies reveal correlations between degree of sinuosity (lobateness) and crater morphology, diameter, latitude, and terrain. Lobateness, together with variations in areal extent of the lobate ejecta blanket with morphology and latitude, probably depends most directly on the ejecta emplacement process. The physical parameters measured here can be compared with those predicted by existing ejecta emplacement models. Some of these parameters are best reproduced by models requiring incorporation of volatiles within the ejecta. However, inconsistencies between other parameters and the models indicate that more detailed modeling is necessary before the location of volatile reservoirs can be confidently predicted based on ejecta morphology studies alone.

  2. The potential to reconstruct broadscale climate indices associated with southeast Australian droughts from Athrotaxis species, Tasmania

    NASA Astrophysics Data System (ADS)

    Allen, K. J.; Ogden, J.; Buckley, B. M.; Cook, E. R.; Baker, P. J.

    2011-11-01

    Occurrence of drought and dry periods in southeastern Australia has been linked to broad scale climate phenomena including the Southern Oscillation, Interdecadal Pacific Oscillation (IPO), Indian Ocean Dipole (IOD), Southern Annular Mode (SAM) and persistence of blocking high pressure in the Tasman Sea. We examine relationships between Athrotaxis tree ring chronologies from southern Australia extending over much of the past millennia and these broad scale indices. We also examine relationships between the chronologies, temperature, precipitation and a standardised precipitation and evapotranspiration index. Timing of significant correlations with maximum temperature varies between species. The responses of the species with broadscale indices vary with location: northern Athrotaxis cupressoides (Pencil Pine) are more strongly related to the Interdecadal Pacific Oscillation (IPO) and Southern Oscillation Index (SOI) than southern sites. As an exception to this, a site in the far south had significant correlations with both the SOI and IPO, opposite in sign to those observed for the northern sites. Significant spectral power at frequencies consistent with the SOI and IPO occur in all chronologies. Western and southern sites are more strongly related to a seasonalised index of SAM. These three systems have played important roles in determining moisture conditions in southeastern Australia over the past millennium. Results suggest that reconstructions of the SOI, IPO or SAM are unlikely based solely on this Athrotaxis network. The Athrotaxis network of tree ring sites, is however, likely to be an important input to multi-proxy models reconstructing the SOI, IPO or SAM in the Australian sector. The Athrotaxis network of sites is also an important extension of the existing network of Australian tree ring sites that could be used to reconstruct historical drought in southeastern Australia.

  3. Seasonally and regionally determined indication potential of bioassays in contaminated river sediments.

    PubMed

    Hilscherová, Klára; Dusek, Ladislav; Sídlová, Tereza; Jálová, Veronika; Cupr, Pavel; Giesy, John P; Nehyba, Slavomír; Jarkovský, Jirí; Klánová, Jana; Holoubek, Ivan

    2010-03-01

    River sediments are a dynamic system, especially in areas where floods occur frequently. In the present study, an integrative approach is used to investigate the seasonal and spatial dynamics of contamination of sediments from a regularly flooded industrial area in the Czech Republic, which presents a suitable model ecosystem for pollutant distribution research at a regional level. Surface sediments were sampled repeatedly to represent two different hydrological situations: spring (after the peak of high flow) and autumn (after longer period of low flow). Samples were characterized for abiotic parameters and concentrations of priority organic pollutants. Toxicity was assessed by Microtox test; genotoxicity by SOS-chromotest and green fluorescent protein (GFP)-yeast test; and the presence of compounds with specific mode of action by in vitro bioassays for dioxin-like activity, anti-/androgenicity, and anti-/estrogenicity. Distribution of organic contaminants varied among regions and seasonally. Although the results of Microtox and genotoxicity tests were relatively inconclusive, all other specific bioassays led to statistically significant regional and seasonal differences in profiles and allowed clear separation of upstream and downstream regions. The outcomes of these bioassays indicated an association with concentrations of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) as master variables. There were significant interrelations among dioxin-like activity, antiandrogenicity and content of organic carbon, clay, and concentration of PAHs and PCBs, which documents the significance of abiotic factors in accumulation of pollutants. The study demonstrates the strength of the specific bioassays in indicating the changes in contamination and emphasizes the crucial role of a well-designed sampling plan, in which both spatial and temporal dynamics should be taken into account, for the correct interpretations of information in risk assessments. PMID:20821474

  4. Targeted Next-generation Sequencing of Advanced Prostate Cancer Identifies Potential Therapeutic Targets and Disease Heterogeneity

    PubMed Central

    Beltran, Himisha; Yelensky, Roman; Frampton, Garrett M.; Park, Kyung; Downing, Sean R.; MacDonald, Theresa Y.; Jarosz, Mirna; Lipson, Doron; Tagawa, Scott T.; Nanus, David M.; Stephens, Philip J.; Mosquera, Juan Miguel; Cronin, Maureen T.; Rubin, Mark A.

    2012-01-01

    Background Most personalized cancer care strategies involving DNA sequencing are highly reliant on acquiring sufficient fresh or frozen tissue. It has been challenging to comprehensively evaluate the genome of advanced prostate cancer (PCa) because of limited access to metastatic tissue. Objective To demonstrate the feasibility of a novel next-generation sequencing (NGS) based platform that can be used with archival formalin-fixed paraffin-embedded (FFPE) biopsy tissue to evaluate the spectrum of DNA alterations seen in advanced PCa. Design, setting, and participants FFPE samples (including archival prostatectomies and prostate needle biopsies) were obtained from 45 patients representing the spectrum of disease: localized PCa, metastatic hormone-naive PCa, and metastatic castration-resistant PCa (CRPC). We also assessed paired primaries and metastases to understand disease heterogeneity and disease progression. Intervention At least 50 ng of tumor DNA was extracted from FFPE samples and used for hybridization capture and NGS using the Illumina HiSeq 2000 platform. Outcome measurements and statistical analysis A total of 3320 exons of 182 cancer-associated genes and 37 introns of 14 commonly rearranged genes were evaluated for genomic alterations. Results and limitations We obtained an average sequencing depth of >900X. Overall, 44% of CRPCs harbored genomic alterations involving the androgen receptor gene (AR), including AR copy number gain (24% of CRPCs) or AR point mutation (20% of CRPCs). Other recurrent mutations included transmembrane protease, serine 2 gene (TMPRSS2):v-ets erythroblastosis virus E26 oncogene homolog (avian) gene (ERG) fusion (44%); phosphatase and tensin homolog gene (PTEN) loss (44%); tumor protein p53 gene (TP53) mutation (40%); retinoblastoma gene (RB) loss (28%); v-myc myelocytomatosis viral oncogene homolog (avian) gene (MYC) gain (12%); and phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit α gene (PIK3CA) mutation (4%). There was a high incidence of genomic alterations involving key genes important for DNA repair, including breast cancer 2, early onset gene (BRCA2) loss (12%) and ataxia telangiectasia mutated gene (ATM) mutations (8%); these alterations are potentially targetable with poly(adenosine diphosphate-ribose)polymerase inhibitors. A novel and actionable rearrangement involving the v-raf murine sarcoma viral oncogene homolog B1 gene (BRAF) was also detected. Conclusions This first-in-principle study demonstrates the feasibility of performing in-depth DNA analyses using FFPE tissue and brings new insight toward understanding the genomic landscape within advanced PCa. PMID:22981675

  5. Evaluation of vegetation indices for early assessment of corn status and yield potential in Southeastern U.S.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The use of crop canopy sensors for variable rate nitrogen (VRN) application in corn (Zea mays L.) production across the southeastern U.S. implies assessment of corn N status as early as the V6 growth stage. Our goals were to identify vegetation indices (VIs) that best: (i) correlate with plant statu...

  6. Novel Peptide Marker Corresponding to Salivary Protein gSG6 Potentially Identifies Exposure to Anopheles Bites

    PubMed Central

    Poinsignon, Anne; Cornelie, Sylvie; Mestres-Simon, Montserrat; Lanfrancotti, Alessandra; Rossignol, Marie; Boulanger, Denis; Cisse, Badara; Sokhna, Cheikh; Arcà, Bruno; Simondon, François; Remoue, Franck

    2008-01-01

    Background In order to improve malaria control, and under the aegis of WHO recommendations, many efforts are being devoted to developing new tools for identifying geographic areas with high risk of parasite transmission. Evaluation of the human antibody response to arthropod salivary proteins could be an epidemiological indicator of exposure to vector bites, and therefore to risk of pathogen transmission. In the case of malaria, which is transmitted only by anopheline mosquitoes, maximal specificity could be achieved through identification of immunogenic proteins specific to the Anopheles genus. The objective of the present study was to determine whether the IgG response to the Anopheles gambiae gSG6 protein, from its recombinant form to derived synthetic peptides, could be an immunological marker of exposure specific to Anopheles gambiae bites. Methodology/Principal Findings Specific IgG antibodies to recombinant gSG6 protein were observed in children living in a Senegalese area exposed to malaria. With the objective of optimizing Anopheles specificity and reproducibility, we designed five gSG6-based peptide sequences using a bioinformatic approach, taking into consideration i) their potential antigenic properties and ii) the absence of cross-reactivity with protein sequences of other arthropods/organisms. The specific anti-peptide IgG antibody response was evaluated in exposed children. The five gSG6 peptides showed differing antigenic properties, with gSG6-P1 and gSG6-P2 exhibiting the highest antigenicity. However, a significant increase in the specific IgG response during the rainy season and a positive association between the IgG level and the level of exposure to Anopheles gambiae bites was significant only for gSG6-P1. Conclusions/Significance This step-by-step approach suggests that gSG6-P1 could be an optimal candidate marker for evaluating exposure to Anopheles gambiae bites. This marker could be employed as a geographic indicator, like remote sensing techniques, for mapping the risk of malaria. It could also represent a direct criterion of efficacy in evaluation of vector control strategies. PMID:18575604

  7. Proteomic profiling identifies the inorganic pyrophosphatase (PPA1) protein as a potential biomarker of metastasis in laryngeal squamous cell carcinoma.

    PubMed

    Bodnar, Magdalena; Luczak, Magdalena; Bednarek, Kinga; Szylberg, Lukasz; Marszalek, Andrzej; Grenman, Reidar; Szyfter, Krzysztof; Jarmuz-Szymczak, Malgorzata; Giefing, Maciej

    2016-06-01

    Relapse and metastasis are the main causes of unfavorable outcome in head and neck cancers. Whereas, understanding of the molecular background of these processes is far from being complete. Therefore, in this study we aimed to identify potential biomarker candidates of relapse and metastasis in laryngeal squamous cell carcinoma (LSCC) by combining the 2D electrophoresis based protein screen and immunohistochemical analysis of candidate proteins. We screened three groups of LSCC cell lines derived from primary tumors, recurrent tumors and metastases and identified seven proteins that differed significantly in relative abundance between the analyzed groups. Among the identified proteins were the heat shock proteins HSP60 and HSP70 that were significantly downregulated both in recurrences- and metastases-derived cell lines but not in primary tumor-derived cell lines. Moreover, we identified significant upregulation of the annexin V, calreticulin and the inorganic pyrophosphatase (PPA1) exclusively in the metastases-derived cell lines. As these upregulated proteins could potentially become novel biomarkers of metastasis, we have compared their abundance in primary tumor LSCC N(0) cases, primary tumor LSCC N(+) cases as well as in LSCC metastases N(+). Our results show an intense increase of cytoplasmic PPA1 abundance in the N(+) (p = 0.000042) compared to the N(0) group. In summary, we show a group of proteins deregulated in recurrences and metastases of LSCC. Moreover, we suggest the PPA1 protein as a potential new biomarker for metastasis in this cancer. PMID:26948660

  8. Evoked potentials to auditory probes as indices of cerebral specialization of function--replication and extension.

    PubMed

    Shucard, D W; Cummins, K R; Thomas, D G; Shucard, J L

    1981-11-01

    This study was an attempt to replicate findings from previous work in our laboratory as well as to study the relationship between vertex-referenced and linked mastoid-referenced responses under conditions purported to produce differential hemispheric activation. Auditory evoked potentials were recorded between T4-Cz, T3-Cz, T4-A1A2, and T3-A1A2 to task-irrelevant tone pips superimposed on a baseline condition and on two experimental conditions (verbal and music) hypothesized to differentially activate areas of the left and right cerebral hemispheres. Significant AEP amplitude asymmetries were obtained as a function of the ongoing tasks, replicating our previous findings. Higher amplitude AEPs were recorded from temporal-to-vertex leads from the hemisphere thought to be most involved in the ongoing task. In addition, temporal-linked mastoids placements showed an effect opposite to that seen for the vertex-referenced leads with lower amplitude AEPs occurring from the hemisphere purported to be most activated by the task. Mastoid-referenced placements were also less sensitive to task effects than vertex-referenced placements. PMID:6171402

  9. Complex forest dynamics indicate potential for slowing carbon accumulation in the southeastern United States

    NASA Astrophysics Data System (ADS)

    Coulston, John W.; Wear, David N.; Vose, James M.

    2015-01-01

    Over the past century forest regrowth in Europe and North America expanded forest carbon (C) sinks and offset C emissions but future C accumulation is uncertain. Policy makers need insights into forest C dynamics as they anticipate emissions futures and goals. We used land use and forest inventory data to estimate how forest C dynamics have changed in the southeastern United States and attribute changes to land use, management, and disturbance causes. From 2007-2012, forests yielded a net sink of C because of net land use change (+6.48 Tg C yr-1) and net biomass accumulation (+75.4 Tg C yr-1). Forests disturbed by weather, insect/disease, and fire show dampened yet positive forest C changes (+1.56, +1.4, +5.48 Tg C yr-1, respectively). Forest cutting caused net decreases in C (-76.7 Tg C yr-1) but was offset by forest growth (+143.77 Tg C yr-1). Forest growth rates depend on age or stage of development and projected C stock changes indicate a gradual slowing of carbon accumulation with anticipated forest aging (a reduction of 9.5% over the next five years). Additionally, small shifts in land use transitions consistent with economic futures resulted in a 40.6% decrease in C accumulation.

  10. Stable isotopes and inorganic elements as potential indicators of timber geographic origin

    NASA Astrophysics Data System (ADS)

    Kagawa, A.; Abe, H.; Fujii, T.; Itoh, Y.

    2008-12-01

    Illegal logging is a major cause of worldwide deforestation. For regulation of such illegally harvested timber, we have to develop identification methods of timber geographic origin. In our 5-year project, chemical fingerprinting techniques using stable isotope ratios (δ13C, δ18O, δ15N) and inorganic element concentrations (Al, Ba, Ca, Fe, Mg, Mn, Sr, V, Zn ) have been applied to tropical (Shorea spp.) and temperate (Pinus spp.) timber. Since the tropical timber does not have visible annual rings, we used wood taken from the whole radius for chemical analysis. Among the chemical parameters tested, oxygen and carbon isotope ratios have shown the strongest correlation with the geographic origin (latitude and longitude). By plotting the data on a δ13C-δ18O map, we could separate wood from Borneo and Philippines, which are 1000km apart. However, separation of wood from among different areas in Borneo was not possible. Temperate timber has clealy visible annual rings and development of stable isotope time series is easier. By applying "dendroprovenancing" method (Eckstein et al., 1975) to carbon isotope time series, we could achieve provenancing of timber at higher spatial resolution. Estimated timber origins were 100-300 km away from the actual origins (Kagawa et al. 2009, submitted). Inorganic elements reflected soil type and soil water conditions rather than longitude and latitude of the habitat and were not effective indicators for provenancing wood.

  11. Complex forest dynamics indicate potential for slowing carbon accumulation in the southeastern United States

    PubMed Central

    Coulston, John W.; Wear, David N.; Vose, James M.

    2015-01-01

    Over the past century forest regrowth in Europe and North America expanded forest carbon (C) sinks and offset C emissions but future C accumulation is uncertain. Policy makers need insights into forest C dynamics as they anticipate emissions futures and goals. We used land use and forest inventory data to estimate how forest C dynamics have changed in the southeastern United States and attribute changes to land use, management, and disturbance causes. From 2007-2012, forests yielded a net sink of C because of net land use change (+6.48 Tg C yr−1) and net biomass accumulation (+75.4 Tg C yr−1). Forests disturbed by weather, insect/disease, and fire show dampened yet positive forest C changes (+1.56, +1.4, +5.48 Tg C yr−1, respectively). Forest cutting caused net decreases in C (−76.7 Tg C yr−1) but was offset by forest growth (+143.77 Tg C yr−1). Forest growth rates depend on age or stage of development and projected C stock changes indicate a gradual slowing of carbon accumulation with anticipated forest aging (a reduction of 9.5% over the next five years). Additionally, small shifts in land use transitions consistent with economic futures resulted in a 40.6% decrease in C accumulation. PMID:25614123

  12. Parasites of the grouper fish Epinephelus coioides (Serranidae) as potential environmental indicators in Indonesian coastal ecosystems.

    PubMed

    Kleinertz, S; Palm, H W

    2015-01-01

    A total of 195 Epinephelus coioides (Hamilton, 1822) were studied for fish parasites from Javanese (Segara Anakan lagoon) and Balinese waters. Up to 25 different parasite species belonging to the following taxa: one Ciliata, one Microsporea, five Digenea, one Monogenea, four Cestoda, four Nematoda, one Acanthocephala, one Hirudinea and seven Crustacea were identified with four new host and locality records. The dominant parasites included the monogenean Pseudorhabdosynochus lantauensis (53.3-97.1%), the nematode Spirophilometra endangae (23.3-42.9%), the digenean Didymodiclinus sp. (2.9-40.0%), the nematodes Philometra sp. (22.6-34.3%) and Raphidascaris sp. (2.9-28.6%), and the isopod Alcirona sp. (6.7-31.4%). Regional differences for E. coioides were found in terms of endoparasite diversity, total diversity according to Shannon-Wiener, Simpson index and Evenness. A comparison with published data from Sumatera revealed highest endoparasite diversity (Shannon-Wiener: 1.86/1.67-2.04) and lowest ectoparasite/endoparasite ratio (0.73/0.57-0.88) off the Balinese coast, followed by Lampung Bay, Sumatera (1.84; 0.67), off the coast of Segara Anakan lagoon (1.71; 0.71), and in the lagoon (0.30/0.19-0.66; 0.85/0.67-1.00). The presented data demonstrate the natural range of these parameters and parasite prevalences according to habitat and region, allowing adjustment of the scale that has been used in the visual integration of the parasite parameters into a star graph. The parasite fauna of E. coioides in Segara Anakan lagoon 'improved' from 2004 until 2008/09, possibly related to earlier oil spill events in 2002 and 2004. The use of grouper fish parasites as an early warning system for environmental change in Indonesian coastal ecosystems is discussed. PMID:24018181

  13. Genomic alterations indicate tumor origin and varied metastatic potential of disseminated cells from prostate cancer patients.

    PubMed

    Holcomb, Ilona N; Grove, Douglas I; Kinnunen, Martin; Friedman, Cynthia L; Gallaher, Ian S; Morgan, Todd M; Sather, Cassandra L; Delrow, Jeffrey J; Nelson, Peter S; Lange, Paul H; Ellis, William J; True, Lawrence D; Young, Janet M; Hsu, Li; Trask, Barbara J; Vessella, Robert L

    2008-07-15

    Disseminated epithelial cells can be isolated from the bone marrow of a far greater fraction of prostate-cancer patients than the fraction of patients who progress to metastatic disease. To provide a better understanding of these cells, we have characterized their genomic alterations. We first present an array comparative genomic hybridization method capable of detecting genomic changes in the small number of disseminated cells (10-20) that can typically be obtained from bone marrow aspirates of prostate-cancer patients. We show multiple regions of copy-number change, including alterations common in prostate cancer, such as 8p loss, 8q gain, and gain encompassing the androgen-receptor gene on Xq, in the disseminated cell pools from 11 metastatic patients. We found fewer and less striking genomic alterations in the 48 pools of disseminated cells from patients with organ-confined disease. However, we identify changes shared by these samples with their corresponding primary tumors and prostate-cancer alterations reported in the literature, evidence that these cells, like those in advanced disease, are disseminated tumor cells (DTC). We also show that DTCs from patients with advanced and localized disease share several abnormalities, including losses containing cell-adhesion genes and alterations reported to associate with progressive disease. These shared alterations might confer the capability to disseminate or establish secondary disease. Overall, the spectrum of genomic deviations is evidence for metastatic capacity in advanced-disease DTCs and for variation in that capacity in DTCs from localized disease. Our analysis lays the foundation for elucidation of the relationship between DTC genomic alterations and progressive prostate cancer. PMID:18632612

  14. Predatory online behavior: modus operandi of convicted sex offenders in identifying potential victims and contacting minors over the internet.

    PubMed

    Malesky, L Alvin

    2007-01-01

    Sex offenders have used the Internet to identify and contact minors for sexual exploitation (Armagh, 1998; Hernandez, 2000; Lamb, 1998; Lanning, 1998). Yet little is known about how these individuals select their online victims. In order to gain a better understanding of this behavior, the online activity of 31 men who perpetrated or attempted to perpetrate contact sex offenses against minors they communicated with via the Internet, was examined. Three-fourths of the participants monitored chat room dialogue and almost one-half reviewed online profiles of minors in an attempt to identify potential victims. Recommendations to increase the online safety of children and adolescents are discussed. PMID:17895230

  15. Mycobacterium bovis DNA Detection in Colostrum as a Potential Indicator of Vaccination Effectiveness against Bovine Tuberculosis

    PubMed Central

    Herrera-Rodríguez, Sara E.; Gordiano-Hidalgo, María Alejandra; López-Rincón, Gonzálo; Bojorquez-Narváez, Luis; Padilla-Ramírez, Francisco Javier; Pereira-Suárez, Ana Laura; Flores-Valdez, Mario Alberto

    2013-01-01

    Bovine tuberculosis (bTB) remains a problem on many dairy farms in Mexico, as well as a public health risk. We previously found a high frequency of Mycobacterium bovis DNA in colostrum from dairy cows using a nested PCR to detect mpb70. Since there are no reliable in vivo tests to determine the effectiveness of booster Mycobacterium bovis BCG vaccination against bTB, in this work we monitored M. bovis DNA in colostrum by using this nested PCR. In order to decrease the risk of adverse reactions in animals likely containing viable M. bovis, a single application of BCG and a subunit vaccine (EEP-1) formulated with M. bovis culture filtrate proteins (CFP) and a copolymer as the adjuvant was performed in tuberculin skin test-negative cattle (TST−), while TST reactor animals (TST+) received EEP-1 only. Booster immunization using EEP-1 was applied to both groups, 2 months after primary vaccination to whole herds and 12 months later to lactating cows. Colostrum samples were collected from 6 farms where the cows were vaccinated over a 12-month period postvaccination and, for comparison, from one control farm where the cows were not vaccinated with comparable bTB prevalence. We observed an inverse relationship between the frequency of M. bovis DNA detection and time postvaccination at the first (P < 0.001) and second (P < 0.0001) 6-month periods. Additionally, the concentration of gamma interferon (IFN-γ) was higher in mpb70 PCR-positive colostrum samples (P = 0.0003). These results suggest that M. bovis DNA frequency in colostrum could be a potentially useful biomarker for bTB vaccine efficacy on commercial dairy farms. PMID:23425597

  16. Estrogen receptor β promoter methylation: a potential indicator of malignant changes in breast cancer

    PubMed Central

    Gao, Lei; Qi, Xiaolong; Hu, Kaiwen; Zhu, Ruili; Xu, Wei; Sun, Shipeng; Zhang, Lixin; Yang, Ximing; Hua, Baojin

    2016-01-01

    Introduction Estrogen receptor β (ERβ) always lacks expression in estrogen-dependent tumors, which may result from gene inactivation by methylation. In this study, we aimed to determine whether aberrant methylation of the ERβ promoter is associated with decreased ERβ gene expression in breast cancer. Material and methods ERβ methylation status was determined for 132 pairs of breast cancer and adjacent normal tissues via the MethyLight method. Additionally, mRNA relative expression was quantified by real-time polymerase chain reaction (RT-PCR) to determine whether aberrant methylation had a negative correlation with expression. The correlation of ERβ promoter methylation and clinical parameters is also discussed. Results Methylation was observed in 96 (72.7%) breast cancer samples, and the median percentage of fully methylated reference (PMR) among methylated tissues was 0.83. Meanwhile, 94 (71.2%) adjacent normal tissues were methylated and the median PMR was 0.48. Compared to adjacent normal tissues, the methylation level of breast cancer was significantly higher (p < 0.001) and mRNA expression was much lower (p < 0.001). There was a significant correlation between ERβ methylation and mRNA expression in adjacent normal breast tissues (p = 0.004). In addition, the methylation rate of cancer tissues whose maximum diameter < 3 cm was significantly higher than those > 3 cm (p = 0.025). Conclusions ERβ promoter methylation level varies between cancerous and adjacent normal breast tissues. There was significant downregulation of ERβ methylation expression in pre-cancerous stages of breast cancer. Therefore, demethylation drugs may offer a potential strategy for preventing the development of pre-cancerous cells. PMID:26925128

  17. Epidemiological pattern of tattoo skin disease: a potential general health indicator for cetaceans.

    PubMed

    Van Bressem, Marie-Françoise; Van Waerebeek, Koen; Aznar, Francisco Javier; Raga, Juan Antonio; Jepson, Paul D; Duignan, Pádraig; Deaville, Rob; Flach, Leonardo; Viddi, Francisco; Baker, John R; Di Beneditto, Ana Paula; Echegaray, Mónica; Genovo, Tilen; Reyes, Julio; Felix, Fernando; Gaspar, Raquel; Ramos, Renata; Peddemors, Vic; Sanino, Gian Paolo; Siebert, Ursula

    2009-07-23

    The presence of tattoo skin disease (TSD) was examined in 1392 free-ranging and dead odontocetes comprising 17 species from the Americas, Europe, South Africa, New Zealand and Greenland. We investigated whether TSD prevalence varied with sex, age and health status. TSD was encountered in cetaceans from the Pacific and Atlantic Oceans as well as in those from the North, Mediterranean and Tasman Seas. No clear patterns related to geography and host phylogeny were detected, except that prevalence of TSD in juveniles and, in 2 species (dusky dolphin Lagenorhynchus obscurus and Burmeister's porpoise Phocoena spinipinnis), in adults was remarkably high in samples from Peru. Environmental factors and virus properties may be responsible for this finding. Sex did not significantly influence TSD prevalence except in the case of Peruvian P. spinipinnis. Generally, there was a pattern of TSD increase in juveniles compared to calves, attributed to the loss of maternal immunity. Also, in most samples, juveniles seemed to have a higher probability of suffering TSD than adults, presumably because more adults had acquired active immunity following infection. This holo-endemic pattern was inverted in poor health short-beaked common dolphins Delphinus delphis and harbour porpoises Phocoena phocoena from the British Isles, and in Chilean dolphins Cephalorhynchus eutropia from Patagonia, where adults showed a higher TSD prevalence than juveniles. Very large tattoos were seen in some adult odontocetes from the SE Pacific, NE Atlantic and Portugal's Sado Estuary, which suggest impaired immune response. The epidemiological pattern of TSD may be an indicator of cetacean population health. PMID:19750811

  18. Tyrosine kinase inhibitors: their on-target toxicities as potential indicators of efficacy.

    PubMed

    Shah, Devron R; Shah, Rashmi R; Morganroth, Joel

    2013-06-01

    Tyrosine kinase inhibitors (TKIs) have revolutionized the treatment of certain forms of cancers, raising hopes for many patients with otherwise unresponsive tumours. While these agents are generally well tolerated, clinical experience with them has highlighted their unexpected association with serious toxic effects on various organs such as the heart, lungs, liver, kidneys, thyroid, skin, blood coagulation, gastrointestinal tract and nervous system. Many of these toxic effects result from downstream inhibition of vascular endothelial growth factor or epidermal growth factor signalling in cells of normal organs. Many of these undesirable effects such as hypertension, hypothyroidism, skin reactions and possibly proteinuria are on-target effects. Since tyrosine kinases are widely distributed with specific functional roles in different organs, this association is not too surprising. Various studies suggest that the development of these on-target effects indicates clinically desirable and effective inhibition of the corresponding ligand-mediated receptor linked with oncogenesis. This is reflected as improved efficacy in the subgroup of patients who develop these on-target adverse effects compared with those who do not. Inevitably, issues arise with respect to the regulatory assessment of efficacy and risk/benefit of the TKIs as well as the clinical approach to managing patients who develop these effects. Routine subgroup analysis of efficacy data from clinical trials (patients with and without on-target toxicity) may enable more effective clinical use of TKIs since (i) discontinuing or reducing the dose of the TKI has a negative impact if the tumour is TKI-responsive; and (ii) it is usually possible to manage these undesirable on-target effects with conventional clinical approaches. Prospective studies are needed to investigate this proposition further. PMID:23620170

  19. Predictive Potential of Heart Rate Complexity Measurement: An Indication for Laparotomy Following Solid Organ Injury

    PubMed Central

    Foroutan, Ali; Paydar, Shahram; Heydari, Seyed Taghi; Erjaee, Gholamhussian; Bagheri Lankarani, Kamran; Nowroozi, Abbas; Moslemi, Sam

    2015-01-01

    Background: Nonlinear analysis of heart rate variability (HRV) has been recently used as a predictor of prognosis in trauma patients. Objectives: We applied nonlinear analysis of HRV in patients with blunt trauma and intraperitoneal bleeding to assess our ability to predict the outcome of conservative management. Patients and Methods: An analysis of electrocardiography (ECG) from 120 patients with blunt trauma was conducted at the onset of admission to the emergency department. ECGs of 65 patients were excluded due to inadequacy of noise-free length. Of the remaining 55 patients, 47 survived (S group) and eight patients died in the hospital (Non-S group). Nineteen patients were found to have intra-abdominal bleeding, eight of which ultimately underwent laparotomy to control bleeding (Op group) and 11 underwent successful non-operative management (non-Op). Demographic data including vital signs, glasgow coma scale (GCS), arterial blood gas and injury severity scores (ISS) were recorded. Heart rate complexity (HRC) methods, including entropy, were used to analyze the ECG. Results: There were no differences in age, gender, heart rate (HR) and blood pressure between the S and Non-S groups. However, approximate entropy, used as a method of HRC measurement, and GCS were significantly higher in S group, compared to the Non-S group. The base deficit and ISS were significantly higher in the Non-S group. Regarding age, sex, ISS, base deficit, vital signs and GCS, no difference was found between Op and Non-Op groups. Approximate entropy was significantly lower in the Op group, compared to the Non-Op group. Conclusions: The loss of HRC at the onset of admission may predict mortality in patients with blunt trauma. Lower entropy, in recently admitted patients with intra-abdominal bleeding, may indicate laparotomy when the vital signs are stable. PMID:26839850

  20. Plant DNA: A new substrate for carbon stable isotope analysis and a potential paleoenvironmental indicator

    NASA Astrophysics Data System (ADS)

    Jahren, H.; Petersen, G.; Seberg, O.

    2003-12-01

    The δ 13C value of fossil plant materials can be used to gain insight into the dominant photosynthetic pathway, as well as other environmental attributes, of ancient plant ecosystems. Nucleotide sequences from land-plant nucleic acids extracted from 400 ka sediments have been recognized as the oldest authenticated fossil DNA, making the inference of plant taxonomy possible in substrates devoid of plant macro- and microfossils. If the C isotope relationship between bulk plant tissue and associated plant nucleic acids were known, fossil plant nucleic acids could be analyzed for δ 13C values and used as land-plant isotopic substrates within mixed organic material. Toward this end, we present δ 13C analyses of nucleic acids isolated from 12 higher-plant species that span the full phylogenetic diversity of seed plants. Extracted nucleic acids were dominated by double-stranded DNA containing fragments of rbcL gene ˜ 350 base pairs in length. The C isotope compositions of plant nucleic acids were found to be enriched in 13C relative to bulk plant tissue by a constant value (1.39 ‰ ). This study represents the first comparison of the δ 13C value of nucleic acids to the δ 13C value of bulk tissue for multicellular organisms; our results contrasted with the minimal fractionations reported for microorganisms. Because the isotopic enrichment δ 13C is constant across tracheophytes, the δ 13C value of fossil plant DNA can be used as a paleoenvironmental indicator, eliminating the need for morphological recognition of fossil plant material in paleoenvironmental studies.

  1. Distribution and Potential Indicators of Hospitalized Cases of Neurocysticercosis and Epilepsy in Ecuador from 1996 to 2008

    PubMed Central

    Gabriël, Sarah; Benitez-Ortiz, Washington; Saegerman, Claude; Dorny, Pierre; Berkvens, Dirk; Abatih, Emmanuel Nji

    2015-01-01

    Background Epilepsy is one of the most common signs of Neurocysticercosis (NCC). In this study, spatial and temporal variations in the incidence of hospitalized cases (IHC) of epilepsy and NCC in Ecuadorian municipalities were analyzed. Additionally, potential socio-economic and landscape indicators were evaluated in order to understand in part the macro-epidemiology of the Taenia solium taeniasis/cysticercosis complex. Methodology Data on the number of hospitalized epilepsy and NCC cases by municipality of residence were obtained from morbidity-hospital systems in Ecuador. SatScan software was used to determine whether variations in the IHC of epilepsy and NCC in space and time. In addition, several socio-economic and landscape variables at municipality level were used to study factors intervening in the macro-epidemiology of these diseases. Negative Binomial regression models through stepwise selection and Bayesian Model Averaging (BMA) were used to explain the variations in the IHC of epilepsy and NCC. Principal findings Different clusters were identified through space and time. Traditional endemic zones for NCC and epilepsy, recognized in other studies were confirmed in our study. However, for both disorders more recent clusters were identified. Among municipalities, an increasing tendency for IHC of epilepsy, and a decreasing tendency for the IHC of NCC were observed over time. In contrast, within municipalities a positive linear relationship between both disorders was found. An increase in the implementation of systems for eliminating excrements would help to reduce the IHC of epilepsy by 1.00% (IC95%; 0.2%–1.8%) and by 5.12% (IC95%; 3.63%-6.59%) for the IHC of NCC. The presence of pig production was related to IHC of NCC. Conclusion/Significance Both disorders were related to the lack of an efficient system for eliminating excrements. Given the appearance of recent epilepsy clusters, these locations should be studied in depth to discriminate epilepsies due to NCC from epilepsies due to other causes. Field studies are needed to evaluate the true prevalence of cysticercosis in humans and pigs in different zones of the country in order to better implement and manage prevention and/or control campaigns. PMID:26580210

  2. Incidents of potential public health significance identified using national surveillance of US poison center data (2008–2012)

    PubMed Central

    LAW, R. K.; SHEIKH, S.; BRONSTEIN, A.; THOMAS, R.; SPILLER, H. A.; SCHIER, J. G.

    2015-01-01

    Background The Centers for Disease Control and Prevention (CDC) and the American Association of Poison Control Centers conduct national surveillance on data collected by US poison centers to identify incidents of potential public health significance (IPHS). The overarching goals of this collaboration are to improve CDC’s national surveillance capacity for public health threats, identify early markers of public health incidents and enhance situational awareness. The National Poison Data System (NPDS) is used as a surveillance system to automatically identify data anomalies. Purpose To characterize data anomalies and IPHS captured by national surveillance of poison center data over 5 years. Methods Data anomalies are identified through three surveillance methodologies: call-volume, clinical effect, and case-based. Anomalies are reviewed by a team of epidemiologists and clinical toxicologists to determine IPHS using standardized criteria. The authors reviewed IPHS identified by these surveillance activities from 2008 through 2012. Results Call-volume surveillance identified 384 IPHS; most were related to gas and fume exposures (n=229; 59.6%) with the most commonly implicated substance being carbon monoxide (CO) (n=92; 22.8%). Clinical-effect surveillance identified 138 IPHS; the majority were related to gas and fume exposures (n=58; 42.0%) and gastrointestinal complaints (n=84; 16.2%), and the most commonly implicated substance was CO (n=20; 14.4%). Among the 11 case-based surveillance definitions, the botulism case definition yielded the highest percentage of identified agent-specific illness. Conclusions A small proportion of data anomalies were designated as IPHS. Of these, CO releases were the most frequently reported IPHS and gastrointestinal syndromes were the most commonly reported illness manifestations. poison center data surveillance may be used as an approach to identify exposures, illnesses, and incidents of importance at the national and state level. PMID:25175899

  3. Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

    PubMed Central

    Halappanavar, Sabina

    2015-01-01

    Summary Background: The presence of diverse types of nanomaterials (NMs) in commerce is growing at an exponential pace. As a result, human exposure to these materials in the environment is inevitable, necessitating the need for rapid and reliable toxicity testing methods to accurately assess the potential hazards associated with NMs. In this study, we applied biclustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related biclusters of genes showing similar expression profiles were identified. The identified biclusters were then used to conduct a gene set enrichment analysis on pulmonary gene expression profiles derived from mice exposed to nano-titanium dioxide (nano-TiO2), carbon black (CB) or carbon nanotubes (CNTs) to determine the disease significance of these data-driven gene sets. Results: Biclusters representing inflammation (chemokine activity), DNA binding, cell cycle, apoptosis, reactive oxygen species (ROS) and fibrosis processes were identified. All of the NM studies were significant with respect to the bicluster related to chemokine activity (DAVID; FDR p-value = 0.032). The bicluster related to pulmonary fibrosis was enriched in studies where toxicity induced by CNT and CB studies was investigated, suggesting the potential for these materials to induce lung fibrosis. The pro-fibrogenic potential of CNTs is well established. Although CB has not been shown to induce fibrosis, it induces stronger inflammatory, oxidative stress and DNA damage responses than nano-TiO2 particles. Conclusion: The results of the analysis correctly identified all NMs to be inflammogenic and only CB and CNTs as potentially fibrogenic. In addition to identifying several previously defined, functionally relevant gene sets, the present study also identified two novel genes sets: a gene set associated with pulmonary fibrosis and a gene set associated with ROS, underlining the advantage of using a data-driven approach to identify novel, functionally related gene sets. The results can be used in future gene set enrichment analysis studies involving NMs or as features for clustering and classifying NMs of diverse properties. PMID:26885455

  4. Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas.

    PubMed

    King, R A; Symondson, W O C; Thomas, R J

    2015-06-01

    Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats. PMID:25572526

  5. Integrated Molecular Profiling of Human Gastric Cancer Identifies DDR2 as a Potential Regulator of Peritoneal Dissemination.

    PubMed

    Kurashige, Junji; Hasegawa, Takanori; Niida, Atsushi; Sugimachi, Keishi; Deng, Niantao; Mima, Kosuke; Uchi, Ryutaro; Sawada, Genta; Takahashi, Yusuke; Eguchi, Hidetoshi; Inomata, Masashi; Kitano, Seigo; Fukagawa, Takeo; Sasako, Mitsuru; Sasaki, Hiroki; Sasaki, Shin; Mori, Masaki; Yanagihara, Kazuyoshi; Baba, Hideo; Miyano, Satoru; Tan, Patrick; Mimori, Koshi

    2016-01-01

    Peritoneal dissemination is the most frequent, incurable metastasis occurring in patients with advanced gastric cancer (GC). However, molecular mechanisms driving peritoneal dissemination still remain poorly understood. Here, we aimed to provide novel insights into the molecular mechanisms that drive the peritoneal dissemination of GC. We performed combined expression analysis with in vivo-selected metastatic cell lines and samples from 200 GC patients to identify driver genes of peritoneal dissemination. The driver-gene functions associated with GC dissemination were examined using a mouse xenograft model. We identified a peritoneal dissemination-associated expression signature, whose profile correlated with those of genes related to development, focal adhesion, and the extracellular matrix. Among the genes comprising the expression signature, we identified that discoidin-domain receptor 2 (DDR2) as a potential regulator of peritoneal dissemination. The DDR2 was upregulated by the loss of DNA methylation and that DDR2 knockdown reduced peritoneal metastasis in a xenograft model. Dasatinib, an inhibitor of the DDR2 signaling pathway, effectively suppressed peritoneal dissemination. DDR2 was identified as a driver gene for GC dissemination from the combined expression signature and can potentially serve as a novel therapeutic target for inhibiting GC peritoneal dissemination. PMID:26934957

  6. Integrated Molecular Profiling of Human Gastric Cancer Identifies DDR2 as a Potential Regulator of Peritoneal Dissemination

    PubMed Central

    Kurashige, Junji; Hasegawa, Takanori; Niida, Atsushi; Sugimachi, Keishi; Deng, Niantao; Mima, Kosuke; Uchi, Ryutaro; Sawada, Genta; Takahashi, Yusuke; Eguchi, Hidetoshi; Inomata, Masashi; Kitano, Seigo; Fukagawa, Takeo; Sasako, Mitsuru; Sasaki, Hiroki; Sasaki, Shin; Mori, Masaki; Yanagihara, Kazuyoshi; Baba, Hideo; Miyano, Satoru; Tan, Patrick; Mimori, Koshi

    2016-01-01

    Peritoneal dissemination is the most frequent, incurable metastasis occurring in patients with advanced gastric cancer (GC). However, molecular mechanisms driving peritoneal dissemination still remain poorly understood. Here, we aimed to provide novel insights into the molecular mechanisms that drive the peritoneal dissemination of GC. We performed combined expression analysis with in vivo-selected metastatic cell lines and samples from 200 GC patients to identify driver genes of peritoneal dissemination. The driver-gene functions associated with GC dissemination were examined using a mouse xenograft model. We identified a peritoneal dissemination-associated expression signature, whose profile correlated with those of genes related to development, focal adhesion, and the extracellular matrix. Among the genes comprising the expression signature, we identified that discoidin-domain receptor 2 (DDR2) as a potential regulator of peritoneal dissemination. The DDR2 was upregulated by the loss of DNA methylation and that DDR2 knockdown reduced peritoneal metastasis in a xenograft model. Dasatinib, an inhibitor of the DDR2 signaling pathway, effectively suppressed peritoneal dissemination. DDR2 was identified as a driver gene for GC dissemination from the combined expression signature and can potentially serve as a novel therapeutic target for inhibiting GC peritoneal dissemination. PMID:26934957

  7. Application of remote sensing and GIS analysis for identifying groundwater potential zone in parts of Kodaikanal Taluk, South India

    NASA Astrophysics Data System (ADS)

    Bagyaraj, Murugesan; Ramkumar, Thirunavukkarasu; Venkatramanan, Senapathi; Gurugnanam, Balasubramanian

    2013-03-01

    Groundwater potential zones were demarcated with the help of remote sensing and Geographic Information System (GIS) techniques. The study area is composed rocks of Archaean age and charnockite dominated over others. The parameters considered for identifying the groundwater potential zone of geology slope, drainage density, geomorphic units and lineament density were generated using the resource sat (IRS P6 LISS IV MX) data and survey of India (SOI) toposheets of scale 1:50000 and integrated them with an inverse distance weighted (IDW) model based on GIS data to identify the groundwater potential of the study area. Suitable weightage factors were assigned for each category of these parameters. For the various geomorphic units, weightage factors were assigned based on their capability to store ground-water. This procedure was repeated for all the other layers and resultant layers were reclassified. The reclassified layers were then combined to demarcate zones as very good, good, moderate, low, and poor. This groundwater potentiality information could be used for effective identification of suitable locations for extraction of potable water for rural populations.

  8. Can inbound and domestic medical tourism improve your bottom line? Identifying the potential of a U.S. tourism market.

    PubMed

    Fottler, Myron D; Malvey, Donna; Asi, Yara; Kirchner, Sarah; Warren, Natalia A

    2014-01-01

    In large part due to current economic conditions and the political uncertainties of healthcare reform legislation, hospitals need to identify new sources of revenue. Two potentially untapped sources are inbound (international) and domestic (within the United States) medical tourists. This case study uses data from a large, urban healthcare system in the southeastern United States to quantify its potential market opportunities for medical tourism. The data were mined from electronic health records, and descriptive frequency analysis was used to provide a preliminary market assessment. This approach permits healthcare systems to move beyond anecdotal information and assess the relative market potential of their particular geographic area and the diagnostic services they offer for attracting inbound and domestic medical tourists. Implications for healthcare executives and guidance on how they can focus marketing efforts are discussed. PMID:24611426

  9. Clonal analyses and gene profiling identify genetic biomarkers of the thermogenic potential of human brown and white preadipocytes.

    PubMed

    Xue, Ruidan; Lynes, Matthew D; Dreyfuss, Jonathan M; Shamsi, Farnaz; Schulz, Tim J; Zhang, Hongbin; Huang, Tian Lian; Townsend, Kristy L; Li, Yiming; Takahashi, Hirokazu; Weiner, Lauren S; White, Andrew P; Lynes, Maureen S; Rubin, Lee L; Goodyear, Laurie J; Cypess, Aaron M; Tseng, Yu-Hua

    2015-07-01

    Targeting brown adipose tissue (BAT) content or activity has therapeutic potential for treating obesity and the metabolic syndrome by increasing energy expenditure. However, both inter- and intra-individual differences contribute to heterogeneity in human BAT and potentially to differential thermogenic capacity in human populations. Here we generated clones of brown and white preadipocytes from human neck fat and characterized their adipogenic and thermogenic differentiation. We combined an uncoupling protein 1 (UCP1) reporter system and expression profiling to define novel sets of gene signatures in human preadipocytes that could predict the thermogenic potential of the cells once they were maturated. Knocking out the positive UCP1 regulators, PREX1 and EDNRB, in brown preadipocytes using CRISPR-Cas9 markedly abolished the high level of UCP1 in brown adipocytes differentiated from the preadipocytes. Finally, we were able to prospectively isolate adipose progenitors with great thermogenic potential using the cell surface marker CD29. These data provide new insights into the cellular heterogeneity in human fat and offer potential biomarkers for identifying thermogenically competent preadipocytes. PMID:26076036

  10. Potentials for Indication of Potentially Harmful Toxic Algal Blooms Using PROBA1-CHRIS Hyperspectral Imagery- A Case Study in Burkina Faso

    NASA Astrophysics Data System (ADS)

    Beiermann, Timo

    2010-12-01

    Toxic algal blooms are an issue affecting water quality and can cause harmful health impacts. The aim of the conducted case study is to assess such blooms by chlorophyll a and phycocyanin detection as indicators of the occurrence. Using demonstrated single reflectance ratio algorithms published as in [7] and processed with provided tools for hyperspectral Proba1-CHRIS imagery in a study site including Loumbila reservoir near Ouagadougou, capital of Burkina Faso to investigate potentials of this approach.

  11. Identifying outcome-based indicators and developing a curriculum for a continuing medical education programme on rational prescribing using a modified Delphi process

    PubMed Central

    Esmaily, Hamideh M; Savage, Carl; Vahidi, Rezagoli; Amini, Abolghasem; Zarrintan, Mohammad Hossein; Wahlstrom, Rolf

    2008-01-01

    Background Continuing medical education (CME) is compulsory for physicians in Iran. Recent studies in Iran show that modifications of CME elements are necessary to improve the effectiveness of the educational programmes. Other studies point to an inappropriate, even irrational drug prescribing. Based on a needs assessment study regarding CME for general physicians in the East Azerbaijan province in Iran, rational prescribing practice was recognized as a high priority issue. Considering different educational methods, outcome-based education has been proposed as a suitable approach for CME. The purpose of the study was to obtain experts' consensus about appropriate educational outcomes of rational prescribing for general physicians in CME and developing curricular contents for this education. Methods The study consisted of two phases: The first phase was conducted using a two-round Delphi consensus process to identify the outcome-based educational indicators regarding rational prescribing for general physicians in primary care (GPs). In the second phase the agreed indicators were submitted to panels of experts for assessment and determination of content for a CME program in the field. Results Twenty one learning outcomes were identified through a modified Delphi process. The indicators were used by the panels of experts and six educational topics were determined for the CME programme and the curricular content of each was defined. The topics were 1) Principles of prescription writing, 2) Adverse drug reactions, 3) Drug interactions, 4) Injections, 5) Antibiotic therapy, and 6) Anti-inflammatory agents therapy. One of the topics was not directly related to any outcome, raising a question about the need for a discussion on constructive alignment. Conclusions Consensus on learning outcomes was achieved and an educational guideline was designed. Before suggesting widespread use in the country the educational package should be tested in the CME context. PMID:18510774

  12. Applying indicator-based geostatistical approaches to determine potential zones of groundwater recharge based on borehole data

    NASA Astrophysics Data System (ADS)

    Jang, C.-S.; Chen, S.-K.

    2012-04-01

    Evaluating a potential zone of groundwater recharge is considerably critical for planning a scheme of quality protection and quantity management of groundwater. This study determined potential zones of groundwater recharge using indicator kriging (IK) based on borehole data in the Pingtung Plain, southern Taiwan. Subsoil data were first classified into four categories - gravel (very high subsoil infiltration), coarse sand to medium sand (high subsoil infiltration), fine sand to very fine sand (low subsoil infiltration), and silt, mud, and clay (very low subsoil infiltration). IK was used to characterize the classifications of subsoil infiltration by selecting a maximum estimation probability. Then, very high and high soil permeability contents in unsaturated aquifers, which represent the capacity of unsaturated aquifer percolation, were estimated spatially and probabilistically using IK. Finally, combinations under different conditions of subsoil infiltration and unsaturated aquifer percolation were recommended to delineate potential zones of groundwater recharge. Owing to limited observed data, estimated probabilities of subsoil infiltration and unsaturated aquifer percolation obtained from IK can explore the uncertainty of estimated parameters. The analyzed results reveal that IK has good functionality for determining potential zones of groundwater recharge. The northeastern and southeastern regions are main groundwater recharge zones, approximately 19.6% of total area. Artificial ponds or wetlands can be established in the suggested zones to enhance groundwater recharge. Keywords: Groundwater recharge; Indicator kriging; Subsoil infiltration; Soil percolation; Uncertainty; Probability

  13. Identifying Factors for Optimal Development of Health-Related Websites: A Delphi Study Among Experts and Potential Future Users

    PubMed Central

    van Osch, Liesbeth; de Vries, Hein

    2012-01-01

    Background The Internet has become a popular medium for offering tailored and targeted health promotion programs to the general public. However, suboptimal levels of program use in the target population limit the public health impact of these programs. Optimizing program development is considered as one of the main processes to increase usage rates. Objective To distinguish factors potentially related to optimal development of health-related websites by involving both experts and potential users. By considering and incorporating the opinions of experts and potential users in the development process, involvement in the program is expected to increase, consequently resulting in increased appreciation, lower levels of attrition, and higher levels of sustained use. Methods We conducted a systematic three-round Delphi study through the Internet. Both national and international experts (from the fields of health promotion, health psychology, e-communication, and technical Web design) and potential users were invited via email to participate. During this study an extensive list of factors potentially related to optimal development of health-related websites was identified, by focusing on factors related to layout, general and risk information provision, questionnaire use, additional services, and ease of use. Furthermore, we assessed the extent to which experts and potential users agreed on the importance of these factors. Differences as well as similarities among experts and potentials users were deduced. Results In total, 20 of 62 contacted experts participated in the first round (32% response rate); 60 of 200 contacted experts (30% response rate) and 210 potential users (95% response rate) completed the second-round questionnaire, and 32 of 60 contacted experts completed the third round (53% response rate). Results revealed important factors consented upon by experts and potential users (eg, ease of use, clear structure, and detailed health information provision), as well as differences regarding important factors consented upon by experts (eg, visual aids, self-monitoring tool, and iterative health feedback) or by potential users only (eg, bread crumb navigation and prevention of receiving spam). Conclusions This study is an important first step in determining the agreed-upon factors that should be taken into account when developing online health promotion programs. The public health impact of these programs will be improved by optimizing the development process in line with these factors. PMID:22357411

  14. Secretome analysis identifies potential virulence factors of Diplodia corticola, a fungal pathogen involved in cork oak (Quercus suber) decline.

    PubMed

    Fernandes, Isabel; Alves, Artur; Correia, António; Devreese, Bart; Esteves, Ana Cristina

    2014-01-01

    The characterisation of the secretome of phytopathogenic fungi may contribute to elucidate the molecular mechanisms of pathogenesis. This is particularly relevant for Diplodia corticola, a fungal plant pathogen belonging to the family Botryosphaeriaceae, whose genome remains unsequenced. This phytopathogenic fungus is recognised as one of the most important pathogens of cork oak, being related to the decline of cork oak forests in the Iberian Peninsula. Unfortunately, secretome analysis of filamentous fungi is limited by the low protein concentration and by the presence of many interfering substances, such as polysaccharides, which affect the separation and analysis by 1D and 2D gel electrophoresis. We compared six protein extraction protocols concerning their suitability for further application with proteomic workflows. The protocols involving protein precipitation were the most efficient, with emphasis on TCA-acetone protocol, allowing us to identify the most abundant proteins on the secretome of this plant pathogen. Approximately 60% of the spots detected were identified, all corresponding to extracellular proteins. Most proteins identified were carbohydrate degrading enzymes and proteases that may be related to D. corticola pathogenicity. Although the secretome was assessed in a noninfection environment, potential virulence factors such as the putative glucan-β-glucosidase, neuraminidase, and the putative ferulic acid esterase were identified. The data obtained forms a useful basis for a deeper understanding of the pathogenicity and infection biology of D. corticola. Moreover, it will contribute to the development of proteomics studies on other members of the Botryosphaeriaceae. PMID:24863480

  15. Exome Sequencing Identifies DLG1 as a Novel Gene for Potential Susceptibility to Crohn's Disease in a Chinese Family Study

    PubMed Central

    Song, Lu; NG, Siew Chien; Wang, Xiaobing; Chen, Liping; Yi, Fengming; Ran, Zhihua; Zhou, Rui; Xia, Bing

    2014-01-01

    Background Genetic variants make some contributions to inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC). More than 100 susceptibility loci were identified in Western IBD studies, but susceptibility gene has not been found in Chinese IBD patients till now. Sequencing of individuals with an IBD family history is a powerful approach toward our understanding of the genetics and pathogenesis of IBD. The aim of this study, which focuses on a Han Chinese CD family, is to identify high-risk variants and potentially novel loci using whole exome sequencing technique. Methods Exome sequence data from 4 individuals belonging to a same family were analyzed using bioinformatics methods to narrow down the variants associated with CD. The potential risk genes were further analyzed by genotyping and Sanger sequencing in family members, additional 401 healthy controls (HC), 278 sporadic CD patients, 123 UC cases, a pair of monozygotic CD twins and another Chinese CD family. Results From the CD family in which the father and daughter were affected, we identified a novel single nucleotide variant (SNV) c.374T>C (p.I125T) in exon 4 of discs large homolog 1 (DLG1), a gene has been reported to play mutiple roles in cell proliferation, T cell polarity and T cell receptor signaling. After genotyping among case and controls, a PLINK analysis showed the variant was of significance (P<0.05). 4 CD patients of the other Chinese family bore another non-synonymous variant c.833G>A (p.R278Q) in exon 9 of DLG1. Conclusions We have discovered novel genetic variants in the coding regions of DLG1 gene, the results support that DLG1 is a novel potential susceptibility gene for CD in Chinese patients. PMID:24937328

  16. The iPLA(2)γ is identified as the membrane potential sensitive phospholipase in liver mitochondria.

    PubMed

    Rauckhorst, Adam J; Pfeiffer, Douglas R; Broekemeier, Kimberly M

    2015-08-19

    Previous reports from our lab identified a mitochondrial calcium-independent phospholipase A2 activity that is activated when the mitochondrial membrane potential is decreased. This activity was demonstrated to influence occurrence of the permeability transition. Originally, this activity was ascribed to the iPLA2β protein. Recently, both iPLA2β and iPLA2γ knock out mice have been generated. It has been shown by others that the iPLA2γ plays a significant role in progression of the permeability transition. In this paper, using the iPLA2β and iPLA2γ knock out mice we show that the membrane potential sensitive activity is the iPLA2γ. PMID:26206229

  17. Machine-learning-based selective sampling procedure for identifying the low-energy region in a potential energy surface: A case study on proton conduction in oxides

    NASA Astrophysics Data System (ADS)

    Toyoura, Kazuaki; Hirano, Daisuke; Seko, Atsuto; Shiga, Motoki; Kuwabara, Akihide; Karasuyama, Masayuki; Shitara, Kazuki; Takeuchi, Ichiro

    2016-02-01

    In this paper, we propose a selective sampling procedure to preferentially evaluate a potential energy surface (PES) in a part of the configuration space governing a physical property of interest. The proposed sampling procedure is based on a machine-learning method called the Gaussian process, which is used to construct a statistical model of the PES for identifying the region of interest in the configuration space. We demonstrate the efficacy of the proposed procedure for atomic diffusion and ionic conduction, specifically, the proton conduction in a well-studied proton-conducting oxide, barium zirconate (BaZrO3) . The results of the demonstration study indicate that our procedure can efficiently identify the low-energy region characterizing the proton conduction in the host crystal lattice and that the descriptors used for the statistical PES model have a great influence on the performance.

  18. Orphan G-protein-coupled receptors : strategies for identifying ligands and potential for use in eating disorders.

    PubMed

    Harrold, Joanne A; Halford, Jason C G

    2007-01-01

    G-protein-coupled receptors (GPCRs) are key regulators of intercellular interactions, participating in almost every physiological response. They exert their effects by being activated by a variety of endogenous ligands. Traditionally, these ligands were identified first, providing tools to characterise the receptors. However, since the late 1980s, homology screening approaches have allowed the GPCRs to be found first, and in turn used as orphan targets to identify their ligands. Over the last decade this method has led to the identification of 12 novel neuropeptide families. Interestingly, four of these deorphanised GPCR systems, melanin-concentrating hormone, ghrelin, orexin and neuropeptide B/neuropeptide W, have been found to play a role in the control of energy balance. This article reviews the role of these GPCR systems in the control of food intake and energy expenditure, and discusses their potential use in therapies directed at eating disorders. As obesity has reached epidemic proportions across the developed world, pharmacotherapy has focused on this condition. However, difficulties in weight control also characterise disorders of binge eating such as bulimia and binge-eating disorder. Consequently, hypophagic treatments may be of potential benefit in normal, overweight or obese individuals displaying aberrant (out of control) eating behaviour. PMID:17767394

  19. A Systematic In Silico Search for Target Similarity Identifies Several Approved Drugs with Potential Activity against the Plasmodium falciparum Apicoplast

    PubMed Central

    Bispo, Nadlla Alves; Culleton, Richard; Silva, Lourival Almeida; Cravo, Pedro

    2013-01-01

    Most of the drugs in use against Plasmodium falciparum share similar modes of action and, consequently, there is a need to identify alternative potential drug targets. Here, we focus on the apicoplast, a malarial plastid-like organelle of algal source which evolved through secondary endosymbiosis. We undertake a systematic in silico target-based identification approach for detecting drugs already approved for clinical use in humans that may be able to interfere with the P. falciparum apicoplast. The P. falciparum genome database GeneDB was used to compile a list of ≈600 proteins containing apicoplast signal peptides. Each of these proteins was treated as a potential drug target and its predicted sequence was used to interrogate three different freely available databases (Therapeutic Target Database, DrugBank and STITCH3.1) that provide synoptic data on drugs and their primary or putative drug targets. We were able to identify several drugs that are expected to interact with forty-seven (47) peptides predicted to be involved in the biology of the P. falciparum apicoplast. Fifteen (15) of these putative targets are predicted to have affinity to drugs that are already approved for clinical use but have never been evaluated against malaria parasites. We suggest that some of these drugs should be experimentally tested and/or serve as leads for engineering new antimalarials. PMID:23555651

  20. Identifying and tracing potential energy surfaces of electronic excitations with specific character via their transition origins: application to oxirane.

    PubMed

    Li, Jian-Hao; Zuehlsdorff, T J; Payne, M C; Hine, N D M

    2015-05-14

    We show that the transition origins of electronic excitations identified by quantified natural transition orbital (QNTO) analysis can be employed to connect potential energy surfaces (PESs) according to their character across a wide range of molecular geometries. This is achieved by locating the switching of transition origins of adiabatic potential surfaces as the geometry changes. The transition vectors for analysing transition origins are provided by linear response time-dependent density functional theory (TDDFT) calculations under the Tamm-Dancoff approximation. We study the photochemical CO ring opening of oxirane as an example and show that the results corroborate the traditional Gomer-Noyes mechanism derived experimentally. The knowledge of specific states for the reaction also agrees well with that given by previous theoretical work using TDDFT surface-hopping dynamics that was validated by high-quality quantum Monte Carlo calculations. We also show that QNTO can be useful for considerably larger and more complex systems: by projecting the excitations to those of a reference oxirane molecule, the approach is able to identify and analyse specific excitations of a trans-2,3-diphenyloxirane molecule. PMID:25875632

  1. Indicator organisms in meat and poultry slaughter operations: their potential use in process control and the role of emerging technologies.

    PubMed

    Saini, Parmesh K; Marks, Harry M; Dreyfuss, Moshe S; Evans, Peter; Cook, L Victor; Dessai, Uday

    2011-08-01

    Measuring commonly occurring, nonpathogenic organisms on poultry products may be used for designing statistical process control systems that could result in reductions of pathogen levels. The extent of pathogen level reduction that could be obtained from actions resulting from monitoring these measurements over time depends upon the degree of understanding cause-effect relationships between processing variables, selected output variables, and pathogens. For such measurements to be effective for controlling or improving processing to some capability level within the statistical process control context, sufficiently frequent measurements would be needed to help identify processing deficiencies. Ultimately the correct balance of sampling and resources is determined by those characteristics of deficient processing that are important to identify. We recommend strategies that emphasize flexibility, depending upon sampling objectives. Coupling the measurement of levels of indicator organisms with practical emerging technologies and suitable on-site platforms that decrease the time between sample collections and interpreting results would enhance monitoring process control. PMID:21819672

  2. A tree-based statistical classification algorithm (CHAID) for identifying variables responsible for the occurrence of faecal indicator bacteria during waterworks operations

    NASA Astrophysics Data System (ADS)

    Bichler, Andrea; Neumaier, Arnold; Hofmann, Thilo

    2014-11-01

    Microbial contamination of groundwater used for drinking water can affect public health and is of major concern to local water authorities and water suppliers. Potential hazards need to be identified in order to protect raw water resources. We propose a non-parametric data mining technique for exploring the presence of total coliforms (TC) in a groundwater abstraction well and its relationship to readily available, continuous time series of hydrometric monitoring parameters (seven year records of precipitation, river water levels, and groundwater heads). The original monitoring parameters were used to create an extensive generic dataset of explanatory variables by considering different accumulation or averaging periods, as well as temporal offsets of the explanatory variables. A classification tree based on the Chi-Squared Automatic Interaction Detection (CHAID) recursive partitioning algorithm revealed statistically significant relationships between precipitation and the presence of TC in both a production well and a nearby monitoring well. Different secondary explanatory variables were identified for the two wells. Elevated water levels and short-term water table fluctuations in the nearby river were found to be associated with TC in the observation well. The presence of TC in the production well was found to relate to elevated groundwater heads and fluctuations in groundwater levels. The generic variables created proved useful for increasing significance levels. The tree-based model was used to predict the occurrence of TC on the basis of hydrometric variables.

  3. SPLAT: Using Spectral Indices to Identify and Characterize Ultracool Stars, Brown Dwarfs and Exoplanets in Deep Surveys and as Companions to Nearby Stars

    NASA Astrophysics Data System (ADS)

    Aganze, Christian; Burgasser, Adam J.; Martin, Eduardo; Konopacky, Quinn; Masters, Daniel C.

    2016-06-01

    The majority of ultracool dwarf stars and brown dwarfs currently known were identified in wide-field red optical and infrared surveys, enabling measures of the local, typically isolated, population in a relatively shallow (<100 pc radius) volume. Constraining the properties of the wider Galactic population (scale height, radial distribution, Population II sources), and close brown dwarf and exoplanet companions to nearby stars, requires specialized instrumentation, such as high-contrast, coronagraphic spectrometers (e.g., Gemini/GPI, VLT/Sphere, Project 1640); and deep spectral surveys (e.g., HST/WFC3 parallel fields, Euclid). We present a set of quantitative methodologies to identify and robustly characterize sources for these specific populations, based on templates and tools developed as part of the SpeX Prism Library Analysis Toolkit. In particular, we define and characterize specifically-tuned sets spectral indices that optimize selection of cool dwarfs and distinguish rare populations (subdwarfs, young planetary-mass objects) based on low-resolution, limited-wavelength-coverage spectral data; and present a template-matching classification method for these instruments. We apply these techniques to HST/WFC3 parallel fields data in the WISPS and HST-3D programs, where our spectral index set allows high completeness and low contamination for searches of late M, L and T dwarfs to distances out to ~3 kpc.The material presented here is based on work supported by the National Aeronautics and Space Administration under Grant No. NNX15AI75G.

  4. Identifying host sources, human health risk and indicators of Cryptosporidium and Giardia in a Canadian watershed influenced by urban and rural activities.

    PubMed

    Van Dyke, Michele I; Ong, Corinne S L; Prystajecky, Natalie A; Isaac-Renton, Judith L; Huck, Peter M

    2012-06-01

    Cryptosporidium and Giardia were characterized in a watershed in southern Ontario, Canada, over a 2 year period. River samples were collected every two weeks, primarily near a municipal drinking water treatment plant intake. Cryptosporidium and Giardia were frequently detected with an overall occurrence rate of 88 and 97%, respectively. Giardia concentrations were higher than Cryptosporidium, with median values of 80 cysts 100 L(-1) and 12 oocysts 100 L(-1), respectively. Although pathogens rarely show a significant relationship with fecal or water quality indicators, this study determined that Cryptosporidium, but not Giardia, was significantly correlated with Escherichia coli, turbidity and river flow. There was no correlation between the two types of protozoa, and only Giardia showed a seasonal trend with higher concentrations at cold water temperatures. Cryptosporidium genotyping of all samples found that farm animals and wildlife were an important contributor of oocysts in the watershed, and that Cryptosporidium strains/genotypes of medium to high risk for human infection (C. hominis, C. parvum and C. ubiquitum) were detected in 16% of samples. This study was able to identify Cryptosporidium host sources and human health risk, and to identify differences between Cryptosporidium and Giardia occurrence in the watershed. PMID:22717756

  5. A chemical biology approach identified PI3K as a potential therapeutic target for neurofibromatosis type 2

    PubMed Central

    Petrilli, Alejandra M; Fuse, Marisa A; Donnan, Mathew S; Bott, Marga; Sparrow, Nicklaus A; Tondera, Daniel; Huffziger, Julia; Frenzel, Corina; Malany, C Siobhan; Echeverri, Christophe J; Smith, Layton; Fernández-Valle, Cristina

    2014-01-01

    Mutations in the merlin tumor suppressor gene cause Neurofibromatosis type 2 (NF2), which is a disease characterized by development of multiple benign tumors in the nervous system. The current standard of care for NF2 calls for surgical resection of the characteristic tumors, often with devastating neurological consequences. There are currently no approved non-surgical therapies for NF2. In an attempt to identify much needed targets and therapeutically active compounds for NF2 treatment, we employed a chemical biology approach using ultra-high-throughput screening. To support this goal, we created a merlin-null mouse Schwann cell (MSC) line to screen for compounds that selectively decrease their viability and proliferation. We optimized conditions for 384-well plate assays and executed a proof-of-concept screen of the Library of Pharmacologically Active Compounds. Further confirmatory and selectivity assays identified phosphatidylinositol 3-kinase (PI3K) as a potential NF2 drug target. Notably, loss of merlin function is associated with activation of the PI3K/Akt pathway in human schwannomas. We report that AS605240, a PI3K inhibitor, decreased merlin-null MSC viability in a dose-dependent manner without significantly decreasing viability of control Schwann cells. AS605240 exerted its action on merlin-null MSCs by promoting caspase-dependent apoptosis and inducing autophagy. Additional PI3K inhibitors tested also decreased viability of merlin-null MSCs in a dose-dependent manner. In summary, our chemical genomic screen and subsequent hit validation studies have identified PI3K as potential target for NF2 therapy. PMID:25360213

  6. Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis

    PubMed Central

    2010-01-01

    Background Cryptocaryon irritans is a parasitic ciliate that causes cryptocaryonosis (white spot disease) in marine fish. Diagnosis of cryptocaryonosis often depends on the appearance of white spots on the surface of the fish, which are usually visible only during later stages of the disease. Identifying suitable biomarkers of this parasite would aid the development of diagnostic tools and control strategies for C. irritans. The C. irritans genome is virtually unexplored; therefore, we generated and analyzed expressed sequence tags (ESTs) of the parasite to identify genes that encode for surface proteins, excretory/secretory proteins and repeat-containing proteins. Results ESTs were generated from a cDNA library of C. irritans tomonts isolated from infected Asian sea bass, Lates calcarifer. Clustering of the 5356 ESTs produced 2659 unique transcripts (UTs) containing 1989 singletons and 670 consensi. BLAST analysis showed that 74% of the UTs had significant similarity (E-value < 10-5) to sequences that are currently available in the GenBank database, with more than 15% of the significant hits showing unknown function. Forty percent of the UTs had significant similarity to ciliates from the genera Tetrahymena and Paramecium. Comparative gene family analysis with related taxa showed that many protein families are conserved among the protozoans. Based on gene ontology annotation, functional groups were successfully assigned to 790 UTs. Genes encoding excretory/secretory proteins and membrane and membrane-associated proteins were identified because these proteins often function as antigens and are good antibody targets. A total of 481 UTs were classified as encoding membrane proteins, 54 were classified as encoding for membrane-bound proteins, and 155 were found to contain excretory/secretory protein-coding sequences. Amino acid repeat-containing proteins and GPI-anchored proteins were also identified as potential candidates for the development of diagnostic and control strategies for C. irritans. Conclusions We successfully discovered and examined a large portion of the previously unexplored C. irritans transcriptome and identified potential genes for the development and validation of diagnostic and control strategies for cryptocaryonosis. PMID:20113487

  7. Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.)

    PubMed Central

    Horvath, David P; Chao, Wun S; Suttle, Jeffrey C; Thimmapuram, Jyothi; Anderson, James V

    2008-01-01

    Background Dormancy of buds is a critical developmental process that allows perennial plants to survive extreme seasonal variations in climate. Dormancy transitions in underground crown buds of the model herbaceous perennial weed leafy spurge were investigated using a 23 K element cDNA microarray. These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. Crown buds collected monthly from August through December, over a five year period, were used to monitor the changes in the transcriptome during dormancy transitions. Results Nearly 1,000 genes were differentially-expressed through seasonal dormancy transitions. Expected patterns of gene expression were observed for previously characterized genes and physiological processes indicated that resolution in our analysis was sufficient for identifying shifts in global gene expression. Conclusion Gene ontology of differentially-expressed genes suggests dormancy transitions require specific alterations in transport functions (including induction of a series of mitochondrial substrate carriers, and sugar transporters), ethylene, jasmonic acid, auxin, gibberellic acid, and abscisic acid responses, and responses to stress (primarily oxidative and cold/drought). Comparison to other dormancy microarray studies indicated that nearly half of the genes identified in our study were also differentially expressed in at least two other plant species during dormancy transitions. This comparison allowed us to identify a particular MADS-box transcription factor related to the DORMANCY ASSOCIATED MADS-BOX genes from peach and hypothesize that it may play a direct role in dormancy induction and maintenance through regulation of FLOWERING LOCUS T. PMID:19014493

  8. Zebrafish: an emerging technology for in vivo pharmacological assessment to identify potential safety liabilities in early drug discovery

    PubMed Central

    Barros, T P; Alderton, W K; Reynolds, H M; Roach, A G; Berghmans, S

    2008-01-01

    The zebrafish is a well-established model organism used in developmental biology. In the last decade, this technology has been extended to the generation of high-value knowledge on safety risks of novel drugs. Indeed, the larval zebrafish appear to combine advantages of whole organism phenotypic assays and those (rapid production of results with minimal resource engagement) of in vitro high-throughput screening techniques. Thus, if appropriately evaluated, it can offer undeniable advantages in drug discovery for identification of target and off-target effects. Here, we review some applications of zebrafish to identify potential safety liabilities, particularly before lead/candidate selection. For instance, zebrafish cardiovascular system can be used to reveal decreases in heart rate and atrial–ventricular dissociation, which may signal human ether-a-go-go-related gene (hERG) channel blockade. Another main area of interest is the CNS, where zebrafish behavioural assays have been and are further being developed into screening platforms for assessment of locomotor activity, convulsant and proconvulsant liability, cognitive impairment, drug dependence potential and impaired visual and auditory functions. Zebrafish also offer interesting possibilities for evaluating effects on bone density and gastrointestinal function. Furthermore, available knowledge of the renal system in larval zebrafish can allow identification of potential safety issues of drug candidates on this often neglected area in early development platforms. Although additional validation is certainly needed, the zebrafish is emerging as a versatile in vivo animal model to identify off-target effects that need investigation and further clarification early in the drug discovery process to reduce the current, high degree of attrition in development. PMID:18552866

  9. Gene expression profiling identifies EPHB4 as a potential predictive biomarker in colorectal cancer patients treated with bevacizumab.

    PubMed

    Guijarro-Muñoz, Irene; Sánchez, Antonio; Martínez-Martínez, Esther; García, Jose M; Salas, Clara; Provencio, Mariano; Alvarez-Vallina, Luis; Sanz, Laura

    2013-01-01

    The anti-VEGF monoclonal antibody bevacizumab was approved in 2004 as a first-line treatment for metastatic colorectal cancer (CRC) in combination with chemotherapy and provided proof of principle for antiangiogenic therapy. However, there is no biomarker that can help to select patients who may benefit from bevacizumab in order to improve cost-effectiveness and therapeutic outcomes. The aim of this study was to compare gene expression profiles in CRC patients treated with bevacizumab who responded to the treatment with those that did not respond, in an effort to identify potential predictive biomarkers. RNA isolated from formalin-fixed paraffin-embedded tumor specimens of patients treated with bevacizumab was subjected to gene expression analysis with quantitative RT-PCR arrays profiling 84 genes implicated in the angiogenic process. Data were validated at the protein level using immunohistochemistry. We identified a gene, EPHB4, whose expression was significantly increased in nonresponders (p = 0.048, Mann-Whitney test). Furthermore, high EPHB4 tumor levels were associated with decreased median overall survival (16 months vs 48, Log-rank p = 0.012). This was not observed in a control group of CRC patients treated only with chemotherapy, suggesting that EPHB4 constitutes a potential predictive biomarker and not a mere prognostic one. These data support the notion of a potential synergy between EPHB4-EFNB2 and VEGF-VEGFR pathways, making patients with high EPHB4 expression more resistant to VEGF blocking. Therefore, determination of EPHB4 levels in CRC samples could be useful for the prediction of response to bevacizumab. PMID:23579861

  10. Percutaneous nephrostomy: current indications and potential uses in obstetrics and gynecology. Literature review and report of a case.

    PubMed

    Hedegaard, C K; Wallace, D

    1987-11-01

    Percutaneous nephrostomy offers a rapid and relatively safe means of short- or long-term management of urinary obstruction, irrespective of the underlying cause. It is particularly useful in patients who cannot undergo general anesthesia or surgery because of potential major risks. At present, the most common indication for percutaneous nephrostomy in OB/GYN is probably urinary tract obstruction secondary to pelvic malignancy. It is not indicated in terminal patients, but can be used to temporize renal function to allow palliative therapy and to assess the residual functional capacity of the obstructed kidney. Percutaneous nephrostomy will most likely be used even more frequently in the future as current roles are expanded particularly in areas such as perinatology. PMID:3684112

  11. Evaluating the potential of vegetation indices for winter wheat LAI estimation under different fertilization and water conditions

    NASA Astrophysics Data System (ADS)

    Xie, Qiaoyun; Huang, Wenjiang; Dash, Jadunandan; Song, Xiaoyu; Huang, Linsheng; Zhao, Jinling; Wang, Renhong

    2015-12-01

    Leaf area index (LAI) is an important indicator for monitoring crop growth conditions and forecasting grain yield. Many algorithms have been developed for remote estimation of the leaf area index of vegetation, such as using spectral vegetation indices, inversion of radiative transfer models, and supervised learning techniques. Spectral vegetation indices, mathematical combination of reflectance bands, are widely used for LAI estimation due to their computational simplicity and their applications ranged from the leaf scale to the entire globe. However, in many cases, their applicability is limited to specific vegetation types or local conditions due to species specific nature of the relationship used to transfer the vegetation indices to LAI. The overall objective of this study is to investigate the most suitable vegetation index for estimating winter wheat LAI under eight different types of fertilizer and irrigation conditions. Regression models were used to estimate LAI using hyperspectral reflectance data from the Pushbroom Hyperspectral Imager (PHI) and in-situ measurements. Our results showed that, among six vegetation indices investigated, the modified soil-adjusted vegetation index (MSAVI) and the normalized difference vegetation index (NDVI) exhibited strong and significant relationships with LAI, and thus were sensitive across different nitrogen and water treatments. The modified triangular vegetation index (MTVI2) confirmed its potential on crop LAI estimation, although second to MSAVI and NDVI in our study. The enhanced vegetation index (EVI) showed moderate performance. However, the ratio vegetation index (RVI) and the modified simple ratio index (MSR) predicted the least accurate estimations of LAI, exposing the simple band ratio index's weakness under different treatment conditions. The results support the use of vegetation indices for a quick and effective LAI mapping procedure that is suitable for winter wheat under different management practices.

  12. Ecology of testate amoebae and their potential use as palaeohydrologic indicators from peatland in Sanjiang Plain, Northeast China

    NASA Astrophysics Data System (ADS)

    Song, Lihong; Li, Hongkai; Wang, Kehong; Wu, Donghui; Wu, Haitao

    2014-12-01

    Testate amoebae are sensitive indicators of substrate moisture in peatlands. Over the last decades, they have been studied to reconstruct hydrological changes since the Holocene. However, these studies have been geographically restricted to North America and Europe. We conducted the first investigation of testate amoebae on the largest continental fresh water wetland in the Sanjiang Plain, China. The objectives of this study were to provide baseline data on the ecology of testate amoebae in the peatlands of Northeast China and to assess the potential of using them as environmental indicators in this ecosystem. We examined modern testate amoeba assemblages and species-environmental relationships at 46 microsites within 5 waterlogged depressions. The environmental parameters measured included: depth to water table, pH, and loss on ignition. The results showed that the dominant species were Trinema complanatum type, Euglypha rotunda type, Euglypha strigosa type, and Centropyxis cassis type. Redundancy analysis demonstrates that water table depth has the most important effect on testate amoeba assemblages, explaining 16.7% ( p = 0.002) of the total variance. pH was not a statistically significant factor for testate amoeba assemblages. Weighted averaging and weighted averaging partial least squares models were used to build transfer functions for depth to water table. The best performing transfer function was generated by the weighted averaging partial least squares model with an r 2 LOSO of 0.62 and RMSEPLOSO of 6.96 cm. Results indicate that testate amoebae in waterlogged depression peatland have the potential to be used as indicators for hydrological changes and for palaeohydrologic reconstructions in the Sanjiang Plain.

  13. Heat tolerance around flowering in wheat identified as a key trait for increased yield potential in Europe under climate change.

    PubMed

    Stratonovitch, Pierre; Semenov, Mikhail A

    2015-06-01

    To deliver food security for the 9 billon population in 2050, a 70% increase in world food supply will be required. Projected climatic and environmental changes emphasize the need for breeding strategies that delivers both a substantial increase in yield potential and resilience to extreme weather events such as heat waves, late frost, and drought. Heat stress around sensitive stages of wheat development has been identified as a possible threat to wheat production in Europe. However, no estimates have been made to assess yield losses due to increased frequency and magnitude of heat stress under climate change. Using existing experimental data, the Sirius wheat model was refined by incorporating the effects of extreme temperature during flowering and grain filling on accelerated leaf senescence, grain number, and grain weight. This allowed us, for the first time, to quantify yield losses resulting from heat stress under climate change. The model was used to optimize wheat ideotypes for CMIP5-based climate scenarios for 2050 at six sites in Europe with diverse climates. The yield potential for heat-tolerant ideotypes can be substantially increased in the future (e.g. by 80% at Seville, 100% at Debrecen) compared with the current cultivars by selecting an optimal combination of wheat traits, e.g. optimal phenology and extended duration of grain filling. However, at two sites, Seville and Debrecen, the grain yields of heat-sensitive ideotypes were substantially lower (by 54% and 16%) and more variable compared with heat-tolerant ideotypes, because the extended grain filling required for the increased yield potential was in conflict with episodes of high temperature during flowering and grain filling. Despite much earlier flowering at these sites, the risk of heat stress affecting yields of heat-sensitive ideotypes remained high. Therefore, heat tolerance in wheat is likely to become a key trait for increased yield potential and yield stability in southern Europe in the future. PMID:25750425

  14. Heat tolerance around flowering in wheat identified as a key trait for increased yield potential in Europe under climate change

    PubMed Central

    Stratonovitch, Pierre; Semenov, Mikhail A.

    2015-01-01

    To deliver food security for the 9 billon population in 2050, a 70% increase in world food supply will be required. Projected climatic and environmental changes emphasize the need for breeding strategies that delivers both a substantial increase in yield potential and resilience to extreme weather events such as heat waves, late frost, and drought. Heat stress around sensitive stages of wheat development has been identified as a possible threat to wheat production in Europe. However, no estimates have been made to assess yield losses due to increased frequency and magnitude of heat stress under climate change. Using existing experimental data, the Sirius wheat model was refined by incorporating the effects of extreme temperature during flowering and grain filling on accelerated leaf senescence, grain number, and grain weight. This allowed us, for the first time, to quantify yield losses resulting from heat stress under climate change. The model was used to optimize wheat ideotypes for CMIP5-based climate scenarios for 2050 at six sites in Europe with diverse climates. The yield potential for heat-tolerant ideotypes can be substantially increased in the future (e.g. by 80% at Seville, 100% at Debrecen) compared with the current cultivars by selecting an optimal combination of wheat traits, e.g. optimal phenology and extended duration of grain filling. However, at two sites, Seville and Debrecen, the grain yields of heat-sensitive ideotypes were substantially lower (by 54% and 16%) and more variable compared with heat-tolerant ideotypes, because the extended grain filling required for the increased yield potential was in conflict with episodes of high temperature during flowering and grain filling. Despite much earlier flowering at these sites, the risk of heat stress affecting yields of heat-sensitive ideotypes remained high. Therefore, heat tolerance in wheat is likely to become a key trait for increased yield potential and yield stability in southern Europe in the future. PMID:25750425

  15. Potential shortcomings of output:input ratios as indicators of economic efficiency in commercial beef breed evaluations.

    PubMed

    Melton, B E; Colette, W A

    1993-03-01

    In recent years animal breeders have increasingly made use of output:input ratios and simple measures of economic efficiency, such as annual profits, as a basis for comparisons and evaluations of the commercial applicability of alternative beef breeds. In many instances, however, output:input ratios may produce fallacious indications of economic efficiency that may, in turn, lead to erroneous conclusions regarding the true commercial applicability of the breeds evaluated. Errors potentially arising from the use of output:input ratios in breed evaluations may be attributed to a combination of 1) a narrow range of input use values under which most breeds are evaluated and 2) the inability of output:input ratios, including average annual profitability, to reflect consistently the economic objectives of commercial cow-calf producers. An alternative basis for breed comparison and evaluation is, therefore, developed from economic theories related to optimal investment and asset replacement. Comparison of the results obtained with this alternative to those obtained from output:input ratio evaluation, including annual profitability, indicate that potential value differences of as much as 33% may result from the use of output:input ratios as a primary basis of commercial breed evaluation. PMID:8463143

  16. Potential of using satellite based vegetation indices and biophysical variables for the assessment of the water footprint of crops

    NASA Astrophysics Data System (ADS)

    Stancalie, Gh.; Nertan, A. T.; Toulios, L.; Spiliotopoulos, M.

    2014-08-01

    Satellite remote sensing techniques play an important role in crop identification, acreage and production estimation, disease and stress detection, and soil and water resources characterization because they provide spatially explicit information and access to remote locations. The main objective of the study is to highlight the potential of using remote sensing techniques in the research field of water management, especially for "water footprint" assessment. In this paper, several vegetation indices (NDVI, NDWI, etc) and biophysical variables (LAI, fAPAR) are key variables to potentially be estimated by remote sensing and used in water footprint studies. The combination of these input parameters brings several limitations regarding the discrepancies in temporal and spatial resolution and data availability, which are described and discussed in detail. MODIS, Landsat, SPOT Vegetation and Meteosat data were used in order to estimate evapotranspiration and vegetation indices. The results of this study show the usefulness of satellite data for water footprint assessment and were obtained by the Remote Sensing Working Group in the framework of the ESSEM COST Action ES1106, "Assessment of EUROpean AGRIculture WATer use and trade under climate change" (EUROAGRIWAT).

  17. Disappointing reliability of pulsatility indices to identify candidates for magnetic resonance imaging screening in population-based studies assessing prevalence of cerebral small vessel disease

    PubMed Central

    Del Brutto, Oscar H.; Mera, Robertino M.; Andrade, María de la Luz; Castillo, Pablo R.; Zambrano, Mauricio; Nader, Juan A.

    2015-01-01

    Background: Diagnosis of cerebral small vessel disease (SVD) is a challenge in remote areas where magnetic resonance imaging (MRI) is not available. Hospital-based studies in high-risk or stroke patients have found an association between the pulsatility index (PI) of intracranial arteries – as derived from transcranial Doppler (TCD) – and white matter hyperintensities (WMH) of presumed vascular origin. We aimed to assess the reliability of cerebral pulsatility indices to identify candidates for MRI screening in population-based studies assessing prevalence of SVD. Methods: A representative sample of stroke-free Atahualpa residents aged ≥65 years investigated with MRI underwent TCD. Using generalized linear models, we evaluated whether the PI of major intracranial arteries correlate with WMH (used as a proxy of diffuse SVD), after adjusting for demographics and cardiovascular risk factors. Results: Out of 70 participants (mean age 70.6 ± 4.6 years, 57% women), 28 (40%) had moderate-to-severe WMH. In multivariate models, there were no differences across categories of WMH in the mean PI of middle cerebral arteries (1.10 ± 0.16 vs. 1.22 ± 0.24, β: 0.065, 95% confidence interval (CI): −0.084–0.177, P = 0.474) or vertebrobasilar arteries (1.11 ± 0.16 vs. 1.29 ± 0.27, β: 0.066, 95% CI: −0.0024–0.156, P = 0.146). Conclusions: Cerebral PI should not be used to identify candidates for MRI screening in population-based studies assessing the burden of SVD. PMID:26167015

  18. Metabolic Profiling and Enzyme Analyses Indicate a Potential Role of Antioxidant Systems in Complementing Glyphosate Resistance in an Amaranthus palmeri Biotype.

    PubMed

    Maroli, Amith S; Nandula, Vijay K; Dayan, Franck E; Duke, Stephen O; Gerard, Patrick; Tharayil, Nishanth

    2015-10-21

    Metabolomics and biochemical assays were employed to identify physiological perturbations induced by a commercial formulation of glyphosate in susceptible (S) and resistant (R) biotypes of Amaranthus palmeri. At 8 h after treatment (HAT), compared to the respective water-treated control, cellular metabolism of both biotypes were similarly perturbed by glyphosate, resulting in abundance of most metabolites including shikimic acid, amino acids, organic acids and sugars. However, by 80 HAT the metabolite pool of glyphosate-treated R-biotype was similar to that of the control S- and R-biotypes, indicating a potential physiological recovery. Furthermore, the glyphosate-treated R-biotype had lower reactive oxygen species (ROS) damage, higher ROS scavenging activity, and higher levels of potential antioxidant compounds derived from the phenylpropanoid pathway. Thus, metabolomics, in conjunction with biochemical assays, indicate that glyphosate-induced metabolic perturbations are not limited to the shikimate pathway, and the oxidant quenching efficiency could potentially complement the glyphosate resistance in this R-biotype. PMID:26329798

  19. Altered platelet indices as potential markers of severe and complicated malaria caused by Plasmodium vivax: a cross-sectional descriptive study

    PubMed Central

    2013-01-01

    Background This study described altered platelet indices in patients with acute malaria caused by Plasmodium vivax and determined whether these alterations are associated with warning signs of severe and complicated malaria. Methods A total of 186 patients attending the Malaria Clinic at the University Hospital from the Federal University of Mato Grosso, Brazil, between 2008 and 2013 were included in this study. After parasitological confirmation of exclusive infection by P. vivax, blood cell counts and platelet indices were determined. Disease gravity was evaluated on the basis of classic signs of Plasmodium falciparum severe malaria, including severe anemia, or by changes in serum levels of glucose, bilirubin, aminotransferases and creatinine at the time of the patient’s admission. Patients with a longer duration of symptoms or those identified as primo infected were considered potential candidates for evolution into the severe form of malaria. Results The mean platelet volume (MPV), platelet distribution width (PDW), and plateletcrit (PCT) values exhibited significant variability. A significant inverse relationship was observed between parasitaemia and PCT. Patients with warning signs for evolution into severe disease, with primo infection, or presenting with symptoms for over three days had the highest MPV and PDW. The adjusted analyses showed the presence of warning signs for the development of severe and complicated malaria remained independently linked to elevated MPV and PDW. Conclusion Altered platelet indices should be analysed as potential markers for the severity of malaria caused by P. vivax. Future studies with appropriate methodology for prognostic evaluation could confirm the potential use of these indices in clinical practice. PMID:24370274

  20. Global miRNA Expression Profiling Identifies miR-1290 as Novel Potential oncomiR in Laryngeal Carcinoma

    PubMed Central

    Kostrzewska-Poczekaj, Magdalena; Bednarek, Kinga; Paczkowska, Julia; Jackowska, Joanna; Grenman, Reidar; Szyfter, Krzysztof; Wierzbicka, Malgorzata; Giefing, Maciej; Jarmuz-Szymczak, Malgorzata

    2015-01-01

    Background Laryngeal squamous cell carcinoma (LSCC) is the most common group among head and neck cancers. LSCC is characterized by a high incidence in Europe. With the aim of better understanding its genetic background we performed global miRNA expression profiling of LSCC cell lines and primary specimens. By this approach we identified a cohort of 33 upregulated and 9 downregulated miRNA genes in LSCC as compared to epithelial no tumor controls. Results Within this group we identified overexpression of the novel miR-1290 gene not reported in the context of LSCC before. Using a combined bioinformatical approach in connection with functional analysis we delineated two putative target genes of miR-1290 namely ITPR2 and MAF which are significantly downregulated in LSCC. They are interesting candidates for tumor suppressor genes as they are implicated in apoptosis and other processes deregulated in cancer. Conclusion Taken together, we propose miR-1290 as the new oncomiR involved in LSCC pathogenesis. Additionally, we suggest that the oncogenic potential of miR-1290 might be expressed by the involvement in downregulation of its target genes MAF and ITPR2. PMID:26694163

  1. In silico repositioning-chemogenomics strategy identifies new drugs with potential activity against multiple life stages of Schistosoma mansoni.

    PubMed

    Neves, Bruno J; Braga, Rodolpho C; Bezerra, Jos C B; Cravo, Pedro V L; Andrade, Carolina H

    2015-01-01

    Morbidity and mortality caused by schistosomiasis are serious public health problems in developing countries. Because praziquantel is the only drug in therapeutic use, the risk of drug resistance is a concern. In the search for new schistosomicidal drugs, we performed a target-based chemogenomics screen of a dataset of 2,114 proteins to identify drugs that are approved for clinical use in humans that may be active against multiple life stages of Schistosoma mansoni. Each of these proteins was treated as a potential drug target, and its amino acid sequence was used to interrogate three databases: Therapeutic Target Database (TTD), DrugBank and STITCH. Predicted drug-target interactions were refined using a combination of approaches, including pairwise alignment, conservation state of functional regions and chemical space analysis. To validate our strategy, several drugs previously shown to be active against Schistosoma species were correctly predicted, such as clonazepam, auranofin, nifedipine, and artesunate. We were also able to identify 115 drugs that have not yet been experimentally tested against schistosomes and that require further assessment. Some examples are aprindine, gentamicin, clotrimazole, tetrabenazine, griseofulvin, and cinnarizine. In conclusion, we have developed a systematic and focused computer-aided approach to propose approved drugs that may warrant testing and/or serve as lead compounds for the design of new drugs against schistosomes. PMID:25569258

  2. A mouse mammary gland involution mRNA signature identifies biological pathways potentially associated with breast cancer metastasis.

    PubMed

    Stein, Torsten; Salomonis, Nathan; Nuyten, Dimitry S A; van de Vijver, Marc J; Gusterson, Barry A

    2009-06-01

    Mouse mammary gland involution resembles a wound healing response with suppressed inflammation. Wound healing and inflammation are also associated with tumour development, and a 'wound-healing' gene expression signature can predict metastasis formation and survival. Recent studies have shown that an involuting mammary gland stroma can promote metastasis. It could therefore be hypothesised that gene expression signatures from an involuting mouse mammary gland may provide new insights into the physiological pathways that promote breast cancer progression. Indeed, using the HOPACH clustering method, the human orthologues of genes that were differentially regulated at day 3 of mammary gland involution and showed prolonged expression throughout the first 4 days of involution distinguished breast cancers in the NKI 295 breast cancer dataset with low and high metastatic activity. Most strikingly, genes associated with copper ion homeostasis and with HIF-1 promoter binding sites were the most over-represented, linking this signature to hypoxia. Further, six out of the ten mRNAs with strongest up-regulation in cancers with poor survival code for secreted factors, identifying potential candidates that may be involved in stromal/matrix-enhanced metastasis formation/breast cancer development. This method therefore identified biological processes that occur during mammary gland involution, which may be critical in promoting breast cancer metastasis that could form a basis for future investigation, and supports a role for copper in breast cancer development. PMID:19408105

  3. In Silico Repositioning-Chemogenomics Strategy Identifies New Drugs with Potential Activity against Multiple Life Stages of Schistosoma mansoni

    PubMed Central

    Neves, Bruno J.; Braga, Rodolpho C.; Bezerra, José C. B.; Cravo, Pedro V. L.; Andrade, Carolina H.

    2015-01-01

    Morbidity and mortality caused by schistosomiasis are serious public health problems in developing countries. Because praziquantel is the only drug in therapeutic use, the risk of drug resistance is a concern. In the search for new schistosomicidal drugs, we performed a target-based chemogenomics screen of a dataset of 2,114 proteins to identify drugs that are approved for clinical use in humans that may be active against multiple life stages of Schistosoma mansoni. Each of these proteins was treated as a potential drug target, and its amino acid sequence was used to interrogate three databases: Therapeutic Target Database (TTD), DrugBank and STITCH. Predicted drug-target interactions were refined using a combination of approaches, including pairwise alignment, conservation state of functional regions and chemical space analysis. To validate our strategy, several drugs previously shown to be active against Schistosoma species were correctly predicted, such as clonazepam, auranofin, nifedipine, and artesunate. We were also able to identify 115 drugs that have not yet been experimentally tested against schistosomes and that require further assessment. Some examples are aprindine, gentamicin, clotrimazole, tetrabenazine, griseofulvin, and cinnarizine. In conclusion, we have developed a systematic and focused computer-aided approach to propose approved drugs that may warrant testing and/or serve as lead compounds for the design of new drugs against schistosomes. PMID:25569258

  4. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations

    PubMed Central

    2011-01-01

    The recent publication of the draft genome sequences of the Neanderthal and a ~50,000-year-old archaic hominin from Denisova Cave in southern Siberia has ushered in a new age in molecular archaeology. We previously cross-compared the human, chimpanzee and Neanderthal genome sequences with respect to a set of disease-causing/disease-associated missense and regulatory mutations (Human Gene Mutation Database) and succeeded in identifying genetic variants which, although apparently pathogenic in humans, may represent a 'compensated' wild-type state in at least one of the other two species. Here, in an attempt to identify further 'potentially compensated mutations' (PCMs) of interest, we have compared our dataset of disease-causing/disease-associated mutations with their corresponding nucleotide positions in the Denisovan hominin, Neanderthal and chimpanzee genomes. Of the 15 human putatively disease-causing mutations that were found to be compensated in chimpanzee, Denisovan or Neanderthal, only a solitary F5 variant (Val1736Met) was specific to the Denisovan. In humans, this missense mutation is associated with activated protein C resistance and an increased risk of thromboembolism and recurrent miscarriage. It is unclear at this juncture whether this variant was indeed a PCM in the Denisovan or whether it could instead have been associated with disease in this ancient hominin. PMID:21807602

  5. Gene Expression Profiling in a Mouse Model Identifies Fetal Liver- and Placenta-Derived Potential Biomarkers for Down Syndrome Screening

    PubMed Central

    Imholz, Sandra; Koster, Maria P. H.; van Oostrom, Conny T. M.; Breit, Timo M.; Schielen, Peter C. J. I.; de Vries, Annemieke

    2011-01-01

    Background As a first step to identify novel potential biomarkers for prenatal Down Syndrome screening, we analyzed gene expression in embryos of wild type mice and the Down Syndrome model Ts1Cje. Since current Down Syndrome screening markers are derived from placenta and fetal liver, these tissues were chosen as target. Methodology/Principal Findings Placenta and fetal liver at 15.5 days gestation were analyzed by microarray profiling. We confirmed increased expression of genes located at the trisomic chromosomal region. Overall, between the two genotypes more differentially expressed genes were found in fetal liver than in placenta. Furthermore, the fetal liver data are in line with the hematological aberrations found in humans with Down Syndrome as well as Ts1Cje mice. Together, we found 25 targets that are predicted (by Gene Ontology, UniProt, or the Human Plasma Proteome project) to be detectable in human serum. Conclusions/Significance Fetal liver might harbor more promising targets for Down Syndrome screening studies. We expect these new targets will help focus further experimental studies on identifying and validating human maternal serum biomarkers for Down Syndrome screening. PMID:21533146

  6. Experimental antibiotic treatment identifies potential pathogens of white band disease in the endangered Caribbean coral Acropora cervicornis.

    PubMed

    Sweet, M J; Croquer, A; Bythell, J C

    2014-08-01

    Coral diseases have been increasingly reported over the past few decades and are a major contributor to coral decline worldwide. The Caribbean, in particular, has been noted as a hotspot for coral disease, and the aptly named white syndromes have caused the decline of the dominant reef building corals throughout their range. White band disease (WBD) has been implicated in the dramatic loss of Acropora cervicornis and Acropora palmata since the 1970s, resulting in both species being listed as critically endangered on the International Union for Conservation of Nature Red list. The causal agent of WBD remains unknown, although recent studies based on challenge experiments with filtrate from infected hosts concluded that the disease is probably caused by bacteria. Here, we report an experiment using four different antibiotic treatments, targeting different members of the disease-associated microbial community. Two antibiotics, ampicillin and paromomycin, arrested the disease completely, and by comparing with community shifts brought about by treatments that did not arrest the disease, we have identified the likely candidate causal agent or agents of WBD. Our interpretation of the experimental treatments is that one or a combination of up to three specific bacterial types, detected consistently in diseased corals but not detectable in healthy corals, are likely causal agents of WBD. In addition, a histophagous ciliate (Philaster lucinda) identical to that found consistently in association with white syndrome in Indo-Pacific acroporas was also consistently detected in all WBD samples and absent in healthy coral. Treatment with metronidazole reduced it to below detection limits, but did not arrest the disease. However, the microscopic disease signs changed, suggesting a secondary role in disease causation for this ciliate. In future studies to identify a causal agent of WBD via tests of Henle-Koch's postulates, it will be vital to experimentally control for populations of the other potential pathogens identified in this study. PMID:24943374

  7. Experimental antibiotic treatment identifies potential pathogens of white band disease in the endangered Caribbean coral Acropora cervicornis

    PubMed Central

    Sweet, M. J.; Croquer, A.; Bythell, J. C.

    2014-01-01

    Coral diseases have been increasingly reported over the past few decades and are a major contributor to coral decline worldwide. The Caribbean, in particular, has been noted as a hotspot for coral disease, and the aptly named white syndromes have caused the decline of the dominant reef building corals throughout their range. White band disease (WBD) has been implicated in the dramatic loss of Acropora cervicornis and Acropora palmata since the 1970s, resulting in both species being listed as critically endangered on the International Union for Conservation of Nature Red list. The causal agent of WBD remains unknown, although recent studies based on challenge experiments with filtrate from infected hosts concluded that the disease is probably caused by bacteria. Here, we report an experiment using four different antibiotic treatments, targeting different members of the disease-associated microbial community. Two antibiotics, ampicillin and paromomycin, arrested the disease completely, and by comparing with community shifts brought about by treatments that did not arrest the disease, we have identified the likely candidate causal agent or agents of WBD. Our interpretation of the experimental treatments is that one or a combination of up to three specific bacterial types, detected consistently in diseased corals but not detectable in healthy corals, are likely causal agents of WBD. In addition, a histophagous ciliate (Philaster lucinda) identical to that found consistently in association with white syndrome in Indo-Pacific acroporas was also consistently detected in all WBD samples and absent in healthy coral. Treatment with metronidazole reduced it to below detection limits, but did not arrest the disease. However, the microscopic disease signs changed, suggesting a secondary role in disease causation for this ciliate. In future studies to identify a causal agent of WBD via tests of Henle–Koch's postulates, it will be vital to experimentally control for populations of the other potential pathogens identified in this study. PMID:24943374

  8. Assessment of the extended Koopmans' theorem for the chemical reactivity: Accurate computations of chemical potentials, chemical hardnesses, and electrophilicity indices.

    PubMed

    Yildiz, Dilan; Bozkaya, Uğur

    2016-01-30

    The extended Koopmans' theorem (EKT) provides a straightforward way to compute ionization potentials and electron affinities from any level of theory. Although it is widely applied to ionization potentials, the EKT approach has not been applied to evaluation of the chemical reactivity. We present the first benchmarking study to investigate the performance of the EKT methods for predictions of chemical potentials (μ) (hence electronegativities), chemical hardnesses (η), and electrophilicity indices (ω). We assess the performance of the EKT approaches for post-Hartree-Fock methods, such as Møller-Plesset perturbation theory, the coupled-electron pair theory, and their orbital-optimized counterparts for the evaluation of the chemical reactivity. Especially, results of the orbital-optimized coupled-electron pair theory method (with the aug-cc-pVQZ basis set) for predictions of the chemical reactivity are very promising; the corresponding mean absolute errors are 0.16, 0.28, and 0.09 eV for μ, η, and ω, respectively. PMID:26458329

  9. Evaluation of voltage-dependent calcium channel γ gene families identified several novel potential susceptible genes to schizophrenia

    PubMed Central

    Guan, Fanglin; Zhang, Tianxiao; Liu, Xinshe; Han, Wei; Lin, Huali; Li, Lu; Chen, Gang; Li, Tao

    2016-01-01

    Voltage-gated L-type calcium channels (VLCC) are distributed widely throughout the brain. Among the genes involved in schizophrenia (SCZ), genes encoding VLCC subunits have attracted widespread attention. Among the four subunits comprising the VLCC (α − 1, α −2/δ, β, and γ), the γ subunit that comprises an eight-member protein family is the least well understood. In our study, to further investigate the risk susceptibility by the γ subunit gene family to SCZ, we conducted a large-scale association study in Han Chinese individuals. The SNP rs17645023 located in the intergenic region of CACNG4 and CACNG5 was identified to be significantly associated with SCZ (OR = 0.856, P = 5.43 × 10−5). Similar results were obtained in the meta-analysis with the current SCZ PGC data (OR = 0.8853). We also identified a two-SNP haplotype (rs10420331-rs11084307, P = 1.4 × 10−6) covering the intronic region of CACNG8 to be significantly associated with SCZ. Epistasis analyses were conducted, and significant statistical interaction (OR = 0.622, P = 2.93 × 10−6, Pperm < 0.001) was observed between rs192808 (CACNG6) and rs2048137 (CACNG5). Our results indicate that CACNG4, CACNG5, CACNG6 and CACNG8 may contribute to the risk of SCZ. The statistical epistasis identified between CACNG5 and CACNG6 suggests that there may be an underlying biological interaction between the two genes. PMID:27102562

  10. Genome-Wide DNA Methylation Analysis Identifies Novel Hypomethylated Non-Pericentromeric Genes with Potential Clinical Implications in ICF Syndrome

    PubMed Central

    Gatto, S.; Gagliardi, M.; Crujeiras, A. B.; Matarazzo, M. R.; Esteller, M.; Sandoval, J.

    2015-01-01

    Introduction and Results Immunodeficiency, centromeric instability and facial anomalies syndrome (ICF) is a rare autosomal recessive disease, characterized by severe hypomethylation in pericentromeric regions of chromosomes (1, 16 and 9), marked immunodeficiency and facial anomalies. The majority of ICF patients present mutations in the DNMT3B gene, affecting the DNA methyltransferase activity of the protein. In the present study, we have used the Infinium 450K DNA methylation array to evaluate the methylation level of 450,000 CpGs in lymphoblastoid cell lines and untrasformed fibroblasts derived from ICF patients and healthy donors. Our results demonstrate that ICF-specific DNMT3B variants A603T/STP807ins and V699G/R54X cause global DNA hypomethylation compared to wild-type protein. We identified 181 novel differentially methylated positions (DMPs) including subtelomeric and intrachromosomic regions, outside the classical ICF-related pericentromeric hypomethylated positions. Interestingly, these sites were mainly located in intergenic regions and inside the CpG islands. Among the identified hypomethylated CpG-island associated genes, we confirmed the overexpression of three selected genes, BOLL, SYCP2 and NCRNA00221, in ICF compared to healthy controls, which are supposed to be expressed in germ line and silenced in somatic tissues. Conclusions In conclusion, this study contributes in clarifying the direct relationship between DNA methylation defect and gene expression impairment in ICF syndrome, identifying novel direct target genes of DNMT3B. A high percentage of the DMPs are located in the subtelomeric regions, indicating a specific role of DNMT3B in methylating these chromosomal sites. Therefore, we provide further evidence that hypomethylation in specific non-pericentromeric regions of chromosomes might be involved in the molecular pathogenesis of ICF syndrome. The detection of DNA hypomethylation at BOLL, SYCP2 and NCRNA00221 may pave the way for the development of specific clinical biomarkers with the aim to facilitate the identification of ICF patients. PMID:26161907

  11. Indicators of hydrological, biogeochemical and ecological integrity for estimating potential loss of ecosystem services from wetlands on domesticated landscapes

    NASA Astrophysics Data System (ADS)

    Creed, I. F.; Aldred, D.; Spargo, A.; Bayley, S.

    2012-12-01

    Wetlands are being lost at an alarming rate in the prairie pothole landscape of North America. The full consequence of this loss is not fully understood or recognized due to (1) inadequate or incomplete wetland inventories (with mapping emphasizing permanent and not ephemeral wetlands, and only capturing "easy to observe" wetland area defined by open water and not the true dynamic wetland extent defined by saturated soils), and (2) lack of appropriate theoretical frameworks to assess the functions and benefits of these wetlands. We present a theoretical framework that integrates indicators to estimate functions and benefits of wetland integrity in central Alberta. We establish indicators using the principles that are representative of the dominant processes operating on the landscape, are simple and are scalable. While some of these indicators may be widely recognized, their implementation is often not comprehensive or complete. First, we develop an automated method for fine scale mapping of permanent and ephemeral wetlands from a fusion of high-resolution elevation data and aerial photography. Second, we estimate historic wetland loss over the past 50 years during which intensive domestication of the landscape occurred by modeling the distribution of wetlands in an undisturbed landscape using area-frequency power functions and calculating the difference in the actual wetland inventory. Third, we define relative wetland assessment units using cluster analysis of hydrological and ecological variables, including climate, geology, topography, soils and land use/land covers. Fourth, for each assessment unit we define indicators of functions and benefits of aquatic ecosystem services including water storage (surface and subsurface), phosphorus retention, nitrate removal, sediment retention, ecological health/biodiversity and human use, and then use practical strategies rooted in the fusion of digital terrain analysis and remote sensing techniques to measure and monitor these indicators over the past years. For a time series of wetlands loss we derive these indicators of functions and benefits to estimate changes in the provision of specific aquatic ecosystem services on the landscape. Last, we develop formulae for integrating these indicators to determine whether a specific wetland or wetland complex should be prioritized for conservation, exemplifying potential trade-offs among ecosystem services in setting conservation targets on this wetland dominated landscapes. The proposed theoretical framework evolved from close collaboration between scientists and resource managers, and will inform those engaged in developing wetland policies for a broad range of jurisdictions.

  12. An Investigation of Circumbinary Planet Orbital Stability and Habitability to Identify Potential Planetary Systems with Several Habitable Planets

    NASA Astrophysics Data System (ADS)

    Mason, Paul A.; Zuluaga, Jorge; Cuartas, Pablo A.

    2015-08-01

    The census of planets orbiting the center of mass of binary stars is rapidly growing. The question of stability for circumbinary planets has been the focus of much recent research. We review this work and present results of new simulations, from which we find criteria for the long term stability of exoplanets orbiting binaries. We are especially concerned with the potential stability of planets in habitable zones surrounding binaries. For this purpose, we merge a long-term orbital stability study with an analysis of the rotational evolution of the stellar components. The stellar evolution and rotational study enables estimates of stellar activity, and the effects on the magnetospheres and atmospheres of planets over the course of history for a potentially habitable circumbinary planet. We find that the long-term orbital stability of circumbinary habitable zone depends sensitively on the initial orbit of the binary and on the masses of the stars. We find that stellar twins (binary mass ratio ~ 1) and binaries with circular orbits provide the most stable solutions. However, if the binary orbit evolves too rapidly, planets may be lost due to changes in resonance locations. A subset of binaries are identified possessing both stable orbital solutions for multiple planets in the habitable zone and reduced stellar aggression due to tidal torqueing of the stellar rotation.

  13. Comparison of genetically encoded calcium indicators for monitoring action potentials in mammalian brain by two-photon excitation fluorescence microscopy

    PubMed Central

    Podor, Borbala; Hu, Yi-ling; Ohkura, Masamichi; Nakai, Junichi; Croll, Roger; Fine, Alan

    2015-01-01

    Abstract. Imaging calcium transients associated with neuronal activity has yielded important insights into neural physiology. Genetically encoded calcium indicators (GECIs) offer conspicuous potential advantages for this purpose, including exquisite targeting. While the catalogue of available GECIs is steadily growing, many newly developed sensors that appear promising in vitro or in model cells appear to be less useful when expressed in mammalian neurons. We have, therefore, evaluated the performance of GECIs from two of the most promising families of sensors, G-CaMPs [Nat. Biotechnol. 19(2), 137–141 (2001)11175727] and GECOs [Science 333(6051), 1888–1891 (2011)21903779], for monitoring action potentials in rat brain. Specifically, we used two-photon excitation fluorescence microscopy to compare calcium transients detected by G-CaMP3; GCaMP6f; G-CaMP7; Green-GECO1.0, 1.1 and 1.2; Blue-GECO; Red-GECO; Rex-GECO0.9; Rex-GECO1; Carmine-GECO; Orange-GECO; and Yellow-GECO1s. After optimizing excitation wavelengths, we monitored fluorescence signals associated with increasing numbers of action potentials evoked by current injection in CA1 pyramidal neurons in rat organotypic hippocampal slices. Some GECIs, particularly Green-GECO1.2, GCaMP6f, and G-CaMP7, were able to detect single action potentials with high reliability. By virtue of greatest sensitivity and fast kinetics, G-CaMP7 may be the best currently available GECI for monitoring calcium transients in mammalian neurons. PMID:26158004

  14. Temporal coupling between neuronal activity and blood flow in rat cerebellar cortex as indicated by field potential analysis

    PubMed Central

    Mathiesen, Claus; Caesar, Kirsten; Lauritzen, Martin

    2000-01-01

    Laser-Doppler flowmetry and extracellular recordings of field potentials were used to examine the temporal coupling between neuronal activity and increases in cerebellar blood flow (CeBF). Climbing fibre-evoked increases in CeBF were dependent on stimulus duration, indicating that increases in CeBF reflected a time integral in neuronal activity. The simplest way to represent neuronal activity over time was to obtain a running summation of evoked field potential amplitudes (runΣFP). RunΣFP was calculated for each stimulus protocol and compared with the time course of the CeBF responses to demonstrate coupling between nerve cell activity and CeBF. In the climbing fibre system, the amplitude and time course of CeBF were in agreement with the calculated postsynaptic runΣFP (2–20 Hz for 60 s). This suggested coupling between CeBF and neuronal activity in this excitatory, monosynaptic, afferent-input system under these conditions. There was no correlation between runΣFP and CeBF during prolonged stimulation. Parallel fibre-evoked increases in CeBF correlated with runΣFP of pre- and postsynaptic potentials (2–15 Hz for 60 s). At higher stimulation frequencies and during longer-lasting stimulation the time course and amplitudes of CeBF responses correlated with runΣFP of presynaptic, but not postsynaptic potentials. This suggested a more complex relationship in this mixed inhibitory-excitatory, disynaptic, afferent-input system. This study has demonstrated temporal coupling between neuronal activity and CeBF in the monosynaptic, excitatory climbing-fibre system. In the mixed mono- and disynaptic parallel fibre system, temporal coupling was most clearly observed at low stimulation frequencies. We propose that appropriate modelling of electrophysiological data is needed to document functional coupling of neuronal activity and blood flow. PMID:10673558

  15. What's down below? Current and potential future applications of geophysical techniques to identify subsurface permafrost conditions (Invited)

    NASA Astrophysics Data System (ADS)

    Douglas, T. A.; Bjella, K.; Campbell, S. W.

    2013-12-01

    For infrastructure design, operations, and maintenance requirements in the North the ability to accurately and efficiently detect the presence (or absence) of ground ice in permafrost terrains is a serious challenge. Ground ice features including ice wedges, thermokarst cave-ice, and segregation ice are present in a variety of spatial scales and patterns. Currently, most engineering applications use borehole logging and sampling to extrapolate conditions at the point scale. However, there is high risk of over or under estimating the presence of frozen or unfrozen features when relying on borehole information alone. In addition, boreholes are costly, especially for planning linear structures like roads or runways. Predicted climate warming will provide further challenges for infrastructure development and transportation operations where permafrost degradation occurs. Accurately identifying the subsurface character in permafrost terrains will allow engineers and planners to cost effectively create novel infrastructure designs to withstand the changing environment. There is thus a great need for a low cost rapidly deployable, spatially extensive means of 'measuring' subsurface conditions. Geophysical measurements, both terrestrial and airborne, have strong potential to revolutionize our way of mapping subsurface conditions. Many studies in continuous and discontinuous permafrost have used geophysical measurements to identify discrete features and repeatable patterns in the subsurface. The most common measurements include galvanic and capacitive coupled resistivity, ground penetrating radar, and multi frequency electromagnetic induction techniques. Each of these measurements has strengths, weaknesses, and limitations. By combining horizontal geophysical measurements, downhole geophysics, multispectral remote sensing images, LiDAR measurements, and soil and vegetation mapping we can start to assemble a holistic view of how surface conditions and standoff measurements can be used to delineate subsurface permafrost geomorphology. This presentation will include examples of projects in Alaska and Greenland where a combination of geophysical and other measurement techniques have been used to identify subsurface conditions. These include projects at multiple locations around Interior Alaska where a variety of ground based and standoff measurements are being used to identify subsurface conditions, and infrastructure projects at Thule, Greenland, where geophysical measurements are being used to cut costs for new construction and maintenance. The expansion of the Cold Regions Research and Engineering Laboratories' Fox Permafrost Tunnel is to provide a three dimensional test bed for geophysical measurements, and construction is aided by geophysical measurements. The array of geophysical research tools used to interrogate the subsurface in permafrost terrains can likely provide worthwhile information in non-frozen ground terrains to support sensor development and geomorphological interpretation.

  16. Naphthenic acids in coastal sediments after the Hebei Spirit oil spill: a potential indicator for oil contamination.

    PubMed

    Wan, Yi; Wang, Beili; Khim, Jong Seong; Hong, Seongjin; Shim, Won Joon; Hu, Jianying

    2014-04-01

    Naphthenic acids (NAs) as toxic components in most petroleum sources are suspected to be one of the major pollutants in the aquatic environment following oil spills, and the polarity and persistence of NAs make it a potential indicator for oil contamination. However, the contamination and potential effects of pollutants in oil spill affected areas remain unknown. To investigate NAs in oil spill affected areas, a sensitive method was first established for analysis of NAs, together with oxy-NAs in sediment samples by UPLC-QTOF-MS. Then the method was applied to determine the NA mixtures in crude oil, weathered oil, and sediments from the spilled sites after the Hebei Spirit oil spill, Taean, South Korea (Dec. 2007). Concentrations of NAs, O3-NAs, and O4-NAs were found to be 7.8-130, 3.6-44, and 0.8-20 mg kg(-1) dw in sediments from the Taean area, respectively, which were much greater than those measured in the reference sites of Manlipo and Anmyundo beaches. Concentrations of NAs were 50-100 times greater than those (0.077-2.5 mg kg(-1) dw) of PAHs in the same sediment samples, thus the ecological risk of NAs in oil spill affected areas deserves more attention. The sedimentary profiles of oil-derived NAs and background NAs centered around compounds with 21-35 and 12-21 carbons, respectively, indicating that the crude-derived NA mixtures originating from the 2007 oil spill were persistent. Acyclic NAsn=5-20 were easily degraded compared to cyclic NAsn=21-41 during the oil weathering processes, and the ratio of oxy-NAsn=21-41 relative to NAsn=21-41 could be a novel index to estimate the degree of oil weathering in sediments. Altogether, the persistent oil-derived NAsn=21-41 could be used as a potential indicator for oil-specific contamination, as such compounds would not be much affected by the properties of coastal sediments possibly due to the high sorption of the negatively charged compounds (NAs) in sediment. PMID:24579908

  17. Pituitary tumor transforming gene and fibroblast growth factor-2 expression: potential prognostic indicators in differentiated thyroid cancer.

    PubMed

    Boelaert, K; McCabe, C J; Tannahill, L A; Gittoes, N J L; Holder, R L; Watkinson, J C; Bradwell, A R; Sheppard, M C; Franklyn, J A

    2003-05-01

    Differentiated thyroid cancers are the most common endocrine cancers, but there are no reliable molecular markers of prognosis. Pituitary tumor transforming gene (PTTG) plays several potential roles in tumor initiation and progression, including regulating mitosis and stimulating expression of fibroblast growth factor (FGF)-2. Increased expression of PTTG has been demonstrated in follicular thyroid lesions, and expression of this oncogene has been identified as a potential prognostic marker in pituitary adenomas and colon carcinomas. We assessed the expression of PTTG and FGF-2 and its receptor FGF-R-1 in 27 differentiated thyroid cancers, and we compared this with expression in 11 normal thyroids, 25 multinodular goiters, and 13 Graves' disease specimens. We also examined the relationship between gene expression and clinical markers of tumor behavior. PTTG and FGF-2 were overexpressed in thyroid carcinomas (9.5-fold increase, P = 0.003, and 5.0-fold increase, P < 0.001, respectively) compared with normal thyroid. Increased FGF-2 mRNA expression was independently associated with the findings of lymph node invasion (R(2) = 0.71; P < 0.001) and distant metastasis (R(2) = 0.55; P = 0.009) at tumor presentation, after taking into account known prognostic factors such as age and gender of the patient and size and type of the tumor. High PTTG expression was independently associated with tumor recurrence (R(2) = 0.64; P = 0.003). We conclude that PTTG and FGF-2 expression are potential prognostic markers (and perhaps therapeutic targets) for differentiated thyroid cancer. PMID:12727994

  18. Overall multi-media persistence as an indicator of potential for population-level intake of environmental contaminants

    SciTech Connect

    MacLeod, Matthew; McKone, Thomas E.

    2003-06-01

    Although it is intuitively apparent that population-level exposure to contaminants dispersed in the environment must related to the persistence of the contaminant, there has been little effort to formally quantify this link. In this paper we investigate the relationship between overall persistence in a multimedia environment and the population-level exposure as expressed by intake fraction (iF), which is the cumulative fraction of chemical emitted to the environment that is taken up by members of the population. We first confirm that for any given chemical contaminant and emission scenario the definition of iF implies that it is directly proportional to the overall multi-media persistence, P{sub OV}. We show that the proportionality constant has dimensions of time and represents the characteristic time for population intake (CTI) of the chemical from the environment. We then apply the CalTOX fate and exposure model to explore how P{sub OV} and CTI combine to determine the magnitude of iF. We find that CTI has a narrow range of possible values relative to P{sub OV} across multiple chemicals and emissions scenarios. We use data from the Canadian Environmental Protection Act Priority Substance List (PSL1) Assessments to show that exposure assessments based on empirical observation are consistent with interpretations from the model. The characteristic time for intake along different dominant exposure pathways is discussed. Results indicate that P{sub OV} derived from screening-level assessments of persistence, bioaccumulation potential, and toxicity (PBT) is a useful indicator of the potential for population-level exposure.

  19. Transcriptional Profiling of Peripheral Blood Mononuclear Cells in Pancreatic Cancer Patients Identifies Novel Genes with Potential Diagnostic Utility

    PubMed Central

    Baine, Michael J.; Chakraborty, Subhankar; Smith, Lynette M.; Mallya, Kavita; Sasson, Aaron R.; Brand, Randall E.; Batra, Surinder K.

    2011-01-01

    Background It is well known that many malignancies, including pancreatic cancer (PC), possess the ability to evade the immune system by indirectly downregulating the mononuclear cell machinery necessary to launch an effective immune response. This knowledge, in conjunction with the fact that the trancriptome of peripheral blood mononuclear cells has been shown to be altered in the context of many diseases, including renal cell carcinoma, lead us to study if any such alteration in gene expression exists in PC as it may have diagnostic utility. Methods and Findings PBMC samples from 26 PC patients and 33 matched healthy controls were analyzed by whole genome cDNA microarray. Three hundred eighty-three genes were found to be significantly different between PC and healthy controls, with 65 having at least a 1.5 fold change in expression. Pathway analysis revealed that many of these genes fell into pathways responsible for hematopoietic differentiation, cytokine signaling, and natural killer (NK) cell and CD8+ T-cell cytotoxic response. Unsupervised hierarchical clustering analysis identified an eight-gene predictor set, consisting of SSBP2, Ube2b-rs1, CA5B, F5, TBC1D8, ANXA3, ARG1, and ADAMTS20, that could distinguish PC patients from healthy controls with an accuracy of 79% in a blinded subset of samples from treatment naïve patients, giving a sensitivity of 83% and a specificity of 75%. Conclusions In summary, we report the first in-depth comparison of global gene expression profiles of PBMCs between PC patients and healthy controls. We have also identified a gene predictor set that can potentially be developed further for use in diagnostic algorithms in PC. Future directions of this research should include analysis of PBMC expression profiles in patients with chronic pancreatitis as well as increasing the number of early-stage patients to assess the utility of PBMCs in the early diagnosis of PC. PMID:21347333

  20. Managing the Risk of Triggered Seismicity: Can We Identify (and Avoid) Potentially Active Faults? - A Practical Case Study in Oklahoma

    NASA Astrophysics Data System (ADS)

    Zoback, M. D.; Alt, R. C., II; Walsh, F. R.; Walters, R. J.

    2014-12-01

    It is well known that throughout the central and eastern U.S. there has been a marked increase in seismicity since 2009, at least some of which appears to increased wastewater injection. No area has seen a greater increase in seismicity than Oklahoma. In this paper, we utilize newly available information on in situ stress orientation and relative magnitudes, the distribution of high volume injection wells and knowledge of the intervals used for waste water disposal to identify the factors potentially contributing to the occurrence of triggered seismicity. While there are a number of sites where in situ stress data has been successfully used to identify potentially active faults, we are investigating whether this methodology can be implemented throughout a state utilizing the types of information frequently available in areas of oil and gas development. As an initial test of this concept, we have been compiling stress orientation data from wells throughout Oklahoma provided by private industry. Over fifty new high quality data points, principally drilling-induced tensile fractures observed in image logs, result in a greatly improved understanding of the stress field in much of the state. A relatively uniform ENE direction of maximum compressive stress is observed, although stress orientations (and possibly relative stress magnitudes) differ in the southern and southwestern parts of the state. The proposed methodology can be tested in the area of the NE-trending fault that produced the M 5+ earthquakes in the Prague, OK sequence in 2011, and the Meers fault in southwestern OK, that produced a M~7 reverse faulting earthquake about 1100 years ago. This methodology can also be used to essentially rule out slip on other major faults in the area, such as the ~N-S trending Nemaha fault system. Additional factors leading to the occurrence of relatively large triggered earthquakes in Oklahoma are 1) the overall increase in injection volumes throughout the state in recent years (especially in some particular areas) 2) the injection of waste water in a geologic formation laying directly above crystalline basement rocks and 3) the widespread distribution of injection wells.

  1. Planting Sentinel European Trees in Eastern Asia as a Novel Method to Identify Potential Insect Pest Invaders

    PubMed Central

    Roques, Alain; Fan, Jian-ting; Courtial, Béatrice; Zhang, Yan-zhuo; Yart, Annie; Auger-Rozenberg, Marie-Anne; Denux, Olivier; Kenis, Marc; Baker, Richard; Sun, Jiang-hua

    2015-01-01

    Quarantine measures to prevent insect invasions tend to focus on well-known pests but a large proportion of the recent invaders were not known to cause significant damage in their native range, or were not even known to science before their introduction. A novel method is proposed to detect new potential pests of woody plants in their region of origin before they are introduced to a new continent. Since Asia is currently considered to be the main supplier of insect invaders to Europe, sentinel trees were planted in China during 2007-2011 as an early warning tool to identify the potential for additional Asian insect species to colonize European trees. Seedlings (1-1.5 m tall) of five broadleaved (Quercus petraea, Q. suber, Q. ilex, Fagus sylvatica, and Carpinus betulus) and two conifer species (Abies alba and Cupressus sempervirens) were planted in blocks of 100 seedlings at two widely separated sites (one in a nursery near Beijing and the other in a forest environment near Fuyang in eastern China), and then regularly surveyed for colonization by insects. A total of 104 insect species, mostly defoliators, were observed on these new hosts, and at least six species were capable of larval development. Although a number of the insects observed were probably incidental feeders, 38 species had more than five colonization events, mostly infesting Q. petraea, and could be considered as being capable of switching to European trees if introduced to Europe. Three years was shown to be an appropriate duration for the experiment, since the rate of colonization then tended to plateau. A majority of the identified species appeared to have switched from agricultural crops and fruit trees rather than from forest trees. Although these results are promising, the method is not appropriate for xylophagous pests and other groups developing on larger trees. Apart from the logistical problems, the identification to species level of the specimens collected was a major difficulty. This situation could be improved by the development of molecular databases. PMID:25993342

  2. Ceriodaphnia dubia as a potential bio-indicator for assessing acute aluminum oxide nanoparticle toxicity in fresh water environment.

    PubMed

    Pakrashi, Sunandan; Dalai, Swayamprava; Humayun, Ahmed; Chakravarty, Sujay; Chandrasekaran, Natarajan; Mukherjee, Amitava

    2013-01-01

    Growing nanomaterials based consumer applications have raised concerns about their potential release into the aquatic ecosystems and the consequent toxicological impacts. So environmental monitoring of the nanomaterials in aqueous systems becomes imperative. The current study reveals the potential of Ceriodaphnia dubia (C. dubia) as a bio-indicator for aluminum oxide nanoparticles in a fresh water aquatic ecosystem where it occupies an important ecological niche as a primary consumer. This study aims to investigate the aluminium oxide nanoparticle induced acute toxicity on Ceriodaphnia dubia in a freshwater system. The bioavailability of the aluminum oxide nanoparticles has been studied with respect to their aggregation behavior in the system and correlated with the toxicity endpoints. The oxidative stress generated by the particles contributed greatly toward their toxicity. The crucial role of leached aluminium ion mediated toxicity in the later phases (48 h and 72 h) in conjunction with the effects from the nano-sized particles in the initial phases (24 h) puts forth the dynamics of nanotoxicity in the test system. The internalization of nanoparticles (both gross and systemic uptake) as substantiated through the transmission electron microscopy (TEM) and inductively coupled plasma optical emission spectral (ICP-OES) analysis was another major contributor toward acute toxicity. Concluding the present study, Ceriodaphnia dubia can be a promising candidate for bio-monitoring the aluminium oxide nanoparticles in a fresh water system. PMID:24040143

  3. Volatile fingerprint of Brazilian defective coffee seeds: corroboration of potential marker compounds and identification of new low quality indicators.

    PubMed

    Toci, Aline T; Farah, Adriana

    2014-06-15

    In the present work, the volatile profiles of green and roasted Brazilian defective coffee seeds and their controls were characterised, totalling 159 compounds. Overall, defective seeds showed higher number and concentration of volatile compounds compared to those of control seeds, especially pyrazines, pyrroles and phenols. Corroborating our previous results, butyrolactone and hexanoic acid, previously considered as potential defective seeds' markers, were observed only in raw and roasted defective seeds, respectively, and not in control seeds. New compounds were suggested as potential defective seeds' markers: hexanoic acid (for raw and roasted defective seeds in general), butyrolactone (for raw defective seeds in general), and 3-ethyl-2-methyl-1,3-hexadiene (for raw black seeds); β-linalool and 2-butyl-3,5-dimethylpyrazine (for roasted defective seeds in general), and 2-pentylfuran (for roasted black seeds). Additional compounds suggested as low quality indicators were 2,3,5,6-tetramethylpyrazine,2,3-butanediol and 4-ethylguaiacol, β-linalool, 2-,3-dimethylbutyl butanoate, 2-phenylethyl acetate, 2,3-butanedione, hexanedioic acid, guaiacol, 2,3-dihydro-2-methyl-1H-benzopyrrol, 3-methylpiperidine, 2-pentylpiperidine, 3-octen-2-one, 2-octenal, 2-pentylfuran and 2-butyl-3-methylpyrazine. PMID:24491734

  4. Ceriodaphnia dubia as a Potential Bio-Indicator for Assessing Acute Aluminum Oxide Nanoparticle Toxicity in Fresh Water Environment

    PubMed Central

    Pakrashi, Sunandan; Dalai, Swayamprava; Humayun, Ahmed; Chakravarty, Sujay; Chandrasekaran, Natarajan; Mukherjee, Amitava

    2013-01-01

    Growing nanomaterials based consumer applications have raised concerns about their potential release into the aquatic ecosystems and the consequent toxicological impacts. So environmental monitoring of the nanomaterials in aqueous systems becomes imperative. The current study reveals the potential of Ceriodaphnia dubia (C. dubia) as a bio-indicator for aluminum oxide nanoparticles in a fresh water aquatic ecosystem where it occupies an important ecological niche as a primary consumer. This study aims to investigate the aluminium oxide nanoparticle induced acute toxicity on Ceriodaphnia dubia in a freshwater system. The bioavailability of the aluminum oxide nanoparticles has been studied with respect to their aggregation behavior in the system and correlated with the toxicity endpoints. The oxidative stress generated by the particles contributed greatly toward their toxicity. The crucial role of leached aluminium ion mediated toxicity in the later phases (48 h and 72 h) in conjunction with the effects from the nano-sized particles in the initial phases (24 h) puts forth the dynamics of nanotoxicity in the test system. The internalization of nanoparticles (both gross and systemic uptake) as substantiated through the transmission electron microscopy (TEM) and inductively coupled plasma optical emission spectral (ICP-OES) analysis was another major contributor toward acute toxicity. Concluding the present study, Ceriodaphnia dubia can be a promising candidate for bio-monitoring the aluminium oxide nanoparticles in a fresh water system. PMID:24040143

  5. Identifying conservation successes, failures and future opportunities; assessing recovery potential of wild ungulates and tigers in Eastern Cambodia.

    PubMed

    O'Kelly, Hannah J; Evans, Tom D; Stokes, Emma J; Clements, Tom J; Dara, An; Gately, Mark; Menghor, Nut; Pollard, Edward H B; Soriyun, Men; Walston, Joe

    2012-01-01

    Conservation investment, particularly for charismatic and wide-ranging large mammal species, needs to be evidence-based. Despite the prevalence of this theme within the literature, examples of robust data being generated to guide conservation policy and funding decisions are rare. We present the first published case-study of tiger conservation in Indochina, from a site where an evidence-based approach has been implemented for this iconic predator and its prey. Despite the persistence of extensive areas of habitat, Indochina's tiger and ungulate prey populations are widely supposed to have precipitously declined in recent decades. The Seima Protection Forest (SPF), and broader Eastern Plains Landscape, was identified in 2000 as representing Cambodia's best hope for tiger recovery; reflected in its designation as a Global Priority Tiger Conservation Landscape. Since 2005 distance sampling, camera-trapping and detection-dog surveys have been employed to assess the recovery potential of ungulate and tiger populations in SPF. Our results show that while conservation efforts have ensured that small but regionally significant populations of larger ungulates persist, and density trends in smaller ungulates are stable, overall ungulate populations remain well below theoretical carrying capacity. Extensive field surveys failed to yield any evidence of tiger, and we contend that there is no longer a resident population within the SPF. This local extirpation is believed to be primarily attributable to two decades of intensive hunting; but importantly, prey densities are also currently below the level necessary to support a viable tiger population. Based on these results and similar findings from neighbouring sites, Eastern Cambodia does not currently constitute a Tiger Source Site nor meet the criteria of a Global Priority Tiger Landscape. However, SPF retains global importance for many other elements of biodiversity. It retains high regional importance for ungulate populations and potentially in the future for Indochinese tigers, given adequate prey and protection. PMID:23077476

  6. Assessing the Connection Between Health and Education: Identifying Potential Leverage Points for Public Health to Improve School Attendance

    PubMed Central

    Kuo, Tony; Coller, Karen; Guerrero, Lourdes R.; Wong, Mitchell D.

    2014-01-01

    Objectives. We examined multiple variables influencing school truancy to identify potential leverage points to improve school attendance. Methods. A cross-sectional observational design was used to analyze inner-city data collected in Los Angeles County, California, during 2010 to 2011. We constructed an ordinal logistic regression model with cluster robust standard errors to examine the association between truancy and various covariates. Results. The sample was predominantly Hispanic (84.3%). Multivariable analysis revealed greater truancy among students (1) with mild (adjusted odds ratio [AOR] = 1.57; 95% confidence interval [CI] = 1.22, 2.01) and severe (AOR = 1.80; 95% CI = 1.04, 3.13) depression (referent: no depression), (2) whose parents were neglectful (AOR = 2.21; 95% CI = 1.21, 4.03) or indulgent (AOR = 1.71; 95% CI = 1.04, 2.82; referent: authoritative parents), (3) who perceived less support from classes, teachers, and other students regarding college preparation (AOR = 0.87; 95% CI = 0.81, 0.95), (4) who had low grade point averages (AOR = 2.34; 95% CI = 1.49, 4.38), and (5) who reported using alcohol (AOR = 3.47; 95% CI = 2.34, 5.14) or marijuana (AOR = 1.59; 95% CI = 1.06, 2.38) during the past month. Conclusions. Study findings suggest depression, substance use, and parental engagement as potential leverage points for public health to intervene to improve school attendance. PMID:25033134

  7. Identifying Conservation Successes, Failures and Future Opportunities; Assessing Recovery Potential of Wild Ungulates and Tigers in Eastern Cambodia

    PubMed Central

    O'Kelly, Hannah J.; Evans, Tom D.; Stokes, Emma J.; Clements, Tom J.; Dara, An; Gately, Mark; Menghor, Nut; Pollard, Edward H. B.; Soriyun, Men; Walston, Joe

    2012-01-01

    Conservation investment, particularly for charismatic and wide-ranging large mammal species, needs to be evidence-based. Despite the prevalence of this theme within the literature, examples of robust data being generated to guide conservation policy and funding decisions are rare. We present the first published case-study of tiger conservation in Indochina, from a site where an evidence-based approach has been implemented for this iconic predator and its prey. Despite the persistence of extensive areas of habitat, Indochina's tiger and ungulate prey populations are widely supposed to have precipitously declined in recent decades. The Seima Protection Forest (SPF), and broader Eastern Plains Landscape, was identified in 2000 as representing Cambodia's best hope for tiger recovery; reflected in its designation as a Global Priority Tiger Conservation Landscape. Since 2005 distance sampling, camera-trapping and detection-dog surveys have been employed to assess the recovery potential of ungulate and tiger populations in SPF. Our results show that while conservation efforts have ensured that small but regionally significant populations of larger ungulates persist, and density trends in smaller ungulates are stable, overall ungulate populations remain well below theoretical carrying capacity. Extensive field surveys failed to yield any evidence of tiger, and we contend that there is no longer a resident population within the SPF. This local extirpation is believed to be primarily attributable to two decades of intensive hunting; but importantly, prey densities are also currently below the level necessary to support a viable tiger population. Based on these results and similar findings from neighbouring sites, Eastern Cambodia does not currently constitute a Tiger Source Site nor meet the criteria of a Global Priority Tiger Landscape. However, SPF retains global importance for many other elements of biodiversity. It retains high regional importance for ungulate populations and potentially in the future for Indochinese tigers, given adequate prey and protection. PMID:23077476

  8. Identifying flood deposits in lake sediments : Changing frequencies and potential links to long-term climate change

    NASA Astrophysics Data System (ADS)

    Støren, E.; Paasche, Ø.; Dahl, S. O.; Nesje, A.; Kolstad, E.

    2012-04-01

    In an effort to improve the understanding of long-term variability in flood frequency and how they relate to climate change, we have developed a method that objectively identifies the sedimentary imprint of individual river floods in downstream lake basins. Here we have applied the method to two lake sediment records collected from two different mountainous areas in Southern Norway, resulting in detailed records of Holocene river-flood activity covering the last c. 10,000 years. Identification of historically known floods during instrumental and historical times (AD 1958, 1938, 1860 and 1789) suggest that the approach is reliable not just for recent times, but also for the entire Holocene. The results indicate that both frequency and distribution of floods over southern Norway has changed significantly during the Holocene. Flood frequency was, for example, highest over the last 2300 years when recorded flood frequency was about 2-3 times higher than the Holocene mean. During the early and middle Holocene flood frequency was on the contrary generally low; around half of the Holocene mean. The two examined flood records, retrieved from lakes lying c. 70 km apart, reveal subtle differences, but nonetheless produce a pattern that alternates on centennial timescales. Our results indicate that these differences cannot be explained by local conditions associated with the respective catchments. Moreover, we rule out possible external factors such as altitudinal changes due to isostatic movement, changes in vegetation cover etc. The present regional discharge regime is dominated by spring-summer snow-melt and we conclude that the observed changes in flood frequency most likely is attributed to changes in snow cover, which primarily is a function of winter precipitation and the accumulation (integrated over decades) of perennial snowfields in the mountains.

  9. Identifying and Mitigating Potential Nutrient and Sediment Hot Spots under a Future Scenario in the Missouri River Basin

    SciTech Connect

    Wu, May; Zhang, Zhonglong

    2015-09-01

    Using the Soil and Water Assessment Tool (SWAT) for large-scale watershed modeling could be useful for evaluating the quality of the water in regions that are dominated by nonpoint sources in order to identify potential “hot spots” for which mitigating strategies could be further developed. An analysis of water quality under future scenarios in which changes in land use would be made to accommodate increased biofuel production was developed for the Missouri River Basin (MoRB) based on a SWAT model application. The analysis covered major agricultural crops and biofuel feedstock in the MoRB, including pasture land, hay, corn, soybeans, wheat, and switchgrass. The analysis examined, at multiple temporal and spatial scales, how nitrate, organic nitrogen, and total nitrogen; phosphorus, organic phosphorus, inorganic phosphorus, and total phosphorus; suspended sediments; and water flow (water yield) would respond to the shifts in land use that would occur under proposed future scenarios. The analysis was conducted at three geospatial scales: (1) large tributary basin scale (two: Upper MoRB and Lower MoRB); (2) regional watershed scale (seven: Upper Missouri River, Middle Missouri River, Middle Lower Missouri River, Lower Missouri River, Yellowstone River, Platte River, and Kansas River); and (3) eight-digit hydrologic unit (HUC-8) subbasin scale (307 subbasins). Results showed that subbasin-level variations were substantial. Nitrogen loadings decreased across the entire Upper MoRB, and they increased in several subbasins in the Lower MoRB. Most nitrate reductions occurred in lateral flow. Also at the subbasin level, phosphorus in organic, sediment, and soluble forms was reduced by 35%, 45%, and 65%, respectively. Suspended sediments increased in 68% of the subbasins. The water yield decreased in 62% of the subbasins. In the Kansas River watershed, the water quality improved significantly with regard to every nitrogen and phosphorus compound. The improvement was clearly attributable to the conversion of a large amount of land to switchgrass. The Middle Lower Missouri River and Lower Missouri River were identified as hot regions. Further analysis identified four subbasins (10240002, 10230007, 10290402, and 10300200) as being the most vulnerable in terms of sediment, nitrogen, and phosphorus loadings. Overall, results suggest that increasing the amount of switchgrass acreage in the hot spots should be considered to mitigate the nutrient loads. The study provides an analytical method to support stakeholders in making informed decisions that balance biofuel production and water sustainability.

  10. Effect of sulphur deprivation on osmotic potential components and nitrogen metabolism in oilseed rape leaves: identification of a new early indicator.

    PubMed

    Sorin, Elise; Etienne, Philippe; Maillard, Anne; Zamarreño, Angel-Mari; Garcia-Mina, José-Maria; Arkoun, Mustapha; Jamois, Frank; Cruz, Florence; Yvin, Jean-Claude; Ourry, Alain

    2015-10-01

    Identification of early sulphur (S) deficiency indicators is important for species such as Brassica napus, an S-demanding crop in which yield and the nutritional quality of seeds are negatively affected by S deficiency. Because S is mostly stored as SO4 (2-) in leaf cell vacuoles and can be mobilized during S deficiency, this study investigated the impact of S deprivation on leaf osmotic potential in order to identify compensation processes. Plants were exposed for 28 days to S or to chlorine deprivation in order to differentiate osmotic and metabolic responses. While chlorine deprivation had no significant effects on growth, osmotic potential and nitrogen metabolism, Brassica napus revealed two response periods to S deprivation. The first one occurred during the first 13 days during which plant growth was maintained as a result of vacuolar SO4 (2-) mobilization. In the meantime, leaf osmotic potential of S-deprived plants remained similar to control plants despite a reduction in the SO4 (2-) osmotic contribution, which was fully compensated by an increase in NO3 (-), PO4 (3-) and Cl(-) accumulation. The second response occurred after 13 days of S deprivation with a significant reduction in growth, leaf osmotic potential, NO3 (-) uptake and NO3 (-) reductase activity, whereas amino acids and NO3 (-) were accumulated. This kinetic analysis of S deprivation suggested that a ([Cl(-)]+[NO3 (-)]+[PO4 (3-)]):[SO4 (2-)] ratio could provide a relevant indicator of S deficiency, modified nearly as early as the over-expression of genes encoding SO4 (2-) tonoplastic or plasmalemmal transporters, with the added advantage that it can be easily quantified under field conditions. PMID:26139826

  11. Land use as an explanatory factor for potential phosphorus loss risk, assessed by P indices and their governing parameters.

    PubMed

    Zhou, Bin; Vogt, Rolf D; Lu, Xueqiang; Yang, Xiaoguang; Lü, Changwei; Mohr, Christian W; Zhu, Liang

    2015-08-01

    The total level of phosphorus (P) and the distribution of P pools in the topsoil are significantly affected by the excessive application of mineral and organic fertilizers connected with intensive agriculture. This leads to an increased potential risk for P loss, and then contributes to freshwater eutrophication. Soil test P (STP), P sorption index (PSI) and degree of P saturation (DPS) are commonly applied as proxies for assessing the risk of P loss. Although conceptually based, the empirical relationships between these operationally defined proxies and the actual P flux exhibit large spatial variations. Herein, a comprehensive synoptic study and monitoring of soil has been conducted in a watershed in north-eastern China. A set of conventional indicators for soil P loss risk were measured along with the main P pools, P sorption indices, texture, organic matter, as well as Fe and Al oxides and other mineral compositions. Moreover, detailed soil P speciation was conducted using phosphorus nuclear magnetic resonance ((31)P NMR) spectroscopy. In addition, phosphatase activities in the soils were determined for each land use soil category. The results reflected that the soil content of total P, total inorganic P and STP increased significantly following the order of increasing management intensity. STP, being strongly coupled to the application of P fertilizers, was a strong explanatory factor for the spatial differences in DPS - both between and within different land uses. The dominant inorganic and organic P species in the soils were orthophosphate and monoester-P, respectively. Their contents were oppositely correlated with the degree of management influence, with the amount of orthophosphate positively related. Alkaline phosphomonoesterase (AlP) represented the highest activities among the four representative phosphatases, i.e. enzymes that hydrolyze organic P - releasing labile orthophosphate. Orchard soils were found to contain the highest levels of monoester P as well as high AlP activities. This indicates a strong capacity to produce labile orthophosphate. Our results suggest that the type of land use can be employed as a general explanatory factor for considering the potential high risk of loss of P. Regionalized P loss parameters will further improve the accuracy of risk assessment. PMID:26151813

  12. Potential groundwater age tracer found: Halon-1301 (CF3Br), as previously identified as CFC-13 (CF3Cl)

    NASA Astrophysics Data System (ADS)

    Beyer, Monique; van der Raaij, Rob; Morgenstern, Uwe; Jackson, Bethanna

    2014-09-01

    Groundwater dating using anthropogenic and natural tracer substances is a powerful tool for understanding groundwater dynamics for improved management of groundwater resources. Due to limitations in individual dating methods, often multiple tracers are used to reduce ambiguities. It is commonly accepted that there is a need for further complementary age tracers, in addition to current ones (e.g., tritium, SF6, and CFCs). We propose a potential new groundwater age tracer, Halon-1301 (CF3Br), which can easily be determined using gas chromatography with an attached electron capture detector (GC/ECD) developed by Busenberg and Plummer (2008). Its peak was noted by Busenberg and Plummer (2008), but they believed it to be CFC-13 (CF3Cl) at that time. We performed rigorous tests on gases containing or excluding Halon-1301 and CFC-13 and modern water samples and concluded that the two compounds have extremely similar retention times. Additionally, we found that the ECD response of CFC-13 is far too low to be detected in groundwater or air using standard volumes and sampling techniques