Science.gov

Sample records for identify potential indicators

  1. Identifying potentially preventable complications using a present on admission indicator.

    PubMed

    Hughes, John S; Averill, Richard F; Goldfield, Norbert I; Gay, James C; Muldoon, John; McCullough, Elizabeth; Xiang, Jean

    2006-01-01

    This article describes the development of Potentially Preventable Complications (PPCs), a new method that uses a present on admission (POA) indicator to identify in-hospital complications among secondary diagnoses that arise after admission. Analyses that used PPCs to obtain risk-adjusted complication rates for California hospitals showed that (1) the POA indicator is essential for identifying complications, (2) frequency of complications varies by reason for admission and severity of illness (SOI), (3) complications are associated with higher hospital charges, longer lengths of stay, and increased mortality, and (4) hospital complication rates tend to be stable over time. PMID:17290649

  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, Lus C; Esteves, Maria P; Carvalheiro, Florbela; Grio, 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. Patient-identified quality indicators for colonoscopy services

    PubMed Central

    Sewitch, Maida J; Dub, Catherine; Brien, Stephanie; Jiang, Mengzhu; Hilsden, Robert J; Barkun, Alan N; Armstrong, David

    2013-01-01

    BACKGROUND: Current quality improvement tools for endoscopy services, such as the Global Rating Scale (GRS), emphasize the need for patient-centred care. However, there are no studies that have investigated patient expectations and/or perceptions of quality indicators in endoscopy services. OBJECTIVES: To identify quality indicators for colonoscopy services from the patient perspective; to rate indicators of importance; to determine factors that influence indicator ratings; and to compare the identified indicators with those of the GRS. METHODS: A two-phase mixed methods study was undertaken in Montreal (Quebec), Calgary (Alberta) and Hamilton (Ontario) among patients ?18 years of age who spoke and read English or French. In phase 1, focus group participants identified quality indicators that were then used to construct a survey questionnaire. In phase 2, survey questionnaires, which were completed immediately after colonoscopy, prompted respondents to rate the 20 focus group-derived indicators according to their level of importance (low, medium, high) and to list up to nine additional items. Multiple logistic regression analysis was used to determine the factors that influenced focus group-derived indicator ratings. Patient-identified indicators were compared with those used in the GRS to identify novel indicators. RESULTS: Three quality indicator themes were identified by 66 participants in 12 focus groups: communication, comfort and service environment. Of the 828 surveys distributed, 402 (48.6%) were returned and 65% of focus group-derived indicators were rated highly important by at least 55% of survey respondents. Indicator ratings differed according to age, sex, site and perceived colorectal cancer risk. Of the 29 patient-identified indicators, 17 (58.6%) were novel. CONCLUSIONS: Patients identified 17 novel quality indicators, suggesting that patients and health professionals differ in their perspectives with respect to quality in colonoscopy services. PMID:23378980

  9. 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…

  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 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

  12. Cambrian potential indicated in Kentucky Rome trough

    SciTech Connect

    Harris, D.C.; Drahovzal, J.A.

    1996-02-19

    This paper reviews recent gas discoveries in the Kentucky Rome trough and the implications for future developments. It reviews the geology and stratigraphy of this structure and identifies the potential zones of production and trapping mechanisms. It provides results from geologic logs and seismic data to provide cross sectional and structural interpretations. Finally it discusses the gas composition of natural gas recovered from the basin.

  13. Debulking procedures: potential device specific indications.

    PubMed

    Schwarzwlder, Uwe; Zeller, Thomas

    2010-03-01

    During the past decade, the endovascular treatment of peripheral arterial disease has become more widespread due to the impressive extension of the endovascular toolbox to include different atherectomy technologies. The promise of atherectomy is to avoid the "barotraumas" defined as complications of traditional angioplasty such as dissection, elastic recoil, and disruption of the internal elastic lamina resulting in overwhelming neointima and smooth muscle cell proliferation. The oldest atherectomy technologies are the excimer laser and the Rotablator. The excimer laser technology is based on the principle of photoablation converting occlusive material into microbubbles being immediately dissolved into the blood. The Rotablator and the newer diamondback device are high speed rotational "sanding" devices particularly developed for the treatment of highly calcified plaque particularly in small vessel lesions, such as the popliteal and infrapopliteal segments. The Silverhawk system, currently the most widespread used device, is a directional atherectomy device particularly designed for eccentric and not severely calcified infrainguinal lesions whereas a variation of this device, the Rockhawk, is dedicated for the treatment of calcified plaques. The Jetstream system is the latest approved rotational atherectomy device focusing on native arteries with a reference vessel diameter of 4-6 mm in its current version; uniquely this device also has an aspiration capability making the device not only an atherectomy device but potentially also a thrombectomy device. This article will review the different indications for the use of these atherectomy devices including tips and specific device limitations. PMID:20123432

  14. Solution Potentials Indicate Aluminum-Alloy Tempers

    NASA Technical Reports Server (NTRS)

    Danford, M. D.

    1985-01-01

    Report discusses use of solution potential as measure of temper of aluminum alloys. Technique based on fact that different tempers or heat treatments exhibit different solution potentials as function of aging time.

  15. 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…

  16. 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

  17. Identifying Quality Indicators of SAE and FFA: A Delphi Approach

    ERIC Educational Resources Information Center

    Jenkins, Charles Cordell, III; Kitchel, Tracy

    2009-01-01

    The purpose of this study was to determine quality indicators for SAE and FFA according to 36 experts across the United States. This is a part of a larger study looking at all components of the traditional three-circle model. The study utilized the Delphi technique to garner expert opinion about quality indicators in Agricultural Education. For

  18. 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...

  19. 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

  20. 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.

  1. Multi-indicator radiation identifier for land mines

    NASA Astrophysics Data System (ADS)

    Hussein, Esam M. A.

    2002-08-01

    This paper presents a radioisotope-based concept for determining whether an anomaly in the ground contains an explosive material or not. Nitrogen-based explosives, commonly used in landmines, are rich in carbon, nitrogen and oxygen. Hydrogen is also present in the explosive material, but can be found as well in the mine casing (if plastic or wood). Moreover, explosive materials have a density that is higher than that of most organic materials, but lower than that of metals. All these features are employed in a detection concept that relies on the use of an isotopic source of neutrons. The amount of slowing-down of the source's fast neutrons, as they scatter to the thermal energy, is indicative of the hydrogen content. The enhancement of the intensity of fast neutrons, due to resonance scattering by carbon, nitrogen and oxygen, is indicative of their combined presence. Moreover, the photons that accompany neutron production, are Compton-scattered, providing an indication of the electron-density of the anomaly. These three measurements, contrasted against those obtained from the surrounding soil, are indicative of the presence or absence of a mine, or a mine-like, target.

  2. 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

  3. Identifying indices of learning for alpha neurofeedback training.

    PubMed

    Dempster, T; Vernon, D

    2009-12-01

    Neurofeedback has been around for decades and has applications for both clinical and healthy populations yet there is no standard method for measuring learning or a way of defining successful learning. Thus the aim of this study was to focus on alpha neurofeedback and examine changes in three different measures: amplitude, percent time, and integrated alpha, across four methods: within sessions, across sessions, within sessions compared to baseline, and across sessions compared to baseline. Participants completed 10 weekly sessions of eyes open alpha (8-12 Hz) neurofeedback training (NFT) at Pz. Whilst all three measures showed changes within sessions, the inclusion of baselines revealed that such changes represented a return to baseline levels rather than an increase in alpha. Changes across sessions were only evident in amplitude and inclusion of baseline showed that NFT did not elicit any changes beyond baseline levels. Given this a case is made for incorporating baseline measures when attempting to identify evidence of learning. It is also suggested that both amplitude and percent time measures are used independently rather than incorporate them into a more conservative and less sensitive integrated measure. Finally, focusing on within sessions changes may be a more useful approach in identifying changes resulting from NFT. PMID:19760142

  4. SELECTING INDICATORS OF BIODIVERSITY FOR CONSERVATION PLANNING: IDENTIFYING THE MECHANISMS BEHIND INDICATOR GROUP PERFORMANCE

    EPA Science Inventory

    Most conservation planning is constrained by time and funding. In particular, the selection of areas to protect biodiversity must often be completed with limited data on species distributions. Consequently, different groups of species have been proposed as indicators or surroga...

  5. Identify potentially eligible participants | accrualnet.cancer.gov

    Cancer.gov

    Your institutions information system is an obvious starting point for identifying potential clinical trial participants. If your medical records are electronic, then the process may be simpler. No matter which tools you use, it is important to know all the potentially eligible participants are being identified.

  6. Identifying indicators of illegal behaviour: carnivore killing in human-managed landscapes

    PubMed Central

    St John, Freya A. V.; Keane, Aidan M.; Edwards-Jones, Gareth; Jones, Lauren; Yarnell, Richard W.; Jones, Julia P. G.

    2012-01-01

    Managing natural resources often depends on influencing people's behaviour, however effectively targeting interventions to discourage environmentally harmful behaviours is challenging because those involved may be unwilling to identify themselves. Non-sensitive indicators of sensitive behaviours are therefore needed. Previous studies have investigated people's attitudes, assuming attitudes reflect behaviour. There has also been interest in using people's estimates of the proportion of their peers involved in sensitive behaviours to identify those involved, since people tend to assume that others behave like themselves. However, there has been little attempt to test the potential of such indicators. We use the randomized response technique (RRT), designed for investigating sensitive behaviours, to estimate the proportion of farmers in north-eastern South Africa killing carnivores, and use a modified logistic regression model to explore relationships between our best estimates of true behaviour (from RRT) and our proposed non-sensitive indicators (including farmers' attitudes, and estimates of peer-behaviour). Farmers' attitudes towards carnivores, question sensitivity and estimates of peers' behaviour, predict the likelihood of farmers killing carnivores. Attitude and estimates of peer-behaviour are useful indicators of involvement in illicit behaviours and may be used to identify groups of people to engage in interventions aimed at changing behaviour. PMID:21795272

  7. 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

  8. 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

  9. 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 ...

  10. 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

  11. Identifying potential cancer driver genes by genomic data integration

    PubMed Central

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

    2013-01-01

    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. PMID:24346768

  12. Identifying potential cancer driver genes by genomic data integration.

    PubMed

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

    2013-01-01

    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. PMID:24346768

  13. 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.

  14. 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

  15. 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.

  16. Paediatric tonsillotomy--an Irish perspective on potential evolving indications.

    PubMed

    Fitzgerald, C; Oosthuizen, J C; Colreavy, M

    2015-04-01

    Tonsillotomy is the preferred treatment of some otolaryngologists for younger patients (under 3 years) with low body weight (under 15 kgs) and a history of obstructive sleep apnoea. The use of the technique in the same patient cohort for recurrent tonsillitis remains controversial. The aim of this study was to evaluate the indications and outcomes of paediatric patients undergoing tonsillotomy (with or without adenoidectomy) at a paediatric ENT centre in Ireland. Patients were identified from a prospectively maintained database and chart review was completed. A total of 23 patients were identified who underwent tonsillotomy. The commonest indication was Obstructive Sleep Apnoea (OSA) in 15 patients (65%). Outcomes following tonsillotomy compared favourably with traditional tonsillectomy. No intra-operative or post-operative complications were recorded (0%). No patients required readmission or later tonsillectomy (0%). At follow-up 19/23 patients with OSA (82.6%) had complete symptom resolution. Tonsillotomy appears to represent a safe, effective treatment option in the paediatric population, however, its role in recurrent tonsillitis remains controversial. PMID:26016307

  17. [Indications for studying evoked potentials in childhood. Methods--indications--value].

    PubMed

    Grke, W

    1986-01-01

    Evoked potentials (EP) represent a valuable addition to currently applied diagnostic methods in neuropediatrics. Profound knowledge of the neurophysiological conditions producing EP-alterations allows basic conclusions, that cannot be gained or replaced by other investigations. EP-investigation demonstrate the existence but not the nature of a lesion in the CNS. Further diagnostic work-up usually will be necessary. Proved EP-alterations produce reproducible diagnostic results and give clues regarding its localization. Evoked potentials can be used as a screening-method for neuropediatric diseases. By follow-up examinations it is possible to show, wether there is progression or not. Testing for evoked potentials is indicated in suspected cerebral palsy in infants, in all cases of psychomotor retardation of unknown origin, impairment of vision or hearing, in cases of brain trauma or in suspected brainstem process, lesions of N. opticus or visual projective systems, neurometabolic or degenerative CNS disease, phacomatosis, progressive myoclonic epilepsy, ceroidlipofuscinosis Jansky-Bielschowski, benign partial epilepsy with extreme somatosensory evoked potentials, Ramsey-Hunt-Syndrome and aplasia of the corpus callosum. PMID:3807249

  18. 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

  19. Scavenging rate ecoassay: a potential indicator of estuary condition.

    PubMed

    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

  20. 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

  1. Identifying bryostatins and potential precursors from the bryozoan Bugula neritina.

    PubMed

    Manning, Thomas J; Land, Michael; Rhodes, Emily; Chamberlin, Linda; Rudloe, Jack; Phillips, Dennis; Lam, Tukiet T; Purcell, Jeremiah; Cooper, Helen J; Emmett, Mark R; Marshall, Alan G

    2005-07-01

    The bryozoan species Bugula neritina contains the anticancer agent bryostatin. Bryostatin has been extracted from these sessile marine invertebrates since the late 1960s from the Gulf of California, Gulf of Mexico, as well as various locations on the eastern and western rims of the Pacific Ocean. In this work we are focusing on animals harvested in the Gulf of Mexico near Alligator Point (Florida). Using Inductively Coupled Plasma-Mass Spectrometry (ICP-MS) we measure the concentration of 70 elements in B. neritina, a sea squirt, and the sediment from the point of harvesting. This data has helped us generate an extraction process for marine natural products. Combining UV/VIS absorbance measurements with Matrix Assisted Laser Desorption Ionization-Time of Flight-Mass Spectrometer (MALDI-TOF-MS), we demonstrated that the specific form of bryostatin extracted is a function of the solvent. A 9.4T Fourier Transform-Ion Cyclotron Resonance (FT-ICR) mass spectrometer, whose sensitivity, mass accuracy, and resolving power allowed the exact empirical formulas of potential precursors of bryostatin to be identified, was employed. Finally we examine extracts of 14 marine species of the Gulf of Mexico, from the sand trout (Cynoscion arenarius) to chicken liver sponge (Chrondrilla nucula), all recently collected, which had shown some medicinal activity thirty years ago in a National Cancer Institute study. By the MALDI-TOF-MS, we were able to identify mass spectral features that correspond to different variations of the basic bryostatin structure, which raises the question if the bryozoans are the original source of bryostatin. PMID:15938194

  2. 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.

  3. 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...

  4. 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...

  5. Comparative analysis of viral pathogens and potential indicators in shellfish.

    PubMed

    Muniain-Mujika, I; Calvo, M; Lucena, F; Girones, R

    2003-05-25

    Shellfish can be responsible of outbreaks of infectious diseases and current health measures do not guarantee the absence of viral pathogens in this product. Here we examine the presence of pathogenic viruses and potential indicators in shellfish in a comparative analysis.Sixty shellfish samples collected in three areas with different levels of faecal contamination were analysed for Escherichia coli, total coliforms, Clostridium perfringens, somatic coliphages, F-specific phages of RNA (F-RNA), bacteriophages infecting Bacteroides fragilis RYC2056, human adenovirus, enterovirus and hepatitis A virus (HAV). Viruses were eluted in a glycine buffer at pH 10. The overall percentage of viral pathogens detected was 47% for human adenoviruses, 19% for enteroviruses and 24% for HAV. Since all the samples positive for enterovirus and HAV were also positives for human adenovirus, the latter may be considered useful as a molecular index of viral contamination in shellfish. No significant differences in the bioaccumulation of bacteria and bacteriophages for oysters or mussels were observed. It was found that the probability of detection of any of the pathogenic virus decreases as the temperature of shellfish growing waters increases. However, the probability of detecting viruses increases when phages of B. fragilis are found. Although more data are needed in order to fulfil the need of viral indicators for controlling the presence of human viruses in shellfish, the obtained results indicate that phages infecting B. fragilis RYC2056 could be a suitable group of bacteriophages to be used as an indicator of the presence of viruses in shellfish. PMID:12672594

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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

  11. Protein phosphorylation profiling identifies potential mechanisms for direct immunotoxicity.

    PubMed

    Shao, Jia; Stout, Inge; Hendriksen, Peter J M; van Loveren, Henk; Peijnenburg, Ad A C M; Volger, Oscar L

    2016-01-01

    Signaling networks are essential elements that are involved in diverse cellular processes. One group of fundamental components in various signaling pathways concerns protein tyrosine kinases (PTK). Various toxicants have been demonstrated to exert their toxicity via modulation of tyrosine kinase activity. The present study aimed to identify common cellular signaling pathways that are involved in chemical-induced direct immunotoxicity. To this end, an antibody array-based profiling approach was applied to assess effects of five immunotoxicants, two immunosuppressive drugs and two non-immunotoxic control chemicals on the phosphorylation of 28 receptor tyrosine kinases and 11 crucial signaling nodes in Jurkat T-cells. The phosphorylation of ribosomal protein S6 (RPS6) and of kinases Akt, Src and p44/42 were found to be commonly regulated by immunotoxicants and/or immunosuppressive drugs (at least three compounds), with the largest effect observed upon RPS6. Flow cytometry and Western blotting were used to further examine the effect of the model immunotoxicant TBTO on the components of the mTOR-p70S6K-RPS6 pathway. These analyses revealed that both TBTO and the mTOR inhibitor rapamycin inactivate RPS6, but via different mechanisms. Finally, a comparison of the protein phosphorylation data to previously obtained transcriptome data of TBTO-treated Jurkat cells resulted in a good correlation at the pathway level and indicated that TBTO affects ribosome biogenesis and leukocyte migration. The effect of TBTO on the latter process was confirmed using a CXCL12 chemotaxis assay. PMID:25715851

  12. 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...

  13. 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…

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Identifying indicators of harmful and problem gambling in a Canadian sample through receiver operating characteristic analysis.

    PubMed

    Quilty, Lena C; Avila Murati, Daniela; Bagby, R Michael

    2014-03-01

    Many gamblers would prefer to reduce gambling on their own rather than to adopt an abstinence approach within the context of a gambling treatment program. Yet responsible gambling guidelines lack quantifiable markers to guide gamblers in wagering safely. To address these issues, the current investigation implemented receiver operating characteristic (ROC) analysis to identify behavioral indicators of harmful and problem gambling. Gambling involvement was assessed in 503 participants (275 psychiatric outpatients and 228 community gamblers) with the Canadian Problem Gambling Index. Overall gambling frequency, duration, and expenditure were able to distinguish harmful and problematic gambling at a moderate level. Indicators of harmful gambling were generated for engagement in specific gambling activities: frequency of tickets and casino; duration of bingo, casino, and investments; and expenditures on bingo, casino, sports betting, games of skill, and investments. Indicators of problem gambling were similarly produced for frequency of tickets and casino, and expenditures on bingo, casino, games of skill, and investments. Logistic regression analyses revealed that overall gambling frequency uniquely predicted the presence of harmful and problem gambling. Furthermore, frequency indicators for tickets and casino uniquely predicted the presence of both harmful and problem gambling. Together, these findings contribute to the development of an empirically based method enabling the minimization of harmful or problem gambling through self-control rather than abstinence. PMID:23647158

  20. Teacher Leadership: A Profile To Identify the Potential.

    ERIC Educational Resources Information Center

    Krisko, Mary Ellen

    This study examined teacher leadership as a step beyond the traditional teacher role, developing a profile of the teacher leader. Formal and informal teacher leaders responded to statements that revealed identifiable descriptors of characteristics or attributes of effective teacher leaders who lead beyond the classroom. These descriptors were

  1. 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

  2. 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...

  3. 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...

  4. 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

  5. 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

  6. 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...

  7. Potential of isotope analysis (C, Cl) to identify dechlorination mechanisms

    NASA Astrophysics Data System (ADS)

    Cretnik, Stefan; Thoreson, Kristen; Bernstein, Anat; Ebert, Karin; Buchner, Daniel; Laskov, Christine; Haderlein, Stefan; Shouakar-Stash, Orfan; Kliegman, Sarah; McNeill, Kristopher; Elsner, Martin

    2013-04-01

    Chloroethenes are commonly used in industrial applications, and detected as carcinogenic contaminants in the environment. Their dehalogenation is of environmental importance in remediation processes. However, a detailed understanding frequently accounted problem is the accumulation of toxic degradation products such as cis-dichloroethylene (cis-DCE) at contaminated sites. Several studies have addressed the reductive dehalogenation reactions using biotic and abiotic model systems, but a crucial question in this context has remained open: Do environmental transformations occur by the same mechanism as in their corresponding in vitro model systems? The presented study shows the potential to close this research gap using the latest developments in compound specific chlorine isotope analysis, which make it possible to routinely measure chlorine isotope fractionation of chloroethenes in environmental samples and complex reaction mixtures.1,2 In particular, such chlorine isotope analysis enables the measurement of isotope fractionation for two elements (i.e., C and Cl) in chloroethenes. When isotope values of both elements are plotted against each other, different slopes reflect different underlying mechanisms and are remarkably insensitive towards masking. Our results suggest that different microbial strains (G. lovleyi strain SZ, D. hafniense Y51) and the isolated cofactor cobalamin employ similar mechanisms of reductive dechlorination of TCE. In contrast, evidence for a different mechanism was obtained with cobaloxime cautioning its use as a model for biodegradation. The study shows the potential of the dual isotope approach as a tool to directly compare transformation mechanisms of environmental scenarios, biotic transformations, and their putative chemical lab scale systems. Furthermore, it serves as an essential reference when using the dual isotope approach to assess the fate of chlorinated compounds in the environment.

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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...

  13. 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...

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

    PubMed

    Graillot, Didier; Paran, Frdric; 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

  15. Identifying potential impact of lead contamination using a geographic information system

    SciTech Connect

    Bocco, G.; Sanchez, R.

    1997-01-01

    The main objective of this research was to identify the potential hazards associated with lead contamination from fixed sources in the city of Tijuana. An exploratory model is presented that describes the potential polluting sources as well as the exposed universe. The results of the analysis provide a clear picture of the geographic distribution of hazards areas for potential lead pollution in Tijuana. The findings are indicative of the dramatic consequences of rapid industrialization and urbanization in a city where there have not been significant planning efforts to mitigate the negative effects of this growth. The approach followed helps to narrow the universe of potential pollution sources, which can help to direct attention, research priorities, and resources to the most critical areas. 16 refs.

  16. IDENTIFYING POTENTIAL MARKERS OF THE SUN'S GIANT CONVECTIVE SCALE

    SciTech Connect

    McIntosh, Scott W.; Wang, Xin; Leamon, Robert J.; Scherrer, Philip H.

    2014-04-01

    Line-of-sight magnetograms from the Helioseismic and Magnetic Imager (HMI) of the Solar Dynamics Observatory (SDO) are analyzed using a diagnostic known as the magnetic range of influence (MRoI). The MRoI is a measure of the length over which a photospheric magnetogram is balanced and so its application gives the user a sense of the connective length scales in the outer solar atmosphere. The MRoI maps and histograms inferred from the SDO/HMI magnetograms primarily exhibit four scales: a scale of a few megameters that can be associated with granulation, a scale of a few tens of megameters that can be associated with super-granulation, a scale of many hundreds to thousands of megameters that can be associated with coronal holes and active regions, and a hitherto unnoticed scale that ranges from 100 to 250Mm. We infer that this final scale is an imprint of the (rotationally driven) giant convective scale on photospheric magnetism. This scale appears in MRoI maps as well-defined, spatially distributed concentrations that we have dubbed ''g-nodes''. Furthermore, using coronal observations from the Atmospheric Imaging Assembly on SDO, we see that the vicinity of these g-nodes appears to be a preferred location for the formation of extreme-ultraviolet (and likely X-Ray) brightpoints. These observations and straightforward diagnostics offer the potential of a near real-time mapping of the Sun's largest convective scale, a scale that possibly reaches to the very bottom of the convective zone.

  17. 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-Prot (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.

  18. Human brain potentials indicate morphological decomposition in visual word recognition.

    PubMed

    Barber, Horacio; Domnguez, Alberto; de Vega, Manuel

    2002-02-01

    Stem homographs are pairs of words with the same orthographic description of their stem but which are semantically and morphologically unrelated (e.g. in Spanish: rata/rato (rat/moment)). In priming tasks, stem homographs produce inhibition, unlike morphologically related words (loca/loco (madwoman/madman)) which produce facilitation. An event-related potentials study was conducted to compare morphological and stem homographic priming effects. The results show a similar attenuation of the N400 component at the 350-500 ms temporal window for the two conditions. In contrast, a broad negativity occurs only for stem homographs at the 500-600 ms window. This late negativity is interpreted as the consequence of an inhibitory effect for stem homographs that delays the stage of meaning integration. PMID:11803121

  19. 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)

  20. 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.

  1. Using Indices of Fidelity to Intervention Core Components to Identify Program Active Ingredients

    ERIC Educational Resources Information Center

    Abry, Tashia; Hulleman, Chris S.; Rimm-Kaufman, Sara E.

    2015-01-01

    Identifying the active ingredients of an intervention--intervention-specific components serving as key levers of change--is crucial for unpacking the intervention black box. Measures of intervention fidelity can be used to identify specific active ingredients, yet such applications are rare. We illustrate how fidelity measures can be used to

  2. 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...

  3. 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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. A Preliminary Examination to Identify the Presence of Quality Indicators in Single-Subject Research

    ERIC Educational Resources Information Center

    Tankersley, Melody; Cook, Bryan G.; Cook, Lysandra

    2008-01-01

    Scholars in the field of special education put forth a series of papers that proposed quality indicators for specific research designs that must be present for a study to be considered of high quality, as well as standards for evaluating a body of research to determine whether a practice is evidence-based. The purpose of this article was to pilot

  9. A simple contact mapping algorithm for identifying potential peptide mimetics in proteinprotein interaction partners

    PubMed Central

    Krall, Alex; Brunn, Jonathan; Kankanala, Spandana; Peters, Michael H

    2014-01-01

    A simple, static contact mapping algorithm has been developed as a first step at identifying potential peptide biomimetics from protein interaction partner structure files. This rapid and simple mapping algorithm, OpenContact provides screened or parsed protein interaction files based on specified criteria for interatomic separation distances and interatomic potential interactions. The algorithm, which uses all-atom Amber03 force field models, was blindly tested on several unrelated cases from the literature where potential peptide mimetics have been experimentally developed to varying degrees of success. In all cases, the screening algorithm efficiently predicted proposed or potential peptide biomimetics, or close variations thereof, and provided complete atom-atom interaction data necessary for further detailed analysis and drug development. In addition, we used the static parsing/mapping method to develop a peptide mimetic to the cancer protein target, epidermal growth factor receptor. In this case, secondary, loop structure for the peptide was indicated from the intra-protein mapping, and the peptide was subsequently synthesized and shown to exhibit successful binding to the target protein. The case studies, which all involved experimental peptide drug advancement, illustrate many of the challenges associated with the development of peptide biomimetics, in general. Proteins 2014; 82:22532262. 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:24756879

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

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

    PubMed

    Melot, Brent C; Scanlon, David O; Reynaud, Marine; Rousse, Gwenalle; Chotard, Jean-Nol; 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

  16. 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.

  17. 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...

  18. 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

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

    PubMed

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

    2015-12-23

    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. PMID:26649627

  20. 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

  1. 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...

  2. Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand Pachycladon

    PubMed Central

    2010-01-01

    Background Transcript profiling of closely related species provides a means for identifying genes potentially important in species diversification. However, the predictive value of transcript profiling for inferring downstream-physiological processes has been unclear. In the present study we use shotgun proteomics to validate inferences from microarray studies regarding physiological differences in three Pachycladon species. We compare transcript and protein profiling and evaluate their predictive value for inferring glucosinolate chemotypes characteristic of these species. Results Evidence from heterologous microarrays and shotgun proteomics revealed differential expression of genes involved in glucosinolate hydrolysis (myrosinase-associated proteins) and biosynthesis (methylthioalkylmalate isomerase and dehydrogenase), the interconversion of carbon dioxide and bicarbonate (carbonic anhydrases), water use efficiency (ascorbate peroxidase, 2 cys peroxiredoxin, 20 kDa chloroplastic chaperonin, mitochondrial succinyl CoA ligase) and others (glutathione-S-transferase, serine racemase, vegetative storage proteins, genes related to translation and photosynthesis). Differences in glucosinolate hydrolysis products were directly confirmed. Overall, prediction of protein abundances from transcript profiles was stronger than prediction of transcript abundance from protein profiles. Protein profiles also proved to be more accurate predictors of glucosinolate profiles than transcript profiles. The similarity of species profiles for both transcripts and proteins reflected previously inferred phylogenetic relationships while glucosinolate chemotypes did not. Conclusions We have used transcript and protein profiling to predict physiological processes that evolved differently during diversification of three Pachycladon species. This approach has also identified candidate genes potentially important in adaptation, which are now the focus of ongoing study. Our results indicate that protein profiling provides a valuable tool for validating transcript profiles in studies of adaptive divergence. PMID:20482888

  3. Improving the Screening Process for Identifying Students with High Academic Potential from Minority Populations.

    ERIC Educational Resources Information Center

    Ratliff, Mary A.

    This practicum was designed to improve screening procedures for identifying students with high potential, to develop and field test screening instruments, and to increase the number of students with high potential from minority populations referred for further testing. Three screening instruments were developed for use in searching for students

  4. 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

  5. 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

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

    PubMed Central

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

    2015-01-01

    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

  7. 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.

  8. Potential of Enterococcus faecalis as a human fecal indicator for microbial source tracking.

    PubMed

    Wheeler, Andrea L; Hartel, Peter G; Godfrey, Dominique G; Hill, Jennifer L; Segars, William I

    2002-01-01

    Regulatory agencies are interested in a fecal indicator bacterium with a host range limited to humans because human fecal contamination represents the greatest hazard to humans, yet is a relatively easy nonpoint source to remedy. Watersheds with human fecal contamination could be given first priority for cleanup. A fecal indicator bacterium with a host range limited to humans and a few other warm-blooded animal species would also simplify microbial source tracking because only a few animal species would be required for any host origin database. The literature suggests that the fecal indicator bacterium Enterococcus faecalis has a limited host range. On this basis, we selected this bacterium for study. Of 583 fecal streptococcal isolates obtained on Enterococcosel agar from Canada goose, cattle, deer, dog, human, chicken, and swine, 392 were considered presumptive enterococci and were subsequently speciated with the API 20 Strep system. Of these isolates, 22 were Ent. durans (5.6%), 61 were Ent. faecalis (15.6%), 98 were Ent. faecium (25.0%), 86 were Ent. gallinarum (21.9%), and 125 were unidentified (31.9%). The host range of the Ent. faecalis isolates was limited to dogs, humans, and chickens. Media were developed to isolate and identify Ent. faecalis quickly from fecal samples and this scheme eliminated Ent. faecalis isolates from dogs. When the remaining Ent. faecalis isolates were ribotyped, it was possible to differentiate clearly among the isolates from human and chicken. It may be that combining the potentially limited host range of Ent. faecalis with ribotyping is useful for prioritizing watersheds with fecal contamination. PMID:12175048

  9. 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 ...

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. 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; Slvia 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

  16. Identifying the potential extracellular electron transfer pathways from a c-type cytochrome network.

    PubMed

    Ding, De-Wu; Xu, Jun; Li, Ling; Xie, Jian-Ming; Sun, Xiao

    2014-12-01

    Extracellular electron transfer (EET) is the key feature of some bacteria, such as Geobacter sulfurreducens and Shewanella oneidensis. Via EET processes, these bacteria can grow on electrode surfaces and make current output of microbial fuel cells. c-Type cytochromes can be used as carriers to transfer electrons, which play an important role in EET processes. Typically, from the inner (cytoplasmic) membrane through the periplasm to the outer membrane, they could form EET pathways. Recent studies suggest that a group of c-type cytochromes could form a network which extended the well-known EET pathways. We obtained the protein interaction information for all 41 c-type cytochromes in Shewanella oneidensis MR-1, constructed a large-scale protein interaction network, and studied its structural characteristics and functional significance. Centrality analysis has identified the top 10 key proteins of the network, and 7 of them are associated with electricity production in the bacteria, which suggests that the ability of Shewanella oneidensis MR-1 to produce electricity might be derived from the unique structure of the c-type cytochrome network. By modularity analysis, we obtained 5 modules from the network. The subcellular localization study has shown that the proteins in these modules all have diversiform cellular compartments, which reflects their potential to form EET pathways. In particular, combination of protein subcellular localization and operon analysis, the well-known and new candidate EET pathways are obtained from the Mtr-like module, indicating that potential EET pathways could be obtained from such a c-type cytochrome network. PMID:25227320

  17. 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

  18. Identifying potential adverse effects using the web: a new approach to medical hypothesis generation

    PubMed Central

    Benton, Adrian; Ungar, Lyle; Hill, Shawndra; Hennessy, Sean; Mao, Jun; Chung, Annie; Leonard, Charles E.; Holmes, John H.

    2011-01-01

    Medical message boards are online resources where users with a particular condition exchange information, some of which they might not otherwise share with medical providers. Many of these boards contain a large number of posts and contain patient opinions and experiences that would be potentially useful to clinicians and researchers. We present an approach that is able to collect a corpus of medical message board posts, de-identify the corpus, and extract information on potential adverse drug effects discussed by users. Using a corpus of posts to breast cancer message boards, we identified drug event pairs using co-occurrence statistics. We then compared the identified drug event pairs with adverse effects listed on the package labels of tamoxifen, anastrozole, exemestane, and letrozole. Of the pairs identified by our system, 7580% were documented on the drug labels. Some of the undocumented pairs may represent previously unidentified adverse drug effects. PMID:21820083

  19. Identifying Women with Indicators of Subfertility in a Statewide Population Database: Operationalizing the Missing Link in ART Research

    PubMed Central

    Declercq, Eugene R; Belanoff, Candice; Diop, Hafsatou; Gopal, Daksha; Hornstein, Mark; Kotelchuck, Milton; Luke, Barbara; Stern, Judy E

    2014-01-01

    Objective To identify a group of deliveries to mothers with indicators of subfertility (SUBFERTILITY) Design Longitudinal cohort study Setting Massachusetts Patients 334,152 deliveries to Massachusetts mothers in a Massachusetts hospital between July 1, 2004-December 31, 2008 Interventions None Main Outcome Measure Subfertility was defined by an indication on current or past birth certificate or hospital utilization data of infertility or assisted reproductive technology (ART) cycle prior to index delivery and no indication of ART use with index delivery. Results Initially 12,367 deliveries met the inclusion criteria for SUBFERTILITY (8,019 from birth certificates; 2,777 from hospital data; 1,571 from prior ART treatment). Removing deliveries from more than one data source resulted in 10,764 unique deliveries. Removing deliveries resulting from ART treatments left 6,238 deliveries in the SUBFERTILITY category. Demographic analysis indicated that deliveries in SUBFERTILITY were more similar to ART than to the fertile population. Conclusions We have demonstrated the feasibility of using existing population based linked public health datasets to identify SUBFERTILITY deliveries and we have used ART data to distinguish ART and SUBFERTILITY births. The SUBFERTILITY category can serve as a comparison group of subfertile patients for studies of ART delivery and longitudinal health outcomes. PMID:24289994

  20. 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

  1. 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

  2. Potentially Hazardous Co-orbiting Materials of Asteroid 138175 Identified by Interplanetary Field Enhancements

    NASA Astrophysics Data System (ADS)

    Lai, Hairong; Russell, Christopher; Wei, Hanying; Delzanno, Gian Luca; Connors, Martin

    2014-05-01

    Interplanetary Field Enhancements (IFEs) were discovered almost 30 years ago in the PVO magnetic-field records. Our current understanding is that IFEs result from interactions between solar wind and clouds of nanometer-scale charged dust released in interplanetary collisions. These charged dust clouds are then accelerated by the solar wind and moving away from the Sun at near solar wind speed. This IFE formation hypothesis is supported by the discovery of co-orbiting materials associated with asteroid 2201 Oljato: IFE rate peaked when Oljato was close and IFE occurrence clustered in the longitudes near which the orbit of Oljato intersects the orbital plane of Venus. A followed up study with Venus Express observations suggested that the co-orbiting materials dissipated in 30 years At 1AU, based on ACE and Wind observations, IFEs have a significant cluster in the longitude range between 195 and 225. Thus we use the same IFE technique to identify the 'parent' Near-Earth Objects of co-orbiting materials which should be responsible for those IFEs. There are more than 5000 JPL documented NEOs whose ecliptic plane crossings are near to or inside the Earth's orbit and whose orbital periods are less than five years. By comparing their trajectories, we find that the asteroid 138175 is a good candidate for the 'parent' body. This asteroid orbits the Sun in a 5.24 inclined elliptical orbit with a period of 367.96 days. Its descending node is at about 206, where the IFE occurrence rate peaks. We also find that there is a spread of the IFE rate around the descending node, indicating that the co-orbiting materials have significant dispersion about the asteroid's orbit. The mass distribution of the associated IFEs indicates that most of the materials had a dimension of tens of meters before the collisions. Interplanetary objects in such size range are difficult to be identified by traditional surveys. Although asteroid 138175 itself has now been removed from the potentially hazardous NEO list, its co-orbiting materials may have high impact probability and cause significant damage due to their dispersed orbits and non-negligible size range. The same technique can be applied to the remaining thousands of known NEOs crossing the ecliptic plane inside the Earth's orbit and find those that have co-orbiting materials which might be hazardous to the Earth. Thus alerts can be issued when the Earth approaches the orbits of objects with co-orbiting debris.

  3. 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.

  4. 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 (?18O, ?13C), 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 ?18O, ?13C, 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

  5. 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

  6. 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)

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

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false How are potential market participants identified for the USDA Farmers Market? 170.6 Section 170.6 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED)...

  8. 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.

  9. A Model for Identifying the Potential Clientele for Substance Abuse Programs.

    ERIC Educational Resources Information Center

    Froland, Charles; Brodsky, Gerry

    1978-01-01

    A model is presented that estimates the rates, numbers, and sociodemographic characteristics of potential clientele for substance abuse programs. Using the synthetic estimates technique and existing bodies of information, the model has been tested and cross validated with substance abuse related problem indicators with good results. (Author/CTM)

  10. 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

  11. Exome resequencing identifies potential tumor-suppressor genes that predispose to colorectal cancer.

    PubMed

    Smith, Christopher G; Naven, Marc; Harris, Rebecca; Colley, James; West, Hannah; Li, Ning; Liu, Yuan; Adams, Richard; Maughan, Timothy S; Nichols, Laura; Kaplan, Richard; Wagner, Michael J; McLeod, Howard L; Cheadle, Jeremy P

    2013-07-01

    Inherited factors account for around one third of all colorectal cancers (CRCs) and include rare high penetrance mutations in APC, MSH2, MSH6, and POLE. Here, we sought novel tumor-suppressor genes that predispose to CRC by exome resequencing 50 sporadic patients with advanced CRC (18 diagnosed ?35 years of age) at a mean coverage of 30. To help identify potentially pathogenic alleles, we initially sought rare or novel germline truncating mutations in 1,138 genes that were likely to play a role in colorectal tumorigenesis. In total, 32 such mutations were identified and confirmed, and included an insertion in APC and a deletion in POLE, thereby validating our approach for identifying disease alleles. We sought somatic mutations in the corresponding genes in the CRCs of the patients harboring the germline lesions and found biallelic inactivation of FANCM, LAMB4, PTCHD3, LAMC3, and TREX2, potentially implicating these genes as tumor suppressors. We also identified a patient who carried a germline truncating mutation in NOTCH3, part of the Notch signaling cascade that maintains intestinal homeostasis. Our whole exome analyses provided further gene lists to facilitate the identification of potential predisposition alleles. PMID:23585368

  12. 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

  13. 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.

  14. 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

  15. 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).

  16. 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...

  17. 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…

  18. 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

  19. A Topology Potential-Based Method for Identifying Essential Proteins from PPI Networks.

    PubMed

    Li, Min; Lu, Yu; Wang, Jianxin; Wu, Fang-Xiang; Pan, Yi

    2015-01-01

    Essential proteins are indispensable for cellular life. It is of great significance to identify essential proteins that can help us understand the minimal requirements for cellular life and is also very important for drug design. However, identification of essential proteins based on experimental approaches are typically time-consuming and expensive. With the development of high-throughput technology in the post-genomic era, more and more protein-protein interaction data can be obtained, which make it possible to study essential proteins from the network level. There have been a series of computational approaches proposed for predicting essential proteins based on network topologies. Most of these topology based essential protein discovery methods were to use network centralities. In this paper, we investigate the essential proteins' topological characters from a completely new perspective. To our knowledge it is the first time that topology potential is used to identify essential proteins from a protein-protein interaction (PPI) network. The basic idea is that each protein in the network can be viewed as a material particle which creates a potential field around itself and the interaction of all proteins forms a topological field over the network. By defining and computing the value of each protein's topology potential, we can obtain a more precise ranking which reflects the importance of proteins from the PPI network. The experimental results show that topology potential-based methods TP and TP-NC outperform traditional topology measures: degree centrality (DC), betweenness centrality (BC), closeness centrality (CC), subgraph centrality (SC), eigenvector centrality (EC), information centrality (IC), and network centrality (NC) for predicting essential proteins. In addition, these centrality measures are improved on their performance for identifying essential proteins in biological network when controlled by topology potential. PMID:26357224

  20. 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.

  1. Indications and potential sources of change in sand transport in the Brazos River, Texas

    USGS Publications Warehouse

    Dunn, David D.; Raines, Timothy H.

    2001-01-01

    Changes in the capacity of the Brazos River to transport sand can be identified within the context of Lane?s relation through changes in channel geometry, changes in the characteristics of suspended loads, and changes in discharge. The Brazos River channel has been undergoing continual adjustment since the 1940s. For a discharge of 5,000 cubic feet per second, the water-surface altitude has decreased 2 to 4 feet at the Hempstead and Richmond streamflow-gaging stations between 1940 and 1995. The characteristics of suspended-sediment samples at the Richmond streamflow-gaging station have changed between the periods 1969?81 and 1982?95. The amount of sand-size sediment transported in suspension has decreased. The distribution of both daily and annual-peak discharges has changed. However, the computed annual loads of suspended sand indicate no statistically significant change in the median annual load. The transport of sand in the Brazos River depends on a complex set of factors, most of which are continually changing. Potential sources of change in sand transport in the Brazos River include the effects of reservoir construction, changes in land use, and instream sand and gravel mining. Extensive reservoir construction in the Brazos River Basin has reduced sand transport by trapping sediment and by reducing the magnitude of peak discharges. However, reductions in sand transport associated with reservoir construction apparently are compensated for by increases associated with tributary sediment inflow and localized bank erosion. The total area of harvested acres of non-hay crops in the lower Brazos River Basin during 1924?92 decreased more than 75 percent from about 32 percent to about 8 percent of the total area. Correspondingly, erosion potential has decreased substantially. Several sand and gravel mining sites are located on the Brazos River between Hempstead and Rosharon. The quantity of sediment extracted by instream sand and gravel mining operations could represent from 11 to 25 percent of the total sand transported by the Brazos River. The effects of mining on sand transport could not be quantified.

  2. 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

  3. 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.

  4. 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.

  5. 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

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

    PubMed

    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

    2015-05-01

    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. Analyses according to tumor stage progression identified TERT promoter mutation as an early event, whereas FGF3, 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. 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

  7. 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.

  8. A realistic assessment of the indicator potential of butterflies and other charismatic taxonomic groups.

    PubMed

    Fleishman, Erica; Murphy, Dennis D

    2009-10-01

    Charismatic groups of animals and plants often are proposed as sentinels of environmental status and trends. Nevertheless, many claims that a certain taxonomic group can provide more-general information on environmental quality are not evaluated critically. To address several of the many definitions of indicator species, we used butterflies to explore in some detail the attributes that affect implementation of indicators generically. There probably are few individual species, or sets of species, that can serve as scientifically valid, cost-effective measures of the status or trend of an environmental phenomenon that is difficult to measure directly. Nevertheless, there are species with distributions, abundances, or demographic characteristics that are responsive to known environmental changes. In this context, single or multiple species can serve as indicators when targets are defined explicitly, ecological relationships between the target and the putative indicators are well understood, and data are sufficient to differentiate between deterministic and stochastic responses. Although these situations exist, they are less common than might be apparent from an extensive and often confounded literature on indicators. Instead, the public appeal of charismatic groups may be driving much of their acclaim as indicators. The same taxon may not be appropriate for marketing a general conservation mission and for drawing strong inference about specific environmental changes. To provide insights into the progress of conservation efforts, it is essential to identify scientific and practical criteria for selection and application of indicators and then to examine whether a given taxonomic group meets those criteria. PMID:19459893

  9. 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

  10. 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

  11. Developing consensus on hospital prescribing indicators of potential harms amenable to decision support

    PubMed Central

    Thomas, Sarah K; McDowell, Sarah E; Hodson, James; Nwulu, Ugochi; Howard, Rachel L; Avery, Anthony J; Slee, Ann; Coleman, Jamie J

    2013-01-01

    Aims To develop a list of prescribing indicators specific for the hospital setting that would facilitate the prospective collection of high-severity and/or high-frequency prescribing errors, which are also amenable to electronic clinical decision support. Methods A two-stage consensus technique (electronic Delphi) was carried out with 20 experts across England. Participants were asked to score prescribing errors using a five-point Likert scale for their likelihood of occurrence and the severity of the most likely outcome. These were combined to produce risk scores, from which median scores were calculated for each indicator across the participants in the study. The degree of consensus between the participants was defined as the proportion that gave a risk score in the same category as the median. Indicators were included if a consensus of 80% or more was achieved. Results A total of 80 prescribing errors were identified by consensus as being high or extreme risk. The most common drug classes named within the indicators were antibiotics (n = 13), antidepressants (n = 8), nonsteroidal anti-inflammatory drugs (n = 6) and opioid analgesics (n = 6). The most frequent error type identified as high or extreme risk were those classified as clinical contraindications (n = 29 of 80). Conclusions Eighty high-risk prescribing errors in the hospital setting have been identified by an expert panel. These indicators can serve as a standardized, validated tool for the collection of prescribing data in both paper-based and electronic prescribing processes. This can assess the impact of safety improvement initiatives, such as the implementation of electronic clinical decision support. PMID:23362926

  12. Comparative oncogenomics identifies PSMB4 and SHMT2 as potential cancer driver genes.

    PubMed

    Lee, Genee Y; Haverty, Peter M; Li, Li; Kljavin, Noelyn M; Bourgon, Richard; Lee, James; Stern, Howard; Modrusan, Zora; Seshagiri, Somasekar; Zhang, Zemin; Davis, David; Stokoe, David; Settleman, Jeffrey; de Sauvage, Frederic J; Neve, Richard M

    2014-06-01

    Cancer genomes maintain a complex array of somatic alterations required for maintenance and progression of the disease, posing a challenge to identify driver genes among this genetic disorder. Toward this end, we mapped regions of recurrent amplification in a large collection (n=392) of primary human cancers and selected 620 genes whose expression is elevated in tumors. An RNAi loss-of-function screen targeting these genes across a panel of 32 cancer cell lines identified potential driver genes. Subsequent functional assays identified SHMT2, a key enzyme in the serine/glycine synthesis pathway, as necessary for tumor cell survival but insufficient for transformation. The 26S proteasomal subunit, PSMB4, was identified as the first proteasomal subunit with oncogenic properties promoting cancer cell survival and tumor growth in vivo. Elevated expression of SHMT2 and PSMB4 was found to be associated with poor prognosis in human cancer, supporting the development of molecular therapies targeting these genes or components of their pathways. PMID:24755469

  13. 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.

  14. 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 ? 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

  15. DRAR-CPI: a server for identifying drug repositioning potential and adverse drug reactions via the chemicalprotein interactome

    PubMed Central

    Luo, Heng; Chen, Jian; Shi, Leming; Mikailov, Mike; Zhu, Huang; Wang, Kejian; He, Lin; Yang, Lun

    2011-01-01

    Identifying new indications for existing drugs (drug repositioning) is an efficient way of maximizing their potential. Adverse drug reaction (ADR) is one of the leading causes of death among hospitalized patients. As both new indications and ADRs are caused by unexpected chemicalprotein interactions on off-targets, it is reasonable to predict these interactions by mining the chemicalprotein interactome (CPI). Making such predictions has recently been facilitated by a web server named DRAR-CPI. This server has a representative collection of drug molecules and targetable human proteins built up from our work in drug repositioning and ADR. When a user submits a molecule, the server will give the positive or negative association scores between the users molecule and our library drugs based on their interaction profiles towards the targets. Users can thus predict the indications or ADRs of their molecule based on the association scores towards our library drugs. We have matched our predictions of drugdrug associations with those predicted via gene-expression profiles, achieving a matching rate as high as 74%. We have also successfully predicted the connections between anti-psychotics and anti-infectives, indicating the underlying relevance of anti-psychotics in the potential treatment of infections, vice versa. This server is freely available at http://cpi.bio-x.cn/drar/. PMID:21558322

  16. Terrestrial Evaporite Analogues for Identifying Extremophiles (Past or Present) from Potential Mars Evaporites

    NASA Astrophysics Data System (ADS)

    Morris, P.; Wentworth, S.; Byrne, M.; Nelman, M.; Longazo, T.; Allen, C.; Brigmon, R.; McKay, D.

    An understanding of terrestrial evaporite microbial biota, their markers and fossilization processes is important for identifying potential present or past life signs from extraterrestrial sources such as Mars meteorites and Mars sample return. Storrs Lake, San Salvador Island, Bahamas, Mono Lake, California and the Dead Sea, Israel represent marine and nonmarine sites for comparative investigative studies of potential Mars analogues. Variations between the sites can be attributed to salinity, pH, water chemistry, and seasonal temperature changes, all of which can affect microbial abundance, fossilization, and mineral formation. Storr's Lake, located at sea level, pH 8, salinity averaging 7 g/l. has extensive stromatolitic structures0 composed of biofilm, rods, filaments, cocci and diatoms. The fossilized organic remains are generally composed of magnesium enriched calcium carbonate. Mono Lake is 2100 meters above sea level, pH and salinity are similar to Storr's Lake, and it has various evaporite and carbonate deposits including tufa structures that vary in height from less than 1 meter to over 4 meters. Algae, cyanobacteria, diatoms, and other microbial forms are present and contribute to t e formation of evaporiteh deposits including tufas. The Dead Sea is 400 m below sea level, pH 6.3 in the upper water mass, salinity averaging 229.9 g/l, and possesses extensive salt deposits with scant evidence of microbial fossilization as large carbonate structures such as tufas and stromatolites are absent. Modern investigative tools can identify microbes from all of these environments, but confirming the presence of fossilized microbes and their biomarkers subsequent to burial and lithification is more difficult. The goal of this study is to identify these biomarkers and test their suitability for identifying extraterrestrial microbial remains.

  17. 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.

  18. Identifying potential prey of the pelagic larvae of the spiny lobster Jasus edwardsii using signature lipids.

    PubMed

    Jeffs, Andrew G; Nichols, Peter D; Mooney, Ben D; Phillips, Katrina L; Phleger, Charles F

    2004-04-01

    Signature lipid analyses were used to identify the natural prey of the pelagic phyllosoma larvae of the spiny lobster Jasus edwardsii. Lipid class, fatty acid and sterol composition were determined for associated potential prey items and for phyllosomes captured between 50 and 90 km offshore from the northeastern coast of New Zealand. Phospholipid was the dominant lipid class in all potential prey items and the transparent phyllosomes. The levels of other lipid classes varied between potential prey items, with the next most abundant classes being triacylglycerols, free fatty acids and sterols. A limited number of the potential prey items also contained wax ester. Major fatty acids in all potential prey items were generally 22:6omega3 (docosahexaenoic acid), 16:0, 18:1omega9c, and 20:5omega3 (eicosapentaenoic acid). Multivariate analyses of fatty acid and sterol content of the samples grouped the phyllosoma samples together regardless of their developmental stage or their collection location. However, the phyllosomes were not associated with any of the general groupings of pelagic ascidians, amphipods, chaetognaths, pteropods, euphausiids, fish, copepods or particulate matter that were formed by the statistical analyses. Although the sterol profiles of the potential prey items showed considerable variation, the phyllosomes contained predominantly cholesterol, suggesting that other dietary sterols are converted to cholesterol or metabolised by the phyllosomes. Therefore, the use of sterols for tracing the prey of J. edwardsii phyllosoma appears to be limited. Our results suggest that phyllosomes are opportunistic predators that feed on a variety of prey and are preferentially retaining specific diet-derived fatty acids. PMID:15082000

  19. 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

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

    PubMed

    Cerero-Lapiedra, Roco; Esparza-Gmez, Germn C; Casado-de la Cruz, Laura; Domnguez-Gordillo, Adelaida A; Corral-Linaza, Csar; 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

  1. Multidisciplinary Team Approach for Identifying Potential Candidate for Transcatheter Aortic Valve Implantation

    PubMed Central

    Hong, Sung-Jin; Ko, Young-Guk; Choi, Donghoon; Hong, Geu-Ru; Shim, Jae-Kwang; Kwak, Young-Lan; Lee, Sak; Chang, Byung-Chul; Jang, Yangsoo

    2014-01-01

    Purpose We sought to evaluate the clinical usefulness of decision making by a multidisciplinary heart team for identifying potential candidates for transcatheter aortic valve implantation (TAVI) in patients with symptomatic severe aortic stenosis. Materials and Methods The multidisciplinary team consisted of two interventional cardiologists, two cardiovascular surgeons, one cardiac imaging specialist, and two cardiac anesthesiologists. Results Out of 60 patients who were screened as potential TAVI candidates, 31 patients were initially recommended as appropriate for TAVI, and 20 of these 31 eventually underwent TAVI. Twenty-two patients underwent surgical aortic valve replacement (AVR), and 17 patients received only medical treatment. Patients who underwent TAVI and medical therapy were older than those who underwent surgical AVR (p<0.001). The logistic Euroscore was significantly highest in the TAVI group and lowest in the surgical AVR group (p=0.012). Most patients in the TAVI group (90%) and the surgical AVR group (91%) had severe cardiac symptoms, but only 47% in the medical therapy group had severe symptoms. The cumulative percentages of survival without re-hospitalization or all-cause death at 6 months for the surgical AVR, TAVI, and medical therapy groups were 84%, 75%, and 28%, respectively (p=0.007, by log-rank). Conclusion TAVI was recommended in half of the potential candidates following a multidisciplinary team approach and was eventually performed in one-third of these patients. One-third of the patients who were initially considered potential candidates received surgical AVR with favorable clinical outcomes. PMID:25048481

  2. The potential for spatial distribution indices to signal thresholds in marine fish biomass.

    PubMed

    Reuchlin-Hugenholtz, Emilie; Shackell, Nancy L; Hutchings, Jeffrey A

    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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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 Blanger, 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 Blanger(2010). Geochim. Cosmochim. Acta, 74, 995-1015

  10. 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=25071.1; BW=60145.4kg) 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=12233.2; BW=61549.1kg) 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

  11. 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

  12. 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.

  13. Ecosystem greenspots: identifying potential drought, fire, and climate-change micro-refuges.

    PubMed

    Mackey, Brendan; Berry, Sandra; Hugh, Sonia; Ferrier, Simon; Harwood, Thomas D; Williams, Kristen J

    2012-09-01

    In response to climate change and other threatening processes there is renewed interest in the role of refugia and refuges. In bioregions that experience drought and fire, micro-refuges can play a vital role in ensuring the persistence of species. We develop and apply an approach to identifying potential micro-refuges based on a time series of remotely sensed vegetation greenness (fraction of photosynthetically active radiation intercepted by the sunlit canopy; fPAR). The primary data for this analysis were NASA MODIS 16-day L3 Global 250 m (MOD13Q1) satellite imagery. This method draws upon relevant ecological theory (source sink habitats, habitat templet) to calculate a micro-refuge index, which is analyzed for each of the major vegetation ecosystems in the case-study region (the Great Eastern Ranges of New South Wales, Australia). Potential ecosystem greenspots were identified, at a range of thresholds, based on an index derived from: the mean and coefficient of variance (COV) of fPAR over the 10-year time series; the minimum mean annual fPAR; and the COV of the 12 values of mean monthly fPAR. These greenspots were mapped and compared with (1) an index of vascular plant species composition, (2) environmental variables, and (3) protected areas. Potential micro-refuges were found within all vegetation ecosystem types. The total area of ecosystem greenspots within the upper 25% threshold was 48 406 ha; around 0.2% of the total area of native vegetation (23.9 x 10(6) ha) in the study region. The total area affected by fire was 3.4 x 10(6) ha. The results of the environmental diagnostic analysis suggest deterministic controls on the geographical distribution of potential micro-refuges that may continue to function under climate change. The approach is relevant to other regions of the world where the role of micro-refuges in the persistence of species is recognized, including across the world's arid zones and, in particular, for the Australian, southern African, and South American continents. Micro-refuge networks may play an important role in maintaining beta-diversity at the bio-region scale and contribute to the stability, resilience, and adaptive capacity of ecosystems in the face of ever-growing pressures from human-forced climate change, land use, and other threatening processes. PMID:23092021

  14. 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.

  15. 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.

  16. 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.

  17. Identifying potential sources of Sudan I contamination in Capsicum fruits over its growth period.

    PubMed

    Wu, Naiying; Gao, Wei; Zhou, Li; Lian, Yunhe; Li, Fengfei; Han, Wenjie

    2015-04-15

    Sudan dyes in spices are often assumed to arise from cross-contamination or malicious addition. Here, experiments were carried out to identify the potential source of Sudan I-IV in Capsicum fruits through investigation of their contents in native Capsicum tissues, soils and associated agronomic materials. Sudan II-IV was not detected in any of the tested samples. Sudan I was found in almost all samples except for the mulching film. Sudan I concentrations decreased from stems to leaves and then to fruits or roots. Sudan I levels in soils were significantly elevated by vegetation treatment. These results exclude the possibility of soil as the main source for Sudan I contamination in Capsicum fruits. Further study found out pesticide and fertilizer constitutes the major source of Sudan I contamination. This work represents a preliminary step for a detailed Sudan I assessment to support Capsicum management and protection in the studied region. PMID:25466000

  18. 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

  19. 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.

  20. 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:2.9190.7)) 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

  1. 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

  2. Assessing urban potential flooding risk and identifying effective risk-reduction measures.

    PubMed

    Cherqui, Frdric; Belmeziti, Ali; Granger, Damien; Sourdril, Antoine; Le Gauffre, Pascal

    2015-05-01

    Flood protection is one of the traditional functions of any drainage system, and it remains a major issue in many cities because of economic and health impact. Heavy rain flooding has been well studied and existing simulation software can be used to predict and improve level of protection. However, simulating minor flooding remains highly complex, due to the numerous possible causes related to operational deficiencies or negligent behaviour. According to the literature, causes of blockages vary widely from one case to another: it is impossible to provide utility managers with effective recommendations on how to improve the level of protection. It is therefore vital to analyse each context in order to define an appropriate strategy. Here we propose a method to represent and assess the flooding risk, using GIS and data gathered during operation and maintenance. Our method also identifies potential management responses. The approach proposed aims to provide decision makers with clear and comprehensible information. Our method has been successfully applied to the Urban Community of Bordeaux (France) on 4895 interventions related to flooding recorded during the 2009-2011 period. Results have shown the relative importance of different issues, such as human behaviour (grease, etc.) or operational deficiencies (roots, etc.), and lead to identify corrective and proactive. This study also confirms that blockages are not always directly due to the network itself and its deterioration. Many causes depend on environmental and operating conditions on the network and often require collaboration between municipal departments in charge of roads, green spaces, etc. PMID:25682359

  3. Exome Sequencing Identifies Potential Risk Variants for Mendelian Disorders at High Prevalence in Qatar

    PubMed Central

    Rodriguez-Flores, Juan L.; Fakhro, Khalid; Hackett, Neil R.; Salit, Jacqueline; Fuller, Jennifer; Agosto-Perez, Francisco; Gharbiah, Maey; Malek, Joel A.; Zirie, Mahmoud; Jayyousi, Amin; Badii, Ramin; Al-Marri, Ajayeb Al-Nabet; Chouchane, Lotfi; Stadler, Dora J.; Hunter-Zinck, Haley; Mezey, Jason G.; Crystal, Ronald G.

    2013-01-01

    Exome sequencing of families of related individuals has been highly successful in identifying genetic polymorphisms responsible for Mendelian disorders. Here, we demonstrate the value of the reverse approach, where we use exome sequencing of a sample of unrelated individuals to analyze allele frequencies of known causal mutations for Mendelian diseases. We sequenced the exomes of 100 individuals representing the three major genetic subgroups of the Qatari population (Q1 Bedouin, Q2 Persian-South Asian, Q3 African) and identified 37 variants in 33 genes with effects on 36 clinically significant Mendelian diseases. These include variants not present in 1000 Genomes and variants at high frequency when compared to 1000 Genomes populations. Several of these Mendelian variants were only segregating in one Qatari subpopulation, where the observed subpopulation specificity trends were confirmed in an independent population of 386 Qataris. Pre-marital genetic screening in Qatar tests for only 4 out of the 37, such that this study provides a set of Mendelian disease variants with potential impact on the epidemiological profile of the population that could be incorporated into the testing program if further experimental and clinical characterization confirms high penetrance. PMID:24123366

  4. 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.

  5. Identifying the Potential Loss of Monitoring Wells Using an Uncertainty Analysis

    SciTech Connect

    Freedman, Vicky L.; Waichler, Scott R.; Cole, Charles R.; Vermeul, Vince R.; Bergeron, Marcel P.

    2005-11-01

    From the mid-1940s through the 1980s, large volumes of wastewater were discharged at the Hanford Site in southeastern Washington State, causing a large-scale rise (in excess of 20 m) in the water table. When wastewater discharges ceased in 1988, groundwater mounds began to dissipate. This caused a large number of wells to go dry and has made it difficult to monitor contaminant plume migration. To identify the wells that could potentially go dry, a first order uncertainty analysis was performed using a three-dimensional, finite element code (CFEST) coupled with UCODE, a nonlinear parameter estimation code. The analysis was conducted in four steps. First, key parameter values were identified by calibrating to historical hydraulic head data. Second, the model was tested for linearity, a strict requirement for representing output uncertainty. Third, results from the calibration period were used to verify model predictions by comparing monitoring wells? wet/dry status with field data. In the final step, predictions on the number and locations of dry wells were made through the year 2048. A non-physically based model that extrapolated trends at each individual well was also tested as a predictor of a well?s wet/dry status. Results demonstrated that when uncertainty in both parameter estimates and measurement error was considered, the CFEST-based model successfully predicted the majority of dry wells, outperforming the trend model. Predictions made through the year 2048 identified approximately 50% of the wells in the monitoring well network are likely to go dry, which can aid in decisions for their replacement.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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

  14. Evoked potentials as indices of adaptation in the somatosensory system in humans: a review and prospectus.

    PubMed

    McLaughlin, D F; Kelly, E F

    1993-01-01

    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 conditions of repetitive stimulation. Similar results have been reported for several mammalian species and with a diversity of stimulation, recording and analysis protocols. The most characteristic finding is a loss of SEP component amplitude as a function of decreasing time between stimulus presentations. The effects become larger and appear at longer ISIs at higher levels of the somatosensory pathway, are more readily evoked by stimulus trains than by stimulus pairs and are most pronounced for response components generated in the upper cortical layers. These findings are consistent with a recently proposed neurophysiological model of short-term plasticity in somatosensory cortex, which incorporates detailed and current information on cortical microcircuitry, receptor and neurotransmitter characteristics, topographical organization and dynamic response to repetitive sensory drive. Recommendations are provided for further research, emphasizing the potential of frequency-domain analysis methods in conjunction with mechanical vibrotactile stimuli as a vehicle for more detailed testing of the proposed neurophysiological model and for closer integration with psychophysical studies of vibrotactile adaptation. PMID:8339106

  15. 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.

  16. 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

  17. 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

  18. 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

  19. Evaluation of potential indicators of viral contamination in shellfish and their applicability to diverse geographical areas.

    PubMed

    Formiga-Cruz, M; Allard, A K; Conden-Hansson, A-C; Henshilwood, K; Hernroth, B E; Jofre, J; Lees, D N; Lucena, F; Papapetropoulou, M; Rangdale, R E; Tsibouxi, A; Vantarakis, A; Girones, R

    2003-03-01

    The distribution of the concentration of potential indicators of fecal viral pollution in shellfish was analyzed under diverse conditions over 18 months in diverse geographical areas. These microorganisms have been evaluated in relation to contamination by human viral pathogens detected in parallel in the analyzed shellfish samples. Thus, significant shellfish-growing areas from diverse countries in the north and south of Europe (Greece, Spain, Sweden, and the United Kingdom) were defined and studied by analyzing different physicochemical parameters in the water and the levels of Escherichia coli, F-specific RNA bacteriophages, and phages infecting Bacteroides fragilis strain RYC2056 in the shellfish produced, before and after depuration treatments. A total of 475 shellfish samples were studied, and the results were statistically analyzed. According to statistical analysis, the presence of human viruses seems to be related to the presence of all potential indicators in the heavily contaminated areas, where E. coli would probably be suitable as a fecal indicator. The F-RNA phages, which are present in higher numbers in Northern Europe, seem to be significantly related to the presence of viral contamination in shellfish, with a very weak predictive value for hepatitis A virus, human adenovirus, and enterovirus and a stronger one for Norwalk-like virus. However, it is important to note that shellfish produced in A or clean B areas can sporadically contain human viruses even in the absence of E. coli or F-RNA phages. The data presented here will be useful in defining microbiological parameters for improving the sanitary control of shellfish consumed raw or barely cooked. PMID:12620843

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. A proton current drives action potentials in genetically identified sour taste cells

    PubMed Central

    Chang, Rui B.; Waters, Hang; Liman, Emily R.

    2010-01-01

    Five tastes have been identified, each of which is transduced by a separate set of taste cells. Of these sour, which is associated with acid stimuli, is the least understood. Genetic ablation experiments have established that sour is detected by a subset of taste cells that express the TRP channel PKD2L1 and its partner PKD1L3, however the mechanisms by which this subset of cells detects acids remain unclear. Previous efforts to understand sour taste transduction have been hindered because sour responsive cells represent only a small fraction of cells in a taste bud, and numerous ion channels with no role in sour sensing are sensitive to acidic pH. To identify acid-sensitive conductances unique to sour cells, we created genetically modified mice in which sour cells were marked by expression of YFP under the control of the PKD2L1 promoter. To measure responses to sour stimuli we developed a method in which suction electrode recording is combined with UV photolysis of NPE-caged proton. Using these methods, we report that responses to sour stimuli are not mediated by Na+ permeable channels as previously thought, but instead are mediated by a proton conductance specific to PKD2L1-expressing taste cells. This conductance is sufficient to drive action potential firing in response to acid stimuli, is enriched in the apical membrane of PKD2L1-expressing taste cells and is not affected by targeted deletion of the PKD1L3 gene. We conclude that, during sour transduction, protons enter through an apical proton conductance to directly depolarize the taste cell membrane. PMID:21098668

  6. Cheap and nasty? The potential perils of using management costs to identify global conservation priorities.

    PubMed

    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

  7. 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

  8. RNA sequencing reveals differentially expressed genes as potential diagnostic and prognostic indicators of gallbladder carcinoma

    PubMed Central

    Jiang, Mingming; Fang, Meng; Ji, Jun; Wang, Aihua; Wang, Mengmeng; Jiang, Xiaoqing; Gao, Chunfang

    2015-01-01

    Gallbladder carcinoma (GBC) is a rare tumor with a dismal survival rate overall. Hence, there is an urgent need for exploring more specific and sensitive biomarkers for the diagnosis and treatment of GBC. At first, amplified total RNAs from two paired GBC tumors and adjacent non-tumorous tissues (ANTTs) were subjected to RNA sequencing. 161 genes were identified differentially expressed between tumors and ANTTs. Functional enrichment analysis indicated that the up-regulated genes in tumor were primarily associated with signaling molecules and enzyme modulators, and mainly involved in cell cycles and pathways in cancer. Twelve differentially expressed genes (DEGs) were further confirmed in another independent cohort of 35 GBC patients. Expression levels of BIRC5, TK1, TNNT1 and MMP9 were found to be positively related to postoperative relapse. There was also a significant correlation between BIRC5 expression and tumor-node-metastasis (TNM) stage. Besides, we observed a positive correlation between serum CA199 concentration and the expression levels of TNNT1, MMP9 and CLIC3. Survival analysis revealed that GBC patients with high TK1 and MMP9 expression levels had worse prognosis. These identified DEGs might not only be promising biomarkers for GBC diagnosis and prognosis, but also expedite the discovery of novel therapeutic strategies. PMID:25970782

  9. 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

  10. A Comparative Reverse Docking Strategy to Identify Potential Antineoplastic Targets of Tea Functional Components and Binding Mode

    PubMed Central

    Zheng, Rong; Chen, Tuan-sheng; Lu, Tun

    2011-01-01

    The main functional components of green tea, such as epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC), are found to have a broad antineoplastic activity. The discovery of their targets plays an important role in revealing the antineoplastic mechanism. Therefore, to identify potential target proteins for tea polyphenols, we have taken a comparative virtual screening approach using two reverse docking systems, one based on Autodock software and the other on Tarfisdock. Two separate in silico workflows were implemented to derive a set of target proteins related to human diseases and ranked by the binding energy score. Several conventional clinically important proteins with anti-tumor effects are screened out from the PDTD protein database as the potential receptors by both procedures. To further analyze the validity of docking results, we study the binding mode of EGCG and the potential target protein Leukotriene A4 hydrolase in detail. We indicate that interactions mediated by electrostatic and hydrogen bond play a key role in ligand binding. EGCG binds to the enzyme with certain orientation and conformation that is suitable for nucleophilic attacks by several electrical residues inside the enzymes activity cavity. This study provides useful information for studying the antitumor mechanism of teas functional components. The comparative reverse docking strategy presented generates a tractable set of antineoplastic proteins for future experimental validation as drug targets against tumors. PMID:21954353

  11. 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

  12. 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.

  13. 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.

  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 1-10μM, 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. Mitochondrial Membrane Potential Identifies Cells with Enhanced Stemness for Cellular Therapy.

    PubMed

    Sukumar, Madhusudhanan; Liu, Jie; Mehta, Gautam U; Patel, Shashank J; Roychoudhuri, Rahul; Crompton, Joseph G; Klebanoff, Christopher A; Ji, Yun; Li, Peng; Yu, Zhiya; Whitehill, Greg D; Clever, David; Eil, Robert L; Palmer, Douglas C; Mitra, Suman; Rao, Mahadev; Keyvanfar, Keyvan; Schrump, David S; Wang, Ena; Marincola, Francesco M; Gattinoni, Luca; Leonard, Warren J; Muranski, Pawel; Finkel, Toren; Restifo, Nicholas P

    2016-01-12

    Long-term survival and antitumor immunity of adoptively transferred CD8(+) Tcells is dependent on their metabolic fitness, but approaches to isolate therapeutic Tcells based on metabolic features are not well established. Here we utilized a lipophilic cationic dye tetramethylrhodamine methyl ester (TMRM) to identify and isolate metabolically robust Tcells based on their mitochondrial membrane potential (??m). Comprehensive metabolomic and gene expression profiling demonstrated global features of improved metabolic fitness in low-??m-sorted CD8(+) Tcells. Transfer of these low-??m Tcells was associated with superior long-term invivo persistence and an enhanced capacity to eradicate established tumors compared with high-??m cells. Use of ??m-based sorting to enrich for cells with superior metabolic features was observed in CD8(+), CD4(+) Tcell subsets, and long-term hematopoietic stem cells. This metabolism-based approach to cell selection may be broadly applicable to therapies involving the transfer of HSC or lymphocytes for the treatment of viral-associated illnesses and cancer. PMID:26674251

  16. 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.

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

    PubMed

    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. PMID:10622770

  18. 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.

  19. High-Throughput Screening for Positive Allosteric Modulators Identified Potential Therapeutics against Acetylcholinesterase Inhibition.

    PubMed

    Chapleau, Richard R; McElroy, Craig A; Ruark, Christopher D; Fleming, Emily J; Ghering, Amy B; Schlager, John J; Poeppelman, Lee D; Gearhart, Jeffery M

    2015-10-01

    The current standard of care for treatment of organophosphate (OP) poisoning includes pretreatment with the weak reversible acetylcholinesterase (AChE) inhibitor pyridostigmine bromide. Because this drug is an AChE inhibitor, similar side effects exist as with OP poisoning. In an attempt to provide a therapeutic capable of mitigating AChE inhibition without such side effects, high-throughput screening was performed to identify a compound capable of increasing the catalytic activity of AChE. Herein, two such novel positive allosteric modulators (PAMs) of AChE are presented. These PAMs increase AChE activity threefold, but they fail to upshift the apparent IC50 of a variety of OPs. Further development and optimization of these compounds may lead to pre- and/or postexposure therapeutics with broad-spectrum efficacy against pesticide and nerve agent poisoning. In addition, they could be used to complement the current therapeutic standard of care to increase the activity of uninhibited AChE, potentially increasing the efficacy of current therapeutics in addition to altering the therapeutic window. PMID:26078409

  20. Antioxidant Potential of a Polyherbal Antimalarial as an Indicator of Its Therapeutic Value

    PubMed Central

    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

  1. 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

  2. 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

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

    PubMed Central

    Hoban, Sean; Arntzen, Jan A; Bruford, Michael W; Godoy, Jos A; Rus Hoelzel, A; Segelbacher, Gernot; Vil, 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 8090% 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

  4. 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...

  5. 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...

  6. 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.

  7. Indicator dyes as probes of electrostatic potential changes on macromolecular surfaces.

    PubMed

    Moller, J V; Kragh-Hansen, U

    1975-06-01

    An indicator dye attached to an electrostatically charged macromolecular surface generally has a pK value (pKb') different from that of uncombined dye (pKf'). The question if changes in (pKb' - pKf'), designated as increment incrementpK, records changes in the electrostatic potential at the binding site has been examined in spectrophotometric and binding experiments, using the interaction of Chlorophenol Red and Phenol Red with human serum albumin and cationic micelles as examples. (1) In serum albumin solutions increment incrementpK is decreased by a reduction of pH. The decrease is correlated with the increase in positive charges on the protein molecule, and the response is attenuated by high ionic strength in accordance with electrostatic theory. (2) Opposite changes in binding affinity to serum albumin and increment incrementpK as a function of pH are observed; the binding of basic (bivalent anion) dye is more susceptible to a change in pH than in the acidic (univalent anion) form. (3) Preferential uptake of the basic as compared to the acidic form of dye is observed by binding to cetyltrimethylammonium chloride and cetylpyridinium chloride micelles (mu equals 0.033, [Cl-] equals 0.033 M). An increase in the ionic strength is accompanied by a positive value of increment incrementpK. The results are consonant with the view that the observed increment incrementpK values reflect changes in the electrostatic potential at the binding site with consequently little, if any, effect on the intrinsic pK. The extension of the method to measure changes in the electrostatic potential at binding sites on cell membranes is briefly discussed. PMID:237529

  8. 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.

  9. 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

  10. 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

  11. Identifying the null subject: evidence from event-related brain potentials.

    PubMed

    Demestre, J; Meltzer, S; Garca-Albea, J E; Vigil, A

    1999-05-01

    Event-related brain potentials (ERPs) were recorded during spoken language comprehension to study the on-line effects of gender agreement violations in controlled infinitival complements. Spanish sentences were constructed in which the complement clause contained a predicate adjective marked for syntactic gender. By manipulating the gender of the antecedent (i.e., the controller) of the implicit subject while holding constant the gender of the adjective, pairs of grammatical and ungrammatical sentences were created. The detection of such a gender agreement violation would indicate that the parser had established the coreference relation between the null subject and its antecedent. The results showed a complex biphasic ERP (i.e., an early negativity with prominence at anterior and central sites, followed by a centroparietal positivity) in the violating condition as compared to the non-violating conditions. The brain reacts to NP-adjective gender agreement violations within a few hundred milliseconds of their occurrence. The data imply that the parser has properly coindexed the null subject of an infinitive clause with its antecedent. PMID:10344021

  12. 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

  13. Identifying patients with axial spondyloarthritis in primary care: how useful are items indicative of inflammatory back pain?

    PubMed Central

    Braun, A; Saracbasi, E; Grifka, J; Schnitker, J; Braun, J

    2011-01-01

    Background The value of clinical items defining inflammatory back pain to identify patients with axial spondyloarthritis (SpA) in primary care is unclear. Objective To identify predictive clinical parameters for a diagnosis of axial SpA in patients with chronic back pain presenting in primary care. Methods Consecutive patients aged <45 years (n=950) with back pain for >2 months who presented to orthopaedic surgeons (n=143) were randomised based on four key questions for referral to rheumatologists (n=36) for diagnosis. Results The rheumatologists saw 322 representative patients (mean age 36 years, 50% female, median duration of back pain 30 months). 113 patients (35%) were diagnosed as axial SpA (62% HLA B27+), 47 (15%) as ankylosing spondylitis (AS) and 66 (21%) as axial non-radiographic SpA (nrSpA). Age at onset ?35 years, improvement by exercise, improvement with non-steroidal anti-inflammatory drugs, waking up in the second half of the night and alternating buttock pain were identified as most relevant for diagnosing axial SpA by multiple regression analysis. Differences between AS and nrSpA were detected. No single item was predictive, but ?3 items proved useful for good sensitivity and specificity by receiver operating characteristic modelling. Conclusion This study shows that a preselection in primary care of patients with back pain based on a combination of clinical items is useful to facilitate the diagnosis of axial SpA. PMID:21821621

  14. 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

  15. 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.

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

    PubMed

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

    2015-10-01

    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

  17. 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.

  18. 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

  19. 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

  20. Using in Vitro High Throughput Screening Assays to Identify Potential Endocrine-Disrupting Chemicals

    PubMed Central

    Rotroff, Daniel M.; Dix, David J.; Houck, Keith A.; Knudsen, Thomas B.; Martin, Matthew T.; McLaurin, Keith W.; Reif, David M.; Crofton, Kevin M.; Singh, Amar V.; Xia, Menghang; Huang, Ruili

    2012-01-01

    Background: Over the past 20 years, an increased focus on detecting environmental chemicals that pose a risk of adverse effects due to endocrine disruption has driven the creation of the U.S. Environmental Protection Agency (EPA) Endocrine Disruptor Screening Program (EDSP). Thousands of chemicals are subject to the EDSP; thus, processing these chemicals using current test batteries could require millions of dollars and decades. A need for increased throughput and efficiency motivated the development of methods using in vitro high throughput screening (HTS) assays to prioritize chemicals for EDSP Tier 1 screening (T1S). Objective: In this study we used U.S. EPA ToxCast HTS assays for estrogen, androgen, steroidogenic, and thyroid-disrupting mechanisms to classify compounds and compare ToxCast results to in vitro and in vivo data from EDSP T1S assays. Method: We implemented an iterative model that optimized the ability of endocrine-related HTS assays to predict components of EDSP T1S and related results. Balanced accuracy was used as a measure of model performance. Results: ToxCast estrogen receptor and androgen receptor assays predicted the results of relevant EDSP T1S assays with balanced accuracies of 0.91 (p < 0.001) and 0.92 (p < 0.001), respectively. Uterotrophic and Hershberger assay results were predicted with balanced accuracies of 0.89 (p < 0.001) and 1 (p < 0.001), respectively. Models for steroidogenic and thyroid-related effects could not be developed with the currently published ToxCast data. Conclusions: Overall, results suggest that current ToxCast assays can accurately identify chemicals with potential to interact with the estrogenic and androgenic pathways, and could help prioritize chemicals for EDSP T1S assays. PMID:23052129

  1. 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

  2. Measured coral luminescence as a freshwater proxy: comparison with visual indices and a potential age artefact

    NASA Astrophysics Data System (ADS)

    Lough, J. M.

    2011-03-01

    Illuminating slices from massive coral skeletons under ultraviolet light can reveal bright luminescent lines in nearshore corals affected by freshwater river flows. The occurrence and intensity of these lines in long-lived corals can then be used to reconstruct past river flow and rainfall, extending the instrumental records of past tropical climate variability considerably. Earlier studies from the Great Barrier Reef, Australia, have used visual assessments of luminescent line intensity to develop semi-quantitative (though potentially subjective) indices of spatial and temporal variations in freshwater flows. Annual visual assessments and relative coral luminescence intensity (measured by fluorescence spectroscopy) and growth variables are first compared for 89 Porites coral colonies from 30 reefs throughout the length and breadth of the GBR. This demonstrates that simple visual assessments can provide useful information, in the absence of quantitative measurements, of this proxy freshwater tracer. The annual range of measured luminescence between the preceding winter minimum and summer maximum, rather than annual average or annual maximum luminescence is shown to be the most robust measure of freshwater flow. Second, from analyses of the coral colony data and over 40-century-long or longer coral core records, attention is drawn to a potential age artefact in annual average and annual maximum measured coral luminescence. These variables show a significant decline through time, similar to the observed decline in average skeletal density. Although the reasons for this decline are unknown, it could compromise interpretation of long-term variations in freshwater flows and subsequent climatic inferences. This artefact does not appear to affect the annual luminescence range which, it is concluded, is a robust proxy for inter-annual variations in river flow and rainfall.

  3. Glycines: Role in ?-Helical Membrane Protein Structures and a Potential Indicator for Native Conformation

    PubMed Central

    Dong, Hao; Sharma, Mukesh; Zhou, Huan-Xiang; Cross, Timothy A.

    2012-01-01

    Among the growing number of membrane protein structures in the Protein Data Bank, there are many transmembrane domains that appear to be native-like; at the same time there are others that appear to have less than complete native-like character. Hence there is an increasing need for validation tools that distinguish native-like from nonnative-like structures. Membrane mimetics used in protein structural characterizations differ in numerous physicochemical properties from native membranes and provide many opportunities for introducing nonnative-like features into membrane protein structures. One possible approach for validating membrane protein structures is based on the use of glycine residues in transmembrane domains. Here, we have reviewed the membrane protein structure database and identified a set of benchmark proteins that appear to be native like. In these structures, conserved glycine residues rarely face the lipid interstices, and many of them participate in close helix-helix packing. Glycine-based validation allowed the identification of nonnative-like features in several membrane proteins and also shows the potential for verifying the native-like character for numerous other membrane protein structures. PMID:22650985

  4. 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, Bjrn 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.

  5. Multiple Indices of Diffusion Identifies White Matter Damage in Mild Cognitive Impairment and Alzheimers Disease

    PubMed Central

    O'Dwyer, Laurence; Lamberton, Franck; Bokde, Arun L. W.; Ewers, Michael; Faluyi, Yetunde O.; Tanner, Colby; Mazoyer, Bernard; O'Neill, Des; Bartley, Mirad; Collins, D. Rnn; Coughlan, Tara; Prvulovic, David; Hampel, Harald

    2011-01-01

    The study of multiple indices of diffusion, including axial (DA), radial (DR) and mean diffusion (MD), as well as fractional anisotropy (FA), enables WM damage in Alzheimer's disease (AD) to be assessed in detail. Here, tract-based spatial statistics (TBSS) were performed on scans of 40 healthy elders, 19 non-amnestic MCI (MCIna) subjects, 14 amnestic MCI (MCIa) subjects and 9 AD patients. Significantly higher DA was found in MCIna subjects compared to healthy elders in the right posterior cingulum/precuneus. Significantly higher DA was also found in MCIa subjects compared to healthy elders in the left prefrontal cortex, particularly in the forceps minor and uncinate fasciculus. In the MCIa versus MCIna comparison, significantly higher DA was found in large areas of the left prefrontal cortex. For AD patients, the overlap of FA and DR changes and the overlap of FA and MD changes were seen in temporal, parietal and frontal lobes, as well as the corpus callosum and fornix. Analysis of differences between the AD versus MCIna, and AD versus MCIa contrasts, highlighted regions that are increasingly compromised in more severe disease stages. Microstructural damage independent of gross tissue loss was widespread in later disease stages. Our findings suggest a scheme where WM damage begins in the core memory network of the temporal lobe, cingulum and prefrontal regions, and spreads beyond these regions in later stages. DA and MD indices were most sensitive at detecting early changes in MCIa. PMID:21738785

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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.

  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. 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

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. Secretomes are a potential source of molecular targets for cancer therapies and indicate that APOE is a candidate biomarker for lung adenocarcinoma metastasis.

    PubMed

    Liu, Zan; Gao, Yuan; Hao, Fengxia; Lou, Xiaomin; Zhang, Xiuwei; Li, Yang; Wu, Di; Xiao, Ting; Yang, Longhai; Li, Qingchang; Qiu, Xueshan; Wang, Enhua

    2014-11-01

    Identifying patients at high risk of metastasis is a major challenge in lung adenocarcinoma (ADC) therapy, therefore discovery of noninvasive biomarkers and therapeutic targets is urgent. We found significant differences between the secretomes of differentially expressed proteins in lung ADC cell lines, clinical tissue samples and serum plasma samples with high and low metastatic potential. In particular, Apolipoprotein E (APOE) levels were three-times greater in cells with lymph node metastases (LNM) than those without. Our study indicates that APOE is a potential indicator of metastatic lung ADC and that secretomes may offer a valuable resource for biomarkers of lung ADC with LNM. PMID:25098600

  7. 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.

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs

    PubMed Central

    Zhang, Rui; Cairelli, Michael J; Fiszman, Marcelo; Kilicoglu, Halil; Rindflesch, Thomas C; Pakhomov, Serguei V; Melton, Genevieve B

    2014-01-01

    In this study, we report on the performance of an automated approach to discovery of potential prostate cancer drugs from the biomedical literature. We used the semantic relationships in SemMedDB, a database of structured knowledge extracted from all MEDLINE citations using SemRep, to extract potential relationships using knowledge of cancer drugs pathways. Two cancer drugs pathway schemas were constructed using these relationships extracted from SemMedDB. Through both pathway schemas, we found drugs already used for prostate cancer therapy and drugs not currently listed as the prostate cancer medications. Our study demonstrates that the appropriate linking of relevant structured semantic relationships stored in SemMedDB can support the discovery of potential prostate cancer drugs. PMID:25392688

  20. 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...

  1. 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...

  2. 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

  3. 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

  4. 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…

  5. 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

  6. Histidine Decarboxylase Is Identified as a Potential Biomarker of Intestinal Mucosal Injury in Patients with Acute Intestinal Obstruction

    PubMed Central

    Yang, Jian-Jun; Ma, Yan-Lei; Zhang, Peng; Chen, Hong-Qi; Liu, Zhi-Hua; Qin, Huan-Long

    2011-01-01

    Various biomarkers currently used for the diagnosis of intestinal mucosal injury (IMI) in patients with acute intestinal obstruction have low sensitivity and specificity. In the present study, IMI, as indicated by the impaired expression of tight junction proteins, including zonula occludens-1, occludin and claudin-1, and inflammation were determined in colonic tissues of patients with 45 strangulated intestinal obstruction (STR-IO) and the adjacent normal colonic tissues of 35 patients with colon cancers by quantitative real-time polymerase chain reaction (QRT-PCR), Western blotting, immunohistochemistry and histological examination, respectively. Then, two-dimensional fluorescent difference gel electrophoresis coupled with linear trap quadrupole mass spectrometry was used to screen for potential biomarkers of IMI in the serum samples of 10 STR-IO, 10 simple intestinal obstruction (SIM-IO) and 10 normal healthy controls. A total of 35 protein spots were differentially expressed among the serum samples, and six of the proteins were identified as potential biomarkers. Among the six proteins, histidine decarboxylase (HDC) and ceruloplasmin (CP) were elevated significantly in patients with STR-IO, compared with patients with SIM-IO and healthy controls. Thus, HDC and CP were further validated by QRT-PCR, Western blotting, immunohistochemistry and enzyme-linked immunosorbent assay, respectively, in colonic tissues, serum and urine samples. Finally, the receiver operating characteristic curves were used to show the area under the curves of HDC, CP and several established biomarkers, followed by the determination of the appropriate cutoff values and their sensitivities and specificities. It was shown that for serum and urine, HDC levels achieved sensitivities and specificities compatible to or even greater than those of established biomarkers for the diagnosis of IMI in patients with acute intestinal obstruction, although further validation in a larger cohort is required. PMID:21915437

  7. 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.

  8. ATP-inhibited K+ channels and membrane potential of identified leech neurons.

    PubMed

    Frey, G; Lucht, M; Schlue, W R

    1998-07-01

    The effect of the ATP-inhibited K+ channel on the membrane potential of leech Retzius neurons was analyzed using electrolyte-filled single-barrelled microelectrodes. The membrane potential was independent of the external nutrient supply during a period of 11 h, probably because the internal energy reserves were sufficient. The K+ channel activator HOE 234 ((3S,4R)-3-hydroxy-2, 2-dimethyl-4-(2-oxo-1-pyrrolidinyl)-6-phenylsulfonylchromane hemihydrate, 500 microM) induced a membrane hyperpolarization. In the presence of HOE 234, action potentials occurred with a reduced after-hyperpolarization and were discharged in bursts, possibly because of an inhibition of Ca2+ channels. The blocker of ATP-inhibited K+ channels tolbutamide did not significantly alter the membrane potential. In the absence of tolbutamide, the metabolic inhibitors iodoacetate, azide and cyanide (10 mM) evoked membrane hyperpolarizations, but in the presence of 1 mM tolbutamide their hyperpolarizing actions were reduced or abolished while membrane depolarizations were intensified. We conclude that ATP-inhibited K+ channels in the soma membrane of leech Retzius neurons provide coupling of cellular metabolism to electrical activity and ionic fluxes. PMID:9666141

  9. 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…

  10. 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…

  11. 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…

  12. 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…

  13. 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

  14. 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…

  15. UNAIDS multiple sexual partners core indicator: promoting sexual networks to reduce potential biases

    PubMed Central

    Dimbuene, Zacharie Tsala; Emina, Jacques B.O.; Sankoh, Osman

    2014-01-01

    UNAIDS proposed a set of core indicators for monitoring changes in the worldwide AIDS epidemic. This paper explores the validity and effectiveness of the multiple sexual partners core indicator, which is only partially captured with current available data. The paper also suggests an innovative approach for collecting more informative data that can be used to provide an accurate measure of the UNAIDSs multiple sexual partners core indicator. Specifically, the paper addresses three major limitations associated with the indicator when it is measured with respondents sexual behaviors. First, the indicator assumes that a persons risk of contracting HIV/AIDS/STIs is merely a function of his/her own sexual behavior. Second, the indicator does not account for a partners sexual history, which is very important in assessing an individuals risk level. Finally, the 12-month period used to define a persons risks can be misleading, especially because HIV/AIDS theoretically has a period of latency longer than a year. The paper concludes that, programmatically, improvements in data collection are a top priority for reducing the observed bias in the multiple sexual partners core indicator. PMID:24647127

  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, Agns

    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. Biominerals on Mars: the potential for carbonates to be life indicators

    NASA Astrophysics Data System (ADS)

    Stalport, Fabien; Person, Alain; Cabane, Michel; Ausset, Patrick; Coll, Patrice; Szopa, Cyril; Navarro-Gonzalez, Rafael

    The question of life on Mars remains open today because recent data provided by the Mars Express orbiter, the Mars Reconnaissance Orbiter and the twin rovers Spirit and Opportunity seem to indicate a past environment of Mars, with liquid water and mild temperatures, favourable for life. We also suggest that a better understanding of the biomineral formation processes, and the discrimination between them and their abiotic counterparts (i.e. minerals with the same chemical and mineralogical composition but formed by abiotic processes) should be considered as a promising approach in order to detect possible traces of a past Martian life. Moreover, biominerals may constitute fossil records of biological activities, which can survive for several millions or billions years, because they are among the oldest know traces of the biological activity on Earth. One of the properties of the biominerals, compared with their abiotic counterparts, is their faster crystalline speed of growing. The higher this speed is, the more the mineral crystallinity decreases, i.e. its crystal lattice will incorporate a significant number of impurities (crystalline defects, trace/minor elements and maybe organic matter). These impurities increase the crystal entropy and also the required energy to stabilize it: the crystal is then thermodynamically less stable. We then propose that the crystallinity differences between the biominerals and their abiotic counterparts induce specific physico-chemical behaviours. Among the analytical techniques capable to characterize this mineral property, we selected DTA-TG analysis (thermogravimetry coupled to differential thermal analysis). We suggest that the crystallinity is an influent parameter for the mineral thermal resistance. The temperature increase could be a "stressing" agent for the crystal lattices and it could involve behaviour differences between the biominerals and their abiotic counterparts. We then quantify this difference by comparing thermal resistance of various calcite and aragonite samples in order to observe a possible discrimination between a biological thermal degradation "domain" and an abiotic one. The carbonates were selected because they are among the oldest biominerals on Earth, widely produced by the terrestrial biological activity, and potentially present at Mars. The studied samples are biogenic, abiotic and diagenetic ones (combining a biological origin and an abiotic evolution). We started this study with calcite samples, including current biogenic samples, fossil biogenic samples, sedimentary samples and abiotic samples. We observed that the thermal resistance temperatures of all the current biogenic calcite samples are at least 15 C lower compared to those of abiotic calcite samples. The second part of the study was based on aragonite samples, including current biogenic samples, fossil biogenic samples and abiotic samples. We also observed a 23 C difference between the biological domain and the abiotic domain.. This demonstrates that the simple technique we chose is capable to differentiate the biotic minerals from the abiotic ones. We then have access to a non-ambiguous biological signature via the thermal resistance comparison of biogenic and abiotic carbonates. This discriminatory method could be used in the framework of several in situ Mars exploration mission: directly by differential thermal analysis (TEGA instrument, Phoenix Lander mission, 2007) or indirectly by analysis in gas chromatography coupled to mass spectrometry (SAM experiment on MSL 2009 or MOMA experiment on ExoMars 2013).

  19. 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...

  20. 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

  1. 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.

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

    PubMed

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

    2015-01-28

    A recently developed instrument for time-resolved infrared detection following pulse radiolysis has been used to measure the ?(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. 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. PMID:25554821

  3. 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

  4. 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

  5. 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

  6. 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

  7. Traits, habitats, and clades: identifying traits of potential importance to environmental filtering.

    PubMed

    Mayfield, Margaret M; Boni, Maciej F; Ackerly, David D

    2009-07-01

    Environmental filtering is a fundamental process in the ecological assembly of communities. Recently developed phylogenetic tools identify patterns associated with environmental filtering across whole communities. Here we introduce a novel method that allows the detection of traits involved in the environmental filtering of species from specific clades in specific habitat types. Our approach identifies nonindependent trait/habitat/clade (THC) associations and also provides a framework for detecting clearly defined two-way trait/clade, trait/habitat, and clade/habitat associations. The THC method relies on exact binomial tests and differentiates THC associations resulting from a three-way interaction from those that are generated by one or more underlying significant two-way interactions. It can also detect THC associations for which there are no significant two-way associations (trait/habitat, trait/clade, clade/habitat). To illustrate the THC method, we examine plant pollination and dispersal traits from six habitat types in a fragmented Costa Rican landscape. Results suggest that these traits are not widely important for the environmental filtering of most clades in this landscape, but animal dispersal and insect pollination are involved in the filtering of monocots and the Piperaceae in rain forest understory. PMID:19463061

  8. Sleep-related eye symptoms and their potential for identifying driver sleepiness.

    PubMed

    Filtness, Ashleigh J; Anund, Anna; Fors, Carina; Ahlstrm, Christer; Akerstedt, Torbjrn; Kecklund, Gran

    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

  9. 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

  10. Surface fluorescence method can identify potential oil pay zones in Permian Basin

    SciTech Connect

    Burrows, R. ); Calhoun, G.G.

    1992-09-28

    This paper points out a direct relationship between the fluorescence signature between the oil produced from a well and that found in the soils overlying that oil accumulation. Under the right conditions, an operator can know before drilling which of the potential pays in its prospect is trapped and microseeping to the surface. Some have suggested that half the oil that has been produced was found using visible oil seeps as indictions of traps. With those obvious opportunities on production, only more subtle microseeps remain. Instruments sensitive enough to measure these miniscule amounts of aromatic hydrocarbons have only recently become available.

  11. 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

  12. Molecular markers and imaging tools to identify malignant potential in Barrett's esophagus

    PubMed Central

    Bennett, Michael; Mashimo, Hiroshi

    2014-01-01

    Due to its rapidly rising incidence and high mortality, esophageal adenocarcinoma is a major public health concern, particularly in Western countries. The steps involved in the progression from its predisposing condition, gastroesophageal reflux disease, to its premalignant disorder, Barretts esophagus, and to cancer, are incompletely understood. Current screening and surveillance methods are limited by the lack of population-wide utility, incomplete sampling of standard biopsies, and subjectivity of evaluation. Advances in endoscopic ablation have raised the hope of effective therapy for eradication of high-risk Barretts lesions, but improvements are needed in determining when to apply this treatment and how to follow patients clinically. Researchers have evaluated numerous potential molecular biomarkers with the goal of detecting dysplasia, with varying degrees of success. The combination of biomarker panels with epidemiologic risk factors to yield clinical risk scoring systems is promising. New approaches to sample tissue may also be combined with these biomarkers for less invasive screening and surveillance. The development of novel endoscopic imaging tools in recent years has the potential to markedly improve detection of small foci of dysplasia in vivo. Current and future efforts will aim to determine the combination of markers and imaging modalities that will most effectively improve the rate of early detection of high-risk lesions in Barretts esophagus. PMID:25400987

  13. 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

  14. 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; Celedn, 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 ? 10g/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

  15. 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

  16. 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...

  17. 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…

  18. 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...

  19. 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...

  20. Acoustic noise alters selective attention processes as indicated by direct current (DC) brain potential changes.

    PubMed

    Trimmel, Karin; Schtzer, 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

  1. Acoustic Noise Alters Selective Attention Processes as Indicated by Direct Current (DC) Brain Potential Changes

    PubMed Central

    Trimmel, Karin; Schtzer, 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 shiftswhich are discussed to represent different states of cortical activationof 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 suggestbesides some limitationsthat 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

  2. 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.

  3. Developing key laboratory performance indicators: a feasibility study. Potential roles for CLMA.

    PubMed

    Zinn, J; Getzen, T

    1995-01-01

    The challenges (and opportunities) for laboratory management posed by cost control, managed care, information networks, and health system integration call for both short- and long-term responses. In rapidly evolving markets, new measures are needed to assess how effectively laboratories manage the information process. The objective of the research described in this report was to determine the feasibility of a system that would collect, analyze, and report nationally standardized indicators of laboratory performance and that would meet the needs of health system executives, managed care plans, and external agencies, as well as laboratory service providers. The feasibility study involved extensive interviews with a broad cross-section of the health-care industry, as well as a literature search of journals, newspapers, marketing brochures, and other documents addressing comparative performance assessment in the health-care industry. The study investigated the current status of comparative performance assessment in the health-care industry. We found that there are several important lessons laboratorians can learn from the experiences of others involved in key indicator development and performance assessment: Key indicators must measure those aspects of performance that are important and meaningful to laboratory customers. Indicators developed for laboratory management performance should be compatible with performance criteria established in other health-care sectors, particularly those that represent managed care and other customers of laboratory services. The identification of participants in the process of consensus development should be as inclusive as possible if the indicators are to gain wide acceptance. Standardized definitions and data collection rules are essential for data comparability. Credibility is key. It is necessary that the chosen measures be not only reliable, valid, and easy to implement, they must also be demonstrably related to patient care outcomes. In order to make meaningful interlaboratory comparisons, an effective system for peer groupings is also required. Currently available systems for collecting and reporting laboratory performance data were also reviewed.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:10143165

  4. 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

  5. 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

  6. 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

  7. 49 CFR 192.917 - How does an operator identify potential threats to pipeline integrity and use the threat...

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 49 Transportation 3 2013-10-01 2013-10-01 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...

  8. 40 CFR Table 5 to Subpart Jj of... - List of VHAP of Potential Concern Identified by Industry

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 11 2012-07-01 2012-07-01 false List of VHAP of Potential Concern Identified by Industry 5 Table 5 to Subpart JJ of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED)...

  9. 40 CFR Table 5 to Subpart Jj of... - List of VHAP of Potential Concern Identified by Industry

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 11 2013-07-01 2013-07-01 false List of VHAP of Potential Concern Identified by Industry 5 Table 5 to Subpart JJ of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED)...

  10. 40 CFR Table 5 to Subpart Jj of... - List of VHAP of Potential Concern Identified by Industry

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 10 2011-07-01 2011-07-01 false List of VHAP of Potential Concern Identified by Industry 5 Table 5 to Subpart JJ of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED)...

  11. 40 CFR Table 5 to Subpart Jj of... - List of VHAP of Potential Concern Identified by Industry

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 11 2014-07-01 2014-07-01 false List of VHAP of Potential Concern Identified by Industry 5 Table 5 to Subpart JJ of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED)...

  12. 40 CFR Table 5 to Subpart Jj of... - List of VHAP of Potential Concern Identified by Industry

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 10 2010-07-01 2010-07-01 false List of VHAP of Potential Concern Identified by Industry 5 Table 5 to Subpart JJ of Part 63 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED)...

  13. 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...

  14. 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...

  15. Petrographic features of solid organic materials as indicators of paleotemperatures and oil potential

    SciTech Connect

    Ammosov, I.I.

    1981-04-01

    We identified temperature zones from quantitative petrographic data on solid organic substances. These zones constitute a system responsible for the generation, migration, and accumulation of organic fluids, which as a whole is responsible for the production of oil pools. The zones are produced mainly by heat fluxes from the asthenosphere and by the heat from intrusions. The paleotemperature gradient is one of the parameters of such heat fluxes.

  16. Application of Polychromatic Flow Cytometry to Identify Novel Subsets of Circulating Cells with Angiogenic Potential

    PubMed Central

    Estes, Myka L.; Mund, Julie A.; Mead, Laura E.; Prater, Daniel N.; Cai, Shanbao; Wang, Haiyan; Pollok, Karen E.; Murphy, Michael P.; An, Caroline S.T.; Srour, Edward F.; Ingram, David A.; Case, Jamie

    2010-01-01

    Defining whether human circulating pro-angiogenic cells represent a subset of the hematopoietic system and express CD45 or are hematopoietic derivatives that do not express CD45 (and are called endothelial progenitor cells) remains controversial. We have previously developed a polychromatic flow cytometry (PFC) protocol to isolate subsets of hematopoietic cells and we now identify the circulating pool of CD34+CD45dim cells representing functional circulating hematopoietic stem and progenitor cells (CHSPCs) that can be separated on the basis of AC133 expression and report that the AC133+ subset of the CHSPCs enhances the growth of tumor blood vessels in vivo in immunodeficient mice. In addition, the ratio of AC133+ pro-angiogenic CHSPCs to AC133? non-angiogenic CHSPCs unambiguously correlates with the severity of the clinical state of patients with peripheral arterial disease. In sum, a PFC protocol validated via in vitro and in vivo analyses, can be used to interrogate the roles of human hematopoietic elements in the growth and maintenance of the vasculature. PMID:20803735

  17. 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

  18. Use of comparative proteomics to identify potential resistance mechanisms in cancer treatment

    PubMed Central

    Zhang, Jian-Ting; Liu, Yang

    2007-01-01

    Drug resistance is a major problem in successful cancer chemotherapy. Many molecular mechanisms that are responsible for drug resistance are known whereas others have yet to be discovered. Determining the exact mechanism activated in a particular case (clinical or laboratory) is a difficult task. Recently, proteomics has been applied to investigate drug resistance mechanisms in model cancer cell lines. As a result, novel mechanisms of resistance have been discovered and known mechanisms of resistance confirmed. In this paper, we wish to review recent developments and progresses in the application of proteomic tools to identify known and novel drug resistance mechanisms in drug-selected model cancer cell lines. Our combined analyses of multiple proteomic studies of various drug resistant cancer cell lines revealed that many mechanisms of resistance likely exist in any given drug-selected cancer cell line and that common mechanisms of resistance may be selected in a spectrum of cancer cell lines. These observations suggest that combination therapies targeting multiple mechanisms to sensitize drug resistant cancers may be necessary to eradicate cancers in the future. PMID:17854999

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. N(8)-acetylspermidine as a potential plasma biomarker for Snyder-Robinson syndrome identified by clinical metabolomics.

    PubMed

    Abela, Lucia; Simmons, Luke; Steindl, Katharina; Schmitt, Bernhard; Mastrangelo, Massimo; Joset, Pascal; Papuc, Mihaela; Sticht, Heinrich; Baumer, Alessandra; Crowther, Lisa M; Mathis, Dborah; Rauch, Anita; Plecko, Barbara

    2016-01-01

    Clinical metabolomics has emerged as a powerful tool to study human metabolism in health and disease. Comparative statistical analysis of untargeted metabolic profiles can reveal perturbations of metabolite levels in diseases and thus has the potential to identify novel biomarkers. Here we have applied a simultaneous genetic-metabolomic approach in twin boys with epileptic encephalopathy of unclear etiology. Clinical exome sequencing identified a novel missense mutation in the spermine synthase gene (SMS) that causes Snyder-Robinson syndrome (SRS). Untargeted plasma metabolome analysis revealed significantly elevated levels of N(8)-acetylspermidine, a precursor derivative of spermine biosynthesis, as a potential novel plasma biomarker for SRS. This result was verified in a third patient with genetically confirmed SRS. This study illustrates the potential of metabolomics as a translational technique to support exome data on a functional and clinical level. PMID:26174906

  4. 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

  5. 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.

  6. The Semaphore crab, Heloecius cordiformis: bio-indication potential for heavy metals in estuarine systems.

    PubMed

    MacFarlane; Booth; Brown

    2000-09-01

    Although alterations at the organism level in decapod crustaceans on exposure to heavy metals have been evidenced in the laboratory, little examination of metal effects on morphology and population parameters have been explored in a field-based situation. Relationships between morphological parameters, population demography and heavy metal sediment loadings were examined in conjunction with the accumulation of metals in the Semaphore crab, Heloecius cordiformis, in the Port Jackson and Hawkesbury River estuaries, Sydney, Australia. H. cordiformis exhibited sexual dimorphism, with males having larger carapace width, carapace length, chelae length and total mass than females. Sexes were subsequently treated separately to assess morphological differences among locations. Locations that had greater proportions of females with purple chelae and less females in the population tended to have higher sediment metal levels. These relationships were maintained over time, and could be employed as population-level biological indicators of heavy metal stress. Copper and zinc were regulated in the hepatopancreas of H. cordiformis. Lead was accumulated in the hepatopancreas of H. cordiformis in proportion to sediment lead levels, suggesting the species is both an appropriate candidate for bio-indication of lead pollution, and Pb is the main metal linked with population level differences. Accumulation of lead varied between sexes, indicating that sexes must be monitored separately. Smaller males accumulated more lead than larger males, suggesting size is an important consideration for lead accumulation. PMID:10958951

  7. 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 ?/?-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

  8. 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

  9. Identifying the Potential for Robotics to Assist Older Adults in Different Living Environments.

    PubMed

    Mitzner, Tracy L; Chen, Tiffany L; Kemp, Charles C; Rogers, Wendy A

    2014-04-01

    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

  10. Identifying potential clinical syndromes of hepatocellular carcinoma using PSO-based hierarchical feature selection algorithm.

    PubMed

    Ji, Zhiwei; Wang, Bing

    2014-01-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. Clinical symptoms attributable to HCC are usually absent, thus often miss the best therapeutic opportunities. Traditional Chinese Medicine (TCM) plays an active role in diagnosis and treatment of HCC. In this paper, we proposed a particle swarm optimization-based hierarchical feature selection (PSOHFS) model to infer potential syndromes for diagnosis of HCC. Firstly, the hierarchical feature representation is developed by a three-layer tree. The clinical symptoms and positive score of patient are leaf nodes and root in the tree, respectively, while each syndrome feature on the middle layer is extracted from a group of symptoms. Secondly, an improved PSO-based algorithm is applied in a new reduced feature space to search an optimal syndrome subset. Based on the result of feature selection, the causal relationships of symptoms and syndromes are inferred via Bayesian networks. In our experiment, 147 symptoms were aggregated into 27 groups and 27 syndrome features were extracted. The proposed approach discovered 24 syndromes which obviously improved the diagnosis accuracy. Finally, the Bayesian approach was applied to represent the causal relationships both at symptom and syndrome levels. The results show that our computational model can facilitate the clinical diagnosis of HCC. PMID:24745007

  11. 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

  12. Identifying Potential Clinical Syndromes of Hepatocellular Carcinoma Using PSO-Based Hierarchical Feature Selection Algorithm

    PubMed Central

    Ji, Zhiwei; Wang, Bing

    2014-01-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. Clinical symptoms attributable to HCC are usually absent, thus often miss the best therapeutic opportunities. Traditional Chinese Medicine (TCM) plays an active role in diagnosis and treatment of HCC. In this paper, we proposed a particle swarm optimization-based hierarchical feature selection (PSOHFS) model to infer potential syndromes for diagnosis of HCC. Firstly, the hierarchical feature representation is developed by a three-layer tree. The clinical symptoms and positive score of patient are leaf nodes and root in the tree, respectively, while each syndrome feature on the middle layer is extracted from a group of symptoms. Secondly, an improved PSO-based algorithm is applied in a new reduced feature space to search an optimal syndrome subset. Based on the result of feature selection, the causal relationships of symptoms and syndromes are inferred via Bayesian networks. In our experiment, 147 symptoms were aggregated into 27 groups and 27 syndrome features were extracted. The proposed approach discovered 24 syndromes which obviously improved the diagnosis accuracy. Finally, the Bayesian approach was applied to represent the causal relationships both at symptom and syndrome levels. The results show that our computational model can facilitate the clinical diagnosis of HCC. PMID:24745007

  13. Docking based virtual screening and molecular dynamics study to identify potential monoacylglycerol lipase inhibitors.

    PubMed

    Afzal, Obaid; Kumar, Suresh; Kumar, Rajiv; Firoz, Ahmad; Jaggi, Manu; Bawa, Sandhya

    2014-08-15

    Monoacylglycerol lipase (MAGL) is one of the key enzymes of the endocannabinoid system (ECS). It hydrolyzes one of the major endocannabinoid, 2-arachidonoylglycerol (2-AG), an endogenous full agonist at G protein coupled cannabinoid receptors CB1 and CB2. Numerous studies showed that MGL inhibitors are potentially useful for the treatment of pain, inflammation, cancer and CNS disorders. These provocative findings suggested that pharmacological inhibition of MAGL function may confer significant therapeutic benefits. In this study, we presented hybrid ligand and structure-based approaches to obtain a novel set of virtual leads as MAGL inhibitors. The constraints used in this study, were Glide score, binding free energy estimates and ADME properties to screen the ZINC database, containing approximately 21 million compounds. A total of seven virtual hits were obtained, which showed significant binding affinity towards MAGL protein. Ligand, ZINC24092691 was employed in complex form with the protein MAGL, for molecular dynamics simulation study, because of its excellent glide score, binding free energy and ADME properties. The RMSD of ZINC24092691 was observed to stay at 0.1 nm (1 ) in most of the trajectories, which further confirmed its ability to inhibit the protein MAGL. The hits were then evaluated for their ability to inhibit human MAGL. The compound ZINC24092691 displayed the noteworthy inhibitory activity reducing MAGL activity to 21.15% at 100 nM concentration, with an IC50 value of 10 nM. PMID:25011912

  14. 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

  15. 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

  16. 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.

  17. Kinase inhibitor screening identifies CDK4 as a potential therapeutic target for melanoma

    PubMed Central

    MAHGOUB, T.; EUSTACE, A.J.; COLLINS, D.M.; WALSH, N.; O'DONOVAN, N.; CROWN, J.

    2015-01-01

    Despite recent advances in targeted therapies and immunotherapies metastatic melanoma remains only rarely curable. The objective of the present study was to identify novel therapeutic targets for metastatic melanoma. A library of 160 well-characterised and potent protein kinase inhibitors was screened in the BRAF mutant cell line Sk-Mel-28, and the NRAS mutant Sk-Mel-2, using proliferation assays. Of the 160 inhibitors tested, 20 achieved >50% growth inhibition in both cell lines. Six of the 20 were cyclin dependent kinase (CDK) inhibitors, including two CDK4 inhibitors. Fascaplysin, a synthetic CDK4 inhibitor, was further tested in 8 melanoma cell lines. The concentration of fascaplysin required to inhibit growth by 50% (IC50 value) ranged from 0.03 to 0.22 ?M. Fascaplysin also inhibited clonogenic growth and induced apoptosis. Sensitivity to PD0332991, a therapeutic CDK4/6 inhibitor was also evaluated in the melanoma cell lines. PD0332991 IC50 values ranged from 0.13 to 2.29 ?M. Similar to fascaplysin, PD0332991 inhibited clonogenic growth of melanoma cells and induced apoptosis. Higher levels of CDK4 protein correlated with lower sensitivity to PD0332991 in the cell lines. Combined treatment with PD0332991 and the BRAF inhibitor PLX4032, showed additive anti-proliferative effects in the BRAF mutant cell line Malme-3M. In summary, targeting CDK4 inhibits growth and induces apoptosis in melanoma cells in vitro, suggesting that CDK4 may be a rational therapeutic target for metastatic melanoma. PMID:26201960

  18. 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.

  19. DNA Microarray Analysis Identifies CKS2 and LEPR as Potential Markers of Meningioma Recurrence

    PubMed Central

    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

    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 ?Ct 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

  20. 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 ?Ct 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

  1. Cross-polar cap potential difference, auroral electrojet indices, and solar wind parameters

    SciTech Connect

    Ahn, B.H. Univ. of Colorado, Boulder ); Kamide, Y. ); Kroehl, H.W.; Gorney, D.J. )

    1992-02-01

    The cross-polar cap potential difference {Phi} (KRM) is estimated from ground magnetic perturbation data through the magnetometer inversion method of Kamide, Richmond, and Matsushita (FRM), combined with an empirical ionospheric conductance distribution estimated from the DMSP X ray image data. A significant correlation is found between {Phi} (KRM) and the AE(12) index. {Phi} (KRM) is then compared with the potential difference estimated from a more direct method of the satellite electric field measurements and also with {Phi}(IMF) is found to be linearly correlated with {Phi} (IMF) based on solar wind parameters. {Phi} IMF is found to be linearly correlated with {Phi}(KRM), as {Phi}(IMF) = 29.8 + 0.999 {Phi} (KRM), with the highest correlation obtained for a 40-min lag in the interplanetary magnetic field (IMF). Note that {Phi}(IMF) is systematically larger than {Phi} (KRM) by 30 kV, suggesting the possibility that the theoretical method overestimates the cross-polar cap potential difference. During steady southward IMF periods were steady {Phi} (IMF) variations are expected, significant fluctuations in calculated {Phi} (KRM) values are obtained. Since the decrease in {Phi} (KRM) is closely associated with enhancements in auroral particle precipitation during these periods, a highly correlative relation between {Phi} (IMF) and {Phi} (KRM) cannot be deduced unless the phases of substorms are taken into account. The overall high correlation between them, however, supports the view expressed by Wolf et al. (1986) that directly driven processes are more important than unloading processes during disturbed periods.

  2. A complementary bioinformatics approach to identify potential plant cell wall glycosyltransferase-encoding genes.

    PubMed

    Egelund, Jack; Skjt, 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

  3. 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.

  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. 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

  6. Potential lung nodules identification for characterization by variable multistep threshold and shape indices from CT images.

    PubMed

    Iqbal, Saleem; Iqbal, Khalid; Arif, Fahim; Shaukat, Arslan; Khanum, Aasia

    2014-01-01

    Computed tomography (CT) is an important imaging modality. Physicians, surgeons, and oncologists prefer CT scan for diagnosis of lung cancer. However, some nodules are missed in CT scan. Computer aided diagnosis methods are useful for radiologists for detection of these nodules and early diagnosis of lung cancer. Early detection of malignant nodule is helpful for treatment. Computer aided diagnosis of lung cancer involves lung segmentation, potential nodules identification, features extraction from the potential nodules, and classification of the nodules. In this paper, we are presenting an automatic method for detection and segmentation of lung nodules from CT scan for subsequent features extraction and classification. Contribution of the work is the detection and segmentation of small sized nodules, low and high contrast nodules, nodules attached with vasculature, nodules attached to pleura membrane, and nodules in close vicinity of the diaphragm and lung wall in one-go. The particular techniques of the method are multistep threshold for the nodule detection and shape index threshold for false positive reduction. We used 60 CT scans of "Lung Image Database Consortium-Image Database Resource Initiative" taken by GE medical systems LightSpeed16 scanner as dataset and correctly detected 92% nodules. The results are reproducible. PMID:25506388

  7. 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 (?FAMEs) 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.

  8. 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

  9. Drainage network extraction of Brazilian semiarid region with potential flood indication areas

    NASA Astrophysics Data System (ADS)

    Rosim, Sergio; de Freitas Oliveira, Joo. Ricardo; de Oliveira Ortiz, Jussara; Cuellar, Miguel Zanic; Jardim, Alexandre Copertino

    2014-10-01

    This region has the particularity of, at the same time, coexisting with sporadic floods and scarcity of water. This situation requires complex studies involving water resources based on runoff of rain waters and on the courses of the rivers. For the extraction of drainage was carried out by using of the system for hydrological modeling treatment TerraHidro, developed by INPE's Image Processing Division. This system uses the PFS method for extraction of drainage, which has provided good results, enabling the reduction of the time spent on manual editing of drainage errors. TerraHidro has a tool called Height Above the Nearest Drainage (HAND) which gives information on potential flood areas. Elevation data were used in the Aster GDEM with spatial resolution of 30 meters for drainage extraction. A qualitative comparison was performed between drainage extracted by TerraHidro and drainage manually extracted by a specialist.

  10. 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

  11. Variations in Environmental Signals in Tree-Ring Indices in Trees with Different Growth Potential.

    PubMed

    Hafner, Polona; Gri?ar, Joica; Skudnik, Mitja; Levani?, 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. ?-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

  12. 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...

  13. Complete mitogenome of the foxface rabbitfish Siganus vulpinus (Perciformes, Siganidae): indication of potential interbreeding in rabbitfishes.

    PubMed

    Yan, Shuai; Wang, Ming; Yang, Tingbao

    2014-10-20

    Abstract In the present study, the complete mitochondrial genome of the foxface rabbitfish Siganus vulpinus (Perciformes, Siganidae) is determined. The entire sequence is 16,505?bp in length, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The genome organization is similar to those found in other rabbitfishes. Apart from ND6 and 8 tRNA genes, all other mitochondrial genes are encoded on the heavy strand. Overall base compositions of mitogenome are 29.3% of A, 29.3% of C, 25.7% of T, and 15.7% of G, showing an obvious anti-G bias which is commonly found in fishes. The high similarity of mitochondrial genome between S. vulpinus and S. unimaculatus indicate that natural interbreeding might exist in breeding season. PMID:25329262

  14. 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.

  15. 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

  16. 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

  17. 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 ? 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 ? 13C values and used as land-plant isotopic substrates within mixed organic material. Toward this end, we present ? 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 ? 13C value of nucleic acids to the ? 13C value of bulk tissue for multicellular organisms; our results contrasted with the minimal fractionations reported for microorganisms. Because the isotopic enrichment ? 13C is constant across tracheophytes, the ? 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.

  18. Plant DNA: A new substrate for carbon stable isotope analysis and a potential paleoenvironmental indicator

    NASA Astrophysics Data System (ADS)

    Jahren, A. Hope; Petersen, Gitte; Seberg, Ole

    2004-03-01

    The ?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 fossil sediments have been recognized as the oldest authenticated fossil deoxyribonucleic acid (DNA), making the inference of plant taxonomy possible in substrates devoid of plant macrofossils 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 ?13C value and used as land plant isotopic substrates within mixed organic material. Toward this end, we present ?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 ?13C value of nucleic acids to the ?13C value of bulk tissue for multicellular organisms; our results contrasted with the minimal fractionations reported for microorganisms. Because the isotopic enrichment is constant across tracheophytes, the ?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.

  19. Soil fungal community shift evaluation as a potential cadaver decomposition indicator.

    PubMed

    Chimutsa, Monica; Olakanye, Ayodeji O; Thompson, Tim J U; Ralebitso-Senior, T Komang

    2015-12-01

    Fungi metabolise organic matter in situ and so alter both the bio-/physico-chemical properties and microbial community structure of the ecosystem. In particular, they are responsible reportedly for specific stages of decomposition. Therefore, this study aimed to extend previous bacteria-based forensic ecogenomics research by investigating soil fungal community and cadaver decomposition interactions in microcosms with garden soil (20kg, fresh weight) and domestic pig (Sus scrofa domesticus) carcass (5kg, leg). Soil samples were collected at depths of 0-10cm, 10-20cm and 20-30cm on days 3, 28 and 77 in the absence (control -Pg) and presence (experimental +Pg) of Sus scrofa domesticus and used for total DNA extraction and nested polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) profiling of the 18S rRNA gene. The Shannon-Wiener (H') community diversity indices were 1.250.21 and 1.490.30 for the control and experimental microcosms, respectively, while comparable Simpson species dominance (S) values were 0.650.109 and 0.750.015. Generally, and in contrast to parallel studies of the bacterial 16S rRNA and 16S rDNA profiles, statistical analysis (t-test) of the 18S dynamics showed no mathematically significant shifts in fungal community diversity (H'; p=0.142) and dominance (S; p=0.392) during carcass decomposition, necessitating further investigations. PMID:26322496

  20. 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.

  1. 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

  2. Complex forest dynamics indicate potential for slowing carbon accumulation in the southeastern United States.

    PubMed

    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

  3. 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

  4. 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

  5. Clinical applications of palifermin: amelioration of oral mucositis and other potential indications

    PubMed Central

    Vadhan-Raj, Saroj; Goldberg, Jenna D; Perales, Miguel-Angel; Berger, Dietmar P; Brink, Marcel RM

    2013-01-01

    Mucositis is one of the most significant toxicities in cancer patients undergoing cytotoxic treatment. It can have a negative impact on both quality of life and health economics. Severe oral mucositis can contribute to hospitalization, need for narcotic analgesics, total parentral nutrition, suboptimal delivery of anti-neoplastic treatment, and morbidity and mortality. Palifermin, a recombinant derivative of human keratinocyte growth factor, is the first active agent approved by the FDA for the prevention of severe oral mucositis in patients undergoing haematopoietic stem cell transplantation (HSCT). Several studies have also shown significant reduction in the incidence, severity and/or duration of oral mucositis in other high-risk settings such as concurrent chemoradiotherapy (CT/RT) for patients with head and neck cancer, and use of mucotoxic chemotherapeutic agents such as doxorubicin in sarcoma and fluorouracil for the treatment of colorectal cancer. The reduction in mucositis has translated into amelioration of symptoms and improvement in daily functioning as measured by patient-reported outcome in multiple studies. The clinical response to palifermin appears to be related in part to epithelial proliferation and mucosal thickening. Palifermin also has other potential clinical applications including the acceleration of immune reconstitution and inhibition of graft-versus-host disease in patients undergoing HSCT, and mitigation of dysphagia in lung cancer patients treated with concurrent CT/RT. Palifermin is generally well tolerated with mild-to-moderate skin and oral adverse events. Future studies may expand the use of palifermin into other areas that would benefit from its cytoprotective and regenerative effects. PMID:24251854

  6. Mycobacterium bovis DNA Detection in Colostrum as a Potential Indicator of Vaccination Effectiveness against Bovine Tuberculosis

    PubMed Central

    Herrera-Rodrguez, Sara E.; Gordiano-Hidalgo, Mara Alejandra; Lpez-Rincn, Gonzlo; Bojorquez-Narvez, Luis; Padilla-Ramrez, Francisco Javier; Pereira-Surez, 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-?) 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

  7. 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

  8. Dissolved Organic Carbon and Optical Properties as Indicators of Trihalomethane Formation Potential in an Agricultural Watershed

    NASA Astrophysics Data System (ADS)

    Pellerin, B. A.; Bergamaschi, B. A.; Spencer, R. G.

    2006-12-01

    Elevated concentrations of dissolved organic carbon (DOC) in the Sacramento-San Joaquin Delta waters may result in the formation of high levels of carcinogenic disinfection byproducts such as trihalomethane during drinking water treatment. The importance of Central Valley agricultural lands as sources of DOC and THM- precursors upstream of the Delta is presently unknown. We are quantifying contributions of DOC and THM- precursors from the Willow Slough watershed, a 425 km2 agriculturally-dominated catchment. During 2006, water samples were collected weekly at the mouth of the watershed and analyzed for DOC concentrations, optical properties (UV absorbance and fluorescence), and trihalomethane formation potential (THMFP). Additional synoptic samples were collected seasonally (winter, spring, summer) from 16 watershed locations and analyzed for optical properties, DOC concentrations, and THMFP. DOC concentrations generally ranged from approximately 2 to 4 mg/L at the watershed outlet during winter and spring, but increased weekly to 8 mg/L following the onset of irrigation. The THMFP at the mouth of the water was correlated with DOC concentration (r2 = 0.87), with higher concentrations during high discharge events and lower concentrations during summer and prolonged rain-free periods. In addition, the species of THM varied between high and low-flow periods, with THM formation dominated by brominated species during low- flow periods and chlorinated species during rainfall-runoff events. Optical characterization of DOC via UV absorbance and fluorescence suggests changes in DOC composition between high- and low-flow periods, likely reflective of changing sources and flowpaths of runoff.

  9. Abnormal indices of cell cycle activity in schizophrenia and their potential association with oligodendrocytes.

    PubMed

    Katsel, Pavel; Davis, Kenneth L; Li, Celeste; Tan, Weilun; Greenstein, Elizabeth; Kleiner Hoffman, Lisa B; Haroutunian, Vahram

    2008-11-01

    The goal of this study was to determine what signaling pathways may elicit myelin-specific gene expression deficits in schizophrenia (SZ). Microarray analyses indicated that genes associated with canonical cell cycle pathways were significantly affected in the anterior cingulate gyrus (ACG), the region exhibiting the most profound myelin-specific gene expression changes, in persons with SZ (N=16) as compared with controls (N=19). Detected gene expression changes of key regulators of G1/S phase transition and genes central to oligodendrocyte differentiation were validated using qPCR in the ACG in an independent cohort (Ns=45/34). The relative abundance of phosphorylated retinoblastoma protein (pRb) was increased in the white matter underlying the ACG in SZ subjects (Ns=12). The upregulation of cyclin D1 gene expression and the downregulation of p57(Kip2), accompanied by increased cyclin D/CDK4-dependent phosphorylation of pRb, acting as a checkpoint for G1/S phase transition, suggest abnormal cell cycle re-entry in postmitotic oligodendrocytes in SZ. Furthermore, gene expression profiling of brain samples from myelin mutant animal models, quaking and myelin-associated glycoprotein (MAG) null mice, showed that cell cycle gene expression changes were not a necessary consequence of the reduced gene expression of structural myelin proteins, such as MAG. While, quaking, a known modulator of cell cycle activity during oligodendrocyte differentiation impairs the expression of multiple myelin genes, including those that are affected in SZ. These data suggest that the normal patterns of cell cycle gene and protein expression are disrupted in SZ and that this disruption may contribute to the oligodendroglial deficits observed in SZ. PMID:18322470

  10. 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

  11. 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

  12. Urban liveability: emerging lessons from Australia for exploring the potential for indicators to measure the social determinants of health.

    PubMed

    Badland, Hannah; Whitzman, Carolyn; Lowe, Melanie; Davern, Melanie; Aye, Lu; Butterworth, Iain; Hes, Dominique; Giles-Corti, Billie

    2014-06-01

    It has long been recognised that urban form impacts on health outcomes and their determinants. There is growing interest in creating indicators of liveability to measure progress towards achieving a wide range of policy outcomes, including enhanced health and wellbeing, and reduced inequalities. This review aimed to: 1) bring together the concepts of urban 'liveability' and social determinants of health; 2) synthesise the various liveability indicators developed to date; and 3) assess their quality using a health and wellbeing lens. Between 2011 and 2013, the research team reviewed 114 international academic and policy documents, as well as reports related to urban liveability. Overall, 233 indicators were found. Of these, 61 indicators were regarded as promising, 57 indicators needed further development, and 115 indicators were not useful for our purposes. Eleven domains of liveability were identified that likely contribute to health and wellbeing through the social determinants of health. These were: crime and safety; education; employment and income; health and social services; housing; leisure and culture; local food and other goods; natural environment; public open space; transport; and social cohesion and local democracy. Many of the indicators came from Australian sources; however most remain relevant from a 'global north' perspective. Although many indicators were identified, there was inconsistency in how these domains were measured. Few have been validated to assess their association with health and wellbeing outcomes, and little information was provided for how they should be applied to guide urban policy and practice. There is a substantial opportunity to further develop these measures to create a series of robust and evidence-based liveability indices, which could be linked with existing health and wellbeing data to better inform urban planning policies within Australia and beyond. PMID:24762261

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML

    PubMed Central

    Lo, Miao-Chia; Peterson, Luke F.; Yan, Ming; Cong, Xiuli; Jin, Fulai; Shia, Wei-Jong; Matsuura, Shinobu; Ahn, Eun-Young; Komeno, Yukiko; Ly, Minh; Ommen, Hans B.; Chen, I-Ming; Hokland, Peter; Willman, Cheryl L.; Ren, Bing

    2012-01-01

    Chromosome translocation 8q22;21q22 [t(8;21)] is commonly associated with acute myeloid leukemia (AML), and the resulting AML1-ETO fusion proteins are involved in the pathogenesis of AML. To identify novel molecular and therapeutic targets, we performed combined gene expression microarray and promoter occupancy (ChIP-chip) profiling using Lin?/Sca1?/cKit+ cells, the major leukemia cell population, from an AML mouse model induced by AML1-ETO9a (AE9a). Approximately 30% of the identified common targets of microarray and ChIP-chip assays overlap with the human t(8;21)gene expression molecular signature. CD45, a protein tyrosine phosphatase and a negative regulator of cytokine/growth factor receptor and JAK/STAT signaling, is among those targets. Its expression is substantially down-regulated in leukemia cells. Consequently, JAK/STAT signaling is enhanced. Re-expression of CD45 suppresses JAK/STAT activation, delays leukemia development, and promotes apoptosis of t(8;21)positive cells. This study demonstrates the benefit of combining gene expression and promoter occupancy profiling assays to identify molecular and potential therapeutic targets in human cancers and describes a previously unappreciated signaling pathway involving t(8;21) fusion proteins, CD45, and JAK/STAT, which could be a potential novel target for treating t(8;21) AML. PMID:22740448

  20. 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

  1. The potential impact of routine testing of individuals with HIV indicator diseases in order to prevent late HIV diagnosis

    PubMed Central

    2013-01-01

    Background The aim of our work was to evaluate the potential impact of the European policy of testing for HIV all individuals presenting with an indicator disease, to prevent late diagnosis of HIV. We report on a retrospective analysis among individuals diagnosed with HIV to assess whether a history of certain diseases prior to HIV diagnosis was associated with the chance of presenting late for care, and to estimate the proportion of individuals presenting late who could have been diagnosed earlier if tested when the indicator disease was diagnosed. Methods We studied a large cohort of individuals newly diagnosed with HIV infection in 13 counselling and testing sites in the Lazio Region, Italy (01/01/2004-30/04/2009). Considered indicator diseases were: viral hepatitis infection (HBV/HCV), sexually transmitted infections, seborrhoeic dermatitis and tuberculosis. Logistic regression analysis was performed to estimate association of occurrence of at least one indicator disease with late HIV diagnosis. Results In our analysis, the prevalence of late HIV diagnosis was 51.3% (890/1735). Individuals reporting at least one indicator disease before HIV diagnosis (29% of the study population) had a lower risk of late diagnosis (OR?=?0.7; 95%CI: 0.5-0.8) compared to those who did not report a previous indicator disease. 52/890 (5.8%) late presenters were probably already infected at the time the indicator disease was diagnosed, a median of 22.6months before HIV diagnosis. Conclusions Our data suggest that testing for HIV following diagnosis of an indicator disease significantly decreases the probability of late HIV diagnosis. Moreover, for 5.5% of late HIV presenters, diagnosis could have been anticipated if they had been tested when an HIV indicator disease was diagnosed. However, this strategy for enhancing early HIV diagnosis needs to be complemented by client-centred interventions that aim to increase awareness in people who do not perceive themselves as being at risk for HIV. PMID:24112129

  2. 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 Crohns 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

  3. 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

  4. The Environmental ``Risky'' Region: Identifying Land Degradation Processes Through Integration of Socio-Economic and Ecological Indicators in a Multivariate Regionalization Model

    NASA Astrophysics Data System (ADS)

    Salvati, Luca; Zitti, Marco

    2009-11-01

    Although several studies have assessed Land Degradation (LD) states in the Mediterranean basin through the use of composite indices, relatively few have evaluated the impact of specific LD drivers at the local scale. In this work, a computational strategy is introduced to define homogeneous areas at risk and the main factors acting as determinants of LD. The procedure consists of three steps and is applied to a set of ten environmental indicators available at the municipality scale in Latium, central Italy. A principal component analysis extracting latent patterns and simplifying data complexity was carried out on the original data matrix. Subsequently, a k-means cluster analysis was applied on a restricted number of meaningful, latent factors extracted by PCA in order to produce a classification of the study area into homogeneous regions. Finally, a stepwise discriminant analysis was performed to determine which indicators contributed the most to the definition of homogeneous regions. Three classes of risky regions were identified according to the main drivers of LD acting at the local scale. These include: (i) soil sealing (coupled with landscape fragmentation, fire risk, and related processes), (ii) soil salinization due to agricultural intensification, and (iii) soil erosion due to farmland depopulation and land abandonment in sloping areas. Areas at risk for LD covered 56 and 63% of the investigated areas in 1970 and 2000, respectively.

  5. 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

  6. 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.

  7. Entering a New Era of Body Indices: The Feasibility of a Body Shape Index and Body Roundness Index to Identify Cardiovascular Health Status

    PubMed Central

    Maessen, Martijn F. H.; Eijsvogels, Thijs M. H.; Verheggen, Rebecca J. H. M.; Hopman, Maria T. E.; Verbeek, Andr L. M.; de Vegt, Femmie

    2014-01-01

    Background The Body Mass Index (BMI) and Waist Circumference (WC) are well-used anthropometric predictors for cardiovascular diseases (CVD), but their validity is regularly questioned. Recently, A Body Shape Index (ABSI) and Body Roundness Index (BRI) were introduced as alternative anthropometric indices that may better reflect health status. Objective This study assessed the capacity of ABSI and BRI in identifying cardiovascular diseases and cardiovascular disease risk factors and determined whether they are superior to BMI and WC. Design and Methods 4627 Participants (5412 years) of the Nijmegen Exercise Study completed an online questionnaire concerning CVD health status (defined as history of CVD or CVD risk factors) and anthropometric characteristics. Quintiles of ABSI, BRI, BMI, and WC were used regarding CVD prevalence. Odds ratios (OR), adjusted for age, sex, and smoking, were calculated per anthropometric index. Results 1332 participants (27.7%) reported presence of CVD or CVD risk factors. The prevalence of CVD increased across quintiles for BMI, ABSI, BRI, and WC. Comparing the lowest with the highest quintile, adjusted OR (95% CI) for CVD were significantly different for BRI 3.2 (1.47.2), BMI 2.4 (1.93.1), and WC 3.0 (1.65.6). The adjusted OR (95% CI) for CVD risk factors was for BRI 2.5 (2.03.3), BMI 3.3 (1.66.8), and WC 2.0 (1.62.5). No association was observed for ABSI in both groups. Conclusions BRI, BMI, and WC are able to determine CVD presence, while ABSI is not capable. Nevertheless, the capacity of BRI as a novel body index to identify CVD was not superior compared to established anthropometric indices like BMI and WC. PMID:25229394

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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

  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. 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

  16. Clinical Proteomics Identifies Urinary CD14 as a Potential Biomarker for Diagnosis of Stable Coronary Artery Disease

    PubMed Central

    Lee, Min-Yi; Huang, Chun-Hao; Kuo, Chao-Jen; Lin, Chen-Lung Steve; Lai, Wen-Ter; Chiou, Shyh-Horng

    2015-01-01

    Inflammation plays a key role in coronary artery disease (CAD) and other manifestations of atherosclerosis. Recently, urinary proteins were found to be useful markers for reflecting inflammation status of different organs. To identify potential biomarker for diagnosis of CAD, we performed one-dimensional SDS-gel electrophoresis followed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Among the proteins differentially expressed in urine samples, monocyte antigen CD14 was found to be consistently expressed in higher amounts in the CAD patients as compared to normal controls. Using enzyme-linked immunosorbent assays to analyze the concentrations of CD14 in urine and serum, we confirmed that urinary CD14 levels were significantly higher in patients (n = 73) with multi-vessel and single vessel CAD than in normal control (n = 35) (P < 0.001). Logistic regression analysis further showed that urinary CD14 concentration level is associated with severity or number of diseased vessels and SYNTAX score after adjustment for potential confounders. Concomitantly, the proportion of CD14+ monocytes was significantly increased in CAD patients (59.7 3.6%) as compared with healthy controls (14.9 2.1%) (P < 0.001), implicating that a high level of urinary CD14 may be potentially involved in mechanism(s) leading to CAD pathogenesis. By performing shotgun proteomics, we further revealed that CD14-associated inflammatory response networks may play an essential role in CAD. In conclusion, the current study has demonstrated that release of CD14 in urine coupled with more CD14+ monocytes in CAD patients is significantly correlated with severity of CAD, pointing to the potential application of urinary CD14 as a novel noninvasive biomarker for large-scale diagnostic screening of susceptible CAD patients. PMID:25668619

  17. 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.

  18. Profiling of the Tox21 Chemical Collection for Mitochondrial Function to Identify Compounds that Acutely Decrease Mitochondrial Membrane Potential

    PubMed Central

    Attene-Ramos, Matias S.; Huang, Ruili; Michael, Sam; Witt, Kristine L.; Richard, Ann; Tice, Raymond R.; Simeonov, Anton; Austin, Christopher P.

    2014-01-01

    Background: Mitochondrial dysfunction has been implicated in the pathogenesis of a variety of disorders including cancer, diabetes, and neurodegenerative and cardiovascular diseases. Understanding whether different environmental chemicals and druglike molecules impact mitochondrial function represents an initial step in predicting exposure-related toxicity and defining a possible role for such compounds in the onset of various diseases. Objectives: We sought to identify individual chemicals and general structural features associated with changes in mitochondrial membrane potential (MMP). Methods: We used a multiplexed [two end points in one screen; MMP and adenosine triphosphate (ATP) content] quantitative high throughput screening (qHTS) approach combined with informatics tools to screen the Tox21 library of 10,000 compounds (~ 8,300 unique chemicals) at 15 concentrations each in triplicate to identify chemicals and structural features that are associated with changes in MMP in HepG2 cells. Results: Approximately 11% of the compounds (913 unique compounds) decreased MMP after 1 hr of treatment without affecting cell viability (ATP content). In addition, 309 compounds decreased MMP over a concentration range that also produced measurable cytotoxicity [half maximal inhibitory concentration (IC50) in MMP assay/IC50 in viability assay ? 3; p < 0.05]. More than 11% of the structural clusters that constitute the Tox21 library (76 of 651 clusters) were significantly enriched for compounds that decreased the MMP. Conclusions: Our multiplexed qHTS approach allowed us to generate a robust and reliable data set to evaluate the ability of thousands of drugs and environmental compounds to decrease MMP. The use of structure-based clustering analysis allowed us to identify molecular features that are likely responsible for the observed activity. Citation: Attene-Ramos MS, Huang R, Michael S, Witt KL, Richard A, Tice RR, Simeonov A, Austin CP, Xia M. 2015. Profiling of the Tox21 chemical collection for mitochondrial function to identify compounds that acutely decrease mitochondrial membrane potential. Environ Health Perspect 123:4956;?http://dx.doi.org/10.1289/ehp.1408642 PMID:25302578

  19. 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.

  20. A cell-based fascin bioassay identifies compounds with potential anti-metastasis or cognition-enhancing functions.

    PubMed

    Kraft, Robert; Kahn, Allon; Medina-Franco, Jos L; Orlowski, Mikayla L; Baynes, Cayla; Lpez-Vallejo, Fabian; Barnard, Kobus; Maggiora, Gerald M; Restifo, Linda L

    2013-01-01

    The actin-bundling protein fascin is a key mediator of tumor invasion and metastasis and its activity drives filopodia formation, cell-shape changes and cell migration. Small-molecule inhibitors of fascin block tumor metastasis in animal models. Conversely, fascin deficiency might underlie the pathogenesis of some developmental brain disorders. To identify fascin-pathway modulators we devised a cell-based assay for fascin function and used it in a bidirectional drug screen. The screen utilized cultured fascin-deficient mutant Drosophila neurons, whose neurite arbors manifest the 'filagree' phenotype. Taking a repurposing approach, we screened a library of 1040 known compounds, many of them FDA-approved drugs, for filagree modifiers. Based on scaffold distribution, molecular-fingerprint similarities, and chemical-space distribution, this library has high structural diversity, supporting its utility as a screening tool. We identified 34 fascin-pathway blockers (with potential anti-metastasis activity) and 48 fascin-pathway enhancers (with potential cognitive-enhancer activity). The structural diversity of the active compounds suggests multiple molecular targets. Comparisons of active and inactive compounds provided preliminary structure-activity relationship information. The screen also revealed diverse neurotoxic effects of other drugs, notably the 'beads-on-a-string' defect, which is induced solely by statins. Statin-induced neurotoxicity is enhanced by fascin deficiency. In summary, we provide evidence that primary neuron culture using a genetic model organism can be valuable for early-stage drug discovery and developmental neurotoxicity testing. Furthermore, we propose that, given an appropriate assay for target-pathway function, bidirectional screening for brain-development disorders and invasive cancers represents an efficient, multipurpose strategy for drug discovery. PMID:22917928

  1. Framework for identifying chemicals with structural features associated with the potential to act as developmental or reproductive toxicants.

    PubMed

    Wu, Shengde; Fisher, Joan; Naciff, Jorge; Laufersweiler, Michael; Lester, Cathy; Daston, George; Blackburn, Karen

    2013-12-16

    Developmental and reproductive toxicity (DART) end points are important hazard end points that need to be addressed in the risk assessment of chemicals to determine whether or not they are the critical effects in the overall risk assessment. These hazard end points are difficult to predict using current in silico tools because of the diversity of mechanisms of action that elicit DART effects and the potential for narrow windows of vulnerability. DART end points have been projected to consume the majority of animals used for compliance with REACH; thus, additional nonanimal predictive tools are urgently needed. This article presents an empirically based decision tree for determining whether or not a chemical has receptor-binding properties and structural features that are consistent with chemical structures known to have toxicity for DART end points. The decision tree is based on a detailed review of 716 chemicals (664 positive, 16 negative, and 36 with insufficient data) that have DART end-point data and are grouped into defined receptor binding and chemical domains. When tested against a group of chemicals not included in the training set, the decision tree is shown to identify a high percentage of chemicals with known DART effects. It is proposed that this decision tree could be used both as a component of a screening system to identify chemicals of potential concern and as a component of weight-of-evidence decisions based on structure-activity relationships (SAR) to fill data gaps without generating additional test data. In addition, the chemical groupings generated could be used as a starting point for the development of hypotheses for in vitro testing to elucidate mode of action and ultimately in the development of refined SAR principles for DART that incorporate mode of action (adverse outcome pathways). PMID:24206190

  2. A cell-based fascin bioassay identifies compounds with potential anti-metastasis or cognition-enhancing functions

    PubMed Central

    Kraft, Robert; Kahn, Allon; Medina-Franco, Jos L.; Orlowski, Mikayla L.; Baynes, Cayla; Lpez-Vallejo, Fabian; Barnard, Kobus; Maggiora, Gerald M.; Restifo, Linda L.

    2013-01-01

    SUMMARY The actin-bundling protein fascin is a key mediator of tumor invasion and metastasis and its activity drives filopodia formation, cell-shape changes and cell migration. Small-molecule inhibitors of fascin block tumor metastasis in animal models. Conversely, fascin deficiency might underlie the pathogenesis of some developmental brain disorders. To identify fascin-pathway modulators we devised a cell-based assay for fascin function and used it in a bidirectional drug screen. The screen utilized cultured fascin-deficient mutant Drosophila neurons, whose neurite arbors manifest the filagree phenotype. Taking a repurposing approach, we screened a library of 1040 known compounds, many of them FDA-approved drugs, for filagree modifiers. Based on scaffold distribution, molecular-fingerprint similarities, and chemical-space distribution, this library has high structural diversity, supporting its utility as a screening tool. We identified 34 fascin-pathway blockers (with potential anti-metastasis activity) and 48 fascin-pathway enhancers (with potential cognitive-enhancer activity). The structural diversity of the active compounds suggests multiple molecular targets. Comparisons of active and inactive compounds provided preliminary structure-activity relationship information. The screen also revealed diverse neurotoxic effects of other drugs, notably the beads-on-a-string defect, which is induced solely by statins. Statin-induced neurotoxicity is enhanced by fascin deficiency. In summary, we provide evidence that primary neuron culture using a genetic model organism can be valuable for early-stage drug discovery and developmental neurotoxicity testing. Furthermore, we propose that, given an appropriate assay for target-pathway function, bidirectional screening for brain-development disorders and invasive cancers represents an efficient, multipurpose strategy for drug discovery. PMID:22917928

  3. 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

  4. Cross-comparison of the genome sequences from human, chimpanzee, Neanderthal and a Denisovan hominin identifies novel potentially compensated mutations.

    PubMed

    Zhang, Guojie; Pei, Zhang; Ball, Edward V; Mort, Matthew; Kehrer-Sawatzki, Hildegard; Cooper, David N

    2011-07-01

    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. 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

  6. 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

  7. 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

  8. 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

  9. 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, Mara 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, ?: 0.065, 95% confidence interval (CI): ?0.0840.177, P = 0.474) or vertebrobasilar arteries (1.11 0.16 vs. 1.29 0.27, ?: 0.066, 95% CI: ?0.00240.156, 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

  10. 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 HenleKoch's postulates, it will be vital to experimentally control for populations of the other potential pathogens identified in this study. PMID:24943374

  11. 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).

  12. 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

  13. A systems biology approach to identify intelligence quotient score-related genomic regions, and pathways relevant to potential therapeutic treatments.

    PubMed

    Zhao, Min; Kong, Lei; Qu, Hong

    2014-01-01

    Although the intelligence quotient (IQ) is the most popular intelligence test in the world, little is known about the underlying biological mechanisms that lead to the differences in human. To improve our understanding of cognitive processes and identify potential biomarkers, we conducted a comprehensive investigation of 158 IQ-related genes selected from the literature. A genomic distribution analysis demonstrated that IQ-related genes were enriched in seven regions of chromosome 7 and the X chromosome. In addition, these genes were enriched in target lists of seven transcription factors and sixteen microRNAs. Using a network-based approach, we further reconstructed an IQ-related pathway from known human pathway interaction data. Based on this reconstructed pathway, we incorporated enriched drugs and described the importance of dopamine and norepinephrine systems in IQ-related biological process. These findings not only reveal several testable genes and processes related to IQ scores, but also have potential therapeutic implications for IQ-related mental disorders. PMID:24566931

  14. A systems biology approach to identify intelligence quotient score-related genomic regions, and pathways relevant to potential therapeutic treatments

    PubMed Central

    Zhao, Min; Kong, Lei; Qu, Hong

    2014-01-01

    Although the intelligence quotient (IQ) is the most popular intelligence test in the world, little is known about the underlying biological mechanisms that lead to the differences in human. To improve our understanding of cognitive processes and identify potential biomarkers, we conducted a comprehensive investigation of 158 IQ-related genes selected from the literature. A genomic distribution analysis demonstrated that IQ-related genes were enriched in seven regions of chromosome 7 and the X chromosome. In addition, these genes were enriched in target lists of seven transcription factors and sixteen microRNAs. Using a network-based approach, we further reconstructed an IQ-related pathway from known human pathway interaction data. Based on this reconstructed pathway, we incorporated enriched drugs and described the importance of dopamine and norepinephrine systems in IQ-related biological process. These findings not only reveal several testable genes and processes related to IQ scores, but also have potential therapeutic implications for IQ-related mental disorders. PMID:24566931

  15. 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.

  16. 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

  17. Recycled water: potential health risks from volatile organic compounds and use of 1,4-dichlorobenzene as treatment performance indicator.

    PubMed

    Rodriguez, Clemencia; Linge, Kathryn; Blair, Palenque; Busetti, Francesco; Devine, Brian; Van Buynder, Paul; Weinstein, Philip; Cook, Angus

    2012-01-01

    Characterisation of the concentrations and potential health risks of chemicals in recycled water is important if this source of water is to be safely used to supplement drinking water sources. This research was conducted to: (i) determine the concentration of volatile organic compounds (VOCs) in secondary treated effluent (STE) and, post-reverse osmosis (RO) treatment and to; (ii) assess the health risk associated with VOCs for indirect potable reuse (IPR). Samples were examined pre and post-RO in one full-scale and one pilot plant in Perth, Western Australia. Risk quotients (RQ) were estimated by expressing the maximum and median concentration as a function of the health value. Of 61 VOCs analysed over a period of three years, twenty one (21) were detected in STE, with 1,4-dichlorobenzene (94%); tetrachloroethene (88%); carbon disulfide (81%) and; chloromethane (58%) most commonly detected. Median concentrations for these compounds in STE ranged from 0.81 ?g/L for 1,4-dichlorobenzene to 0.02 ?g/L for carbon disulphide. After RO, twenty six (26) VOCs were detected, of which 1,4-dichlorobenzene (89%); acrylonitrile (83%) chloromethane (63%) and carbon disulfide (40%) were the more frequently detected. RQ(max) were all below health values in the STE and after RO. Median removal efficiency for RO was variable, ranging from -77% (dichlorodifluoromethane) to 91.2% (tetrachloroethene). The results indicate that despite the detection of VOCs in STE and after RO, their human health impact in IPR is negligible due to the low concentrations detected. The results indicate that 1,4-dichlorobenzene is a potential treatment chemical indicator for assessment of VOCs in IPR using RO treatment. PMID:22078226

  18. Assessment of the extended Koopmans' theorem for the chemical reactivity: Accurate computations of chemical potentials, chemical hardnesses, and electrophilicity indices.

    PubMed

    Yildiz, Dilan; Bozkaya, U?ur

    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 (?) (hence electronegativities), chemical hardnesses (?), and electrophilicity indices (?). We assess the performance of the EKT approaches for post-Hartree-Fock methods, such as Mller-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 ?, ?, and ?, respectively. 2015 Wiley Periodicals, Inc. PMID:26458329

  19. Duodenal bile examination in identifying potential non-responders to bile salt treatment and its comparison with gall bladder bile examination.

    PubMed

    Agarwal, D K; Choudhuri, G; Saraswat, V A; Negi, T S; Kapoor, V K; Saxena, R

    1994-01-01

    The results of bile salt treatment in patients with radiolucent stones and a functioning gall bladder have been poor. In 42 of these patients awaiting cholecystectomy we determined the value of duodenal bile examination in predicting gall stone composition, and thus identifying those less likely to respond to bile salt therapy. Based on chemical analysis and scanning electron microscopy, 28 of 42 (67%) gall stones retrieved at surgery were potentially insoluble. Microscopic examination of duodenal bile correctly identified 21 (75%) of them: it predicted all four (100%) pigment stones, three of six (50%) calcium carbonate containing cholesterol stones, and 14 of 18 (78%) cholesterol stones with pigment shells. It was nearly as reliable as microscopic examination of bile aspirated directly from the gall bladder during surgery (21 (75%) v 23 (82%); p = NS). Furthermore, the presence of cholesterol crystals in duodenal bile was a more sensitive indicator than chemical detection of supersaturation (34 of 38 (89%) v 25 of 35 (71%); p < 0.05) for prediction of cholesterol gall stones. Microscopic examination of duodenal bile, if used as a screening test, could help to exclude potential non-responders and thereby improve considerably the results of oral bile salt treatment for gall stone dissolution. PMID:8307430

  20. 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

  1. Genetic screening test for psoriatic arthritis and UVB irradiation potential responders: A new tool to identify psoriasis subpopulation patients?

    PubMed Central

    Lotti, Torello; Tognetti, Linda; Galeone, Massimiliano; Bruscino, Nicola; Moretti, Silvia; Giorgini, Simonetta

    2011-01-01

    Psoriatic arthritis (PsA) is a psoriasis-associated inflammatory disease of the joints and enthuses. The occurrence of PsA is linked to the complex interplay of gene environment, and immune system. Genetic factors have long been recognized to play an important role in PsA. Genes within the major histocompatibility complex (MHC) region have been shown to be associated with PsA. These include genes coded in the HLA region, (especially Class I antigens) and non-HLA genes (i.e., MHC class I chain-related antigen A, MICA, and TNF-? genes). Association studies in PsA have also identified a number of genes outside MHC region, including interleukin-1 (IL-1) gene cluster, killer-cell immunoglobulin-like receptors (KIRs), and IL-23R genes. Established systemic treatments for moderate-severe psoriasis and PsA may be potentially dangerous and usually time consuming for the patient and often expensive for the National Health Systems. Tests which could predict which subset of psoriatic patients could develop the most severe forms of the disease (i.e., PsA) or will respond to well-established (UVB irradiation) or other systemic treatments are now required. The goal of genetic test screening is to rapidly and safely identify subjects for preventive or early treatment or extended surveillance prior to the onset of signs and symptoms. Genetic tests today represent a reliable investigation procedure which could rapidly and consistently improve the diagnostic ability of the dermatologist and contribute to the early and correct treatment of the different subsets of PsA. PMID:23130225

  2. Subtractive Phage Display Selection from Canine Visceral Leishmaniasis Identifies Novel Epitopes That Mimic Leishmania infantum Antigens with Potential Serodiagnosis Applications

    PubMed Central

    Costa, Lourena E.; Lima, Mayara I. S.; Chvez-Fumagalli, Miguel A.; Menezes-Souza, Daniel; Martins, Vivian T.; Duarte, Mariana C.; Lage, Paula S.; Lopes, Eliane G. P.; Lage, Daniela P.; Ribeiro, Tatiana G.; Andrade, Pedro H. R.; de Magalhes-Soares, Danielle F.; Soto, Manuel; Tavares, Carlos A. P.; Goulart, Luiz R.

    2014-01-01

    Visceral leishmaniasis (VL) is a zoonotic disease that is endemic to Brazil, where dogs are the main domestic parasite reservoirs, and the percentages of infected dogs living in regions where canine VL (CVL) is endemic have ranged from 10% to 62%. Despite technological advances, some problems have been reported with CVL serodiagnosis. The present study describes a sequential subtractive selection through phage display technology from polyclonal antibodies of negative and positive sera that resulted in the identification of potential bacteriophage-fused peptides that were highly sensitive and specific to antibodies of CVL. A negative selection was performed in which phage clones were adhered to purified IgGs from healthy and Trypanosoma cruzi-infected dogs to eliminate cross-reactive phages. The remaining supernatant nonadhered phages were submitted to positive selection against IgG from the blood serum of dogs that were infected with Leishmania infantum. Phage clones that adhered to purified IgGs from the CVL-infected serum samples were selected. Eighteen clones were identified and their reactivities tested by a phage enzyme-linked immunosorbent assay (phage-ELISA) against the serum samples from infected dogs (n = 31) compared to those from vaccinated dogs (n = 21), experimentally infected dogs with cross-reactive parasites (n = 23), and healthy controls (n = 17). Eight clones presented sensitivity, specificity, and positive and negative predictive values of 100%, and they showed no cross-reactivity with T. cruzi- or Ehrlichia canis-infected dogs or with dogs vaccinated with two different commercial CVL vaccines in Brazil. Our study identified eight mimotopes of L. infantum antigens with 100% accuracy for CVL serodiagnosis. The use of these mimotopes by phage-ELISA proved to be an excellent assay that was reproducible, simple, fast, and inexpensive, and it can be applied in CVL-monitoring programs. PMID:24256622

  3. 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

  4. 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

  5. Planting sentinel European trees in eastern Asia as a novel method to identify potential insect pest invaders.

    PubMed

    Roques, Alain; Fan, Jian-Ting; Courtial, Batrice; 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

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Relative abundance and treatment reduction of viruses during wastewater treatment processes--identification of potential viral indicators.

    PubMed

    Kitajima, Masaaki; Iker, Brandon C; Pepper, Ian L; Gerba, Charles P

    2014-08-01

    Waterborne pathogenic viruses discharged from wastewater treatment plants (WWTPs) pose potential public health risks. In the present study, we investigated the relative abundance, occurrence, and reduction of eleven different viruses at two WWTPs in southern Arizona over a 12-month period, from August 2011 to July 2012. Influent and effluent samples from the two WWTPs were collected monthly. Viruses were concentrated using an electronegative filter method and quantified using TaqMan-based quantitative PCR (qPCR) assays for each of the virus types (i.e., genogroup I, II and IV noroviruses, sapovirus, enterovirus, group A rotavirus, Aichi virus, pepper mild mottle virus, adenovirus, and JC and BK polyomaviruses), with murine norovirus internal control for the monitoring of extraction-RT-qPCR efficiencies. The pepper mild mottle virus, a plant virus, was found to be the most prevalent virus in both influent and effluent wastewater (annual mean concentration of 3.7-4.410(6) copies/L and 4.6-6.310(5) copies/L in influent and effluent wastewater, respectively), showing a low reduction by the treatment processes (0.76-0.99 annual mean log10 reduction), and no significant seasonal change in concentration. Aichi virus, a human enteric virus, was also found in greater abundance, and showed lower reduction during wastewater treatment than other human enteric viruses. Our results suggest that these viruses could be used as potential indicators of wastewater reclamation system performance, with respect to virus occurrence and removal. PMID:24836386

  15. 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

  16. Plasmodium falciparum Gametocyte-Specific Antibody Profiling Reveals Boosting through Natural Infection and Identifies Potential Markers of Gametocyte Exposure

    PubMed Central

    Skinner, Jeff; Huang, Chiung-Yu; Waisberg, Michael; Felgner, Philip L.; Doumbo, Ogobara K.; Ongoiba, Aissata; Kayentao, Kassoum; Traore, Boubacar

    2015-01-01