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Sample records for identifying potential environmental

  1. Identifying potential environmental impacts of waste handling strategies in textile industry.

    PubMed

    Yacout, Dalia M M; Hassouna, M S

    2016-08-01

    Waste management is a successful instrument to minimize generated waste and improve environmental conditions. In spite of the large share of developing countries in the textile industry, limited information is available concerning the waste management strategies implemented for textiles on those countries and their environmental impacts. In the current study, two waste management approaches for hazardous solid waste treatment of acrylic fibers (landfill and incineration) were investigated. The main research questions were: What are the different impacts of each waste management strategy? Which waste management strategy is more ecofriendly? Life cycle assessment was employed in order to model the environmental impacts of each waste streaming approach separately then compare them together. Results revealed that incineration was the more ecofriendly approach. Highest impacts of both approaches were on ecotoxicity and carcinogenic potentials due to release of metals from pigment wastes. Landfill had an impact of 46.8 % on human health as compared to 28 % by incineration. Incineration impact on ecosystem quality was higher than landfill impact (68.4 and 51.3 %, respectively). As for resources category, incineration had a higher impact than landfill (3.5 and 2.0 %, respectively). Those impacts could be mitigated if state-of-the-art landfill or incinerator were used and could be reduced by applying waste to energy approaches for both management systems In conclusion, shifting waste treatment from landfill to incineration would decrease the overall environmental impacts and allow energy recovery. The potential of waste to energy approach by incineration with heat recovery could be considered in further studies. Future research is needed in order to assess the implementation of waste management systems and the preferable waste management strategies in the textile industry on developing countries. PMID:27372905

  2. 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. PMID:27331226

  3. Identifying potential areas for biofuel production and evaluating the environmental effects: a case study of the James River Basin in the Midwestern United States

    USGS Publications Warehouse

    Wu, Yiping; Liu, Shu-Guang; Li, Zhengpeng

    2012-01-01

    Biofuels are now an important resource in the United States because of the Energy Independence and Security Act of 2007. Both increased corn growth for ethanol production and perennial dedicated energy crop growth for cellulosic feedstocks are potential sources to meet the rising demand for biofuels. However, these measures may cause adverse environmental consequences that are not yet fully understood. This study 1) evaluates the long-term impacts of increased frequency of corn in the crop rotation system on water quantity and quality as well as soil fertility in the James River Basin and 2) identifies potential grasslands for cultivating bioenergy crops (e.g. switchgrass), estimating the water quality impacts. We selected the soil and water assessment tool, a physically based multidisciplinary model, as the modeling approach to simulate a series of biofuel production scenarios involving crop rotation and land cover changes. The model simulations with different crop rotation scenarios indicate that decreases in water yield and soil nitrate nitrogen (NO3-N) concentration along with an increase in NO3-N load to stream water could justify serious concerns regarding increased corn rotations in this basin. Simulations with land cover change scenarios helped us spatially classify the grasslands in terms of biomass productivity and nitrogen loads, and we further derived the relationship of biomass production targets and the resulting nitrogen loads against switchgrass planting acreages. The suggested economically efficient (planting acreage) and environmentally friendly (water quality) planting locations and acreages can be a valuable guide for cultivating switchgrass in this basin. This information, along with the projected environmental costs (i.e. reduced water yield and increased nitrogen load), can contribute to decision support tools for land managers to seek the sustainability of biofuel development in this region.

  4. 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…

  5. Identifying environmental correlates of intraspecific genetic variation.

    PubMed

    Harrisson, K A; Yen, J D L; Pavlova, A; Rourke, M L; Gilligan, D; Ingram, B A; Lyon, J; Tonkin, Z; Sunnucks, P

    2016-09-01

    Genetic variation is critical to the persistence of populations and their capacity to adapt to environmental change. The distribution of genetic variation across a species' range can reveal critical information that is not necessarily represented in species occurrence or abundance patterns. We identified environmental factors associated with the amount of intraspecific, individual-based genetic variation across the range of a widespread freshwater fish species, the Murray cod Maccullochella peelii. We used two different approaches to statistically quantify the relative importance of predictor variables, allowing for nonlinear relationships: a random forest model and a Bayesian approach. The latter also accounted for population history. Both approaches identified associations between homozygosity by locus and both disturbance to the natural flow regime and mean annual flow. Homozygosity by locus was negatively associated with disturbance to the natural flow regime, suggesting that river reaches with more disturbed flow regimes may support larger, more genetically diverse populations. Our findings are consistent with the hypothesis that artificially induced perennial flows in regulated channels may provide greater and more consistent habitat and reduce the frequency of population bottlenecks that can occur frequently under the highly variable and unpredictable natural flow regime of the system. Although extensive river regulation across eastern Australia has not had an overall positive effect on Murray cod numbers over the past century, regulation may not represent the primary threat to Murray cod survival. Instead, pressures other than flow regulation may be more critical to the persistence of Murray cod (for example, reduced frequency of large floods, overfishing and chemical pollution). PMID:27273322

  6. Identifying populations at risk from environmental contamination from point sources

    PubMed Central

    Williams, F; Ogston, S

    2002-01-01

    Objectives: To compare methods for defining the population at risk from a point source of air pollution. A major challenge for environmental epidemiology lies in correctly identifying populations at risk from exposure to environmental pollutants. The complexity of today's environment makes it essential that the methods chosen are accurate and sensitive. Methods: Environmental and mathematical methods were used to identify the population potentially exposed to a point source of airborne pollution emanating from a waste incinerator. Soil sampling was undertaken at 83 sites throughout the city and environs. The concentrations of arsenic and copper were measured at each site. Computer software produced smoothed contour plots of the distribution of arsenic and copper in the soil based on the information derived from the sampling sites. The population at risk was also identified using concentric rings of varying radii, with the source of pollution at the centre. Lastly, we used the sites that had previously been selected and measured the frequency of wind direction, speed and distance from the source of pollution at each site. Theoretical contour plots were constructed using the distance from the source of pollution at each site, with and without incorporating wind frequency as a function of direction. Results: Each method identified different populations at risk from airborne pollution. The use of circles was a very imprecise way of identifying exposed populations. Mathematical modelling that incorporated wind direction was better. Soil sampling at many sites was accurate, as the method is direct; but it is very costly and the close proximity of high and low concentrations hindered interpretation. The smoothed contour plots derived from the soil sampling sites identified an exposed population that was similar to that derived from the spot sampling. Conclusions: Using circles as the only means of identifying the exposed population leads to dilution of the potential

  7. Identifying Potential Noise Sources within Acoustic Signals

    NASA Astrophysics Data System (ADS)

    Holcomb, Victoria; Lewalle, Jacques

    2013-11-01

    We test a new algorithm for its ability to detect sources of noise within random background. The goal of these tests is to better understand how to identify sources within acoustic signals while simultaneously determining the strengths and weaknesses of the algorithm in question. Unlike previously published algorithms, the antenna method does not pinpoint events by looking for the most energetic portions of a signal. The algorithm searches for the ideal lag combinations between three signals by taking excerpts of possible events. The excerpt with the lowest calculated minimum distance between possible events is how the algorithm identifies sources. At the minimum distance, the events are close in time and frequency. This method can be compared to the cross correlation and denoising methods to better understand its effectiveness. This work is supported in part by Spectral Energies LLC, under an SBIR grant from AFRL, as well as the Syracuse University MAE department.

  8. Identifying environmental sounds: a multimodal mapping study

    PubMed Central

    Tomasino, Barbara; Canderan, Cinzia; Marin, Dario; Maieron, Marta; Gremese, Michele; D'Agostini, Serena; Fabbro, Franco; Skrap, Miran

    2015-01-01

    Our environment is full of auditory events such as warnings or hazards, and their correct recognition is essential. We explored environmental sounds (ES) recognition in a series of studies. In study 1 we performed an Activation Likelihood Estimation (ALE) meta-analysis of neuroimaging experiments addressing ES processing to delineate the network of areas consistently involved in ES processing. Areas consistently activated in the ALE meta-analysis were the STG/MTG, insula/rolandic operculum, parahippocampal gyrus and inferior frontal gyrus bilaterally. Some of these areas truly reflect ES processing, whereas others are related to design choices, e.g., type of task, type of control condition, type of stimulus. In study 2 we report on 7 neurosurgical patients with lesions involving the areas which were found to be activated by the ALE meta-analysis. We tested their ES recognition abilities and found an impairment of ES recognition. These results indicate that deficits of ES recognition do not exclusively reflect lesions to the right or to the left hemisphere but both hemispheres are involved. The most frequently lesioned area is the hippocampus/insula/STG. We made sure that any impairment in ES recognition would not be related to language problems, but reflect impaired ES processing. In study 3 we carried out an fMRI study on patients (vs. healthy controls) to investigate how the areas involved in ES might be functionally deregulated because of a lesion. The fMRI evidenced that controls activated the right IFG, the STG bilaterally and the left insula. We applied a multimodal mapping approach and found that, although the meta-analysis showed that part of the left and right STG/MTG activation during ES processing might in part be related to design choices, this area was one of the most frequently lesioned areas in our patients, thus highlighting its causal role in ES processing. We found that the ROIs we drew on the two clusters of activation found in the left and in

  9. Environmental Journalism and Environmental Communication Education: Identifying an Educational Model.

    ERIC Educational Resources Information Center

    Casey, William E.

    News coverage of the environment has been the subject of intense scrutiny for some 25 years. Content analyses have suggested that environmental coverage is plagued by omission of important information in areas of economics, health, safety, and consumer concerns. Surveys of reporters show high levels of frustration and dissatisfaction with their…

  10. IDENTIFYING AND MONITORING ENVIRONMENTAL TOXICITY USING CERIODAPHNIA MICROARRAYS - PHASE I

    EPA Science Inventory

    The current U.S. Environmental Protection Agency (EPA) SBIR solicitation states that “technology is needed to better identify and monitor sources of pollution and protect water quality.” Microarrays may be particularly well suited to identifying environmental toxic...

  11. POTENTIAL ENVIRONMENTAL IMPACTS OF SOLAR HEATING AND COOLING SYSTEMS

    EPA Science Inventory

    This report discusses potential environmental consequences of solar energy utilization for heating and cooling buildings. It identifies the areas in which both positive and negative impacts are possible, summarizes the national research and development program directed toward sol...

  12. A procedure for identifying significant environmental aspects in sea ports.

    PubMed

    Darbra, R M; Ronza, A; Stojanovic, T A; Wooldridge, C; Casal, J

    2005-08-01

    A new methodology has been designed to identify and rank the significant environmental aspects in sea ports. The main objective of the Strategic Overview of Significant Environmental Aspects (SOSEA) is to help port managers to identify significant environmental aspects and to reinforce the awareness about them in order to prioritise work in environmental management. Developed in close collaboration with port environmental managers and tested in a set of ports, it is a user-friendly tool that can be applied in approximately half a working day. It is based on ISO 14001 vocabulary and requirements and it can be considered as the base for the implementation of any Environmental Management System for port communities. PMID:15946703

  13. Identifying Environmental Contributions to Autism: Provocative Clues and False Leads

    ERIC Educational Resources Information Center

    Lawler, Cindy P.; Croen, Lisa A.; Grether, Judith K.; Van de Water, Judy

    2004-01-01

    The potential role of environmental factors in autism spectrum disorders (ASD) is an area of emerging interest within the public and scientific communities. The high degree of heritability of ASD suggests that environmental influences are likely to operate through their interaction with genetic susceptibility during vulnerable periods of…

  14. 3 Drugs Identified to Potentially Fight Zika Virus

    MedlinePlus

    ... 160680.html 3 Drugs Identified to Potentially Fight Zika Virus But only one is already approved in ... developing fetuses protection against the damaging effects of Zika virus, a new multicenter study reports. Researchers identified ...

  15. Using Environmental Correlations to Identify Loci Underlying Local Adaptation

    PubMed Central

    Coop, Graham; Witonsky, David; Di Rienzo, Anna; Pritchard, Jonathan K.

    2010-01-01

    Loci involved in local adaptation can potentially be identified by an unusual correlation between allele frequencies and important ecological variables or by extreme allele frequency differences between geographic regions. However, such comparisons are complicated by differences in sample sizes and the neutral correlation of allele frequencies across populations due to shared history and gene flow. To overcome these difficulties, we have developed a Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers and then uses this as a null model for a test at individual SNPs. In our model the sample frequencies of an allele across populations are drawn from a set of underlying population frequencies; a transform of these population frequencies is assumed to follow a multivariate normal distribution. We first estimate the covariance matrix of this multivariate normal across loci using a Monte Carlo Markov chain. At each SNP, we then provide a measure of the support, a Bayes factor, for a model where an environmental variable has a linear effect on the transformed allele frequencies compared to a model given by the covariance matrix alone. This test is shown through power simulations to outperform existing correlation tests. We also demonstrate that our method can be used to identify SNPs with unusually large allele frequency differentiation and offers a powerful alternative to tests based on pairwise or global FST. Software is available at http://www.eve.ucdavis.edu/gmcoop/. PMID:20516501

  16. Harnessing genomics to identify environmental determinants of heritable disease

    PubMed Central

    Yauk, Carole Lyn; Argueso, J. Lucas; Auerbach, Scott S.; Awadalla, Philip; Davis, Sean R.; DeMarini, David M.; Douglas, George R.; Dubrova, Yuri E.; Elespuru, Rosalie K.; Glover, Thomas W.; Hales, Barbara F.; Hurles, Matthew E.; Klein, Catherine B.; Lupski, James R.; Manchester, David K.; Marchetti, Francesco; Montpetit, Alexandre; Mulvihill, John J.; Robaire, Bernard; Robbins, Wendie A.; Rouleau, Guy A.; Shaughnessy, Daniel T.; Somers, Christopher M.; Taylor, James G.; Trasler, Jacquetta; Waters, Michael D.; Wilson, Thomas E.; Witt, Kristine L.; Bishop, Jack B.

    2012-01-01

    Next-generation sequencing technologies can now be used to directly measure heritable de novo DNA sequence mutations in humans. However, these techniques have not been used to examine environmental factors that induce such mutations and their associated diseases. To address this issue, a working group on environmentally induced germline mutation analysis (ENIGMA) met in October 2011 to propose the necessary foundational studies, which include sequencing of parent–offspring trios from highly exposed human populations, and controlled dose–response experiments in animals. These studies will establish background levels of variability in germline mutation rates and identify environmental agents that influence these rates and heritable disease. Guidance for the types of exposures to examine come from rodent studies that have identified agents such as cancer chemotherapeutic drugs, ionizing radiation, cigarette smoke, and air pollution as germ-cell mutagens. Research is urgently needed to establish the health consequences of parental exposures on subsequent generations. PMID:22935230

  17. Environmental Perchlorate Exposure: Potential Adverse Thyroid Effects

    PubMed Central

    Leung, Angela M.; Pearce, Elizabeth N.; Braverman, Lewis E.

    2014-01-01

    Purpose of review This review will present a general overview of the sources, human studies, and proposed regulatory action regarding environmental perchlorate exposure. Recent findings Some recent studies have reported significant associations between urinary perchlorate concentrations, thyroid dysfunction, and decreased infant IQ in groups who would be particularly susceptible to perchlorate effects. An update regarding the recent proposed regulatory actions and potential costs surrounding amelioration of perchlorate contamination is provided. Summary The potential adverse thyroidal effects of environmental perchlorate exposure remain controversial, and further research is needed to further define its relationship to human health among pregnant and lactating women and their infants. PMID:25106002

  18. EPA - NEW ENGLAND CENSUS 2000 POTENTIAL ENVIRONMENTAL JUSTICE AREAS

    EPA Science Inventory

    The Region's Potential Environmental Justice (EJ Areas) are based on the 2000 Census Block Group Boundary layer. The methodology used to determine how the areas are coded involved identifying those blockgroups with percentages in the top 15% of the region for low-income res...

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

    PubMed

    Boesch, Michael Elias; Hellweg, Stefanie

    2010-12-01

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

  20. 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.

  1. Potential environmental implications of nanoscale zero-valent iron particles for environmental remediation

    PubMed Central

    Jang, Min-Hee; Lim, Myunghee; Hwang, Yu Sik

    2014-01-01

    Objectives Nanoscale zero-valent iron (nZVI) particles are widely used in the field of various environmental contaminant remediation. Although the potential benefits of nZVI are considerable, there is a distinct need to identify any potential risks after environmental exposure. In this respect, we review recent studies on the environmental applications and implications of nZVI, highlighting research gaps and suggesting future research directions. Methods Environmental application of nZVI is briefly summarized, focusing on its unique properties. Ecotoxicity of nZVI is reviewed according to type of organism, including bacteria, terrestrial organisms, and aquatic organisms. The environmental fate and transport of nZVI are also summarized with regards to exposure scenarios. Finally, the current limitations of risk determination are thoroughly provided. Results The ecotoxicity of nZVI depends on the composition, concentration, size and surface properties of the nanoparticles and the experimental method used, including the species investigated. In addition, the environmental fate and transport of nZVI appear to be complex and depend on the exposure duration and the exposure conditions. To date, field-scale data are limited and only short-term studies using simple exposure methods have been conducted. Conclusions In this regard, the primary focus of future study should be on 1) the development of an appropriate and valid testing method of the environmental fate and ecotoxicity of reactive nanoparticles used in environmental applications and 2) assessing their potential environmental risks using in situ field scale applications. PMID:25518840

  2. Potential environmental effects of energy conservation measures in northwest industries

    SciTech Connect

    Baechler, M C; Gygi, K F; Hendrickson, P L

    1992-01-01

    The Bonneville Power Administration (Bonneville) has identified 101 plants in the Pacific Northwest that account for 80% of the region's industrial electricity consumption. These plants offer a precise target for a conservation program. PNL determined that most of these 101 plants were represented by 11 major industries. We then reviewed 36 major conservation technologies used in these 11 industrial settings to determine their potential environmental impacts. Energy efficiency technologies designed for industrial use may result in direct or indirect environmental impacts. Effects may result from the production of the conservation measure technology, changes in the working environment due to different energy and material requirements, or changes to waste streams. Industry type, work-place conditions, worker training, and environmental conditions inside and outside the plant are all key variables that may affect environmental outcomes. To address these issues this report has three objectives: Describe potential conservation measures that Bonneville may employ in industrial programs and discuss potential primary impacts. Characterize industrial systems and processes where the measure may be employed and describe general environmental issues associated with each industry type. Review environmental permitting, licensing, and other regulatory actions required for industries and summarize the type of information available from these sources for further analysis.

  3. A screening approach for identifying environmental justice issues in environmental impact statements

    SciTech Connect

    Schexnayder, S.S.

    1995-12-01

    Executive Order 12898 and the accompanying memorandum addressed to Federal agency heads, both issued on February 11, 1994, require NEPA processes to incorporate environmental justice. The NEPA processes affected are: (1) public involvement formats, (2) analyses of potential impacts. The Executive Order clearly indicates that research strategies and mitigation measure should be developed with the input of the populations mentioned in the Executive Order, i.e., minority and low-income populations. However, an enhanced public involvement process may not occur because the NEPA activity may have been underway before the Executive Order was issued or because the agency chooses not to change traditional public participation mechanisms. It is also possible that enhanced mechanisms may not effectively elicit involvement. In either case, analysis that considers environmental justice must proceed. These analyses could be highly data-intensive--requiring new or modified methodological approaches-- and time-intensive, particularly if the process elements of the executive order are interpreted broadly, Federal agencies and NEPA project managers already have expressed concern about the potential cost of conducting exhaustive environmental justice related analyses where they may not be warranted. Also, the time and resources required to conduct a full environmental justice analysis is counter to recent trends to streamline the NEPA process. In light of this, a process to screen for indicators of the potential for environmental justice issues has been developed. The method incorporates separate screens for human health impacts, socioeconomic impacts, and social structural impacts. Positive results of any screen indicates the need for full-scale, environmental-justice-related analysis of that category of impact. The screen is intended as a useful tool in implementing environmental justice in environmental impact statements.

  4. 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.

  5. A potential method to identify poor breast screening performance

    NASA Astrophysics Data System (ADS)

    Dong, Leng; Chen, Yan; Gale, Alastair G.; Chakraborty, Dev P.

    2012-02-01

    In the UK all breast screeners undertake the PERFORMS scheme where they annually read case sets of challenging cases. From the subsequent data it is possible to identify any individual who is performing significantly lower than their peers. This can then facilitate them being offered further targeted training to improve performance. However, currently this under-performance can only be calculated once all screeners have taken part, which means the feedback can potentially take several months. To determine whether such performance outliers could usefully be identified approximately much earlier the data from the last round of the scheme were re-analysed. From the information of 283 participants, 1,000 groups of them were selected randomly for fixed group sizes varying from four to 50 individuals. After applying bootstrapping on 1,000 groups, a distribution of low performance threshold values was constructed. Then the accuracy of estimation was determined by calculating the median value and standard error of this distribution as compared with the known actual results. Data indicate that increasing sample sizes improved the estimation of the median and decreased the standard error. Using information from as few as 25 individuals allowed an approximation of the known outlier cut off value and this improved with larger sample sizes. This approach is now implemented in the PERFORMS scheme to enable individuals who have difficulties, as compared to their peers, to be identified very early after taking part which can then help them to improve their performance.

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

    PubMed

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

    2016-01-01

    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

  7. Potential environmental impacts of future halocarbon emissions

    SciTech Connect

    Holmes, K.J.; Ellis, J.H.

    1996-08-01

    An integrated analysis of future halocarbon emissions and their environmental impacts shows that strict global compliance is required if the Montreal Protocol is to accomplish the goal of eliminating the lower stratospheric ozone hole. This analysis is integrated in the sense that demographic, economic, and regulatory processes controlling future production were linked explicitly to the technological factors translating production into emissions and the environmental processes transforming emissions into environmental impacts. Given current models of halocarbon transformation and atmospheric response, this research suggests that if a small percentage of nations continues to expand production at modest rates, the ozone hole will not be eliminated. In addition, high growth rate assumptions for halocarbon production by noncompliance nations will result in significantly increased ozone depletion. This research also shows that the continued use of small amounts of ozone-depleting substances for essential uses and the failure to adequately replace all ozone-depleting substances can eliminate the possibility of returning the atmosphere to pre-ozone hole conditions. The global climate change potential of halocarbons is fairly small if growth rates for chlorofluorocarbon substitutes remain low. If growth rates return to precontrol levels, these substitutes could contribute significantly to global climate change. 41 refs., 3 figs., 3 tabs.

  8. Identifying indoor environmental patterns from bioaerosol material using HPLC

    PubMed Central

    Staton, Sarah J. R.; Castillo, Josemar A.; Taylor, Thomas J.; Herckes, Pierre; Hayes, Mark A.

    2012-01-01

    A substantial portion of the atmospheric particle budget is of biological origin (human and animal dander, plant and insect debris, etc.). These bioaerosols can be considered information-rich packets of biochemical data specific to the organism of origin. In this study, bioaerosol samples from various indoor environments were analyzed to create identifiable patterns attributable to a source level of occupation. Air samples were collected from environments representative of human high-traffic and low-traffic indoor spaces along with direct human skin sampling. In all settings, total suspended particulate matter (TSP) was collected and the total aerosol protein concentration ranged from 0.03–1.2 μg/m3. High performance liquid chromatography (HPLC) was chosen as a standard analysis technique for the examination of aqueous aerosol extracts to distinguish signatures of occupation compared to environmental background. The results of this study suggest that bioaerosol “fingerprinting” is possible with the two test environments being distinguishable at a 97% confidence interval. PMID:23092966

  9. Simplified LCA and matrix methods in identifying the environmental aspects of a product system.

    PubMed

    Hur, Tak; Lee, Jiyong; Ryu, Jiyeon; Kwon, Eunsun

    2005-05-01

    In order to effectively integrate environmental attributes into the product design and development processes, it is crucial to identify the significant environmental aspects related to a product system within a relatively short period of time. In this study, the usefulness of life cycle assessment (LCA) and a matrix method as tools for identifying the key environmental issues of a product system were examined. For this, a simplified LCA (SLCA) method that can be applied to Electrical and Electronic Equipment (EEE) was developed to efficiently identify their significant environmental aspects for eco-design, since a full scale LCA study is usually very detailed, expensive and time-consuming. The environmentally responsible product assessment (ERPA) method, which is one of the matrix methods, was also analyzed. Then, the usefulness of each method in eco-design processes was evaluated and compared using the case studies of the cellular phone and vacuum cleaner systems. It was found that the SLCA and the ERPA methods provided different information but they complemented each other to some extent. The SLCA method generated more information on the inherent environmental characteristics of a product system so that it might be useful for new design/eco-innovation when developing a completely new product or method where environmental considerations play a major role from the beginning. On the other hand, the ERPA method gave more information on the potential for improving a product so that it could be effectively used in eco-redesign which intends to alleviate environmental impacts of an existing product or process. PMID:15829365

  10. Identifying Potential Regions of Copy Number Variation for Bipolar Disorder

    PubMed Central

    Chen, Yi-Hsuan; Lu, Ru-Band; Hung, Hung; Kuo, Po-Hsiu

    2014-01-01

    Bipolar disorder is a complex psychiatric disorder with high heritability, but its genetic determinants are still largely unknown. Copy number variation (CNV) is one of the sources to explain part of the heritability. However, it is a challenge to estimate discrete values of the copy numbers using continuous signals calling from a set of markers, and to simultaneously perform association testing between CNVs and phenotypic outcomes. The goal of the present study is to perform a series of data filtering and analysis procedures using a DNA pooling strategy to identify potential CNV regions that are related to bipolar disorder. A total of 200 normal controls and 200 clinically diagnosed bipolar patients were recruited in this study, and were randomly divided into eight control and eight case pools. Genome-wide genotyping was employed using Illumina Human Omni1-Quad array with approximately one million markers for CNV calling. We aimed at setting a series of criteria to filter out the signal noise of marker data and to reduce the chance of false-positive findings for CNV regions. We first defined CNV regions for each pool. Potential CNV regions were reported based on the different patterns of CNV status between cases and controls. Genes that were mapped into the potential CNV regions were examined with association testing, Gene Ontology enrichment analysis, and checked with existing literature for their associations with bipolar disorder. We reported several CNV regions that are related to bipolar disorder. Two CNV regions on chromosome 11 and 22 showed significant signal differences between cases and controls (p < 0.05). Another five CNV regions on chromosome 6, 9, and 19 were overlapped with results in previous CNV studies. Experimental validation of two CNV regions lent some support to our reported findings. Further experimental and replication studies could be designed for these selected regions.

  11. Chrysophyte cysts as potential environmental indicators.

    USGS Publications Warehouse

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

    1981-01-01

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

  12. Identifying environmental safety and health requirements for the Fernald Environmental Restoration Management Corporation

    SciTech Connect

    Beckman, W.H.; Cossel, S.C.; Alhadeff, N.; Porco, D.J.; Lindamood, S.B.; Beers, J.A.

    1994-01-14

    This presentation will describe the Fernald Environmental Restoration Management Corporation`s (FERMCO) Standards/Requirements Identification Documents (S/RlDs) Program, the unique process used to implement it, and the status of the program. We will also discuss the lessons learned as the program was implemented. The Department of Energy (DOE) established the Fernald site to produce uranium metals for the nation`s defense programs in 1953. In 1989, DOE suspended production and, in 1991, the mission of the site was formally changed to one of environmental cleanup and restoration. The site was renamed the Fernald Environmental Management Project (FEMP). FERMCO`s mission is to provide safe, early, and least-cost final clean-up of the site in compliance with all regulations and commitments. DOE has managed nuclear facilities primarily through its oversight of Management and Operating contractors. Comprehensive nuclear industry standards were absent when most DOE sites were first established, Management and Operating contractors had to apply existing non-nuclear industry standards and, in many cases, formulate new technical standards. Because it was satisfied with the operation of its facilities, DOE did not incorporate modern practices and standards as they became available. In March 1990, the Defense Nuclear Facilities Safety Board issued Recommendation 90-2, which called for DOE to identify relevant standards and requirements, conduct adequacy assessments of requirements in protecting environmental, public, and worker health and safety, and determine the extent to which the requirements are being implemented. The Environmental Restoration and Waste Management Office of DOE embraced the recommendation for facilities under its control. Strict accountability requirements made it essential that FERMCO and DOE clearly identify applicable requirements necessary, determine the requirements` adequacy, and assess FERMCO`s level of compliance.

  13. 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

  14. Environmentally induced autoimmune diseases: potential mechanisms.

    PubMed Central

    Rao, T; Richardson, B

    1999-01-01

    Environmental and other xenobiotic agents can cause autoimmunity. Examples include drug-induced lupus, toxic oil syndrome, and contaminated l-tryptophan ingestion. Numerous mechanisms, based on (italic)in vitro(/italic) evidence and animal models, have been proposed to explain how xenobiotics induce or accelerate autoimmunity. The majority of these can be divided into three general categories. The first is those inhibiting the processes involved in establishing tolerance by deletion. Inhibiting deletion can result in the release of newly generated autoreactive cells into the periphery. The second mechanism is the modification of gene expression in the cells participating in the immune response, permitting lymphocytes to respond to signals normally insufficient to initiate a response or allowing the antigen-presenting cells to abnormally stimulate a response. Abnormal gene expression can thus disrupt tolerance maintained by suppression or anergy, permitting activation of autoreactive cells. The third is the modification of self-molecules such that they are recognized by the immune system as foreign. Examples illustrating these concepts are presented, and related mechanisms that have the potential to similarly affect the immune system are noted. Some mechanisms appear to be common to a variety of agents, and different mechanisms appear to produce similar diseases. However, evidence that any of these mechanisms are actually responsible for xenobiotic-induced human autoimmune disease is still largely lacking, and the potential for numerous and as yet unidentified mechanisms also exists. PMID:10502539

  15. OXPHOS-Dependent Cells Identify Environmental Disruptors of Mitochondrial Function

    EPA Science Inventory

    Mitochondrial dysfunction is associated with numerous chronic diseases including metabolic syndrome. Environmental chemicals can impair mitochondrial function through numerous mechanisms such as membrane disruption, complex inhibition and electron transport chain uncoupling. Curr...

  16. Potential effects of environmental chemical contamination in congenital heart disease.

    PubMed

    Gorini, Francesca; Chiappa, Enrico; Gargani, Luna; Picano, Eugenio

    2014-04-01

    There is compelling evidence that prenatal exposures to environmental xenobiotics adversely affect human development and childhood. Among all birth defects, congenital heart disease (CHD) is the most prevalent of all congenital malformations and remains the leading cause of death. It has been estimated that in most cases the causes of heart defects remain unknown, while a growing number of studies have indicated the potential role of environmental agents as risk factors in CHD occurrence. In particular, maternal exposure to chemicals during the first trimester of pregnancy represents the most critical window of exposure for CHD. Specific classes of xenobiotics (e.g. organochlorine pesticides, organic solvents, air pollutants) have been identified as potential risk factors for CHD. Nonetheless, the knowledge gained is currently still incomplete as a consequence of the frequent heterogeneity of the methods applied and the difficulty in estimating the net effect of environmental pollution on the pregnant mother. The presence of multiple sources of pollution, both indoor and outdoor, together with individual lifestyle factors, may represent a further confounding element for association with the disease. A future new approach for research should probably focus on individual measurements of professional, domestic, and urban exposure to physical and chemical pollutants in order to accurately retrace the environmental exposure of parents of affected offspring during the pre-conceptional and pregnancy periods. PMID:24452958

  17. Potential environmental toxicity from hemodialysis effluent.

    PubMed

    Machado, Carla Keite; Pinto, Luciano Henrique; Del Ciampo, Lineu Fernando; Lorenzi, Luciano; Correia, Cláudia Hack Gumz; Häder, Donat Peter; Erzinger, Gilmar Sidnei

    2014-04-01

    Understanding the toxicity of certain potentially toxic compounds on various aquatic organisms allows to assess the impact that these pollutants on the aquatic biota. One source of pollution is the wastewater from hemodialysis. The process of sewage treatment is inefficient in inhibition and removal of pathogenic bacteria resistant to antibiotics in this wastewater. In many countries, such as Brazil, during emergencies, sewage and effluents from hospitals are often dumped directly into waterways without any previous treatment. The objective of this study was to characterize the effluents generated by hemodialysis and to assess the degree of acute and chronic environmental toxicity. The effluents of hemodialysis showed high concentrations of nitrites, phosphates, sulfates, ammonia, and total nitrogen, as well as elevated conductivity, turbidity, salinity, biochemical and chemical oxygen demand, exceeding the thresholds defined in the CONAMA Resolution 430. The samples showed acute toxicity to the green flagellate Euglena gracilis affecting different physiological parameters used as endpoints in an automatic bioassay such as motility, precision of gravitational orientation (r-value), compactness, upward movement, and alignment, with mean EC50 values of recalculate as 76.90 percent (±4.68 percent) of the undiluted effluents. In tests with Daphnia magna, the acute toxicity EC50 was 86.91 percent (±0.39 percent) and a NOEC value of 72.97 percent and a LEOC value 94.66 percent. PMID:24580820

  18. National variety trials identify clones with high potential

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Quality potato varieties are the backbone of a strong potato industry. Variety trials have been used to identify promising new varieties for well over a century. Trials are repeated and information collected over many years in order to confidently identify lines that may be well suited for productio...

  19. Environmental Health Related Socio-Spatial Inequalities: Identifying "Hotspots" of Environmental Burdens and Social Vulnerability.

    PubMed

    Shrestha, Rehana; Flacke, Johannes; Martinez, Javier; van Maarseveen, Martin

    2016-01-01

    Differential exposure to multiple environmental burdens and benefits and their distribution across a population with varying vulnerability can contribute heavily to health inequalities. Particularly relevant are areas with high cumulative burdens and high social vulnerability termed as "hotspots". This paper develops an index-based approach to assess these multiple burdens and benefits in combination with vulnerability factors at detailed intra-urban level. The method is applied to the city of Dortmund, Germany. Using non-spatial and spatial methods we assessed inequalities and identified "hotspot" areas in the city. We found modest inequalities burdening higher vulnerable groups in Dortmund (CI = -0.020 at p < 0.05). At the detailed intra-urban level, however, inequalities showed strong geographical patterns. Large numbers of "hotspots" exist in the northern part of the city compared to the southern part. A holistic assessment, particularly at a detailed local level, considering both environmental burdens and benefits and their distribution across the population with the different vulnerability, is essential to inform environmental justice debates and to mobilize local stakeholders. Locating "hotspot" areas at this detailed spatial level can serve as a basis to develop interventions that target vulnerable groups to ensure a health conducive equal environment. PMID:27409625

  20. Potential effects of environmental regulatory procedures on geothermal development

    SciTech Connect

    Beeland, G.V.; Boies, D.B.

    1981-01-01

    The potential effects of several types of applicable environmental regulatory procedures on geothermal development were assessed, and particular problem areas were identified. The possible impact of procedures adopted pursuant to the following Federal statutes were analyzed: Clean Air Act; Clean Water Act; Safe Drinking Water Act; and Resource Conservation and Recovery Act. State regulations applicable, or potentially applicable, to geothermal facilities were also reviewed to determine: permit information requirements; pre-permit air or water quality monitoring requirements; effect of mandated time frames for permit approval; and potential for exemption of small facilities. The regulations of the following states were covered in the review: Alaska; Arizona; California; Colorado; Hawaii; Idaho; Montana; Nevada; New Mexico; Oregon; Utah; Washington; and Wyoming. (MHR)

  1. Applying genotoxicology tools to identify environmental stressors in support of river management.

    PubMed

    Oberholster, Paul J; Hill, Liesl; Jappie, Shaamiela; Truter, Johannes C; Botha, Anna-Maria

    2016-02-01

    Although bioassay approaches are useful for identifying chemicals of potential concern, they provide little understanding of the mechanisms of chemical toxicity. Without this understanding, it is difficult to address some of the key challenges that currently face aquatic ecotoxicology. To overcome this, the toxicity potential of the water samples was assessed and surviving organisms (Physa acuta) were used for protein activity measurements and gene expression profiling by making use of complementary DNA amplified fragment length polymorphism (cDNA-AFLP) analysis. From the data it was evident that the impacts of specific pollutants (e.g. sewage) on organisms at the cellular level could be identified, and that the expressed stressor genes can be used as bioindicators/markers/genetic signatures or fingerprints during identification of point source pollution. From an ecosystem management point of view these insights could assist with the forecasting and reduction of environmental risks on catchment level by implementing suitable management interventions. PMID:26372886

  2. 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).

  3. Assessing potential future environmental legal events

    SciTech Connect

    Tonn, B.; Petrich, C.

    1997-10-28

    This report addresses the topic of environmental citizenship in the United States. The term refers to responsibilities each of us have with respect to helping our communities and nation make sound environmental decisions. This research centers on the citizens and what we ought to be doing, as opposed to what the government ought to be doing for us, to improve environmental citizenship. This report examines four central questions: What are the requirements (i.e., responsibilities) of citizenship vis-a-vis environmental decision- making processes; what constraints limit people`s ability to meet these requirements; what does our form of governance do to help or hinder in meeting these requirements; and what recommendations can be put forth to improve public participation in environmental decision making?

  4. Vibrio parahaemolyticus Strains of Pandemic Serotypes Identified from Clinical and Environmental Samples from Jiangsu, China.

    PubMed

    Li, Jingjiao; Xue, Feng; Yang, Zhenquan; Zhang, Xiaoping; Zeng, Dexin; Chao, Guoxiang; Jiang, Yuan; Li, Baoguang

    2016-01-01

    Vibrio parahaemolyticus has emerged as a major foodborne pathogen in China, Japan, Thailand, and other Asian countries. In this study, 72 strains of V. parahaemolyticus were isolated from clinical and environmental samples between 2006 and 2014 in Jiangsu, China. The serotypes and six virulence genes including thermostable direct hemolysin (TDR) and TDR-related hemolysin (TRH) genes were assessed among the isolates. Twenty five serotypes were identified and O3:K6 was one of the dominant serotypes. The genetic diversity was assessed by multilocus sequence typing (MLST) analysis, and 48 sequence types (STs) were found, suggesting this V. parahaemolyticus group is widely dispersed and undergoing rapid evolution. A total of 25 strains of pandemic serotypes such as O3:K6, O5:K17, and O1:KUT were identified. It is worth noting that the pandemic serotypes were not exclusively identified from clinical samples, rather, nine strains were also isolated from environmental samples; and some of these strains harbored several virulence genes, which may render those strains pathogenicity potential. Therefore, the emergence of these "environmental" pandemic V. parahaemolyticus strains may poses a new threat to the public health in China. Furthermore, six novel serotypes and 34 novel STs were identified among the 72 isolates, indicating that V. parahaemolyticus were widely distributed and fast evolving in the environment in Jiangsu, China. The findings of this study provide new insight into the phylogenic relationship between V. parahaemolyticus strains of pandemic serotypes from clinical and environmental sources and enhance the MLST database; and our proposed possible O- and K- antigen evolving paths of V. parahaemolyticus may help understand how the serotypes of this dispersed bacterial population evolve. PMID:27303379

  5. An overview of algae biofuel production and potential environmental impact.

    PubMed

    Menetrez, Marc Y

    2012-07-01

    Algae are among the most potentially significant sources of sustainable biofuels in the future of renewable energy. A feedstock with virtually unlimited applicability, algae can metabolize various waste streams (e.g., municipal wastewater, carbon dioxide from industrial flue gas) and produce products with a wide variety of compositions and uses. These products include lipids, which can be processed into biodiesel; carbohydrates, which can be processed into ethanol; and proteins, which can be used for human and animal consumption. Algae are commonly genetically engineered to allow for advantageous process modification or optimization. However, issues remain regarding human exposure to algae-derived toxins, allergens, and carcinogens from both existing and genetically modified organisms (GMOs), as well as the overall environmental impact of GMOs. A literature review was performed to highlight issues related to the growth and use of algal products for generating biofuels. Human exposure and environmental impact issues are identified and discussed, as well as current research and development activities of academic, commercial, and governmental groups. It is hoped that the ideas contained in this paper will increase environmental awareness of issues surrounding the production of algae and will help the algae industry develop to its full potential. PMID:22681590

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

    ERIC Educational Resources Information Center

    Benson, Nicholas; Newman, Isadore

    2010-01-01

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

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

    PubMed

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

    2006-08-01

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

  8. 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...

  9. Potential Metabolic Biomarkers to Identify Interstitial Lung Abnormalities

    PubMed Central

    Tan, Yong; Jia, Dongmei; Lin, Zhang; Guo, Baosheng; He, Bing; Lu, Cheng; Xiao, Cheng; Liu, Zhongdi; Zhao, Ning; Bian, Zhaoxiang; Zhang, Ge; Zhang, Weidong; Liu, Xinru; Lu, Aiping

    2016-01-01

    Determining sensitive biomarkers in the peripheral blood to identify interstitial lung abnormalities (ILAs) is essential for the simple early diagnosis of ILAs. This study aimed to determine serum metabolic biomarkers of ILAs and the corresponding pathogenesis. Three groups of subjects undergoing health screening, including healthy subjects, subjects with ILAs, and subjects who were healthy initially and with ILAs one year later (Healthy→ILAs), were recruited for this study. The metabolic profiles of all of the subjects’ serum were analyzed by liquid chromatography quadruple time-of-flight mass spectrometry. The metabolic characteristics of the ILAs subjects were discovered, and the corresponding biomarkers were predicted. The metabolomic data from the Healthy→ILAs subjects were collected for further verification. The results indicated that five serum metabolite alterations (up-regulated phosphatidylcholine, phosphatidic acid, betaine aldehyde and phosphatidylethanolamine, as well as down-regulated 1-acylglycerophosphocholine) were sensitive and reliable biomarkers for identifying ILAs. Perturbation of the corresponding biological pathways (RhoA signaling, mTOR/P70S6K signaling and phospholipase C signaling) might be at least partially responsible for the pathogenesis of ILAs. This study may provide a good template for determining the early diagnostic markers of subclinical disease status and for obtaining a better understanding of their pathogenesis. PMID:27438829

  10. Framework for Identifying Key Environmental Concerns in Marine Renewable Energy Projects- Appendices

    SciTech Connect

    Kramer, Sharon; Previsic, Mirko; Nelson, Peter; Woo, Sheri

    2010-06-17

    Marine wave and tidal energy technology could interact with marine resources in ways that are not well understood. As wave and tidal energy conversion projects are planned, tested, and deployed, a wide range of stakeholders will be engaged; these include developers, state and federal regulatory agencies, environmental groups, tribal governments, recreational and commercial fishermen, and local communities. Identifying stakeholders’ environmental concerns in the early stages of the industry’s development will help developers address and minimize potential environmental effects. Identifying important concerns will also assist with streamlining siting and associated permitting processes, which are considered key hurdles by the industry in the U.S. today. In September 2008, RE Vision consulting, LLC was selected by the Department of Energy (DoE) to conduct a scenario-based evaluation of emerging hydrokinetic technologies. The purpose of this evaluation is to identify and characterize environmental impacts that are likely to occur, demonstrate a process for analyzing these impacts, identify the “key” environmental concerns for each scenario, identify areas of uncertainty, and describe studies that could address that uncertainty. This process is intended to provide an objective and transparent tool to assist in decision-making for siting and selection of technology for wave and tidal energy development. RE Vision worked with H. T. Harvey & Associates, to develop a framework for identifying key environmental concerns with marine renewable technology. This report describes the results of this study. This framework was applied to varying wave and tidal power conversion technologies, scales, and locations. The following wave and tidal energy scenarios were considered: 4 wave energy generation technologies 3 tidal energy generation technologies 3 sites: Humboldt coast, California (wave); Makapu’u Point, Oahu, Hawaii (wave); and the Tacoma Narrows, Washington (tidal

  11. The role of Life Cycle Assessment in identifying and reducing environmental impacts of CCS

    SciTech Connect

    Sathre, Roger; Masanet, Eric; Cain, Jennifer; Chester, Mikhail

    2011-04-20

    Life Cycle Assessment (LCA) should be used to assist carbon capture and sequestration (CCS) planners to reduce greenhouse gas (GHG) emissions and avoid unintended environmental trade-offs. LCA is an analytical framework for determining environmental impacts resulting from processes, products, and services. All life cycle stages are evaluated including raw material sourcing, processing, operation, maintenance, and component end-of-life, as well as intermediate stages such as transportation. In recent years a growing number of LCA studies have analyzed CCS systems. We reviewed 50+ LCA studies, and selected 11 studies that compared the environmental performance of 23 electric power plants with and without CCS. Here we summarize and interpret the findings of these studies. Regarding overall climatemitigation effectiveness of CCS, we distinguish between the capture percentage of carbon in the fuels, the net carbon dioxide (CO2) emission reduction, and the net GHG emission reduction. We also identify trade-offs between the climate benefits and the potential increased non-climate impacts of CCS. Emissions of non-CO2 flue gases such as NOx may increase due to the greater throughput of fuel, and toxicity issues may arise due to the use of monoethanolamine (MEA) capture solvent, resulting in ecological and human health impacts. We discuss areas where improvements in LCA data or methods are needed. The decision to implement CCS should be based on knowledge of the overall environmental impacts of the technologies, not just their carbon capture effectiveness. LCA will be an important tool in providing that knowledge.

  12. Vibrio parahaemolyticus Strains of Pandemic Serotypes Identified from Clinical and Environmental Samples from Jiangsu, China

    PubMed Central

    Li, Jingjiao; Xue, Feng; Yang, Zhenquan; Zhang, Xiaoping; Zeng, Dexin; Chao, Guoxiang; Jiang, Yuan; Li, Baoguang

    2016-01-01

    Vibrio parahaemolyticus has emerged as a major foodborne pathogen in China, Japan, Thailand, and other Asian countries. In this study, 72 strains of V. parahaemolyticus were isolated from clinical and environmental samples between 2006 and 2014 in Jiangsu, China. The serotypes and six virulence genes including thermostable direct hemolysin (TDR) and TDR-related hemolysin (TRH) genes were assessed among the isolates. Twenty five serotypes were identified and O3:K6 was one of the dominant serotypes. The genetic diversity was assessed by multilocus sequence typing (MLST) analysis, and 48 sequence types (STs) were found, suggesting this V. parahaemolyticus group is widely dispersed and undergoing rapid evolution. A total of 25 strains of pandemic serotypes such as O3:K6, O5:K17, and O1:KUT were identified. It is worth noting that the pandemic serotypes were not exclusively identified from clinical samples, rather, nine strains were also isolated from environmental samples; and some of these strains harbored several virulence genes, which may render those strains pathogenicity potential. Therefore, the emergence of these “environmental” pandemic V. parahaemolyticus strains may poses a new threat to the public health in China. Furthermore, six novel serotypes and 34 novel STs were identified among the 72 isolates, indicating that V. parahaemolyticus were widely distributed and fast evolving in the environment in Jiangsu, China. The findings of this study provide new insight into the phylogenic relationship between V. parahaemolyticus strains of pandemic serotypes from clinical and environmental sources and enhance the MLST database; and our proposed possible O- and K- antigen evolving paths of V. parahaemolyticus may help understand how the serotypes of this dispersed bacterial population evolve. PMID:27303379

  13. Identifying crater potential improves shallow gas kick control

    SciTech Connect

    Rocha, L.A. ); Bourgoyne, A.T. )

    1993-12-27

    An understanding of sea floor crater mechanisms can help drillers determine whether to divert or shut in a shallow gas kick. Proper well planning that considers potential shallow gas sources can eliminate some of the more common failure situations with both diverting and shutting in of a well. Current well control practice for land and bottom-supported marine rigs usually calls for shutting in the well when a kick is detected, providing sufficient casing has been set to keep any flow underground. The casing and surface equipment must have an adequately high working pressure to ensure that formation fracture occurs before the equipment fails. Even for high shut-in pressures, an underground blowout is preferable to a surface blowout. An operator may choose to divert the flow if the surface casing is not set deep enough to keep the underground flow outside the casing from breaking through the sediments to the surface. Once the flow reaches the surface, a crater may form at the sea bed, possibly sinking or damaging the rig. Craters increase the difficulty and time required to kill a blowout. The paper describes shallow gas environments, the decision to divert or shut in the well, fluid migration, cement bond failure, hydraulic fracture, shear failure, the effect of fault planes, crater mechanisms, formation liquefaction, piping, caving, historical cases, and a deepwater crater.

  14. Identifying Potential Markers of the Sun's Giant Convective Scale

    NASA Astrophysics Data System (ADS)

    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 250 Mm. 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.

  15. 42 CFR 137.301 - How are project and program environmental review costs identified?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Construction Nepa Process § 137.301 How are project and program environmental review costs identified? (a) The... identified during the performance of the construction project, the Self-Governance Tribe or, at the request... 42 Public Health 1 2010-10-01 2010-10-01 false How are project and program environmental...

  16. 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

    ... by Industry CAS No. Chemical name EPA de minimis, tons/yr 68122 Dimethyl formamide 1.0 50000... 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...

  17. 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

    ... by Industry CAS No. Chemical name EPA de minimis, tons/yr 68122 Dimethyl formamide 1.0 50000... 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...

  18. 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

    ... by Industry CAS No. Chemical name EPA de minimis, tons/yr 68122 Dimethyl formamide 1.0 50000... 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...

  19. 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

    ... by Industry CAS No. Chemical name EPA de minimis, tons/yr 68122 Dimethyl formamide 1.0 50000... 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...

  20. 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

    ... by Industry CAS No. Chemical name EPA de minimis, tons/yr 68122 Dimethyl formamide 1.0 50000... 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...

  1. Molecular Modeling of Environmentally Important Processes: Reduction Potentials

    ERIC Educational Resources Information Center

    Lewis, Anne; Bumpus, John A.; Truhlar, Donald G.; Cramer, Christopher J.

    2004-01-01

    The increasing use of computational quantum chemistry in the modeling of environmentally important processes is described. The employment of computational quantum mechanics for the prediction of oxidation-reduction potential for solutes in an aqueous medium is discussed.

  2. COMPETITION POTENTIALS OF ENVIRONMENTALLY APPLIED BACTERIA WITH HUMAN FECAL MICROBIOTA

    EPA Science Inventory

    One of the potential human health effects associated with the environmental release. his of genetically engineered microorganisms is colonization of the intestinal tract study uses serial transfer techniques to monitor the in vitro survival and competition with human fecal microb...

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

    NASA Astrophysics Data System (ADS)

    Nelson, William R.; Haney, Lon N.; Ostrom, Lee T.; Richards, Robert E.

    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 identify 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.

  4. Potential Application of Environmental Noise Recordings in Geoarchaeological Site Characterization

    NASA Astrophysics Data System (ADS)

    Di Luzio, E.

    2015-12-01

    Environmental noise recordings are commonly applied in seismic microzonation studies. By calculating the H/V spectral ratio, the fundamental frequency of soft terrains overlying a rigid bedrock can be determined (Nakamura (1989). In such a simple two-layer system, equation f = n Vs/4H (1) links the resonance frequency "f" to the thickness "H" and shear waves velocity "Vs "of the resonating layer. In recent years, this methodology has been applied generally to obtain information on the seismostratigraphy of an investigated site in different environmental context. In this work, its potential application in the characterization of archaeological features hosted in shallow geological levels is discussed. Field cases are identified in the Appia Antica archaeological site which is placed in central Italy. Here, acknowledged targets correspond to: i) empty tanks carved by the Romans into Cretaceous limestone in the IV-III cen. BC and ii): the basaltic stone paving of the ancient road track which is locally buried beneath colluvial deposits. Narrowly-spaced recordings of environmental noise were carried using a portable digital seismograph equipped with three electrodynamic orthogonal sensors (velocimeters) responding in the band 0.1 ÷1024 Hz and adopting a sampling frequency of 256 Hz.. Results are discussed in terms of absolute H/V values and related distribution maps in the very high-frequency interval of 10-40Hz. In the tanks hosting area, interpolation of H/V maximum values around 13Hz matches caves location and alignment, which is also evidenced by clear inversions (H/V<1) at lower frequencies (10-1Hz). Correlation between H/V peaks and the top surface of the buried stone paving along the prosecution of the road track is even more straightforward. Finally, the depth variations of the tank roofs and the basaltic paving were reconstructed combining in equation (1) results of noise recordings with borehole data and geophysical surveys (SASW analysis).

  5. Exergy: its potential and limitations in environmental science and technology.

    PubMed

    Dewulf, Jo; Van Langenhove, Herman; Muys, Bart; Bruers, Stijn; Bakshi, Bhavik R; Grubb, Geoffrey F; Paulus, D M; Sciubba, Enrico

    2008-04-01

    New technologies, either renewables-based or not, are confronted with both economic and technical constraints. Their development takes advantage of considering the basic laws of economics and thermodynamics. With respect to the latter, the exergy concept pops up. Although its fundamentals, that is, the Second Law of Thermodynamics, were already established in the 1800s, it is only in the last years that the exergy concept has gained a more widespread interest in process analysis, typically employed to identify inefficiencies. However, exergy analysis today is implemented far beyond technical analysis; it is also employed in environmental, (thermo)economic, and even sustainability analysis of industrial systems. Because natural ecosystems are also subjected to the basic laws of thermodynamics, it is another subject of exergy analysis. After an introduction on the concept itself, this review focuses on the potential and limitations of the exergy conceptin (1) ecosystem analysis, utilized to describe maximum storage and maximum dissipation of energy flows (2); industrial system analysis: from single process analysis to complete process chain analysis (3); (thermo)economic analysis, with extended exergy accounting; and (4) environmental impact assessment throughout the whole life cycle with quantification of the resource intake and emission effects. Apart from technical system analysis, it proves that exergy as a tool in environmental impact analysis may be the most mature field of application, particularly with respect to resource and efficiency accounting, one of the major challenges in the development of sustainable technology. Far less mature is the exergy analysis of natural ecosystems and the coupling with economic analysis, where a lively debate is presently going on about the actual merits of an exergy-based approach. PMID:18504947

  6. CAPABILITY OF GC/FT-IR TO IDENTIFY TOXIC SUBSTANCES IN ENVIRONMENTAL SAMPLE EXTRACTS

    EPA Science Inventory

    The minimum identifiable quantities of 55 toxic substances have been determined by packed column gas chromatography/Fourier transform infrared spectroscopy (GC/FT-IR) at conditions compatible with environmental extract analysis. Identification of each GC effluent component was ac...

  7. Identifying and managing adverse environmental health effects: 5. Persistent organic pollutants

    PubMed Central

    Abelsohn, Alan; Gibson, Brian L.; Sanborn, Margaret D.; Weir, Erica

    2002-01-01

    CONCERN AND AWARENESS IS GROWING about the health effects of exposures to environmental contaminants, including those found in food. Most primary care physicians lack knowledge and training in the clinical recognition and management of the health effects of environmental exposures. We have found that the use of a simple history-taking tool — the CH2OPD2 mnemonic (Community, Home, Hobbies, Occupation, Personal habits, Diet and Drugs) — can help physicians identify patients at risk of such health effects. We present an illustrative case of a mother who is concerned about eating fish and wild game because her 7-year-old son has been found to have learning difficulties and she is planning another pregnancy. Potential exposures to persistent organic pollutants (POPs) and mercury are considered. The neurodevelopmental effects of POPs on the fetus are reviewed. We provide advice to limit a patient's exposure to these contaminants and discuss the relevance of these exposures to the learning difficulties of the 7-year-old child and to the planning of future pregnancies. PMID:12074124

  8. Betweenness-Based Method to Identify Critical Transmission Sectors for Supply Chain Environmental Pressure Mitigation.

    PubMed

    Liang, Sai; Qu, Shen; Xu, Ming

    2016-02-01

    To develop industry-specific policies for mitigating environmental pressures, previous studies primarily focus on identifying sectors that directly generate large amounts of environmental pressures (a.k.a. production-based method) or indirectly drive large amounts of environmental pressures through supply chains (e.g., consumption-based method). In addition to those sectors as important environmental pressure producers or drivers, there exist sectors that are also important to environmental pressure mitigation as transmission centers. Economy-wide environmental pressure mitigation might be achieved by improving production efficiency of these key transmission sectors, that is, using less upstream inputs to produce unitary output. We develop a betweenness-based method to measure the importance of transmission sectors, borrowing the betweenness concept from network analysis. We quantify the betweenness of sectors by examining supply chain paths extracted from structural path analysis that pass through a particular sector. We take China as an example and find that those critical transmission sectors identified by betweenness-based method are not always identifiable by existing methods. This indicates that betweenness-based method can provide additional insights that cannot be obtained with existing methods on the roles individual sectors play in generating economy-wide environmental pressures. Betweenness-based method proposed here can therefore complement existing methods for guiding sector-level environmental pressure mitigation strategies. PMID:26727352

  9. 42 CFR 137.301 - How are project and program environmental review costs identified?

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... HUMAN SERVICES INDIAN HEALTH SERVICE, DEPARTMENT OF HEALTH AND HUMAN SERVICES TRIBAL SELF-GOVERNANCE... development to identify program and project related costs associated with carrying out environmental responsibilities for proposed projects. The goal in this process is to identify the costs associated with...

  10. Mars Environmental Compatibility Assessment (MECA): Identifying the Hazards of the Martian Soil

    NASA Astrophysics Data System (ADS)

    Meloy, T. P.; Hecht, M. H.; Anderson, M. S.; Frant, M. A.; Fuerstenau, S. D.; Keller, H. U.; Markiewicz, W. J.; Marshall, J.; Pike, W. T.; Quate, C. F.

    1999-09-01

    Sometime in the next decade NASA will decide whether to send a human expedition to explore the planet Mars. The Mars Environmental Compatibility Assessment (MECA) has been selected by NASA to evaluate the Martian environment for soil and dust hazards to human exploration. The integrated MECA payload contains three elements: a wet-chemistry laboratory, a microscopy station, and enhancements to a lander robot-arm system incorporating arrays of material patches and an electrometer to identify triboelectric charging during soil excavation. The wet-chemistry laboratory will evaluate samples of Martian soil in water to determine the total dissolved solids, redox potential, pH, and quantify the concentration of many soluble ions using ion-selective electrodes. These electrodes can detect potentially dangerous heavy-metal ions, emitted pathogenic gases, and the soil's corrosive potential. MECA's microscopy station combines optical and atomic-force microscopy with a robot-arm camera to provide imaging over nine orders of magnitude, from meters to nanometers. Soil particle properties including size, shape, color, hardness, adhesive potential (electrostatic and magnetic), will be determined on the microscope stage using an ar-ray of sample receptacles and collection substrates, and an abrasion tool,. The simple, rugged atomic-force microscope will image in the submicron size range and has the capability of performing a particle-by-particle analysis of the dust and soil. Although selected by NASA's Human Exploration and Development of Space Enterprise, the MECA instrument suite also has the capability to address basic geology, paleoclimate, and exobiology issues. To understand both contemporaneous and ancient processes on Mars, the mineralogical, petrological, and reactivity of Martian surface materials should be constrained: the NMCA experiment will shed light on these quantities through its combination of chemistry and microscopy. On Earth, the earliest forms of life are

  11. Mars Environmental Compatibility Assessment (MECA): Identifying the Hazards of the Martian Soil

    NASA Technical Reports Server (NTRS)

    Meloy, T. P.; Hecht, M. H.; Anderson, M. S.; Frant, M. A.; Fuerstenau, S. D.; Keller, H. U.; Markiewicz, W. J.; Marshall, J.; Pike, W. T.; Quate, C. F.

    1999-01-01

    Sometime in the next decade NASA will decide whether to send a human expedition to explore the planet Mars. The Mars Environmental Compatibility Assessment (MECA) has been selected by NASA to evaluate the Martian environment for soil and dust hazards to human exploration. The integrated MECA payload contains three elements: a wet-chemistry laboratory, a microscopy station, and enhancements to a lander robot-arm system incorporating arrays of material patches and an electrometer to identify triboelectric charging during soil excavation. The wet-chemistry laboratory will evaluate samples of Martian soil in water to determine the total dissolved solids, redox potential, pH, and quantify the concentration of many soluble ions using ion-selective electrodes. These electrodes can detect potentially dangerous heavy-metal ions, emitted pathogenic gases, and the soil's corrosive potential. MECA's microscopy station combines optical and atomic-force microscopy with a robot-arm camera to provide imaging over nine orders of magnitude, from meters to nanometers. Soil particle properties including size, shape, color, hardness, adhesive potential (electrostatic and magnetic), will be determined on the microscope stage using an ar-ray of sample receptacles and collection substrates, and an abrasion tool,. The simple, rugged atomic-force microscope will image in the submicron size range and has the capability of performing a particle-by-particle analysis of the dust and soil. Although selected by NASA's Human Exploration and Development of Space Enterprise, the MECA instrument suite also has the capability to address basic geology, paleoclimate, and exobiology issues. To understand both contemporaneous and ancient processes on Mars, the mineralogical, petrological, and reactivity of Martian surface materials should be constrained: the NMCA experiment will shed light on these quantities through its combination of chemistry and microscopy. On Earth, the earliest forms of life are

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

    PubMed

    Cherqui, Frédéric; 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

  13. 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

  14. AN INTEGRATED NETWORK APPROACH TO IDENTIFYING BIOLOGICAL PATHWAYS AND ENVIRONMENTAL EXPOSURE INTERACTIONS IN COMPLEX DISEASES

    PubMed Central

    DARABOS, CHRISTIAN; QIU, JINGYA; MOORE, JASON H.

    2015-01-01

    Complex diseases are the result of intricate interactions between genetic, epigenetic and environmental factors. In previous studies, we used epidemiological and genetic data linking environmental exposure or genetic variants to phenotypic disease to construct Human Phenotype Networks and separately analyze the effects of both environment and genetic factors on disease interactions. To better capture the intricacies of the interactions between environmental exposure and the biological pathways in complex disorders, we integrate both aspects into a single “tripartite” network. Despite extensive research, the mechanisms by which chemical agents disrupt biological pathways are still poorly understood. In this study, we use our integrated network model to identify specific biological pathway candidates possibly disrupted by environmental agents. We conjecture that a higher number of co-occurrences between an environmental substance and biological pathway pair can be associated with a higher likelihood that the substance is involved in disrupting that pathway. We validate our model by demonstrating its ability to detect known arsenic and signal transduction pathway interactions and speculate on candidate cell-cell junction organization pathways disrupted by cadmium. The validation was supported by distinct publications of cell biology and genetic studies that associated environmental exposure to pathway disruption. The integrated network approach is a novel method for detecting the biological effects of environmental exposures. A better understanding of the molecular processes associated with specific environmental exposures will help in developing targeted molecular therapies for patients who have been exposed to the toxicity of environmental chemicals. PMID:26776169

  15. Predicting Fish Growth Potential and Identifying Water Quality Constraints: A Spatially-Explicit Bioenergetics Approach

    NASA Astrophysics Data System (ADS)

    Budy, Phaedra; Baker, Matthew; Dahle, Samuel K.

    2011-10-01

    Anthropogenic impairment of water bodies represents a global environmental concern, yet few attempts have successfully linked fish performance to thermal habitat suitability and fewer have distinguished co-varying water quality constraints. We interfaced fish bioenergetics, field measurements, and Thermal Remote Imaging to generate a spatially-explicit, high-resolution surface of fish growth potential, and next employed a structured hypothesis to detect relationships among measures of fish performance and co-varying water quality constraints. Our thermal surface of fish performance captured the amount and spatial-temporal arrangement of thermally-suitable habitat for three focal species in an extremely heterogeneous reservoir, but interpretation of this pattern was initially confounded by seasonal covariation of water residence time and water quality. Subsequent path analysis revealed that in terms of seasonal patterns in growth potential, catfish and walleye responded to temperature, positively and negatively, respectively; crappie and walleye responded to eutrophy (negatively). At the high eutrophy levels observed in this system, some desired fishes appear to suffer from excessive cultural eutrophication within the context of elevated temperatures whereas others appear to be largely unaffected or even enhanced. Our overall findings do not lead to the conclusion that this system is degraded by pollution; however, they do highlight the need to use a sensitive focal species in the process of determining allowable nutrient loading and as integrators of habitat suitability across multiple spatial and temporal scales. We provide an integrated approach useful for quantifying fish growth potential and identifying water quality constraints on fish performance at spatial scales appropriate for whole-system management.

  16. Integrated Bioinformatics, Environmental Epidemiologic and Genomic Approaches to Identify Environmental and Molecular Links between Endometriosis and Breast Cancer

    PubMed Central

    Roy, Deodutta; Morgan, Marisa; Yoo, Changwon; Deoraj, Alok; Roy, Sandhya; Yadav, Vijay Kumar; Garoub, Mohannad; Assaggaf, Hamza; Doke, Mayur

    2015-01-01

    We present a combined environmental epidemiologic, genomic, and bioinformatics approach to identify: exposure of environmental chemicals with estrogenic activity; epidemiologic association between endocrine disrupting chemical (EDC) and health effects, such as, breast cancer or endometriosis; and gene-EDC interactions and disease associations. Human exposure measurement and modeling confirmed estrogenic activity of three selected class of environmental chemicals, polychlorinated biphenyls (PCBs), bisphenols (BPs), and phthalates. Meta-analysis showed that PCBs exposure, not Bisphenol A (BPA) and phthalates, increased the summary odds ratio for breast cancer and endometriosis. Bioinformatics analysis of gene-EDC interactions and disease associations identified several hundred genes that were altered by exposure to PCBs, phthalate or BPA. EDCs-modified genes in breast neoplasms and endometriosis are part of steroid hormone signaling and inflammation pathways. All three EDCs–PCB 153, phthalates, and BPA influenced five common genes—CYP19A1, EGFR, ESR2, FOS, and IGF1—in breast cancer as well as in endometriosis. These genes are environmentally and estrogen responsive, altered in human breast and uterine tumors and endometriosis lesions, and part of Mitogen Activated Protein Kinase (MAPK) signaling pathways in cancer. Our findings suggest that breast cancer and endometriosis share some common environmental and molecular risk factors. PMID:26512648

  17. Identifying the role of conservation biology for solving the environmental crisis.

    PubMed

    Dalerum, Fredrik

    2014-11-01

    Humans are altering their living environment to an extent that could cause environmental collapse. Promoting change into environmental sustainability is therefore urgent. Despite a rapid expansion in conservation biology, appreciation of underlying causes and identification of long-term solutions have largely been lacking. I summarized knowledge regarding the environmental crisis, and argue that the most important contributions toward solutions come from economy, political sciences, and psychology. Roles of conservation biology include providing environmental protection until sustainable solutions have been found, evaluating the effectiveness of implemented solutions, and providing societies with information necessary to align effectively with environmental values. Because of the potential disciplinary discrepancy between finding long-term solutions and short-term protection, we may face critical trade-offs between allocations of resources toward achieving sustainability. Since biological knowledge is required for such trade-offs, an additional role for conservation biologists may be to provide guidance toward finding optimal strategies in such trade-offs. PMID:25081492

  18. POTENTIAL ENVIRONMENTAL PROBLEMS OF ENHANCED OIL AND GAS RECOVERY TECHNIQUES

    EPA Science Inventory

    This report provides: (a) an identification of and analysis of available data regarding EOR/EGR related pollutants; (b) an assessment of potential environmental impacts and an identification of possible controls; and (c) recommendations as to research needs. The following process...

  19. 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...

  20. A novel technique for identifying opportunities to improve environmental hygiene in the operating room.

    PubMed

    Jefferson, Julie; Whelan, Rita; Dick, Brian; Carling, Philip

    2011-03-01

    Environmental cleaning and disinfection is essential for optimizing safe patient care in the OR; however, perioperative staff members have not had an easy-to-use, objective method for determining whether high-touch, potentially contaminated surfaces have been cleaned during terminal room cleaning. To address this issue, members of the Healthcare Environmental Hygiene Study Group used a transparent, removable, environmentally stable disclosing agent and handheld ultraviolet light to determine whether potentially contaminated surfaces had been contacted by a wet disinfection cleaning cloth during terminal cleaning of ORs. Results from the project showed that 237 of 946 targeted surfaces (25%) had the disclosing agent removed (ie, were cleaned). The use of the disclosing agent for staff education and process monitoring has led to significant improvements in the disinfection cleaning process. PMID:21353808

  1. Delphi analysis: a technique for identifying and ranking environmental and natural resource policy issues

    SciTech Connect

    Leitch, J.A.; Leistritz, F.L.

    1984-01-01

    A Delphi-type survey and a consensus-building workshop were carried out to identify the most significant natural resource issues and problems emerging in the Great Plains and Rocky Mountain states. Approximately 107 issues initially were identified through a literature search and an inquiry Delphi round. Delphi round enabled the list to be narrowed to 25 issues. While consensus was found on the top 25 issues as a group, neither the Delphi panel nor the workshop participants agreed on the top five. Specific issues related to water and energy comprised the majority of those identified as most significant. Overall, the Delphi method appears to be a powerful and flexible tool for evaluating emerging environmental issues and problems. The analysis suggests that Delphi findings are quite robust with respect to minor changes in panel composition. Delphi thus appears to be an approach that may find increasing application in environmental policy analysis. 11 references, 3 figures, 4 tables.

  2. Noble metals: a toxicological appraisal of potential new environmental contaminants.

    PubMed Central

    Brubaker, P E; Moran, J P; Bridbord, K; Hueter, F G

    1975-01-01

    The public health benefits expected by reducing known hazardous emissions from mobile sources should not be compromised by increasing levels of other potentially hazardous unregulated emissions. Catalytic converters are going to be used to meet the statutory requirements on carbon monoxide and hydrocarbon emissions from light duty motor vehicles. Platinum and palladium metals are the catalytic materials to be used in these emission control devices. Preliminary experimental evidence and analysis of the impact of these control devices on the future use and demand for platinum indicates that this metal may appear at detectable levels in the environment by the end of this decade. At the present time, platinum and palladium are not present in the public environment and represent potentially new environmental contaminants as a consequence of use of this new abatement control technology. There is relatively little information available to adequately assess the potential health hazards that may be associated with exposure to these metals and their compounds. Analysis of the environmental problems and concerns associated with possible new environmental contaminants are discussed. Limited estimates are made on community exposure by use of a meteorological dispersion model. Biodegradation potential and attention is also given to the limited toxicological information available. PMID:50939

  3. Potential environmental benefits of prospective genetic changes in broiler traits.

    PubMed

    Leinonen, I; Williams, A G; Kyriazakis, I

    2016-02-01

    A system approach-based Life Cycle Assessment (LCA) framework, combined with a simple mechanistic model of bird energy balance was used to predict the potential effects of 15 y prospective broiler breeding on the environmental impacts of the standard UK broiler production system. The year 2014 Ross 308 genotype was used as a baseline, and a future scenario was specified from rates of genetic improvement predicted by the industry. The scenario included changes in the traits of growth rate (reducing the time to reach a target weight 2.05 kg from 34 d to 27 d), body lipid content, carcass yield, mortality and the number of chicks produced by a breeder hen. Diet composition was adjusted in order to accommodate the future nutrient requirements of the birds following the genetic change. The results showed that predicted changes in biological performance due to selective breeding could lead to reduced environmental impacts of the broiler production chain, most notably in the Eutrophication Potential (by 12%), Acidification Potential (by 10%) and Abiotic Resource Use (by 9%) and Global Warming Potential (by 9%). These reductions were mainly caused by the reduced maintenance energy requirement and thus lower feed intake, resulting from the shorter production cycle, together with the increased carcass yield. However, some environmental benefits were limited by the required changes in feed composition (e.g., increased inclusion of soy meal and vegetable oil) as a result of the changes in bird nutrient requirements. This study is the first one aiming to link the mechanistic animal modeling approach to predicted genetic changes in order to produce quantitative estimates of the future environmental impacts of broiler production. Although a more detailed understanding on the mechanisms of the potential changes in bird performance and their consequences on feeding and husbandry would be still be needed, the modeling framework produced in this study provides a starting point for

  4. Mapping environmental injustices: pitfalls and potential of geographic information systems in assessing environmental health and equity.

    PubMed Central

    Maantay, Juliana

    2002-01-01

    Geographic Information Systems (GIS) have been used increasingly to map instances of environmental injustice, the disproportionate exposure of certain populations to environmental hazards. Some of the technical and analytic difficulties of mapping environmental injustice are outlined in this article, along with suggestions for using GIS to better assess and predict environmental health and equity. I examine 13 GIS-based environmental equity studies conducted within the past decade and use a study of noxious land use locations in the Bronx, New York, to illustrate and evaluate the differences in two common methods of determining exposure extent and the characteristics of proximate populations. Unresolved issues in mapping environmental equity and health include lack of comprehensive hazards databases; the inadequacy of current exposure indices; the need to develop realistic methodologies for determining the geographic extent of exposure and the characteristics of the affected populations; and the paucity and insufficiency of health assessment data. GIS have great potential to help us understand the spatial relationship between pollution and health. Refinements in exposure indices; the use of dispersion modeling and advanced proximity analysis; the application of neighborhood-scale analysis; and the consideration of other factors such as zoning and planning policies will enable more conclusive findings. The environmental equity studies reviewed in this article found a disproportionate environmental burden based on race and/or income. It is critical now to demonstrate correspondence between environmental burdens and adverse health impacts--to show the disproportionate effects of pollution rather than just the disproportionate distribution of pollution sources. PMID:11929725

  5. Mapping environmental injustices: pitfalls and potential of geographic information systems in assessing environmental health and equity.

    PubMed

    Maantay, Juliana

    2002-04-01

    Geographic Information Systems (GIS) have been used increasingly to map instances of environmental injustice, the disproportionate exposure of certain populations to environmental hazards. Some of the technical and analytic difficulties of mapping environmental injustice are outlined in this article, along with suggestions for using GIS to better assess and predict environmental health and equity. I examine 13 GIS-based environmental equity studies conducted within the past decade and use a study of noxious land use locations in the Bronx, New York, to illustrate and evaluate the differences in two common methods of determining exposure extent and the characteristics of proximate populations. Unresolved issues in mapping environmental equity and health include lack of comprehensive hazards databases; the inadequacy of current exposure indices; the need to develop realistic methodologies for determining the geographic extent of exposure and the characteristics of the affected populations; and the paucity and insufficiency of health assessment data. GIS have great potential to help us understand the spatial relationship between pollution and health. Refinements in exposure indices; the use of dispersion modeling and advanced proximity analysis; the application of neighborhood-scale analysis; and the consideration of other factors such as zoning and planning policies will enable more conclusive findings. The environmental equity studies reviewed in this article found a disproportionate environmental burden based on race and/or income. It is critical now to demonstrate correspondence between environmental burdens and adverse health impacts--to show the disproportionate effects of pollution rather than just the disproportionate distribution of pollution sources. PMID:11929725

  6. Identifying environmental health priorities in underserved populations: a study of rural versus urban communities

    PubMed Central

    Bernhard, M.C.; Evans, M.B.; Kent, S.T.; Johnson, E.; Threadgill, S.L.; Tyson, S.; Becker, S.M.; Gohlke, J.M.

    2013-01-01

    Objectives Understanding and effectively addressing persistent health disparities in minority communities requires a clear picture of members’ concerns and priorities. This study was intended to engage residents in urban and rural communities in order to identify environmental health priorities. Specific emphasis was placed on how the communities defined the term environment, their perceptions of environmental exposures as affecting their health, specific priorities in their communities, and differences in urban versus rural populations. Study design A community-engaged approach was used to develop and implement focus groups and compare environmental health priorities in urban versus rural communities. Methods A total of eight focus groups were conducted: four in rural and four in urban communities. Topics included defining the term environment, how the environment may affect health, and environmental priorities within their communities, using both open discussion and a predefined list. Data were analysed both qualitatively and quantitatively to identify patterns and trends. Results There were important areas of overlap in priorities between urban and rural communities; both emphasized the importance of the social environment and shared a concern over air pollution from industrial sources. In contrast, for urban focus groups, abandoned houses and their social and physical sequelae were a high priority while concerns about adequate sewer and water services and road maintenance were high priorities in rural communities. Conclusions This study was able to identify environmental health priorities in urban versus rural minority communities. In contrast to some previous risk perception research, the results of this study suggest prioritization of tangible, known risks in everyday life instead of rare, disaster-related events, even in communities that have recently experienced devastating damage from tornadoes. The findings can help inform future efforts to study

  7. Potential environmental benefits from regulatory consideration of synthetic drilling muds

    SciTech Connect

    Burke, C.J.; Veil, J.A.

    1995-02-01

    When drilling exploration and production wells for oil and gas, drillers use specialized drilling fluids, referred to as muds, to help maintain well control and to remove drill cuttings from the hole. Historically, either water-based muds (WBMs) or oil-based muds (OBMs) have been used for offshore wells. Recently, in response to US Environmental Protection Agency (EPA) regulations and drilling-waste discharge requirements imposed by North Sea nations, the drilling industry has developed several types of synthetic-based muds (SBMs) that combine the desirable operating qualities of OBMs with the lower toxicity and environmental impact qualities of WBMs. This report describes the operational, environmental, and economic features of all three types of muds and discusses potential EPA regulatory barriers to wider use of SBMs.

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

    ERIC Educational Resources Information Center

    Neyman, C. A., Jr.

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

  9. Use of Event-Related Potentials to Identify Language and Reading Skills

    ERIC Educational Resources Information Center

    Molfese, Victoria J.; Molfese, Dennis L.; Beswick, Jennifer L.; Jacobi-Vessels, Jill; Molfese, Peter J.; Molnar, Andrew E.; Wagner, Mary C.; Haines, Brittany L.

    2008-01-01

    The extent to which oral language and emergent literacy skills are influenced by event-related potential measures of phonological processing was examined. Results revealed that event-related potential responses identify differences in letter naming but not receptive language skills.

  10. Environmentally induced epigenetic toxicity: potential public health concerns.

    PubMed

    Marczylo, Emma L; Jacobs, Miriam N; Gant, Timothy W

    2016-09-01

    Throughout our lives, epigenetic processes shape our development and enable us to adapt to a constantly changing environment. Identifying and understanding environmentally induced epigenetic change(s) that may lead to adverse outcomes is vital for protecting public health. This review, therefore, examines the present understanding of epigenetic mechanisms involved in the mammalian life cycle, evaluates the current evidence for environmentally induced epigenetic toxicity in human cohorts and rodent models and highlights the research considerations and implications of this emerging knowledge for public health and regulatory toxicology. Many hundreds of studies have investigated such toxicity, yet relatively few have demonstrated a mechanistic association among specific environmental exposures, epigenetic changes and adverse health outcomes in human epidemiological cohorts and/or rodent models. While this small body of evidence is largely composed of exploratory in vivo high-dose range studies, it does set a precedent for the existence of environmentally induced epigenetic toxicity. Consequently, there is worldwide recognition of this phenomenon, and discussion on how to both guide further scientific research towards a greater mechanistic understanding of environmentally induced epigenetic toxicity in humans, and translate relevant research outcomes into appropriate regulatory policies for effective public health protection. PMID:27278298

  11. 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

  12. Identifying the effects of environmental and policy change interventions on healthy eating.

    PubMed

    Bowen, Deborah J; Barrington, Wendy E; Beresford, Shirley A A

    2015-03-18

    Obesity has been characterized as a disease. Strategies to change the incidence and prevalence of this disease include a focus on changing physical and social environments, over and above individual-level strategies, using a multilevel or systems approach. We focus our attention on evidence published between 2008 and 2013 on the effectiveness of interventions in nutrition environments, i.e., environmental interventions designed to influence the intake of healthful foods and amount of energy consumed. An overarching socioecological framework that has guided much of this research was used to characterize different types of environmental strategies. Intervention examples in each area of the framework are provided with a discussion of key findings and related conceptual and methodological issues. The emphasis in this review is on adults, but clearly this literature is only one part of the picture. Much research has been focused on child-specific interventions, including environmental interventions. Some evidence suggests effectiveness of policy-based or other types of interventions that aim to regulate or restructure environments to promote healthy dietary choices, and these strategies would apply to both children and adults. Opportunities to evaluate these policy changes in adults' social and physical environments are rare. Much of the existing research has been with children. As conceptual and methodological issues continue to be identified and resolved, we hope that future research in this domain will identify environmental strategies that can be included in intervention toolboxes to build healthy nutrition environments for both adults and children. PMID:25785891

  13. Identifying the Effects of Environmental and Policy Change Interventions on Healthy Eating

    PubMed Central

    Bowen, Deborah J.; Barrington, Wendy E.; Beresford, Shirley A.A.

    2015-01-01

    Obesity has been characterized as a disease. Strategies to change the incidence and prevalence of this disease include a focus on changing physical and social environments, over and above individual-level strategies, using a multilevel or systems approach. We focus our attention on evidence published between 2008 and 2013 on the effectiveness of interventions in nutrition environments, i.e., environmental interventions designed to influence the intake of healthful foods and amount of energy consumed. An overarching socioecological framework that has guided much of this research was used to characterize different types of environmental strategies. Intervention examples in each area of the framework are provided with a discussion of key findings and related conceptual and methodological issues. The emphasis in this review is on adults, but clearly this literature is only one part of the picture. Much research has been focused on child-specific interventions, including environmental interventions. Some evidence suggests effectiveness of policy-based or other types of interventions that aim to regulate or restructure environments to promote healthy dietary choices, and these strategies would apply to both children and adults. Opportunities to evaluate these policy changes in adults’ social and physical environments are rare. Much of the existing research has been with children. As conceptual and methodological issues continue to be identified and resolved, we hope that future research in this domain will identify environmental strategies that can be included in intervention toolboxes to build healthy nutrition environments for both adults and children. PMID:25785891

  14. 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

  15. Environmental engineering of navigation infrastructure: a survey of existing practices, challenges, and potential opportunities.

    PubMed

    Fredette, Thomas J; Foran, Christy M; Brasfield, Sandra M; Suedel, Burton C

    2012-01-01

    Navigation infrastructure such as channels, jetties, river training structures, and lock-and-dam facilities are primary components of a safe and efficient water transportation system. Planning for such infrastructure has until recently involved efforts to minimize impacts on the environment through a standardized environmental assessment process. More recently, consistent with environmental sustainability concepts, planners have begun to consider how such projects can also be constructed with environmental enhancements. This study examined the existing institutional conditions within the US Army Corps of Engineers and cooperating federal agencies relative to incorporating environmental enhancements into navigation infrastructure projects. The study sought to (1) investigate institutional attitudes towards the environmental enhancement of navigation infrastructure (EENI) concept, (2) identify potential impediments to implementation and solutions to such impediments, (3) identify existing navigation projects designed with the express intent of enhancing environmental benefit in addition to the primary project purpose, (4) identify innovative ideas for increasing environmental benefits for navigation projects, (5) identify needs for additional technical information or research, and (6) identify laws, regulations, and policies that both support and hinder such design features. The principal investigation tool was an Internet-based survey with 53 questions. The survey captured a wide range of perspectives on the EENI concept including ideas, concerns, research needs, and relevant laws and policies. Study recommendations included further promotion of the concept of EENI to planners and designers, documentation of existing projects, initiation of pilot studies on some of the innovative ideas provided through the survey, and development of national goals and interagency agreements to facilitate implementation. PMID:21796771

  16. Potential environmental impacts of offshore UK geological CO2 storage

    NASA Astrophysics Data System (ADS)

    Carruthers, Kit; Wilkinson, Mark; Butler, Ian B.

    2016-04-01

    Geological carbon dioxide storage in the United Kingdom (UK) will almost certainly be entirely offshore, with storage for over 100 years' worth of UK CO2 output from industry and power generation in offshore depleted hydrocarbon fields and sandstone formations. Storage capacity can be limited by the increase in formation water pressure upon CO2 injection, therefore removal and disposal of formation waters ('produced waters') can control formation water pressures, and increase CO2 storage capacity. Formation waters could also be produced during CO2-Enhanced Oil Recovery (CO2-EOR). The precedent from current UK North Sea hydrocarbon extraction is to 'overboard' produced waters into the ocean, under current regulations. However, laboratory and field scale studies, with an emphasis on the effects on onshore shallow potable groundwaters, have shown that CO2 dissolution in formation waters during injection and storage acidifies the waters and promotes mobilisation from the reservoir sandstones of major and trace elements into solution, including heavy metals. Eight of these elements are specifically identified in the UK as potentially hazardous to the marine environment (As, Cd, Cr, Cu, Hg, Ni, Pb, Zn). A comparison was made between the concentrations of these eight trace elements in the results of laboratory batch leaching experiments of reservoir rock in CO2-rich saline solutions and overboarded waters from current offshore UK hydrocarbon production. This showed that, taking the North Sea as a whole, the experimental results fall within the range of concentrations of current oil and gas activities. However, on a field-by-field basis, concentrations may be enhanced with CO2 storage, such that they are higher than waters normally produced from a particular field. Lead, nickel and zinc showed the greatest concentration increases in the experiments with the addition of CO2, with the other five elements of interest not showing any strong trends with respect to enhanced CO2

  17. Potential for use of environmental factors in urban planning

    NASA Astrophysics Data System (ADS)

    Teixeira da Silva, Ricardo; van der Ploeg, Martine; van Delden, Hedwig; Fleskens, Luuk

    2016-04-01

    Projections for population growth estimate, on top of the current 7.4 billion world population, an increase of 2 billion people for the next 40 years. It is also projected that 66 per cent of the world population in 2050 will live in urban areas. To accommodate the urban population growth cities are changing continuously land cover to urban areas. Such changes are a threat for natural resources and food production systems stability and capability to provide food and other functions. However, little has been done concerning a rational soil management for food production in urban and peri-urban areas. This study focuses on the assessment of soil lost due to urban expansion and discusses the potential loss regarding the quality of the soil for food production and environmental functions. It is relevant to increase the knowledge on the role of soils in peri-urban areas and in the interaction of physical, environmental and social factors. The methodology consists of assessing the soil quality in and around urban and peri-urban areas. It focuses particularly on the physical properties and the environmental factors, for two periods of time and account the potential losses due to urban expansion. This project is on-going, therefore current advances will be presented and will look for a discussion on the contribution of soil quality for decision-making and land management in urban and peri-urban areas.

  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, 75–80% were documented on the drug labels. Some of the undocumented pairs may represent previously unidentified adverse drug effects. PMID:21820083

  19. Environmental Health Related Socio-Spatial Inequalities: Identifying “Hotspots” of Environmental Burdens and Social Vulnerability

    PubMed Central

    Shrestha, Rehana; Flacke, Johannes; Martinez, Javier; van Maarseveen, Martin

    2016-01-01

    Differential exposure to multiple environmental burdens and benefits and their distribution across a population with varying vulnerability can contribute heavily to health inequalities. Particularly relevant are areas with high cumulative burdens and high social vulnerability termed as “hotspots”. This paper develops an index-based approach to assess these multiple burdens and benefits in combination with vulnerability factors at detailed intra-urban level. The method is applied to the city of Dortmund, Germany. Using non-spatial and spatial methods we assessed inequalities and identified “hotspot” areas in the city. We found modest inequalities burdening higher vulnerable groups in Dortmund (CI = −0.020 at p < 0.05). At the detailed intra-urban level, however, inequalities showed strong geographical patterns. Large numbers of “hotspots” exist in the northern part of the city compared to the southern part. A holistic assessment, particularly at a detailed local level, considering both environmental burdens and benefits and their distribution across the population with the different vulnerability, is essential to inform environmental justice debates and to mobilize local stakeholders. Locating “hotspot” areas at this detailed spatial level can serve as a basis to develop interventions that target vulnerable groups to ensure a health conducive equal environment. PMID:27409625

  20. Potentials and Limitations of Wireless Sensor Networks for Environmental

    NASA Astrophysics Data System (ADS)

    Bumberger, J.; Remmler, P.; Hutschenreuther, T.; Toepfer, H.; Dietrich, P.

    2013-12-01

    Understanding and dealing with environmental challenges worldwide requires suitable interdisciplinary methods and a level of expertise to be able to implement these solutions, so that the lifestyles of future generations can be secured in the years to come. To characterize environmental systems it is necessary to identify and describe processes with suitable methods. Environmental systems are often characterized by their high heterogeneity, so individual measurements for their complete representation are often not sufficient. The application of wireless sensor networks in terrestrial and aquatic ecosystems offer significant benefits as a better consideration of the local test conditions becomes possible. This can be essential for the monitoring of heterogeneous environmental systems. Significant advantages in the application of wireless sensor networks are their self-organizing behaviour, resulting in a major reduction in installation and operation costs and time. In addition, a point measurement with a sensor is significantly improved by measuring at several points. It is also possible to perform analog and digital signal processing and computation on the basis of the measured data close to the sensor. Hence, a significant reduction of the data to be transmitted can be achieved which leads to a better energy management of sensor nodes. Furthermore, their localization via satellite, the miniaturization of the nodes and long-term energy self-sufficiency are current topics under investigation. In this presentation, the possibilities and limitations of the applicability of wireless sensor networks for long-term environmental monitoring are presented. To underline the importance of this future technology, example concepts are given in the field of near-surface geothermics, groundwater observation, measurement of spatial radiation intensity and air humidity on soils, measurement of matter fluxes, greenhouse gas measurement, and landslide monitoring.

  1. Using Social Media Data to Identify Potential Candidates for Drug Repurposing: A Feasibility Study

    PubMed Central

    Liu, Hongfang; Nambisan, Priya

    2016-01-01

    Background Drug repurposing (defined as discovering new indications for existing drugs) could play a significant role in drug development, especially considering the declining success rates of developing novel drugs. Typically, new indications for existing medications are identified by accident. However, new technologies and a large number of available resources enable the development of systematic approaches to identify and validate drug-repurposing candidates. Patients today report their experiences with medications on social media and reveal side effects as well as beneficial effects of those medications. Objective Our aim was to assess the feasibility of using patient reviews from social media to identify potential candidates for drug repurposing. Methods We retrieved patient reviews of 180 medications from an online forum, WebMD. Using dictionary-based and machine learning approaches, we identified disease names in the reviews. Several publicly available resources were used to exclude comments containing known indications and adverse drug effects. After manually reviewing some of the remaining comments, we implemented a rule-based system to identify beneficial effects. Results The dictionary-based system and machine learning system identified 2178 and 6171 disease names respectively in 64,616 patient comments. We provided a list of 10 common patterns that patients used to report any beneficial effects or uses of medication. After manually reviewing the comments tagged by our rule-based system, we identified five potential drug repurposing candidates. Conclusions To our knowledge, this is the first study to consider using social media data to identify drug-repurposing candidates. We found that even a rule-based system, with a limited number of rules, could identify beneficial effect mentions in patient comments. Our preliminary study shows that social media has the potential to be used in drug repurposing. PMID:27311964

  2. Potential environmental consequences of administration of ectoparasiticides to sheep.

    PubMed

    Beynon, S A

    2012-09-30

    Sheep ectoparasiticides, which include the synthetic pyrethroids, the organophosphates, the 'insect'-growth regulators, the formamidines and the spinocyns, enter into the environment primarily through disposal of dip or fleece scours, as well as with contaminated faeces and urine. Due to the large quantities of spent dip, risks associated with environmental contamination are high. Synthetic pyrethroids and organophosphates pose risks to dung, soil and aquatic fauna; concerns over potential ecotoxicity to vertebrates and invertebrates have resulted in the cessation of their use in many countries. There is very little information regarding the ecotoxicity of 'insect'-growth regulators, formamidines or spinocyns, with no studies focussing on sheep. Here, the impact of sheep ectoparasiticides is discussed in terms of their potential to enter into the environment, their toxicity and their impact on ecosystem functioning. Where there are no data for excretion or toxicity of the ectoparasiticides used in sheep production, examples to demonstrate potential impacts are taken from laboratory ecotoxicity tests and the cattle literature, as well on work with foliar insecticides. Future research priorities are suggested to allow assessment of the environmental consequences of sheep ectoparasiticide treatments, which are essential for future sustainable sheep production. PMID:22538092

  3. Assessing potential future environmental legislative, regulatory, and judicial events

    SciTech Connect

    Tonn, B.; Schweitzer, M.; Godfrey, G.; Wagner, C.; MacGregor, D.G.

    1998-03-01

    This report describes a methodology to proactively and methodically assess future potential environmental legislative, regulatory, and judicial events. This is an important endeavor because new, revised, and reauthorized legislation, proposed and final regulations, and outcomes of judicial proceedings have the potential to impose new actions, directions, and costs of many organizations in the United States (related to capital investments, operating approaches, and research and development) and to affect the quality of life. The electric power industry is particularly impacted by environmental regulatory events (the term `regulatory` is used to cover all the types of legal events listed above), as the generation, transmission, and distribution of electricity affects air and water quality, require disposal of solid, hazardous, and radioactive wastes, and at times, impacts wetlands and endangered species. Numerous potential regulatory events, such as the reauthorization of the Clean Water Act and new regulations associated with global climate change, can greatly affect the power industry. Organizations poised to respond proactively to such events will improve their competitive positions, reduce their costs in the long-term, and improve their public images.

  4. Identifying trends for understanding the role of humic substances in the environmental behavior of radionuclides

    SciTech Connect

    Czerwinski, K.R.; Buckau, G.

    1999-07-01

    Humic substances are expected to have a major role in the environmental speciation of radionuclides. If the speciation of the radionuclide humic complex can be adequately modeled, predictions of its fate and transport may be possible. Additionally, humic substances have been shown to adsorb to a variety of mineral surfaces. The humic coated surfaces also interact with aqueous radionuclides, complicating environmental behavior. Studies indicate the importance of pH, ionic strength, and humic substance concentration in understanding the impact of humic substances on radionuclide speciation. However, values obtained to describe complexation or sorption vary and are difficult to compare and incorporate into existing geochemical codes due to variations in humic complexation models or concepts. This obscures intercomparison and the utility of the resulting values. This work shows results based on different concepts can be evaluated with the charge neutralization model, yielding similar stability constant values. The consistent stability constants found with the charge neutralization model can be used for intercomparison and identification of behavioral trends. A speciation calculation of a contaminated site using identified trends between humic and fulvic acid are given. The results yield good agreement between calculation and environmental observations. Laboratory experiments validate the identified trend. Comparisons between aquatic and sorb humic acid are presented and similarities useful for modeling are given.

  5. Prioritizing chemicals for environmental management in China based on screening of potential risks

    NASA Astrophysics Data System (ADS)

    Yu, Xiangyi; Mao, Yan; Sun, Jinye; Shen, Yingwa

    2014-03-01

    The rapid development of China's chemical industry has created increasing pressure to improve the environmental management of chemicals. To bridge the large gap between the use and safe management of chemicals, we performed a comprehensive review of the international methods used to prioritize chemicals for environmental management. By comparing domestic and foreign methods, we confirmed the presence of this gap and identified potential solutions. Based on our literature review, we developed an appropriate screening method that accounts for the unique characteristics of chemical use within China. The proposed method is based on an evaluation using nine indices of the potential hazard posed by a chemical: three environmental hazard indices (persistence, bioaccumulation, and eco-toxicity), four health hazard indices (acute toxicity, carcinogenicity, mutagenicity, and reproductive and developmental toxicity), and two environmental exposure hazard indices (chemical amount and utilization pattern). The results of our screening agree with results of previous efforts from around the world, confirming the validity of the new system. The classification method will help decisionmakers to prioritize and identify the chemicals with the highest environmental risk, thereby providing a basis for improving chemical management in China.

  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. Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans.

    PubMed

    Anderson, Justin E; Kono, Thomas J Y; Stupar, Robert M; Kantar, Michael B; Morrell, Peter L

    2016-01-01

    Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections. PMID:26818076

  8. Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

    PubMed Central

    Anderson, Justin E.; Kono, Thomas J. Y.; Stupar, Robert M.; Kantar, Michael B.; Morrell, Peter L.

    2016-01-01

    Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections. PMID:26818076

  9. High Incidence of Mammalian Orthoreovirus Identified by Environmental Surveillance in Taiwan

    PubMed Central

    Huang, Sheng-Wen; Yang, Jyh-Yuan; Wang, Jen-Ren

    2015-01-01

    Wild poliovirus (WPV) persists in diverse locales worldwide, spreading outward from endemic areas. In response to the international threat of WPV transmission and changes in the national vaccination policy, we established an environmental surveillance system to monitor the circulation of wild and vaccine-related poliovirus in Taiwan. From July 2012 to December 2013, we collected sewage specimens every month from 10 sewage treatment plants located throughout Taiwan. The specimens were concentrated by the two-phase separation method and then inoculated into L20B, RD, and A549 cells for virus isolation. Viral isolates were identified and serotyped by immunofluorescence assay or molecular analysis. A total of 300 sewage samples were collected, and the results showed 163 samples (54.3%) were positive for virus, and 268 isolates were identified. Among these, 75 samples (25%) were positive for enterovirus (EV), but no poliovirus was found. In addition, 92 isolates were identified as enteroviruses and the most common serotypes were coxsackievirus B4, coxsackievirus B3, and coxsackievirus B2. Interestingly, 102 (34%) and 82 (27.3%) specimens were positive for mammalian orthoreovirus (MRV) and adenovirus, respectively. This study confirmed that sewage surveillance can be a useful additional modality for monitoring the possible presence of wild-type or vaccine-derived poliovirus in wastewater, and can indicate the current types of viruses circulating in the population. Furthermore, since MRV was found in children with acute necrotizing encephalopathy and meningitis, the high incidence of MRV detected by environmental surveillance warrants further investigation. PMID:26555962

  10. Biosensor Zebrafish Provide New Insights into Potential Health Effects of Environmental Estrogens

    PubMed Central

    Lee, Okhyun; Takesono, Aya; Tada, Masazumi; Kudoh, Tetsuhiro

    2012-01-01

    Background: Environmental estrogens alter hormone signaling in the body that can induce reproductive abnormalities in both humans and wildlife. Available testing systems for estrogens are focused on specific systems such as reproduction. Crucially, however, the potential for significant health impacts of environmental estrogen exposures on a variety of body systems may have been overlooked. Objective: Our aim was to develop and apply a sensitive transgenic zebrafish model to assess real-time effects of environmental estrogens on signaling mechanisms in a whole body system for use in integrated health assessments. Methods: We created a novel transgenic biosensor zebrafish containing an estrogen-inducible promoter derived with multiple tandem estrogen responsive elements (EREs) and a Gal4ff-UAS system for enhanced response sensitivity. Results: Using our novel estrogen-responsive transgenic (TG) zebrafish, we identified target tissues for environmental estrogens; these tissues have very high sensitivity even at environmentally relevant concentrations. Exposure of the TG fish to estrogenic endocrine-disrupting chemicals (EDCs) induced specific expression of green fluorescent protein (GFP) in a wide variety of tissues including the liver, heart, skeletal muscle, otic vesicle, forebrain, lateral line, and ganglions, most of which have not been established previously as targets for estrogens in fish. Furthermore, we found that different EDCs induced GFP expression with different tissue response patterns and time trajectories, suggesting different potential health effects. Conclusion: We have developed a powerful new model for understanding toxicological effects, mechanisms, and health impacts of environmental estrogens in vertebrates. PMID:22510978

  11. Environmental potential of carbon dioxide utilization in the polyurethane supply chain.

    PubMed

    von der Assen, Niklas; Sternberg, André; Kätelhön, Arne; Bardow, André

    2015-01-01

    Potential environmental benefits have been identified for the utilization of carbon dioxide (CO2) as a feedstock for polyurethanes (PUR). CO2 can be utilized in the PUR supply chain in a wide variety of ways ranging from direct CO2 utilization for polyols as a PUR precursor, to indirect CO2 utilization for basic chemicals in the PUR supply chain. In this paper, we present a systematic exploration and environmental evaluation of all direct and indirect CO2 utilization options for flexible and rigid PUR foams. The analysis is based on an LCA-based PUR supply chain optimization model using linear programming to identify PUR production with minimal environmental impacts. The direct utilization of CO2 for polyols allows for large specific impact reductions of up to 4 kg CO2-eq. and 2 kg oil-eq. per kg CO2 utilized, but the amounts of CO2 that can be utilized are limited to 0.30 kg CO2 per kg PUR. The amount of CO2 utilized can be increased to up to 1.7 kg CO2 per kg PUR by indirect CO2 utilization in the PUR supply chain. Indirect CO2 utilization requires hydrogen (H2). The environmental impacts of H2 production strongly affect the impact of indirect CO2 utilization in PUR. To achieve optimal environmental performance under the current fossil-based H2 generation, PUR production can only utilize much less CO2 than theoretically possible. Thus, utilizing as much CO2 in the PUR supply chain as possible is not always environmentally optimal. Clean H2 production is required to exploit the full CO2 utilization potential for environmental impact reduction in PUR production. PMID:26381106

  12. Identifying potential indicators of conservation value using natural heritage occurrence data.

    PubMed

    Pearman, Peter B; Penskar, Michael R; Schools, Edward H; Enander, Helen D

    2006-02-01

    Conservation planning based on the occurrence of rare species has been criticized as being too limited in scope to conserve biodiversity as a whole. Conversely, planning based on indicator taxa may lack sufficient focus to conserve those species in greatest need of conservation. An alternative approach is to identify a variety of species at risk that are associated with areas of conservation value, which is defined based on species-independent characteristics. We identified potential indicators of conservation value using occurrence data on species at risk and independent information on conservation value that incorporated indices of ecosystem integrity. We propose a taxonomically diverse group of indicator species that are strongly associated with areas of exceptional ecosystem integrity, to serve as a focus for further research and in planning for biodiversity conservation. We identify potential indicator species by defining a null model in which species at risk are equally associated with areas of high ecosystem integrity, then by conducting randomization tests to identify noncompliant species in the state of Michigan, USA. Areas of high ecosystem integrity are selected using criteria to flag (1) secure biotic communities with structural integrity and few exotic species, (2) natural areas subjected to expert review, (3) contiguous relict areas of forest interior, (4) contiguous areas of unmodified wetland, and (5) all these areas combined. We determine the spatial occurrence of species at risk using data from Michigan's statewide Natural Heritage database. The potential indicators include plants, insects, and birds. Their species identity and distribution of occurrences varies with the five scenarios, and together the species broadly cover the entire state. These species at risk, many of which occur throughout the Great Lakes region, may be used to identify additional areas potentially high in conservation value and to monitor their conservation. The ecological

  13. Identifying Potential Impact of Lead Contamination Using a Geographic Information System

    PubMed

    BOCCO; SANCHEZ

    1997-01-01

    / The main objective of this research was to identify the potential hazards associated with lead contami-nation 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.KEY WORDS: Lead contamination; Industrial hazards; GIS; Tijuana; Mexico PMID:8939792

  14. 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.

  15. Identifying the Environmental Factors That Determine the Genetic Structure of Populations

    PubMed Central

    Foll, Matthieu; Gaggiotti, Oscar

    2006-01-01

    The study of population genetic structure is a fundamental problem in population biology because it helps us obtain a deeper understanding of the evolutionary process. One of the issues most assiduously studied in this context is the assessment of the relative importance of environmental factors (geographic distance, language, temperature, altitude, etc.) on the genetic structure of populations. The most widely used method to address this question is the multivariate Mantel test, a nonparametric method that calculates a correlation coefficient between a dependent matrix of pairwise population genetic distances and one or more independent matrices of environmental differences. Here we present a hierarchical Bayesian method that estimates FST values for each local population and relates them to environmental factors using a generalized linear model. The method is demonstrated by applying it to two data sets, a data set for a population of the argan tree and a human data set comprising 51 populations distributed worldwide. We also carry out a simulation study to investigate the performance of the method and find that it can correctly identify the factors that play a role in the structuring of genetic diversity under a wide range of scenarios. PMID:16951078

  16. CO2 Sequestration in Unmineable Coal Seams: Potential Environmental Impacts

    SciTech Connect

    Hedges, S.W.; Soong, Yee; McCarthy Jones, J.R.; Harrison, D.K.; Irdi, G.A.; Frommell, E.A.; Dilmore, R.M.; Pique, P.J.; Brown, T.D

    2005-09-01

    An initial investigation into the potential environmental impacts of CO2 sequestration in unmineable coal seams has been conducted, focusing on changes in the produced water during enhanced coalbed methane (ECBM) production using a CO2 injection process (CO2-ECBM). Two coals have been used in this study, the medium volatile bituminous Upper Freeport coal (APCS 1) of the Argonne Premium Coal Samples series, and an as-mined Pittsburgh #8 coal, which is a high volatile bituminous coal. Coal samples were reacted with either synthetic produced water or field collected produced water and gaseous carbon dioxide at 40 οC and 50 bar to evaluate the potential for mobilizing toxic metals during CO2-ECBM/sequestration. Microscopic and x-ray diffraction analysis of the post-reaction coal samples clearly show evidence of chemical reaction, and chemical analysis of the produced water shows substantial changes in composition. These results suggest that changes to the produced water chemistry and the potential for mobilizing toxic trace elements from coalbeds are important factors to be considered when evaluating deep, unmineable coal seams for CO2 sequestration.

  17. Potential Environmental Benefits from Increased Use of Bioenergy in China

    NASA Astrophysics Data System (ADS)

    Fan, Shuyang; Freedman, Bill; Gao, Jixi

    2007-09-01

    Because of its large population and rapidly growing economy, China is confronting a serious energy shortage and daunting environmental problems. An increased use of fuels derived from biomass could relieve some demand for nonrenewable sources of energy while providing environmental benefits in terms of cleaner air and reduced emissions of greenhouse gases. In 2003, China generated about 25.9 × 108 metric tons of industrial waste (liquid + solid), 14.7 × 108 metric tons/year (t/y) of manure (livestock + human), 7.1 × 108 t/y of crop residues and food-processing byproducts, 2 × 108 t/y of fuelwood and wood manufacturing residues, and 1.5 × 108 t/y of municipal waste. Biofuels derived from these materials could potentially displace the use of about 4.12 × 108 t/y of coal and 3.75 × 106 t/y of petroleum. An increased bioenergy use of this magnitude would help to reduce the emissions of key air pollutants: SO2 by 11.6 × 106 t/y, NOX by 1.48 × 106 t/y, CO2 by 1.07 × 109 t/y, and CH4 by 50 × 106 t/y. The reduced SO2 emissions would be equivalent to 54% of the national emissions in 2003, whereas those for CO2 are 30%. It is important to recognize, however, that large increases in the use of biomass fuels also could result in socioeconomic and environmental problems such as less production of food and damage caused to natural habitats.

  18. Potential environmental benefits from increased use of bioenergy in China.

    PubMed

    Fan, Shuyang; Freedman, Bill; Gao, Jixi

    2007-09-01

    Because of its large population and rapidly growing economy, China is confronting a serious energy shortage and daunting environmental problems. An increased use of fuels derived from biomass could relieve some demand for nonrenewable sources of energy while providing environmental benefits in terms of cleaner air and reduced emissions of greenhouse gases. In 2003, China generated about 25.9 x 10(8) metric tons of industrial waste (liquid + solid), 14.7 x 10(8) metric tons/year (t/y) of manure (livestock + human), 7.1 x 10(8) t/y of crop residues and food-processing byproducts, 2 x 10(8) t/y of fuelwood and wood manufacturing residues, and 1.5 x 10(8) t/y of municipal waste. Biofuels derived from these materials could potentially displace the use of about 4.12 x 10(8) t/y of coal and 3.75 x 10(6) t/y of petroleum. An increased bioenergy use of this magnitude would help to reduce the emissions of key air pollutants: SO(2 )by 11.6 x 10(6) t/y, NO(X) by 1.48 x 10(6) t/y, CO2 by 1.07 x 10(9) t/y, and CH4 by 50 x 10(6) t/y. The reduced SO(2) emissions would be equivalent to 54% of the national emissions in 2003, whereas those for CO2 are 30%. It is important to recognize, however, that large increases in the use of biomass fuels also could result in socioeconomic and environmental problems such as less production of food and damage caused to natural habitats. PMID:17638052

  19. 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.

  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. Spatial epidemiology of blastomycosis hospitalizations: detecting clusters and identifying environmental risk factors.

    PubMed

    Seitz, Amy E; Adjemian, Jennifer; Steiner, Claudia A; Prevots, D Rebecca

    2015-06-01

    Blastomycosis is a disease caused by endemic fungi that ranges from severe pulmonary or disseminated to mild or asymptomatic. Environmental factors associated with it are not well described throughout the endemic area. We used the intramural State Inpatient Database from the Agency for Healthcare Research and Quality and ArcMap GIS to identify geographic high-risk clusters of blastomycosis hospitalizations in 13 states in the US endemic regions (AR, IA, IL, IN, KY, LA, MI, MN, MO, MS, OH, TN, and WI). We then used logistic regression to identify risk factors associated with these high-risk clusters. We describe six clusters of counties in which there was an elevated incidence of blastomycosis hospitalizations. We identified maximum mean annual temperature, percentage of persons aged ≥65 years, and mercury and copper soil content as being associated with high-risk clusters. Specifically, the odds of a county being part of a high-risk cluster was associated with increasing percentage of population over age 65, decreasing maximum temperature, increasing mercury, and decreasing copper soil content. Healthcare providers should be aware of these high-risk areas so that blastomycosis can be included, as appropriate, in a differential diagnosis for patients currently or previously residing in these areas. PMID:25908653

  2. Tree growth variability under environmental changes - identifying underlying physiological mechanisms by stable C and O isotopes

    NASA Astrophysics Data System (ADS)

    Weigt, Rosemarie; Saurer, Matthias; Siegwolf, Rolf T. W.

    2014-05-01

    Long-term variability of tree growth is a result of changing environmental factors and physiological response mechanisms. Information about these relationships can be retrieved from tree ring width, but also from tree ring isotopes as proxies of photosynthetic rates (13C), stomatal conductance (13C, 18O), and source water (18O) used by the tree. With the interdisciplinary project iTREE, we aim to identify physiological mechanisms by relating time-series of tree ring isotopes from a network of sites to environmental factors, and compare resulting growth reponses with stand surveys and vegetation models. Linking these different scales - from individual trees to site and landscape - will contribute to reduce uncertainties in modeling large-scale variability of forest biomass production under current climate change. At a high altitude site in Switzerland (Loetschental, 2100m asl), ~400 yrs old larch (Larix dedicua) trees showed enhanced tree growth towards the end of the 20th century along with increasing CO2 concentrations and temperature, but also increasing variability between individual trees. At this temperature limited site, both environmental factors seem to act as growth drivers by increasing photosynthesis and cell growth. Because δ18O and δ13C (after correction for atmospheric CO2 increase and 13C decrease) remained rather unchanged over the past ~100 yrs, the stomatal behavior did not change according to the dual isotope model, indicating relatively constant water supply over time. At other sites throughout Central Europe, physiological responses to environmental changes may result in different carbon assimilation or allocation other than stem growth. First data of different sites and species along a temperature gradient in Central Europe show that year-to-year variability of tree ring δ13C and δ18O are positively correlated at most sites indicating pronounced responsiveness of stomatal conductance. A trend of increasing isotopic values across the past

  3. 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.

  4. 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

  5. Environmental surface cleanliness and the potential for contamination during handwashing.

    PubMed

    Griffith, Christopher J; Malik, Rifhat; Cooper, Rose A; Looker, Nick; Michaels, Barry

    2003-04-01

    Effective handwashing (including drying) is important in infection control. The ability of the various stages of handwashing to decrease skin-surface microbial counts has been documented. However, an important element, environmental surface cleanliness, and the potential for contamination of hands during the process has not been well studied or quantified. An examination of the adenosine triphosphate (a measure of residual organic soil), bacterial, and staphylococcal load on ward handwash station surfaces, which could be touched during handwashing, is reported. Hand contact surfaces tested consisted of approximately 620 each of: faucet handles, soap dispenser activator mechanisms, and folded paper-towel dispenser exits. Failure rates in excess of benchmark clean values were higher with adenosine triphosphate assays than microbial counts. This could indicate the presence of a higher level of general organic debris (eg, skin cells) as opposed to microbial contamination or could reflect greater assay sensitivity. Faucet handles were more likely to be contaminated and be in excess of benchmark values than paper-towel dispenser exits. However, the latter are likely to be the final surface touched during the handwashing process and overall nearly 20% were above microbiologic benchmark values. Many of the organisms isolated were staphylococci and the results are discussed within the context of microbial cross-contamination and potential pathogen spread. PMID:12665742

  6. Extracellular polymeric substances of bacteria and their potential environmental applications.

    PubMed

    More, T T; Yadav, J S S; Yan, S; Tyagi, R D; Surampalli, R Y

    2014-11-01

    Biopolymers are considered a potential alternative to conventional chemical polymers because of their ease of biodegradability, high efficiency, non-toxicity and non-secondary pollution. Recently, extracellular polymeric substances (EPS, biopolymers produced by the microorganisms) have been recognised by many researchers as a potential flocculent for their applications in various water, wastewater and sludge treatment processes. In this context, literature information on EPS is widely dispersed and is very scarce. Thus, this review marginalizes various studies conducted so far about EPS nature-production-recovery, properties, environmental applications and moreover, critically examines future research needs and advanced application prospective of the EPS. One of the most important aspect of chemical composition and structural details of different moieties of EPS in terms of carbohydrates, proteins, extracellular DNA, lipid and surfactants and humic substances are described. These chemical characteristics of EPS in relation to formation and properties of microbial aggregates as well as degradation of EPS in the matrix (biomass, flocs etc) are analyzed. The important engineering properties (based on structural characteristics) such as adsorption, biodegradability, hydrophilicity/hydrophobicity of EPS matrix are also discussed in details. Different aspects of EPS production process such as bacterial strain maintenance; inoculum and factors affecting EPS production were presented. The important factors affecting EPS production include growth phase, carbon and nitrogen sources and their ratio, role of other nutrients (phosphorus, micronutrients/trace elements, and vitamins), impact of pH, temperature, metals, aerobic versus anaerobic conditions and pure and mixed culture. The production of EPS in high concentration with high productivity is essential due to economic reasons. Therefore, the knowledge about all the aspects of EPS production (listed above) is highly

  7. Environmental effects and individual body condition drive seasonal fecundity of rabbits: identifying acute and lagged processes.

    PubMed

    Wells, Konstans; O'Hara, Robert B; Cooke, Brian D; Mutze, Greg J; Prowse, Thomas A A; Fordham, Damien A

    2016-07-01

    The reproduction of many species is determined by seasonally-driven resource supply. But it is difficult to quantify whether the fecundity is sensitive to short- or long-term exposure to environmental conditions such as rainfall that drive resource supply. Using 25 years of data on individual fecundity of European female rabbits, Oryctolagus cuniculus, from semiarid Australia, we investigate the role of individual body condition, rainfall and temperature as drivers of seasonal and long-term and population-level changes in fecundity (breeding probability, ovulation rate, embryo survival). We built distributed lag models in a hierarchical Bayesian framework to account for both immediate and time-lagged effects of climate and other environmental drivers, and possible shifts in reproduction over consecutive seasons. We show that rainfall during summer, when rabbits typically breed only rarely, increased breeding probability immediately and with time lags of up to 10 weeks. However, an earlier onset of the yearly breeding period did not result in more overall reproductive output. Better body condition was associated with an earlier onset of breeding and higher embryo survival. Breeding probability in the main breeding season declined with increased breeding activity in the preceding season and only individuals in good body condition were able to breed late in the season. Higher temperatures reduce breeding success across seasons. We conclude that a better understanding of seasonal dynamics and plasticity (and their interplay) in reproduction will provide crucial insights into how lagomorphs are likely to respond and potentially adapt to the influence of future climate and other environmental change. PMID:27028444

  8. Using high frequency consumption data to identify demand response potential for solar energy integration

    NASA Astrophysics Data System (ADS)

    Jin, L.; Borgeson, S.; Fredman, D.; Hans, L.; Spurlock, A.; Todd, A.

    2015-12-01

    California's renewable portfolio standard (2012) requires the state to get 33% of its electricity from renewable sources by 2020. Increased share of variable renewable sources such as solar and wind in the California electricity system may require more grid flexibility to insure reliable power services. Such grid flexibility can be potentially provided by changes in end use electricity consumptions in response to grid conditions (demand-response). In the solar case, residential consumption in the late afternoon can be used as reserve capacity to balance the drop in solar generation. This study presents our initial attempt to identify, from a behavior perspective, residential demand response potentials in relation to solar ramp events using a data-driven approach. Based on hourly residential energy consumption data, we derive representative daily load shapes focusing on discretionary consumption with an innovative clustering analysis technique. We aggregate the representative load shapes into behavior groups in terms of the timing and rhythm of energy use in the context of solar ramp events. Households of different behavior groups that are active during hours with high solar ramp rates are identified for capturing demand response potential. Insights into the nature and predictability of response to demand-response programs are provided.

  9. High-Throughput Yeast-Based Reporter Assay to Identify Compounds with Anti-inflammatory Potential.

    PubMed

    Garcia, G; Santos, C Nunes do; Menezes, R

    2016-01-01

    The association between altered proteostasis and inflammatory responses has been increasingly recognized, therefore the identification and characterization of novel compounds with anti-inflammatory potential will certainly have a great impact in the therapeutics of protein-misfolding diseases such as degenerative disorders. Although cell-based screens are powerful approaches to identify potential therapeutic compounds, establishing robust inflammation models amenable to high-throughput screening remains a challenge. To bridge this gap, we have exploited the use of yeasts as a platform to identify lead compounds with anti-inflammatory properties. The yeast cell model described here relies on the high-degree homology between mammalian and yeast Ca(2+)/calcineurin pathways converging into the activation of NFAT and Crz1 orthologous proteins, respectively. It consists of a recombinant yeast strain encoding the lacZ gene under the control of Crz1-recongition elements to facilitate the identification of compounds interfering with Crz1 activation through the easy monitoring of β-galactosidase activity. Here, we describe in detail a protocol optimized for high-throughput screening of compounds with potential anti-inflammatory activity as well as a protocol to validate the positive hits using an alternative β-galactosidase substrate. PMID:27613055

  10. 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.

  11. 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

  12. Calculations supporting evaluation of potential environmental standards for Yucca Mountain

    SciTech Connect

    Duguid, J.O.; Andrews, R.W.; Brandstetter, E.; Dale, T.F.; Reeves, M.

    1994-04-01

    The Energy Policy Act of 1992, Section 801 (US Congress, 1992) provides for the US Environmental Protection Agency (EPA) to contract the National Academy of Sciences (NAS) to conduct a study and provide findings and recommendations on reasonable standards for the disposal of high-level wastes at the Yucca Mountain site. The NAS study is to provide findings and recommendations which include, among other things, whether a health-based standard based on dose to individual members of the public from releases to the accessible environment will provide a reasonable standard for the protection of the health and safety of the public. The EPA, based upon and consistent with the findings and recommendations of the NAS, is required to promulgate standards for protection of the public from releases from radioactive materials stored or disposed of in a repository at the Yucca Mountain site. This document presents a number of different ``simple`` analyses of undisturbed repository performance that are intended to provide input to those responsible for setting appropriate environmental standards for a potential repository at the Yucca Mountain site in Nevada. Each of the processes included in the analyses has been simplified to capture the primary significance of that process in containing or isolating the waste from the biosphere. In these simplified analyses, the complex waste package interactions were approximated by a simple waste package ``failure`` distribution which is defined by the initiation and rate of waste package ``failures``. Similarly, releases from the waste package and the engineered barrier system are controlled by the very near field environment and the presence and rate of advective and diffusive release processes. Release was approximated by either a simple alteration-controlled release for the high solubility radionuclides and either a diffusive or advective-controlled release for the solubility-limited radionuclides.

  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. 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.

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

    PubMed

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

    2015-08-01

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

  16. 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

  17. A simple contact mapping algorithm for identifying potential peptide mimetics in protein–protein 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; 82:2253–2262. © 2014 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc. PMID:24756879

  18. Cytotoxicity Potential and Genotypic Characterization of Escherichia coli Isolates from Environmental and Food Sources

    PubMed Central

    Maldonado, Yadilka; Fiser, Jennifer C.; Nakatsu, Cindy H.; Bhunia, Arun K.

    2005-01-01

    The presence of Escherichia coli isolates in the environment is a potential source of contamination of food and water supplies. Moreover, these isolates may harbor virulence genes that can be a source of new forms of pathogenic strains. Here, using multiplex PCR, we examined the presence of virulence gene markers (stx1, stx2, eaeA, hlyA) in 1,698 environmental isolates of E. coli and 81 isolates from food and clinical sources. The PCR analysis showed that ∼5% (79 of 1,698) of the total environmental isolates and 96% (79 of 81) of the food and clinical isolates were positive for at least one of the genes. Of the food and clinical isolates, 84% (68 of 81 isolates) were positive for all four genes. Of the subset of environmental isolates chosen for further analysis, 16% (13 of 79 isolates) were positive for stx2 and 84% (66 of 79 isolates) were positive for eaeA; 16 of the latter strains were also positive for hlyA. The pathogenic potentials of 174 isolates (81 isolates from food and clinical sources and 93 isolates from environmental sources) were tested by using a cytotoxicity assay based on lactate dehydrogenase release from Vero cells. In general, 97% (79 of 81) of the food and clinical isolates and 41% (39 of 93) of the environmental isolates exhibited positive cytotoxicity. High cytotoxicity values correlated to the presence of stx genes. The majority of hly-positive but stx-negative environmental isolates also exhibited a certain degree of cytotoxicity. Isolates were also tested for sorbitol utilization and were genotyped by ribotyping and by repetitive extragenic palindromic PCR (REP-PCR) as potential means of quickly identifying virulent strains from the environment, but none of these methods could be used to distinguish cytotoxic environmental isolates. Only 31% of the isolates were negative for sorbitol fermentation, and none of the isolates had common ribotypes or REP-PCR fingerprints. This study suggests that overall higher cytotoxicity values

  19. 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 Tox

  20. GIS-based decision support system for identifying potential sites for rainwater harvesting

    NASA Astrophysics Data System (ADS)

    Mbilinyi, B. P.; Tumbo, S. D.; Mahoo, H. F.; Mkiramwinyi, F. O.

    Identification of potential sites for rainwater harvesting (RWH) is an important step towards maximizing water availability and land productivity in the semi-arid areas. However, selection of appropriate sites for different RWH technologies on a large scale presents a great challenge, since the necessary biophysical data and infrastructure are often lacking. This paper presents a geographic information system (GIS)-based decision support system (DSS) that uses remote sensing (RS), limited field survey to identify potential sites for RWH technologies. The input into the DSS include maps of rainfall, slope, soil texture, soil depth, drainage and land use/cover and the outputs are maps showing potential sites of water storage systems (ndiva), stone terraces, bench terraces and borders. The Model Builder in the Arc View GIS was used as a platform for the DSS. Two sites in the Makanya watershed, in Kilimanjaro Region, Tanzania, were used for testing and validation of the DSS. The results reflect specific suitability levels of parameters and weight of factors; for example, near streams (drainage) with slope ranges from moderately steep to steep (10°-30°) are potential sites for ndiva locations whereas moderately undulating to steep slopes (5°-30°) with unstable soils are potential sites for stone terraces. Moderately undulating slopes (5°-10°) with clay, silt clay and sandy clay soils are potential sites for bench terrace and gently undulating slopes (2°-5°) with clay, silt clay and sandy clay soils are potential sites for borders. The results from testing and validation of the developed DSS indicated that the tool can be used reliably to predict potential sites for RWH technologies in semi-arid areas. Most of predicted RWH technologies during testing were found within very highly and highly suitable locations (41.4% and 40%, respectively) also in validation 36.9% of RWH technologies were found within the moderately suitable followed by very highly suitable and

  1. Hot spot analysis applied to identify ecosystem services potential in Lithuania

    NASA Astrophysics Data System (ADS)

    Pereira, Paulo; Depellegrin, Daniel; Misiune, Ieva

    2016-04-01

    Hot spot analysis are very useful to identify areas with similar characteristics. This is important for a sustainable use of the territory, since we can identify areas that need to be protected, or restored. This is a great advantage in terms of land use planning and management, since we can allocate resources, reduce the economical costs and do a better intervention in the landscape. Ecosystem services (ES) are different according land use. Since landscape is very heterogeneous, it is of major importance understand their spatial pattern and where are located the areas that provide better ES and the others that provide less services. The objective of this work is to use hot-spot analysis to identify areas with the most valuable ES in Lithuania. CORINE land-cover (CLC) of 2006 was used as the main spatial information. This classification uses a grid of 100 m resolution and extracted a total of 31 land use types. ES ranking was carried out based on expert knowledge. They were asked to evaluate the ES potential of each different CLC from 0 (no potential) to 5 (very high potential). Hot spot analysis were evaluated using the Getis-ord test, which identifies cluster analysis available in ArcGIS toolbox. This tool identifies areas with significantly high low values and significant high values at a p level of 0.05. In this work we used hot spot analysis to assess the distribution of providing, regulating cultural and total (sum of the previous 3) ES. The Z value calculated from Getis-ord was used to statistical analysis to access the clusters of providing, regulating cultural and total ES. ES with high Z value show that they have a high number of cluster areas with high potential of ES. The results showed that the Z-score was significantly different among services (Kruskal Wallis ANOVA =834. 607, p<0.001). The Z score of providing services (0.096±2.239) were significantly higher than the total (0.093±2.045), cultural (0.080±1.979) and regulating (0.076±1.961). These

  2. Developments in the EPA Computational Toxicology Program to Identify Environmental Endocrine Disruptors ( Environmental Endocrine Disruptors Gordon Conference)

    EPA Science Inventory

    Presentation at the Environmental Endocrine Disruptors Gordon Conference in Newry, ME June 22, 2016 to give an overview of the use of high throughput screening and high throughput toxicokinetics to build models for endocrine disruption by environmental chemicals for estrogen rece...

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

    PubMed Central

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

    2015-01-01

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

  4. Identifying the decision to be supported: a review of papers from environmental modelling and software

    USGS Publications Warehouse

    Sojda, Richard S.; Chen, Serena H.; El Sawah, Sondoss; Guillaume, Joseph H.A.; Jakeman, A.J.; Lautenbach, Sven; McIntosh, Brian S.; Rizzoli, A.E.; Seppelt, Ralf; Struss, Peter; Voinov, Alexey; Volk, Martin

    2012-01-01

    Two of the basic tenets of decision support system efforts are to help identify and structure the decisions to be supported, and to then provide analysis in how those decisions might be best made. One example from wetland management would be that wildlife biologists must decide when to draw down water levels to optimise aquatic invertebrates as food for breeding ducks. Once such a decision is identified, a system or tool to help them make that decision in the face of current and projected climate conditions could be developed. We examined a random sample of 100 papers published from 2001-2011 in Environmental Modelling and Software that used the phrase “decision support system” or “decision support tool”, and which are characteristic of different sectors. In our review, 41% of the systems and tools related to the water resources sector, 34% were related to agriculture, and 22% to the conservation of fish, wildlife, and protected area management. Only 60% of the papers were deemed to be reporting on DSS. This was based on the papers reviewed not having directly identified a specific decision to be supported. We also report on the techniques that were used to identify the decisions, such as formal survey, focus group, expert opinion, or sole judgment of the author(s). The primary underlying modelling system, e.g., expert system, agent based model, Bayesian belief network, geographical information system (GIS), and the like was categorised next. Finally, since decision support typically should target some aspect of unstructured decisions, we subjectively determined to what degree this was the case. In only 23% of the papers reviewed, did the system appear to tackle unstructured decisions. This knowledge should be useful in helping workers in the field develop more effective systems and tools, especially by being exposed to the approaches in different, but related, disciplines. We propose that a standard blueprint for reporting on DSS be developed for

  5. Residential energy use in Mexico: Structure, evolution, environmental impacts, and savings potential

    SciTech Connect

    Masera, O.; Friedmann, R.; deBuen, O.

    1993-05-01

    This article examines the characteristics of residential energy use in Mexico, its environmental impacts, and the savings potential of the major end-uses. The main options and barriers to increase the efficiency of energy use are discussed. The energy analysis is based on a disaggregation of residential energy use by end-uses. The dynamics of the evolution of the residential energy sector during the past 20 years are also addressed when the information is available. Major areas for research and for innovative decision-making are identified and prioritized.

  6. 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

  7. 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.

  8. A New Bayesian Method to Identify the Environmental Factors That Influence Recent Migration

    PubMed Central

    Faubet, Pierre; Gaggiotti, Oscar E.

    2008-01-01

    We present a new multilocus genotype method that makes inferences about recent immigration rates and identifies the environmental factors that are more likely to explain observed gene flow patterns. It also estimates population-specific inbreeding coefficients, allele frequencies, and local population FST's and performs individual assignments. We generate synthetic data sets to determine the region of the parameter space where our method is and is not able to provide accurate estimates. Our simulation study indicates that reliable results can be obtained when the global level of genetic differentiation (FST) is >1%, the number of loci is only 10, and sample sizes are of the order of 50 individuals per population. We illustrate our method by applying it to Pakistani human data, considering altitude and geographic distance as explanatory factors. Our results suggest that altitude explains better the genetic data than geographic distance. Additionally, they show that southern low-altitude populations have higher migration rates than northern high-altitude ones. PMID:18245344

  9. Identifying and managing adverse environmental health effects: 2. Outdoor air pollution.

    PubMed

    Abelsohn, Alan; Stieb, David; Sanborn, Margaret D; Weir, Erica

    2002-04-30

    Air pollution contributes to preventable illness and death. Subgroups of patients who appear to be more sensitive to the effects of air pollution include young children, the elderly and people with existing chronic cardiac and respiratory disease such as chronic obstructive pulmonary disease and asthma. It is unclear whether air pollution contributes to the development of asthma, but it does trigger asthma episodes. Physicians are in a position to identify patients at particular risk of health effects from air pollution exposure and to suggest timely and appropriate actions that these patients can take to protect themselves. A simple tool that uses the CH2OPD2 mnemonic (Community, Home, Hobbies, Occupation, Personal habits, Diet and Drugs) can help physicians take patients' environmental exposure histories to assess those who may be at risk. As public health advocates, physicians contribute to the primary prevention of illness and death related to air pollution in the population. In this article we review the origins of air pollutants, the pathophysiology of health effects, the burden of illness and the clinical implications of smog exposure using the illustrative case of an adolescent patient with asthma. PMID:12000251

  10. 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.

  11. Manure-borne estrogens as potential environmental contaminants: a review.

    PubMed

    Hanselman, Travis A; Graetz, Donald A; Wilkie, Ann C

    2003-12-15

    Livestock wastes are potential sources of endocrine disrupting compounds to the environment. Steroidal estrogen hormones such as estradiol, estrone, and estriol are a particular concern because there is evidence that low nanogram per liter concentrations of estrogens in water can adversely affect the reproductive biology of fish and other aquatic vertebrate species. We performed a literature review to assess the current state of science regarding estrogen physicochemical properties, livestock excretion, and the fate of manure-borne estrogens in the environment. Unconjugated steroidal estrogens have low solubility in water (0.8-13.3 mg L(-1)) and are moderately hydrophobic (log Kow 2.6-4.0). Cattle excrete mostly 17alpha-estradiol, 17beta-estradiol, estrone, and respective sulfated and glucuronidated counterparts, whereas swine and poultry excrete mostly 17beta-estradiol, estrone, estriol, and respective sulfated and glucuronidated counterparts. The environmental fate of estrogens is not clearly known. Laboratory-based studies have found that the biological activity of these compounds is greatly reduced or eliminated within several hours to days due to degradation and sorption. On the other hand, field studies have demonstrated that estrogens are sufficiently mobile and persistent to impact surface and groundwater quality. Future research should use standardized methods for the analysis of manure, soil, and water. More information is needed about the types and amounts of estrogens that exist in livestock wastes and the fate of manure-borne estrogens applied to agricultural lands. Field and laboratory studies should work toward revealing the mechanisms of estrogen degradation, sorption, and transport so that the risk of estrogen contamination of waterways can be minimized. PMID:14717153

  12. 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.

  13. Utilization of intrinsic boron isotopes as co-migrating tracers for identifying potential nitrate contamination sources

    SciTech Connect

    Leenhouts, J.M.; Bassett, R.L.; Maddock, T. III

    1998-03-01

    The stable isotopes of the conservative element boron, {sup 11}B and {sup 10}B, have been employed as co-migrating isotopic tracers to trace potential sources of nitrate observed in ground water pumped from a large capacity 0.167 m{sup 3}/s irrigation well in the Avra Valley of southeastern Arizona. The isotopic ratios provided an identifying signature for two nitrogen carrying source waters: municipal waste water and agricultural return flow. Additional chemical parameters were also examined to corroborate the isotopic indications. Boron isotopes provided a superior delineation of mixing processes in the system compared to the general inorganic chemical parameters. Findings of this investigation indicate that the water pumped by the study well at the beginning of the 1993 irrigation season was composed of a mixture of approximately 25% municipal waste water and 75% background ground water. As the irrigation season progressed, an increasing proportion of water was contributed by irrigation return flow from neighboring agricultural fields.

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

    PubMed Central

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

    2012-01-01

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

  15. 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

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

    PubMed

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

    2016-10-01

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

  17. OIL SHALE: POTENTIAL ENVIRONMENTAL IMPACTS AND CONTROL TECHNOLOGY

    EPA Science Inventory

    The U. S. Environmental Protection Agency's Industrial Environmental Research Laboratory in Cincinnati, Ohio (IERL-Ci) has performed research related to oil shale processing and disposal since 1973. This research is in support of the Clean Air Act, The Federal Water Pollution Con...

  18. Environmental stressors during space flight: potential effects on body temperature

    NASA Technical Reports Server (NTRS)

    Jauchem, J. R.

    1988-01-01

    1. Organisms may be affected by many environmental factors during space flight, e.g., acceleration, weightlessness, decreased pressure, changes in oxygen tension, radiofrequency radiation and vibration. 2. Previous studies of change in body temperature--one response to these environmental factors--are reviewed. 3. Conditions leading to heat stress and hypothermia are discussed.

  19. Potential Perils of Changing Environmental Context on Examination Scores

    ERIC Educational Resources Information Center

    Van Der Wege, Mija; Barry, Leslie A.

    2008-01-01

    Environmental context can affect memory retrieval in a wide range of situations. The authors investigate the relationship between the location of a collegiate final examination and student performance. Although several other studies have looked at the impact of environmental context on test taking, this study does so in a real-world environment,…

  20. Patient Safety Indicators: using administrative data to identify potential patient safety concerns.

    PubMed Central

    Miller, M R; Elixhauser, A; Zhan, C; Meyer, G S

    2001-01-01

    OBJECTIVE: To develop Patient Safety Indicators (PSI) to identify potential in-hospital patient safety problems for the purpose of quality improvement. DATA SOURCE/STUDY DESIGN: The data source was 2,400,000 discharge records in the 1997 New York State Inpatient Database. PSI algorithms were developed using systematic literature reviews of indicators and hand searches of the ICD-9-CM code book. The prevalence of PSI events and associations between PSI events and patient-level and hospital-level characteristics, length of stay, in-hospital mortality, and hospital charges were examined. PRINCIPAL FINDINGS: PSIs were developed for 12 distinct clinical situations and an overall summary measure. The 1997 event rates per 10,000 discharges varied from 1.1 for foreign bodies left during procedure to 84.7 for birth traumas. Discharge records with PSI events had twofold to threefold longer hospital stays, twofold to 20-fold higher rates of in-hospital mortality, and twofold to eightfold higher total charges than records without PSI events. Multivariate logistic regression revealed that PSI events were primarily associated with increasing age (p < .001), hospitals performing more inpatient surgery (p < .001), and hospitals with higher percentage of beds in intensive care units (p < .001). CONCLUSIONS: The PSIs provide an efficient and user-friendly tool to identify potential inhospital patient safety problems for targeted institution-level quality improvement efforts. Until better error-reporting systems are developed the PSIs can serve to shed light on the problem of medical errors not limited solely to mortality because of errors. PMID:16148964

  1. Potential of zerovalent iron nanoparticles for remediation of environmental organic contaminants in water: a review.

    PubMed

    Raychoudhury, Trishikhi; Scheytt, Traugott

    2013-01-01

    Zerovalent iron (ZVI) has the potential to degrade different organic contaminants. Nanoscale zerovalent iron (NZVI) can reduce the contaminants even more rapidly due to its small size and large specific surface area (SSA), compared to granular ZVI. The main objective of this paper is to assess and compare the potential of NZVI for degradation of different contaminants in water under specific environmental conditions. As a first step, the potential reactive functional groups/bonds associated with different contaminants are identified and possible reaction mechanisms are discussed. Thereafter, the reaction efficiencies of different organic contaminants with NZVI are compared. Mass of ZVI and reaction time required to transform a certain amount of contaminated water are calculated based on literature data. Sources of contaminants in the environment and their environmental occurrences are discussed to understand the potential locations where NZVI could be applied for removal of different contaminants. Overall it is observed that azo-compounds are readily transformed in the presence of NZVI particles. Reaction efficiencies of ZVI for reduction of nitro-organic compounds are also reasonably high. However, halogenated compounds with high molecular weights or complex structures (i.e., iodinated contrast media, DDT, polychlorinated biphenyls, etc.) show lower reaction rates with NZVI compared to the widely studied chlorinated hydrocarbons (i.e., trichloroethylene). PMID:24135090

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

    PubMed

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

    2016-04-21

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

  3. 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.

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

    PubMed

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

    2012-08-01

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

  5. A feasibility study on the influence of the geomorphological feature in identifying the potential landslide hazard

    NASA Astrophysics Data System (ADS)

    Baek, M. H.; Kim, T. H.

    2014-11-01

    In this study we focused on identifying geomorphological features that control the location of landslides. The representation of these features is based on a high resolution DEM (Digital Elevation Model) derived from airborne laser altimetry (LiDAR) and evaluated by statistical analysis of axial orientation data. The main principle of this analysis is generating eigenvalues from axial orientation data and comparing them. The Planarity, a ratio of eigenvalues, would tell the degree of roughness on ground surface based on their ratios. Results are compared to the recent landslide case in Korea in order to evaluate the feasibility of the proposed methodology in identifying the potential landslide hazard. The preliminary landslide assessment based on the Planarity analysis well discriminates features between stable and unstable domain in the study area especially in the landslide initiation zones. Results also show it is beneficial to build the preliminary landslide hazard especially inventory mapping where none of information on historical records of landslides is existed. By combining other physical procedures such as geotechnical monitoring, the landslide hazard assessment using geomorphological features will promise a better understanding of landslides and their mechanisms, and provide an enhanced methodology to evaluate their hazards and appropriate actions.

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

    PubMed

    Bisset, L R; Fierz, W

    1993-03-01

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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. Microarray Analysis of Transcriptome of Medulla Identifies Potential Biomarkers for Parkinson's Disease

    PubMed Central

    Liao, Xiao-Yang; Yang, Zheng-Hui; Wang, Jun; Lin, Hang; Wang, Qing-Song; Wu, Yu-Xian; Liu, Yu

    2013-01-01

    To complement the molecular pathways contributing to Parkinson's disease (PD) and identify potential biomarkers, gene expression profiles of two regions of the medulla were compared between PD patients and control. GSE19587 containing two groups of gene expression profiles [6 dorsal motor nucleus of the vagus (DMNV) samples from PD patients and 5 from controls, 6 inferior olivary nucleus (ION) samples from PD patients and 5 from controls] was downloaded from Gene Expression Omnibus. As a result, a total of 1569 and 1647 differentially expressed genes (DEGs) were, respectively, screened in DMNV and ION with limma package of R. The functional enrichment analysis by DAVID server (the Database for Annotation, Visualization and Integrated Discovery) indicated that the above DEGs may be involved in the following processes, such as regulation of cell proliferation, positive regulation of macromolecule metabolic process, and regulation of apoptosis. Further analysis showed that there were 365 common DEGs presented in both regions (DMNV and ION), which may be further regulated by eight clusters of microRNAs retrieved with WebGestalt. The genes in the common DEGs-miRNAs regulatory network were enriched in regulation of apoptosis process via DAVID analysis. These findings could not only advance the understandings about the pathogenesis of PD, but also suggest potential biomarkers for this disease. PMID:24350239

  12. POTENTIAL ENVIRONMENTAL IMPACT OF COMPOUNDING AND FABRICATING INDUSTRIES: A PRELIMINARY ASSESSMENT

    EPA Science Inventory

    The overall objectives of this research effort were to identify compounding and fabricating industries from a selected number of Standard Industrial Classification codes, and identify the environmental impact resulting from processing steps used by fabrication or compounding indu...

  13. 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

  14. Permafrost as palaeo-environmental archive - potentials and limitations

    NASA Astrophysics Data System (ADS)

    Schirrmeister, L.; Wetterich, S.; Meyer, H.; Grosse, G.; Schwamborn, G.; Siegert, C.

    2009-04-01

    temperatures, mean winter temperatures, mean Juli temperatures, precipitation, humidity, soil climate and chemistry, hydrology and hydrochemistry of waters). The general potential of permafrost archives includes spatial (circumarctic, high arctic to boreal zones) and temporal (Mid Pleistocene to modern) environmental gradients. Lateral cross sections contain information about permafrost degradation during interglacial periods, the aggradation of ice-rich sequences during stadial and interstadial periods, and extreme changes in periglacial hydrology during the late Quaternary. The spatial reconstruction of ancient landscapes is possible by detailed study of kilometer-long coastal exposures. Temporally relative high resolution (about 50 years) isotope data from ice wedges reflect the Late Pleistocene to Holocene climate transition. Using transfer functions for pollen, plant macro remains or chironomids, the numerical estimation of palaeo-climate data (temperature and precipitation) is possible. The limitations of permafrost archives are the frequent lack of continuous sequences due to thermokarst or thermo-erosion events. Local stratigraphies are sometimes difficult to correlate on a regional scale because of permafrost degradation and neotectonic influence on the accumulative/erosive environment in some regions. Until now there are still uncertainties for comparing different geochronological methods, some of them related to unknown influences of permafrost processes on chemical and physical parameters important to the age determination technique. Due to strong cryoturbation patterns and sometimes challenging sampling situations on near-vertical frozen exposures the geochronological resolution in permafrost sequences is usually lower than in lacustrine sequences or glacial ice cores. Eventually, as for any other archive, we need to consider the effect of local versus regional signals derived from the palaeo-ecological interpretation of fossil records.

  15. MicroRNAs as Potential Signatures of Environmental Exposure or Effect: A Systematic Review

    PubMed Central

    Vrijens, Karen; Bollati, Valentina

    2015-01-01

    Background: The exposome encompasses all life-course environmental exposures from the prenatal period onward that influence health. MicroRNAs (miRNAs) are interesting entities within this concept as markers and causation of disease. MicroRNAs are short oligonucleotide sequences that can interact with several mRNA targets. Objectives: We reviewed the current state of the field on the potential of using miRNAs as biomarkers for environmental exposure. We investigated miRNA signatures in response to all types of environmental exposure to which a human can be exposed, including cigarette smoke, air pollution, nanoparticles, and diverse chemicals; and we examined the health conditions for which the identified miRNAs have been reported (i.e., cardiovascular disease, cancer, and diabetes). Methods: We searched the PubMed and ScienceDirect databases to identify relevant studies. Results: For all exposures incorporated in this review, 27 miRNAs were differentially expressed in at least two independent studies. miRNAs that had expression alterations associated with smoking observed in multiple studies are miR-21, miR-34b, miR-125b, miR-146a, miR-223, and miR-340; and those miRNAs that were observed in multiple air pollution studies are miR-9, miR-10b, miR-21, miR-128, miR-143, miR-155, miR-222, miR-223, and miR-338. We found little overlap among in vitro, in vivo, and human studies between miRNAs and exposure. Here, we report on disease associations for those miRNAs identified in multiple studies on exposure. Conclusions: miRNA changes may be sensitive indicators of the effects of acute and chronic environmental exposure. Therefore, miRNAs are valuable novel biomarkers for exposure. Further studies should elucidate the role of the mediation effect of miRNA between exposures and effect through all stages of life to provide a more accurate assessment of the consequences of miRNA changes. Citation: Vrijens K, Bollati V, Nawrot TS. 2015. MicroRNAs as potential signatures of

  16. Using a Physical Education Environmental Survey to Identify Areas of Concern and Improve Conditions

    ERIC Educational Resources Information Center

    Hill, Grant; Hulbert, George

    2007-01-01

    School environmental conditions can impact learning in physical educational classes. It is important for schools to control environmental health hazards, not only to promote a conducive school learning environment, but to also reduce associated health risks. To help physical education leaders determine the quality of physical education facilities…

  17. Identifying the dominant metabolic strategies used by microorganisms within basalt-hosted, anoxic deep subsurface basement fluids via environmental genomics

    NASA Astrophysics Data System (ADS)

    Rappe, M. S.; Jungbluth, S.; Carr, S. A.; Lin, H. T.; Hsieh, C. C.; Nigro, O. D.; Steward, G. F.; Orcutt, B.

    2014-12-01

    A microbial ecosystem distinct from both overlying sediments and bottom seawater lies within the basaltic crust of the Juan de Fuca Ridge flank. The metabolic potential and genomic characteristics of microbes residing in fluids of this remote, anoxic region of the subsurface ocean were investigated using environmental DNA extracted from large-volume fluid samples obtained from advanced borehole observatories installed at two recently drilled IODP Boreholes, U1362A and U1362B. Fluids were collected from the deep (204 meters sub-basement) horizon of Borehole U1362A and shallow (40 meters sub-basement) horizon of Borehole U1362B and used to generate 503 and 705 million base-pairs of genomic DNA sequence data, respectively. Phylogenetically informative genes revealed that the community structure recovered via metagenomics was generally consistent with that obtained previously by 16S rRNA gene sequencing and was dominated by uncultivated bacterial lineages of Proteobacteria, Nitrospirae, Candidate Division OP8 (Aminicenantes), Thermotoga and archaeal groups THSCG, MCG (Bathyarchaeota), MBGE, and Archaeoglobus. Genes involved in phage integration, chemotaxis, nitrate reduction, methanogenesis, and amino acid degradation were all detected, revealing potentially dynamic microbial communities. Putative sulfate reduction genes were discovered within previously identified Firmicutes lineage Candidatus Desulforudis, along with other groups (e.g. Archaeoglobus). Significant metagenome assembly resulted in 72 and 105 contigs of >100 Kbp from U1362B and U1362A, respectively, including 1137, 977 and 356 Kbp-long contigs from Candidate Division OP8 residing in U1362B. These assemblies have revealed novel metabolic potential within abundant members of the deep subsurface microbial community, which can be directly related to their survival in the deep oceanic crust.

  18. Visual Indicators on Vaccine Boxes as Early Warning Tools to Identify Potential Freeze Damage

    PubMed Central

    Angoff, Ronald; Wood, Jillian; Chernock, Maria C.; Tipping, Diane

    2015-01-01

    Background The aim of this study was to determine whether the use of visual freeze indicators on vaccines would assist health care providers in identifying vaccines that may have been exposed to potentially damaging temperatures. Methods Twenty-seven sites in Connecticut involved in the Vaccine for Children Program participated. In addition to standard procedures, visual freeze indicators (FREEZEmarker® L; Temptime Corporation, Morris Plains, NJ) were affixed to each box of vaccine that required refrigeration but must not be frozen. Temperatures were monitored twice daily. Results During the 24 weeks, all 27 sites experienced triggered visual freeze indicator events in 40 of the 45 refrigerators. A total of 66 triggered freeze indicator events occurred in all 4 types of refrigerators used. Only 1 of the freeze events was identified by a temperature-monitoring device. Temperatures recorded on vaccine data logs before freeze indicator events were within the 35°F to 46°F (2°C to 8°C) range in all but 1 instance. A total of 46,954 doses of freeze-sensitive vaccine were stored at the time of a visual freeze indicator event. Triggered visual freeze indicators were found on boxes containing 6566 doses (14.0% of total doses). Of all doses stored, 14,323 doses (30.5%) were of highly freeze-sensitive vaccine; 1789 of these doses (12.5%) had triggered indicators on the boxes. Conclusions Visual freeze indicators are useful in the early identification of freeze events involving vaccines. Consideration should be given to including these devices as a component of the temperature-monitoring system for vaccines. PMID:27330265

  19. A genetic database can be utilized to identify potential biomarkers for biphenotypic hepatocellular carcinoma-cholangiocarcinoma

    PubMed Central

    Mohan, Sachin; Grewal, Navjot; Elfant, Adam B.; Judge, Thomas A.

    2016-01-01

    Background Biphenotypic hepatocellular carcinoma-cholangiocarcinoma (HCC-CC) is an uncommon primary liver neoplasm. Due to limitations in radiologic imaging for the diagnosis of this condition, biopsy is a common method for diagnosis, which is invasive and holds potential complications. To identify alternative means for obtaining the diagnosis and assessing the prognosis of this condition, we evaluated biomarkers for biphenotypic HCC-CC using a genetic database. Methods To evaluate the genetic associations with each variable we utilized GeneCards®, The Human Gene Compendium (http://www.genecards.org). The results of our search were entered into the Pathway Interaction Database from the National Cancer Institute (PID-NCI) (http://pid.nci.nih.gov), to generate a biomolecule interaction map. Results The results of our query yielded 690 genes for HCC, 98 genes for CC and 50 genes for HCC-CC. Genes depicted in this analysis demonstrate the role of hormonal regulation, embryonic development, cell surface adhesion, cytokeratin stability, mucin production, metalloproteinase regulation, Ras signaling, metabolism and apoptosis. Examples of previously described markers included hepatocyte growth factor (HGF), mesenchymal epithelial transition (MET) and Kirsten rat sarcoma viral oncogene homolog (KRAS). Novel markers included phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA), GPC3, choline kinase alpha (CHKA), prostaglandin-endoperoxide synthase 2 (PTGS2), telomerase reverse transcriptase (TERT), myeloid cell leukemia 1 (MCL1) and N-acetyltransferase 2 (NAT2). Conclusions GeneCards is a useful research tool in the genetic analysis of low frequency malignancies. Utilizing this tool we identified several biomarkers are methods for diagnosing HCC-CC. Finally, utilizing these methods, HCC-CC was found to be predominantly a subtype of CC. PMID:27563447

  20. 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.

  1. A Riemannian geometric mapping technique for identifying incompressible equivalents to subsonic potential flows

    NASA Astrophysics Data System (ADS)

    German, Brian Joseph

    much the same way that general relativity ascribes gravitational forces to the curvature of space-time. Although the analogy with general relativity is fruitful, it is important not to overstate the similarities between compressibility and the physics of gravity, as the interest for this thesis is primarily in the mathematical framework and not physical phenomenology or epistemology. The thesis presents the philosophy and theory for the transformation method followed by a numerical method for practical solutions of equivalent incompressible flows over arbitrary closed profiles. The numerical method employs an iterative approach involving the solution of the equivalent incompressible flow with a panel method, the calculation of the metric tensor for the gauge transformation, and the solution of the curvilinear coordinate mapping to the canonical flow with a finite difference approach for the elliptic boundary value problem. This method is demonstrated for non-circulatory flow over a circular cylinder and both symmetric and lifting flows over a NACA 0012 profile. Results are validated with accepted subcritical full potential test cases available in the literature. For chord-preserving mapping boundary conditions, the results indicate that the equivalent incompressible profiles thicken with Mach number and develop a leading edge droop with increased angle of attack. Two promising areas of potential applicability of the method have been identified. The first is in airfoil inverse design methods leveraging incompressible flow knowledge including heuristics and empirical data for the potential field effects on viscous phenomena such as boundary layer transition and separation. The second is in aerodynamic testing using distorted similarity-scaled models.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-05-01

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

  4. Evaluating the Pathogenic Potential of Environmental Escherichia coli by Using the Caenorhabditis elegans Infection Model

    PubMed Central

    Merkx-Jacques, Alexandra; Coors, Anja; Brousseau, Roland; Masson, Luke; Mazza, Alberto; Tien, Yuan-Ching

    2013-01-01

    The detection and abundance of Escherichia coli in water is used to monitor and mandate the quality of drinking and recreational water. Distinguishing commensal waterborne E. coli isolates from those that cause diarrhea or extraintestinal disease in humans is important for quantifying human health risk. A DNA microarray was used to evaluate the distribution of virulence genes in 148 E. coli environmental isolates from a watershed in eastern Ontario, Canada, and in eight clinical isolates. Their pathogenic potential was evaluated with Caenorhabditis elegans, and the concordance between the bioassay result and the pathotype deduced by genotyping was explored. Isolates identified as potentially pathogenic on the basis of their complement of virulence genes were significantly more likely to be pathogenic to C. elegans than those determined to be potentially nonpathogenic. A number of isolates that were identified as nonpathogenic on the basis of genotyping were pathogenic in the infection assay, suggesting that genotyping did not capture all potentially pathogenic types. The detection of the adhesin-encoding genes sfaD, focA, and focG, which encode adhesins; of iroN2, which encodes a siderophore receptor; of pic, which encodes an autotransporter protein; and of b1432, which encodes a putative transposase, was significantly associated with pathogenicity in the infection assay. Overall, E. coli isolates predicted to be pathogenic on the basis of genotyping were indeed so in the C. elegans infection assay. Furthermore, the detection of C. elegans-infective environmental isolates predicted to be nonpathogenic on the basis of genotyping suggests that there are hitherto-unrecognized virulence factors or combinations thereof that are important in the establishment of infection. PMID:23377948

  5. 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

  6. Identifying Hydrologic Flowpaths on Arctic Hillslopes Using Electrical Resistivity and Self Potential

    NASA Astrophysics Data System (ADS)

    Voytek, E.; Rushlow, C. R.; Godsey, S.; Singha, K.

    2015-12-01

    Shallow subsurface flow is a dominant process controlling hillslope runoff generation, soil development, and solute reaction and transport. Despite their importance, the location and geometry of flowpaths are difficult to determine. In arctic environments, shallow subsurface flowpaths are limited to a thin zone of seasonal thaw above continuous permafrost, which is traditionally assumed to mimic to surface topography. Here we use a combined approach of electrical resistivity imaging (ERI) and self-potential measurements (SP) to map shallow subsurface flowpaths in and around water tracks, drainage features common to arctic hillslopes. ERI measurements delineate thawed zones in the subsurface that control flowpaths, while SP is sensitive to groundwater flow. We find that areas of low electrical resistivity in the water tracks are deeper than manual thaw depth estimates and variations from surface topography. This finding suggests that traditional techniques significantly underestimate active layer thaw and the extent of the flowpath network on arctic hillslopes. SP measurements identify complex 3-D flowpaths in the thawed zone. Our results lay the groundwork for investigations into the seasonal dynamics, hydrologic connectivity, and climate sensitivity of spatially distributed flowpath networks on arctic hillslopes.

  7. Urine metabolomic analysis identifies potential biomarkers and pathogenic pathways in kidney cancer.

    PubMed

    Kim, Kyoungmi; Taylor, Sandra L; Ganti, Sheila; Guo, Lining; Osier, Michael V; Weiss, Robert H

    2011-05-01

    Kidney cancer is the seventh most common cancer in the Western world, its incidence is increasing, and it is frequently metastatic at presentation, at which stage patient survival statistics are grim. In addition, there are no useful biofluid markers for this disease, such that diagnosis is dependent on imaging techniques that are not generally used for screening. In the present study, we use metabolomics techniques to identify metabolites in kidney cancer patients' urine, which appear at different levels (when normalized to account for urine volume and concentration) from the same metabolites in nonkidney cancer patients. We found that quinolinate, 4-hydroxybenzoate, and gentisate are differentially expressed at a false discovery rate of 0.26, and these metabolites are involved in common pathways of specific amino acid and energetic metabolism, consistent with high tumor protein breakdown and utilization, and the Warburg effect. When added to four different (three kidney cancer-derived and one "normal") cell lines, several of the significantly altered metabolites, quinolinate, α-ketoglutarate, and gentisate, showed increased or unchanged cell proliferation that was cell line-dependent. Further evaluation of the global metabolomics analysis, as well as confirmation of the specific potential biomarkers using a larger sample size, will lead to new avenues of kidney cancer diagnosis and therapy. PMID:21348635

  8. 2D-DIGE proteomic analysis identifies new potential therapeutic targets for adrenocortical carcinoma

    PubMed Central

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

    2015-01-01

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

  9. 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.

  10. Correlation Analysis between SNP and Expression Arrays in Gliomas Identify Potentially Relevant Targets Genes1

    PubMed Central

    Kotliarov, Yuri; Kotliarova, Svetlana; Charong, Nurdina; Li, Aiguo; Walling, Jennifer; Aquilanti, Elisa; Ahn, Susie; Steed, Mary Ellen; Su, Qin; Center, Angela; Zenklusen, Jean C; Fine, Howard A.

    2008-01-01

    Primary brain tumors are a major cause of cancer mortality in the United States. Therapy for gliomas, the most common type of primary brain tumors, remains suboptimal. The development of improved therapeutics will require greater knowledge of the biology of gliomas at both the genomic and transcriptional levels. We have previously reported whole genome profiling of chromosome copy number alterations (CNA) in gliomas, and now present our findings on how those changes may affect transcription of genes that may be involved in tumor induction and progression. By calculating correlation values of mRNA expression vs. DNA copy number average in a moving window around a given RNA probeset, biologically relevant information can be gained that is obscured by the analysis of a single data type. Correlation coefficients ranged from −0.6 to 0.7; highly significant when compared to previously studies. Most correlated genes are located on chromosomes 1, 7, 9, 10, 13, 14, 19, 20 and 22, chromosomes known to have genomic alterations in gliomas. Additionally, we were able to identify CNAs whose gene expression correlation suggests possible epigenetic regulation. This analysis revealed a number of interesting candidates such as CXCL12, PTER, LRRN6C, among others. The results have been verified using real-time PCR and methylation sequencing assays. These data will further help differentiate genes involved in the induction and/or maintenance of the tumorigenic process from those that are mere passenger mutations, thereby enriching for a population of potentially new therapeutic molecular targets. PMID:19190341

  11. Global transcriptional responses to cisplatin in Dictyostelium discoideum identify potential drug targets

    PubMed Central

    Van Driessche, Nancy; Alexander, Hannah; Min, Junxia; Kuspa, Adam; Alexander, Stephen; Shaulsky, Gad

    2007-01-01

    Dictyostelium discoideum is a useful model for studying mechanisms of cisplatin drug sensitivity. Our previous findings, that mutations in sphingolipid metabolism genes confer cisplatin resistance in D. discoideum and in human cells, raised interest in the resistance mechanisms and their implications for cisplatin chemotherapy. Here we used expression microarrays to monitor physiological changes and to identify pathways that are affected by cisplatin treatment of D. discoideum. We found >400 genes whose regulation was altered by cisplatin treatment of wild-type cells, including groups of genes that participate in cell proliferation and in nucleotide and protein metabolism, showing that the cisplatin response is orderly and multifaceted. Transcriptional profiling of two isogenic cisplatin-resistant mutants, impaired in different sphingolipid metabolism steps, showed that the effect of cisplatin treatment was greater than the effect of the mutations, indicating that cisplatin resistance in the mutants is due to specific abilities to overcome the drug effects rather than to general drug insensitivity. Nevertheless, the mutants exhibited significantly different responses to cisplatin compared with the parent, and >200 genes accounted for that difference. Mutations in five cisplatin response genes (sgkB, csbA, acbA, smlA, and atg8) resulted in altered drug sensitivity, implicating novel pathways in cisplatin response. Our data illustrate how modeling complex cellular responses to drugs in genetically stable and tractable systems can uncover new targets with the potential for improving chemotherapy. PMID:17878305

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

    PubMed Central

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

    2016-01-01

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

  13. Habitable Zone Limits as a Guide to Count, Identify and Characterize Potential Habitable Planets

    NASA Astrophysics Data System (ADS)

    Kopparapu, R.

    2014-04-01

    Identifying terrestrial planets in the habitable zones (HZs) of other stars is one of the primary goals of ongoing exoplanet surveys and proposed space-based flagship missions. I will present our recent results on the new estimates of HZs around Main-sequence stars with Earth and super-Earth planets. According to our new model, a conservative estimate of the inner (moist greenhouse) and outer (maximum greenhouse) HZ limits for our Solar System are at 0.99 AU and 1.67 AU, respectively, and more massive planets (superEarths) have wider HZs. I will also discuss HZ limits from 3D climate models, which point to a sharp shift in the width of the HZs from F to M stars. Applying the new HZ limits to extrasolar planetary systems in NASA's "Kepler" data, we find that potentially habitable planets around M-dwarfs are more common than previously reported, and the frequency of Earth-size planets around G & K stars may be lower (~ 10-15%) than recent estimates (~22%).

  14. 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.

  15. 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

  16. Through Their Lens: The Potential of Photovoice for Documentation of Environmental Perspectives among Kenyan Teachers

    ERIC Educational Resources Information Center

    Quigley, Cassie F.; Dogbey, James; Che, S. Megan; Hallo, Jeffrey; Womac, Patrick

    2014-01-01

    This study explores the potential of photovoice for understanding environmental perspectives of teachers in the Narok District of Kenya. The objective of this paper is to share this photo-methodology with environmental educators so they may use it as an innovative methodological tool to understand the construction of environmental perspectives.…

  17. Identifying Environmental Risk Factors of Cholera in a Coastal Area with Geospatial Technologies

    PubMed Central

    Xu, Min; Cao, Chunxiang; Wang, Duochun; Kan, Biao

    2014-01-01

    Satellites contribute significantly to environmental quality and public health. Environmental factors are important indicators for the prediction of disease outbreaks. This study reveals the environmental factors associated with cholera in Zhejiang, a coastal province of China, using both Remote Sensing (RS) and Geographic information System (GIS). The analysis validated the correlation between the indirect satellite measurements of sea surface temperature (SST), sea surface height (SSH) and ocean chlorophyll concentration (OCC) and the local cholera magnitude based on a ten-year monthly data from the year 1999 to 2008. Cholera magnitude has been strongly affected by the concurrent variables of SST and SSH, while OCC has a one-month time lag effect. A cholera prediction model has been established based on the sea environmental factors. The results of hot spot analysis showed the local cholera magnitude in counties significantly associated with the estuaries and rivers. PMID:25551518

  18. Sediment Toxicity Identification Evaluations (TIEs): Manipulating Bioavailability to Whole Organisms to Identify Environmental Toxins

    EPA Science Inventory

    Toxicity tests are a common method for determining whether sediment contaminants represent an environmental risk. Toxicity tests indicate if contaminants in sediments are bioavailable and capable of causing adverse biological effects to whole aquatic organisms. Several environmen...

  19. Why Study Geoscience? Identifying Effective Recruitment and Retention Strategies for an Undergraduate Earth & Environmental Sciences Program

    NASA Astrophysics Data System (ADS)

    Vajoczki, S.; Eyles, C. H.; Stewart, J.; Dasilva, L.

    2005-12-01

    McMaster University is a `research intensive' university with 17,000+ full time undergraduate students. The School of Geography and Earth Sciences (SGES) is located within the Faculty of Science, offers B.Sc., B.A., M.Sc., M.A. and PhD degree programs and teaches more than 70 undergraduate courses on an annual basis. The Honours B.Sc program in Earth and Environmental Sciences (EES) graduates approximately 25 students per year. Students enroll in undergraduate SGES programs in their second year, after completion of an introductory first year in the Faculty of Science in which they take compulsory science courses including math, physics, chemistry, and biology. First year students, as well as those in upper years, may also elect to take one or more of three introductory courses offered by SGES (Earth & the Environment, The Living Environment, Atmosphere & Hydrosphere) to complete their science requirements. Most students entering the Faculty of Science know little about geoscience as it does not form an important part of the Ontario secondary school curriculum. Hence, recruitment into the EES program is primarily via the first year courses. In order to establish reasons why students elected to take the introductory courses offered by SGES, and their reasons for considering subsequent entry to the B.Sc program, a survey of students taking one of the courses was conducted in the fall of 2003. Results from the survey indicate that students enroll in the course, and subsequently the EES program, for a variety of reasons including: general interest in how the planet works, concern for the environment, interesting title of the course and reputation of the instructor. Student concern over lack of potential jobs is cited as the main reason for not pursuing a degree in geoscience. This survey has helped to direct the multifaceted recruitment strategies used by SGES to continue to develop its undergraduate program through delivery of high quality first year courses

  20. Education in Environmental Remote Sensing: Potentials and Problems.

    ERIC Educational Resources Information Center

    Kiefer, Ralph W.; Lillesand, Thomas M.

    1983-01-01

    Discusses remote sensing principles and applications and the status and needs of remote sensing education in the United States. A summary of the fundamental policy issues that will determine remote sensing's future role in environmental and resource managements is included. (Author/BC)

  1. Biased Data and Potential Solutions for Health and Environmental Assessments

    EPA Science Inventory

    The utility and credibility of environmental assessments depend on the use of unbiased data. However, it is increasingly clear that, despite peer review, much of the scientific literature is biased. Sources of bias may include publication practices, research design and implemen...

  2. Evaluating the potential effectiveness of proposed environmental justice initiatives

    SciTech Connect

    Greenfield, N.L.; Namovicz, C.R.

    1994-12-31

    Congress directed the US Environmental Protection Agency (EPA) to create the Technical Assistance Grant (TAG) program to address the concerns of these citizens and, thereby improve community relations at Superfund sites. TAGs provide funding to allow affected residents to hire independent scientific and technical consultants to help them understand the issues at the site and better participate in remedy selection. This study will not directly assess the experience of Environmental Justice sites within the Superfund program. Rather, this study examines existing data on TAGs and the applicability of an expanded TAG program in addressing expressed Environmental Justice concerns. Specifically, the study compares the characteristics of sites with TAGs to a matched control group of sites/communities without TAGs. The study establishes a rigorous statistical baseline upon which it can evaluate the marginal contribution of outreach initiatives to the needs and concerns of minority and low income communities. The results of these analyses will serve as a foundation for evaluating proposed changes in the scope and emphasis of Superfund`s community relations and Environmental Justice outreach programs.

  3. UMEL: A new regression tool to identify measurement peaks in LIDAR/DIAL systems for environmental physics applications

    NASA Astrophysics Data System (ADS)

    Gelfusa, M.; Gaudio, P.; Malizia, A.; Murari, A.; Vega, J.; Richetta, M.; Gonzalez, S.

    2014-06-01

    Recently, surveying large areas in an automatic way, for early detection of both harmful chemical agents and forest fires, has become a strategic objective of defence and public health organisations. The Lidar and Dial techniques are widely recognized as a cost-effective alternative to monitor large portions of the atmosphere. To maximize the effectiveness of the measurements and to guarantee reliable monitoring of large areas, new data analysis techniques are required. In this paper, an original tool, the Universal Multi Event Locator, is applied to the problem of automatically identifying the time location of peaks in Lidar and Dial measurements for environmental physics applications. This analysis technique improves various aspects of the measurements, ranging from the resilience to drift in the laser sources to the increase of the system sensitivity. The method is also fully general, purely software, and can therefore be applied to a large variety of problems without any additional cost. The potential of the proposed technique is exemplified with the help of data of various instruments acquired during several experimental campaigns in the field.

  4. THE USE OF SPATIAL ANALYTICAL TECHNIQUES TO IDENTIFY POTENTIAL BROWNFIELDS SITES

    EPA Science Inventory

    Brownfields are abandoned, idled, or underutilized properties where expansion or redevelopment is complicated by real or perceived environmental contamination. Most Brownfields sites are located in urban, commercial, and industrial areas. Under the Brownfields Program, the United...

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

    PubMed Central

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

    2014-01-01

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

  6. 76 FR 21938 - Potential Environmental Impacts of the Proposed Runway 13 Extension and Associated Actions for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-19

    ... Federal Aviation Administration Potential Environmental Impacts of the Proposed Runway 13 Extension and... Administration (FAA), Department of Transportation (DOT). ACTION: Notice of availability of a final EA and FONSI/ROD for the evaluation of the potential environmental impacts associated with the proposed Runway...

  7. A fibrinogen-related protein identified from hepatopancreas of crayfish is a potential pattern recognition receptor.

    PubMed

    Chen, Qiming; Bai, Suhua; Dong, Chaohua

    2016-09-01

    Fibrinogen-related protein (FREP) family is a large group of proteins containing fibrinogen-like (FBG) domain and plays multiple physiological roles in animals. However, their immune functions in crayfish are not fully explored. In the present study, a novel fibrinogen-like protein (designated as PcFBN1) was identified and characterized from hepatopancreas of red swamp crayfish Procambarus clarkii. The cDNA sequence of PcFBN1 contains an open reading frame (ORF) of 1353 bp encoding a protein of 450 amino acids. Sequence and structural analysis indicated that PcFBN1 contains an FBG domain in C-terminal and a putative signal peptide of 19 amino acids in N-terminal. Semi-quantitative PCR revealed that the main expression of PcFBN1 was observed in hepatopancreas and hemocyte. Temporal expression analysis exhibited that PcFBN1 expression could be significantly induced by heat-killed Aeromonas hydrophila. Tissue distribution and temporal change of PcFBN1 suggested that PcFBN1 may be involved in immune responses of red swamp crayfish. Recombinant PcFBN1 protein binds and agglutinates both gram-negative bacteria Escherichia coli and gram-positive bacteria Micrococcus lysodeikticus. Moreover, binding and agglutination is Ca(2+) dependent. Further analysis indicated that PcFBN1 recognizes some acetyl group-containing substance LPS and PGN. RNAi experiment revealed that PcFBN1 is required for bacterial clearance and survival from A. hydrophila infection. Reduction of PcFBN1 expression significantly decreased the survival and enhanced the number of A. hydrophila in the hemolymph. These results indicated that PcFBN1 plays an important role in the innate immunity of red swamp crayfish as a potential pattern recognition receptor. PMID:27417229

  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. 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

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

    PubMed Central

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

    2015-01-01

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

  11. Investigation of gene-environment interactions between 47 newly identified breast cancer susceptibility loci and environmental risk factors.

    PubMed

    Rudolph, Anja; Milne, Roger L; Truong, Thérèse; Knight, Julia A; Seibold, Petra; Flesch-Janys, Dieter; Behrens, Sabine; Eilber, Ursula; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Dunning, Alison M; Shah, Mitul; Munday, Hannah R; Darabi, Hatef; Eriksson, Mikael; Brand, Judith S; Olson, Janet; Vachon, Celine M; Hallberg, Emily; Castelao, J Esteban; Carracedo, Angel; Torres, Maria; Li, Jingmei; Humphreys, Keith; Cordina-Duverger, Emilie; Menegaux, Florence; Flyger, Henrik; Nordestgaard, Børge G; Nielsen, Sune F; Yesilyurt, Betul T; Floris, Giuseppe; Leunen, Karin; Engelhardt, Ellen G; Broeks, Annegien; Rutgers, Emiel J; Glendon, Gord; Mulligan, Anna Marie; Cross, Simon; Reed, Malcolm; Gonzalez-Neira, Anna; Arias Perez, José Ignacio; Provenzano, Elena; Apicella, Carmel; Southey, Melissa C; Spurdle, Amanda; Häberle, Lothar; Beckmann, Matthias W; Ekici, Arif B; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; McLean, Catriona; Baglietto, Laura; Chanock, Stephen J; Lissowska, Jolanta; Sherman, Mark E; Brüning, Thomas; Hamann, Ute; Ko, Yon-Dschun; Orr, Nick; Schoemaker, Minouk; Ashworth, Alan; Kosma, Veli-Matti; Kataja, Vesa; Hartikainen, Jaana M; Mannermaa, Arto; Swerdlow, Anthony; Giles, Graham G; Brenner, Hermann; Fasching, Peter A; Chenevix-Trench, Georgia; Hopper, John; Benítez, Javier; Cox, Angela; Andrulis, Irene L; Lambrechts, Diether; Gago-Dominguez, Manuela; Couch, Fergus; Czene, Kamila; Bojesen, Stig E; Easton, Doug F; Schmidt, Marjanka K; Guénel, Pascal; Hall, Per; Pharoah, Paul D P; Garcia-Closas, Montserrat; Chang-Claude, Jenny

    2015-03-15

    A large genotyping project within the Breast Cancer Association Consortium (BCAC) recently identified 41 associations between single nucleotide polymorphisms (SNPs) and overall breast cancer (BC) risk. We investigated whether the effects of these 41 SNPs, as well as six SNPs associated with estrogen receptor (ER) negative BC risk are modified by 13 environmental risk factors for BC. Data from 22 studies participating in BCAC were pooled, comprising up to 26,633 cases and 30,119 controls. Interactions between SNPs and environmental factors were evaluated using an empirical Bayes-type shrinkage estimator. Six SNPs showed interactions with associated p-values (pint ) <1.1 × 10(-3) . None of the observed interactions was significant after accounting for multiple testing. The Bayesian False Discovery Probability was used to rank the findings, which indicated three interactions as being noteworthy at 1% prior probability of interaction. SNP rs6828523 was associated with increased ER-negative BC risk in women ≥170 cm (OR = 1.22, p = 0.017), but inversely associated with ER-negative BC risk in women <160 cm (OR = 0.83, p = 0.039, pint = 1.9 × 10(-4) ). The inverse association between rs4808801 and overall BC risk was stronger for women who had had four or more pregnancies (OR = 0.85, p = 2.0 × 10(-4) ), and absent in women who had had just one (OR = 0.96, p = 0.19, pint = 6.1 × 10(-4) ). SNP rs11242675 was inversely associated with overall BC risk in never/former smokers (OR = 0.93, p = 2.8 × 10(-5) ), but no association was observed in current smokers (OR = 1.07, p = 0.14, pint = 3.4 × 10(-4) ). In conclusion, recently identified BC susceptibility loci are not strongly modified by established risk factors and the observed potential interactions require confirmation in independent studies. PMID:25227710

  12. An investigation of gene-environment interactions between 47 newly identified breast cancer susceptibility loci and environmental risk factors

    PubMed Central

    Rudolph, Anja; Milne, Roger L.; Truong, Thérèse; Knight, Julia A.; Seibold, Petra; Flesch-Janys, Dieter; Behrens, Sabine; Eilber, Ursula; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Dunning, Alison M.; Shah, Mitul; Munday, Hannah R.; Darabi, Hatef; Eriksson, Mikael; Brand, Judith S.; Olson, Janet; Vachon, Celine M.; Hallberg, Emily; Castelao, J. Esteban; Carracedo, Angel; Torres, Maria; Li, Jingmei; Humphreys, Keith; Cordina-Duverger, Emilie; Menegaux, Florence; Flyger, Henrik; Nordestgaard, Børge G.; Nielsen, Sune F.; Yesilyurt, Betul T.; Floris, Giuseppe; Leunen, Karin; Engelhardt, Ellen G.; Broeks, Annegien; Rutgers, Emiel J.; Glendon, Gord; Mulligan, Anna Marie; Cross, Simon; Reed, Malcolm; Gonzalez-Neira, Anna; Perez, José Ignacio Arias; Provenzano, Elena; Apicella, Carmel; Southey, Melissa C.; Spurdle, Amanda; Investigators, kConFab; Group, AOCS; Häberle, Lothar; Beckmann, Matthias W.; Ekici, Arif B.; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; McLean, Catriona; Baglietto, Laura; Chanock, Stephen J.; Lissowska, Jolanta; Sherman, Mark E.; Brüning, Thomas; Hamann, Ute; Ko, Yon-Dschun; Orr, Nick; Schoemaker, Minouk; Ashworth, Alan; Kosma, Veli-Matti; Kataja, Vesa; Hartikainen, Jaana M.; Mannermaa, Arto; Swerdlow, Anthony; Giles, Graham G.; Brenner, Hermann; Fasching, Peter A.; Chenevix-Trench, Georgia; Hopper, John; Benítez, Javier; Cox, Angela; Andrulis, Irene L.; Lambrechts, Diether; Gago-Dominguez, Manuela; Couch, Fergus; Czene, Kamila; Bojesen, Stig E.; Easton, Doug F.; Schmidt, Marjanka K.; Guénel, Pascal; Hall, Per; Pharoah, Paul D. P.; Garcia-Closas, Montserrat; Chang-Claude, Jenny

    2014-01-01

    A large genotyping project within the Breast Cancer Association Consortium (BCAC) recently identified 41 associations between single nucleotide polymorphisms (SNPs) and overall breast cancer (BC) risk. We investigated whether the effects of these 41 SNPs, as well as six SNPs associated with estrogen receptor (ER) negative BC risk are modified by 13 environmental risk factors for BC. Data from 22 studies participating in BCAC were pooled, comprising up to 26,633 cases and 30,119 controls. Interactions between SNPs and environmental factors were evaluated using an empirical Bayes-type shrinkage estimator. Six SNPs showed interactions with associated p-values (pint) <1.1×10−3. None of the observed interactions was significant after accounting for multiple testing. The Bayesian False Discovery Probability was used to rank the findings, which indicated three interactions as being noteworthy at 1% prior probability of interaction. SNP rs6828523 was associated with increased ER-negative BC risk in women ≥170cm (OR=1.22, p=0.017), but inversely associated with ER-negative BC risk in women <160cm (OR=0.83, p=0.039, pint=1.9×10−4). The inverse association between rs4808801 and overall BC risk was stronger for women who had had four or more pregnancies (OR=0.85, p=2.0×10−4), and absent in women who had had just one (OR=0.96, p=0.19, pint = 6.1×10−4). SNP rs11242675 was inversely associated with overall BC risk in never/former smokers (OR=0.93, p=2.8×10−5), but no association was observed in current smokers (OR=1.07, p=0.14, pint = 3.4×10−4). In conclusion, recently identified breast cancer susceptibility loci are not strongly modified by established risk factors and the observed potential interactions require confirmation in independent studies. PMID:25227710

  13. 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.

  14. ISO 14000 - the International Environmental Management Standard: Potential impacts on environmental management and auditing in the electric power generation industry

    SciTech Connect

    Gauntlett, S.B.; Pierce, J.L.; Pierce, J.L.

    1995-12-31

    In the framework of environmental management, the concept of voluntary environmental compliance auditing is not in itself a new development. Environmentally conscious firms have for more than a decade, undertaken voluntary audits to help achieve and maintain compliance with environmental regulations and to help identify and correct unregulated or poorly regulated environmental hazard. The firms undertaking the audits were motivated by a desire to mitigate legal and financial risks and/or the desire to be a highly responsible member of the corporate community. Much of the early attention to environmental auditing was in the chemical process industries. Today, there are four current trends affecting environmental auditing: (1) the practice is becoming widespread in all industry groups in both large and small firms; (2) environmental management and audit methodolgies and approaches are being codified in the form of written national and International standards; (3) environmental management programs and in-house audits are increasingly being certified by independent auditors (who are not associated with regulatory agencies); and (4) the certifications are being viewed as marketing and public relations tools. The adoption of ISO 14000 is destined to become the most significant development in international environmental management and auditing. International standards for the development of Environmental Management Systems and the execution of environmental audits do not currently exist. Individual countries, such as England and France, have national standards. One multi-national standard currently exists--the European Economic Community`s Eco-Management and Audit Scheme (EMAS). The United States does not have a national environmental management and auditing standard.

  15. Potential environmental impact of a hydrogen economy on the stratosphere.

    PubMed

    Tromp, Tracey K; Shia, Run-Lie; Allen, Mark; Eiler, John M; Yung, Y L

    2003-06-13

    The widespread use of hydrogen fuel cells could have hitherto unknown environmental impacts due to unintended emissions of molecular hydrogen, including an increase in the abundance of water vapor in the stratosphere (plausibly by as much as approximately 1 part per million by volume). This would cause stratospheric cooling, enhancement of the heterogeneous chemistry that destroys ozone, an increase in noctilucent clouds, and changes in tropospheric chemistry and atmosphere-biosphere interactions. PMID:12805546

  16. A Potential Link between Environmental Triggers and Autoimmunity.

    PubMed

    Vojdani, Aristo

    2014-01-01

    Autoimmune diseases have registered an alarming rise worldwide in recent years. Accumulated evidence indicates that the immune system's ability to distinguish self from nonself is negatively impacted by genetic factors and environmental triggers. Genetics is certainly a factor, but since it normally takes a very long time for the human genetic pattern to change enough to register on a worldwide scale, increasingly the attention of studies has been focused on the environmental factors of a rapidly changing and evolving civilization. New technology, new industries, new inventions, new chemicals and drugs, and new foods and diets are constantly and rapidly being introduced in this fast-paced ever-changing world. Toxicants, infections, epitope spreading, dysfunctions of immune homeostasis, and dietary components can all have an impact on the body's delicate immune recognition system. Although the precise etiology and pathogenesis of many autoimmune diseases are still unknown, it would appear from the collated studies that there are common mechanisms in the immunopathogenesis of multiple autoimmune reactivities. Of particular interest is the citrullination of host proteins and their conversion to autoantigens by the aforementioned environmental triggers. The identification of these specific triggers of autoimmune reactivity is essential then for the development of new therapies for autoimmune diseases. PMID:24688790

  17. Using Canonical Correlation Analysis to Identify Environmental Attitude Groups: Considerations for National Forest Planning in the Southwestern U.S.

    NASA Astrophysics Data System (ADS)

    Prera, Alejandro J.; Grimsrud, Kristine M.; Thacher, Jennifer A.; McCollum, Dan W.; Berrens, Robert P.

    2014-10-01

    As public land management agencies pursue region-specific resource management plans, with meaningful consideration of public attitudes and values, there is a need to characterize the complex mix of environmental attitudes in a diverse population. The contribution of this investigation is to make use of a unique household, mail/internet survey data set collected in 2007 in the Southwestern United States (Region 3 of the U.S. Forest Service). With over 5,800 survey responses to a set of 25 Public Land Value statements, canonical correlation analysis is able to identify 7 statistically distinct environmental attitudinal groups. We also examine the effect of expected changes in regional demographics on overall environmental attitudes, which may help guide in the development of socially acceptable long-term forest management policies. Results show significant support for conservationist management policies and passive environmental values, as well as a greater role for stakeholder groups in generating consensus for current and future forest management policies.

  18. Early evaluation of potential environmental impacts of carbon nanotube synthesis by chemical vapor deposition.

    PubMed

    Plata, Desirée L; Hart, A John; Reddy, Christopher M; Gschwend, Philip M

    2009-11-01

    The carbon nanotube (CNT) industry is expanding rapidly, yet little is known about the potential environmental impacts of CNT manufacture. Here, we evaluate the effluent composition of a representative multiwalled CNT synthesis by catalytic chemical vapor deposition (CVD) in order to provide data needed to design strategies for mitigating any unacceptable emissions. During thermal pretreatment of the reactant gases (ethene and H(2)), we found over 45 side-products were formed, including methane, volatile organic compounds (VOCs), and polycyclic aromatic hydrocarbons (PAHs). This finding suggests several environmental concerns with the existing process, including potential discharges of the potent greenhouse gas, methane (up to 1.7%), and toxic compounds such as benzene and 1,3-butadiene (up to 36000 ppmv). Extrapolating these laboratory-scale data to future industrial CNT production, we estimate that (1) contributions of atmospheric methane will be negligible compared to other existing sources and (2) VOC and PAH emissions may become important on local scales but will be small when compared to national industrial sources. As a first step toward reducing such unwanted emissions, we used continuous in situ measures of CNT length during growth and sought to identify which thermally generated compounds correlated with CNT growth rate. The results suggested that, in future CNT production approaches, key reaction intermediates could be delivered to the catalyst without thermal treatment. This would eliminate the most energetically expensive component of CVD synthesis (heating reactant gases), while reducing the formation of unintended byproducts. PMID:19924971

  19. An Overview of Algae Biofuel Production and Potential Environmental Impact

    EPA Science Inventory

    Algae are among the most potentially significant sources of sustainable biofuels in the future of renewable energy. A feedstock with virtually unlimited applicability, algae can metabolize various waste streams (e.g., municipal wastewater, carbon dioxide from industrial flue gas)...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. RNA-Based Methods Increase the Detection of Fecal Bacteria and Fecal Identifiers in Environmental Waters

    EPA Science Inventory

    We evaluated the use of qPCR RNA-based methods in the detection of fecal bacteria in environmental waters. We showed that RNA methods can increase the detection of fecal bacteria in multiple water matrices. The data suggest that this is a viable alternative for the detection of a...

  2. 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

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

    EPA Science Inventory

    Over the past 20 years, an increased focus on detecting environmental chemicals posing a risk of adverse effects due to endocrine disruption has driven the creation of the U.S. EPA Endocrine Disruptor Screening Program (EDSP). Thousands of chemicals are subject to the EDSP, whic...

  4. USING A GEOGRAPHIC INFORMATION SYSTEM TO IDENTIFY AREAS WITH POTENTIAL FOR OFF-TARGET PESTICIDE EXPOSURE

    EPA Science Inventory

    In many countries, numerous tests are required as part of the risk assessment process before chemical registration to protect human health and the environment from unintended effects of chemical releases. Most of these tests are not based on ecological or environmental relevance ...

  5. Potential pitfalls of relying on hydrogen sulfide (H2S) production to identify Salmonella in feed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Salmonella can be difficult to assess and isolate in poultry feed due to stress, uneven distribution and poor growth. Previous studies have shown that several strains of Salmonella can be affected by environmental changes, resulting in H2S-negative colonies. This is a major concern, as H2S productio...

  6. 49 CFR 192.917 - How does an operator identify potential threats to pipeline integrity and use the threat...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... pipeline integrity and use the threat identification in its integrity program? 192.917 Section 192.917....917 How does an operator identify potential threats to pipeline integrity and use the threat identification in its integrity program? (a) Threat identification. An operator must identify and evaluate...

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

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... pipeline integrity and use the threat identification in its integrity program? 192.917 Section 192.917....917 How does an operator identify potential threats to pipeline integrity and use the threat identification in its integrity program? (a) Threat identification. An operator must identify and evaluate...

  8. 49 CFR 192.917 - How does an operator identify potential threats to pipeline integrity and use the threat...

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... pipeline integrity and use the threat identification in its integrity program? 192.917 Section 192.917....917 How does an operator identify potential threats to pipeline integrity and use the threat identification in its integrity program? (a) Threat identification. An operator must identify and evaluate...

  9. 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

    ... pipeline integrity and use the threat identification in its integrity program? 192.917 Section 192.917....917 How does an operator identify potential threats to pipeline integrity and use the threat identification in its integrity program? (a) Threat identification. An operator must identify and evaluate...

  10. 49 CFR 192.917 - How does an operator identify potential threats to pipeline integrity and use the threat...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... pipeline integrity and use the threat identification in its integrity program? 192.917 Section 192.917....917 How does an operator identify potential threats to pipeline integrity and use the threat identification in its integrity program? (a) Threat identification. An operator must identify and evaluate...

  11. Nanoparticles: Their potential toxicity, waste and environmental management

    SciTech Connect

    Bystrzejewska-Piotrowska, Grazyna Golimowski, Jerzy; Urban, Pawel L.

    2009-09-15

    This literature review discusses specific issues related to handling of waste containing nanomaterials. The aims are (1) to highlight problems related to uncontrolled release of nanoparticles to the environment through waste disposal, and (2) to introduce the topics of nanowaste and nanotoxicology to the waste management community. Many nanoparticles used by industry contain heavy metals, thus toxicity and bioaccumulation of heavy metals contained in nanoparticles may become important environmental issues. Although bioavailability of heavy metals contained in nanoparticles can be lower than those present in soluble form, the toxicity resulting from their intrinsic nature (e.g. their size, shape or density) may be significant. An approach to the treatment of nanowaste requires understanding of all its properties - not only chemical, but also physical and biological. Progress in nanowaste management also requires studies of the environmental impact of the new materials. The authors believe Amara's law is applicable to the impact of nanotechnologies, and society might overestimate the short-term effects of these technologies, while underestimating the long-term effects. It is necessary to have basic information from companies about the level and nature of nanomaterials produced or emitted and about the expectation of the life cycle time of nanoproducts as a basis to estimate the level of nanowaste in the future. Without knowing how companies plan to use and store recycled and nonrecycled nanomaterials, development of regulations is difficult. Tagging of nanoproducts is proposed as a means to facilitate separation and recovery of nanomaterials.

  12. Potential applications of environmental sampling and analysis for the IAEA

    SciTech Connect

    Raber, E.

    1993-03-01

    This objective of this paper is to address the usefulness of envirorunental sampling and analysis in support of the IAEA. In particular, whether state-of-the-art analytical methods may provide detection of undeclared nuclear activities. It is important to emphasize that envirorunental sampling offers the IAEA a method of improving the assurance that a particular facility has no ongoing undeclared nuclear activities. It is suggested as a supplement to the existing IAEA safeguards inspections and activities. Enviromental sampling with appropriate analytical techniques can detect unknown activity fairly well, but it is not very reliable for determining how much or when activity has actually occured. Additionally, it is important to point out that the cost of such an envirorunental sampling program needs to be balanced with the confidence provided to detect undeclared nuclear activities. Environmental sampling wig probably not allow the IAEA to reduce or eliminate some of its existing baseline activities. The addition of an environmental sampling and analysis program will entail a cost of its own, and adding such a program may not reduce IAEA total costs. The overall cost of such a program will depend on the level of confidence required, (e.g. number and type of samples and analyses), the Quality Assurance plan to be implemented and the number of sites to be inspected. A more detailed cost analysis is not within the scope of this paper.

  13. Bioconcentration potential of organic environmental chemicals in humans

    SciTech Connect

    Geyer, H.; Scheunert, I.; Korte, F.

    1986-12-01

    A list of environmental chemicals detectable in adipose tissue and/or milk of non-occupationally exposed humans is presented. Besides their physiochemical properties (n-octanol/water partition coefficient and water solubility), their acceptable daily intake (ADI) values, production figures, fate in the environment, concentrations in human adipose tissue, and data from total diet studies from market basket investigations are given. Average bioconcentration factors (BCF) of polychlorinated biphenyls (PCBs), 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), DDT, hexachlorobenzene (HCB), dieldrin, hexachlorocyclohexane isomers (alpha-HCH, beta-HCH, gamma-HCH, delta-HCH), pentachlorophenol (PCP), and 3,5-di-tert-butyl-4-hydroxytoluene (BHT) in human adipose tissue are calculated. The bioconcentration factors (wet wt basis) of these compounds are between 3 and 47 times higher in humans than in rats. The environmental chemicals are divided into three groups in respect to their bioconcentration factors in human adipose tissue: group I, high BCF (greater than 100); group II, medium BCF (10-100); and group III, low BCF (less than 10). The bioconcentration factors are useful for hazard assessment of chemicals to humans.

  14. Potential health and environmental effects of trace elements and radionuclides from increased coal utilization.

    PubMed Central

    Van Hook, R I

    1979-01-01

    This report addresses the effects of coal-derived trace and radioactive elements. A summary of our current understanding of health and environmental effects of trace and radioactive elements released during coal mining, cleaning, combustion, and ash disposal is presented. Physical and biological transport phenomena which are important in determining organism exposure are also discussed. Biological concentration and transformation as well as synergistic and antagonistic actions among trace contaminants are discussed in terms of their importance in mobility, persistence, availability, and ultimate toxicity. The consequences of implementing the President's National Energy Plan are considered in terms of the impact of the NEP in 1985 and 2000 on the potential effects of trace and radioactive elements from the coal fuel cycle. Areas of needed research are identified in specific recommendations. PMID:540619

  15. Potential environmental effects of pack stock on meadow ecosystems of the Sierra Nevada, USA

    USGS Publications Warehouse

    Ostoja, Steven M.; Brooks, Matthew L.; Moore, Peggy E.; Berlow, Eric L.; Robert Blank; Roche, Jim; Chase, Jennifer T.; Sylvia Haultain

    2014-01-01

    Pack and saddle stock, including, but not limited to domesticated horses, mules, and burros, are used to support commercial, private and administrative activities in the Sierra Nevada. The use of pack stock has become a contentious and litigious issue for land management agencies in the region inter alia due to concerns over effects on the environment. The potential environmental effects of pack stock on Sierra Nevada meadow ecosystems are reviewed and it is concluded that the use of pack stock has the potential to influence the following: (1) water nutrient dynamics, sedimentation, temperature, and microbial pathogen content; (2) soil chemistry, nutrient cycling, soil compaction and hydrology; (3) plant individuals, populations and community dynamics, non-native invasive species, and encroachment of woody species; and (4) wildlife individuals, populations and communities. It is considered from currently available information that management objectives of pack stock should include the following: minimise bare ground, maximise plant cover, maintain species composition of native plants, minimise trampling, especially on wet soils and stream banks, and minimise direct urination and defecation by pack stock into water. However, incomplete documentation of patterns of pack stock use and limited past research limits current understanding of the effects of pack stock, especially their effects on water, soils and wildlife. To improve management of pack stock in this region, research is needed on linking measurable monitoring variables (e.g. plant cover) with environmental relevancy (e.g. soil erosion processes, wildlife habitat use), and identifying specific environmental thresholds of degradation along gradients of pack stock use in Sierra Nevada meadows.

  16. Identifying barriers and catalysts to fostering pro-environmental behavior: opportunities and challenges for community psychology.

    PubMed

    Quimby, Christine C; Angelique, Holly

    2011-06-01

    In this paper, we report on an exploratory study of perceived barriers and catalysts to increasing pro-environmental behavior among people associated with the environmental movement. Perceived barriers include time, money, low efficacy and hopelessness. Catalysts focus on changing social norms, especially through education and institutional support. We discuss the tragedy of the commons and free-riding as impediments to change. We use this study as an entryway to hypothesize opportunities and challenges that community psychologists face in motivating and supporting actions to reduce the impact of global climate change. We provide examples of how community psychologists can foster these changes. In short, we argue that community psychology is well positioned to take a leading role in the fight for a carbon neutral future. PMID:21203832

  17. Environmental Trigger(s) of Type 1 Diabetes: Why So Difficult to Identify?

    PubMed Central

    2015-01-01

    Type 1 diabetes (T1D) is one of the most common chronic diseases with childhood onset, and the disease has increased two- to fivefold over the past half century by as yet unknown means. T1D occurs when the body's immune system turns against itself so that, in a very specific and targeted way, it destroys the pancreatic β-cells. T1D results from poorly defined interactions between susceptibility genes and environmental determinants. In contrast to the rapid progress in finding T1D genes, identification and confirmation of environmental determinants remain a formidable challenge. This review article will focus on factors which have to be evaluated and decision to take before starting a new prospective cohort study. Considering all the large ongoing prospective studies, new and more conclusive data than that obtained so far should instead come from international collaboration on the ongoing cohort studies. PMID:25883954

  18. ASSESSMENT OF POTENTIAL ENVIRONMENTAL PROBLEMS CONCERNING WATER AVAILABILITY

    EPA Science Inventory

    This study analyzes national supply and demand and summarizes data on all water resources regions. Estimates of the potential for wastewater reuse and recycling are also presented. The technology for improving the water supply through augmentation and conservation is reviewed, an...

  19. Identifying the Environmental Conditions Favouring West Nile Virus Outbreaks in Europe

    PubMed Central

    Metz, Markus; Rosà, Roberto; Marini, Giovanni; Chadwick, Elizabeth; Neteler, Markus

    2015-01-01

    West Nile Virus (WNV) is a globally important mosquito borne virus, with significant implications for human and animal health. The emergence and spread of new lineages, and increased pathogenicity, is the cause of escalating public health concern. Pinpointing the environmental conditions that favour WNV circulation and transmission to humans is challenging, due both to the complexity of its biological cycle, and the under-diagnosis and reporting of epidemiological data. Here, we used remote sensing and GIS to enable collation of multiple types of environmental data over a continental spatial scale, in order to model annual West Nile Fever (WNF) incidence across Europe and neighbouring countries. Multi-model selection and inference were used to gain a consensus from multiple linear mixed models. Climate and landscape were key predictors of WNF outbreaks (specifically, high precipitation in late winter/early spring, high summer temperatures, summer drought, occurrence of irrigated croplands and highly fragmented forests). Identification of the environmental conditions associated with WNF outbreaks is key to enabling public health bodies to properly focus surveillance and mitigation of West Nile virus impact, but more work needs to be done to enable accurate predictions of WNF risk. PMID:25803814

  20. Identifying the environmental conditions favouring West Nile Virus outbreaks in Europe.

    PubMed

    Marcantonio, Matteo; Rizzoli, Annapaola; Metz, Markus; Rosà, Roberto; Marini, Giovanni; Chadwick, Elizabeth; Neteler, Markus

    2015-01-01

    West Nile Virus (WNV) is a globally important mosquito borne virus, with significant implications for human and animal health. The emergence and spread of new lineages, and increased pathogenicity, is the cause of escalating public health concern. Pinpointing the environmental conditions that favour WNV circulation and transmission to humans is challenging, due both to the complexity of its biological cycle, and the under-diagnosis and reporting of epidemiological data. Here, we used remote sensing and GIS to enable collation of multiple types of environmental data over a continental spatial scale, in order to model annual West Nile Fever (WNF) incidence across Europe and neighbouring countries. Multi-model selection and inference were used to gain a consensus from multiple linear mixed models. Climate and landscape were key predictors of WNF outbreaks (specifically, high precipitation in late winter/early spring, high summer temperatures, summer drought, occurrence of irrigated croplands and highly fragmented forests). Identification of the environmental conditions associated with WNF outbreaks is key to enabling public health bodies to properly focus surveillance and mitigation of West Nile virus impact, but more work needs to be done to enable accurate predictions of WNF risk. PMID:25803814

  1. Potential for ag residue collection, economics and environmental benefits

    NASA Astrophysics Data System (ADS)

    Hettenhaus, J. R.

    2003-12-01

    Removing excess corn stover and cereal straws after erosion requirements have been satisfied offers much potential as a renewable feedstock for initial biorefineries, producing fuels, chemicals and materials while reducing crop inputs, increasing farm income and offsetting greenhouse gas emissions. Two biorefinery site studies are presented for the production of fuel ethanol: SW Nebraska and Western Oklahoma. Results include excess available, delivered cost, net income to the farmer, improved SOM from move to no-till and GHG reduction from fossil fuel offset

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

    This study aims to better understand the role of vegetation on the Ca cycle at the level of the critical zone of the Earth, in order to specify the mechanisms controlling the Ca absorption by plants at the rock/plant interface. To do this, we performed experiments using hydroponic plant cultures in a way that we could control the cooccuring geochemical and biological processes and determine the impact of the nutritive solution on the Ca cycle within plants. A dicotyledon and calcicole plant with rapid growth, the French bean (Phaseolus vulgaris L.), has been chosen to have access to one complete growth cycle. Several experiments have been conducted with two Ca concentrations, 5 (L) and 60 (H) ppm and two pH values (4 and 6) in the nutritive solution, for which the Ca concentration was maintained constant, so its Ca content is considered to be infinite. We determined Ca concentrations and isotopic ratios in the nutritive solution and in different organs (main roots, secondary roots, old and young stems, old and young leaves and fruits) at two different growth stages (10 days and 6 weeks). Our results show, in accord with previously published field studies, that the bean organs are all enriched in the light 40Ca isotope compared to the nutritive solution (e.g. Wigand et al., 2005; Page et al., 2008; Cenki-Tok et al., 2009; Holmden and Bélanger, 2010). We identify two fractionation levels. The first occurs during the uptake of the nutrient elements by the lateral roots. This implies that the main mechanisms of light isotope enrichments in the plant are due to electrochemical gradient transport processes taking place at this interface. The second fractionation can be observed within the plant itself and is due to the nature of the considered organ itself. Indeed structural reservoirs (primary roots, stem, reproductive organs) incorporate more the light 40Ca isotope compared to the transfer reservoirs (lateral roots, xylem sap, leaves). This could be linked to ion

  3. Identifying Determinants of Oncomelania hupensis Habitats and Assessing the Effects of Environmental Control Strategies in the Plain Regions with the Waterway Network of China at the Microscale

    PubMed Central

    Qiu, Juan; Li, Rendong; Xu, Xingjian; Yu, Chuanhua; Xia, Xin; Hong, Xicheng; Chang, Bianrong; Yi, Fengjia; Shi, Yuanyuan

    2014-01-01

    This study aims to identify the landscape ecological determinants related to Oncomelania hupensis distribution, map the potential high risk of O. hupensis habitats at the microscale, and assess the effects of two environmental control strategies. Sampling was performed on 242 snail sites and 726 non-snail sites throughout Qianjiang City, Hubei Province, China. An integrated approach of landscape pattern analysis coupled with multiple logistic regression modeling was applied to investigate the effects of environmental factors on snail habitats. The risk probability of snail habitats positively correlated with patch fractal dimension (FD), paddy farm land proportion, and wetness index but inversely correlated with categorized normalized difference vegetation index (NDVI) and elevation. These findings indicate that FD can identify irregular features (e.g., irrigation ditches) in plain regions and that a moderate NDVI increases the microscale risk probability. Basing on the observed determinants, we predicted a map showing high-risk areas of snail habitats and simulated the effects of conduit hardening and paddy farming land rotation to dry farming land. The two approaches were confirmed effective for snail control. These findings provide an empirical basis for health professionals in local schistosomiasis control stations to identify priority areas and promising environmental control strategies for snail control and prevention. PMID:25003174

  4. 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...

  5. 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...

  6. 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...

  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

    ... (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...

  8. 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...

  9. Evaluating environmental modeling and sampling data with biomarker data to identify sources and routes of exposure

    NASA Astrophysics Data System (ADS)

    Shin, Hyeong-Moo; McKone, Thomas E.; Bennett, Deborah H.

    2013-04-01

    Exposure to environmental chemicals results from multiple sources, environmental media, and exposure routes. Ideally, modeled exposures should be compared to biomonitoring data. This study compares the magnitude and variation of modeled polycyclic aromatic hydrocarbons (PAHs) exposures resulting from emissions to outdoor and indoor air and estimated exposure inferred from biomarker levels. Outdoor emissions result in both inhalation and food-based exposures. We modeled PAH intake doses using U.S. EPA's 2002 National Air Toxics Assessment (NATA) county-level emissions data for outdoor inhalation, the CalTOX model for food ingestion (based on NATA emissions), and indoor air concentrations from field studies for indoor inhalation. We then compared the modeled intake with the measured urine levels of hydroxy-PAH metabolites from the 2001-2002 National Health and Nutrition Examination Survey (NHANES) survey as quantifiable human intake of PAH parent-compounds. Lognormal probability plots of modeled intakes and estimated intakes inferred from biomarkers suggest that a primary route of exposure to naphthalene, fluorene, and phenanthrene for the U.S. population is likely inhalation from indoor sources. For benzo(a)pyrene, the predominant exposure route is likely from food ingestion resulting from multi-pathway transport and bioaccumulation due to outdoor emissions. Multiple routes of exposure are important for pyrene. We also considered the sensitivity of the predicted exposure to the proportion of the total naphthalene production volume emitted to the indoor environment. The comparison of PAH biomarkers with exposure variability estimated from models and sample data for various exposure pathways supports that both indoor and outdoor models are needed to capture the sources and routes of exposure to environmental contaminants.

  10. 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.

  11. 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

  12. Triclosan: current status, occurrence, environmental risks and bioaccumulation potential.

    PubMed

    Dhillon, Gurpreet Singh; Kaur, Surinder; Pulicharla, Rama; Brar, Satinder Kaur; Cledón, Maximiliano; Verma, Mausam; Surampalli, Rao Y

    2015-05-01

    Triclosan (TCS) is a multi-purpose antimicrobial agent used as a common ingredient in everyday household personal care and consumer products. The expanded use of TCS provides a number of pathways for the compound to enter the environment and it has been detected in sewage treatment plant effluents; surface; ground and drinking water. The physico-chemical properties indicate the bioaccumulation and persistence potential of TCS in the environment. Hence, there is an increasing concern about the presence of TCS in the environment and its potential negative effects on human and animal health. Nevertheless, scarce monitoring data could be one reason for not prioritizing TCS as emerging contaminant. Conventional water and wastewater treatment processes are unable to completely remove the TCS and even form toxic intermediates. Considering the worldwide application of personal care products containing TCS and inefficient removal and its toxic effects on aquatic organisms, the compound should be considered on the priority list of emerging contaminants and its utilization in all products should be regulated. PMID:26006133

  13. Triclosan: Current Status, Occurrence, Environmental Risks and Bioaccumulation Potential

    PubMed Central

    Dhillon, Gurpreet Singh; Kaur, Surinder; Pulicharla, Rama; Brar, Satinder Kaur; Cledón, Maximiliano; Verma, Mausam; Surampalli, Rao Y.

    2015-01-01

    Triclosan (TCS) is a multi-purpose antimicrobial agent used as a common ingredient in everyday household personal care and consumer products. The expanded use of TCS provides a number of pathways for the compound to enter the environment and it has been detected in sewage treatment plant effluents; surface; ground and drinking water. The physico-chemical properties indicate the bioaccumulation and persistence potential of TCS in the environment. Hence, there is an increasing concern about the presence of TCS in the environment and its potential negative effects on human and animal health. Nevertheless, scarce monitoring data could be one reason for not prioritizing TCS as emerging contaminant. Conventional water and wastewater treatment processes are unable to completely remove the TCS and even form toxic intermediates. Considering the worldwide application of personal care products containing TCS and inefficient removal and its toxic effects on aquatic organisms, the compound should be considered on the priority list of emerging contaminants and its utilization in all products should be regulated. PMID:26006133

  14. Mapping the Racial Inequality in Place: Using Youth Perceptions to Identify Unequal Exposure to Neighborhood Environmental Hazards.

    PubMed

    Teixeira, Samantha; Zuberi, Anita

    2016-01-01

    Black youth are more likely than white youth to grow up in poor, segregated neighborhoods. This racial inequality in the neighborhood environments of black youth increases their contact with hazardous neighborhood environmental features including violence and toxic exposures that contribute to racial inequality in youth health and well-being. While the concept of neighborhood effects has been studied at length by social scientists, this work has not been as frequently situated within an environmental justice (EJ) paradigm. The present study used youth perceptions gained from in-depth interviews with youth from one Pittsburgh, Pennsylvania neighborhood to identify neighborhood environmental health hazards. We then mapped these youth-identified features to examine how they are spatially and racially distributed across the city. Our results suggest that the intersection of race and poverty, neighborhood disorder, housing abandonment, and crime were salient issues for youth. The maps show support for the youths' assertions that the environments of black and white individuals across the city of Pittsburgh differ in noteworthy ways. This multi-lens, mixed-method analysis was designed to challenge some of the assumptions we make about addressing environmental inequality using youths' own opinions on the issue to drive our inquiry. PMID:27571086

  15. Permafrost as palaeo-environmental archive - potentials and limitations

    NASA Astrophysics Data System (ADS)

    Schirrmeister, L.; Wetterich, S.; Meyer, H.; Grosse, G.; Schwamborn, G.; Siegert, C.

    2009-04-01

    Since 1994, the Periglacial Research Group of the Alfred Wegener Institute is studying permafrost sequences of the Beringian landmass. The study sites in Siberia cover lake banks on Taymyr Peninsula, coastal sites at the Laptev and the East Siberian Seas, locations in the Lena Delta, at the lower Kolyma river, the middle Lena and the lower Aldan rivers, and the catchment area of the El'gygytgyn crater lake in Chukotka. In Alaska, permafrost tunnels near Fairbanks and Barrow, and coastal sites on the Seward Peninsula coast were studied. In addition, Canadian sites on Herschel Island in the Beaufort Sea and at the adjacent coast of the Yukon plain were studied. Subsurface exposures like tunnels and cellars provided the opportunity for three-dimensional studies of sedimentary and ground ice features, relatively ‘clean' field conditions for in-situ experiments, monitoring procedures, and detailed and repeatable sampling. Permafrost cores were drilled in order to study inaccessible sequences below the terrain surface and shelf sea floor. Cores were transported and stored frozen for further high-resolution analysis. Reference core sections were preserved for subsequent later studies. Terrestrial sediment cores are highly localized records, sometimes problematic in extrapolating horizons in inhomogeneous sediments like ground ice-deformed permafrost deposits, and drill campaigns are usually cost intensive and logistical challenging. Coastal permafrost cliffs often naturally expose large cross sections trough modern and ancient landscapes. Contrary to cores, they provide an opportunity to study the wider context of depositional environments and ground ice features. Due to the relative easy access to coasts and the recurring natural exposure of cliffs by thermo-abrasive wave action they are very convenient study objects for regional comparisons and correlation of past environmental conditions. Finally, palaeogeographical reconstructions are also guided by remote sensing

  16. 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…

  17. An Evaluation of Selected Procedures for Identifying Potential High School Dropouts.

    ERIC Educational Resources Information Center

    Weber, James M.

    Many students who enter public schools leave without achieving what has become the expected minimum level of educational attainment, a high school diploma. The purpose of this study was to contribute to existing dropout-prevention research by identifying and validating reliable decision rules for differentiating actual dropouts from high school…

  18. 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...

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

    EPA Science Inventory

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

  20. 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

  1. An aggregate analysis of personal care products in the environment: Identifying the distribution of environmentally-relevant concentrations.

    PubMed

    Hopkins, Zachary R; Blaney, Lee

    2016-01-01

    Over the past 3-4 decades, per capita consumption of personal care products (PCPs) has steadily risen, resulting in increased discharge of the active and inactive ingredients present in these products into wastewater collection systems. PCPs comprise a long list of compounds employed in toothpaste, sunscreen, lotions, soaps, body washes, and insect repellants, among others. While comprehensive toxicological studies are not yet available, an increasing body of literature has shown that PCPs of all classes can impact aquatic wildlife, bacteria, and/or mammalian cells at low concentrations. Ongoing research efforts have identified PCPs in a variety of environmental compartments, including raw wastewater, wastewater effluent, surface water, wastewater solids, sediment, groundwater, and drinking water. Here, an aggregate analysis of over 5000 reported detections was conducted to better understand the distribution of environmentally-relevant PCP concentrations in, and between, these compartments. The distributions were used to identify whether aggregated environmentally-relevant concentration ranges intersected with available toxicity data. For raw wastewater, wastewater effluent, and surface water, a clear overlap was present between the 25th-75th percentiles and identified toxicity levels. This analysis suggests that improved wastewater treatment of antimicrobials, UV filters, and polycyclic musks is required to prevent negative impacts on aquatic species. PMID:27128715

  2. Cluster analysis of spontaneous preterm birth phenotypes identifies potential associations among preterm birth mechanisms

    PubMed Central

    Esplin, M Sean; Manuck, Tracy A.; Varner, Michael W.; Christensen, Bryce; Biggio, Joseph; Bukowski, Radek; Parry, Samuel; Zhang, Heping; Huang, Hao; Andrews, William; Saade, George; Sadovsky, Yoel; Reddy, Uma M.; Ilekis, John

    2015-01-01

    Objective We sought to employ an innovative tool based on common biological pathways to identify specific phenotypes among women with spontaneous preterm birth (SPTB), in order to enhance investigators' ability to identify to highlight common mechanisms and underlying genetic factors responsible for SPTB. Study Design A secondary analysis of a prospective case-control multicenter study of SPTB. All cases delivered a preterm singleton at SPTB ≤34.0 weeks gestation. Each woman was assessed for the presence of underlying SPTB etiologies. A hierarchical cluster analysis was used to identify groups of women with homogeneous phenotypic profiles. One of the phenotypic clusters was selected for candidate gene association analysis using VEGAS software. Results 1028 women with SPTB were assigned phenotypes. Hierarchical clustering of the phenotypes revealed five major clusters. Cluster 1 (N=445) was characterized by maternal stress, cluster 2 (N=294) by premature membrane rupture, cluster 3 (N=120) by familial factors, and cluster 4 (N=63) by maternal comorbidities. Cluster 5 (N=106) was multifactorial, characterized by infection (INF), decidual hemorrhage (DH) and placental dysfunction (PD). These three phenotypes were highly correlated by Chi-square analysis [PD and DH (p<2.2e-6); PD and INF (p=6.2e-10); INF and DH (p=0.0036)]. Gene-based testing identified the INS (insulin) gene as significantly associated with cluster 3 of SPTB. Conclusion We identified 5 major clusters of SPTB based on a phenotype tool and hierarchal clustering. There was significant correlation between several of the phenotypes. The INS gene was associated with familial factors underlying SPTB. PMID:26070700

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

    PubMed

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

    2005-06-01

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

  4. Characteristics of mannosylerythritol lipids and their environmental potential.

    PubMed

    Yu, Mingda; Liu, Zhifeng; Zeng, Guangming; Zhong, Hua; Liu, Yang; Jiang, Yongbing; Li, Min; He, Xiaoxiao; He, Yan

    2015-04-30

    Mannosylerythritol lipids (MELs) are promising biosurfactants containing two glycosyl derivatives and various fatty acids, which are mainly secreted by Pseudozyma as well as Ustilago. In this review, the latest research is demonstrated on production conditions, structural diversity, self-assembling properties and versatile biochemical functions of MELs. The genetic study and synthetic pathways, which mainly influence the type and yield of MELs production. Due to the excellent surface activity, biocompatibility and restorative function, MELs can be used in enviornmental industry, which has not been widely noted. In this paper, the current status of research on enviornmental potential of MELs has been discussed including petroleum degradation, bioconversion of chemical wastes and enhanced bioremediation of amphiphilic wastes. PMID:25723622

  5. Potential environmental impacts of bioenergy crop production. Background paper

    SciTech Connect

    Not Available

    1993-09-01

    Bioenergy crops have the potential to improve the environment, increase rural incomes, and reduce Federal budget deficits and the U.S. trade imbalance. In the wake of the devastating Midwest floods, bioenergy crops may also offer a more robust crop for flood-prone regions. Bioenergy crops include annual row crops such as corn, herbaceous perennial grasses (herbaceous energy crops--HECs) such as switchgrass, and short-rotation woody crops (SRWCs) such as poplar. HECs are analogous to growing hay, harvesting the crop for energy rather than for forage. SRWCs typically consist of a plantation of closely spaced (2 to 3 meters apart on a grid) trees that are harvested on a cycle of 3 to 10 years.

  6. Fishers' knowledge identifies environmental changes and fish abundance trends in impounded tropical rivers.

    PubMed

    Hallwass, Gustavo; Lopes, Priscila F; Juras, Anastácio A; Silvano, Renato A M

    2013-03-01

    The long-term impacts of large hydroelectric dams on small-scale fisheries in tropical rivers are poorly known. A promising way to investigate such impacts is to compare and integrate the local ecological knowledge (LEK) of resource users with biological data for the same region. We analyzed the accuracy of fishers' LEK to investigate fisheries dynamics and environmental changes in the Lower Tocantins River (Brazilian Amazon) downstream from a large dam. We estimated fishers' LEK through interviews with 300 fishers in nine villages and collected data on 601 fish landings in five of these villages, 22 years after the dam's establishment (2006-2008). We compared these two databases with each other and with data on fish landings from before the dam's establishment (1981) gathered from the literature. The data obtained based on the fishers' LEK (interviews) and from fisheries agreed regarding the primary fish species caught, the most commonly used type of fishing gear (gill nets) and even the most often used gill net mesh sizes but disagreed regarding seasonal fish abundance. According to the interviewed fishers, the primary environmental changes that occurred after the impoundment were an overall decrease in fish abundance, an increase in the abundance of some fish species and, possibly, the local extinction of a commercial fish species (Semaprochilodus brama). These changes were corroborated by comparing fish landings sampled before and 22 years after the impoundment, which indicated changes in the composition of fish landings and a decrease in the total annual fish production. Our results reinforce the hypothesis that large dams may adversely affect small-scale fisheries downstream and establish a feasible approach for applying fishers' LEK to fisheries management, especially in regions with a low research capacity. PMID:23634590

  7. THE USE OF VISUAL AND CHEMOSENSORY EVOKED POTENTIALS IN ENVIRONMENTAL AND OCCUPATIONAL HEALTH

    EPA Science Inventory

    The application of visual (VEP) and chemosensory evoked potentials (CSEP) in occupational and environmental health is briefly reviewed. EPs have been used extensively in experimental neurotoxicology and play an increasing role in human neurotoxicity testing. he similarity of VEP ...

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

    SciTech Connect

    Liu Funing )

    1993-05-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  10. 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…

  11. Anti-tubercular drug development: computational strategies to identify potential compounds.

    PubMed

    Rajkhowa, Sanchaita; Jha, Anupam Nath; Deka, Ramesh Chandra

    2015-11-01

    InhA is an attractive target to combat tuberculosis (TB), which is targeted by many pro-drugs (isoniazid, etc.) and drugs such as triclosan. However, triclosan is less useful as an antitubercular drug due to its low bioavailability and therefore, in order to overcome this difficulty, many derivatives of triclosan were prepared. Here, we have combined various computational techniques to virtually screen out four potential triclosan derivatives. Molecular docking methods have been employed to screen out 32 out of 62 triclosan derivatives considering the mode of binding and the top re-rank scores. A comparative study on the chemical properties of triclosan and some of its derivatives has been performed using density functional theory (DFT) calculations. DFT based global reactivity descriptors (GRD), such as hardness, chemical potential, chemical softness, electrophilicity index, Fukui function, and local philicity calculated at the optimized geometries were used to investigate the usefulness of these descriptors for understanding the reactive nature and sites of the molecules. QSAR equations were built using these descriptors considering these 32 compounds. Four common compounds showing the best correlation and the best docking scores were considered for the ADMET property calculations and their dynamical movements have been studied using molecular dynamics simulations. Our results showed that these four compounds are chemically more active than triclosan and have the potential to inhibit the Mycobacterium tuberculosis enoyl acyl carrier protein reductase. This work shows that combination of different computational techniques may help to screen out potential drug candidates from a list of possible ones. PMID:26386453

  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. 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…

  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. 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…

  16. A national effort to identify fry processing clones with low acrylamide-forming potential

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Acrylamide is a suspected human carcinogen. Processed potato products, such as chips and fries, contribute to dietary intake of acrylamide. One of the most promising approaches to reducing acrylamide consumption is to develop and commercialize new potato varieties with low acrylamide-forming potenti...

  17. 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…

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

    PubMed

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

    2015-05-01

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

  19. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants

    PubMed Central

    Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J.; Carlson, Christopher S.; Casey, Graham; Chang-Claude, Jenny; Conti, David V.; Curtis, Keith R.; Duggan, David; Gallinger, Steven; Haile, Robert W.; Harrison, Tabitha A.; Hayes, Richard B.; Hoffmeister, Michael; Hopper, John L.; Hudson, Thomas J.; Jenkins, Mark A.; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M.; Newcomb, Polly A.; Nickerson, Deborah A.; Potter, John D.; Schoen, Robert E.; Schumacher, Fredrick R.; Seminara, Daniela; Slattery, Martha L.; Hsu, Li; Chan, Andrew T.; White, Emily; Berndt, Sonja I.; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). PMID:27379672

  20. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants.

    PubMed

    Du, Mengmeng; Jiao, Shuo; Bien, Stephanie A; Gala, Manish; Abecasis, Goncalo; Bezieau, Stephane; Brenner, Hermann; Butterbach, Katja; Caan, Bette J; Carlson, Christopher S; Casey, Graham; Chang-Claude, Jenny; Conti, David V; Curtis, Keith R; Duggan, David; Gallinger, Steven; Haile, Robert W; Harrison, Tabitha A; Hayes, Richard B; Hoffmeister, Michael; Hopper, John L; Hudson, Thomas J; Jenkins, Mark A; Küry, Sébastien; Le Marchand, Loic; Leal, Suzanne M; Newcomb, Polly A; Nickerson, Deborah A; Potter, John D; Schoen, Robert E; Schumacher, Fredrick R; Seminara, Daniela; Slattery, Martha L; Hsu, Li; Chan, Andrew T; White, Emily; Berndt, Sonja I; Peters, Ulrike

    2016-01-01

    Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s). PMID:27379672

  1. Potential environmental benefits of ionophores in ruminant diets.

    PubMed

    Tedeschi, Luis Orlindo; Fox, Danny Gene; Tylutki, Thomas Paul

    2003-01-01

    A concern of the USEPA is the volatilization of NH3 from animal manure and CH4 produced from ruminal fermentation. Excess N in the environment has been associated with adverse effects on human health, and CH4 and N2O emissions are sources of greenhouse gases. The objectives of this paper are to summarize and quantify the benefits of ionophores, principally monensin, in decreasing NH3 and CH4 emissions to the environment and reducing resource utilization in cattle (Bos spp.) production. The data indicate that monensin in the diets of ruminants may decrease protein degradation in the rumen and may increase feed protein utilization by an average of 3.5 percentage units. These changes would have an effect in reducing N losses and decreasing fecal N and the amount of protein that must be fed to meet animal requirements. Additionally, CH4 is produced by enteric fermentation in ruminants, which is responsible for about 33 to 39% of CH4 emissions from agriculture. Ionophores can reduce CH4 production by 25% and decrease feed intake by 4% without affecting animal performance. The inclusion of monensin in beef and dairy cattle diets may benefit air quality by reducing CH4 and N emissions and water quality by reducing N in manure, which can potentially leave the farm through leaching into ground water and through runoff into surface water. PMID:14535299

  2. Potential for the environmental impact of transgenic crops.

    PubMed

    Dale, Philip J; Clarke, Belinda; Fontes, Eliana M G

    2002-06-01

    In recent years, there has been increasing interest in how changes in agricultural practice associated with the introduction of particular genetically modified (GM) crops might indirectly impact the environment. There is also interest in any effects that might be associated with recombinant and novel combinations of DNA passing into the environment, and the possibility that they may be taken up by microorganisms or other live biological material. From the current state of knowledge, the impact of free DNA of transgenic origin is likely to be negligible compared with the large amount of total free DNA. We can find no compelling scientific arguments to demonstrate that GM crops are innately different from non-GM crops. The kinds of potential impacts of GM crops fall into classes familiar from the cultivation of non-GM crops (e.g., invasiveness, weediness, toxicity, or biodiversity). It is likely, however, that the novelty of some of the products of GM crop improvement will present new challenges and perhaps opportunities to manage particular crops in creative ways. PMID:12042859

  3. 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

  4. 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.

  5. Development and Use of a Selectable, Broad-Host-Range Reporter Transposon for Identifying Environmentally Regulated Promoters in Bacteria

    PubMed Central

    Spinler, Jennifer K.; Zajdowicz, Sheryl L. W.; Haller, Jon C.; Oram, Diana Marra; Gill, Ronald E.; Holmes, Randall K.

    2009-01-01

    This report describes the development and use of TnKnXSp, a selectable broad-host-range reporter transposon with a promoterless aphA gene. Insertion of TnKnXSp into the chromosome of a kanamycin-susceptible bacterium confers resistance to kanamycin only if aphA is transcribed from an active promoter adjacent to the insertion site. We designed TnKnXSp as a tool for identifying environmentally regulated promoters in bacteria and developed general methods for initial characterization of any TnKnXSp integrant. To identify putative iron-regulated promoters in Corynebacterium diphtheriae, we constructed TnKnXSp integrants and identified a subgroup that expressed kanamycin resistance under low-iron, but not high-iron, conditions. We characterized representative integrants with this phenotype, located the TnKnXSp insertion in each, and demonstrated that transcription of aphA was repressed under high-iron vs. low-iron growth conditions. We also demonstrated that TnKnXSp can be used in bacteria other than C. diphtheriae, including Escherichia coli and Bacillus subtilus. Our findings validate TnKnXSp as a useful tool for identifying environmentally regulated promoters in bacteria. PMID:19146571

  6. Potential Environmental and Environmental-Health Implications of the SAFRR Tsunami Scenario in California: Chapter F in The SAFRR (Science Application for Risk Reduction) Tsunami Scenario

    USGS Publications Warehouse

    Plumlee, Geoffrey S.; Morman, Suzette A.; San Juan, Carma

    2013-01-01

    If human populations are successfully evacuated prior to the tsunami arrival, there would be no or limited numbers of drownings, other casualties, or related injuries, wounds, and infections. Immediately after the tsunami, human populations away from the inundation zone could be transiently exposed to airborne gases, smoke, and ash from tsunamigenic fires. Cleanup and disposal, particularly of hazardous materials, would pose substantial logistical challenges and economic costs. Given the high value of the coastal residential and commercial properties in the inundation zone, it can be postulated that there would be substantial insurance claims for environmental restoration, mold mitigation, disposal of debris that contains hazardous materials, and costs of litigation related to environmental liability. Post-tsunami cleanup, if done with appropriate mitigation (for example, dust control), personal protection, and disposal measures, would help reduce the potential for cleanup-worker and resident exposures to toxicants and pathogens in harbor waters, debris, soils, ponded waters, and buildings. A number of other steps can be taken by governments, businesses, and residents to help reduce the environmental impacts of tsunamis and to recover more quickly from these environmental impacts. For example, development of State and local policies that foster rapid assessment of potential contamination, as well as rapid decision making for disposal options should hazardous debris or sediment be identified, would help enhance recovery by speeding cleanup.

  7. A molecular approach to identify active microbes in environmental eukaryote clone libraries.

    PubMed

    Stoeck, Thorsten; Zuendorf, Alexandra; Breiner, Hans-Werner; Behnke, Anke

    2007-02-01

    A rapid method for the simultaneous extraction of RNA and DNA from eukaryote plankton samples was developed in order to discriminate between indigenous active cells and signals from inactive or even dead organisms. The method was tested using samples from below the chemocline of an anoxic Danish fjord. The simple protocol yielded RNA and DNA of a purity suitable for amplification by reverse transcription-polymerase chain reaction (RT-PCR) and PCR, respectively. We constructed an rRNA-derived and an rDNA-derived clone library to assess the composition of the microeukaryote assemblage under study and to identify physiologically active constituents of the community. We retrieved nearly 600 protistan target clones, which grouped into 84 different phylotypes (98% sequence similarity). Of these phylotypes, 27% occurred in both libraries, 25% exclusively in the rRNA library, and 48% exclusively in the rDNA library. Both libraries revealed good correspondence of the general community composition in terms of higher taxonomic ranks. They were dominated by anaerobic ciliates and heterotrophic stramenopile flagellates thriving below the fjord's chemocline. The high abundance of these bacterivore organisms points out their role as a major trophic link in anoxic marine systems. A comparison of the two libraries identified phototrophic dinoflagellates, "uncultured marine alveolates group I," and different parasites, which were exclusively detected with the rDNA-derived library, as nonindigenous members of the anoxic microeukaryote community under study. PMID:17264997

  8. Identifying the potential loss of monitoring wells using an uncertainty analysis.

    PubMed

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

    2005-01-01

    From the mid-1940s through the 1980s, large volumes of waste water were discharged at the Hanford Site in southeastern Washington State, causing a large-scale rise (>20 m) in the water table. When waste water discharges ceased in 1988, ground water 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 monitoring wells that will need replacement, a methodology has been developed using a first-order uncertainty analysis with UCODE, a nonlinear parameter estimation code. Using a three-dimensional, finite-element ground water flow code, key parameters were identified by calibrating to historical hydraulic head data. Results from the calibration period were then used to check model predictions by comparing monitoring wells' wet/dry status with field data. This status was analyzed using a methodology that incorporated the 0.3 cumulative probability derived from the confidence and prediction intervals. For comparison, a nonphysically based trend model was also used as a predictor of wells' wet/dry status. Although the numerical model outperformed the trend model, for both models, the central value of the intervals was a better predictor of a wet well status. The prediction interval, however, was more successful at identifying dry wells. Predictions made through the year 2048 indicated that 46% of the wells in the monitoring well network are likely to go dry in areas near the river and where the ground water mound is dissipating. PMID:16324012

  9. 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

  10. Envisioning a metropolitan foodshed: potential environmental consequences of increasing food-crop production around Chicago

    NASA Astrophysics Data System (ADS)

    Bowen, E. E.; Martin, P. A.; Schuble, T. J.

    2009-12-01

    Nationwide, cities are increasingly developing policies aimed at greater sustainability, particularly focusing on reducing environmental impact. Such policies commonly emphasize more efficiently using energy to decrease the greenhouse gas (GHG) footprint of the city. However, most plans ignore the food system as a factor in regional energy use and GHG emissions. Yet, the food system in the United States accounts for ~20% of per capita greenhouse gas emissions. Local, sustainable food production is cited as one strategy for mitigating GHG emissions of large metropolitan areas. “Sustainable” for regional agriculture is often identified as small-scale, diversified food crop production using best practices management. Localized food production (termed “foodshed”) using sustainable agriculture could mitigate climate change in multiple ways: (1) energy and therefore CO2-intensive portions of the conventional food system might be replaced by local, lower-input food production resulting in carbon offsets; (2) increased regional carbon storage might result from well-managed food crop production vs. commodity crop production; and (3) averted N2O emissions might result from closing nutrient cycles on agricultural lands following changes in management practices. The broader implications for environmental impact of widespread conversion to sustainable food crop agriculture, however, remain largely unknown. We examine the Chicago metropolitan region to quantify the impact of increased local food production on regional energy efficiency and GHG emissions. Geospatial analysis is used to quantify the resource potential for establishing a Chicago metropolitan foodshed. A regional foodshed is defined by minimizing cost through transportation mode (road, rail, or water) and maximizing the production potential of different soil types. Simple biogeochemical modeling is used to predict changes in N2O emissions and nutrient flows following changes in land management practices

  11. Environmental characterization of two potential locations at Hanford for a new production reactor

    SciTech Connect

    Watson, E.C.; Becker, C.D.; Fitzner, R.E.; Gano, K.A.; Imhoff, K.L.; McCallum, R.F.; Myers, D.A.; Page, T.L.; Price, K.R.; Ramsdell, J.V.; Rice D.G.; Schreiber D.L.; Skumatz L.A.; Sommer D.J.; Tawil J.J.; Wallace R.W.; Watson D.G.

    1984-09-01

    This report describes various environmental aspects of two areas on the Hanford Site that are potential locations for a New Production Reactor (NPR). The area known as the Skagit Hanford Site is considered the primary or reference site. The second area, termed the Firehouse Site, is considered the alternate site. The report encompasses an environmental characterization of these two potential NPR locations. Eight subject areas are covered: geography and demography; ecology; meteorology; hydrology; geology; cultural resources assessment; economic and social effects of station construction and operation; and environmental monitoring. 80 refs., 68 figs., 109 tabs.

  12. Potential of infrared spectroscopy in combination with extended canonical variate analysis for identifying different paper types

    NASA Astrophysics Data System (ADS)

    Riba, Jordi-Roger; Canals, Trini; Cantero, Rosa; Iturriaga, Hortensia

    2011-02-01

    The increasing use of secondary fiber in papermaking has led to the production of paper containing a wide range of contaminants. Wastepaper mills need to develop quality control methods for evaluating the incoming wastepaper stock as well as testing the specifications of the final product. The goal of this work is to present a fast and successful methodology for identifying different paper types. In this way, undesirable paper types can be refused, thus improving the runnability of the paper machine and the quality of the paper manufactured. In this work we examine various types of paper using information obtained by an appropriate chemometric treatment of infrared spectral data. For this purpose, we studied a large number of paper sheets of three different types (namely coated, offset and cast-coated) supplied by several paper manufacturers. We recorded Fourier transform infrared (FTIR) spectra with the aid of an attenuated total reflectance (ATR) module and near-infrared (NIR) reflectance spectra by means of fiber optics. Both techniques proved expeditious and required no sample pretreatment. The primary objective of this work was to develop a methodology for the accurate identification of samples of different paper types. For this purpose, we used the chemometric discrimination technique extended canonical variate analysis (ECVA) in combination with the k nearest neighbor (kNN) method to classify samples in the prediction set. Use of the NIR and FTIR techniques under these conditions allowed paper types to be identified with 100% success in prediction samples.

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

    PubMed Central

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

    2014-01-01

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

  14. 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

  15. A Quantitative High-Throughput Screen Identifies Potential Epigenetic Modulators of Gene Expression

    PubMed Central

    Johnson, Ronald L.; Huang, Wenwei; Jadhav, Ajit; Austin, Christopher P.; Inglese, James; Martinez, Elisabeth D.

    2008-01-01

    Epigenetic regulation of gene expression is essential in embryonic development and contributes to cancer pathology. We used a cell-based imaging assay that measures derepression of a silenced GFP reporter to identify novel classes of compounds involved in epigenetic regulation. This Locus Derepression (LDR) assay was screened against a 69,137-member chemical library using quantitative high-throughput screening (qHTS), a titration-response method that assays compounds at multiple concentrations. From structure-activity relationships of the 411 actives recovered from the qHTS, six distinct chemical series were chosen for further study. Forty-eight qHTS actives and analogs were counter screened using the parental line of the LDR cells, which lack the GFP reporter. Three series, 8-hydroxy quinoline, quinoline-8-thiol and 1,3,5-thiadiazinane-2-thione, were not fluorescent and re-confirmed activity in the LDR cells. The three active series did not inhibit histone deacetylase activity in nuclear extracts or reactivate the expression of the densely methylated p16 gene in cancer cells. However, one series induced expression of the methylated CDH13 gene and inhibited the viability of several lung cancer lines at submicromolar concentrations. These results suggest that the identified small molecules act on epigenetic or transcriptional components and validate our approach of using a cell-based imaging assay in conjunction with qHTS. PMID:18211814

  16. 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

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

    PubMed Central

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

    2013-01-01

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

  18. New potential markers of in vitro tomato morphogenesis identified by mRNA differential display.

    PubMed

    Torelli, A; Soragni, E; Bolchi, A; Petrucco, S; Ottonello, S; Branca, C

    1996-12-01

    The identification of plant genes involved in early phases of in vitro morphogenesis can not only contribute to our understanding of the processes underlying growth regulator-controlled determination, but also provide novel markers for evaluating the outcome of in vitro regeneration experiments. To search for such genes and to monitor changes in gene expression accompanying in vitro regeneration, we have adapted the mRNA differential display technique to the comparative analysis of a model system of tomato cotyledons that can be driven selectively toward either shoot or callus formation by means of previously determined growth regulator supplementations. Hormone-independent transcriptional modulation (mainly down-regulation) has been found to be the most common event, indicating that a non-specific reprogramming of gene expression quantitatively predominates during the early phases of in vitro culture. However, cDNA fragments representative of genes that are either down-regulated or induced in a programme-specific manner could also be identified, and two of them (G35, G36) were further characterized. One of these cDNA fragments, G35, corresponds to an mRNA that is down-regulated much earlier in callus- (day 2) than in shoot-determined explants (day 6). The other, G36, identifies an mRNA that is transiently expressed in shoot-determined explants only, well before any macroscopic signs of differentiation become apparent, and thus exhibits typical features of a morphogenetic marker. PMID:8980540

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

    PubMed

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

    2010-12-01

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

  20. 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

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  2. Infrared Spectroscopy of Pollen Identifies Plant Species and Genus as Well as Environmental Conditions

    PubMed Central

    Zimmermann, Boris; Kohler, Achim

    2014-01-01

    Background It is imperative to have reliable and timely methodologies for analysis and monitoring of seed plants in order to determine climate-related plant processes. Moreover, impact of environment on plant fitness is predominantly based on studies of female functions, while the contribution of male gametophytes is mostly ignored due to missing data on pollen quality. We explored the use of infrared spectroscopy of pollen for an inexpensive and rapid characterization of plants. Methodology The study was based on measurement of pollen samples by two Fourier transform infrared techniques: single reflectance attenuated total reflectance and transmission measurement of sample pellets. The experimental set, with a total of 813 samples, included five pollination seasons and 300 different plant species belonging to all principal spermatophyte clades (conifers, monocotyledons, eudicots, and magnoliids). Results The spectroscopic-based methodology enables detection of phylogenetic variations, including the separation of confamiliar and congeneric species. Furthermore, the methodology enables measurement of phenotypic plasticity by the detection of inter-annual variations within the populations. The spectral differences related to environment and taxonomy are interpreted biochemically, specifically variations of pollen lipids, proteins, carbohydrates, and sporopollenins. The study shows large variations of absolute content of nutrients for congenital species pollinating in the same environmental conditions. Moreover, clear correlation between carbohydrate-to-protein ratio and pollination strategy has been detected. Infrared spectral database with respect to biochemical variation among the range of species, climate and biogeography will significantly improve comprehension of plant-environment interactions, including impact of global climate change on plant communities. PMID:24748390

  3. X-ray Absorption Spectroscopy Identifies Calcium-Uranyl-Carbonate Complexes at Environmental Concentrations

    SciTech Connect

    Kelly, Shelly D; Kemner, Kenneth M; Brooks, Scott C

    2007-01-01

    Current research on bioremediation of uranium-contaminated groundwater focuses on supplying indigenous metal-reducing bacteria with the appropriate metabolic requirements to induce microbiological reduction of soluble uranium(VI) to poorly soluble uranium(IV). Recent studies of uranium(VI) bioreduction in the presence of environmentally relevant levels of calcium revealed limited and slowed uranium(VI) reduction and the formation of a Ca-UO2-CO3 complex. However, the stoichiometry of the complex is poorly defined and may be complicated by the presence of a Na-UO2-CO3 complex. Such a complex might exist even at high calcium concentrations, as some UO2-CO3 complexes will still be present. The number of calcium and/or sodium atoms coordinated to a uranyl carbonate complex will determine the net charge of the complex. Such a change in aqueous speciation of uranium(VI) in calcareous groundwater may affect the fate and transport properties of uranium. In this paper, we present the results from X-ray absorption fine structure (XAFS) measurements of a series of solutions containing 50 lM uranium(VI) and 30 mM sodium bicarbonate, with various calcium concentrations of 0-5 mM. Use of the data series reduces the uncertainty in the number of calcium atoms bound to the UO2-CO3 complex to approximately 0.6 and enables spectroscopic identification of the Na-UO2-CO3 complex. At nearly neutral pH values, the numbers of sodium and calcium atoms bound to the uranyl triscarbonate species are found to depend on the calcium concentration, as predicted by speciation calculations.

  4. X-ray absorption spectroscopy identifies calcium-uranyl-carbonate complexes at environmental concentrations.

    SciTech Connect

    Kelly, S. D.; Kemner, K. M.; Brooks, S. C.; Biosciences Division; ORNL

    2007-01-01

    Current research on bioremediation of uranium-contaminated groundwater focuses on supplying indigenous metal-reducing bacteria with the appropriate metabolic requirements to induce microbiological reduction of soluble uranium(VI) to poorly soluble uranium(IV). Recent studies of uranium(VI) bioreduction in the presence of environmentally relevant levels of calcium revealed limited and slowed uranium(VI) reduction and the formation of a Ca-UO{sub 2}-CO{sub 3} complex. However, the stoichiometry of the complex is poorly defined and may be complicated by the presence of a Na-UO{sub 2}-CO{sub 3} complex. Such a complex might exist even at high calcium concentrations, as some UO{sub 2}-CO{sub 3} complexes will still be present. The number of calcium and/or sodium atoms coordinated to a uranyl carbonate complex will determine the net charge of the complex. Such a change in aqueous speciation of uranium(VI) in calcareous groundwater may affect the fate and transport properties of uranium. In this paper, we present the results from X-ray absorption fine structure (XAFS) measurements of a series of solutions containing 50 {micro}M uranium(VI) and 30 mM sodium bicarbonate, with various calcium concentrations of 0-5 mM. Use of the data series reduces the uncertainty in the number of calcium atoms bound to the UO{sub 2}-CO{sub 3} complex to approximately 0.6 and enables spectroscopic identification of the Na-UO{sub 2}-CO{sub 3} complex. At nearly neutral pH values, the numbers of sodium and calcium atoms bound to the uranyl triscarbonate species are found to depend on the calcium concentration, as predicted by speciation calculations.

  5. Evoked Potential Monitoring Identifies Possible Neurological Injury During Positioning for Craniotomy

    PubMed Central

    Anastasian, Zirka H.; Ramnath, Brian; Komotar, Ricardo J.; Bruce, Jeffrey N.; Sisti, Michael B.; Gallo, Edward J.; Emerson, Ronald G.; Heyer, Eric J.

    2009-01-01

    Somatosensory evoked potential (SSEP) monitoring is commonly used to detect changes in nerve conduction and prevent impending nerve injury. We present a case series of 2 patients who had SSEP monitoring for their surgical craniotomy procedure, and who, upon positioning supine with their head tilted 30–45 degrees, developed unilateral upper extremity SSEP changes. These SSEP changes were reversed when the patients were repositioned. These cases indicate the clinical usefulness of monitoring SSEPs while positioning the patient and adjusting position accordingly to prevent injury. PMID:19690251

  6. Endocrine-Disrupting Chemicals and Oil and Natural Gas Operations: Potential Environmental Contamination and Recommendations to Assess Complex Environmental Mixtures

    PubMed Central

    Kassotis, Christopher D.; Tillitt, Donald E.; Lin, Chung-Ho; McElroy, Jane A.; Nagel, Susan C.

    2015-01-01

    Background Hydraulic fracturing technologies, developed over the last 65 years, have only recently been combined with horizontal drilling to unlock oil and gas reserves previously deemed inaccessible. Although these technologies have dramatically increased domestic oil and natural gas production, they have also raised concerns for the potential contamination of local water supplies with the approximately 1,000 chemicals that are used throughout the process, including many known or suspected endocrine-disrupting chemicals. Objectives We discuss the need for an endocrine component to health assessments for drilling-dense regions in the context of hormonal and antihormonal activities for chemicals used. Methods We discuss the literature on a) surface and groundwater contamination by oil and gas extraction operations, and b) potential human exposure, particularly in the context of the total hormonal and antihormonal activities present in surface and groundwater from natural and anthropogenic sources; we also discuss initial analytical results and critical knowledge gaps. Discussion In light of the potential for environmental release of oil and gas chemicals that can disrupt hormone receptor systems, we recommend methods for assessing complex hormonally active environmental mixtures. Conclusions We describe a need for an endocrine-centric component for overall health assessments and provide information supporting the idea that using such a component will help explain reported adverse health trends as well as help develop recommendations for environmental impact assessments and monitoring programs. Citation Kassotis CD, Tillitt DE, Lin CH, McElroy JA, Nagel SC. 2016. Endocrine-disrupting chemicals and oil and natural gas operations: potential environmental contamination and recommendations to assess complex environmental mixtures. Environ Health Perspect 124:256–264; http://dx.doi.org/10.1289/ehp.1409535 PMID:26311476

  7. 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, Barrett’s 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 Barrett’s 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 Barrett’s esophagus. PMID:25400987

  8. 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

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

    PubMed

    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

  10. Conflict on the coast: using geographic information systems to map potential environmental disputes in Matagorda Bay, Texas.

    PubMed

    Brody, Samuel D; Highfield, Wes; Arlikatti, Sudha; Bierling, David H; Ismailova, Roubabah M; Lee, Lai; Butzler, Rachel

    2004-07-01

    The sustainable management of coastal natural resources inevitably involves identifying stakeholder conflicts and developing planning processes that prevent these conflicts from becoming intractable disputes. This study links environmental conflict to specific areas within a large ecological system. Specifically, we use Geographic Information Systems (GIS) to map potentially competing stakeholder values associated with establishing protected areas in Matagorda Bay, Texas. By overlaying multiple values associated with a range of stakeholders across space, we are able to identify hotspots of potential conflict as well as areas of opportunity for maximizing joint gains. Mapping stakeholder conflict is an approach to proactively locate potential controversy in response to a specific environmental management proposal and guide decision makers in crafting planning processes that mitigate the possibility of intractable disputes and facilitate the implementation of sustainable coastal policies. Results indicate that under different management scenarios, protected area proposals will generate more conflict in specific areas. Most notably, regulated uses would produce the greatest degree of conflict on or near shore, particularly at the mouth of the Colorado River. Additionally, of all the management scenarios evaluated, the prohibition of coastal structural development would generate the overall highest level of conflict within the Bay. Based on the results, we discuss the policy implications for environmental managers and provide guidance for future research on location-based conflict management within the coastal margin. PMID:15156354

  11. Niche Divergence versus Neutral Processes: Combined Environmental and Genetic Analyses Identify Contrasting Patterns of Differentiation in Recently Diverged Pine Species

    PubMed Central

    Moreno-Letelier, Alejandra; Ortíz-Medrano, Alejandra; Piñero, Daniel

    2013-01-01

    Background and Aims Solving relationships of recently diverged taxa, poses a challenge due to shared polymorphism and weak reproductive barriers. Multiple lines of evidence are needed to identify independently evolving lineages. This is especially true of long-lived species with large effective population sizes, and slow rates of lineage sorting. North American pines are an interesting group to test this multiple approach. Our aim is to combine cytoplasmic genetic markers with environmental information to clarify species boundaries and relationships of the species complex of Pinus flexilis, Pinus ayacahuite, and Pinus strobiformis. Methods Mitochondrial and chloroplast sequences were combined with previously obtained microsatellite data and contrasted with environmental information to reconstruct phylogenetic relationships of the species complex. Ecological niche models were compared to test if ecological divergence is significant among species. Key Results and Conclusion Separately, both genetic and ecological evidence support a clear differentiation of all three species but with different topology, but also reveal an ancestral contact zone between P. strobiformis and P. ayacahuite. The marked ecological differentiation of P. flexilis suggests that ecological speciation has occurred in this lineage, but this is not reflected in neutral markers. The inclusion of environmental traits in phylogenetic reconstruction improved the resolution of internal branches. We suggest that combining environmental and genetic information would be useful for species delimitation and phylogenetic studies in other recently diverged species complexes. PMID:24205167

  12. Using canonical correlation analysis to identify environmental attitude groups: considerations for national forest planning in the southwestern U.S.

    PubMed

    Prera, Alejandro J; Grimsrud, Kristine M; Thacher, Jennifer A; McCollum, Dan W; Berrens, Robert P

    2014-10-01

    As public land management agencies pursue region-specific resource management plans, with meaningful consideration of public attitudes and values, there is a need to characterize the complex mix of environmental attitudes in a diverse population. The contribution of this investigation is to make use of a unique household, mail/internet survey data set collected in 2007 in the Southwestern United States (Region 3 of the U.S. Forest Service). With over 5,800 survey responses to a set of 25 Public Land Value statements, canonical correlation analysis is able to identify 7 statistically distinct environmental attitudinal groups. We also examine the effect of expected changes in regional demographics on overall environmental attitudes, which may help guide in the development of socially acceptable long-term forest management policies. Results show significant support for conservationist management policies and passive environmental values, as well as a greater role for stakeholder groups in generating consensus for current and future forest management policies. PMID:25108659

  13. Use of laboratory and field testing to identify potential production problems in the Troll field

    SciTech Connect

    Hartley, R.; Jadid, M.B.

    1989-02-01

    The areal extent of the oil found in Troll made it clear at a very early stage in the field's appraisal that subsea wells would be required if the oil were developed. Owing to cooling in the subsea flowline, subsea wells can be expected to pose more production chemistry problems than would be expected with conventional platform wells. Consequently, a number of laboratory tests were carried out during the appraisal campaign to identify problems to be expected with scaling, foaming, emulsification, wax deposition, and hydrates. Dehydration and wax deposition tests were also carried out offshore during appraisal-well testing. These tests are described, together with the methods subsequently adopted to minimize future production problems.

  14. Pharmaceutical screen identifies novel target processes for activation of autophagy with a broad translational potential.

    PubMed

    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

  15. 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.

  16. 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

  17. Melatonin identified in meats and other food stuffs: potentially nutritional impact.

    PubMed

    Tan, Dun-Xian; Zanghi, Brian M; Manchester, Lucien C; Reiter, Russel J

    2014-09-01

    Melatonin has been identified in primitive photosynthetic bacteria, fungi, plants, and animals including humans. Vegetables, fruits, cereals, wine, and beers all contain melatonin. However, the melatonin content in meats has not been reported previously. Here, for the first time, we report melatonin in meats, eggs, colostrum, and in other edible food products. The levels of melatonin measured by HPLC, in lamb, beef, pork, chicken, and fish, are comparable to other food stuffs (in the range of ng/g). These levels are significantly higher than melatonin concentrations in the blood of vertebrates. As melatonin is a potent antioxidant, its presence in the meat could contribute to shelf life duration as well as preserve their quality and taste. In addition, the consumption of these foods by humans or animals could have health benefits considering the important functions of melatonin as a potent free radical scavenger and antioxidant. PMID:24942090

  18. 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

  19. 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

  20. Integrative Analysis of Genomics and Transcriptome Data to Identify Potential Functional Genes of BMDs in Females.

    PubMed

    Chen, Yuan-Cheng; Guo, Yan-Fang; He, Hao; Lin, Xu; Wang, Xia-Fang; Zhou, Rou; Li, Wen-Ting; Pan, Dao-Yan; Shen, Jie; Deng, Hong-Wen

    2016-05-01

    Osteoporosis is known to be highly heritable. However, to date, the findings from more than 20 genome-wide association studies (GWASs) have explained less than 6% of genetic risks. Studies suggest that the missing heritability data may be because of joint effects among genes. To identify novel heritability for osteoporosis, we performed a system-level study on bone mineral density (BMD) by weighted gene coexpression network analysis (WGCNA), using the largest GWAS data set for BMD in the field, Genetic Factors for Osteoporosis Consortium (GEFOS-2), and a transcriptomic gene expression data set generated from transiliac bone biopsies in women. A weighted gene coexpression network was generated for 1574 genes with GWAS nominal evidence of association (p ≤ 0.05) based on dissimilarity measurement on the expression data. Twelve distinct gene modules were identified, and four modules showed nominally significant associations with BMD (p ≤ 0.05), but only one module, the yellow module, demonstrated a good correlation between module membership (MM) and gene significance (GS), suggesting that the yellow module serves an important biological role in bone regulation. Interestingly, through characterization of module content and topology, the yellow module was found to be significantly enriched with contractile fiber part (GO:044449), which is widely recognized as having a close relationship between muscle and bone. Furthermore, detailed submodule analyses of important candidate genes (HOMER1, SPTBN1) by all edges within the yellow module implied significant enrichment of functional connections between bone and cytoskeletal protein binding. Our study yielded novel information from system genetics analyses of GWAS data jointly with transcriptomic data. The findings highlighted a module and several genes in the model as playing important roles in the regulation of bone mass in females, which may yield novel insights into the genetic basis of osteoporosis. © 2016

  1. Kinase analysis in alcoholic hepatitis identifies p90RSK as a potential mediator of liver fibrogenesis

    PubMed Central

    Morales-Ibanez, Oriol; Affò, Silvia; Rodrigo-Torres, Daniel; Blaya, Delia; Millán, Cristina; Coll, Mar; Perea, Luis; Odena, Gemma; Knorpp, Thomas; Templin, Markus F; Moreno, Montserrat; Altamirano, José; Miquel, Rosa; Arroyo, Vicente; Ginès, Pere; Caballería, Juan; Sancho-Bru, Pau; Bataller, Ramon

    2015-01-01

    Objective Alcoholic hepatitis (AH) is often associated with advanced fibrosis, which negatively impacts survival. We aimed at identifying kinases deregulated in livers from patients with AH and advanced fibrosis in order to discover novel molecular targets. Design Extensive phosphoprotein analysis by reverse phase protein microarrays was performed in AH (n=12) and normal human livers (n=7). Ribosomal S6 kinase (p90RSK) hepatic expression was assessed by qPCR, Western blot and immunohistochemistry. Kaempferol was used as a selective pharmacological inhibitor of the p90RSK pathway to assess the regulation of experimentally-induced liver fibrosis and injury, using in vivo and in vitro approaches. Results Proteomic analysis identified p90RSK as one of the most deregulated kinases in AH. Hepatic p90RSK gene and protein expression was also upregulated in livers with chronic liver disease. Immunohistochemistry studies showed increased p90RSK staining in areas of active fibrogenesis in cirrhotic livers. Therapeutic administration of kaempferol to carbon tetrachloride-treated mice resulted in decreased hepatic collagen deposition, and expression of profibrogenic and proinflammatory genes, compared to vehicle administration. In addition, kaempferol reduced the extent of hepatocellular injury and degree of apoptosis. In primary hepatic stellate cells, kaempferol and small interfering RNA decreased activation of p90RSK, which in turn regulated key profibrogenic actions. In primary hepatocytes, kaempferol attenuated proapoptotic signalling. Conclusions p90RSK is upregulated in patients with chronic liver disease and mediates liver fibrogenesis in vivo and in vitro. These results suggest that the p90RSK pathway could be a new therapeutic approach for liver diseases characterised by advanced fibrosis. PMID:25652085

  2. 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...

  3. Results of an Assessment to Identify Potential Barriers to Sustainable Agriculture on American Indian Reservations in the Western United States

    ERIC Educational Resources Information Center

    Singletary, Loretta; Emm, Staci; Brummer, Fara Ann; Hill, George C.; Lewis, Steve; Hebb, Vicki

    2016-01-01

    Purpose: This paper reports the results of survey research conducted with tribal producers between 2011 and 2012 on 19 of the largest American Indian reservations in Idaho, Nevada, North Dakota, Oregon, South Dakota, and Washington. The purpose of the research was to identify potential barriers to sustainable agriculture on reservation lands. This…

  4. 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.

  5. 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.

  6. 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

  7. Mercury Isotopes as Proxies to Identify Sources and Environmental Impacts of Mercury in Sphalerites

    PubMed Central

    Yin, Runsheng; Feng, Xinbin; Hurley, James P.; Krabbenhoft, David P.; Lepak, Ryan F.; Hu, Ruizhong; Zhang, Qian; Li, Zhonggen; Bi, Xianwu

    2016-01-01

    During the past few years, evidence of mass independent fractionation (MIF) for mercury (Hg) isotopes have been reported in the Earth’s surface reservoirs, mainly assumed to be formed during photochemical processes. However, the magnitude of Hg-MIF in interior pools of the crust is largely unknown. Here, we reported significant variation in Hg-MIF signature (Δ199Hg: −0.24 ~ + 0.18‰) in sphalerites collected from 102 zinc (Zn) deposits in China, indicating that Hg-MIF can be recorded into the Earth’s crust during geological recycling of crustal material. Changing magnitudes of Hg-MIF signals were observed in Zn deposits with different formations, evidence that Hg isotopes (especially Hg-MIF) can be a useful tracer to identify sources (syngenetic and epigenetic) of Hg in mineral deposits. The average isotopic composition in studied sphalerites (δ202Hgaverage: −0.58‰; Δ199Hgaverage: +0.03‰) may be used to fingerprint Zn smelting activities, one of the largest global Hg emission sources. PMID:26728705

  8. Mercury Isotopes as Proxies to Identify Sources and Environmental Impacts of Mercury in Sphalerites.

    PubMed

    Yin, Runsheng; Feng, Xinbin; Hurley, James P; Krabbenhoft, David P; Lepak, Ryan F; Hu, Ruizhong; Zhang, Qian; Li, Zhonggen; Bi, Xianwu

    2016-01-01

    During the past few years, evidence of mass independent fractionation (MIF) for mercury (Hg) isotopes have been reported in the Earth's surface reservoirs, mainly assumed to be formed during photochemical processes. However, the magnitude of Hg-MIF in interior pools of the crust is largely unknown. Here, we reported significant variation in Hg-MIF signature (Δ(199)Hg: -0.24 ~ + 0.18‰) in sphalerites collected from 102 zinc (Zn) deposits in China, indicating that Hg-MIF can be recorded into the Earth's crust during geological recycling of crustal material. Changing magnitudes of Hg-MIF signals were observed in Zn deposits with different formations, evidence that Hg isotopes (especially Hg-MIF) can be a useful tracer to identify sources (syngenetic and epigenetic) of Hg in mineral deposits. The average isotopic composition in studied sphalerites (δ(202)Hg average: -0.58‰; Δ(199)Hg average: +0.03‰) may be used to fingerprint Zn smelting activities, one of the largest global Hg emission sources. PMID:26728705

  9. Mercury Isotopes as Proxies to Identify Sources and Environmental Impacts of Mercury in Sphalerites

    NASA Astrophysics Data System (ADS)

    Yin, Runsheng; Feng, Xinbin; Hurley, James P.; Krabbenhoft, David P.; Lepak, Ryan F.; Hu, Ruizhong; Zhang, Qian; Li, Zhonggen; Bi, Xianwu

    2016-01-01

    During the past few years, evidence of mass independent fractionation (MIF) for mercury (Hg) isotopes have been reported in the Earth’s surface reservoirs, mainly assumed to be formed during photochemical processes. However, the magnitude of Hg-MIF in interior pools of the crust is largely unknown. Here, we reported significant variation in Hg-MIF signature (Δ199Hg: -0.24 ~ + 0.18‰) in sphalerites collected from 102 zinc (Zn) deposits in China, indicating that Hg-MIF can be recorded into the Earth’s crust during geological recycling of crustal material. Changing magnitudes of Hg-MIF signals were observed in Zn deposits with different formations, evidence that Hg isotopes (especially Hg-MIF) can be a useful tracer to identify sources (syngenetic and epigenetic) of Hg in mineral deposits. The average isotopic composition in studied sphalerites (δ202Hgaverage: -0.58‰ Δ199Hgaverage: +0.03‰) may be used to fingerprint Zn smelting activities, one of the largest global Hg emission sources.

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

    PubMed

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

    2015-01-01

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

  11. Assessment of the in vitro antimicrobial activity of Lactobacillus species for identifying new potential antibiotics.

    PubMed

    Dubourg, Grégory; Elsawi, Ziena; Raoult, Didier

    2015-11-01

    The bacteriocin-mediated antimicrobial properties of Lactobacillus spp. have been widely studied, leading to the use of these micro-organisms in the food industry as preservative agents against foodborne pathogens. In an era in which antibiotic resistance is becoming a public health issue, the antimicrobial activity of Lactobacillus spp. could be used for the discovery of new potential antibiotics. Thus, it is essential to have an accurate method of screening the production of antimicrobial agents by prokaryotes. Many in vitro assays have been published to date, largely concerning but not limited to Lactobacillus spp. However, these methods mainly use the spot-on-the-lawn method, which is prone to contamination during the overlay stage, with protocols using methanol vapours or the reverse side agar technique being applied to avoid such contamination. In this study, a method combining the spot-on-the-lawn and well diffusion methods was tested, permitting clear identification of inhibition zones from eight Lactobacillus spp. towards clinical isolates of 12 species (11 bacteria and 1 yeast) commonly found in human pathology. Lactobacillus plantarum CIP 106786 and Lactobacillus rhamnosus CSUR P567 exhibited the widest antimicrobial activity, whereas Lactobacillus acidophilus strain DSM 20079 was relatively inactive. In addition, the putative MIC(50) of L. rhamnosus against Proteus mirabilis was estimated at 1.1×10(9)CFU/mL using culture broth dilution. In conclusion, considering the increasing cultivable bacterial human repertoire, these findings open the way of an effective method to screen in vitro for the production of potential antimicrobial compounds. PMID:26163158

  12. 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

  13. 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

  14. Estimating juniper cover from NAIP imagery and evaluating relationships between potential cover and environmental variables

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Juniper management is constrained by limited tools to estimate juniper cover and potential cover at stand closure across landscapes. We evaluated if remotely sensed imagery (NAIP) could be used to estimate juniper cover and if environmental characteristic could be used to determine potential junipe...

  15. 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

  16. Yeast model identifies ENTPD6 as a potential non-obstructive azoospermia pathogenic gene.

    PubMed

    Wang, Qian; Liu, Chao; Tang, Chaoming; Guo, Huiping; Liu, Yujiao; Wang, Lina; Zhao, Haichao; Shang, Yongliang; Wen, Yang; Lin, Yuan; Zhou, Tao; Zhou, Zuomin; Dong, Wen; Hu, Zhibin; Guo, Xuejiang; Sha, Jiahao; Li, Wei

    2015-01-01

    Approximately ten percent of male infertility is caused by non-obstructive azoospermia (NOA), but the etiologies of many NOA remain elusive. Recently, a genome-wide association study (GWAS) of NOA in Han Chinese men was conducted, and only a few genetic variants associated with NOA were found, which might have resulted from genetic heterogeneity. However, those variants that lack genome-wide significance might still be essential for fertility. Functional analysis of genes surrounding these variants in Drosophila identified some spermatogenesis-essential genes. As a complementary method of Drosophila screening, SK1 background Saccharomvces cerevisiae was used as a model to screen meiosis-related genes from the NOA GWAS data in this study. After functional screening, GDA1 (orthologous to humanENTPD6) was found to be a novel meiosis-related gene. The deletion of GDA1 resulted in the failure of yeast sporulation. Further investigations showed that Gda1p was important for pre-meiotic S phase entry. Interestingly, the meiotic role of Gda1p was dependent on its guanosine diphosphatase activity, but not it's cytoplasmic, transmembrane or stem domains. These yeast data suggest that ENTPD6 may be a novel meiosis-associated NOA-related gene, and the yeast model provides a good approach to analyze GWAS results of NOA. PMID:26152596

  17. 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, Déborah; 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

  18. 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

  19. Principal components analysis to identify influences on research communication and engagement during an environmental disaster

    PubMed Central

    Winters, Charlene A; Moore, Colleen F; Kuntz, Sandra W; Weinert, Clarann; Hernandez, Tanis; Black, Brad

    2016-01-01

    Objectives To discern community attitudes towards research engagement in Libby, Montana, the only Superfund site for which a public health emergency has been declared. Study design Survey study of convenience samples of residents near the Libby, Montana Superfund site. Participants Residents of the Libby, Montana area were recruited from a local retail establishment (N=120, survey 1) or a community event (N=127, survey 2). Measures Two surveys were developed in consultation with a Community Advisory Panel. Results Principal components of survey 1 showed four dimensions of community members' attitudes towards research engagement: (1) researcher communication and contributions to the community, (2) identity and affiliation of the researchers requesting participation, (3) potential personal barriers, including data confidentiality, painful or invasive procedures and effects on health insurance and (4) research benefits for the community, oneself or family. The score on the first factor was positively related to desire to participate in research (r=0.31, p=0.01). Scores on factors 2 and 3 were higher for those with diagnosis of asbestos-related disease (ARD) in the family (Cohen's d=0.41, 0.57). Survey 2 also found more positive attitudes towards research when a family member had ARD (Cohen's d=0.48). Conclusions Principal components analysis shows different dimensions of attitudes towards research engagement. The different dimensions are related to community members' desire to be invited to participate in research, awareness of past research in the community and having been screened or diagnosed with a health condition related to the Superfund contaminant. PMID:27507235

  20. Identifying the role of environmental drivers in organic carbon export from a forested peat catchment.

    PubMed

    Ryder, Elizabeth; de Eyto, Elvira; Dillane, Mary; Poole, Russell; Jennings, Eleanor

    2014-08-15

    Carbon export in streams draining peat catchments represents a potential loss of carbon from long-term stores to downstream aquatic systems and ultimately, through mineralisation, to the atmosphere. There is now a large body of evidence that dissolved organic carbon (DOC) export has increased significantly in recent decades at many sites, although there is still debate about the drivers of this increase. In this study, DOC export and particulate organic carbon (POC) export were quantified from a forested peatland catchment in the west of Ireland over two years at a fine temporal resolution. The principle drivers of change in stream DOC and POC concentrations were investigated using a general additive modelling (GAM) approach. The study period included drought conditions in the early summer of 2010 and clearfelling of some commercial forestry in early 2011. The results indicated that annual loads of 9.5 t DOC km(2) year(-1) and 6.2 t POC km(2) year(-1) were exported from the catchment in 2010. This combined annual load of 15.7 t C km(2) year(-1) would represent between 0.01% and 0.02% of typical estimates for peat soil carbon storage in the region. Soil temperature, river discharge and drought explained 59.7% the deviance in DOC concentrations, while soil temperature, river discharge, and rainfall were the significant drivers of variation in POC concentrations, explaining 58.3% of deviance. Although clearfelling was not a significant factor in either model, large spikes in POC export occurred in 2011 after the first forestry clearance. The results illustrate the complexity of the interactions between climate and land management in driving stream water carbon export. They also highlight the sensitivity of peatland carbon stores to changes in temperature and precipitation, which are projected to be more extreme and variable under future climate scenarios. PMID:24840277

  1. In silico approaches to identify the potential inhibitors of glutamate carboxypeptidase II (GCPII) for neuroprotection.

    PubMed

    Naushad, Shaik Mohammad; Janaki Ramaiah, M; Stanley, Balraj Alex; Prasanna Lakshmi, S; Vishnu Priya, J; Hussain, Tajamul; Alrokayan, Salman A; Kutala, Vijay Kumar

    2016-10-01

    To develop a potential inhibitor for glutamate carboxypeptidase II (GCPII) effective against all the eight common genetic variants reported, PyMOL molecular visualization system was used to generate models of variants using the crystal structure of GCPII i.e. 2OOT as a template. High-throughput virtual screening of 29 compounds revealed differential efficacy across the eight genetic variants (pIC50: 4.70 to 10.22). Pharmacophore analysis and quantitative structure-activity relationship (QSAR) studies revealed a urea-based N-acetyl aspartyl glutamate (NAAG) analogue as more potent inhibitor, which was effective across all the genetic variants of GCPII as evidenced by glide scores (-4.32 to -7.08) and protein-ligand interaction plots (13 interactions in wild GCPII). This molecule satisfied Lipinski rule of five and rule of three for drug-likeliness. Being a NAAG-analogue, this molecule might confer neuroprotection by inhibiting glutamatergic neurotransmission mediated by N-acetylated alpha-linked acidic dipeptidase (NAALADase), a splice variant of GCPII. PMID:27430729

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

    PubMed

    Demestre, J; Meltzer, S; García-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

  3. 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

  4. Blood DNA methylation markers in potentially identified Chinese patients with hepatocellular carcinoma.

    PubMed

    Liu, Zongying; Yan, Haixiu; Zhang, Jinshu

    2016-07-01

    To determine whether blood DNA methylation is associated with hepatocellular carcinoma (HCC) for Chinese patients, we used genome-wide DNA methylation detection to access the blood samples of Chinese patients by Illumina Human methylation 450K arrays. Sixty potentially gene locis which had different methylated levels significantly among tumor and adjacent normal tissues would be tested in this study. A previous study was conducted in China communities and followed with 7 years. The DNA from white blood cells (WBC) from 192 patients with HCC and 215 matched controls were assayed in this study. The χ2 test was used to measure data to categorize variables and t -test was used to evaluate the different characteristics among groups. Besides, odds ratios (OR) and 95%CI was calculated for matching factors by conditional logistic regression models. We found that high methylation in WNK2 was related to increased risk of HCC, and high methylation in TPO were related to decreased risk of HCC. In our multivariable conditional logistic regression models, these results all exist. Those findings support the methylated changes of WNK2 and TPO may become a new detection index for HCC patients in clinical laboratory. However, the results should be replicated in additional prospective studies with lager samples. PMID:27592479

  5. 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

  6. Identifying solar energy potentials and intensifying the climate-friendly use of photovoltaics within urban areas.

    NASA Astrophysics Data System (ADS)

    de Lange, N.

    2016-04-01

    Limited non-renewable fossil energy reserves and the essential ideas of sustainability have caused an increase in the demand for solar energy. The intensified use of renewable energy in Germany is primarily encouraged by the German renewable-energy-law. Solar panels mounted on roofs generate electricity using the energy radiated from the sun by taking advantage of the photovoltaic effect. However, not every roof is usable for power generation through solar energy. Therefore, web-based solar energy registers for multiple regions in Germany have been developed that provide detailed information on roofs suitable for carrying solar panels. The analyses are based on a digital object model derived from airborne laser scanning data of high accuracy and a fully automated technology to classify the points. First, roof points are separated according to their single roof sides and are converted into polygons. Then, exposure, slope, size of the roof, and particularly shading effects are computed to calculate the solar potential of each roof side. The web-GIS provides detailed information about the roof's suitability, such as the installable capacity and the expected generation of electricity. Thus, it helps house owners to calculate their investment and later revenues.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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 μM. 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 μM. 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

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

    PubMed

    Egelund, Jack; Skjøt, Michael; Geshi, Naomi; Ulvskov, Peter; Petersen, Bent Larsen

    2004-09-01

    Plant cell wall (CW) synthesizing enzymes can be divided into the glycan (i.e. cellulose and callose) synthases, which are multimembrane spanning proteins located at the plasma membrane, and the glycosyltransferases (GTs), which are Golgi localized single membrane spanning proteins, believed to participate in the synthesis of hemicellulose, pectin, mannans, and various glycoproteins. At the Carbohydrate-Active enZYmes (CAZy) database where e.g. glucoside hydrolases and GTs are classified into gene families primarily based on amino acid sequence similarities, 415 Arabidopsis GTs have been classified. Although much is known with regard to composition and fine structures of the plant CW, only a handful of CW biosynthetic GT genes-all classified in the CAZy system-have been characterized. In an effort to identify CW GTs that have not yet been classified in the CAZy database, a simple bioinformatics approach was adopted. First, the entire Arabidopsis proteome was run through the Transmembrane Hidden Markov Model 2.0 server and proteins containing one or, more rarely, two transmembrane domains within the N-terminal 150 amino acids were collected. Second, these sequences were submitted to the SUPERFAMILY prediction server, and sequences that were predicted to belong to the superfamilies NDP-sugartransferase, UDP-glycosyltransferase/glucogen-phosphorylase, carbohydrate-binding domain, Gal-binding domain, or Rossman fold were collected, yielding a total of 191 sequences. Fifty-two accessions already classified in CAZy were discarded. The resulting 139 sequences were then analyzed using the Three-Dimensional-Position-Specific Scoring Matrix and mGenTHREADER servers, and 27 sequences with similarity to either the GT-A or the GT-B fold were obtained. Proof of concept of the present approach has to some extent been provided by our recent demonstration that two members of this pool of 27 non-CAZy-classified putative GTs are xylosyltransferases involved in synthesis of pectin

  13. Establishing an in vivo assay system to identify components involved in environmental RNA interference in the western corn rootworm.

    PubMed

    Miyata, Keita; Ramaseshadri, Parthasarathy; Zhang, Yuanji; Segers, Gerrit; Bolognesi, Renata; Tomoyasu, Yoshinori

    2014-01-01

    The discovery of environmental RNA interference (RNAi), in which gene expression is suppressed via feeding with double-stranded RNA (dsRNA) molecules, opened the door to the practical application of RNAi-based techniques in crop pest management. The western corn rootworm (WCR, Diabrotica virgifera virgifera) is one of the most devastating corn pests in North America. Interestingly, WCR displays a robust environmental RNAi response, raising the possibility of applying an RNAi-based pest management strategy to this pest. Understanding the molecular mechanisms involved in the WCR environmental RNAi process will allow for determining the rate limiting steps involved with dsRNA toxicity and potential dsRNA resistance mechanisms in WCR. In this study, we have established a two-step in vivo assay system, which allows us to evaluate the involvement of genes in environmental RNAi in WCR. We show that laccase 2 and ebony, critical cuticle pigmentation/tanning genes, can be used as marker genes in our assay system, with ebony being a more stable marker to monitor RNAi activity. In addition, we optimized the dsRNA dose and length for the assay, and confirmed that this assay system is sensitive to detect well-known RNAi components such as Dicer-2 and Argonaute-2. We also evaluated two WCR sid1- like (sil) genes with this assay system. This system will be useful to quickly survey candidate systemic RNAi genes in WCR, and also will be adaptable for a genome-wide RNAi screening to give us an unbiased view of the environmental/systemic RNAi pathway in WCR. PMID:25003334

  14. Kennecott Utah Copper Corporation: Facility Utilizes Energy Assessments to Identify $930,000 in Potential Annual Savings

    SciTech Connect

    2004-07-01

    Kennecott Utah Copper Corporation (KUCC) used targeted energy assessments in the smelter and refinery at its Bingham Canyon Mine, near Salt Lake City, Utah. The assessment focused mainly on the energy-intensive processes of copper smelting and refining. By implementing the projects identified, KUCC could realize annual cost savings of $930,000 and annual energy savings of 452,000 MMBtu. The projects would also reduce maintenance, repair costs, waste, and environmental emissions. One project would use methane gas from an adjacent municipal dump to replace natural gas currently used to heat the refinery electrolyte.

  15. Endocrine-disrupting chemicals and oil and natural gas operations: Potential environmental contamination and recommendations to assess complex environmental mixtures

    USGS Publications Warehouse

    Kassotis, Christopher D.; Tillitt, Donald E.; Lin, Chung-Ho; McElroy, Jane A.; Nagel, Susan C.

    2015-01-01

    Background: Hydraulic fracturing technologies, developed over the last 65 years, have only recently been combined with horizontal drilling to unlock oil and gas reserves previously deemed inaccessible. While these technologies have dramatically increased domestic oil and natural gas production, they have also raised concerns for the potential contamination of local water supplies with the approximately 1,000 chemicals used throughout the process, including many known or suspected endocrine-disrupting chemicals.Objectives: We discuss the need for an endocrine component to health assessments for drilling-dense regions in the context of hormonal and anti-hormonal activities for chemicals used.Methods: We discuss the literature on 1) surface and ground water contamination by oil and gas extraction operations, and 2) potential human exposure, particularly in context of the total hormonal and anti-hormonal activities present in surface and ground water from natural and anthropogenic sources, with initial analytical results and critical knowledge gaps discussed.Discussion: In light of the potential for environmental release of oil and gas chemicals that can disrupt hormone receptor systems, we recommend methods for assessing complex hormonally active environmental mixtures.Conclusions: We describe a need for an endocrine-centric component for overall health assessments and provide supporting information that using this may help explain reported adverse health trends as well as help develop recommendations for environmental impact assessments and monitoring programs.

  16. 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

    %). 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

  17. Proteomic profiling identifies the inorganic pyrophosphatase (PPA1) protein as a potential biomarker of metastasis in laryngeal squamous cell carcinoma.

    PubMed

    Bodnar, Magdalena; Luczak, Magdalena; Bednarek, Kinga; Szylberg, Lukasz; Marszalek, Andrzej; Grenman, Reidar; Szyfter, Krzysztof; Jarmuz-Szymczak, Malgorzata; Giefing, Maciej

    2016-06-01

    Relapse and metastasis are the main causes of unfavorable outcome in head and neck cancers. Whereas, understanding of the molecular background of these processes is far from being complete. Therefore, in this study we aimed to identify potential biomarker candidates of relapse and metastasis in laryngeal squamous cell carcinoma (LSCC) by combining the 2D electrophoresis based protein screen and immunohistochemical analysis of candidate proteins. We screened three groups of LSCC cell lines derived from primary tumors, recurrent tumors and metastases and identified seven proteins that differed significantly in relative abundance between the analyzed groups. Among the identified proteins were the heat shock proteins HSP60 and HSP70 that were significantly downregulated both in recurrences- and metastases-derived cell lines but not in primary tumor-derived cell lines. Moreover, we identified significant upregulation of the annexin V, calreticulin and the inorganic pyrophosphatase (PPA1) exclusively in the metastases-derived cell lines. As these upregulated proteins could potentially become novel biomarkers of metastasis, we have compared their abundance in primary tumor LSCC N(0) cases, primary tumor LSCC N(+) cases as well as in LSCC metastases N(+). Our results show an intense increase of cytoplasmic PPA1 abundance in the N(+) (p = 0.000042) compared to the N(0) group. In summary, we show a group of proteins deregulated in recurrences and metastases of LSCC. Moreover, we suggest the PPA1 protein as a potential new biomarker for metastasis in this cancer. PMID:26948660

  18. Big Data in Chemical Toxicity Research: The Use of High-Throughput Screening Assays To Identify Potential Toxicants

    PubMed Central

    2015-01-01

    High-throughput screening (HTS) assays that measure the in vitro toxicity of environmental compounds have been widely applied as an alternative to in vivo animal tests of chemical toxicity. Current HTS studies provide the community with rich toxicology information that has the potential to be integrated into toxicity research. The available in vitro toxicity data is updated daily in structured formats (e.g., deposited into PubChem and other data-sharing web portals) or in an unstructured way (papers, laboratory reports, toxicity Web site updates, etc.). The information derived from the current toxicity data is so large and complex that it becomes difficult to process using available database management tools or traditional data processing applications. For this reason, it is necessary to develop a big data approach when conducting modern chemical toxicity research. In vitro data for a compound, obtained from meaningful bioassays, can be viewed as a response profile that gives detailed information about the compound’s ability to affect relevant biological proteins/receptors. This information is critical for the evaluation of complex bioactivities (e.g., animal toxicities) and grows rapidly as big data in toxicology communities. This review focuses mainly on the existing structured in vitro data (e.g., PubChem data sets) as response profiles for compounds of environmental interest (e.g., potential human/animal toxicants). Potential modeling and mining tools to use the current big data pool in chemical toxicity research are also described. PMID:25195622

  19. Big data in chemical toxicity research: the use of high-throughput screening assays to identify potential toxicants.

    PubMed

    Zhu, Hao; Zhang, Jun; Kim, Marlene T; Boison, Abena; Sedykh, Alexander; Moran, Kimberlee

    2014-10-20

    High-throughput screening (HTS) assays that measure the in vitro toxicity of environmental compounds have been widely applied as an alternative to in vivo animal tests of chemical toxicity. Current HTS studies provide the community with rich toxicology information that has the potential to be integrated into toxicity research. The available in vitro toxicity data is updated daily in structured formats (e.g., deposited into PubChem and other data-sharing web portals) or in an unstructured way (papers, laboratory reports, toxicity Web site updates, etc.). The information derived from the current toxicity data is so large and complex that it becomes difficult to process using available database management tools or traditional data processing applications. For this reason, it is necessary to develop a big data approach when conducting modern chemical toxicity research. In vitro data for a compound, obtained from meaningful bioassays, can be viewed as a response profile that gives detailed information about the compound's ability to affect relevant biological proteins/receptors. This information is critical for the evaluation of complex bioactivities (e.g., animal toxicities) and grows rapidly as big data in toxicology communities. This review focuses mainly on the existing structured in vitro data (e.g., PubChem data sets) as response profiles for compounds of environmental interest (e.g., potential human/animal toxicants). Potential modeling and mining tools to use the current big data pool in chemical toxicity research are also described. PMID:25195622

  20. Assessing the potential of farming regions to fulfill agro-environmental functions: a case study in tuscany (Italy).

    PubMed

    Marraccini, Elisa; Rapey, Hélène; Galli, Mariassunta; Lardon, Sylvie; Bonari, Enrico

    2013-03-01

    The increasing interest in agro-environmental management entails having tools to assess, monitor and map agro-environmental functions (AEFs) in different regional contexts. In Europe, decision-making in agro-environmental policies generally targets single functions instead of multiple ones and rarely considers the regional variability of agricultural or geo-physical conditions that may influence the fulfillment of functions. We propose and test a method to assess the potential of farming regions to fulfill a set of AEFs. The method was applied in the "Collina interna grossetana" farming region (Italy) and concerned three functions: protection of surface water from nitrates, protection of soil from erosion, and conservation of landscape diversity. These functions were qualified and mapped using various geo-physical and land cover descriptors from common geographical datasets. All of the descriptors were combined using geographical cluster analysis to identify their contribution to the three functions, and thus to assess the potential of the farming region to fulfill these functions. Three levels of potential were calculated, according to the more or less favorable fulfillment of soil and water functions. No totally favorable contribution to the functions was identified in the studied area. Moreover, we mapped the spatial patterns obtained for the different levels of potential. The landscape diversity function was found to be the least variable in the study area, while different patterns were identified for the other functions. In fact, the northern and central sections of the study region were organized more in the form of large core areas of different levels of potential, whereas the southern section presented more boundary areas, small core areas and isolated pixels. The method may help to establish local priorities in agro-environmental management pointing out where the set of functions is completely or partially fulfilled, as well as where and how it is more or

  1. Predatory online behavior: modus operandi of convicted sex offenders in identifying potential victims and contacting minors over the internet.

    PubMed

    Malesky, L Alvin

    2007-01-01

    Sex offenders have used the Internet to identify and contact minors for sexual exploitation (Armagh, 1998; Hernandez, 2000; Lamb, 1998; Lanning, 1998). Yet little is known about how these individuals select their online victims. In order to gain a better understanding of this behavior, the online activity of 31 men who perpetrated or attempted to perpetrate contact sex offenses against minors they communicated with via the Internet, was examined. Three-fourths of the participants monitored chat room dialogue and almost one-half reviewed online profiles of minors in an attempt to identify potential victims. Recommendations to increase the online safety of children and adolescents are discussed. PMID:17895230

  2. Simple indicator to identify the environmental soundness of growth of consumption and technology: "eco-velocity of consumption".

    PubMed

    Nansai, Keisuke; Kagawa, Shigemi; Suh, Sangwon; Inaba, Rokuta; Moriguchi, Yuichi

    2007-02-15

    Today's material welfare has been achieved at the expense of consumption of finite resources and generation of environmental burdens. Over the past few decades the volume of global consumption has grown dramatically, while at the same time technological advances have enabled products with greater efficiencies. These two directions of change, consumption growth and technological advance, are the foci of the present paper. Using quantitative measures for these two factors, we define a new indicator, "eco-velocity of consumption", analogous to velocity in physics. The indicator not only identifies the environmental soundness of consumption growth and technological advance but also indicates whether and to what extent our society is shifting toward sustainable consumption. This study demonstrates the practicability of the indicator through a case study in which we calculate the eco-velocities of Japanese household consumption in 2 years: 1995 and 2000. The rate of technological advance during the periods concerned is quantified in terms of the embodied carbon dioxide emission per yen of product. The results show that the current growth rate of Japanese household consumption is greater than the rate of technological advance to mitigate carbon dioxide emissions. The eco-velocities at the level of individual commodity groups are also examined, and the sources of changes in eco-velocity for each commodity are identified using structural decomposition analysis. PMID:17593758

  3. 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

  4. Environmental assessment of two different crop systems in terms of biomethane potential production.

    PubMed

    Bacenetti, Jacopo; Fusi, Alessandra; Negri, Marco; Guidetti, Riccardo; Fiala, Marco

    2014-01-01

    The interest in renewable energy sources has gained great importance in Europe due to the need to reduce fossil energy consumption and greenhouse gas emissions, as required by the Renewable Energy Directive (RED) of the European Parliament. The production of energy from energy crops appears to be consistent with RED. The environmental impact related to this kind of energy primarily originates from crop cultivation. This research aimed to evaluate the environmental impact of different crop systems for biomass production: single and double crop. The environmental performances of maize and maize plus wheat were assessed from a life cycle perspective. Two alternative scenarios considering different yields, crop management, and climatic conditions, were also addressed. One normal cubic metre of potential methane was chosen as a functional unit. Methane potential production data were obtained through lab experimental tests. For both of the crop systems, the factors that have the greatest influence on the overall environmental burden are: fertilizer emissions, diesel fuel emissions, diesel fuel production, and pesticide production. Notwithstanding the greater level of methane potential production, the double crop system appears to have the worse environmental performance with respect to its single crop counterpart. This result is due to the bigger quantity of inputs needed for the double crop system. Therefore, the greater amount of biomass (silage) obtained through the double crop system is less than proportional to the environmental burden that results from the bigger quantity of inputs requested for double crop. PMID:23994820

  5. Characterization and Potential Environmental Risks of Leachate from Shredded Rubber Mulches

    PubMed Central

    Kanematsu, Masakazu; Hayashi, Ai; Denison, Michael S.; Young, Thomas M.

    2009-01-01

    In order to determine whether shredded rubber mulches (RM) posed water quality risks when used in stormwater best management practices (BMPs) such as bioretention basins, batch leaching tests were conducted to identify and quantify constituents in leachates from RM such as metal ions, nutrients, total organic carbon (TOC), and aryl hydrocarbon receptor (AhR) activity (determined by the chemically activated luciferase gene expression (CALUX) bioassay) at varied temperature and initial pH values. The results indicate that aqueous extracts of RM contain high concentrations of zinc (Zn) compared with wood mulches (WM), and its concentration increased at lower pH and higher temperature. Although methanol extracts of RM displayed high AhR activity, none of the aqueous extracts of RM had significant activity. Hence, while unknown constituents that have significant AhR activity are present in RM, they appear to be not measurably extracted by water under environmental conditions relevant for stormwater (5 < pH < 9, 10 < T < 40°C). Our results suggests that organic constituents in water extracts of RM which have AhR activity may not be of significant concern while leaching of Zn from RM appears to be a potentially larger water quality issue for RM. PMID:19450864

  6. 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

  7. Identifying/Quantifying Environmental Trade-offs Inherent in GHG Reduction Strategies for Coal-Fired Power.

    PubMed

    Schivley, Greg; Ingwersen, Wesley W; Marriott, Joe; Hawkins, Troy R; Skone, Timothy J

    2015-07-01

    Improvements to coal power plant technology and the cofired combustion of biomass promise direct greenhouse gas (GHG) reductions for existing coal-fired power plants. Questions remain as to what the reduction potentials are from a life cycle perspective and if it will result in unintended increases in impacts to air and water quality and human health. This study provides a unique analysis of the potential environmental impact reductions from upgrading existing subcritical pulverized coal power plants to increase their efficiency, improving environmental controls, cofiring biomass, and exporting steam for industrial use. The climate impacts are examined in both a traditional-100 year GWP-method and a time series analysis that accounts for emission and uptake timing over the life of the power plant. Compared to fleet average pulverized bed boilers (33% efficiency), we find that circulating fluidized bed boilers (39% efficiency) may provide GHG reductions of about 13% when using 100% coal and reductions of about 20-37% when cofiring with 30% biomass. Additional greenhouse gas reductions from combined heat and power are minimal if the steam coproduct displaces steam from an efficient natural gas boiler. These upgrades and cofiring biomass can also reduce other life cycle impacts, although there may be increased impacts to water quality (eutrophication) when using biomass from an intensely cultivated source. Climate change impacts are sensitive to the timing of emissions and carbon sequestration as well as the time horizon over which impacts are considered, particularly for long growth woody biomass. PMID:26001040

  8. 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

  9. 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

  10. Report: Potential environmental impact of exempt site materials - a case study of bituminous road planings and waste soils.

    PubMed

    Bark, Marjorie; Bland, Michael; Grimes, Sue

    2009-09-01

    The use of waste materials for ecological benefit, agricultural improvement or as part of construction works are often exempt from waste management control in order to maximize the reuse of material that would otherwise be disposed of to landfill. It is important, however, to determine whether there is potential for such waste to cause environmental harm in the context of the basis for granting exemptions under the relevant framework objective to ensure that waste is recovered or disposed of without risk to water, air, soil, plants or animals. The potential for environmental harm was investigated by leaching studies on two wastes commonly found at exempt sites: bituminous road planings and waste soils. For bituminous road planings, the organic components of the waste were identified by their solubility in organic solvents but these components would have low environmental impact in terms of bioavailability. Leaching studies of the heavy metals copper, lead and zinc, into the environment, under specific conditions and particularly those modelling acid rain and landfill leachate conditions showed that, except for copper, the amounts leached fell within Waste Acceptance Criteria compliance limits for defining waste as inert waste. The fact that the amount of copper leached was greater than the Waste Acceptance Criteria level suggests that either additional testing of wastes regarded as exempt should be carried out to ensure that they are in analytical compliance or that legislation should allow for the potential benefits of reuse to supersede deviations from analytical compliance. PMID:19423579

  11. 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

  12. 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

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

    PubMed Central

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

    2009-01-01

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

  14. SILAC-based quantitative proteomic approach to identify potential biomarkers from the esophageal squamous cell carcinoma secretome

    PubMed Central

    Kashyap, Manoj Kumar; Harsha, HC; Renuse, Santosh; Pawar, Harsh; Sahasrabuddhe, Nandini A; Kim, Min-Sik; Marimuthu, Arivusudar; Keerthikumar, Shivakumar; Muthusamy, Babylakshmi; Kandasamy, Kumaran; Subbannayya, Yashwanth; Prasad, Thottethodi Subrahmanya Keshava; Mahmood, Riaz; Chaerkady, Raghothama; Meltzer, Stephen J; Kumar, Rekha V; Rustgi, Anil K

    2010-01-01

    The identification of secreted proteins that are differentially expressed between non-neoplastic and esophageal squamous cell carcinoma (ESCC) cells can provide potential biomarkers of ESCC. We used a SILAC-based quantitative proteomic approach to compare the secretome of ESCC cells with that of non-neoplastic esophageal squamous epithelial cells. Proteins were resolved by SDS-PAGE and tandem mass spectrometry analysis (LC-MS/MS) of in-gel trypsindigested peptides was carried out on a high-accuracy qTOF mass spectrometer. In total, we identified 441 proteins in the combined secretomes, including 120 proteins with ≥ 2-fold upregulation in the ESCC secretome vs. that of non-neoplastic esophageal squamous epithelial cells. In this study, several potential protein biomarkers previously known to be increased in ESCC including matrix metalloproteinase 1, transferrin receptor and transforming growth factor beta-induced 68 kDa were identified as overexpressed in the ESCC-derived secretome. In addition, we identified several novel proteins that have not been previously reported to be associated with ESCC. Among the novel candidate proteins identified, protein disulfide isomerase family a member 3 (PDIA3), GDP dissociation inhibitor 2 (GDI2) and lectin galactoside binding soluble 3 binding protein (LGALS3BP) were further validated by immunoblot analysis and immunohistochemical labeling using tissue microarrays. This tissue microarray analysis showed overexpression of protein disulfide isomerase family a member 3, GDP dissociation inhibitor 2 and lectin galactoside binding soluble 3 binding protein in 93, 93 and 87% of 137 ESCC cases, respectively. Hence, we conclude that these potential biomarkers are excellent candidates for further evaluation to test their role and efficacy in the early detection of ESCC. PMID:20686364

  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; Sílvia Soares Pires, Carmen; Imperatriz-Fonseca, Vera Lucia

    2015-08-01

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

  16. Genomic profiling of murine mammary tumors identifies potential personalized drug targets for p53-deficient mammary cancers

    PubMed Central

    Agrawal, Yash N.; Koboldt, Daniel C.; Kanchi, Krishna L.; Herschkowitz, Jason I.; Mardis, Elaine R.; Rosen, Jeffrey M.; Perou, Charles M.

    2016-01-01

    ABSTRACT Targeted therapies against basal-like breast tumors, which are typically ‘triple-negative breast cancers (TNBCs)’, remain an important unmet clinical need. Somatic TP53 mutations are the most common genetic event in basal-like breast tumors and TNBC. To identify additional drivers and possible drug targets of this subtype, a comparative study between human and murine tumors was performed by utilizing a murine Trp53-null mammary transplant tumor model. We show that two subsets of murine Trp53-null mammary transplant tumors resemble aspects of the human basal-like subtype. DNA-microarray, whole-genome and exome-based sequencing approaches were used to interrogate the secondary genetic aberrations of these tumors, which were then compared to human basal-like tumors to identify conserved somatic genetic features. DNA copy-number variation produced the largest number of conserved candidate personalized drug targets. These candidates were filtered using a DNA-RNA Pearson correlation cut-off and a requirement that the gene was deemed essential in at least 5% of human breast cancer cell lines from an RNA-mediated interference screen database. Five potential personalized drug target genes, which were spontaneously amplified loci in both murine and human basal-like tumors, were identified: Cul4a, Lamp1, Met, Pnpla6 and Tubgcp3. As a proof of concept, inhibition of Met using crizotinib caused Met-amplified murine tumors to initially undergo complete regression. This study identifies Met as a promising drug target in a subset of murine Trp53-null tumors, thus identifying a potential shared driver with a subset of human basal-like breast cancers. Our results also highlight the importance of comparative genomic studies for discovering personalized drug targets and for providing a preclinical model for further investigations of key tumor signaling pathways. PMID:27149990

  17. Comparable measures of cognitive function in human infants and laboratory animals to identify environmental health risks to children.

    PubMed Central

    Sharbaugh, Carolyn; Viet, Susan Marie; Fraser, Alexa; McMaster, Suzanne B

    2003-01-01

    The importance of including neurodevelopmental end points in environmental studies is clear. A validated measure of cognitive function in human infants that also has a homologous or parallel test in laboratory animal studies will provide a valuable approach for large-scale studies. Such a comparable test will allow researchers to observe the effect of environmental neurotoxicants in animals and relate those findings to humans. In this article, we present the results of a review of post-1990, peer-reviewed literature and current research examining measures of cognitive function that can be applied to both human infants (0-12 months old) and laboratory animals. We begin with a discussion of the definition of cognitive function and important considerations in cross-species research. We then describe identified comparable measures, providing a description of the test in human infants and animal subjects. Available information on test reliability, validity, and population norms, as well as test limitations and constraints, is also presented. PMID:14527843

  18. Childhood Obesity Prevention in Childcare Settings: the Potential of Policy and Environmental Change Interventions.

    PubMed

    Lessard, Laura; Breck, Andrew

    2015-06-01

    Current obesity rates in young children are a serious public health concern; developing and implementing obesity prevention interventions in childcare settings is a promising avenue to address this issue. In recent years, there has been increasing focus on environmental and policy change interventions for this setting. Improving access to and quality of outdoor play spaces and implementing the Nutrition and Physical Activity Self-Assessment for Child Care (NAP SACC) are two promising environmental change strategies in this setting. Laws at the local, state, and federal level have also been implemented; New York City and Delaware are two jurisdictions that have passed policies and provided preliminary evidence of the potential of policy interventions to change child outcomes. A combination of programmatic, environmental, and policy change strategies will likely be most effective in maximizing the potential of childcare settings to promote healthy weight in children. PMID:26627214

  19. Using Community-Based Participatory Research to Identify Environmental Justice Issues in an Inner-City Community and Inform Urban Planning.

    PubMed

    Mansyur, Carol Leler; Jeng, Hueiwang Anna; Holloman, Erica; DeBrew, Linwood

    2016-01-01

    The Southeast CARE Coalition has been using community-based participatory research to examine environmental degradation in the Southeast Community, Newport News, Virginia. A survey was developed to collect assessment data. Up to 66% of respondents were concerned about environmental problems in their community. Those with health conditions were significantly more likely to identify specific environmental problems. The top 5 environmental concerns included coal dust, air quality, crime, water quality, and trash. The community-based participatory research process is building community capacity and participation, providing community input into strategic planning, and empowering community members to take control of environmental justice issues in their community. PMID:27214672

  20. MYSID CRUSTACEANS AS POTENTIAL TEST ORGANISMS FOR THE EVALUATION OF ENVIRONMENTAL ENDOCRINE DISRUPTORS: A REVIEW

    EPA Science Inventory

    Verslycke, Tim A., Nancy Fockedey, Charles L. McKenney, Jr., Stephen D. Roast, Malcolm B. Jones, Jan Mees and Colin R. Janssen. 2004. Mysid Crustaceans as Potential Test Organisms for the Evaluation of Environmental Endocrine Disruption: A Review. Environ. Toxicol. Chem. 23(5):12...

  1. 77 FR 66185 - Environmental Assessment for Potential Commercial Wind Lease Issuance and Site Assessment...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-11-02

    ... around the Call Area (77 FR 5830). The Call Area is located offshore Massachusetts. Issues and impacts... Bureau of Ocean Energy Management Environmental Assessment for Potential Commercial Wind Lease Issuance and Site Assessment Activities on the Atlantic Outer Continental Shelf (OCS) Offshore...

  2. HOLISTIC APPROACH FOR ASSESSING THE PRESENCE AND POTENTIAL IMPACTS OF WATERBORNE ENVIRONMENTAL CONTAMINANTS

    EPA Science Inventory

    As an integral part of our continuing research in environmental quality assessment approaches, we have developed a variety of passive integrative sampling devices widely applicable for use in defining the presence and potential impacts of a broad array of contaminants. The semipe...

  3. Chemical and biological methods for the analysis and remediation of environmental contaminants frequently identified at superfund sites

    SciTech Connect

    Melinda Christine Wiles

    2004-08-15

    Substantial environmental contamination has occurred from coal tar creosote and pentachlorophenol (C5P) in wood preserving solutions. The present studies focused on the characterization and remediation of these contaminants. The first objective was to delineate a sequence of biological changes caused by chlorinated phenol (CP) exposure. The second study was to develop multi-functional sorbents to remediate CPs and other components of wood preserving waste from groundwater. Following water remediation, the final aim of this work was to explore the safety of the parent clay minerals as potential enterosorbents for contaminants ingested in water and food. Based on evaluations of toxicity and neutron activation analysis of tissues, no significant differences were observed between animals receiving clay supplements and control animals, with the exception of slightly decreased brain Rb in animals ingesting clay. Overall, the results suggest that neither clay mineral, at relatively high dietary concentrations, influences mineral uptake or utilization in the pregnant rat. 420 refs., 28 figs, 15 tabs.

  4. Health Impact Assessment Practice and Potential for Integration within Environmental Impact and Strategic Environmental Assessments in Italy

    PubMed Central

    Linzalone, Nunzia; Assennato, Giorgio; Ballarini, Adele; Cadum, Ennio; Cirillo, Mario; Cori, Liliana; De Maio, Francesca; Musmeci, Loredana; Natali, Marinella; Rieti, Sabrina; Soggiu, Maria Eleonora; Bianchi, Fabrizio

    2014-01-01

    Avoiding or minimizing potential environmental impact is the driving idea behind protecting a population’s health via Environmental Impact Assessments (EIAs) and Strategic Environmental Assessments (SEAs). However, both are often carried out without any systematic approach. This paper describes the findings of a review of HIA, EIA and SEA experiences carried out by the authors, who act as institutional competent subjects at the national and regional levels in Italy. The analysis of how health is tackled in EIA and SEA procedures could support the definition of a protocol for the integration of HIA with EIA and SEA. Although EIA and SEA approaches include the aim of protecting health, significant technical and methodological gaps are present when assessing health systematically, and their basic principles regarding assessment are unsatisfactory for promoting and addressing healthcare concepts stated by the WHO. HIA is still poorly integrated into the decision-making process, screening and monitoring phases are only occasionally implemented, and operational details are not well-defined. The collaborative approach of institutions involved in environment and health is a core element in a systematic advancement toward supporting effective decisions and effective protection of the environment and health. At the Italian national level, the definition of guidelines and tools for HIA, also in relation with EIA and SEA, is of great interest. PMID:25493391

  5. 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

  6. Quantification for total demethylation potential of environmental samples utilizing the EGFP reporter gene.

    PubMed

    Qian, Yan; Wang, Xiao-li; Lv, Zhan-lu; Tysklind, Mats; Guo, Chen; Liang, Bao; Wu, Jia-bing; Yang, Yong-jian; Yang, Yi-shu; Wang, Fei-fei; Duan, Xiao-li; Ma, Jin; Wei, Yong-jie; Wang, Chun-hui; Yang, Li-xin; Zhang, Jin-liang; Shi, Xiao-ming; Wang, Xian-liang

    2016-04-01

    The demethylation potential of pollutants is arguably an innate component of their toxicity in environmental samples. A method was developed for determining the total demethylation potential of food samples (TDQ). The demethylation epigenetic toxicity was determined using the Hep G2 cell line transfected with pEGFP-C3 plasmids containing a methylated promoter of the EGFP reporter gene. The total demethylation potential of the sample extracts (the 5-AZA-CdR demethylation toxic equivalency) can be quantified within one week by using a standard curve of the 5-AZA-CdR demethylation agent. To explore the applicability of TDQ for environmental samples, 17 groundwater samples were collected from heavy polluted Kuihe river and the total demethylation potentials of the sample extracts were measured successfully. Meaningful demethylation toxic equivalencies ranging from 0.00050 to 0.01747μM were found in all groundwater sample extracts. Among 19 kinds of inorganic substance, As and Cd played important roles for individual contribution to the total demethylation epigenetic toxicity. The TDQ assay is reliable and fast for quantifying the DNA demethylation potential of environmental sample extracts, which may improve epigenetic toxicity evaluations for human risk assessment, and the consistent consuming of groundwater alongside the Kuihe river pose unexpected epigenetic health risk to the local residents. PMID:26774982

  7. Speciation Methods Used to Assess Potential Health Effects of Toxic Metals in Environmental Materials

    USGS Publications Warehouse

    Wolf, Ruth E.; Morman, Suzette A.; Plumlee, Geoffrey S.

    2008-01-01

    Assessing potential exposures to toxic metals or metalloids such as arsenic and chromium in environmental materials is important in protecting public health. The chemical form of an element in, or released from, a material is also important, since some forms, such as Cr(VI), are more toxic than others, for example, Cr(III). We have used a variety of procedures to assess potential exposures to hexavalent chromium in ash and burned soils from October 2007 southern California wildfires. Synthetic lung-fluid and de-ionized water extractions simulate release in the lungs and potential environmental releases due to rainfall. Extracts were analyzed for specific chromium and arsenic species using HPLC-ICP-MS methodology. Results indicate that the highly oxidizing environment in wildfires promotes some chromium conversion to Cr(VI), and that the caustic alkalinity of ash enhances Cr(VI) release and stability in lung fluids and rainfall.

  8. A brief overview of the potential environmental hazards of ionic liquids.

    PubMed

    Bubalo, Marina Cvjetko; Radošević, Kristina; Redovniković, Ivana Radojčić; Halambek, Jasna; Srček, Višnja Gaurina

    2014-01-01

    Over past decades ionic liquids, a promising alternative to traditional organic solvents, have been dramatically expanding in popularity as a new generation of chemicals with potential uses in various areas in industry. In the literature these compounds have often been referred to as environmentally friendly; however, in recent years the perception of their greenness dramatically changed as the scientific community began to proactively assess the risk of their application based on the entire life-cycle. This review gives a brief overview of the current knowledge regarding the potential risks linked to the application of ionic liquids - from preparation to their disposal, with special emphasis on their potential environmental impacts and future directions in designing inherently safer ionic liquids. PMID:24210364

  9. A GIS based MCE model for identifying water colour generation potential in UK upland drinking water supply catchments

    NASA Astrophysics Data System (ADS)

    Grayson, Richard; Kay, Paul; Foulger, Miles; Gledhill, Sarah

    2012-02-01

    SummaryWater discolouration is one of the key water quality problems faced by UK water companies taking raw water from peatland catchments. A water colour model has been developed using a combined Geographical Information System and Multicriteria Evaluation approach. The model was used to predict water colour production potential based on key land management practices controlling colour production in UK upland catchments. Calibration of the model with historic data collected at water treatment works treating water from upland areas showed that the model was potentially capable of accurately predicting water colour production potential at the catchment scale (c. 90%). Subsequent validation has shown this to be the case. Rotational heather burning and vegetation type (particularly heather) were identified as the two most statistically significant variables influencing water colour generation in the study catchments. It was predicted that colour is generated in particular hotspots and management to improve water quality should, therefore, focus on such areas. Blending of water is also an important process in controlling colour at the catchment scale and at water treatment works, with high colour often being diluted by runoff from land elsewhere in the catchment with lower potential to generate colour.

  10. Application of human haploid cell genetic screening model in identifying the genes required for resistance to environmental toxicants: Chlorpyrifos as a case study

    PubMed Central

    Zhu, Jinqiu; Dubois, Amber; Ge, Yichen; Olson, James A.; Ren, Xuefeng

    2016-01-01

    Introduction High-throughput loss-of-function genetic screening tools in yeast or other model systems except in mammalian cells have been implemented to study human susceptibility to chemical toxicity. Here, we employed a newly developed human haploid cell (KBM7)-based mutagenic screening model (KBM7-mu cells) and examined its applicability in identifying genes whose absence allows cells to survive and proliferate in the presence of chemicals. Methods KBM7-mucells were exposed to 200 µM Chlorpyrifos (CPF), a widely used organophosphate pesticide, a dose causing approximately 50% death of cells after 48 h of treatment. After a 2–3 week period of continuous CPF exposure, survived single cell colonies were recovered and used for further analysis. DNA isolated from these cells was amplified using Splinkerette PCR with specific designed primers, and sequenced to determine the genomic locations with virus insertion and identify genes affected by the insertion. Quantitative realtime reverse transcription PCR (qRT-PCR) was used to confirm the knockdown of transcription of identified target genes. Results We identified total 9 human genes in which the cells carrying these genes conferred the resistance to CPF, including AGPAT6, AIG1, ATP8B2, BIK, DCAF12, FNBP4, LAT2, MZF1-AS1 and PPTC7. MZF1-AS1 is an antisense RNA and not included in the further analysis. qRT-PCR results showed that the expression of 6 genes was either significantly reduced or completely lost. There were no changes in the expression of DCAF12 and AGPAT6 genes between the KBM7-mu and the control KBM7 cells. Discussion The KBM7-mu genetic screening system can be modified and applied to identify novel susceptibility genes in response to environmental toxicants, which could provide valuable insights into potential mechanisms of toxicity. PMID:26299976

  11. Pile Driving at the New Bridge at Tappan Zee: Potential Environmental Impacts.

    PubMed

    Popper, Arthur N; Moese, Mark; Rollino, John; Krebs, Justin; Racca, Roberto; Martin, Bruce; Zeddies, David; MacGillivray, Alexander; Jacobs, Fred

    2016-01-01

    A new bridge will be constructed to replace the aging Tappan Zee Bridge over the Hudson River in New York. Construction will potentially result in hydroacoustic impacts to the local fish fauna. As a consequence, a substantial environmental impact analysis had to be conducted to obtain construction permits. This paper describes the process of environmental analysis and some of the results of the studies that led up to the final permitting. The process included modeling of pile-driving acoustics, analysis of river ambient noise, analysis of test piling, and observations on fish behavior during these tests. PMID:26611043

  12. Space Toxicology: Environmental Health Considerations during Spaceflight Operations and Potential Paths for Research

    NASA Technical Reports Server (NTRS)

    Khan-Mayberry, Noreen N.; Sundaresan, Alemalu

    2009-01-01

    Space Toxicology is a specialized discipline for spaceflight, space habitation and occupation of celestial bodies including planets, moons and asteroids [1]. Astronaut explorers face unique challenges to their health while working and living with limited resources for rescue and medical care during space operation. At its core the practice of space toxicology to identify, assess and predict potential chemical contaminants and limit the astronaut s exposure to these environmental factors in order to protect crew health. Space toxicologists are also charged with setting safe exposure limits that will protect the astronaut against a multitude of chemical exposures, in a physiologically altered state. In order to maintain sustained occupation in space, toxicological risks are gauged and managed within the context of isolation, continual exposures, reuse of air and water, limited rescue options, and the necessary use of highly toxic compounds required for propulsion. As the space program move towards human presence and exploration other celestial bodies in situ toxicological risks, such as inhalation of unusual and/or reactive mineral dusts must also be analyzed and controlled. Placing humans for long-term presence in space creates several problems and challenges to the long-term health of the crew, such as bone-loss and immunological challenges and has spurred research into acute, chronic and episodic exposure of the pulmonary system to mineral dusts [2]. NASA has demonstrated that lunar soil contains several types of reactive dusts, including an extremely fine respirable component. In order to protect astronaut health, NASA is now investigating the toxicity of this unique class of dusts. Understanding how these reactive components behave "biochemically" in a moisture-rich pulmonary environment will aid in determining how toxic these particles are to humans. The data obtained from toxicological examination of lunar dusts will determine the human risk criteria for lunar

  13. Identifying and tracing potential energy surfaces of electronic excitations with specific character via their transition origins: application to oxirane.

    PubMed

    Li, Jian-Hao; Zuehlsdorff, T J; Payne, M C; Hine, N D M

    2015-05-14

    We show that the transition origins of electronic excitations identified by quantified natural transition orbital (QNTO) analysis can be employed to connect potential energy surfaces (PESs) according to their character across a wide range of molecular geometries. This is achieved by locating the switching of transition origins of adiabatic potential surfaces as the geometry changes. The transition vectors for analysing transition origins are provided by linear response time-dependent density functional theory (TDDFT) calculations under the Tamm-Dancoff approximation. We study the photochemical CO ring opening of oxirane as an example and show that the results corroborate the traditional Gomer-Noyes mechanism derived experimentally. The knowledge of specific states for the reaction also agrees well with that given by previous theoretical work using TDDFT surface-hopping dynamics that was validated by high-quality quantum Monte Carlo calculations. We also show that QNTO can be useful for considerably larger and more complex systems: by projecting the excitations to those of a reference oxirane molecule, the approach is able to identify and analyse specific excitations of a trans-2,3-diphenyloxirane molecule. PMID:25875632

  14. The E-SCREEN assay as a tool to identify estrogens: an update on estrogenic environmental pollutants.

    PubMed Central

    Soto, A M; Sonnenschein, C; Chung, K L; Fernandez, M F; Olea, N; Serrano, F O

    1995-01-01

    Estrogens are defined by their ability to induce the proliferation of cells of the female genital tract. The wide chemical diversity of estrogenic compounds precludes an accurate prediction of estrogenic activity on the basis of chemical structure. Rodent bioassays are not suited for the large-scale screening of chemicals before their release into the environment because of their cost, complexity, and ethical concerns. The E-SCREEN assay was developed to assess the estrogenicity of environmental chemicals using the proliferative effect of estrogens on their target cells as an end point. This quantitative assay compares the cell number achieved by similar inocula of MCF-7 cells in the absence of estrogens (negative control) and in the presence of 17 beta-estradiol (positive control) and a range of concentrations of chemicals suspected to be estrogenic. Among the compounds tested, several "new" estrogens were found; alkylphenols, phthalates, some PCB congeners and hydroxylated PCBs, and the insecticides dieldrin, endosulfan, and toxaphene were estrogenic by the E-SCREEN assay. In addition, these compounds competed with estradiol for binding to the estrogen receptor and increased the levels of progesterone receptor and pS2 in MCF-7 cells, as expected from estrogen mimics. Recombinant human growth factors (bFGF, EGF, IGF-1) and insulin did not increase in cell yields. The aims of the work summarized in this paper were a) to validate the E-SCREEN assay; b) to screen a variety of chemicals present in the environment to identify those that may be causing reproductive effects in wildlife and humans; c) to assess whether environmental estrogens may act cumulatively; and finally d) to discuss the reliability of this and other assays to screen chemicals for their estrogenicity before they are released into the environment. PMID:8593856

  15. Cellulolytic potential under environmental changes in microbial communities from grassland litter

    DOE PAGESBeta

    Berlemont, Renaud; Allison, Steven D.; Weihe, Claudia; Lu, Ying; Brodie, Eoin L.; Martiny, Jennifer B. H.; Martiny, Adam C.

    2014-11-25

    In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of natural variation. Fungal andmore » bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.« less

  16. Cellulolytic potential under environmental changes in microbial communities from grassland litter

    SciTech Connect

    Berlemont, Renaud; Allison, Steven D.; Weihe, Claudia; Lu, Ying; Brodie, Eoin L.; Martiny, Jennifer B. H.; Martiny, Adam C.

    2014-11-25

    In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.

  17. Environmental potentials of policy instruments to mitigate nutrient emissions in Chinese livestock production.

    PubMed

    Zheng, Chaohui; Liu, Yi; Bluemling, Bettina; Mol, Arthur P J; Chen, Jining

    2015-01-01

    To minimize negative environmental impact of livestock production, policy-makers face a challenge to design and implement more effective policy instruments for livestock farmers at different scales. This research builds an assessment framework on the basis of an agent-based model, named ANEM, to explore nutrient mitigation potentials of five policy instruments, using pig production in Zhongjiang county, southwest China, as the empirical filling. The effects of different policy scenarios are simulated and compared using four indicators and differentiating between small, medium and large scale pig farms. Technology standards, biogas subsidies and information provisioning prove to be the most effective policies, while pollution fees and manure markets fail to environmentally improve manure management in pig livestock farming. Medium-scale farms are the more relevant scale category for a more environmentally sound development of Chinese livestock production. A number of policy recommendations are formulated as conclusion, as well as some limitations and prospects of the simulations are discussed. PMID:25247484

  18. Integration of photomosaics and stratigraphy in the Western Appalachian Basin as an aid to identify potential hydrocarbon reservoirs

    SciTech Connect

    Wegweiser, M.D.

    1996-09-01

    Paleozoic stratigraphy of the southern Lake Erie region is commonly interpreted as being dominated by flat-lying sedimentary rocks. Recent surface stratigraphic studies in New York, Pennsylvania, and Ohio have revealed the widespread presence of NW- and NE-trending folds and faults exposed along stream beds, and in bluffs along the southern Lake Erie shoreline. A black shale unit, previously unknown in northwestern Pennsylvania, was also discovered and its lateral continuity mapped. The shale forms a disconformable contact with the overlying Northeast Shale. Ship-based photomosaics were made of bluffs along Lake Erie, and integrated with land-based stratigraphic sections to map the continuity of units, identify displacement zones, and identify low amplitude folds. The black shale unit aided identification of offset and folding. Faults observed at the surface off-set Devonian and Mississippian rocks, and unconsolidated Quaternary sediments. Subsurface wrench faults, apparently extending into Precambrian rocks, have been identified by others. These wrench faults are generally perpendicular to the strike of the Appalachian Mountains, and are known as cross-strike discontinuities (CSDs). Principle zones of displacement associated with the CSDs can be recognized at the surface by numerous fractures having little offset, aligned drainage systems, and zones of increased hydrocarbon productivity and fluid migration. Increased hydrocarbons production occurs where reservoirs are cross-cut by the faults. The faults offset various reservoirs in Pennsylvania and Ohio in the subsurface. Identifying the location of these faults at the surface may provide information that leads top the discovery of new potential reservoirs.

  19. Next-generation sequencing identifies high frequency of mutations in potentially clinically actionable genes in sebaceous carcinoma.

    PubMed

    Tetzlaff, Michael T; Singh, Rajesh R; Seviour, Elena G; Curry, Jonathan L; Hudgens, Courtney W; Bell, Diana; Wimmer, Daniel A; Ning, Jing; Czerniak, Bogdan A; Zhang, Li; Davies, Michael A; Prieto, Victor G; Broaddus, Russell R; Ram, Prahlad; Luthra, Rajyalakshmi; Esmaeli, Bita

    2016-09-01

    Sebaceous carcinoma (SC) is a rare but aggressive malignancy with frequent recurrence and metastases. Surgery is the mainstay of therapy, but effective systemic therapies are lacking because the molecular alterations driving SC remain poorly understood. To identify these, we performed whole-exome next-generation sequencing of 409 cancer-associated genes on 27 SCs (18 primary/locally recurrent ocular, 5 paired metastatic ocular, and 4 primary extraocular) from 20 patients. In ocular SC, we identified 139 non-synonymous somatic mutations (median/lesion 3; range 0-23). Twenty-five of 139 mutations (18%) occurred in potentially clinically actionable genes in 6 of 16 patients. The most common mutations were mutations in TP53 (n = 9), RB1 (n = 6), PIK3CA (n = 2), PTEN (n = 2), ERBB2 (n = 2), and NF1 (n = 2). TP53 and RB1 mutations were restricted to ocular SC and correlated with aberrant TP53 and RB protein expression. Systematic pathway analyses demonstrated convergence of these mutations to activation of the PI3K signalling cascade, and PI3K pathway activation was confirmed in tumours with PTEN and/or PIK3CA mutations. Considerable inter-tumoural heterogeneity was observed between paired primary and metastatic ocular SCs. In primary extraocular SC, we identified 77 non-synonymous somatic mutations (median/lesion 22.5; range 3-29). This overall higher mutational load was attributed to a microsatellite instability phenotype in three of four patients and somatically acquired mutations in mismatch repair genes in two of four patients. Eighteen of 77 mutations (23%) were in potentially clinically actionable genes in three of four patients, including BTK, FGFR2, PDGFRB, HRAS, and NF1 mutations. Identification of potentially clinically actionable mutations in 9 of 20 SC patients (45%) underscores the importance of next-generation sequencing to expand the spectrum of genotype-matched targeted therapies. Frequent activation of PI3K signalling pathways provides a strong

  20. The potential of current- and wind-driven transport for environmental management of the Baltic Sea.

    PubMed

    Soomere, Tarmo; Döös, Kristofer; Lehmann, Andreas; Meier, H E Markus; Murawski, Jens; Myrberg, Kai; Stanev, Emil

    2014-02-01

    The ever increasing impact of the marine industry and transport on vulnerable sea areas puts the marine environment under exceptional pressure and calls for inspired methods for mitigating the impact of the related risks. We describe a method for preventive reduction of remote environmental risks caused by the shipping and maritime industry that are transported by surface currents and wind impact to the coasts. This method is based on characterizing systematically the damaging potential of the offshore areas in terms of potential transport to vulnerable regions of an oil spill or other pollution that has occurred in a particular area. The resulting maps of probabilities of pollution to be transported to the nearshore and the time it takes for the pollution to reach the nearshore are used to design environmentally optimized fairways for the Gulf of Finland, Baltic Proper, and south-western Baltic Sea. PMID:24414808

  1. 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

  2. DNA typing of ancient parasite eggs from environmental samples identifies human and animal worm infections in Viking-age settlement.

    PubMed

    Søe, Martin Jensen; Nejsum, Peter; Fredensborg, Brian Lund; Kapel, Christian Moliin Outzen

    2015-02-01

    Ancient parasite eggs were recovered from environmental samples collected at a Viking-age settlement in Viborg, Denmark, dated 1018-1030 A.D. Morphological examination identified Ascaris sp., Trichuris sp., and Fasciola sp. eggs, but size and shape did not allow species identification. By carefully selecting genetic markers, PCR amplification and sequencing of ancient DNA (aDNA) isolates resulted in identification of: the human whipworm, Trichuris trichiura , using SSUrRNA sequence homology; Ascaris sp. with 100% homology to cox1 haplotype 07; and Fasciola hepatica using ITS1 sequence homology. The identification of T. trichiura eggs indicates that human fecal material is present and, hence, that the Ascaris sp. haplotype 07 was most likely a human variant in Viking-age Denmark. The location of the F. hepatica finding suggests that sheep or cattle are the most likely hosts. Further, we sequenced the Ascaris sp. 18S rRNA gene in recent isolates from humans and pigs of global distribution and show that this is not a suited marker for species-specific identification. Finally, we discuss ancient parasitism in Denmark and the implementation of aDNA analysis methods in paleoparasitological studies. We argue that when employing species-specific identification, soil samples offer excellent opportunities for studies of human parasite infections and of human and animal interactions of the past. PMID:25357228

  3. Fiber contamination of vermiculites: a potential occupational and environmental health hazard

    SciTech Connect

    Moatamed, F.; Lockey, J.E.; Parry, W.T.

    1986-10-01

    Vermiculite ores from Montana, Virginia, and South Africa have been analyzed for the presence of amphibole contamination. Fibrous actinolite was found in unexpanded Montana vermiculite ore at a maximum concentration of 0.2%. The fibers persisted in the expanded ore at a maximum concentration of 0.6%. Actinolite was also found in the Virginia vermiculite ore but at a lower concentration and mostly as cleavage fragments with low length-to-width ratios. South African ore contained rare anthophyllite fibers also with low length-to-width ratios. Vermiculite ores have the potential for amphibole contamination and can represent potential health hazards without proper occupational and environmental control measures.

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

    PubMed

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

    2014-09-01

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

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

    PubMed Central

    Kraft, Robert; Kahn, Allon; Medina-Franco, José L.; Orlowski, Mikayla L.; Baynes, Cayla; López-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

  6. 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, 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

  7. 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

  8. In Silico Approach To Identify Potential Thyroid Hormone Disruptors among Currently Known Dust Contaminants and Their Metabolites.

    PubMed

    Zhang, Jin; Kamstra, Jorke H; Ghorbanzadeh, Mehdi; Weiss, Jana M; Hamers, Timo; Andersson, Patrik L

    2015-08-18

    Thyroid hormone disrupting chemicals (THDCs) interfere with the thyroid hormone system and may induce multiple severe physiological disorders. Indoor dust ingestion is a major route of THDCs exposure in humans, and one of the molecular targets of these chemicals is the hormone transporter transthyretin (TTR). To virtually screen indoor dust contaminants and their metabolites for THDCs targeting TTR, we developed a quantitative structure-activity relationship (QSAR) classification model. The QSAR model was applied to an in-house database including 485 organic dust contaminants reported from literature data and their 433 in silico derived metabolites. The model predicted 37 (7.6%) dust contaminants and 230 (53.1%) metabolites as potential TTR binders. Four new THDCs were identified after testing 23 selected parent dust contaminants in a radio-ligand TTR binding assay; 2,2',4,4'-tetrahydroxybenzophenone, perfluoroheptanesulfonic acid, 3,5,6-trichloro-2-pyridinol, and 2,4,5-trichlorophenoxyacetic acid. These chemicals competitively bind to TTR with 50% inhibition (IC50) values at or below 10 μM. Molecular docking studies suggested that these THDCs interacted similarly with TTR via the residue Ser117A, but their binding poses were dissimilar to the endogenous ligand T4. This study identified new THDCs using an in silico approach in combination with bioassay testing and highlighted the importance of metabolic activation for TTR binding. PMID:26207645

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2007-01-01

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

  11. A framework to gauge the epidemic potential of plant pathogens in environmental reservoirs: the example of kiwifruit canker.

    PubMed

    Bartoli, Claudia; Lamichhane, Jay Ram; Berge, Odile; Guilbaud, Caroline; Varvaro, Leonardo; Balestra, Giorgio M; Vinatzer, Boris A; Morris, Cindy E

    2015-02-01

    New economically important diseases on crops and forest trees emerge recurrently. An understanding of where new pathogenic lines come from and how they evolve is fundamental for the deployment of accurate surveillance methods. We used kiwifruit bacterial canker as a model to assess the importance of potential reservoirs of new pathogenic lineages. The current kiwifruit canker epidemic is at least the fourth outbreak of the disease on kiwifruit caused by Pseudomonas syringae in the mere 50 years in which this crop has been cultivated worldwide, with each outbreak being caused by different genetic lines of the bacterium. Here, we ask whether strains in natural (non-agricultural) environments could cause future epidemics of canker on kiwifruit. To answer this question, we evaluated the pathogenicity, endophytic colonization capacity and competitiveness on kiwifruit of P. syringae strains genetically similar to epidemic strains and originally isolated from aquatic and subalpine habitats. All environmental strains possessing an operon involved in the degradation of aromatic compounds via the catechol pathway grew endophytically and caused symptoms in kiwifruit vascular tissue. Environmental and epidemic strains showed a wide host range, revealing their potential as future pathogens of a variety of hosts. Environmental strains co-existed endophytically with CFBP 7286, an epidemic strain, and shared about 20 virulence genes, but were missing six virulence genes found in all epidemic strains. By identifying the specific gene content in genetic backgrounds similar to known epidemic strains, we developed criteria to assess the epidemic potential and to survey for such strains as a means of forecasting and managing disease emergence. PMID:24986268

  12. Genetic Diversity of Giardia duodenalis: Multilocus Genotyping Reveals Zoonotic Potential between Clinical and Environmental Sources in a Metropolitan Region of Brazil

    PubMed Central

    Durigan, Mauricio; Abreu, Aluana Gonçalves; Zucchi, Maria Imaculada; Franco, Regina Maura Bueno; de Souza, Anete Pereira

    2014-01-01

    Background Giardia duodenalis is a flagellate protozoan that parasitizes humans and several other mammals. Protozoan contamination has been regularly documented at important environmental sites, although most of these studies were performed at the species level. There is a lack of studies that correlate environmental contamination and clinical infections in the same region. The aim of this study is to evaluate the genetic diversity of a set of clinical and environmental samples and to use the obtained data to characterize the genetic profile of the distribution of G. duodenalis and the potential for zoonotic transmission in a metropolitan region of Brazil. Methodology/Principal Findings The genetic assemblages and subtypes of G. duodenalis isolates obtained from hospitals, a veterinary clinic, a day-care center and important environmental sites were determined via multilocus sequence-based genotyping using three unlinked gene loci. Cysts of Giardia were detected at all of the environmental sites. Mixed assemblages were detected in 25% of the total samples, and an elevated number of haplotypes was identified. The main haplotypes were shared among the groups, and new subtypes were identified at all loci. Ten multilocus genotypes were identified: 7 for assemblage A and 3 for assemblage B. Conclusions/Significance There is persistent G. duodenalis contamination at important environmental sites in the city. The identified mixed assemblages likely represent mixed infections, suggesting high endemicity of Giardia in these hosts. Most Giardia isolates obtained in this study displayed zoonotic potential. The high degree of genetic diversity in the isolates obtained from both clinical and environmental samples suggests that multiple sources of infection are likely responsible for the detected contamination events. The finding that many multilocus genotypes (MLGs) and haplotypes are shared by different groups suggests that these sources of infection may be related and

  13. Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas.

    PubMed

    Gorkhali, Neena Amatya; Dong, Kunzhe; Yang, Min; Song, Shen; Kader, Adiljian; Shrestha, Bhola Shankar; He, Xiaohong; Zhao, Qianjun; Pu, Yabin; Li, Xiangchen; Kijas, James; Guan, Weijun; Han, Jianlin; Jiang, Lin; Ma, Yuehui

    2016-01-01

    Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas. PMID:27444145

  14. Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas

    PubMed Central

    Gorkhali, Neena Amatya; Dong, Kunzhe; Yang, Min; Song, Shen; Kader, Adiljian; Shrestha, Bhola Shankar; He, Xiaohong; Zhao, Qianjun; Pu, Yabin; Li, Xiangchen; Kijas, James; Guan, Weijun; Han, Jianlin; Jiang, Lin; Ma, Yuehui

    2016-01-01

    Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas. PMID:27444145

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

    PubMed

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

    2011-07-01

    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 chemical-protein interactions on off-targets, it is reasonable to predict these interactions by mining the chemical-protein 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 user's 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 drug-drug 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

  17. Identifying Active Faults in Northeast North America Using Hypocenters and Multiscale Edge Wavelet Analyses of Potential Fields

    NASA Astrophysics Data System (ADS)

    Carpenter, K.; Horowitz, F.; Ebinger, C. J.; Navarrete, L. C.; Diaz-Etchevehere, D.

    2015-12-01

    Multiscale edge Poisson wavelet analyses of potential field data ("worms") have a physical interpretation as the locations of lateral boundaries in a source distribution that exactly generates the observed field. The worm technique is therefore well-suited to analyses of crustal-scale stuctures that could be reactivated by tectonic stress or by fluid injection processes, providing new tools to analyze existing continental-scale data sets. Northeastern North America (US, Canada) hosts potentially damaging intraplate earthquakes, yet many of the Proterozoic structures are covered by thick sedimentary sequences or dense vegetation, and crustal structure is relatively poorly known.For the purpose of extending basement structure beneath the Appalachian basin and establishing a consistent regional basis for comparison, we use worms to identify steeply dipping structures in compiled gravity and magnetic anomaly data sets. We compare results to intraplate earthquake locations to assess seismic hazards. Clearly, not all locations of lateral boundaries are faults, and we do not expect all faults to have shown activity in the ~50 years of seismic records available. However, proximity statistics between hypocenters and worms are of interest since they assist in the identification and location of a subset of potentially active faults. We compare structures of lateral mass-density or magnetization contrast with locations of earthquake hypocenters cataloged from the ISC, the NEIC, and the ANF from the EarthScope Transportable Array. We develop a GIS based method for calculating hypocenter/worm proximity, and we will show statistics and maps from this method for the region at the meeting.

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

    PubMed

    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

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

    PubMed Central

    Hafner, Polona; Gričar, Jožica; Skudnik, Mitja; Levanič, Tom

    2015-01-01

    We analysed two groups of Quercus robur trees, growing at nearby plots with different micro-location condition (W-wet and D-dry) in the floodplain Krakovo forest, Slovenia. In the study we compared the growth response of two different tree groups to environmental variables, the potential signal stored in earlywood (EW) structure and the potential difference of the information stored in carbon isotope discrimination of EW and latewood (LW). For that purpose EW and LW widths and carbon isotope discrimination for the period 1970–2008 AD were measured. EW and LW widths were measured on stained microscopic slides and chronologies were standardised using the ARSTAN program. α-cellulose was extracted from pooled EW and LW samples and homogenized samples were further analysed using an elemental analyser and IRMS. We discovered that W oaks grew significantly better over the whole analysed period. The difference between D and W oaks was significant in all analysed variables with the exception of stable carbon isotope discrimination in latewood. In W oaks, latewood widths correlated with summer (June to August) climatic variables, while carbon isotope discrimination was more connected to River Krka flow during the summer. EW discrimination correlated with summer and autumn River Krka flow of the previous year, while latewood discrimination correlated with flow during the current year. In the case of D oaks, the environmental signal appears to be vague, probably due to less favourable growth conditions resulting in markedly reduced increments. Our study revealed important differences in responses to environmental factors between the two oak groups of different physiological conditions that are preconditioned by environmental stress. Environmental information stored in tree-ring features may vary, even within the same forest stand, and largely depends on the micro-environment. Our analysis confirmed our assumptions that separate EW and LW analysis of widths and carbon

  20. Identifying coherent patterns of environmental change between multiple, multivariate records: an application to four 1000-year diatom records from Victoria, Australia

    NASA Astrophysics Data System (ADS)

    Tyler, Jonathan J.; Mills, Keely; Barr, Cameron; Sniderman, J. M. Kale; Gell, Peter A.; Karoly, David J.

    2015-07-01

    Empirical orthogonal functions (EOFs) of indirect archives of environmental change are increasingly used to identify coherent trends between palaeoclimate records, to separate externally forced patterns from locally driven idiosyncrasies. Lake sediments are particularly suited to such syntheses: they are abundant in most landscapes and record a wide array of information, yet local complexities often conceal or confuse the climate signal recorded at individual sites. Lake sediment parameters usually exhibit non-linear, multivariate and indirect responses to climate, therefore identifying coherent patterns between two or more lake records presents a complex challenge. Ideally, the selection of representative variables should be non-subjective and inclusive of as many different variables as possible, allowing for unexpected correlations between sites. In order to meet such demands, we propose a two-tier ordination procedure whereby site-specific (local) ordinations, obtained using Detrended Correspondence Analysis (DCA), are nested within a second, regional EOF. Using the local DCAs as representative variables allows the retention of a larger fraction of variance from each site, removes any subjectivity from variable selection and retains the potential for observing multiple, coherent signals from within and between each dataset. We explore this potential using four decadally resolved diatom records from volcanic lakes in Western Victoria, Australia. The records span the 1000 years prior to European settlement in CE 1803. Our analyses reveal at least two coherent patterns of ecological change that are manifest in each of the four datasets, patterns which may have been overlooked by a single-variable, empirical orthogonal function approach. This intra-site coherency provides a valuable step towards understanding multi-decadal hydroclimate variability in southeastern Australia.

  1. An algorithm for estimating potential deposition of corn pollen for environmental assessment.

    PubMed

    Kawashima, Shigeto; Matsuo, Kazuhito; Du, Mingyuan; Takahashi, Yuichi; Inoue, Satoshi; Yonemura, Seiichiro

    2004-01-01

    The safety and impact on the environment of transgenic crops are important issues, and studies have shown that pollen from transgenic Bt (Bacillus thuringiensis) corn (Zea mays L.) may kill nontarget insects. To develop an algorithm for assessing the environmental effect of transgenic crops, we arranged a field experiment in Tsukuba, Japan. Pollen dispersal and deposition were measured inside and outside a cornfield throughout the flowering period. Weather conditions such as wind speed and direction were measured at the same time. Pollen dispersal peaked 1 week after the start of flowering and continued for 12 days thereafter. The variation in daily pollen dispersal was similar at all observation points. Both pollen dispersal and deposition decreased exponentially with distance from the cornfield on all days. We estimated potential pollen deposition with a quasi-mechanistic model that incorporates the effects of wind direction, wind speed, and flowering intensity. The daily potential deposition was summed over the flowering period, and then the relationship between distance from the cornfield and the integrated potential deposition was estimated. It was possible to show the effective area of the environmental risk zone posed by genetically modified pollen by combining the distance/deposition relationship with the dose/response relationship derived from a laboratory assay. The algorithm described here can be applied to various wind-pollinated plants to estimate both potential and integrated pollen deposition. PMID:16028796

  2. What's down below? Current and potential future applications of geophysical techniques to identify subsurface permafrost conditions (Invited)

    NASA Astrophysics Data System (ADS)

    Douglas, T. A.; Bjella, K.; Campbell, S. W.

    2013-12-01

    For infrastructure design, operations, and maintenance requirements in the North the ability to accurately and efficiently detect the presence (or absence) of ground ice in permafrost terrains is a serious challenge. Ground ice features including ice wedges, thermokarst cave-ice, and segregation ice are present in a variety of spatial scales and patterns. Currently, most engineering applications use borehole logging and sampling to extrapolate conditions at the point scale. However, there is high risk of over or under estimating the presence of frozen or unfrozen features when relying on borehole information alone. In addition, boreholes are costly, especially for planning linear structures like roads or runways. Predicted climate warming will provide further challenges for infrastructure development and transportation operations where permafrost degradation occurs. Accurately identifying the subsurface character in permafrost terrains will allow engineers and planners to cost effectively create novel infrastructure designs to withstand the changing environment. There is thus a great need for a low cost rapidly deployable, spatially extensive means of 'measuring' subsurface conditions. Geophysical measurements, both terrestrial and airborne, have strong potential to revolutionize our way of mapping subsurface conditions. Many studies in continuous and discontinuous permafrost have used geophysical measurements to identify discrete features and repeatable patterns in the subsurface. The most common measurements include galvanic and capacitive coupled resistivity, ground penetrating radar, and multi frequency electromagnetic induction techniques. Each of these measurements has strengths, weaknesses, and limitations. By combining horizontal geophysical measurements, downhole geophysics, multispectral remote sensing images, LiDAR measurements, and soil and vegetation mapping we can start to assemble a holistic view of how surface conditions and standoff measurements

  3. Polymerase chain reaction-based screening method applicable universally to environmental haloarchaea and halobacteria for identifying polyhydroxyalkanoate producers among them.

    PubMed

    Mahansaria, Riddhi; Choudhury, Jayanta Debabrata; Mukherjee, Joydeep

    2015-09-01

    The existing techniques for detection of polyhydroxyalkanoates (PHA) in halophilic archaea/bacteria are either imprecise or require prior PHA production before screening. The proposed method involves amplification of the approximately 280-300 bp conserved region of Class III PHA synthase (phaC) gene of halophiles using the primers codehopCF and codehopCR (Han et al. Appl Environ Microb 76:7811-7819, 2010). In this study, the best reaction condition was ascertained after repeated trials. This developed method was tested on nine haloarchaeal and halobacterial type strains and 28 environmental halophilic archaea and bacteria isolated from the salt pans of the east and west coasts of India. 29 strains were found to be phaC-positive, while eight were found to be phaC-negative although they appeared PHA positive through conventional Nile Red staining. 16S rRNA-based phylogenetic analysis identified 9 haloarchaeal and 9 halobacterial species as novel PHA producers. Multiple sequence alignment of the phaC gene-derived amino acid sequences showed that only 7 amino acid residues were conserved within all four classes of phaC enzymes, whereas 61 amino acids were identical among the phaC enzyme specific to the haloarchaeal and halobacterial strains presently investigated. All phaC-positive strains produced PHA in standard nutrient deficient medium, whereas the phaC-negative strains did not accumulate any PHA as detected by gas chromatography and nuclear magnetic resonance analyses, thus proving the precision of the developed method and elimination of false positives seen with the traditional Nile Red staining procedure. PMID:26240023

  4. Exploratory study of some potential environmental impacts of CO2 sequestration in unmineable coal seams

    SciTech Connect

    Hedges, S.W.; Soong, Y.; Jones, R.J.; Harrison, D.K.; Irdi, G.A.; Frommell, E.A.; Dilmore, R.M.; White, C.M.

    2007-01-01

    An initial investigation into the potential environmental impacts of CO2 sequestration in unmineable coal seams has been conducted, focusing on changes in the produced water during enhanced coalbed methane (ECBM) production, using a CO2 injection process (CO2-ECBM). A high volatile bituminous coal, Pittsburgh No. 8, was reacted with synthetic produced water and gaseous carbon dioxide at 40°C and 50 bar to evaluate the potential for mobilisation of toxic metals during CO2-ECBM/sequestration. Microscopic and X-ray diffraction analysis of the post-reaction coal samples clearly show evidence of chemical reaction and chemical analysis of the synthetic produced water shows substantial changes in composition. These results suggest that changes to the produced water chemistry and the potential for mobilising toxic trace elements from coal beds are important factors to be considered when evaluating deep, unmineable coal seams for CO2 sequestration.

  5. Suitable Environmental Ranges for Potential Coral Reef Habitats in the Tropical Ocean

    PubMed Central

    Guan, Yi; Hohn, Sönke; Merico, Agostino

    2015-01-01

    Coral reefs are found within a limited range of environmental conditions or tolerance limits. Estimating these limits is a critical prerequisite for understanding the impacts of climate change on the biogeography of coral reefs. Here we used the diagnostic model ReefHab to determine the current environmental tolerance limits for coral reefs and the global distribution of potential coral reef habitats as a function of six factors: temperature, salinity, nitrate, phosphate, aragonite saturation state, and light. To determine these tolerance limits, we extracted maximum and minimum values of all environmental variables in corresponding locations where coral reefs are present. We found that the global, annually averaged tolerance limits for coral reefs are 21.7—29.6 °C for temperature, 28.7—40.4 psu for salinity, 4.51 μmol L-1 for nitrate, 0.63 μmol L-1 for phosphate, and 2.82 for aragonite saturation state. The averaged minimum light intensity in coral reefs is 450 μmol photons m-2 s-1. The global area of potential reef habitats calculated by the model is 330.5 × 103 km2. Compared with previous studies, the tolerance limits for temperature, salinity, and nutrients have not changed much, whereas the minimum value of aragonite saturation in coral reef waters has decreased from 3.28 to 2.82. The potential reef habitat area calculated with ReefHab is about 121×103 km2 larger than the area estimated from the charted reefs, suggesting that the growth potential of coral reefs is higher than currently observed. PMID:26030287

  6. Potential pathogenicity of Aeromonas hydrophila complex strains isolated from clinical, food, and environmental sources.

    PubMed

    Albarral, Vicenta; Sanglas, Ariadna; Palau, Montserrat; Miñana-Galbis, David; Fusté, M Carmen

    2016-04-01

    Aeromonas are autochthonous inhabitants of aquatic environments, including chlorinated and polluted waters, although they can also be isolated from a wide variety of environmental and clinical sources. They cause infections in vertebrates and invertebrates and are considered to be an emerging pathogen in humans, producing intestinal and extra-intestinal diseases. Most of the clinical isolates correspond to A. hydrophila, A. caviae, and A. veronii bv. Sobria, which are described as the causative agents of wound infections, septicaemia, and meningitis in immunocompromised people, and diarrhoea and dysenteric infections in the elderly and children. The pathogenic factors associated with Aeromonas are multifactorial and involve structural components, siderophores, quorum-sensing mechanisms, secretion systems, extracellular enzymes, and exotoxins. In this study, we analysed a representative number of clinical and environmental strains belonging to the A. hydrophila species complex to evaluate their potential pathogenicity. We thereby detected their enzymatic activities and antibiotic susceptibility pattern and the presence of virulence genes (aer, alt, ast, and ascV). The notably high prevalence of these virulence factors, even in environmental strains, indicated a potential pathogenic capacity. Additionally, we determined the adhesion capacity and cytopathic effects of this group of strains in Caco-2 cells. Most of the strains exhibited adherence and caused complete lysis. PMID:26889703

  7. Aluminum is a potential environmental factor for Crohn's disease induction: extended hypothesis.

    PubMed

    Lerner, Aaron

    2007-06-01

    Aluminum (Al) is a common environmental compound with immune-adjuvant activity and granulomatous inflammation inducer. Al exposure in food, additives, air, pharmaceuticals, and water pollution is ubiquitous in Western culture. Crohn's disease (CD) is a chronic relapsing intestinal inflammation in genetically susceptible individuals and is influenced by yet unidentified environmental factors. It is hypothesized, in the present review, that Al is a potential factor for induction or maintaining the inflammation in CD. Epidemiologically, CD incidence is higher in urban areas, where microparticle pollution is prevalent. Al immune activities share many characteristics with the immune pathology of CD: increased antigen presentation and APCs activation, many luminal bacterial or dietary compounds can be adsorbed to the metal and induce Th1 profile activity, promotion of humoral and cellular immune responses, proinflammatory, apoptotic, oxidative activity, and stress-related molecule expression enhancement, affecting intestinal bacterial composition and virulence, granuloma formation, colitis induction in an animal model of CD, and terminal ileum uptake. The Al-bacterial interaction, the microparticles homing the intestine together with the extensive immune activity, put Al as a potential environmental candidate for CD induction and maintenance. PMID:17804561

  8. Forecasting potential global environmental costs of livestock production 2000–2050

    PubMed Central

    Pelletier, Nathan; Tyedmers, Peter

    2010-01-01

    Food systems—in particular, livestock production—are key drivers of environmental change. Here, we compare the contributions of the global livestock sector in 2000 with estimated contributions of this sector in 2050 to three important environmental concerns: climate change, reactive nitrogen mobilization, and appropriation of plant biomass at planetary scales. Because environmental sustainability ultimately requires that human activities as a whole respect critical thresholds in each of these domains, we quantify the extent to which current and future livestock production contributes to published estimates of sustainability thresholds at projected production levels and under several alternative endpoint scenarios intended to illustrate the potential range of impacts associated with dietary choice. We suggest that, by 2050, the livestock sector alone may either occupy the majority of, or significantly overshoot, recently published estimates of humanity’s “safe operating space” in each of these domains. In light of the magnitude of estimated impacts relative to these proposed (albeit uncertain) sustainability boundary conditions, we suggest that reining in growth of this sector should be prioritized in environmental governance. PMID:20921375

  9. Maternal Expressed Emotion Predicts Children's Antisocial Behavior Problems: Using Monozygotic-Twin Differences to Identify Environmental Effects on Behavioral Development

    ERIC Educational Resources Information Center

    Caspi, Avshalom; Moffitt, Terrie E.; Morgan, Julia; Rutter,Michael; Taylor,Alan; Arseneault, Louise; Tully, Lucy; Jacobs, Catherine; Kim-Cohen, Julia

    2004-01-01

    If maternal expressed emotion is an environmental risk factor for children's antisocial behavior problems, it should account for behavioral differences between siblings growing up in the same family even after genetic influences on children's behavior problems are taken into account. This hypothesis was tested in the Environmental Risk…

  10. Identifying Patient-Specific Epstein-Barr Nuclear Antigen-1 Genetic Variation and Potential Autoreactive Targets Relevant to Multiple Sclerosis Pathogenesis

    PubMed Central

    Tschochner, Monika; Leary, Shay; Cooper, Don; Strautins, Kaija; Chopra, Abha; Clark, Hayley; Choo, Linda; Dunn, David; James, Ian; Carroll, William M.; Kermode, Allan G.; Nolan, David

    2016-01-01

    Background Epstein-Barr virus (EBV) infection represents a major environmental risk factor for multiple sclerosis (MS), with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1)-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome. Methods Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan) and candidates were evaluated for cross recognition with human brain proteins. Results EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3% nucleotide positions at a 1% cut-off). In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes (‘AEG’: aa 481–496 and ‘MVF’: aa 562–577), and two putative epitopes between positions 502–543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogenesis. Conclusions This study demonstrates the feasibility of obtaining autologous EBNA-1 sequences directly from buffy coat samples, and confirms divergence of these sequences from standard laboratory strains

  11. Kinase Gene Expression Profiling of Metastatic Clear Cell Renal Cell Carcinoma Tissue Identifies Potential New Therapeutic Targets.

    PubMed

    Ghatalia, Pooja; Yang, Eddy S; Lasseigne, Brittany N; Ramaker, Ryne C; Cooper, Sara J; Chen, Dongquan; Sudarshan, Sunil; Wei, Shi; Guru, Arjun S; Zhao, Amy; Cooper, Tiffiny; Della Manna, Deborah L; Naik, Gurudatta; Myers, Richard M; Sonpavde, Guru

    2016-01-01

    Kinases are therapeutically actionable targets. Kinase inhibitors targeting vascular endothelial growth factor receptors (VEGFR) and mammalian target of rapamycin (mTOR) improve outcomes in metastatic clear cell renal cell carcinoma (ccRCC), but are not curative. Metastatic tumor tissue has not been comprehensively studied for kinase gene expression. Paired intra-patient kinase gene expression analysis in primary tumor (T), matched normal kidney (N) and metastatic tumor tissue (M) may assist in identifying drivers of metastasis and prioritizing therapeutic targets. We compared the expression of 519 kinase genes using NanoString in T, N and M in 35 patients to discover genes over-expressed in M compared to T and N tissue. RNA-seq data derived from ccRCC tumors in The Cancer Genome Atlas (TCGA) were used to demonstrate differential expression of genes in primary tumor tissue from patients that had metastasis at baseline (n = 79) compared to those that did not develop metastasis for at least 2 years (n = 187). Functional analysis was conducted to identify key signaling pathways by using Ingenuity Pathway Analysis. Of 10 kinase genes overexpressed in metastases compared to primary tumor in the discovery cohort, 9 genes were also differentially expressed in TCGA primary tumors with metastasis at baseline compared to primary tumors without metastasis for at least 2 years: EPHB2, AURKA, GSG2, IKBKE, MELK, CSK, CHEK2, CDC7 and MAP3K8; p<0.001). The top pathways overexpressed in M tissue were pyridoxal 5'-phosphate salvage, salvage pathways of pyrimidine ribonucleotides, NF-kB signaling, NGF signaling and cell cycle control of chromosomal replication. The 9 kinase genes validated to be over-expressed in metastatic ccRCC may represent currently unrecognized but potentially actionable therapeutic targets that warrant functional validation. PMID:27574806

  12. Kinase Gene Expression Profiling of Metastatic Clear Cell Renal Cell Carcinoma Tissue Identifies Potential New Therapeutic Targets

    PubMed Central

    Ramaker, Ryne C.; Cooper, Sara J.; Chen, Dongquan; Sudarshan, Sunil; Wei, Shi; Guru, Arjun S.; Zhao, Amy; Cooper, Tiffiny; Della Manna, Deborah L.; Naik, Gurudatta; Myers, Richard M.; Sonpavde, Guru

    2016-01-01

    Kinases are therapeutically actionable targets. Kinase inhibitors targeting vascular endothelial growth factor receptors (VEGFR) and mammalian target of rapamycin (mTOR) improve outcomes in metastatic clear cell renal cell carcinoma (ccRCC), but are not curative. Metastatic tumor tissue has not been comprehensively studied for kinase gene expression. Paired intra-patient kinase gene expression analysis in primary tumor (T), matched normal kidney (N) and metastatic tumor tissue (M) may assist in identifying drivers of metastasis and prioritizing therapeutic targets. We compared the expression of 519 kinase genes using NanoString in T, N and M in 35 patients to discover genes over-expressed in M compared to T and N tissue. RNA-seq data derived from ccRCC tumors in The Cancer Genome Atlas (TCGA) were used to demonstrate differential expression of genes in primary tumor tissue from patients that had metastasis at baseline (n = 79) compared to those that did not develop metastasis for at least 2 years (n = 187). Functional analysis was conducted to identify key signaling pathways by using Ingenuity Pathway Analysis. Of 10 kinase genes overexpressed in metastases compared to primary tumor in the discovery cohort, 9 genes were also differentially expressed in TCGA primary tumors with metastasis at baseline compared to primary tumors without metastasis for at least 2 years: EPHB2, AURKA, GSG2, IKBKE, MELK, CSK, CHEK2, CDC7 and MAP3K8; p<0.001). The top pathways overexpressed in M tissue were pyridoxal 5'-phosphate salvage, salvage pathways of pyrimidine ribonucleotides, NF-kB signaling, NGF signaling and cell cycle control of chromosomal replication. The 9 kinase genes validated to be over-expressed in metastatic ccRCC may represent currently unrecognized but potentially actionable therapeutic targets that warrant functional validation. PMID:27574806

  13. 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

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

    PubMed

    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

  15. 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

  16. 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

  17. 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

  18. The environmental and economic sustainability of potential bioethanol from willow in the UK.

    PubMed

    Stephenson, A L; Dupree, P; Scott, S A; Dennis, J S

    2010-12-01

    Life cycle assessment has been used to investigate the environmental and economic sustainability of a potential operation in the UK in which bioethanol is produced from the hydrolysis and subsequent fermentation of coppice willow. If the willow were grown on idle arable land in the UK, or, indeed, in Eastern Europe and imported as wood chips into the UK, it was found that savings of greenhouse gas emissions of 70-90%, when compared to fossil-derived gasoline on an energy basis, would be possible. The process would be energetically self-sufficient, as the co-products, e.g. lignin and unfermented sugars, could be used to produce the process heat and electricity, with surplus electricity being exported to the National Grid. Despite the environmental benefits, the economic viability is doubtful at present. However, the cost of production could be reduced significantly if the willow were altered by breeding to improve its suitability for hydrolysis and fermentation. PMID:20727740

  19. Environmental Conditions Influence the Plant Functional Diversity Effect on Potential Denitrification

    PubMed Central

    Sutton-Grier, Ariana E.; Wright, Justin P.; McGill, Bonnie M.; Richardson, Curtis

    2011-01-01

    Global biodiversity loss has prompted research on the relationship between species diversity and ecosystem functioning. Few studies have examined how plant diversity impacts belowground processes; even fewer have examined how varying resource levels can influence the effect of plant diversity on microbial activity. In a field experiment in a restored wetland, we examined the role of plant trait diversity (or functional diversity, (FD)) and its interactions with natural levels of variability of soil properties, on a microbial process, denitrification potential (DNP). We demonstrated that FD significantly affected microbial DNP through its interactions with soil conditions; increasing FD led to increased DNP but mainly at higher levels of soil resources. Our results suggest that the effect of species diversity on ecosystem functioning may depend on environmental factors such as resource availability. Future biodiversity experiments should examine how natural levels of environmental variability impact the importance of biodiversity to ecosystem functioning. PMID:21311768

  20. 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

  1. Appraisal of potential environmental risks associated with human antibiotic consumption in Turkey.

    PubMed

    Turkdogan, F Ilter; Yetilmezsoy, Kaan

    2009-07-15

    A comprehensive analysis of Turkish antibiotic data was conducted to evaluate potential environmental risks associated with antibiotic consumption in Turkey for year 2007. Antibiotics were defined for systemic use or group J01 of the WHO Anatomical Therapeutic Chemical (ATC) classification system. Total emissions and prescriptions for each ATC group were classified separately into 17 different J01 categories and three forms of medication (capsule/tablets, injectables and suspensions). Capsules and tablets were found as the most emitted form of medication in year 2007, with a total emission rate of about 585.5 tons/year (76%). Total antibiotic emission rates including all forms of medications were determined to be about 664.2 tons/year (86%) and 110.1 tons/year (14%) for adult and pediatric patients, respectively. An environmental risk assessment of 8 human antibiotics was conducted according to the EU draft guidance (CEC/III/5504/94, draft 6, version 4) and the risk was indicated by the ratio of predicted environmental concentration (PEC) to predicted no effect concentration (PNEC) for the aquatic environment. Available acute and chronic toxicity data were collected from the open peer-reviewed literature to derive PNEC. Risk quotients (PEC/PNEC) were then calculated for 8 pharmaceutical substances. PEC/PNEC ratio exceeded 1.0 for beta-lactams (cephalosporins and penicillins), fluoroquinolones, macrolides and aminoglycosides. The findings of this study concluded that the release of these compounds from wastewater treatment plants may potentially be of an important environmental concern based on today's use of antibiotics in Turkey. PMID:19100684

  2. Environmental Dynamics and the Habitability Potential at Gale Crater, Mars (Invited)

    NASA Astrophysics Data System (ADS)

    Conrad, P. G.; Eigenbrode, J. L.; Atreya, S. K.; Blake, D.; Coll, P. J.; de la Torre Juarez, M.; Edgett, K. S.; Fairen, A.; Fisk, M. R.; Franz, H.; Glavin, D. P.; Gómez, F. G.; Haberle, R. M.; Hamilton, V. E.; Leshin, L. A.; Martin-Torres, F. J.; Martinez-Frias, J.; McAdam, A.; McKay, C. P.; Ming, D. W.; Navarro-Gonzalez, R.; Pavlov, A.; Steele, A.; Stern, J. C.; Zorzano, M.; Mahaffy, P. R.; Grotzinger, J. P.

    2013-12-01

    The assessment of environmental habitability potential involves measurement of the chemical and physical attributes of the system as well as their dynamic interplay. The environmental dynamics describe the availability of both energy sources and raw materials for meeting the requirements of organisms and for altering the environment. Energetic exchange can also determine the preservation potential for organic materials in the rock record. During its first year at Gale Crater, the Mars Science Laboratory payload has directly measured the chemistry and physical attributes, e.g., temperature, humidity, radiation, pressure, etc. of the martian atmosphere. Curiosity has also acquired chemical and mineralogical data, both from a wind drift deposit of fines and from two examples of a sedimentary rock formation in a region of Gale Crater called Yellowknife Bay, some 445 meters to the east of Bradbury Landing, where Curiosity initially touched down. These data enabled inferences to be made regarding depositional environment and past habitability potential at Gale Crater. The rock chemistry data reveal signs of aqueous interaction i.e., H2O, OH and H2 and sufficient elemental basis (C, H, O, S and possibly N) for plausible nutrient supply, should Mars have ever had autotrophic prokaryotes to exploit it, and a range of redox conditions tolerable to Earth microbes is indicated by the presence of clay minerals. Curiosity's observations of the chemical, physical and geologic features of Yellowknife Bay point to a formerly habitable environment.

  3. Potential bud bank responses to apical meristem damage and environmental variables: matching or complementing axillary meristems?

    PubMed

    Klimešová, Jitka; Malíková, Lenka; Rosenthal, Jonathan; Šmilauer, Petr

    2014-01-01

    Soil nutrients, dormant axillary meristem availability, and competition can influence plant tolerance to damage. However, the role of potential bud banks (adventitious meristems initiated only after injury) is not known. Examining Central European field populations of 22 species of short-lived monocarpic herbs exposed to various sources of damage, we hypothesized that: (1) with increasing injury severity, the number of axillary branches would decrease, due to axillary meristem limitation, whereas the number of adventitious shoots (typically induced by severe injury) would increase; (2) favorable environmental conditions would allow intact plants to branch more, resulting in stronger axillary meristem limitation than in unfavorable conditions; and (3) consequently, adventitious sprouting would be better enabled in favorable than unfavorable conditions. We found strong support for the first hypothesis, only limited support for the second, and none for the third. Our results imply that whereas soil nutrients and competition marginally influence plant tolerance to damage, potential bud banks enable plants to overcome meristem limitation from severe damage, and therefore better tolerate it. All the significant effects were found in intraspecific comparisons, whereas interspecific differences were not found. Monocarpic plants with potential bud banks therefore represent a distinct strategy occupying a narrow environmental niche. The disturbance regime typical for this niche remains to be examined, as do the costs associated with the banks of adventitious and axillary reserve meristems. PMID:24516587

  4. Experimental investigation to evaluate the potential environmental hazards of photovoltaic panels.

    PubMed

    Tammaro, Marco; Salluzzo, Antonio; Rimauro, Juri; Schiavo, Simona; Manzo, Sonia

    2016-04-01

    Recently the potential environmental hazard of photovoltaic modules together with their management as waste has attracted the attention of scientists. Particular concern is aroused by the several metals contained in photovoltaic panels whose potential release in the environment were scarcely investigated. Here, for the first time, the potential environmental hazard of panels produced in the last 30 years was investigated through the assessment of up to 18 releasable metals. Besides, the corresponding ecotoxicological effects were also evaluated. Experimental data were compared with the current European and Italian law limits for drinking water, discharge on soil and landfill inert disposal in order to understand the actual pollution load. Results showed that less than 3% of the samples respected all law limits and around 21% was not ecotoxic. By considering the technological evolutions in manufacturing, we have shown that during the years crystalline silicon panels have lower tendency to release hazardous metals with respect to thin film panels. In addition, a prediction of the amounts of lead, chromium, cadmium and nickel releasable from next photovoltaic waste was performed. The prevision up to 2050 showed high amounts of lead (30t) and cadmium (2.9t) releasable from crystalline and thin film panels respectively. PMID:26829098

  5. Potential groundwater age tracer found: Halon-1301 (CF3Br), as previously identified as CFC-13 (CF3Cl)

    NASA Astrophysics Data System (ADS)

    Beyer, Monique; van der Raaij, Rob; Morgenstern, Uwe; Jackson, Bethanna

    2014-09-01

    Groundwater dating using anthropogenic and natural tracer substances is a powerful tool for understanding groundwater dynamics for improved management of groundwater resources. Due to limitations in individual dating methods, often multiple tracers are used to reduce ambiguities. It is commonly accepted that there is a need for further complementary age tracers, in addition to current ones (e.g., tritium, SF6, and CFCs). We propose a potential new groundwater age tracer, Halon-1301 (CF3Br), which can easily be determined using gas chromatography with an attached electron capture detector (GC/ECD) developed by Busenberg and Plummer (2008). Its peak was noted by Busenberg and Plummer (2008), but they believed it to be CFC-13 (CF3Cl) at that time. We performed rigorous tests on gases containing or excluding Halon-1301 and CFC-13 and modern water samples and concluded that the two compounds have extremely similar retention times. Additionally, we found that the ECD response of CFC-13 is far too low to be detected in groundwater or air using standard volumes and sampling techniques. However, the peak areas and concentrations Busenberg and Plummer (2008) reported are in line with what would be expected for Halon-1301. Thus, we are confident that the peak formerly identified as CFC-13 is actually Halon-1301. Busenberg agrees with our findings. We further suggest that Halon-1301 has potential as a (complementary) age tracer, due to its established atmospheric history, and could hypothetically be used to date groundwater recharged in the 1970s or onward. We discuss known relevant properties, such as solubility and stability of Halon-1301 in the context of how these effect its potential application as a groundwater age tracer. Some open questions remain concerning how conservative Halon-1301 is—is it subject to degradation, retardation, and/or local contamination in groundwater. We are confident that Halon-1301 possesses important tracer relevant properties, but further

  6. Hodgkin–Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods

    PubMed Central

    Daly, Aidan C.; Holmes, Chris

    2015-01-01

    As cardiac cell models become increasingly complex, a correspondingly complex ‘genealogy’ of inherited parameter values has also emerged. The result has been the loss of a direct link between model parameters and experimental data, limiting both reproducibility and the ability to re-fit to new data. We examine the ability of approximate Bayesian computation (ABC) to infer parameter distributions in the seminal action potential model of Hodgkin and Huxley, for which an immediate and documented connection to experimental results exists. The ability of ABC to produce tight posteriors around the reported values for the gating rates of sodium and potassium ion channels validates the precision of this early work, while the highly variable posteriors around certain voltage dependency parameters suggests that voltage clamp experiments alone are insufficient to constrain the full model. Despite this, Hodgkin and Huxley's estimates are shown to be competitive with those produced by ABC, and the variable behaviour of posterior parametrized models under complex voltage protocols suggests that with additional data the model could be fully constrained. This work will provide the starting point for a full identifiability analysis of commonly used cardiac models, as well as a template for informative, data-driven parametrization of newly proposed models. PMID:27019736

  7. Comparative study of Saccharomyces cerevisiae wine strains to identify potential marker genes correlated to desiccation stress tolerance.

    PubMed

    Capece, Angela; Votta, Sonia; Guaragnella, Nicoletta; Zambuto, Marianna; Romaniello, Rossana; Romano, Patrizia

    2016-05-01

    The most diffused formulation of starter for winemaking is active dry yeast (ADY). ADYs production process is essentially characterized by air-drying stress, a combination of several stresses, including thermal, hyperosmotic and oxidative and cell capacity to counteract such multiple stresses will determine its survival. The molecular mechanisms underlying cell stress response to desiccation have been mostly studied in laboratory and commercial yeast strains, but a growing interest is currently developing for indigenous yeast strains which represent a valuable and alternative source of genetic and molecular biodiversity to be exploited. In this work, a comparative study of different Saccharomyces cerevisiae indigenous wine strains, previously selected for their technological traits, has been carried out to identify potentially relevant genes involved in desiccation stress tolerance. Cell viability was evaluated along desiccation treatment and gene expression was analyzed by real-time PCR before and during the stress. Our data show that the observed differences in individual strain sensitivity to desiccation stress could be associated to specific gene expression over time. In particular, either the basal or the stress-induced mRNA levels of certain genes, such as HSP12, SSA3, TPS1, TPS2, CTT1 and SOD1, result tightly correlated to the strain survival advantage. This study provides a reliable and sensitive method to predict desiccation stress tolerance of indigenous wine yeast strains which could be preliminary to biotechnological applications. PMID:26882930

  8. Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots.

    PubMed

    Franta, Zdeněk; Vogel, Heiko; Lehmann, Rüdiger; Rupp, Oliver; Goesmann, Alexander; Vilcinskas, Andreas

    2016-01-01

    Lucilia sericata larvae are used as an alternative treatment for recalcitrant and chronic wounds. Their excretions/secretions contain molecules that facilitate tissue debridement, disinfect, or accelerate wound healing and have therefore been recognized as a potential source of novel therapeutic compounds. Among the substances present in excretions/secretions various peptidase activities promoting the wound healing processes have been detected but the peptidases responsible for these activities remain mostly unidentified. To explore these enzymes we applied next generation sequencing to analyze the transcriptomes of different maggot tissues (salivary glands, gut, and crop) associated with the production of excretions/secretions and/or with digestion as well as the rest of the larval body. As a result we obtained more than 123.8 million paired-end reads, which were assembled de novo using Trinity and Oases assemblers, yielding 41,421 contigs with an N50 contig length of 2.22 kb and a total length of 67.79 Mb. BLASTp analysis against the MEROPS database identified 1729 contigs in 577 clusters encoding five peptidase classes (serine, cysteine, aspartic, threonine, and metallopeptidases), which were assigned to 26 clans, 48 families, and 185 peptidase species. The individual enzymes were differentially expressed among maggot tissues and included peptidase activities related to the therapeutic effects of maggot excretions/secretions. PMID:27119084

  9. Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots

    PubMed Central

    Franta, Zdeněk; Vogel, Heiko; Lehmann, Rüdiger; Rupp, Oliver; Goesmann, Alexander; Vilcinskas, Andreas

    2016-01-01

    Lucilia sericata larvae are used as an alternative treatment for recalcitrant and chronic wounds. Their excretions/secretions contain molecules that facilitate tissue debridement, disinfect, or accelerate wound healing and have therefore been recognized as a potential source of novel therapeutic compounds. Among the substances present in excretions/secretions various peptidase activities promoting the wound healing processes have been detected but the peptidases responsible for these activities remain mostly unidentified. To explore these enzymes we applied next generation sequencing to analyze the transcriptomes of different maggot tissues (salivary glands, gut, and crop) associated with the production of excretions/secretions and/or with digestion as well as the rest of the larval body. As a result we obtained more than 123.8 million paired-end reads, which were assembled de novo using Trinity and Oases assemblers, yielding 41,421 contigs with an N50 contig length of 2.22 kb and a total length of 67.79 Mb. BLASTp analysis against the MEROPS database identified 1729 contigs in 577 clusters encoding five peptidase classes (serine, cysteine, aspartic, threonine, and metallopeptidases), which were assigned to 26 clans, 48 families, and 185 peptidase species. The individual enzymes were differentially expressed among maggot tissues and included peptidase activities related to the therapeutic effects of maggot excretions/secretions. PMID:27119084

  10. A Targeted Metabolomics MRM-MS Study on Identifying Potential Hypertension Biomarkers in Human Plasma and Evaluating Acupuncture Effects.

    PubMed

    Yang, Mingxiao; Yu, Zheng; Deng, Shufang; Chen, Xiaomin; Chen, Liang; Guo, Zhenyu; Zheng, Hui; Chen, Lin; Cai, Dingjun; Wen, Bo; Wu, Qiaofeng; Liang, Fanrong

    2016-01-01

    The critical role of metabolic abnormality in hypertension is increasingly recognized, but its biomarkers are not clearly identified. In this study, 47 chemical compounds recorded by literature were employed as target metabolites of essential hypertension (EH). We detected their content in the plasma of EH patients and healthy subjects by using the Multiple Reaction Monitoring-Mass Spectrometry (MRM-MS). After screening the most altered compounds, acupuncture was used to treat patients for 3 months and these plasma metabolites were tested again. The results showed that oleic acid (OA) and myoinositol (MI) were the most important differential metabolites between the hypertensive plasma and the healthy plasma. They were also closely correlated with 24-hour blood pressure and nocturnal dipping. Moreover, plasma OA and MI could be restored to normal levels by acupuncture, accompanying with reduction of 24-hour systolic and diastolic blood pressure [from 145.10 ± 9.28 mm Hg to 140.70 ± 9.59 mm Hg (P < 0.0001), and 88.35 ± 7.92 mm Hg to 85.86 ± 7.95 mm Hg (P = 0.0024), respectively] and improvement of circadian blood pressure rhythm. This study demonstrated that plasma OA and MI were potential hypertension biomarkers and they could be used to preliminarily assess the treating effects such as acupuncture. PMID:27181907

  11. USING PharmGKB TO TRAIN TEXT MINING APPROACHES FOR IDENTIFYING POTENTIAL GENE TARGETS FOR PHARMACOGENOMIC STUDIES

    PubMed Central

    PAKHOMOV, S.; MCINNES, B.T.; LAMBA, J.; LIU, Y.; MELTON, G.B.; GHODKE, Y.; BHISE, N.; LAMBA, V.; BIRNBAUM, A.K.

    2012-01-01

    The main objective of this study was to investigate the feasibility of using PharmGKB, a pharmacogenomic database, as a source of training data in combination with text of MEDLINE abstracts for a text mining approach to identification of potential gene targets for pathway-driven pharmacogenomics research. We used the manually curated relations between drugs and genes in PharmGKB database to train a support vector machine predictive model and applied this model prospectively to MEDLINE abstracts. The gene targets suggested by this approach were subsequently manually reviewed. Our quantitative analysis showed that a support vector machine classifiers trained on MEDLINE abstracts with single words (unigrams) used as features and PharmGKB relations used for supervision, achieve an overall sensitivity of 85% and specificity of 69%. The subsequent qualitative analysis showed that gene targets “suggested” by the automatic classifier were not anticipated by expert reviewers but were subsequently found to be relevant to the three drugs that were investigated: carbamazepine, lamivudine and zidovudine. Our results show that this approach is not only feasible but may also find new gene targets not identifiable by other methods thus making it a valuable tool for pathway-driven pharmacogenomics research. PMID:22564551

  12. A Targeted Metabolomics MRM-MS Study on Identifying Potential Hypertension Biomarkers in Human Plasma and Evaluating Acupuncture Effects

    PubMed Central

    Yang, Mingxiao; Yu, Zheng; Deng, Shufang; Chen, Xiaomin; Chen, Liang; Guo, Zhenyu; Zheng, Hui; Chen, Lin; Cai, Dingjun; Wen, Bo; Wu, Qiaofeng; Liang, Fanrong

    2016-01-01

    The critical role of metabolic abnormality in hypertension is increasingly recognized, but its biomarkers are not clearly identified. In this study, 47 chemical compounds recorded by literature were employed as target metabolites of essential hypertension (EH). We detected their content in the plasma of EH patients and healthy subjects by using the Multiple Reaction Monitoring-Mass Spectrometry (MRM-MS). After screening the most altered compounds, acupuncture was used to treat patients for 3 months and these plasma metabolites were tested again. The results showed that oleic acid (OA) and myoinositol (MI) were the most important differential metabolites between the hypertensive plasma and the healthy plasma. They were also closely correlated with 24-hour blood pressure and nocturnal dipping. Moreover, plasma OA and MI could be restored to normal levels by acupuncture, accompanying with reduction of 24-hour systolic and diastolic blood pressure [from 145.10 ± 9.28 mm Hg to 140.70 ± 9.59 mm Hg (P < 0.0001), and 88.35 ± 7.92 mm Hg to 85.86 ± 7.95 mm Hg (P = 0.0024), respectively] and improvement of circadian blood pressure rhythm. This study demonstrated that plasma OA and MI were potential hypertension biomarkers and they could be used to preliminarily assess the treating effects such as acupuncture. PMID:27181907

  13. Hodgkin-Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods.

    PubMed

    Daly, Aidan C; Gavaghan, David J; Holmes, Chris; Cooper, Jonathan

    2015-12-01

    As cardiac cell models become increasingly complex, a correspondingly complex 'genealogy' of inherited parameter values has also emerged. The result has been the loss of a direct link between model parameters and experimental data, limiting both reproducibility and the ability to re-fit to new data. We examine the ability of approximate Bayesian computation (ABC) to infer parameter distributions in the seminal action potential model of Hodgkin and Huxley, for which an immediate and documented connection to experimental results exists. The ability of ABC to produce tight posteriors around the reported values for the gating rates of sodium and potassium ion channels validates the precision of this early work, while the highly variable posteriors around certain voltage dependency parameters suggests that voltage clamp experiments alone are insufficient to constrain the full model. Despite this, Hodgkin and Huxley's estimates are shown to be competitive with those produced by ABC, and the variable behaviour of posterior parametrized models under complex voltage protocols suggests that with additional data the model could be fully constrained. This work will provide the starting point for a full identifiability analysis of commonly used cardiac models, as well as a template for informative, data-driven parametrization of newly proposed models. PMID:27019736

  14. Potential environmental impacts of light-emitting diodes (LEDs): metallic resources, toxicity, and hazardous waste classification.

    PubMed

    Lim, Seong-Rin; Kang, Daniel; Ogunseitan, Oladele A; Schoenung, Julie M

    2011-01-01

    Light-emitting diodes (LEDs) are advertised as environmentally friendly because they are energy efficient and mercury-free. This study aimed to determine if LEDs engender other forms of environmental and human health impacts, and to characterize variation across different LEDs based on color and intensity. The objectives are as follows: (i) to use standardized leachability tests to examine whether LEDs are to be categorized as hazardous waste under existing United States federal and California state regulations; and (ii) to use material life cycle impact and hazard assessment methods to evaluate resource depletion and toxicity potentials of LEDs based on their metallic constituents. According to federal standards, LEDs are not hazardous except for low-intensity red LEDs, which leached Pb at levels exceeding regulatory limits (186 mg/L; regulatory limit: 5). However, according to California regulations, excessive levels of copper (up to 3892 mg/kg; limit: 2500), Pb (up to 8103 mg/kg; limit: 1000), nickel (up to 4797 mg/kg; limit: 2000), or silver (up to 721 mg/kg; limit: 500) render all except low-intensity yellow LEDs hazardous. The environmental burden associated with resource depletion potentials derives primarily from gold and silver, whereas the burden from toxicity potentials is associated primarily with arsenic, copper, nickel, lead, iron, and silver. Establishing benchmark levels of these substances can help manufacturers implement design for environment through informed materials substitution, can motivate recyclers and waste management teams to recognize resource value and occupational hazards, and can inform policymakers who establish waste management policies for LEDs. PMID:21138290

  15. A Literature Survey to Identify Potentially Volatile Iodine-Bearing Species Present in Off-Gas Streams

    SciTech Connect

    Bruffey, S. H.; Spencer, B. B.; Strachan, D. M.; Jubin, R. T.; Soelberg, N. R.; Riley, B. J.

    2015-06-30

    Four radionuclides have been identified as being sufficiently volatile in the reprocessing of nuclear fuel that their gaseous release needs to be controlled to meet regulatory requirements (Jubin et al. 2011, 2012). These radionuclides are 3H, 14C, 85Kr, and 129I. Of these, 129I has the longest half-life and potentially high biological impact. Accordingly, control of the release of 129I is most critical with respect to the regulations for the release of radioactive material in stack emissions. It is estimated that current EPA regulations (EPA 2010) would require any reprocessing plant in the United States to limit 129I release to less than 0.05 Ci/MTIHM for a typical fuel burnup of 55 gigawatt days per metric tonne (GWd/t) (Jubin 2011). The study of inorganic iodide in off-gas systems has been almost exclusively limited to I2 and the focus of organic iodide studies has been CH3I. In this document, we provide the results of an examination of publically available literature that is relevant to the presence and sources of both inorganic and organic iodine-bearing species in reprocessing plants. We especially focus on those that have the potential to be poorly sequestered with traditional capture methodologies. Based on the results of the literature survey and some limited thermodynamic modeling, the inorganic iodine species hypoiodous acid (HOI) and iodine monochloride (ICl) were identified as potentially low-sorbing iodine species that could present in off-gas systems. Organic species of interest included both short chain alkyl iodides such as methyl iodide (CH3I) and longer alkyl iodides up to iodododecane (C10H21I). It was found that fuel dissolution may provide conditions conducive to HOI formation and has been shown to result in volatile long-chain alkyl iodides, though these may not volatilize until later in the reprocessing sequence. Solvent extraction processes were found to be significant sources of various organic iodine-bearing species; formation of these

  16. Air quality models and unusually large ozone increases: Identifying model failures, understanding environmental causes, and improving modeled chemistry

    NASA Astrophysics Data System (ADS)

    Couzo, Evan A.

    Several factors combine to make ozone (O3) pollution in Houston, Texas, unique when compared to other metropolitan areas. These include complex meteorology, intense clustering of industrial activity, and significant precursor emissions from the heavily urbanized eight-county area. Decades of air pollution research have borne out two different causes, or conceptual models, of O 3 formation. One conceptual model describes a gradual region-wide increase in O3 concentrations "typical" of many large U.S. cities. The other conceptual model links episodic emissions of volatile organic compounds to spatially limited plumes of high O3, which lead to large hourly increases that have exceeded 100 parts per billion (ppb) per hour. These large hourly increases are known to lead to violations of the federal O 3 standard and impact Houston's status as a non-attainment area. There is a need to further understand and characterize the causes of peak O 3 levels in Houston and simulate them correctly so that environmental regulators can find the most cost-effective pollution controls. This work provides a detailed understanding of unusually large O 3 increases in the natural and modeled environments. First, we probe regulatory model simulations and assess their ability to reproduce the observed phenomenon. As configured for the purpose of demonstrating future attainment of the O3 standard, the model fails to predict the spatially limited O3 plumes observed in Houston. Second, we combine ambient meteorological and pollutant measurement data to identify the most likely geographic origins and preconditions of the concentrated O3 plumes. We find evidence that the O3 plumes are the result of photochemical activity accelerated by industrial emissions. And, third, we implement changes to the modeled chemistry to add missing formation mechanisms of nitrous acid, which is an important radical precursor. Radicals control the chemical reactivity of atmospheric systems, and perturbations to

  17. A systematic approach to evaluate erosion potential at environmental restoration sites

    SciTech Connect

    Veenis, S.J.; Mays, D.C.

    1998-12-01

    The Environmental Restoration (ER) Project at the Los Alamos National Laboratory (LANL) is responsible for investigation and remediation of solid waste management units (SWMUs) under the Resource Conservation and Recovery Act and area of concerns (AOCs) under the direction of the Department of Energy. During the investigation and remediation phases, information may be gathered that indicates that conditions may be present at the site which may effect surface water quality. Depending on the constituent found, its concentration, and erosion/sediment transport potential, it may be necessary to implement temporary or permanent mitigative measures.

  18. Public health and the potential benefits of Crime Prevention Through Environmental Design.

    PubMed

    Cozens, Paul

    2007-01-01

    Studies have consistently found that safety and security are major public concerns; however, crime is rarely considered as an outcome in public health. The recent shift by planning policy towards promoting compact, 'walkable' communities close to public transport aims to redress many of the problems associated with urban sprawl. However, communities that do not feel safe are less likely to be active citizens. This paper argues that Crime Prevention Through Environmental Design has potential benefits for public health in the provision of local crime risk assessments and in delivering safer environments, which can support active living, walkable communities and public health. PMID:18093465

  19. Achieving Land, Energy, and Environmental Compatibility: Utility-Scale Solar Energy Potential and Land-Use in California

    NASA Astrophysics Data System (ADS)

    Hoffacker, M. K.; Hernandez, R. R.; Field, C. B.

    2013-12-01

    Solar energy is an archetype renewable energy technology with great potential to reduce greenhouse gas emissions when substituted for carbon-intensive energy. Utility-scale solar energy (USSE; i.e., > 1 MW) necessitates large quantities of space making the efficient use of land for USSE development critical to realizing its full potential. However, studies elucidating the interaction between land-use and utility-scale solar energy (USSE) are limited. In this study, we assessed 1) the theoretical and technical potential of terrestrial-based USSE systems, and 2) land-use and land-cover change impacts from actual USSE installations (> 20 MW; planned, under construction, operating), using California as a case study due to its early adoption of renewable energy systems, unique constraints on land availability, immense energy demand, and vast natural resources. We used topo-climatic (e.g., slope, irradiance), infrastructural (e.g., proximity to transmission lines), and ecological constraints (e.g., threatened and endangered species) to determine highly favorable, favorable, and unfavorable locations for USSE and to assess its technical potential. We found that the theoretical potential of photovoltaic (PV) and concentrating solar power (CSP) in California is 26,097 and 29,422 kWh/m2/day, respectively. We identified over 150 planned, under construction, and operating USSE installations in California, ranging in size from 20 to 1,000 MW. Currently, 29% are located on shrub- and scrublands, 23% on cultivated crop land, 13% on pasture/hay areas, 11% on grassland/herbaceous and developed open space, and 7% in the built environment. Understanding current land-use decisions of USSE systems and assessing its future potential can be instructive for achieving land, energy, and environmental compatibility, especially for other global regions that share similar resource demands and limitations.

  20. Integrating Demographic, Clinical,and Environmental Exposure Information to Identify Genomic Biomarkers Associated With Subtypes of Childhood Asthma

    EPA Science Inventory

    Childhood asthma is a multifactorial disease with a disturbingly high incidence in urbanized areas. The pathogenesis of asthma is poorly understood due to the complex relationship between genetic susceptibility and modulating environmental factors. The Mechanistic Indicators of C...

  1. ION COMPOSITION ELUCIDATION (ICE): A HIGH RESOLUTION MASS SPECTROMETRIC TOOL FOR IDENTIFYING ORGANIC COMPOUNDS IN COMPLEX EXTRACTS OF ENVIRONMENTAL SAMPLES

    EPA Science Inventory


    Unidentified Organic Compounds. For target analytes, standards are purchased, extraction and clean-up procedures are optimized, and mass spectra and retention times for the chromatographic separation are obtained for comparison to the target compounds in environmental sample ...

  2. Human Leptospirosis Infection in Fiji: An Eco-epidemiological Approach to Identifying Risk Factors and Environmental Drivers for Transmission

    PubMed Central

    Lau, Colleen L.; Watson, Conall H.; Lowry, John H.; David, Michael C.; Craig, Scott B.; Wynwood, Sarah J.; Kama, Mike; Nilles, Eric J.

    2016-01-01

    Leptospirosis is an important zoonotic disease in the Pacific Islands. In Fiji, two successive cyclones and severe flooding in 2012 resulted in outbreaks with 576 reported cases and 7% case-fatality. We conducted a cross-sectional seroprevalence study and used an eco-epidemiological approach to characterize risk factors and drivers for human leptospirosis infection in Fiji, and aimed to provide an evidence base for improving the effectiveness of public health mitigation and intervention strategies. Antibodies indicative of previous or recent infection were found in 19.4% of 2152 participants (81 communities on the 3 main islands). Questionnaires and geographic information systems data were used to assess variables related to demographics, individual behaviour, contact with animals, socioeconomics, living conditions, land use, and the natural environment. On multivariable logistic regression analysis, variables associated with the presence of Leptospira antibodies included male gender (OR 1.55), iTaukei ethnicity (OR 3.51), living in villages (OR 1.64), lack of treated water at home (OR 1.52), working outdoors (1.64), living in rural areas (OR 1.43), high poverty rate (OR 1.74), living <100m from a major river (OR 1.41), pigs in the community (OR 1.54), high cattle density in the district (OR 1.04 per head/sqkm), and high maximum rainfall in the wettest month (OR 1.003 per mm). Risk factors and drivers for human leptospirosis infection in Fiji are complex and multifactorial, with environmental factors playing crucial roles. With global climate change, severe weather events and flooding are expected to intensify in the South Pacific. Population growth could also lead to more intensive livestock farming; and urbanization in developing countries is often associated with urban and peri-urban slums where diseases of poverty proliferate. Climate change, flooding, population growth, urbanization, poverty and agricultural intensification are important drivers of zoonotic

  3. Human Leptospirosis Infection in Fiji: An Eco-epidemiological Approach to Identifying Risk Factors and Environmental Drivers for Transmission.

    PubMed

    Lau, Colleen L; Watson, Conall H; Lowry, John H; David, Michael C; Craig, Scott B; Wynwood, Sarah J; Kama, Mike; Nilles, Eric J

    2016-01-01

    Leptospirosis is an important zoonotic disease in the Pacific Islands. In Fiji, two successive cyclones and severe flooding in 2012 resulted in outbreaks with 576 reported cases and 7% case-fatality. We conducted a cross-sectional seroprevalence study and used an eco-epidemiological approach to characterize risk factors and drivers for human leptospirosis infection in Fiji, and aimed to provide an evidence base for improving the effectiveness of public health mitigation and intervention strategies. Antibodies indicative of previous or recent infection were found in 19.4% of 2152 participants (81 communities on the 3 main islands). Questionnaires and geographic information systems data were used to assess variables related to demographics, individual behaviour, contact with animals, socioeconomics, living conditions, land use, and the natural environment. On multivariable logistic regression analysis, variables associated with the presence of Leptospira antibodies included male gender (OR 1.55), iTaukei ethnicity (OR 3.51), living in villages (OR 1.64), lack of treated water at home (OR 1.52), working outdoors (1.64), living in rural areas (OR 1.43), high poverty rate (OR 1.74), living <100m from a major river (OR 1.41), pigs in the community (OR 1.54), high cattle density in the district (OR 1.04 per head/sqkm), and high maximum rainfall in the wettest month (OR 1.003 per mm). Risk factors and drivers for human leptospirosis infection in Fiji are complex and multifactorial, with environmental factors playing crucial roles. With global climate change, severe weather events and flooding are expected to intensify in the South Pacific. Population growth could also lead to more intensive livestock farming; and urbanization in developing countries is often associated with urban and peri-urban slums where diseases of poverty proliferate. Climate change, flooding, population growth, urbanization, poverty and agricultural intensification are important drivers of zoonotic

  4. The exposome concept: a challenge and a potential driver for environmental health research.

    PubMed

    Siroux, Valérie; Agier, Lydiane; Slama, Rémy

    2016-06-01

    The exposome concept was defined in 2005 as encompassing all environmental exposures from conception onwards, as a new strategy to evidence environmental disease risk factors. Although very appealing, the exposome concept is challenging in many respects. In terms of assessment, several hundreds of time-varying exposures need to be considered, but increasing the number of exposures assessed should not be done at the cost of increased exposure misclassification. Accurately assessing the exposome currently requires numerous measurements, which rely on different technologies; resulting in an expensive set of protocols. In the future, high-throughput 'omics technologies may be a promising technique to integrate a wide range of exposures from a small numbers of biological matrices. Assessing the association between many exposures and health raises statistical challenges. Due to the correlation structure of the exposome, existing statistical methods cannot fully and efficiently untangle the exposures truly affecting the health outcome from correlated exposures. Other statistical challenges relate to accounting for exposure misclassification or identifying synergistic effects between exposures. On-going exposome projects are trying to overcome technical and statistical challenges. From a public health perspective, a better understanding of the environmental risk factors should open the way to improved prevention strategies. PMID:27246588

  5. Phenotypic Screening of Primary Human Cell Culture Systems to Identify Potential for Compound Toxicity (CHI Phenotypic Screening)

    EPA Science Inventory

    Addressing safety aspects of drugs and environmental chemicals has historically been undertaken through animal testing. However, the quantity of chemicals needing assessment and the challenge of species extrapolation require development of alternative approaches. Assessing phenot...

  6. Hydrologic modeling to screen potential environmental management methods for malaria vector control in Niger

    NASA Astrophysics Data System (ADS)

    Gianotti, Rebecca L.; Bomblies, Arne; Eltahir, Elfatih A. B.

    2009-08-01

    This paper describes the first use of Hydrology-Entomology and Malaria Transmission Simulator (HYDREMATS), a physically based distributed hydrology model, to investigate environmental management methods for malaria vector control in the Sahelian village of Banizoumbou, Niger. The investigation showed that leveling of topographic depressions where temporary breeding habitats form during the rainy season, by altering pool basin microtopography, could reduce the pool persistence time to less than the time needed for establishment of mosquito breeding, approximately 7 days. Undertaking soil surface plowing can also reduce pool persistence time by increasing the infiltration rate through an existing pool basin. Reduction of the pool persistence time to less than the rainfall interstorm period increases the frequency of pool drying events, removing habitat for subadult mosquitoes. Both management approaches could potentially be considered within a given context. This investigation demonstrates that management methods that modify the hydrologic environment have significant potential to contribute to malaria vector control in water-limited, Sahelian Africa.

  7. Environmental assessment of the potential effects of aquifer thermal energy storage systems on microorganisms in groundwater

    SciTech Connect

    Hicks, R.J.; Stewart, D.L.

    1988-03-01

    The primary objective of this study was to evaluate the potential environmental effects (both adverse and beneficials) of aquifer thermal energy storage (ATES) technology pertaining to microbial communities indigenous to subsurface environments (i.e., aquifers) and the propagation, movement, and potential release of pathogenic microorganisms (specifically, Legionella) within ATES systems. Seasonal storage of thermal energy in aquifers shows great promise to reduce peak demand; reduce electric utility load problems; contribute to establishing favorable economics for district heating and cooling systems; and reduce pollution from extraction, refining, and combustion of fossil fuels. However, concerns that the widespread implementation of this technology may have adverse effects on biological systems indigeneous to aquifers, as well as help to propagate and release pathogenic organisms that enter thee environments need to be resolved. 101 refs., 2 tabs.

  8. Occurrence, properties and pollution potential of environmental minerals in acid mine drainage.

    PubMed

    Valente, T Maria; Leal Gomes, C

    2009-01-15

    This paper describes the occurrences, the mineralogical assemblages and the environmental relevance of the AMD-precipitates from the abandoned mine of Valdarcas, Northern Portugal. At this mining site, these precipitates are particularly related with the chemical speciation of iron, which is in according to the abundance of mine wastes enriched in pyrrhotite and pyrite. The more relevant supergene mineralogical assemblages include the following environmental minerals: soluble metal-salts, mainly sulphates, revealing seasonal behaviour, iron-hydroxysulphates and iron-oxyhydroxides, both forming ochre precipitates of poorly and well-crystalline minerals. Pollution potential of the most highly water soluble salts was analysed in order to evaluate the environmental effect of their dissolution by rainfall. Laboratory experiments, carried out with iron and aluminium sulphates, demonstrated the facility to release metals, sulphate and acidity upon dissolution. Regarding the ochre precipitates, composed by several less soluble iron (III)-minerals, the spatial distribution on the nearby aqueous system as well as the proportion of Jarosite, Schwertmannite and Goethite in the mixtures gave information about the halo's contamination promoted by the AMD emerging from the waste-dumps. PMID:19004477

  9. 76 FR 70429 - Notice of Intent To Prepare an Environmental Impact Statement and Notice of Potential Floodplain...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-14

    ... of Intent To Prepare an Environmental Impact Statement and Notice of Potential Floodplain and... Statement and Notice of Potential Floodplain and Wetlands Involvement. SUMMARY: The U.S. Department of...; and (5) provide notice that the proposed project may involve potential impacts to floodplains...

  10. Potential environmental and human health impacts of rechargeable lithium batteries in electronic waste.

    PubMed

    Kang, Daniel Hsing Po; Chen, Mengjun; Ogunseitan, Oladele A

    2013-05-21

    Rechargeable lithium-ion (Li-ion) and lithium-polymer (Li-poly) batteries have recently become dominant in consumer electronic products because of advantages associated with energy density and product longevity. However, the small size of these batteries, the high rate of disposal of consumer products in which they are used, and the lack of uniform regulatory policy on their disposal means that lithium batteries may contribute substantially to environmental pollution and adverse human health impacts due to potentially toxic materials. In this research, we used standardized leaching tests, life-cycle impact assessment (LCIA), and hazard assessment models to evaluate hazardous waste classification, resource depletion potential, and toxicity potentials of lithium batteries used in cellphones. Our results demonstrate that according to U.S. federal regulations, defunct Li-ion batteries are classified hazardous due to their lead (Pb) content (average 6.29 mg/L; σ = 11.1; limit 5). However, according to California regulations, all lithium batteries tested are classified hazardous due to excessive levels of cobalt (average 163,544 mg/kg; σ = 62,897; limit 8000), copper (average 98,694 mg/kg; σ = 28,734; limit 2500), and nickel (average 9525 mg/kg; σ = 11,438; limit 2000). In some of the Li-ion batteries, the leached concentrations of chromium, lead, and thallium exceeded the California regulation limits. The environmental impact associated with resource depletion and human toxicity is mainly associated with cobalt, copper, nickel, thallium, and silver, whereas the ecotoxicity potential is primarily associated with cobalt, copper, nickel, thallium, and silver. However, the relative contribution of aluminum and lithium to human toxicity and ecotoxicity could not be estimated due to insufficient toxicity data in the models. These findings support the need for stronger government policy at the local, national, and international levels to encourage recovery, recycling, and

  11. Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling

    PubMed Central

    Muthamilarasan, Mehanathan; Bonthala, Venkata S.; Khandelwal, Rohit; Jaishankar, Jananee; Shweta, Shweta; Nawaz, Kashif; Prasad, Manoj

    2015-01-01

    Transcription factors (TFs) are major players in stress signaling and constitute an integral part of signaling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4model plants, Setaria italica (SiWRKY) and S. viridis (SvWRKY), respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analyzed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II, and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY), followed by group III (39 SiWRKY and 11 SvWRKY) and group I (10 SiWRKY and 6 SvWRKY). Group II proteins were further classified into 5 subgroups (IIa to IIe) based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling. PMID:26635818

  12. Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling.

    PubMed

    Muthamilarasan, Mehanathan; Bonthala, Venkata S; Khandelwal, Rohit; Jaishankar, Jananee; Shweta, Shweta; Nawaz, Kashif; Prasad, Manoj

    2015-01-01

    Transcription factors (TFs) are major players in stress signaling and constitute an integral part of signaling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4model plants, Setaria italica (SiWRKY) and S. viridis (SvWRKY), respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analyzed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II, and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY), followed by group III (39 SiWRKY and 11 SvWRKY) and group I (10 SiWRKY and 6 SvWRKY). Group II proteins were further classified into 5 subgroups (IIa to IIe) based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling. PMID:26635818

  13. The IGF-1 Receptor Identifies a Pool of Human Cardiac Stem Cells with Superior Therapeutic Potential for Myocardial Regeneration

    PubMed Central

    D’Amario, Domenico; Cabral-Da-Silva, Mauricio; Zheng, Hanqiao; Fiorini, Claudia; Goichberg, Polina; Steadman, Elisabeth; Ferreira-Martins, João; Sanada, Fumihiro; Piccoli, Marco; Cappetta, Donato; D’Alessandro, David A.; Michler, Robert E.; Hosoda, Toru; Anastasia, Luigi; Rota, Marcello; Leri, Annarosa; Anversa, Piero; Kajstura, Jan

    2012-01-01

    Rationale Age and coronary artery disease may negatively affect the function of human cardiac stem cells (hCSCs) and their potential therapeutic efficacy for autologous cell transplantation in the failing heart. Objective Insulin-like growth factor 1 (IGF-1) and 2 (IGF-2), and angiotensin II (Ang II) and their receptors, IGF-1R, IGF-2R and AT1R, were characterized in c-kit-positive-hCSCs to establish whether these systems would allow us to separate hCSC classes with different growth reserve in the aging and diseased myocardium. Methods and Results C-kit-positive-hCSCs were collected from myocardial samples obtained from 24 patients, 48 to 86 years of age, undergoing elective cardiac surgery for coronary artery disease. The expression of IGF-1R in hCSCs recognized a young cell phenotype defined by long telomeres, high telomerase activity, enhanced cell proliferation and attenuated apoptosis. In addition to IGF-1, IGF-1R-positive-hCSCs secreted IGF-2 that promoted myocyte differentiation. Conversely, the presence of IGF-2R and AT1R, in the absence of IGF-1R, identified senescent hCSCs with impaired growth reserve and increased susceptibility to apoptosis. The ability of IGF-1R-positive-hCSCs to regenerate infarcted myocardium was then compared with that of unselected c-kit-positive-hCSCs. IGF-1R-positive-hCSCs improved cardiomyogenesis and vasculogenesis. Pretreatment of IGF-1R-positive-hCSCs with IGF-2 resulted in the formation of more mature myocytes and superior recovery of ventricular structure. Conclusions hCSCs expressing only IGF-1R synthesize both IGF-1 and IGF-2, which are potent modulators of stem cell replication, commitment to the myocyte lineage and myocyte differentiation, pointing to this hCSC subset as the ideal candidate cell for the management of human heart failure. PMID:21546606

  14. Early T Cell Recognition of B Cells following Epstein-Barr Virus Infection: Identifying Potential Targets for Prophylactic Vaccination

    PubMed Central

    Brooks, Jill M.; Long, Heather M.; Tierney, Rose J.; Shannon-Lowe, Claire; Leese, Alison M.; Fitzpatrick, Martin; Taylor, Graham S.; Rickinson, Alan B.

    2016-01-01

    Epstein-Barr virus, a B-lymphotropic herpesvirus, is the cause of infectious mononucleosis, has strong aetiologic links with several malignancies and has been implicated in certain autoimmune diseases. Efforts to develop a prophylactic vaccine to prevent or reduce EBV-associated disease have, to date, focused on the induction of neutralising antibody responses. However, such vaccines might be further improved by inducing T cell responses capable of recognising and killing recently-infected B cells. In that context, EBNA2, EBNA-LP and BHRF1 are