Science.gov

Sample records for linking biomarker community

  1. Community Links

    ERIC Educational Resources Information Center

    Nelson, Mary

    1975-01-01

    At Moraine Valley Community College (Illinois), a chain of events, programs, activities, and services has linked the college and community in such areas as fine arts, ethnic groups, public services, community action, community service, and community education. (Author/NHM)

  2. Linking Archaeal Molecular Diversity and Lipid Biomarker Composition in a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda; Orphan, Victoria; Turk, Kendra; Embaye, Tsegereda; Kubo, Mike; Summons, Roger

    2005-01-01

    Lipid biomarkers for discrete microbial groups are a valuable tool for establishing links to ancient microbial ecosystems. Lipid biomarkers can establish organism source and function in contemporary microbial ecosystems (membrane lipids) and by analogy, potential relevance to the fossilized carbon skeletons (geolipids) extracted from ancient sedimentary rock. The Mars Exploration Rovers have provided clear evidence for an early wet Mars and the presence of hypersaline evaporitic basins. Ongoing work on an early Earth analog, the hypersaline benthic mats in Guerrero Negro, Baja California Sur, may provide clues to what may have evolved and flourished on an early wet Mars, if only for a short period. Cyanobacterial mats are a pertinent early Earth analog for consideration of evolutionary and microbial processes within the aerobic photosynthetic and adjacent anoxic layers. Fluctuations in physio-chemical parameters associated with spatial and temporal scales are expressed through vast microbial metabolic diversity. Our recent work hopes to establish the dynamic of archaeal diversity, particularly as it relates to methane production in this high sulfate environment, through the use of lipid biomarker and phylogenetic analyses. Archaeal 16s rRNA and mcrA gene assemblages, demonstrated distinct spatial separation over the 130 mm core of at least three distinct genera within the order Methanosarcinales, as well as an abundance of uncultured members of the Thermoplasmales and Crenarchaeota. Ether-bound lipid analysis identified abundant 0-alkyl and 0-isopranyl chains throughout the core, and the presence of sn-2 hydroxyarchaeol, a biomarker for methylotrophic methanogens. A unique ether isoprenoid chain, a C30:1 , possibly related to the geolipid squalane, a paleobiomarker associated with hypersaline environments, was most abundant within the oxic-anoxic transition zone.

  3. Developing community friendly appropriate biomarkers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this presentation we discuss the statistical methodology used in the development of biomarkers to track disease as an outcome for nutrition or exercise interventions in community settings. Obesity and co-morbidities are of growing concern. Nutrition and physical activity interventions have been d...

  4. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

    2003-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

  5. Community Links as Resources.

    ERIC Educational Resources Information Center

    Kleine, Patricia A.; Webb, James T.

    This chapter examines issues in cultivating community resources in programs for gifted and talented children. First, ways to meet the affective needs of gifted children are considered and the importance of bridging the gap between home and school and resolving conflicts is stressed. Ten hindrances to the optimum development of children are…

  6. Lymphangioleiomyomatosis Biomarkers Linked to Lung Metastatic Potential and Cell Stemness

    PubMed Central

    Ruiz de Garibay, Gorka; Herranz, Carmen; Llorente, Alicia; Boni, Jacopo; Serra-Musach, Jordi; Mateo, Francesca; Aguilar, Helena; Gómez-Baldó, Laia; Petit, Anna; Vidal, August; Climent, Fina; Hernández-Losa, Javier; Cordero, Álex; González-Suárez, Eva; Sánchez-Mut, José Vicente; Esteller, Manel; Llatjós, Roger; Varela, Mar; López, José Ignacio; García, Nadia; Extremera, Ana I.; Gumà, Anna; Ortega, Raúl; Plà, María Jesús; Fernández, Adela; Pernas, Sònia; Falo, Catalina; Morilla, Idoia; Campos, Miriam; Gil, Miguel; Román, Antonio; Molina-Molina, María; Ussetti, Piedad; Laporta, Rosalía; Valenzuela, Claudia; Ancochea, Julio; Xaubet, Antoni; Casanova, Álvaro; Pujana, Miguel Angel

    2015-01-01

    Lymphangioleiomyomatosis (LAM) is a rare lung-metastasizing neoplasm caused by the proliferation of smooth muscle-like cells that commonly carry loss-of-function mutations in either the tuberous sclerosis complex 1 or 2 (TSC1 or TSC2) genes. While allosteric inhibition of the mechanistic target of rapamycin (mTOR) has shown substantial clinical benefit, complementary therapies are required to improve response and/or to treat specific patients. However, there is a lack of LAM biomarkers that could potentially be used to monitor the disease and to develop other targeted therapies. We hypothesized that the mediators of cancer metastasis to lung, particularly in breast cancer, also play a relevant role in LAM. Analyses across independent breast cancer datasets revealed associations between low TSC1/2 expression, altered mTOR complex 1 (mTORC1) pathway signaling, and metastasis to lung. Subsequently, immunohistochemical analyses of 23 LAM lesions revealed positivity in all cases for the lung metastasis mediators fascin 1 (FSCN1) and inhibitor of DNA binding 1 (ID1). Moreover, assessment of breast cancer stem or luminal progenitor cell biomarkers showed positivity in most LAM tissue for the aldehyde dehydrogenase 1 (ALDH1), integrin-ß3 (ITGB3/CD61), and/or the sex-determining region Y-box 9 (SOX9) proteins. The immunohistochemical analyses also provided evidence of heterogeneity between and within LAM cases. The analysis of Tsc2-deficient cells revealed relative over-expression of FSCN1 and ID1; however, Tsc2-deficient cells did not show higher sensitivity to ID1-based cancer inhibitors. Collectively, the results of this study reveal novel LAM biomarkers linked to breast cancer metastasis to lung and to cell stemness, which in turn might guide the assessment of additional or complementary therapeutic opportunities for LAM. PMID:26167915

  7. Lymphangioleiomyomatosis Biomarkers Linked to Lung Metastatic Potential and Cell Stemness.

    PubMed

    Ruiz de Garibay, Gorka; Herranz, Carmen; Llorente, Alicia; Boni, Jacopo; Serra-Musach, Jordi; Mateo, Francesca; Aguilar, Helena; Gómez-Baldó, Laia; Petit, Anna; Vidal, August; Climent, Fina; Hernández-Losa, Javier; Cordero, Álex; González-Suárez, Eva; Sánchez-Mut, José Vicente; Esteller, Manel; Llatjós, Roger; Varela, Mar; López, José Ignacio; García, Nadia; Extremera, Ana I; Gumà, Anna; Ortega, Raúl; Plà, María Jesús; Fernández, Adela; Pernas, Sònia; Falo, Catalina; Morilla, Idoia; Campos, Miriam; Gil, Miguel; Román, Antonio; Molina-Molina, María; Ussetti, Piedad; Laporta, Rosalía; Valenzuela, Claudia; Ancochea, Julio; Xaubet, Antoni; Casanova, Álvaro; Pujana, Miguel Angel

    2015-01-01

    Lymphangioleiomyomatosis (LAM) is a rare lung-metastasizing neoplasm caused by the proliferation of smooth muscle-like cells that commonly carry loss-of-function mutations in either the tuberous sclerosis complex 1 or 2 (TSC1 or TSC2) genes. While allosteric inhibition of the mechanistic target of rapamycin (mTOR) has shown substantial clinical benefit, complementary therapies are required to improve response and/or to treat specific patients. However, there is a lack of LAM biomarkers that could potentially be used to monitor the disease and to develop other targeted therapies. We hypothesized that the mediators of cancer metastasis to lung, particularly in breast cancer, also play a relevant role in LAM. Analyses across independent breast cancer datasets revealed associations between low TSC1/2 expression, altered mTOR complex 1 (mTORC1) pathway signaling, and metastasis to lung. Subsequently, immunohistochemical analyses of 23 LAM lesions revealed positivity in all cases for the lung metastasis mediators fascin 1 (FSCN1) and inhibitor of DNA binding 1 (ID1). Moreover, assessment of breast cancer stem or luminal progenitor cell biomarkers showed positivity in most LAM tissue for the aldehyde dehydrogenase 1 (ALDH1), integrin-ß3 (ITGB3/CD61), and/or the sex-determining region Y-box 9 (SOX9) proteins. The immunohistochemical analyses also provided evidence of heterogeneity between and within LAM cases. The analysis of Tsc2-deficient cells revealed relative over-expression of FSCN1 and ID1; however, Tsc2-deficient cells did not show higher sensitivity to ID1-based cancer inhibitors. Collectively, the results of this study reveal novel LAM biomarkers linked to breast cancer metastasis to lung and to cell stemness, which in turn might guide the assessment of additional or complementary therapeutic opportunities for LAM. PMID:26167915

  8. Mobile Recommendation Based on Link Community Detection

    PubMed Central

    Zhang, Jianpei; Yang, Jing

    2014-01-01

    Since traditional mobile recommendation systems have difficulty in acquiring complete and accurate user information in mobile networks, the accuracy of recommendation is not high. In order to solve this problem, this paper proposes a novel mobile recommendation algorithm based on link community detection (MRLD). MRLD executes link label diffusion algorithm and maximal extended modularity (EQ) of greedy search to obtain the link community structure, and overlapping nodes belonging analysis (ONBA) is adopted to adjust the overlapping nodes in order to get the more accurate community structure. MRLD is tested on both synthetic and real-world networks, and the experimental results show that our approach is valid and feasible. PMID:25243204

  9. Teachers' Link to Community Resources.

    ERIC Educational Resources Information Center

    West Virginia Education Fund, Charleston.

    This directory consists of profiles of more than 500 companies and organizations which responded to a West Virginia Education Fund survey during the summer of 1990. The purposes of the directory are: (1) to provide a reference that helps educators locate resources from business, industry and community groups; (2) to initiate and facilitate…

  10. Linking community health improvement with clinical strategies.

    PubMed

    Hattis, P; Matheny, P

    2001-01-01

    In most health care organizations, there is a separation between community health improvement (CHI) efforts and other strategic goals--in particular, clinical care strategies. By carefully managing their approach to CHI, health care organizations can successfully link these areas and reap significant tangible and intangible rewards, including cost savings and better outcomes of care. PMID:11372277

  11. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda; Orphan, Victoria; Embaye, Tsegereda; Turk, Kendra; Kubo, Mike; Summons, Roger

    2004-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. Various lipids associated with specific microbial groups can serve as biomarkers for establishing organism source and function in contemporary microbial ecosystems (membrane lipids), and by analogy, potential relevance to ancient organic-rich sedimentary rocks (geolipids). As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments. Our recent work has focused on lipid biomarker analysis of a potential analogue for such ancient mats growing in a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. The aerobic, surface layer of this mat (0 to 1 mm) contained a variety of ester-bound fatty acids (FA) representing a diverse bacterial population including cyanobacteria, sulphate reducers (SRB) and heterotrophs. Biomarkers for microeukaryotes detected in this layer included sterols, C-20 polyunsaturated FA and a highly branched isoprenoid, diagnostic for diatoms. Cyanobacteria were also indicated by the presence of a diagnostic set of mid-chain methylalkanes. C-28, to C-34 wax esters (WXE) present in relatively small amounts in the upper 3 mm of the mat are considered biomarkers for green non-sulphur bacteria. Ether-bound isoprenoids were also identified although in considerably lower abundance than ester-bound FA (approx. 1:l0). These complex ether lipids included archatol, hydroxyarchaeol and a C-40 tetraether, all in small amounts. After ether cleavage with boron tribromide, the major recovered isoprenyl was a C-30:1. This C(sub 30;1) yelded squalane after hydrogenation, a known geobiomarker for hypersaline environments in ancient oils and sediments. In this mat, it represents the dominant Archaeal population. The carbon isotopic composition of biomarker lipids were generally depleted relative to the bulk organic material (delta C-13 TOC -10%). Most

  12. Linking Biomarker and Comparative Omics to Pathogens in Legumes.

    PubMed

    Diapari, Marwan

    2016-01-01

    It is envisioned that a more precise study of the association between the traits and biomarkers will dramatically decrease the time and costs required to bring new improved disease resistance lines to market. The field of omics has an enormous potential to assess diseases more precise, including the identification and understanding of pathogenic mechanisms in legume crops, and have been exemplified by a relatively large number of studies. Recently, molecular genetic studies have accumulated a huge amount of genotypic data, through a more affordable next generation sequencing (NGS) technology, causing the omics approaches to fall behind. In this paper I provide an overview of genomics and proteomics and their use in legume crops, including the use of comparative genomics to identify homologous markers within legume crops. PMID:26364313

  13. Ubiquitousness of link-density and link-pattern communities in real-world networks

    NASA Astrophysics Data System (ADS)

    Šubelj, L.; Bajec, M.

    2012-01-01

    Community structure appears to be an intrinsic property of many complex real-world networks. However, recent work shows that real-world networks reveal even more sophisticated modules than classical cohesive (link-density) communities. In particular, networks can also be naturally partitioned according to similar patterns of connectedness among the nodes, revealing link-pattern communities. We here propose a propagation based algorithm that can extract both link-density and link-pattern communities, without any prior knowledge of the true structure. The algorithm was first validated on different classes of synthetic benchmark networks with community structure, and also on random networks. We have further applied the algorithm to different social, information, technological and biological networks, where it indeed reveals meaningful (composites of) link-density and link-pattern communities. The results thus seem to imply that, similarly as link-density counterparts, link-pattern communities appear ubiquitous in nature and design.

  14. Identification of hybrid node and link communities in complex networks

    NASA Astrophysics Data System (ADS)

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-03-01

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

  15. Identification of hybrid node and link communities in complex networks

    PubMed Central

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-01-01

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately. PMID:25728010

  16. Ecology and distribution of a new biomarker linked to 1,2-dichloropropane dechlorination in subsurface environments

    NASA Astrophysics Data System (ADS)

    Padilla-Crespo, E.; Loeffler, F. E.

    2011-12-01

    Reductive dechlorination plays a major role in the transformation and detoxification of chlorinated solvents, including chlorinated ethenes. Molecular biological tools are being applied at contaminated sites in order to assess the process-specific biomarkers that impact site performance, and to monitor the progress of bioremediation approaches. The few current biomarker genes in use provide an incomplete picture of the reductively dechlorinating bacterial community; this is a limitation for implementing enhanced bioremediation and monitored natural attenuation as cleanup strategies at chlorinated solvent contaminated sites. Reductively dehalogenating organisms, particularly Dehalococcoides (Dhc) strains, possess multiple reductive dehalogenase (RDase) genes, which are promising targets to specifically monitor dehalogenation processes of interest. Dehalococcoides populations in two highly enriched cultures (RC and KS) have been implicated in the reductive dechlorination of dechlorination of 1,2-dichloropropane (1,2-D), a widespread halogenated organic pollutant, to the non-toxic propene. Using a combined approach of transcription, expression and molecular analysis a new biomarker linked to 1,2-dichloropropane has been identified in Dhc strains RC and KS providing for the first time, convincing evidence of a specific RDase implicated in 1,2-D dechlorination to propene. Further analyses imply that new biomarker is in a "mobile DNA segment", a genomic island (GI) of horizontal gene transfer origin. A valid quantitative PCR approach was designed to detect and enumerate this gene in cultures and environmental samples; this will be a useful to bioremediation practitioners to more efficiently implement reductive dechlorination as a remediation tool. The new biomarker has been identified in fresh water sediment samples from different geographical locations in Europe, North and South America. Further research aims to shed light on RDase gene dissemination and the adaptation

  17. Biomarker as a Research Tool in Linking Exposure to Air Particles and Respiratory Health

    PubMed Central

    2015-01-01

    Some of the environmental toxicants from air pollution include particulate matter (PM10), fine particulate matter (PM2.5), and ultrafine particles (UFP). Both short- and long-term exposure could result in various degrees of respiratory health outcomes among exposed persons, which rely on the individuals' health status. Methods. In this paper, we highlight a review of the studies that have used biomarkers to understand the association between air particles exposure and the development of respiratory problems resulting from the damage in the respiratory system. Data from previous epidemiological studies relevant to the application of biomarkers in respiratory system damage reported from exposure to air particles are also summarized. Results. Based on these analyses, the findings agree with the hypothesis that biomarkers are relevant in linking harmful air particles concentrations to increased respiratory health effects. Biomarkers are used in epidemiological studies to provide an understanding of the mechanisms that follow airborne particles exposure in the airway. However, application of biomarkers in epidemiological studies of health effects caused by air particles in both environmental and occupational health is inchoate. Conclusion. Biomarkers unravel the complexity of the connection between exposure to air particles and respiratory health. PMID:25984536

  18. Immunization Coverage Surveys and Linked Biomarker Serosurveys in Three Regions in Ethiopia

    PubMed Central

    Travassos, Mark A.; Beyene, Berhane; Adam, Zenaw; Campbell, James D.; Mulholland, Nigisti; Diarra, Seydou S.; Kassa, Tassew; Oot, Lisa; Sequeira, Jenny; Reymann, Mardi; Blackwelder, William C.; Wu, Yukun; Ruslanova, Inna; Goswami, Jaya; Sow, Samba O.; Pasetti, Marcela F.; Steinglass, Robert; Kebede, Amha; Levine, Myron M.

    2016-01-01

    Objective Demographic and health surveys, immunization coverage surveys and administrative data often divergently estimate vaccination coverage, which hinders pinpointing districts where immunization services require strengthening. We assayed vaccination coverage in three regions in Ethiopia by coverage surveys and linked serosurveys. Methods Households with children aged 12–23 (N = 300) or 6–8 months (N = 100) in each of three districts (woredas) were randomly selected for immunization coverage surveys (inspection of vaccination cards and immunization clinic records and maternal recall) and linked serosurveys. IgG-ELISA serologic biomarkers included tetanus antitoxin ≥ 0.15 IU/ml in toddlers (receipt of tetanus toxoid) and Haemophilus influenzae type b (Hib) anti-capsular titers ≥ 1.0 mcg/ml in infants (timely receipt of Hib vaccine). Findings Coverage surveys enrolled 1,181 children across three woredas; 1,023 (87%) also enrolled in linked serosurveys. Administrative data over-estimated coverage compared to surveys, while maternal recall was unreliable. Serologic biomarkers documented a hierarchy among the districts. Biomarker measurement in infants provided insight on timeliness of vaccination not deducible from toddler results. Conclusion Neither administrative projections, vaccination card or EPI register inspections, nor parental recall, substitute for objective serological biomarker measurement. Including infants in serosurveys informs on vaccination timeliness. PMID:26934372

  19. AGE metabolites: a biomarker linked to cancer disparity?

    PubMed

    Foster, Dion; Spruill, Laura; Walter, Katherine R; Nogueira, Lourdes M; Fedarovich, Hleb; Turner, Ryan Y; Ahmed, Mahtabuddin; Salley, Judith D; Ford, Marvella E; Findlay, Victoria J; Turner, David P

    2014-10-01

    Socioeconomic and environmental influences are established factors promoting cancer disparity, but the contribution of biologic factors is not clear. We report a mechanistic link between carbohydrate-derived metabolites and cancer that may provide a biologic consequence of established factors of cancer disparity. Glycation is the nonenzymatic glycosylation of carbohydrates to macromolecules, which produces reactive metabolites called advanced glycation end products (AGE). A sedentary lifestyle and poor diet all promote disease and the AGE accumulation pool in our bodies and also increase cancer risk. We examined AGE metabolites in clinical specimens of African American and European American patients with prostate cancer and found a higher AGE concentration in these specimens among African American patients when compared with European American patients. Elevated AGE levels corresponded with expression of the receptor for AGE (RAGE or AGER). We show that AGE-mediated increases in cancer-associated processes are dependent upon RAGE. Aberrant AGE accumulation may represent a metabolic susceptibility difference that contributes to cancer disparity. PMID:25053712

  20. Biomarkers Linking PCB Exposure and Obesity£

    PubMed Central

    Ghosh, Somiranjan; Murinova, Lubica; Trnovec, Tomas; Loffredo, Christopher A.; Washington, Kareem; Mitra, Partha S.; Dutta, Sisir K.

    2015-01-01

    Recently the prevalence of obesity has increased dramatically across much of the world. Obesity, as a complex, multifactorial disease, and its health consequences probably result from the interplay of environmental, genetic, and behavioral factors. Several lines of evidence support the theory that obesity is programmed during early development and that environmental exposures can play a key role. We therefore hypothesize that the current epidemic might associated with the influence of chemical exposures upon genetically controlled developmental pathways, leading to metabolic disorders. Some environmental chemicals, such as PCBs and pesticide residues, are widespread in food, drinking water, soil, and they exert multiple effects including estrogenic on cellular processes; some have been shown to affect the development of obesity, insulin resistance, type 2 diabetes, and metabolic syndrome. To bring these lines of evidence together and address an important health problem, this narrative review has been primarily designed to address PCBs exposures that have linked with human disease, obesity in particular, and to assess the effects of PCBs on gene expression in a highly-exposed population. The results strongly suggest that further research into the specific mechanisms of PCBs-associated diseases is warranted. PMID:25420728

  1. AGE metabolites: A biomarker linked to cancer disparity?

    PubMed Central

    Foster, Dion; Spruill, Laura; Walter, Katherine R.; Nogueira, Lourdes M.; Fedarovich, Hleb; Turner, Ryan Y.; Ahmed, Mahtabuddin; Salley, Judith D.; Ford, Marvella E.; Findlay, Victoria J.; Turner, David P.

    2014-01-01

    Socioeconomic and environmental influences are established factors promoting cancer disparity but the contribution of biological factors is not clear. We report a mechanistic link between carbohydrate derived metabolites and cancer which may provide a biological consequence of established factors of cancer disparity. Glycation is the non-enzymatic glycosylation of carbohydrates to macromolecules which produces reactive metabolites called advanced glycation end products (AGEs). A sedentary lifestyle and poor diet all promote disease and the AGE accumulation pool in our bodies and also increase cancer risk. We examined AGE metabolites in clinical specimens of African American and European American prostate cancer patients and found a higher AGE concentration in these specimens among African American patients when compared to European American patients. Elevated AGE levels corresponded with expression of the receptor for AGE (RAGE or AGER). We show that AGE mediated increases in cancer associated processes is dependent upon RAGE. Aberrant AGE accumulation may represent a metabolic susceptibility difference that contributes to cancer disparity. PMID:25053712

  2. Linking biomarkers to reproductive success of caged fathead minnows in streams with increasing urbanization.

    PubMed

    Crago, Jordan; Corsi, Steven R; Weber, Daniel; Bannerman, Roger; Klaper, Rebecca

    2011-03-01

    Reproductive and oxidative stress biomarkers have been recommended as tools to assess the health of aquatic organisms. Though validated in the laboratory, there are few studies that tie a change in gene expression to adverse reproductive or population outcomes in the field. This paper looked at 17 streams with varying degrees of urbanization to assess the use of biomarkers associated with reproduction or stress in predicting reproductive success of fathead minnows. In addition, the relationship between biomarkers and water quality measures in streams with varying degrees of urbanization was examined. Liver vitellogenin mRNA was correlated with reproduction within a period of 11d prior to sampling irrespective of habitat, but its correlation with egg output declined at 12d and beyond indicating its usefulness as a short-term biomarker but its limits as a biomarker of total reproductive output. Stress biomarkers such as glutathione S-transferase may be better correlated with factors affecting reproduction over a longer term. There was a significant correlation between GST mRNA and a variety of anthropogenic pollutants. There was also an inverse correlation between glutathione S-transferase and the amount of the watershed designated as wetland. Egg production over the 21-d was negatively correlated with the amount of urbanization and positively correlated to wetland habitats. This study supports the development of multiple biomarkers linking oxidative stress and other non-reproductive endpoints to changes in aquatic habitats will be useful for predicting the health of fish populations and identifying the environmental factors that may need mitigation for sustainable population management. PMID:21147497

  3. Linking biomarkers to reproductive success of caged fathead minnows in streams with increasing urbanization

    USGS Publications Warehouse

    Crago, J.; Corsi, S.R.; Weber, D.; Bannerman, R.; Klaper, R.

    2011-01-01

    Reproductive and oxidative stress biomarkers have been recommended as tools to assess the health of aquatic organisms. Though validated in the laboratory, there are few studies that tie a change in gene expression to adverse reproductive or population outcomes in the field. This paper looked at 17 streams with varying degrees of urbanization to assess the use of biomarkers associated with reproduction or stress in predicting reproductive success of fathead minnows. In addition, the relationship between biomarkers and water quality measures in streams with varying degrees of urbanization was examined. Liver vitellogenin mRNA was correlated with reproduction within a period of 11. d prior to sampling irrespective of habitat, but its correlation with egg output declined at 12. d and beyond indicating its usefulness as a short-term biomarker but its limits as a biomarker of total reproductive output. Stress biomarkers such as glutathione S-transferase may be better correlated with factors affecting reproduction over a longer term. There was a significant correlation between GST mRNA and a variety of anthropogenic pollutants. There was also an inverse correlation between glutathione S-transferase and the amount of the watershed designated as wetland. Egg production over the 21-d was negatively correlated with the amount of urbanization and positively correlated to wetland habitats. This study supports the development of multiple biomarkers linking oxidative stress and other non-reproductive endpoints to changes in aquatic habitats will be useful for predicting the health of fish populations and identifying the environmental factors that may need mitigation for sustainable population management. ?? 2010 Elsevier Ltd.

  4. Correlations between Community Structure and Link Formation in Complex Networks

    PubMed Central

    Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

    2013-01-01

    Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

  5. Linking Knowledge and Action: PRI's Community Consultant.

    ERIC Educational Resources Information Center

    Spencer, Gregory P.

    Within the Partnership for Rural Improvement (PRI), community consultants operate within three complex sets of relationships: client groups, the organizational structure of PRI, and the local operational base. Community consultants are responsible for developing and facilitating rural development and for providing assistance in community and…

  6. Virtual Rural Community Development: Human Links That Sustain Web Links.

    ERIC Educational Resources Information Center

    Bright, Larry K.; Evans, Wayne H.; Marmet, Kathy

    Outmigration in the rural Upper Midwest prompted a group of citizens and University of South Dakota faculty to form the Center for the Advancement of Rural Communities (ARC). ARC considers how to stimulate traditionally competitive and isolated South Dakota peoples to collaborate for economic, social, educational, political, and cultural gains. As…

  7. Link community detection using generative model and nonnegative matrix factorization.

    PubMed

    He, Dongxiao; Jin, Di; Baquero, Carlos; Liu, Dayou

    2014-01-01

    Discovery of communities in complex networks is a fundamental data analysis problem with applications in various domains. While most of the existing approaches have focused on discovering communities of nodes, recent studies have shown the advantages and uses of link community discovery in networks. Generative models provide a promising class of techniques for the identification of modular structures in networks, but most generative models mainly focus on the detection of node communities rather than link communities. In this work, we propose a generative model, which is based on the importance of each node when forming links in each community, to describe the structure of link communities. We proceed to fit the model parameters by taking it as an optimization problem, and solve it using nonnegative matrix factorization. Thereafter, in order to automatically determine the number of communities, we extend the above method by introducing a strategy of iterative bipartition. This extended method not only finds the number of communities all by itself, but also obtains high efficiency, and thus it is more suitable to deal with large and unexplored real networks. We test this approach on both synthetic benchmarks and real-world networks including an application on a large biological network, and compare it with two highly related methods. Results demonstrate the superior performance of our approach over competing methods for the detection of link communities. PMID:24489803

  8. Link Community Detection Using Generative Model and Nonnegative Matrix Factorization

    PubMed Central

    He, Dongxiao; Jin, Di; Baquero, Carlos; Liu, Dayou

    2014-01-01

    Discovery of communities in complex networks is a fundamental data analysis problem with applications in various domains. While most of the existing approaches have focused on discovering communities of nodes, recent studies have shown the advantages and uses of link community discovery in networks. Generative models provide a promising class of techniques for the identification of modular structures in networks, but most generative models mainly focus on the detection of node communities rather than link communities. In this work, we propose a generative model, which is based on the importance of each node when forming links in each community, to describe the structure of link communities. We proceed to fit the model parameters by taking it as an optimization problem, and solve it using nonnegative matrix factorization. Thereafter, in order to automatically determine the number of communities, we extend the above method by introducing a strategy of iterative bipartition. This extended method not only finds the number of communities all by itself, but also obtains high efficiency, and thus it is more suitable to deal with large and unexplored real networks. We test this approach on both synthetic benchmarks and real-world networks including an application on a large biological network, and compare it with two highly related methods. Results demonstrate the superior performance of our approach over competing methods for the detection of link communities. PMID:24489803

  9. Link community detection based on line graphs with a novel link similarity measure

    NASA Astrophysics Data System (ADS)

    Wang, Guishen; Huang, Lan; Wang, Yan; Pang, Wei; Ma, Qin

    2016-02-01

    Link community gradually unfolds its capacity in complex network research. In this paper, a novel link similarity measure on line graphs is proposed. This measure can be adapted to different types of networks with an adjustable parameter. We prove its value converges to a limit on line graphs with the relationship of the nonneighbor links taken into account. Based on this similarity measure, we propose a novel link community detection algorithm for link clustering on line graphs. The detection algorithm combines the novel link similarity measure with the classic Markov Cluster (MCL) Algorithm and determines the link community partitions by calculating an extended modularity measure. Extensive experiments on two types of complex networks demonstrate the effectiveness, reliability and rationality of our solution in contrast to the other two classical algorithms.

  10. Strong Community, Deep Learning: Exploring the Link

    ERIC Educational Resources Information Center

    Chapman, Carole; Ramondt, Leonie; Smiley, Glenn

    2005-01-01

    This explores the constructivist understanding that shared practitioner research in collaborative online spaces leads to deeper learning. The research was developed within the context of building the National College of School Leaderships (NCSLs) online learning communities. A community and a learning scale, both emerging through grounded…

  11. Biomarkers in community-acquired pneumonia: A state-of-the-art review

    PubMed Central

    Seligman, Renato; Ramos-Lima, Luis Francisco; do Amaral Oliveira, Vivian; Sanvicente, Carina; Pacheco, Elyara F.; Rosa, Karoline Dalla

    2012-01-01

    Community-acquired pneumonia (CAP) exhibits mortality rates, between 20% and 50% in severe cases. Biomarkers are useful tools for searching for antibiotic therapy modifications and for CAP diagnosis, prognosis and follow-up treatment. This non-systematic state-of-the-art review presents the biological and clinical features of biomarkers in CAP patients, including procalcitonin, C-reactive protein, copeptin, pro-ANP (atrial natriuretic peptide), adrenomedullin, cortisol and D-dimers. PMID:23184211

  12. Linking Schools & Community Services: Resource Directory.

    ERIC Educational Resources Information Center

    Mastny, Aleta You, Comp.

    This resource directory begins by asserting that a lack of information sharing across interprofessional disciplines presents a barrier to the development of school-community partnerships. It attempts to address this problem by bringing together a body of information and resources that deal with a variety of social issues. All organizations listed…

  13. Communities of Coaches: The Missing Link

    ERIC Educational Resources Information Center

    Barnson, Steven C.

    2010-01-01

    Interscholastic coaches have unique needs relative to how they learn their practice and progress toward higher levels of professional comfort and competence. The purpose of this article is to review the professional development needs of interscholastic coaches and suggest the use of social-learning techniques, specifically communities of practice,…

  14. Linking a Community of Learners with a Community of Scholars

    ERIC Educational Resources Information Center

    Pagano, Jules O.

    1977-01-01

    Florida International University, a new upper level public university established in 1972, implemented a philosophical and programmatic objective of service to the community and fostering international understanding through the education of students. Its students are comprised of adult graduates of community colleges and older continuing education…

  15. Linking Academic and Community Guidelines for Community-Engaged Scholarship

    ERIC Educational Resources Information Center

    DeLugan, Robin Maria; Roussos, Stergios; Skram, Geneva

    2014-01-01

    Research universities seeking to promote community-engaged scholarship (CES), defined here as research of mutual benefit to community and academic interests, will discover that it requires capacity building and institutional support. At the University of California at Merced, our 7-year experience in building a new public research university that…

  16. Environmental Justice: A Crucial Link between Environmentalism and Community Development?

    ERIC Educational Resources Information Center

    Hillman, Mick

    2002-01-01

    Environmental justice provides a linking theme with which community development workers and environmental activists can build cross-sectoral coalitions. Examples of Australian environmental problems illustrate constraints that must be overcome. Building vertical and horizontal links between and within nongovernmental organizations is one solution.…

  17. Evaluation and Impacts of Linking Family and Community Strengths Conference.

    ERIC Educational Resources Information Center

    Garkovich, Lori; Tisdale, Jacque

    This report summarizes a postconference evaluation of the "Linking Family and Community Strengths" conference, held in Louisville, Kentucky, in June 1996, and describes 12 community projects based on conference lessons. Six months after the conference, an evaluation was completed by 100 of 192 participants. The conference aimed to provide a…

  18. Linked Learning Communities. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2014

    2014-01-01

    Linked learning communities in postsecondary education are programs defined by having social and curricular linkages that provide undergraduate students with intentional integration of the themes and concepts that they are learning. The theory behind these programs is that active learning in a community-based setting can improve academic outcomes…

  19. Linked Vocabulary API for the Earth Sciences Community

    NASA Astrophysics Data System (ADS)

    Zednik, S.; Fox, P. A.; Fu, L.; West, P.; Ma, X.

    2014-12-01

    The Linked Vocabulary API is a specification for publishing RESTful APIs of vocabularies represented in the Simple Knowledge Organization System (SKOS) as Linked Data on the web. This work began as part of the Coastal and Marine Spatial Planning Vocabularies (CMSPV) project in response to the need for a standard manner for agencies to publish and consume hierarchical vocabularies on the web. The RESTful architecture of the API provides a simple mechanism for consumption of full vocabularies, single vocabulary terms, related terms, and searches on terms. The Linked Data nature of the API promotes interoperability by exposing vocabulary resources as resolvable URIs that may be referenced from other vocabularies or sources of Linked Data and by allowing the published vocabulary to contain references as links to terms from other vocabularies. The Linked Vocabulary API is formally defined in a Linked Data API specification and may be deployed using standard implementations of the Linked Data API such as the Epimorphics Linked Data API (ELDA). Recent presentations of work done with the Linked Vocabulary API as part of the CMSPV project have resulted in the API receiving growing interest from the broader scientific community. In this contribution we present the Linked Vocabulary API design and deployment process.

  20. Acute effects of copper and mercury on the estuarine fish Pomatoschistus microps: linking biomarkers to behaviour.

    PubMed

    Vieira, L R; Gravato, C; Soares, A M V M; Morgado, F; Guilhermino, L

    2009-09-01

    The main objective of the present study was to investigate possible links between biomarkers and swimming performance in the estuarine fish Pomatoschistus microps acutely exposed to metals (copper and mercury). In independent bioassays, P. microps juveniles were individually exposed for 96 h to sub-lethal concentrations of copper or mercury. At the end of the assays, swimming performance of fish was measured using a device specially developed for epibenthic fish (SPEDE). Furthermore, the following biomarkers were measured: lipid peroxidation (LPO) and the activity of the enzymes acetylcholinesterase (AChE), lactate dehydrogenase (LDH), glutathione S-transferases (GST), 7-ethoxyresorufin-O-deethylase (EROD), superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR) and glutathione peroxidase (GPx). LC(50)s of copper and mercury (dissolved throughout metal concentrations) at 96h were 568 microg L(-1), and 62 microg L(-1), respectively. Significant and concentration-dependent effects of both metals on swimming resistance and covered distance against water flow were found at concentrations equal or higher than 50 microg L(-1) for copper and 3 microg L(-1) for mercury (dissolved throughout metal concentrations). These results indicate that SPEDE was efficacious to quantify behavioural alterations in the epibenthic fish P. microps at ecologically relevant concentrations. Significant alterations by both metals on biomarkers were found including: inhibition of AChE and EROD activities, induction of LDH, GST and anti-oxidant enzymes, and increased LPO levels, with LOEC values ranging from 25 to 200 microg L(-1), for copper and from 3 to 25 microg L(-1) for mercury (dissolved throughout metal concentrations). Furthermore, significant and positive correlations were found between some biomarkers (AChE and EROD) and behavioural parameters, while negative correlations were found for others (LPO, anti-oxidant enzymes and LDH) suggesting that disruption of cholinergic

  1. Links between deep-sea respiration and community dynamics.

    PubMed

    Ruhl, Henry A; Bett, Brian J; Hughes, Sarah J M; Alt, Claudia H S; Ross, Elizabeth J; Lampitt, Richard S; Pebody, Corinne A; Smith, Kenneth L; Billett, David S M

    2014-06-01

    It has been challenging to establish the mechanisms that link ecosystem functioning to environmental and resource variation, as well as community structure, composition, and compensatory dynamics. A compelling hypothesis of compensatory dynamics, known as "zero-sum" dynamics, is framed in terms of energy resource and demand units, where there is an inverse link between the number of individuals in a community and the mean individual metabolic rate. However, body size energy distributions that are nonuniform suggest a niche advantage at a particular size class, which suggests a limit to which metabolism can explain community structuring. Since 1989, the composition and structure of abyssal seafloor communities in the northeast Pacific and northeast Atlantic have varied interannually with links to climate and resource variation. Here, for the first time, class and mass-specific individual respiration rates were examined along with resource supply and time series of density and biomass data of the dominant abyssal megafauna, echinoderms. Both sites had inverse relationships between density and mean individual metabolic rate. We found fourfold variation in echinoderm respiration over interannual timescales at both sites, which were linked to shifts in species composition and structure. In the northeastern Pacific, the respiration of mobile surface deposit feeding echinoderms was positively linked to climate-driven particulate organic carbon fluxes with a temporal lag of about one year, respiring - 1-6% of the annual particulate organic carbon flux. PMID:25039229

  2. Community Websites: Linking the Personal to Urban History

    ERIC Educational Resources Information Center

    de Wildt, Annemarie

    2013-01-01

    New technology enables museums and other heritage institutions to establish more personal links with their audience, and hopefully by doing so make history more compelling to them. The author explores some Dutch practices with interactive community websites and other ways of making connections between personal stories and urban history.

  3. Community detection in networks with positive and negative links

    NASA Astrophysics Data System (ADS)

    Traag, V. A.; Bruggeman, Jeroen

    2009-09-01

    Detecting communities in complex networks accurately is a prime challenge, preceding further analyses of network characteristics and dynamics. Until now, community detection took into account only positively valued links, while many actual networks also feature negative links. We extend an existing Potts model to incorporate negative links as well, resulting in a method similar to the clustering of signed graphs, as dealt with in social balance theory, but more general. To illustrate our method, we applied it to a network of international alliances and disputes. Using data from 1993-2001, it turns out that the world can be divided into six power blocs similar to Huntington’s civilizations, with some notable exceptions.

  4. Active link selection for efficient semi-supervised community detection

    PubMed Central

    Yang, Liang; Jin, Di; Wang, Xiao; Cao, Xiaochun

    2015-01-01

    Several semi-supervised community detection algorithms have been proposed recently to improve the performance of traditional topology-based methods. However, most of them focus on how to integrate supervised information with topology information; few of them pay attention to which information is critical for performance improvement. This leads to large amounts of demand for supervised information, which is expensive or difficult to obtain in most fields. For this problem we propose an active link selection framework, that is we actively select the most uncertain and informative links for human labeling for the efficient utilization of the supervised information. We also disconnect the most likely inter-community edges to further improve the efficiency. Our main idea is that, by connecting uncertain nodes to their community hubs and disconnecting the inter-community edges, one can sharpen the block structure of adjacency matrix more efficiently than randomly labeling links as the existing methods did. Experiments on both synthetic and real networks demonstrate that our new approach significantly outperforms the existing methods in terms of the efficiency of using supervised information. It needs ~13% of the supervised information to achieve a performance similar to that of the original semi-supervised approaches. PMID:25761385

  5. Active link selection for efficient semi-supervised community detection.

    PubMed

    Yang, Liang; Jin, Di; Wang, Xiao; Cao, Xiaochun

    2015-01-01

    Several semi-supervised community detection algorithms have been proposed recently to improve the performance of traditional topology-based methods. However, most of them focus on how to integrate supervised information with topology information; few of them pay attention to which information is critical for performance improvement. This leads to large amounts of demand for supervised information, which is expensive or difficult to obtain in most fields. For this problem we propose an active link selection framework, that is we actively select the most uncertain and informative links for human labeling for the efficient utilization of the supervised information. We also disconnect the most likely inter-community edges to further improve the efficiency. Our main idea is that, by connecting uncertain nodes to their community hubs and disconnecting the inter-community edges, one can sharpen the block structure of adjacency matrix more efficiently than randomly labeling links as the existing methods did. Experiments on both synthetic and real networks demonstrate that our new approach significantly outperforms the existing methods in terms of the efficiency of using supervised information. It needs ~13% of the supervised information to achieve a performance similar to that of the original semi-supervised approaches. PMID:25761385

  6. Linking the levels: network and relational perspectives for community psychology.

    PubMed

    Neal, Jennifer Watling; Christens, Brian D

    2014-06-01

    In this article, we assert that relationships and networks are of paramount importance for understanding and improving settings, neighborhoods, communities, and larger social systems. Despite previous acknowledgements of their relevance, relational and social network perspectives and analyses remain underrepresented in community psychological research and action. Here, we claim that network and relational perspectives can provide conceptual and empirical 'links' between levels of analysis, more fully reflecting a transactional view. We also describe some of the sophisticated methodologies that can be employed in empirical studies drawing on these perspectives. Additionally, we contend that core concepts in community psychology such as health promotion, empowerment, coalition building, and dissemination and implementation can be better understood when employing relational and network perspectives. As an introduction to this special issue of American Journal of Community Psychology, we draw out themes and key points from the articles in the issue, and offer recommendations for future advancement of these perspectives in the field. PMID:24752731

  7. Community of Communities: An Electronic Link to Integrating Cultural Diversity in Nursing Curriculum.

    ERIC Educational Resources Information Center

    Ryan, Marilyn; Ali, Nagia; Carlton, Kay Hodson

    2002-01-01

    The Community of Communities (COC) website contains information and case studies based on cultural assessment. Online nursing courses are linked to a cultural module in the COC. Evaluation results from 63 students showed that the COC increased awareness of the role of culture in health care and knowledge of international health practices.…

  8. MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data.

    PubMed

    Wang, Xiaojun; Su, Xiaoquan; Cui, Xinping; Ning, Kang

    2015-01-01

    As more than 90% of species in a microbial community could not be isolated and cultivated, the metagenomic methods have become one of the most important methods to analyze microbial community as a whole. With the fast accumulation of metagenomic samples and the advance of next-generation sequencing techniques, it is now possible to qualitatively and quantitatively assess all taxa (features) in a microbial community. A set of taxa with presence/absence or their different abundances could potentially be used as taxonomical biomarkers for identification of the corresponding microbial community's phenotype. Though there exist some bioinformatics methods for metagenomic biomarker discovery, current methods are not robust, accurate and fast enough at selection of non-redundant biomarkers for prediction of microbial community's phenotype. In this study, we have proposed a novel method, MetaBoot, that combines the techniques of mRMR (minimal redundancy maximal relevance) and bootstrapping, for discover of non-redundant biomarkers for microbial communities through mining of metagenomic data. MetaBoot has been tested and compared with other methods on well-designed simulated datasets considering normal and gamma distribution as well as publicly available metagenomic datasets. Results have shown that MetaBoot was robust across datasets of varied complexity and taxonomical distribution patterns and could also select discriminative biomarkers with quite high accuracy and biological consistency. Thus, MetaBoot is suitable for robustly and accurately discover taxonomical biomarkers for different microbial communities. PMID:26213658

  9. Molecular and lipid biomarker analysis of a gypsum-hosted endoevaporitic microbial community.

    PubMed

    Jahnke, L L; Turk-Kubo, K A; N Parenteau, M; Green, S J; Kubo, M D Y; Vogel, M; Summons, R E; Des Marais, D J

    2014-01-01

    Modern evaporitic microbial ecosystems are important analogs for understanding the record of earliest life on Earth. Although mineral-depositing shallow-marine environments were prevalent during the Precambrian, few such environments are now available today for study. We investigated the molecular and lipid biomarker composition of an endoevaporitic gypsarenite microbial mat community in Guerrero Negro, Mexico. The 16S ribosomal RNA gene-based phylogenetic analyses of this mat corroborate prior observations indicating that characteristic layered microbial communities colonize gypsum deposits world-wide despite considerable textural and morphological variability. Membrane fatty acid analysis of the surface tan/orange and lower green mat crust layers indicated cell densities of 1.6 × 10(9) and 4.2 × 10(9)  cells cm(-3) , respectively. Several biomarker fatty acids, ∆7,10-hexadecadienoic, iso-heptadecenoic, 10-methylhexadecanoic, and a ∆12-methyloctadecenoic, correlated well with distributions of Euhalothece, Stenotrophomonas, Desulfohalobium, and Rhodobacterales, respectively, revealed by the phylogenetic analyses. Chlorophyll (Chl) a and cyanobacterial phylotypes were present at all depths in the mat. Bacteriochlorophyl (Bchl) a and Bchl c were first detected in the oxic-anoxic transition zone and increased with depth. A series of monomethylalkanes (MMA), 8-methylhexadecane, 8-methylheptadecane, and 9-methyloctadecane were present in the surface crust but increased in abundance in the lower anoxic layers. The MMA structures are similar to those identified previously in cultures of the marine Chloroflexus-like organism 'Candidatus Chlorothrix halophila' gen. nov., sp. nov., and may represent the Bchl c community. Novel 3-methylhopanoids were identified in cultures of marine purple non-sulfur bacteria and serve as a probable biomarker for this group in the lower anoxic purple and olive-black layers. Together microbial culture and environmental analyses

  10. Linking sub-cellular biomarkers to embryo aberrations in the benthic amphipod Monoporeia affinis.

    PubMed

    Reutgard, Martin; Furuhagen, Sara

    2016-04-01

    To adequately assess and monitor environmental status in the aquatic environment a broad approach is needed that integrates physical variables, chemical analyses and biological effects at different levels of the biological organization. Embryo aberrations in the Baltic Sea key species Monoporeia affinis can be induced by both metals and organic substances as well as by hypoxia, increasing temperatures and malnutrition. This amphipod has therefore been used for more than three decades as a biological effect indicator in monitoring and assessment of chemical pollution and environmental stress. However, little is known about the sub-cellular mechanisms underlying embryo aberrations. An improved mechanistic understanding may open up the possibility of including sub-cellular alterations as sensitive warning signals of stress-induced embryo aberrations. In the present study, M. affinis was exposed in microcosms to 4 different sediments from the Baltic Sea. After 88-95 days of exposure, survival and fecundity were determined as well as the frequency and type of embryo aberrations. Moreover, oxygen radical absorption capacity (ORAC) was assayed as a proxy for antioxidant defense, thiobarbituric acid reactive substances (TBARS) level as a measure of lipid peroxidation and acetylcholinesterase (AChE) activity as an indicator of neurotoxicity. The results show that AChE and ORAC can be linked to the frequency of malformed embryos and arrested embryo development. The occurrence of dead broods was significantly associated with elevated TBARS levels. It can be concluded that these sub-cellular biomarkers are indicative of effects that could affect Darwinian fitness and that oxidative stress is a likely mechanism in the development of aberrant embryos in M. affinis. PMID:26836507

  11. MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data

    PubMed Central

    Wang, Xiaojun; Su, Xiaoquan

    2015-01-01

    As more than 90% of species in a microbial community could not be isolated and cultivated, the metagenomic methods have become one of the most important methods to analyze microbial community as a whole. With the fast accumulation of metagenomic samples and the advance of next-generation sequencing techniques, it is now possible to qualitatively and quantitatively assess all taxa (features) in a microbial community. A set of taxa with presence/absence or their different abundances could potentially be used as taxonomical biomarkers for identification of the corresponding microbial community’s phenotype. Though there exist some bioinformatics methods for metagenomic biomarker discovery, current methods are not robust, accurate and fast enough at selection of non-redundant biomarkers for prediction of microbial community’s phenotype. In this study, we have proposed a novel method, MetaBoot, that combines the techniques of mRMR (minimal redundancy maximal relevance) and bootstrapping, for discover of non-redundant biomarkers for microbial communities through mining of metagenomic data. MetaBoot has been tested and compared with other methods on well-designed simulated datasets considering normal and gamma distribution as well as publicly available metagenomic datasets. Results have shown that MetaBoot was robust across datasets of varied complexity and taxonomical distribution patterns and could also select discriminative biomarkers with quite high accuracy and biological consistency. Thus, MetaBoot is suitable for robustly and accurately discover taxonomical biomarkers for different microbial communities. PMID:26213658

  12. Linking ‘toxic outliers’ to environmental justice communities

    NASA Astrophysics Data System (ADS)

    Collins, Mary B.; Munoz, Ian; JaJa, Joseph

    2016-01-01

    Several key studies have found that a small minority of producers, polluting at levels far exceeding group averages, generate the majority of overall exposure to industrial toxics. Frequently, such patterns go unnoticed and are understudied outside of the academic community. To our knowledge, no research to date has systematically described the scope and extent of extreme variations in industrially based exposure estimates and sought to link inequities in harm produced to inequities in exposure. In an analysis of all permitted industrial facilities across the United States, we show that there exists a class of hyper-polluters—the worst-of-the-worst—that disproportionately expose communities of color and low income populations to chemical releases. This study hopes to move beyond a traditional environmental justice research frame, bringing new computational methods and perspectives aimed at the empirical study of societal power dynamics. Our findings suggest the possibility that substantial environmental gains may be made through selective environmental enforcement, rather than sweeping initiatives.

  13. Inter-individual variation in expression: a missing link in biomarker biology?

    PubMed

    Little, Peter F R; Williams, Rohan B H; Wilkins, Marc R

    2009-01-01

    The past decade has seen an explosion of variation data demonstrating that diversity of both protein-coding sequences and of regulatory elements of protein-coding genes is common and of functional importance. In this article, we argue that genetic diversity can no longer be ignored in studies of human biology, even research projects without explicit genetic experimental design, and that this knowledge can, and must, inform research. By way of illustration, we focus on the potential role of genetic data in case-control studies to identify and validate cancer protein biomarkers. We argue that a consideration of genetics, in conjunction with proteomic biomarker discovery projects, should improve the proportion of biomarkers that can accurately classify patients. PMID:19010558

  14. Protein Biomarkers for Insulin Resistance and Type 2 Diabetes Risk in Two Large Community Cohorts.

    PubMed

    Nowak, Christoph; Sundström, Johan; Gustafsson, Stefan; Giedraitis, Vilmantas; Lind, Lars; Ingelsson, Erik; Fall, Tove

    2016-01-01

    Insulin resistance (IR) is a precursor of type 2 diabetes (T2D), and improved risk prediction and understanding of the pathogenesis are needed. We used a novel high-throughput 92-protein assay to identify circulating biomarkers for HOMA of IR in two cohorts of community residents without diabetes (n = 1,367) (mean age 73 ± 3.6 years). Adjusted linear regression identified cathepsin D and confirmed six proteins (leptin, renin, interleukin-1 receptor antagonist [IL-1ra], hepatocyte growth factor, fatty acid-binding protein 4, and tissue plasminogen activator [t-PA]) as IR biomarkers. Mendelian randomization analysis indicated a positive causal effect of IR on t-PA concentrations. Two biomarkers, IL-1ra (hazard ratio [HR] 1.28, 95% CI 1.03-1.59) and t-PA (HR 1.30, 1.02-1.65) were associated with incident T2D, and t-PA predicted 5-year transition to hyperglycemia (odds ratio 1.30, 95% CI 1.02-1.65). Additional adjustment for fasting glucose rendered both coefficients insignificant and revealed an association between renin and T2D (HR 0.79, 0.62-0.99). LASSO regression suggested a risk model including IL-1ra, t-PA, and the Framingham Offspring Study T2D score, but prediction improvement was nonsignificant (difference in C-index 0.02, 95% CI -0.08 to 0.12) over the T2D score only. In conclusion, proteomic blood profiling indicated cathepsin D as a new IR biomarker and suggested a causal effect of IR on t-PA. PMID:26420861

  15. EarthTrek - linking real research to the community

    NASA Astrophysics Data System (ADS)

    Lewis, G. B.

    2011-12-01

    EarthTrek is a citizen science program that links scientists undertaking real scientific research with the broader community through their active participation in the collection of real scientific data. EarthTrek projects focus on environmental issues in which community involvement is the key to understanding the real nature of the issue at a local, regional or even global scale. Scientists involved in EarthTrek can increase the amount of data collected on their local, regional or global projects as well as dramatically raise the profile of their research in the broader community. Scientists also have the opportunity to mentor young people in career paths which lead to being involved in their scientific field. Participants involved in EarthTrek contribute to scientific research by collecting data following scientific protocols, and then see their contributions reflected in the real outcomes of scientific research. Participants, especially the young, can also discover potential pathways for careers in science. Participant receive rewards for their participation in the form of EarthTrek points and awards based on the number and scope of projects in which they participate. EarthTrek is really a database portal that links the scientists and the community together. Scientists use the portal as a information tool and data collection mechanism for their projects. They also use the portal as a way on communicate their research results to the people who participated. Participants use the portal as a way to seek projects in which they can become involved, learn about protocols and then collect and record data. They also use the portal as a way to discover more about careers in science. The data collected through EarthTrek will become open access once a project is complete and the scientist 'embargo' time is met. This allows other scientists and students to use the data for their own research projects. EarthTrek is a program developed and managed by the Geological Society of

  16. Interpreting Recent Water Quality Changes in Florida Bay in a Paleoecological Context Using Diatoms and Linked Organic Biomarkers

    NASA Astrophysics Data System (ADS)

    Gaiser, E. E.; Wachnicka, A.; Xu, Y.; Jaffe, R.; Fourqurean, J.

    2005-05-01

    Recent alterations in the quality and quantity of freshwater flowing into Florida Bay from the Everglades and surrounding landscape of south Florida has altered the salinity and nutrient regime of the Bay. To interpret these changes with respect to natural variability in this ecosystem we conducted a multiproxy paleoecological investigation at several sites in the Bay. Sediments were cored to bedrock, chronologically calibrated using conventional radiometric methods and sampled at 2 cm intervals for a variety of paleoenvironmental proxies including diatoms, organic biomarkers and nutrient concentrations. Interpretations of paleoenvironmental settings were based on habitat specificities of diatoms and their relationships to biomarkers and nutrients determined by a survey of the modern environment. Signatures in basal peat deposits suggest fresh to brackish-water mangrove-dominated communities existed in central Florida Bay as little as 2000 YBP. Overlying marl contains benthic diatom assemblages indicative of a shallow, seagrass-dominated marine environment that experienced large, decadal-scale fluctuations in salinity. Recent sediments (<100 years) reveal a third zone that contains a flora that is compositionally dissimilar to those occurring in the past. Together with organic biomarkers, phosphorus and nitrogen data, the recent diatom record generally suggests a transition to conditions favoring proliferation of planktonic algae over benthic epiphytes, suggesting displacement of primary production from seagrass beds (which have declined in aerial extent) to the plankton as water-borne nutrients become more available. Several sites show an increase in diatom-inferred salinity after 1990, while the amplitude of fluctuation in salinity has declined.

  17. Lipid metabolites as potential diagnostic and prognostic biomarkers for acute community acquired pneumonia.

    PubMed

    To, Kelvin K W; Lee, Kim-Chung; Wong, Samson S Y; Sze, Kong-Hung; Ke, Yi-Hong; Lui, Yin-Ming; Tang, Bone S F; Li, Iris W S; Lau, Susanna K P; Hung, Ivan F N; Law, Chun-Yiu; Lam, Ching-Wan; Yuen, Kwok-Yung

    2016-06-01

    Early diagnosis of acute community-acquired pneumonia (CAP) is important in patient triage and treatment decisions. To identify biomarkers that distinguish patients with CAP from non-CAP controls, we conducted an untargeted global metabolome analysis for plasma samples from 142 patients with CAP (CAP cases) and 97 without CAP (non-CAP controls). Thirteen lipid metabolites could discriminate between CAP cases and non-CAP controls with area-under-the-receiver-operating-characteristic curve of >0.8 (P ≤ 10(-9)). The levels of glycosphingolipids, sphingomyelins, lysophosphatidylcholines and L-palmitoylcarnitine were higher, while the levels of lysophosphatidylethanolamines were lower in the CAP cases than those in non-CAP controls. All 13 metabolites could distinguish CAP cases from the non-infection, extrapulmonary infection and non-CAP respiratory tract infection subgroups. The levels of trihexosylceramide (d18:1/16:0) were higher, while the levels of lysophosphatidylethanolamines were lower, in the fatal than those of non-fatal CAP cases. Our findings suggest that lipid metabolites are potential diagnostic and prognostic biomarkers for CAP. PMID:27105773

  18. Five Cities, One Vision. CORAL: Linking Communities, Children and Learning.

    ERIC Educational Resources Information Center

    James G. Irvine Foundation, San Francisco, CA.

    This booklet describes the CORAL (Communities Organizing Resources To Advance Learning) program within five California communities: Pasadena, Long Beach, San Jose, Fresno, and Sacramento. This initiative, begun in 1999, is committed to a community-based and community-building approach to supporting learning and focuses on improving academic…

  19. Enzyme-Encapsulated Liposome-Linked Immunosorbent Assay Enabling Sensitive Personal Glucose Meter Readout for Portable Detection of Disease Biomarkers.

    PubMed

    Lin, Bingqian; Liu, Dan; Yan, Jinmao; Qiao, Zhi; Zhong, Yunxin; Yan, Jiawei; Zhu, Zhi; Ji, Tianhai; Yang, Chaoyong James

    2016-03-23

    There is considerable demand for sensitive, selective, and portable detection of disease-associated proteins, particularly in clinical practice and diagnostic applications. Portable devices are highly desired for detection of disease biomarkers in daily life due to the advantages of being simple, rapid, user-friendly, and low-cost. Herein we report an enzyme-encapsulated liposome-linked immunosorbent assay for sensitive detection of proteins using personal glucose meters (PGM) for portable quantitative readout. Liposomes encapsulating a large amount of amyloglucosidase or invertase are surface-coated with recognition elements such as aptamers or antibodies for target recognition. By translating molecular recognition signal into a large amount of glucose with the encapsulated enzyme, disease biomarkers such as thrombin or C-reactive protein (CRP) can be quantitatively detected by a PGM with a high detection limit of 1.8 or 0.30 nM, respectively. With the advantages of portability, ease of use, and low-cost, the method reported here has potential for portable and quantitative detection of various targets for different POC testing scenarios, such as rapid diagnosis in clinic offices, health monitoring at the bedside, and chemical/biochemical safety control in the field. PMID:26918445

  20. Lipid Biomarker and Isotopic Study of Community Distribution and Biomarker Preservation in a Laminated Microbial Mat from Shark Bay, Western Australia.

    PubMed

    Pagès, Anais; Grice, Kliti; Welsh, David T; Teasdale, Peter T; Van Kranendonk, Martin J; Greenwood, Paul

    2015-08-01

    Modern microbial mats from Shark Bay present some structural similarities with ancient stromatolites; thus, the functionality of microbial communities and processes of diagenetic preservation of modern mats may provide an insight into ancient microbial assemblages and preservation. In this study, the vertical distribution of microbial communities was investigated in a well-laminated smooth mat from Shark Bay. Biolipid and compound-specific isotopic analyses were performed to investigate the distribution of microbial communities in four distinct layers of the mat. Biomarkers indicative of cyanobacteria were more abundant in the uppermost oxic layer. Diatom markers (e.g. C25 HBI alkene, C20:4ω6 and C20:5ω3 polar lipid fatty acids (PLFAs)) were also detected in high abundance in the uppermost layer, but also in the deepest layer under conditions of permanent darkness and anoxia, where they probably used NO3 (-) for respiration. CycC19:0, an abundant PLFA of purple sulfur bacteria (PSB), was detected in all layers and presented the most (13)C-depleted values of all PLFAs, consistent with photoautotrophic PSB. Sulfur-bound aliphatic and aromatic biomarkers were detected in all layers, highlighting the occurrence of early sulfurisation which may be an important mechanism in the sedimentary preservation of functional biolipids in living and, thus, also ancient mats. PMID:25812998

  1. Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

    PubMed Central

    Yrjälä, Kim; Alakukku, Laura; Palojärvi, Ansa

    2012-01-01

    The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy. PMID:22983972

  2. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

  3. The Critical Link: Community Colleges and the Workforce.

    ERIC Educational Resources Information Center

    Falcone, Lisa, Ed.

    In 1993, the American Association of Community Colleges (AACC) sponsored five activities designed to build the capacity of community colleges to respond to workforce development needs of employers and employees through contract training services. Three of these activities targeted community college-based business/industry liaisons, who provide a…

  4. Linking Spirituality, School Communities, Grief and Well-Being

    ERIC Educational Resources Information Center

    Rowling, Louise

    2008-01-01

    This article proposes that school communities are significant public places that help shape identity and can also contribute to social and emotional well-being. If school communities respond appropriately to crises and trauma that affect the young, learning becomes social and emotional as well as academic. School communities offer an opportunity…

  5. Linking Workforce Development to Economic Development: A Casebook for Community Colleges

    ERIC Educational Resources Information Center

    Rothwell, William J., Ed.; Gerity, Patrick E., Ed.

    2008-01-01

    "Linking Workforce Development to Economic Development: A Casebook for Community Colleges" is a compilation of best practice examples, which illustrate what it takes for community colleges to achieve their goal of helping people acquire education and skills, helping employers, supporting communities, and building the nation. The book is written…

  6. Learning communities: the link to recruitment and retention.

    PubMed

    Bassi, Sherry; Polifroni, E Carol

    2005-01-01

    The professional learning community is a strategy to help staff development educators address recruitment and retention and organizational culture. The purpose of this article is to analyze the concept of learning communities and discuss their potential to increase the recruitment and retention of new graduate nurses and returning practitioners to the nursing profession. Incorporating learning communities into the healthcare organization will decrease the number of nurses leaving nursing, foster retention, and thus, enhance recruitment. PMID:15940026

  7. Metal-linked Immunosorbent Assay (MeLISA): the Enzyme-Free Alternative to ELISA for Biomarker Detection in Serum

    PubMed Central

    Yu, Ru-Jia; Ma, Wei; Liu, Xiao-Yuan; Jin, Hong-Ying; Han, Huan-Xing; Wang, Hong-Yang; Tian, He; Long, Yi-Tao

    2016-01-01

    Determination of disease biomarkers in clinical samples is of crucial significance for disease monitoring and public health. The dominating format is enzyme-linked immunosorbent assay (ELISA), which subtly exploits both the antigen-antibody reaction and biocatalytic property of enzymes. Although enzymes play an important role in this platform, they generally suffer from inferior stability and less tolerant of temperature, pH condition compared with general chemical product. Here, we demonstrate a metal-linked immunosorbent assay (MeLISA) based on a robust signal amplification mechanism that faithfully replaces the essential element of the enzyme. As an enzyme-free alternative to ELISA, this methodology works by the detection of α-fetoprotein (AFP), prostatic specific antigen (PSA) and C-reactive protein (CRP) at concentrations of 0.1 ng mL-1, 0.1 ng mL-1 and 1 ng mL-1 respectively. It exhibits approximately two magnitudes higher sensitivity and is 4 times faster for chromogenic reaction than ELISA. The detection of AFP and PSA was further confirmed by over a hundred serum samples from hepatocellular carcinoma (HCC) and prostate cancer patients respectively. PMID:27446504

  8. Metal-linked Immunosorbent Assay (MeLISA): the Enzyme-Free Alternative to ELISA for Biomarker Detection in Serum.

    PubMed

    Yu, Ru-Jia; Ma, Wei; Liu, Xiao-Yuan; Jin, Hong-Ying; Han, Huan-Xing; Wang, Hong-Yang; Tian, He; Long, Yi-Tao

    2016-01-01

    Determination of disease biomarkers in clinical samples is of crucial significance for disease monitoring and public health. The dominating format is enzyme-linked immunosorbent assay (ELISA), which subtly exploits both the antigen-antibody reaction and biocatalytic property of enzymes. Although enzymes play an important role in this platform, they generally suffer from inferior stability and less tolerant of temperature, pH condition compared with general chemical product. Here, we demonstrate a metal-linked immunosorbent assay (MeLISA) based on a robust signal amplification mechanism that faithfully replaces the essential element of the enzyme. As an enzyme-free alternative to ELISA, this methodology works by the detection of α-fetoprotein (AFP), prostatic specific antigen (PSA) and C-reactive protein (CRP) at concentrations of 0.1 ng mL(-1), 0.1 ng mL(-1) and 1 ng mL(-1) respectively. It exhibits approximately two magnitudes higher sensitivity and is 4 times faster for chromogenic reaction than ELISA. The detection of AFP and PSA was further confirmed by over a hundred serum samples from hepatocellular carcinoma (HCC) and prostate cancer patients respectively. PMID:27446504

  9. Using Ethnography to Link School and Community in Rural Yucatan.

    ERIC Educational Resources Information Center

    Stearns, Robert David

    1986-01-01

    Examines the use of "directed ethnography," a collaborative ethnographic approach, found to improve the work of Ladino teachers in rural Yucatan community schools. The participating teachers analyze the collected community data and modify their teaching style/curriculum materials to reflect the experience of their Maya Grade 3 students. (KH)

  10. Utilization of DNA-protein cross-links as a biomarker of chromium exposure.

    PubMed Central

    Zhitkovich, A; Voitkun, V; Kluz, T; Costa, M

    1998-01-01

    Human exposure to carcinogenic Cr(VI) compounds is found among workers in a large number of professional groups, and it can also occur through environmental pollution. A significant number of toxic waste sites contain Cr as a major contaminant. In this paper we summarize our efforts to apply measurements of DNA-protein cross-links (DPC) as test for biologically active doses of Cr(VI). DPC were found at elevated levels in lymphocytes in several human populations with low to medium Cr exposures. At high exposure to Cr(VI), exemplified by a group of Bulgarian chromeplaters, DPC plateaued and adducts' levels were similar to those found in environmentally exposed individuals. Lymphocytic DPC correlated strongly with Cr levels in erythrocytes that are indicative of Cr(VI) exposure. DPC in lymphocytes were not confounded by such variables as smoking, age, body weight, gender, or ethnicity. A new version of the cross-link assay offers improved sensitivity and requires a small amount of biologic material. Preliminary results indicate that the ability of DPC to reach detectable levels at low levels of Cr exposure could be related to a lack of repair of these lesions in lymphoid cells. Cr(III)-mediated cross-links of DNA with peptide glutathione or single amino acids were mutagenic in human cells, with a relationship of higher molecular weight of the peptide/amino acid correlating with a more potent mutagenic response. We speculate that bulky DPC could also have a significant promutagenic effect. The current methodology does not allow specific determination of Cr-induced DPC; however, demonstrated sensitivity of DPC measurements and the assay's large sample capacity may allow this assay to be used as the initial screening test for the occurrence of DNA damage in Cr(VI)-exposed populations. PMID:9703480

  11. Modelling Optimal Control of Cholera in Communities Linked by Migration.

    PubMed

    Njagarah, J B H; Nyabadza, F

    2015-01-01

    A mathematical model for the dynamics of cholera transmission with permissible controls between two connected communities is developed and analysed. The dynamics of the disease in the adjacent communities are assumed to be similar, with the main differences only reflected in the transmission and disease related parameters. This assumption is based on the fact that adjacent communities often have different living conditions and movement is inclined toward the community with better living conditions. Community specific reproduction numbers are given assuming movement of those susceptible, infected, and recovered, between communities. We carry out sensitivity analysis of the model parameters using the Latin Hypercube Sampling scheme to ascertain the degree of effect the parameters and controls have on progression of the infection. Using principles from optimal control theory, a temporal relationship between the distribution of controls and severity of the infection is ascertained. Our results indicate that implementation of controls such as proper hygiene, sanitation, and vaccination across both affected communities is likely to annihilate the infection within half the time it would take through self-limitation. In addition, although an infection may still break out in the presence of controls, it may be up to 8 times less devastating when compared with the case when no controls are in place. PMID:26246850

  12. Modelling Optimal Control of Cholera in Communities Linked by Migration

    PubMed Central

    Njagarah, J. B. H.; Nyabadza, F.

    2015-01-01

    A mathematical model for the dynamics of cholera transmission with permissible controls between two connected communities is developed and analysed. The dynamics of the disease in the adjacent communities are assumed to be similar, with the main differences only reflected in the transmission and disease related parameters. This assumption is based on the fact that adjacent communities often have different living conditions and movement is inclined toward the community with better living conditions. Community specific reproduction numbers are given assuming movement of those susceptible, infected, and recovered, between communities. We carry out sensitivity analysis of the model parameters using the Latin Hypercube Sampling scheme to ascertain the degree of effect the parameters and controls have on progression of the infection. Using principles from optimal control theory, a temporal relationship between the distribution of controls and severity of the infection is ascertained. Our results indicate that implementation of controls such as proper hygiene, sanitation, and vaccination across both affected communities is likely to annihilate the infection within half the time it would take through self-limitation. In addition, although an infection may still break out in the presence of controls, it may be up to 8 times less devastating when compared with the case when no controls are in place. PMID:26246850

  13. Structured decision making as a method for linking quantitative decision support to community fundamental objectives

    EPA Science Inventory

    Decision support intended to improve ecosystem sustainability requires that we link stakeholder priorities directly to quantitative tools and measures of desired outcomes. Actions taken at the community level can have large impacts on production and delivery of ecosystem service...

  14. Building healthy communities for children: The transportation link

    SciTech Connect

    Holmes, H.

    1995-09-01

    Two concepts are essential to a definition of a healthy community: social justice and ecological sustainability. These principles must be at the heart of creating healthy communities, cities, and regions. Children and young people are an integral part of socially just and ecologically sustainable communities. Transportation and land-use policies are critical tools for shaping healthy communities, cities, and regions. The health impacts of the private automobile and its full cost to society, including public health and environmental damage costs, need to be clearly understood. The developing physiology of children put them at particular risk to medical impacts of automobile emissions and air pollution. The public health impacts of transportation and land-use policies cannot be divorced from the planning and decision-making process. Transit, bicycle, and pedestrian-oriented transportation modes can serve the transportation needs of children and can stimulate land uses more conducive to a healthy social, economic, and environmental quality of life. This article comments on the combined issues of social justice and ecological sustainability for building the best communities for meeting the needs of children and young adults. 3 refs.

  15. C26:0-Carnitine Is a New Biomarker for X-Linked Adrenoleukodystrophy in Mice and Man

    PubMed Central

    van de Beek, Malu-Clair; Dijkstra, Inge M. E.; van Lenthe, Henk; Ofman, Rob; Goldhaber-Pasillas, Dalia; Schauer, Nicolas; Schackmann, Martin; Engelen-Lee, Joo-Yeon; Vaz, Frédéric M.; Kulik, Wim; Wanders, Ronald J. A.; Engelen, Marc; Kemp, Stephan

    2016-01-01

    X-linked adrenoleukodystrophy (ALD), a progressive neurodegenerative disease, is caused by mutations in ABCD1 and characterized by very-long-chain fatty acids (VLCFA) accumulation. Virtually all males develop progressive myelopathy (AMN). A subset of patients, however, develops a fatal cerebral demyelinating disease (cerebral ALD). Hematopoietic stem cell transplantation is curative for cerebral ALD provided the procedure is performed in an early stage of the disease. Unfortunately, this narrow therapeutic window is often missed. Therefore, an increasing number of newborn screening programs are including ALD. To identify new biomarkers for ALD, we developed an Abcd1 knockout mouse with enhanced VLCFA synthesis either ubiquitous or restricted to oligodendrocytes. Biochemical analysis revealed VLCFA accumulation in different lipid classes and acylcarnitines. Both C26:0-lysoPC and C26:0-carnitine were highly elevated in brain, spinal cord, but also in bloodspots. We extended the analysis to patients and confirmed that C26:0-carnitine is also elevated in bloodspots from ALD patients. We anticipate that validation of C26:0-carnitine for the diagnosis of ALD in newborn bloodspots may lead to a faster inclusion of ALD in newborn screening programs in countries that already screen for other inborn errors of metabolism. PMID:27124591

  16. Injuries and Safe Communities Accreditation: Is there a link?

    PubMed

    Sinelnikov, Sergey; Friedman, Lee S; Chavez, Emily A

    2016-06-01

    Safe Communities (SC) is a global movement that brings together community stakeholders to collaboratively address injury concerns. SC accreditation is a formal process through which communities are recognized for strengthening local injury prevention capacity. Six million Americans live in 25 SC sites, but no research has been done to understand the model's potential impact on this population. This study explored the temporal relationship between SC accreditation and injury trends in three SC sites from the state of Illinois-Arlington Heights, Itasca, and New Lenox. Hospitalization data, including patient demographics, exposure information, injury outcomes, and economic variables, were obtained from a statewide hospital discharge database for a 12-year period (1999-2011). Joinpoint regression models were fitted to identify any periods of significant change, examine the direction of the injury trend, and to estimate monthly percent changes in injury counts and rates. Poisson random-intercept regression measured the average total change since the official SC accreditation for the three communities combined and compared them to three matched control sites. In joinpoint regression, one of the SC sites showed a 10-year increase in hospitalization cases and rates followed by a two-year decline, and the trend reversal occurred while the community was pursuing the SC accreditation. Injury hospitalizations decreased after accreditation compared to the pre-accreditation period when SC sites were compared to their control counterparts using Poisson modeling. Our findings suggest that the SC model may be a promising approach to reduce injuries. Further research is warranted to replicate these findings in other communities. PMID:26974025

  17. Linking Community Resources in Diabetes Care: a Role for Technology?

    PubMed Central

    Peek, Monica E.

    2015-01-01

    Designing and implementing effective lifestyle modification strategies remains one of the great challenges in diabetes care. Historically, programs have focused on individual behavior change with little or no attempt to integrate change within the broader social framework or community context. However, these contextual factors have been shown to be associated with poor diabetes outcomes, particularly in low-income minority populations. Recent evidence suggests that one way to address these disparities is to match patient needs to existing community resources. Not only does this position patients to more quickly adapt behavior in a practical way, but this also refers patients back to their local communities where a support mechanism is in place to sustain healthy behavior. Technology offers a new and promising platform for connecting patients to meaningful resources (also referred to as “assets”). This paper summarizes several noteworthy innovations that use technology as a practical bridge between healthcare and community-based resources that promote diabetes self-care. PMID:25994856

  18. School-Community Links: Supporting Learning in the Middle Years

    ERIC Educational Resources Information Center

    Hayes, Debra; Chodkiewicz, Andrew

    2006-01-01

    This paper reports on research into how schools, parents and local communities work together to support students' learning during the transition from primary to secondary schools in what is referred to as the middle years of schooling. The research was conducted in four Australian schools within one urban school district. These schools were…

  19. Strengthening Links Which Promote Community/School Partnerships.

    ERIC Educational Resources Information Center

    Ramos, Nancy J.; Santos, Ricardo S.

    Issues in establishing and improving school-community partnerships are presented in this paper. Following a review of literature, the essential elements of strong parental involvement programs are described. Five major types of parental involvement programs are identified, and strategies and activities for improving them are offered. A conclusion…

  20. "Why Fly That Way?" Linking Community and Academic Achievement.

    ERIC Educational Resources Information Center

    Greely, Kathy

    This book tells the story of a year in one middle school teacher's class full of lively young adolescents, highlighting exemplary ways of learning and types of schooling. This alternative model of education shows how a strong, supportive community is essential in helping students reach their highest potential. The book includes: specific projects…

  1. Linking Microbial Community Structure to Function in Representative Simulated Systems

    PubMed Central

    Marcus, Ian M.; Wilder, Hailey A.; Quazi, Shanin J.

    2013-01-01

    Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present. PMID:23396331

  2. Employer Roles in Linking School and Work: Lessons from Four Urban Communities.

    ERIC Educational Resources Information Center

    Committee for Economic Development, New York, NY.

    To identify ways employers can strengthen the link between school and work, case studies of efforts to link school to work were conducted in four urban communities: Boston, Massachusetts; Fort Worth, Texas; Louisville/Jefferson County, Kentucky; and Philadelphia, Pennsylvania. Data were gathered from interviews with educators, members of the…

  3. Multimarker Analysis for New Biomarkers in Relation to Central Arterial Stiffness and Hemodynamics in a Chinese Community-Dwelling Population.

    PubMed

    Fu, Shihui; Luo, Leiming; Ye, Ping; Xiao, Wenkai

    2015-11-01

    Central arterial stiffness and hemodynamics independently reflect the risk of cardiovascular events. This Chinese community-based analysis was performed to evaluate the relationships of new biomarkers with central arterial stiffness and hemodynamics by a multimarker method. This analysis consisted of 1540 participants who were fully tested for the new biomarkers including N-terminal prohormone of brain natriuretic peptide, lipid accumulation product, triglyceride-high-density lipoprotein cholesterol (TG-HDL-c) ratio, uric acid, high-sensitivity C-reactive protein, and homocysteine. Carotid-femoral pulse wave velocity (cfPWV), central pulse pressure (cPP), and central augmentation index (cAIx) were measured. The median (range) age of entire cohort was 62 years (21-96 years), and 40.5% were males. The median (interquartile range) of cfPWV, cPP, and cAIx was 11.0 m/s (9.6-13.0 m/s), 42 mm Hg (35-52 mm Hg), and 28% (21%-33%), respectively. In multivariate analysis, participants with higher cfPWV had significantly higher age, peripheral pulse pressure, TG, TG-HDL-c ratio, and homocysteine levels compared with others (P < .05 for all). Multimarker analysis in a Chinese community-dwelling population reinforced the potential clinical value of plasma TG-HDL-c ratio and homocysteine levels as the biomarkers of increased arterial stiffness. PMID:25883364

  4. The Effect of a Community-Based, Primary Health Care Exercise Program on Inflammatory Biomarkers and Hormone Levels

    PubMed Central

    Papini, Camila Bosquiero; Nakamura, Priscila M.; Zorzetto, Lucas P.; Thompson, Janice L.; Phillips, Anna C.; Kokubun, Eduardo

    2014-01-01

    The aim of this study was to analyze the impact of a community-based exercise program in primary care on inflammatory biomarkers and hormone levels. The 1-year quasiexperimental study involved 13 women (mean age = 56.8 ± 11.4 years) and it was developed in two basic health care units in Rio Claro City, Brazil. The physical exercise intervention was comprised of two, 60-minute sessions/week. The inflammatory biomarkers were measured at baseline, 6 months, and 1 year. Repeated measures ANOVA analyses indicated that the intervention was effective in reducing CRP and TNFα after 1 year compared to baseline and 6 months (P < 0.05). There were no changes in IL10, IL6, and insulin after 1 year. However, leptin significantly increased at 1 year (P = 0.016). The major finding of this study is that a community-based exercise program can result in a decrease or maintenance of inflammatory biomarkers after 1 year, and thus has the potential to be a viable public health approach for chronic disease prevention. PMID:25136143

  5. The Community Links of a Sample of People with Intellectual Disabilities

    ERIC Educational Resources Information Center

    Hall, Louise; Hewson, Simon

    2006-01-01

    Background: In 1995, an unpublished study (S. Hewson & C. Waters) showed that the community links of residents in 11 local National Health Services (NHS) trust houses were meagre, despite the service's stated commitment to community presence and participation. The 1995 study was repeated for the same 11 houses in 2002 to examine whether any…

  6. Continuing Medical Education: Linking the Community Hospital and the Medical School.

    ERIC Educational Resources Information Center

    Manning, Phil R.; And Others

    1979-01-01

    A group of community hospitals has been linked to the University of Southern California School of Medicine in a continuing medical education network. An educational development team based at the school helps community hospital physicians identify educational needs and develop responses using local and medical school experts as faculty. (Author/JMD)

  7. Sound Links: Exploring the Social, Cultural and Educational Dynamics of Musical Communities in Australia

    ERIC Educational Resources Information Center

    Bartleet, Brydie-Leigh

    2009-01-01

    "Sound Links" examines the dynamics of community music in Australia, and the models it represents for informal music learning and teaching. This involves researching a selection of vibrant musical communities across the country, exploring their potential for complementarity and synergy with music in schools. This article focuses on the most…

  8. Linking Research and Practice through Teacher Communities: A Place Where Formal and Practical Knowledge Meet?

    ERIC Educational Resources Information Center

    Pareja Roblin, Natalie N.; Ormel, Bart J. B.; McKenney, Susan E.; Voogt, Joke M.; Pieters, Jules M.

    2014-01-01

    This study characterises the links between research and practice across 12 projects concerned with the collaborative design of lesson plans by teacher communities (TCs). Analyses focused on sources of knowledge used to inform lesson design, participants' roles and knowledge generated by the teacher community. Three patterns emerged pertaining…

  9. Phospholipid fatty acid biomarkers in a freshwater periphyton community exposed to uranium: discovery by non-linear statistical learning

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Bunn, Amoret L.; Bailey, Vanessa L.

    2011-01-01

    Phospholipid fatty acids (PLFA) have been widely used to characterize environmental microbial communities, generating community profiles that can distinguish phylogenetic or functional groups within the community. The poor specificity of organism groups with fatty acid biomarkers in the classic PLFA-microorganism associations is a confounding factor in many of the statistical classification/clustering approaches traditionally used to interpret PLFA profiles. In this paper we demonstrate that non-linear statistical learning methods, such as a support vector machine (SVM), can more accurately find patterns related to uranyl nitrate exposure in a freshwater periphyton community than linear methods, such as partial least squares discriminant analysis. In addition, probabilistic models of exposure can be derived from the identified lipid biomarkers to demonstrate the potential model-based approach that could be used in remediation. The SVM probability model separates dose groups at accuracies of ~87.0%, ~71.4%, ~87.5%, and 100% for the four groups; Control (non-amended system), low-dose (amended at 10 µg U L-1), medium dose (amended at 100 µg U L-1), and high dose (500 µg U L-1). The SVM model achieved an overall cross-validated classification accuracy of ~87% in contrast to ~59% for the best linear classifier.

  10. Geochip: A high throughput genomic tool for linking community structure to functions

    SciTech Connect

    Van Nostrand, Joy D.; Liang, Yuting; He, Zhili; Li, Guanghe; Zhou, Jizhong

    2009-01-30

    GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial community structure. However, several challenges remain regarding the development and applications of microarrays for microbial community analysis.

  11. Linking community and ecosystem development on Mount St. Helens.

    PubMed

    Gill, Richard A; Boie, Jennifer A; Bishop, John G; Larsen, Lindsay; Apple, Jennifer L; Evans, R David

    2006-06-01

    In the two decades following the 1980 eruption of Mount St. Helens in Washington State, the N2-fixing colonizer Lupinus lepidus is associated with striking heterogeneity in plant community and soil development. We report on differences in nutrient availability and plant tissue chemistry between older, dense patches (core) of L. lepidus and more recently established low density patches (edge). In addition, we conducted a factorial nitrogen and phosphorus fertilization experiment in core patches to examine the degree of N and P limitation in early primary succession. We found that there were no significant differences in N or P availability between core and edge L. lepidus patches during the dry summer months, although nutrient availability is very low across the landscape. In the high density patches we found lower tissue N content and higher fiber content in L. lepidus tissue than in the younger edge patches. The addition of nutrients substantially altered plant community composition, with N addition causing an increase in other forb biomass and a corresponding competition-induced decline in L. lepidus biomass. The majority of the positive biomass response came from Hypochaeris radicata. In the second year of the fertilization experiment, the addition of N significantly increased total community biomass while L. lepidus biomass declined by more than 50%. The response of every species other than L. lepidus to N additions suggests that N may be the macronutrient most limiting plant production on Mount St. Helens but that the gains in productivity were somewhat offset by a decline of the dominant species. By the third year of the experiment, L. lepidus began to increase in abundance with P addition. This result suggests co-limitation of the community by N and P. PMID:16463176

  12. Enzyme-linked immunosorbent assay for detection of organophosphorylated butyrylcholinesterase: A biomarker of exposure to organophosphate agents

    SciTech Connect

    Wang, Liming; Du, Dan; Lu, Donglai; Lin, Chiann Tso; Smith, Jordan N.; Timchalk, Charles; Liu, Fengquan; Wang, Jun; Lin, Yuehe

    2011-05-05

    A sandwich enzyme-linked immunosorbent assay (sELISA) is developed for detection of organophosphorylated butyrylcholinesterase (OP-BChE), a potential biomarker for human exposure to organophosphate insecticides and nerve agents. A pair of antibodies specific to OP-BChE adduct were identified through systematic screening of several anti BChE antibodies (anti-BChE) and anti-phosphoserine antibodies (anti-Pser) from different sources. The selected anti-BChE (set as capture antibody) antibodies recognize both phosphorylated and nonphosphorylated BChE. These antibodies can therefore be used to capture both BChE and OP-BChE from the sample matrices. The anti- Pser (set as detecting antibody) was used to recognize the OP moiety of OP-BChE adducts. With the combination of the selected antibody pair, several key parameters (such as the concentration of anti-BChE and anti-Pser, and the blocking agent) were optimized to enhance the sensitivity and selectivity of the sELISA. Under the optimal conditions, the sELISA has shown a wide linear range from 0.03 nM to 30 nM, with a detection limit of 0.03 nM. Furthermore, the sELISA was successfully applied to detect OP-BChE using in-vitro biological samples such as rat plasma spiked with OP-BChE with excellent adduct recovery (z>99 %). These results demonstrate that this novel approach holds great promise to develop an ELISA kit and offers a simple and cost-effective tool for screening/evaluating exposure to organophosphate insecticides and nerve agents.

  13. Using the Women's Community Education Approach to Deliver Community Employment Training: A Case Study from Longford Women's Link

    ERIC Educational Resources Information Center

    Patterson, Lorne; Dowd, Kathleen

    2010-01-01

    The recent economic downturn and surge in unemployment has focused attention on education and training as a strategic response to Ireland's socio-economic crisis. However, that attention has been concentrated on training through statutory institutions, particularly FAS and the VECs. Longford Women's Link, a Women's Community Education centre in Co…

  14. Instrument development to search for biomarkers on mars: Terrestrial acidophile, iron-powered chemolithoautotrophic communities as model systems

    NASA Astrophysics Data System (ADS)

    Parro, V.; Rodríguez-Manfredi, J. A.; Briones, C.; Compostizo, C.; Herrero, P. L.; Vez, E.; Sebastián, E.; Moreno-Paz, M.; García-Villadangos, M.; Fernández-Calvo, P.; González-Toril, E.; Pérez-Mercader, J.; Fernández-Remolar, D.; Gómez-Elvira, J.

    2005-06-01

    Recent findings by the MER rover opportunity confirming the presence of iron minerals that can only be formed in the presence of water emphasize the study of analogous environments to Mars on Earth. The study of chemolithoautotrophic communities living in acidic iron-rich habitats is highly relevant in order to identify Mars analog environment-specific biomarkers. Iron oxidizing bacteria like Leptospirillum ferrooxidans and Acidithiobacillus ferrooxidans have ways of life for which it is feasible to identify a past or present hypothetical niche on Mars. We have developed a strategy for biomarker identification based on: (i) search for biosignatures on acid and metal-rich environments; (ii) development of an immunosensor microarray; and (iii) integration into an instrument for autonomous and remote operation. The instrument that we have built, called Signs Of LIfe Detector (SOLID), is capable of processing a variety of samples for the detection of specific biomarkers. Antibodies against several bacterial strains have been developed and tested in a microarray biosensor on SOLID. Tests with field samples have been successfully performed, allowing the detection of L. ferrooxidans, A. ferrooxidans present in sediment samples.

  15. Link prediction based on hyperbolic mapping with community structure for complex networks

    NASA Astrophysics Data System (ADS)

    Wang, Zuxi; Wu, Yao; Li, Qingguang; Jin, Fengdong; Xiong, Wei

    2016-05-01

    Link prediction is becoming a concerned topic in the complex network field in recent years. However, the existing link prediction methods are unsatisfactory for processing topological information and have high time complexity. This paper presents a novel method of Link Prediction with Community Structure (LPCS) based on hyperbolic mapping. Different from the existing link prediction methods, to utilize global structure information of the network, LPCS deals with the network from an overall perspective. LPCS takes full advantage of the community structure and its hierarchical organization to map networks into hyperbolic space, and obtains the hyperbolic coordinates which depict the global structure information of the network, then uses hyperbolic distance to describe the similarity between the nodes, finally predicts missing links according to the degree of the similarity between unconnected node pairs. The combination of the hyperbolic geometry framework and the community structure makes LPCS perform well in predicting missing links, and the time complexity of LPCS is linear, which makes LPCS can be applied to handle large scale networks in acceptable time. LPCS outperforms many state-of-the-art link prediction methods in the networks obeying power-law degree distribution.

  16. Environmental quality assessment combining sediment metal levels, biomarkers and macrobenthic communities: application to the Óbidos coastal lagoon (Portugal).

    PubMed

    Pereira, Patrícia; Carvalho, Susana; Pereira, Fábio; de Pablo, Hilda; Gaspar, Miguel B; Pacheco, Mário; Vale, Carlos

    2012-12-01

    Macroinvertebrate benthic communities are one of the key biological components considered for the assessment of benthic integrity in the context of the Water Framework Directive (WFD). However, under moderate contamination scenarios, the assessment of macrobenthic alterations at community level alone could be insufficient to discriminate the environmental quality of coastal and transitional waters. Keeping this in view, sediment quality of moderately contaminated sites in a coastal lagoon (Óbidos lagoon, Portugal) was assessed by the combination of sediment metal levels, Carcinus maenas biomarkers (accumulated metals and oxidative stress responses) and macrobenthic communities. Two sites were selected in confined inner branches (BS and BB) and a third one in the middle lagoon (ML). The site BB presented slightly higher levels of metals in sediment but biological variables calculated for macrobenthic data were not significantly different between sites. The biotic index M-AMBI that is being applied to assess environmental quality of transitional waters in the scope of the WFD pointed either to high (site ML) or good quality status (BS and BB) in the selected sites. However, crabs from BB site presented significantly higher levels of Ni in hepatopancreas than those from ML and macrobenthic community structure was significantly different between BB and ML. Additionally, spatial differences were obtained for oxidative stress parameters suggesting that BB site presented stressors for crabs (higher GST and lower GSH(t) at BB site). Factor analysis (PCA) integrating sediment contamination, biomarkers in crabs and macrobenthic data also distinguished BB site as the most environmentally disturbed. On the other hand, at ML site, some macrobenthic variables (equitability and polychaetes' diversity) were found to be enhanced by current environmental conditions, suggesting the existence of a better sediment quality. Current results pointed to the usefulness of integrating

  17. Hypersaline Microbial Mat Lipid Biomarkers

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsegereda; Turk, Kendra A.; Summons, Roger E.

    2002-01-01

    Lipid biomarkers and compound specific isotopic abundances are powerful tools for studies of contemporary microbial ecosystems. Knowledge of the relationship of biomarkers to microbial physiology and community structure creates important links for understanding the nature of early organisms and paleoenvironments. Our recent work has focused on the hypersaline microbial mats in evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, sulfur oxidizing and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface. The delta C-13 of cyanobacterial biomarkers such as the monomethylalkanes and hopanoids are consistent with the delta C-13 measured for bulk mat (-10%o), while a GNS biomarker, wax esters (WXE), suggests a more depleted delta C-13 for GNS biomass (-16%o). This isotopic relationship is different than that observed in mats at Octopus Spring, Yellowstone National Park (YSNP) where GNS appear to grow photoheterotrophic ally. WXE abundance, while relatively low, is most pronounced in an anaerobic zone just below the cyanobacterial layer. The WXE isotope composition at GN suggests that these bacteria utilize photoautotrophy incorporating dissolved inorganic carbon (DIC) via the 3-hydroxypropionate pathway using H2S or H2.

  18. Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest.

    PubMed

    Mueller, Rebecca C; Paula, Fabiana S; Mirza, Babur S; Rodrigues, Jorge L M; Nüsslein, Klaus; Bohannan, Brendan J M

    2014-07-01

    Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests. PMID:24451208

  19. INTEGRATING INNOVATIVE BIOMARKERS OF ENVIRONMENTALLY INDUCED DISEASE FOR CHILDREN IN AGRICULTURAL COMMUNITIES

    EPA Science Inventory

    The proposed study is a supplement to our EPA/NIEHS funded Center for Child Environmental Health Risks Research (CHC). We propose to develop an integrative tool for evaluating the importance of knowledge of biomarkers of susceptibility and early response for establishing the e...

  20. Biomarker-derived phytoplankton community for summer monsoon reconstruction in the western South China Sea over the past 450 ka

    NASA Astrophysics Data System (ADS)

    Li, Li; Li, Qianyu; He, Juan; Wang, Hui; Ruan, Yanming; Li, Jianru

    2015-12-01

    Marine algal-derived lipid biomarkers (alkenones, brassicasterol, dinosterol, and long-chain diol/keto-ol representing haptophytes, diatoms, dinoflagellates, and eustigmatophytes, respectively) were used to evaluate the phytoplankton productivity and community structure changes in core MD05-2901 from the western South China Sea, which features distinct summer upwelling induced by southwest Asian monsoon. The results revealed substantial differences in the distribution patterns between the four major marine primary producers. Diatom and dinoflagellate biomarkers displayed slightly higher abundances, mostly in interglacials especially after MIS 8, while alkenones exhibited lower values in MIS 12 and MIS 1, with higher values in between especially in the middle of MIS 7, but eustigmatophytes increased in most glaciations, indicating complex responses of different phytoplanktons to paleoclimatic and paleoenvironmental changes over the past 450 ka. The sum of the four phytoplanktons shows subtle glacial-interglacial patterns, probably reflecting the combined hydrological dynamics driven by enhanced summer monsoon during summer/interglacials and enhanced winter monsoon during winter/glacials in the region. The biomarker-based community structure showed relative high contribution from diatoms and dinoflagellates during interglacials, high contribution in the middle part of the section centered at ~210 ka from the coccolithophorids, but varying levels from the eustigmatophytes with high percentages in most glacials. Diatoms show strong nutrient sensitivity and positive relation with other paleo-proxies, and their enrichments during interglacials can be attributed to enhanced nutrient level induced by the East Asian summer monsoon, which could have been coupled with the influence of the global ice volume, the summer insolation and the Southern Hemisphere latent heat.

  1. Sterols and fatty acid biomarkers as indicators of changes in soil microbial communities in a uranium mine area.

    PubMed

    Guedes, Maria J; Pereira, Ruth; Duarte, Kátia; Rocha-Santos, Teresa A P; Antunes, Sara C; Gonçalves, Fernando; Duarte, Armando C; Freitas, Ana C

    2011-01-01

    Included in the 2nd tier of a site specific risk assessment that is being carried out in an abandoned uranium mine (Cunha Baixa uranium mine, Central Portugal), fatty acids biomarkers and sterols were analyzed to assess the impact of soil contamination with metals and radionuclides in the structure of the microbial community in seven sampling sites located at different distances from the mine. Surface soil samples were collected in those sampling sites in the four different seasons of the year. Principal component analysis (PCA) was performed on fatty acid biomarkers and sterols. Subsequently PCA scores obtained for both components were used to test the effect of sites and seasons, on soil samples collected in the Cunha Baixa uranium mine, through bi-factorial ANOVAs. Through PCA analysis, two distinct groups were set apart along the first two components. One group included sites at a great distance from the mine which were negatively correlated with higher contents of iC15:0 and iC17:0, both indicators of Gram-positive bacteria, as well as with ergosterol, cholestanol and cholesterol. The second group, in turn, was composed of the sampling sites most impacted by ore exploration, in situ leaching of poor ore, and spread of sludge from the effluent treatment pond. These sites were positively correlated with higher levels of iC16:0 (Gram-positive bacteria indicator), cyC17:0 (generally common in gram negative bacteria) and C18:0 and C17:0 biomarkers of non-specific bacteria. The profile of fatty acids obtained in the sampling sites revealed variable predominance of groups of bacteria which are a clear indication of differences in the soil microbial communities that are directly related to the environmental conditions prevailing in the uranium mine area. PMID:21547821

  2. Lipid biomarker and microbial community of 49.6°E hydrothermal field at Southwest Indian Ocean Ridge

    NASA Astrophysics Data System (ADS)

    Lei, J.; Chu, F.; Yu, X.; Li, X.; Tao, C.

    2012-12-01

    In 2007, Chinese Research Cruises Discovered the First Active Hydrothermal Vent Field at the Ultraslow Spreading Southwest Indian Ridge. This study intent to get composition, evolution and origin information of lipid compounds in SWIR, and recognize the style of lipid biomarkers which have obviously indicative significance for community structure.Soluble organic matter were extracted from geological samples (including chimney sulfide, oxide, around hydrothermal vents) in Southwest Indian Ridge (SWIR), and divided into hydrocarbon, fatty acid component by column chromatography. GC, GC-MS, HPLC-MS were applied for composition and abundance analysis. Lipid in hydrothermal sulfide contains obvious isoprenoidal hydrocarbon biomarkers (Sq, IS40) and GDGTs (m/z=653) that associated with methanogenic archaea which belongs to Euryarchaeota, and iso /anti-iso fatty acid (iC15:0, aiC15:0, iC17:0, aiC17:0)which may originated from sulfate reducing bacteria (SRB).Lipids extracted from hydrothermal oxide lack isoprenoidal hydrocarbon, and Ph/C18 (0.57) is much lower than sulfide (1.22). Fatty acid compound of oxide include abundant saturated fatty (C16:0, C18:0) acid and mono-unsaturated fatty acids (C16:1n7, C18:1n7), but much less iso/anti-iso was detected. Lipid composition of hydrothermal oxide showed that archaea activity was seldom in hydrothermal oxide, and sulfur-oxidizing bacteria was the main microbial community.Study of Jaeschke (2010) showed that high temperature hydrothermal venting encompassed different microbial community from low temperature hydrothermal venting. Our study showed that in different stage of hydrothermal, microbial community structure may be distinct.

  3. Integrating the environment, the economy, and community health: a Community Health Center's initiative to link health benefits to smart growth.

    PubMed

    McAvoy, Peter V; Driscoll, Mary Beth; Gramling, Benjamin J

    2004-04-01

    The Sixteenth Street Community Health Center (SSCHC) in Milwaukee, Wis, is making a difference in the livability of surrounding neighborhoods and the overall health of the families it serves. SSCHC is going beyond traditional health care provider models and working to link the environment, the economy, and community health through urban brownfield redevelopment and sustainable land-use planning. In 1997, SSCHC recognized that restoration of local air and water quality and other environmental conditions, coupled with restoring family-supporting jobs in the neighborhood, could have a substantial impact on the overall health of families. Recent events indicate that SSCHC's pursuit of smart growth strategies has begun to pay off. PMID:15053995

  4. Red Blood Cell Fatty Acids and Biomarkers of Inflammation: A Cross-sectional Study in a Community-based Cohort

    PubMed Central

    Fontes, João D.; Rahman, Faisal; Lacey, Sean; Larson, Martin G.; Vasan, Ramachandran S.; Benjamin, Emelia J.; Harris, William S.; Robins, Sander J.

    2015-01-01

    Introduction Inflammation and inflammatory biomarkers have emerged as integral components and predictors of incident cardiovascular (CV) disease. Omega-3 fatty acids, particularly eicosapentaenoic and docosahexaenoic acids (EPA and DHA) have anti-inflammatory properties, and have been variably associated with lower blood pressure, favorable blood lipid changes, and reduced CV events. Methods and Results We examined the cross-sectional association of red blood cell (RBC) fatty acids, representative of body membrane fatty acid composition, with 10 biomarkers active in multiple inflammatory pathways in 2724 participants (mean age 66±9 years, 54% women, 8% minorities) from the Framingham Offspring and minority Omni Cohorts. . After multivariable adjustment, the RBC EPA and DHA content was inversely correlated (all P≤0.001) with 8 markers of inflammation, receptors, or pathways: urinary isoprostanes (r=−0.16); and soluble interleukin-6 (r=−0.10); C-reactive protein (r=−0.08); tumor necrosis factor receptor 2 (r=−0.08); intercellular adhesion molecule-1 (r=−0.08); P-selectin (r=−0.06); lipoprotein-associated phospholipase-A2 mass (r=−0.11) and activity (r=−0.08). The correlations for monocyte chemoattractant protein-1 was −0.05, P=0.006 and osteoprotegerin (r= −0.06, P=0.002) were only nominally significant. Conclusion In our large community-based study, we observed modest inverse associations between several types of inflammatory biomarkers with RBC omega-3 fatty acid levels. Our findings are consistent with the hypothesis that omega-3 fatty acids have anti-inflammatory properties. PMID:25897795

  5. Methods for Linking Community Views to Measureable Outcomes in a Youth Violence Prevention Program

    PubMed Central

    McDonald, Catherine C.; Richmond, Therese S.; Guerra, Terry; Thomas, Nicole A.; Walker, Alia; Branas, Charles C.; TenHave, Thomas R.; Vaughn, Nicole A.; Leff, Stephen S.; Hausman, Alice J.

    2013-01-01

    Background All parties in community–academic partnerships have a vested interest prevention program success. Markers of success that reflect community’s experiences of programmatic prevention success are not always measurable, but critically speak to community-defined needs. Objective The purpose of this manuscript was to (1) describe our systematic process for linking locally relevant community views (community-defined indicators) to measurable outcomes in the context of a youth violence prevention program and (2) discuss lessons learned, next steps, and recommendations for others trying to replicate a similar process. Methods A research team composed of both academic and community researchers conducted a systematic process of matching community-defined indicators of youth violence prevention programmatic success to standardized youth survey items being administered in the course of a program evaluation. The research team of three community partners and Five academic partners considered 43 community-defined indicators and 208 items from the youth surveys being utilized within the context of a community-based aggression prevention program. At the end of the matching process, 92 youth survey items were identified and agreed upon as potential matches to 11 of the community-defined indicators. Conclusions We applied rigorous action steps to match community-defined indicators to survey data collected in the youth violence prevention intervention. We learned important lessons that inform recommendations for others interested in such endeavors. The process used to derive and assess community-defined indicators of success emphasized the principles of community-based participatory research (CBPR) and use of existing and available data to reduce participant burden. PMID:23221296

  6. Service Learning: A Strategy for Rural School Improvement and Community Revitalization. (Benefits)[Squared]: The Exponential Results of Linking School Improvement and Community Development, Issue Number Two.

    ERIC Educational Resources Information Center

    Boethel, Martha

    The future of rural schools is inextricably linked to the future of their surrounding communities, and service learning is a powerful tool for capitalizing on those links. Service learning makes students active participants in service projects that respond to community needs while furthering the academic goals of students. Service learning…

  7. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

    PubMed

    Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

    2015-09-01

    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions. PMID:26184407

  8. Bring the Poles to Your Classroom & Community Through Linked Hands-on Learning & IPY Data

    NASA Astrophysics Data System (ADS)

    Turrin, M.; Bell, R. E.; Kastens, K. A.; Pfirman, S. L.

    2009-12-01

    Two major legacies of the 4th International Polar Year (IPY 2007-9) are a newly galvanized educational community and an immense volume of polar data collected by the global science community. The tremendous new polar datasets represent a unique opportunity to communicate the nature of the changing poles to student and public audiences through this polar savvy educational community if effective approaches to link data and understanding are employed. We have developed a strategy for polar education that leverages the IPY data resources, linked with the polar education hands-on ‘manipulatives’ (materials that students can manipulate in a dynamic manner). This linked approach leverages the fundamental inquiry based learning but recognizes that particularly in the polar sciences the size of the earth, the remoteness of the poles and the scale of its processes make it difficult for students to explore in a hands-on manner. The linking of polar hands-on ‘manipulatives’ with IPY data provides a bridge between the tangible and the global. Alone manipulative activities can be beneficial in their ability to help students visualize a process or behavior, but without a strong link back to the Earth through data or evidence the understanding of the process is not transferred from the classroom model to the full scale Earth. The use of activities or models is beneficial in connecting the learner to the polar process(es), while the IPY data provides a unique opportunity to ground the polar manipulative experiments in real data. This linked strategy emerged from a series of NSF sponsored IPY Polar Fairs at major science museums that reached in excess of 12,000 people. The design of the fairs was that polar scientists developed activities linking low cost hands-on manipulatives to scientific evidence/data that was displayed in posters, images, and video clips. The participating scientists walked the ‘audience’ through the hands-on manipulative, then discussed their

  9. Carotenoid biomarkers as an imperfect reflection of the anoxygenic phototrophic community in meromictic Fayetteville Green Lake.

    PubMed

    Meyer, K M; Macalady, J L; Fulton, J M; Kump, L R; Schaperdoth, I; Freeman, K H

    2011-07-01

    Organic biomarkers in marine sedimentary rocks hold important clues about the early history of Earth's surface environment. The chemical relicts of carotenoids from anoxygenic sulfur bacteria are of particular interest to geoscientists because of their potential to signal episodes of marine photic-zone euxinia such as those proposed for extended periods in the Proterozoic as well as brief intervals during the Phanerozoic. It is therefore critical to constrain the environmental and physiological factors that influence carotenoid production and preservation in modern environments. Here, we present the results of coupled pigment and nucleic acid clone library analyses from planktonic and benthic samples collected from a microbially dominated meromictic lake, Fayetteville Green Lake (New York). Purple sulfur bacteria (PSB) are abundant and diverse both in the water column at the chemocline and in benthic mats below oxygenated shallow waters, with different PSB species inhabiting the two environments. Okenone (from PSB) is an abundant carotenoid in both the chemocline waters and in benthic mats. Green sulfur bacteria and their primary pigment Bchl e are also represented in and below the chemocline. However, the water column and sediments are devoid of the green sulfur bacteria carotenoid isorenieratene. The unexpected absence of isorenieratene and apparent benthic production of okenone provide strong rationale for continued exploration of the microbial ecology of biomarker production in modern euxinic environments. PMID:21682840

  10. Biomarkers of Manganese Exposure in Pregnant Women and Children Living in an Agricultural Community in California

    PubMed Central

    2015-01-01

    Manganese (Mn) is an essential nutrient but at high exposure levels is a neurotoxicant. There is no well-validated biomarker to assess perinatal Mn exposure. A total of 75 mother-child pairs provided blood, urine, and/or deciduous tooth samples. We analyzed Mn in dentin and enamel of shed teeth; maternal, cord, and child blood; and maternal and child urine and examined the interrelationships of Mn levels in all matrices. We observed higher Mn levels in prenatal than postnatal dentin (geometric mean (GM) = 0.51 vs 0.16 Mn:Ca, p < 0.001), maternal blood at delivery than 26 weeks gestation (GM = 20.7 vs. 14.6 μg/L, p = 0.001), and cord blood than child blood at 24 months of age (39.9 vs 25.0 μg/L, p = 0.005). There were no significant correlations between Mn in dentin and Mn concentrations in maternal blood or maternal or child urine. Levels of Mn in prenatal dentin, prenatal maternal blood, and 24 month urine were higher (p < 0.05) among mothers and children living with a farm worker. Prenatal Mn levels in dentin were correlated with Mn loadings and concentrations in prenatal house dust. Levels of Mn measured in tooth dentin constitute a promising biomarker of perinatal exposure. PMID:25390650

  11. The application of a biometric identification technique for linking community and hospital data in rural Ghana

    PubMed Central

    Odei-Lartey, Eliezer Ofori; Boateng, Dennis; Danso, Samuel; Kwarteng, Anthony; Abokyi, Livesy; Amenga-Etego, Seeba; Gyaase, Stephaney; Asante, Kwaku Poku; Owusu-Agyei, Seth

    2016-01-01

    Background The reliability of counts for estimating population dynamics and disease burdens in communities depends on the availability of a common unique identifier for matching general population data with health facility data. Biometric data has been explored as a feasible common identifier between the health data and sociocultural data of resident members in rural communities within the Kintampo Health and Demographic Surveillance System located in the central part of Ghana. Objective Our goal was to assess the feasibility of using fingerprint identification to link community data and hospital data in a rural African setting. Design A combination of biometrics and other personal identification techniques were used to identify individual's resident within a surveillance population seeking care in two district hospitals. Visits from resident individuals were successfully recorded and categorized by the success of the techniques applied during identification. The successes of visits that involved identification by fingerprint were further examined by age. Results A total of 27,662 hospital visits were linked to resident individuals. Over 85% of those visits were successfully identified using at least one identification method. Over 65% were successfully identified and linked using their fingerprints. Supervisory support from the hospital administration was critical in integrating this identification system into its routine activities. No concerns were expressed by community members about the fingerprint registration and identification processes. Conclusions Fingerprint identification should be combined with other methods to be feasible in identifying community members in African rural settings. This can be enhanced in communities with some basic Demographic Surveillance System or census information. PMID:26993473

  12. Characterization of the deep-sea microbial community and investigation of their carbon sources using lipid biomarkers

    NASA Astrophysics Data System (ADS)

    Rampen, S. W.; Sinninghe Damsté, J. S.; Schouten, S.; Middelburg, J. J.

    2012-12-01

    Most marine microbiology studies so far have been devoted to the photic zone, as this is the area where most of the primary production occurs. However, recently several groups of autotrophic organisms belonging to the Thaumarchaeota have been identified in the deep-sea. Thaumarchaeota belong to the Archaea, which form one of the three Domains of life, next to the Eukarya and the Bacteria. While until the 1990s the Archaea were viewed as extremophilic organisms, results obtained over the last twenty years indicate that Thaumarchaeota are an ubiquitous component of marine plankton, being among the most widely distributed and most abundant groups of microorganisms on the planet; Thaumarchaeota even exceed Bacteria in abundance below 1000 m water depth. Despite these findings, our understanding on their physiology and their biogeochemical function remains mostly speculative because only very few of these organisms could be cultivated. The aim of our project is 1) to characterize the microbial community in the deep-sea using lipid biomarkers for Bacteria, Archaea and Eukarya, 2) to investigate the carbon sources for these organisms using compound specific 13C and 14C analyses and 3) to elucidate the flow of carbon in deep-sea microbial communities using 13C labeling studies. To this end, organic matter has been collected from several locations in the Mediterranean Sea and from the Iceland Basin. Water volumes up to 160 liters were sampled using Niskin bottles which were then filtered on board, while larger volumes, up to 5000 liters, were sampled by deployment of two McLane in-situ pumps at depth. Additional water samples were filtered from the subsurface to distinguish in-situ production from settling organic biomass produced in the upper water column. In addition, 13C labeled glucose, amino acids and sodium bicarbonate were each added to deep-sea water kept in separate 20 liter Nalgene bottles. Incubated water samples and control samples were kept at deep

  13. Linking physical education with community sport and recreation: a program for adolescent girls.

    PubMed

    Casey, Meghan; Mooney, Amanda; Eime, Rochelle; Harvey, Jack; Smyth, John; Telford, Amanda; Payne, Warren

    2013-09-01

    The engagement of adolescent girls in physical activity (PA) is a persistent challenge. School-based PA programs have often met with little success because of the lack of linkages between school and community PA settings. The Triple G program aimed to improve PA levels of secondary school girls (12-15 years) in regional Victoria, Australia. The program included a school-based physical education (PE) component that uniquely incorporated student-centered teaching and behavioral skill development. The school component was conceptually and practically linked to a community component that emphasized appropriate structures for participation. The program was informed by ethnographic fieldwork to understand the contextual factors that affect girls' participation in PA. A collaborative intervention design was undertaken to align with PE curriculum and coaching and instructional approaches in community PA settings. The theoretical framework for the intervention was the socioecological model that was underpinned by both individual-level (social cognitive theory) and organizational-level (building organizational/community capacity) strategies. The program model provides an innovative conceptual framework for linking school PE with community sport and recreation and may benefit other PA programs seeking to engage adolescent girls. The objective of this article is to describe program development and the unique theoretical framework and curriculum approaches. PMID:23159996

  14. Effects of GSTM1/GSTT1 Gene Polymorphism and Fruit & Vegetable Consumption on Antioxidant Biomarkers and Cognitive Function in the Elderly: A Community Based Cross-Sectional Study

    PubMed Central

    Liu, Jinmeng; Meng, Liping; Liu, Jixia; Li, Shuang; Han, Jing; Liu, Quanri; Feng, Lingli; Wang, Chao; Xiao, Rong

    2014-01-01

    Background It was reported that Glutathione S-transferase (GST) gene polymorphism and fruit and vegetable (FV) intake were associated with body antioxidant capacity. The oxidative/anti-oxidative imbalance played an important role in the pathogenesis of AD. However, the association of GST genotype, dietary FV consumption with body antioxidant biomarkers and cognitive function in the elderly is not clear. Objective The aim of the present study was to determine the association of GST genotype, and dietary FV intake, with antioxidant biomarkers and cognitive function in the elderly. Methods Food frequency questionnaire was used to collect data of dietary FV intakes in 504 community dwelling elderly aged from 55 to 75 years old. GSTM1 and GSTT1 genotypes were determined by using multiple-PCR method. Plasma and erythrocyte antioxidant biomarkers were measured. Cognitive function was measured by using Montreal Cognitive Assessment. Statistical analysis was applied for exploring the association of GST genotype and FV intake with antioxidant biomarkers level and cognitive function in the elderly. Results Individual GSTM1 or GSTT1 gene deletion affects body antioxidant biomarkers levels, including erythrocyte GST activity, plasma total antioxidant capacity, and glutathione levels. GSTM1and/or GSTT1 gene deletion have no effects on cognitive function in the surveyed participants. The effect of GST genotype on antioxidant biomarkers are FV intake dependent. There is interaction of FV intake and GST genotype on cognitive function in the elderly. Conclusion GST genotype or daily FV consumption impact body antioxidant biomarkers, but not cognitive function in the elderly. There were combined effects of GST genotype and FV consumption on cognitive function in the elderly population. Large scale perspective population study is required to explore the association of GST genetic polymorphism, FV consumption and antioxidant biomarkers and cognitive function in the elderly. PMID

  15. Linking Microbial Community Structure to β-Glucosidic Function in Soil Aggregates

    SciTech Connect

    Bailey, Vanessa L.; Fansler, Sarah J.; Stegen, James C.; McCue, Lee Ann

    2013-10-01

    To link microbial community 16S structure to a measured function in a natural soil we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-glucosidase activity was assayed in 450 individual aggregates which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differences in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be that observed functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to presence or absence of particular taxonomic groups.

  16. Structural changes in soil communities after triclopyr application in soils invaded by Acacia dealbata Link.

    PubMed

    Souza-Alonso, Pablo; Guisande, Alejandra; González, Luís

    2015-01-01

    Triclopyr is a commonly used herbicide in the control of woody plants and can exhibit toxic effects to soil microorganisms. However, the impact on soils invaded by plant exotics has not yet been addressed. Here, we present the results of an 18-month field study conducted to evaluate the impact of triclopyr on the structure of fungal and bacterial communities in soils invaded by Acacia dealbata Link, through the use of denature gradient gel electrophoresis. After triclopyr application, analyses of bacterial fingerprints suggested a change in the structure of the soil bacterial community, whereas the structure of the soil fungal community remained unaltered. Bacterial density and F:B ratio values changed across the year but were not altered due to herbicide spraying. On the contrary, fungal diversity was increased in plots sprayed with triclopyr 5 months after the first application. Richness and diversity (H') of both bacteria and fungi were not modified after triclopyr application. PMID:25602151

  17. Signature lipid biomarkers for in situ microbial biomass, community structure and nutritional status of deep subsurface microbiota in relation to geochemical gradients. Final technical report

    SciTech Connect

    White, D.C.; Ringelberg, D.B.

    1998-02-01

    To obtain a better understanding of the microbial ecology of the deep subsurface, it was necessary to employ alternate techniques for the identification of microorganisms in situ. Classical microbiological techniques assay only those organisms which are culturable with bias occurring towards the media selected. Since culturable microorganisms typically represents only 0.1 to 10% of the extant microbiota, techniques for the direct assay of microorganisms in situ were needed. The analysis of cellular lipid biomarkers is a technique whereby microbial communities can be assayed directly in a variety of environmental matrices. Through the quantitative recovery of lipid biomarkers, estimations of cell biomass, community composition and community nutritional and/or physiological status can be obtained.

  18. Community-based lifestyle intervention improves weight loss, fitness and chronic disease risk biomarkers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Although lifestyle modification of diet, physical activity and behavior is a proven methodology for weight loss and health improvement it is typically resource intensive, particularly when administered in a medical setting. We examined a locally designed, community-based lifestyle intervention progr...

  19. In situ experiments to assess effects of constraints linked to caging on ecotoxicity biomarkers of the three-spined stickleback (Gasterosteus aculeatus L.).

    PubMed

    Le Guernic, Antoine; Sanchez, Wilfried; Palluel, Olivier; Bado-Nilles, Anne; Turies, Cyril; Chadili, Edith; Cavalié, Isabelle; Adam-Guillermin, Christelle; Porcher, Jean-Marc; Geffard, Alain; Betoulle, Stéphane; Gagnaire, Béatrice

    2016-04-01

    The aim of this study was to evaluate the effects of caging constraints on multiple fish biomarkers used during ecotoxicological studies (biometric data, immune and antioxidant systems, and energetic status). Two of these constraints were linked to caging: starvation and fish density in cages, and one in relation to the post-caging handling: a short transport. Three in situ experiments were conducted with three-spined sticklebacks (Gasterosteus aculeatus). The first experiment compared the effects of three densities (low, medium, and high). The second experiment compared effects of starvation in fish fed every two days with fish that were not fed. Finally comparisons between sticklebacks which have suffered a short car transport after caging and sticklebacks killed without preliminary transport were made. The lack of food had no effect on fish energetic reserves but negatively affected their condition index and their immune system. Transport and high density induced oxidative stress, defined as an overproduction of reactive oxygen species and a stimulation of the antioxidant system. These two constraints also harmed the leucocyte viability. In order not to have any impact on ecotoxicity biomarkers during in situ experiments, it is preferable to decrease fish density in cages, prevent transport before dissections, and feed fish when the caging lasts more than two weeks. PMID:26585997

  20. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    PubMed Central

    Al-Najjar, Mohammad A. A.; Ramette, Alban; Kühl, Michael; Hamza, Waleed; Klatt, Judith M.; Polerecky, Lubos

    2014-01-01

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. PMID:25147548

  1. Associations between vitamin K status and haemostatic and inflammatory biomarkers in community-dwelling adults. The Multi-Ethnic Study of Atherosclerosis.

    PubMed

    Shea, M K; Cushman, M; Booth, S L; Burke, G L; Chen, H; Kritchevsky, S B

    2014-09-01

    Vitamin K is integral to haemostatic function, and in vitro and animal experiments suggest that vitamin K can suppress production of inflammatory cytokines. To test the hypothesis that higher vitamin K status is associated with lower haemostatic activation and inflammation in community-dwelling adults, we analysed the cross-sectional association between serum phylloquinone (vitamin K1) with haemostatic and inflammatory biomarkers in 662 participants in the Multi-Ethnic Study of Atherosclerosis (MESA) [mean (SD) age=62 (10) years; 46% female; 37% Caucasian, 25% African-American, 25% Hispanic, 13% Chinese-American]. Following adjustment for demographic and lifestyle characteristics, medication use, triglycerides and body mass index, those in the highest quartile of serum phylloquinone had significantly lower circulating interleukin-6 [adjusted mean (SEM) pmol/l: quartile 4 (Q4)=1.22 (0.07), quartile 1 (Q1)=1.45 (0.07); p-trend<0.01], C-reactive protein [adjusted mean (SEM) mg/dl: Q4=1.57 (0.11), Q1=2.08 (0.18); p-trend=0.02], soluble intercellular adhesion molecule-1 [adjusted mean (SEM) ng/ml: Q4=247 (11), Q1=288 (11); p-trend=0.02], and plasmin-antiplasmin complex [adjusted mean (SEM) nmol/l: Q4=4.02 (0.1), Q1=4.31 (0.1), p-trend=0.04]. We detected an interaction between age and serum phylloquinone with respect to factor VIII and D-dimer (interaction p-values=0.03 and 0.09, respectively). Among participants ≥70 years, serum phylloquinone was inversely associated with factor VIII activity (p-trend=0.06) and positively associated with D-dimer (p-trend=0.01), but was not associated with either marker among participants <70 years (both p≥0.38). In contrast, dietary phylloquinone intake was not associated with any inflammatory or haemostatic biomarker evaluated (all p-trend>0.11). These findings are consistent with laboratory-based studies that suggest a possible anti-inflammatory role for vitamin K. Whether or not these associations predict clinical outcomes linked

  2. Associations between vitamin K status and haemostatic and inflammatory biomarkers in community-dwelling adults: The Multi-Ethnic Study of Atherosclerosis

    PubMed Central

    Shea, M Kyla; Cushman, Mary; Booth, Sarah L; Burke, Gregory L; Chen, Haiying; Kritchevsky, Stephen B

    2014-01-01

    SUMMARY Vitamin K is integral to haemostatic function, and in vitro and animal experiments suggest that vitamin K can suppress production of inflammatory cytokines. To test the hypothesis that higher vitamin K status is associated with lower hemostatic activation and inflammation in community-dwelling adults, we analyzed the cross-sectional association between serum phylloquinone (vitamin K1) with haemostatic and inflammatory biomarkers in 662 participants in the Multi-Ethnic Study of Atherosclerosis (MESA) [mean(SD) age=62(10)y; 46% female; 37% Caucasian, 25% African-American, 25% Hispanic, 13% Chinese-American]. Following adjustment for demographic and lifestyle characteristics, medication use, triglycerides and BMI, those in the highest quartile of serum phylloquinone had significantly lower circulating interleukin-6 [adjusted mean(SEM) pmol/L: quartile 4 (Q4)=1.22(0.07), quartile 1(Q1)=1.45(0.07); p-trend<0.01], CRP [adjusted mean(SEM) mg/dl: Q4=1.57(0.11), Q1=2.08(0.18); p-trend=0.02], soluble intercellular adhesion molecule-1 [adjusted mean(SEM) ng/ml: Q4=247(11), Q1=288(11); p-trend=0.02], and plasmin-antiplasmin complex [adjusted mean(SEM) nmol/L: Q4=4.02(0.1), Q1=4.31(0.1), p-trend=0.04]. We detected an interaction between age and serum phylloquinone with respect to factor VIII and D-dimer (interaction p-values=0.03 and 0.09 respectively). Among participants ≥70y, serum phylloquinone was inversely associated with factor VIII activity (p-trend=0.06) and positively associated with D-dimer (p-trend=0.01), but was not associated with either marker among participants <70y (both p≥0.38). In contrast, dietary phylloquinone intake was not associated with any inflammatory or haemostatic biomarker evaluated (all p-trend>0.11). These findings are consistent with laboratory-based studies that suggest a possible anti-inflammatory role for vitamin K. Whether or not these associations predict clinical outcomes linked to elevated inflammation or haemostatic activation

  3. Common neighbours and the local-community-paradigm for topological link prediction in bipartite networks

    NASA Astrophysics Data System (ADS)

    Daminelli, Simone; Thomas, Josephine Maria; Durán, Claudio; Vittorio Cannistraci, Carlo

    2015-11-01

    Bipartite networks are powerful descriptions of complex systems characterized by two different classes of nodes and connections allowed only across but not within the two classes. Unveiling physical principles, building theories and suggesting physical models to predict bipartite links such as product-consumer connections in recommendation systems or drug-target interactions in molecular networks can provide priceless information to improve e-commerce or to accelerate pharmaceutical research. The prediction of nonobserved connections starting from those already present in the topology of a network is known as the link-prediction problem. It represents an important subject both in many-body interaction theory in physics and in new algorithms for applied tools in computer science. The rationale is that the existing connectivity structure of a network can suggest where new connections can appear with higher likelihood in an evolving network, or where nonobserved connections are missing in a partially known network. Surprisingly, current complex network theory presents a theoretical bottle-neck: a general framework for local-based link prediction directly in the bipartite domain is missing. Here, we overcome this theoretical obstacle and present a formal definition of common neighbour index and local-community-paradigm (LCP) for bipartite networks. As a consequence, we are able to introduce the first node-neighbourhood-based and LCP-based models for topological link prediction that utilize the bipartite domain. We performed link prediction evaluations in several networks of different size and of disparate origin, including technological, social and biological systems. Our models significantly improve topological prediction in many bipartite networks because they exploit local physical driving-forces that participate in the formation and organization of many real-world bipartite networks. Furthermore, we present a local-based formalism that allows to intuitively

  4. Biological database of images and genomes: tools for community annotations linking image and genomic information.

    PubMed

    Oberlin, Andrew T; Jurkovic, Dominika A; Balish, Mitchell F; Friedberg, Iddo

    2013-01-01

    Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two. We present a generic set of software tools, BioDIG, that allows linking of image data to genomic data. BioDIG tools can be applied to a wide range of research problems that require linking images to genomes. BioDIG features the following: rapid construction of web-based workbenches, community-based annotation, user management and web services. By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information. Here we present the BioDIG software tools that include an image module, a genome module and a user management module. We also introduce a BioDIG-based website, MyDIG, which is being used to annotate images of mycoplasmas. PMID:23550062

  5. Value Co-creation and Co-innovation: Linking Networked Organisations and Customer Communities

    NASA Astrophysics Data System (ADS)

    Romero, David; Molina, Arturo

    Strategic networks such as Collaborative Networked Organisations (CNOs) and Virtual Customer Communities (VCCs) show a high potential as drivers of value co-creation and collaborative innovation in today’s Networking Era. Both look at the network structures as a source of jointly value creation and open innovation through access to new skills, knowledge, markets and technologies by sharing risk and integrating complementary competencies. This collaborative endeavour has proven to be able to enhance the adaptability and flexibility of CNOs and VCCs value creating systems in order to react in response to external drivers such as collaborative (business) opportunities. This paper presents a reference framework for creating interface networks, also known as ‘experience-centric networks’, as enablers for linking networked organisations and customer communities in order to support the establishment of user-driven and collaborative innovation networks.

  6. Variation in Parasite Communities in Spottail Shiners (Notropis hudsonius) Linked with Precipitation.

    PubMed

    Marcogliese, David J; Locke, Sean A; Gélinas, Malorie; Gendron, Andrée D

    2016-02-01

    The Richelieu River, Quebec, is a highly-regulated waterway subject to numerous anthropogenic influences from municipal effluents and agricultural activities. Parasite communities in 234 spottail shiners (Notropis hudsonius) were examined from 4 localities in late spring 2003 and 2004. Component species richness varied between 15 and 18 species in 2003 but declined to 9 to 13 in 2004, while total parasite abundance was consistently lower in 2003. Parasite component community similarity among localities could not be directly linked to available upstream water quality measurements or anthropogenic activity and was best explained by precipitation. Total precipitation in May 2003 was approximately 40% more than in May 2004, presumably altering patterns of runoff, river flow rates, and water quality. This study suggests that fish parasite species composition and richness in the Richelieu River are influenced by environmental parameters which in turn ultimately are driven by a combination of climatic conditions and anthropogenic activities in the watershed. PMID:26465386

  7. Stress and the microbiome: linking glucocorticoids to bacterial community dynamics in wild red squirrels.

    PubMed

    Stothart, Mason R; Bobbie, Colleen B; Schulte-Hostedde, Albrecht I; Boonstra, Rudy; Palme, Rupert; Mykytczuk, Nadia C S; Newman, Amy E M

    2016-01-01

    Bacterial diversity within animals is emerging as an essential component of health, but it is unknown how stress may influence the microbiome. We quantify a proximate link between the oral microbiome and hypothalamic-pituitary-adrenal (HPA) axis activity using faecal glucocorticoid metabolites (FGM) in wild red squirrels (Tamiasciurus hudsonicus). Not only was bacterial diversity lower at higher levels of FGM, but also between capture periods a change in bacterial relative abundance was related to an increase in FGM. These linkages between the HPA axis and microbiome communities represent a powerful capacity for stress to have multi-dimensional effects on health. PMID:26740566

  8. Development of a linked perinatal data resource from state administrative and community-based program data.

    PubMed

    Hall, Eric S; Goyal, Neera K; Ammerman, Robert T; Miller, Megan M; Jones, David E; Short, Jodie A; Van Ginkel, Judith B

    2014-01-01

    To demonstrate a generalizable approach for developing maternal-child health data resources using state administrative records and community-based program data. We used a probabilistic and deterministic linking strategy to join vital records, hospital discharge records, and home visiting data for a population-based cohort of at-risk, first time mothers enrolled in a regional home visiting program in Southwestern Ohio and Northern Kentucky from 2007 to 2010. Because data sources shared no universal identifier, common identifying elements were selected and evaluated for discriminating power. Vital records then served as a hub to which other records were linked. Variables were recoded into clinically significant categories and a cross-set of composite analytic variables was constructed. Finally, individual-level data were linked to corresponding area-level measures by census tract using the American Communities Survey. The final data set represented 2,330 maternal-infant pairs with both home visiting and vital records data. Of these, 56 pairs (2.4 %) did not link to either maternal or infant hospital discharge records. In a 10 % validation subset (n = 233), 100 % of the reviewed matches between home visiting data and vital records were true matches. Combining multiple data sources provided more comprehensive details of perinatal health service utilization and demographic, clinical, psychosocial, and behavioral characteristics than available from a single data source. Our approach offers a template for leveraging disparate sources of data to support a platform of research that evaluates the timeliness and reach of home visiting as well as its association with key maternal-child health outcomes. PMID:23420307

  9. Beyond the Classroom: International Education and the Community College. Volume III: Creating Institutional Links in Asia and the Pacific.

    ERIC Educational Resources Information Center

    Franco, Robert W., Ed.; Shimabukuro, James N., Ed.

    Part of a four-volume set in which community college educators discuss their efforts to internationalize the educational experience of the students and communities they serve, volume III in this series addresses the development of programmatic links among five two-year colleges and institutions in Japan, Taiwan, the People's Republic of China,…

  10. Invader Assisted Enzyme-Linked Immunosorbent Assay for Colorimetric Detection of Disease Biomarkers Using Oligonucleotide Probe-Modified Gold Nanoparticles.

    PubMed

    Song, Qinxin; Qi, Xiemin; Jia, Huning; He, Liang; Kumar, Shalen; Pitman, Janet L; Zou, Bingjie; Zhou, Guohua

    2016-04-01

    We successfully developed an invader assisted ELISA assay (iaELISA) for sensitive detection of disease biomarkers. The method includes three key steps as follows; biotinylated detection antibody was at first used to capture targeted antigen by sandwich ELISA. The biotinylated oligonucleotide was then attached to detection antibody via streptavidin. Finally, the cascade invader reactions were employed to amplify the biotinylated oligonucleotide specific to the antigen so that detection of the antigen was transformed into signal amplification of the antigen-specific DNA. To achieve colorimetric detection, oligonucleotide probe and modified gold nanoparticles (AuNPs) were coupled with the invader assay. Utilization of the hairpin probes in the invader reaction brought about free AuNPs, resulting in the positive read-out (red color). On the other hand, aggregation of the AuNPs occurred when the hairpin probes were not utilized in the reaction. This method was successfully used to detect as low as 2.4 x 10(-11) g/mL of HBsAg by both naked eye and spectrophotometer. This sensitivity was about 100 times higher than that of conventional ELISA method. The method was also used to assay 16 serum specimens from HBV-infected patients and 8 serum specimens from HBV-negative donors and results were in good agreement with those obtained from the conventional ELISA. As the invader assay is sensitive to one base sequence, a good specificity was also obtained by detecting other antigens like hepatitis A virus (HAV) and BSA. The method has therefore much potential for ultrasensitive and cost-effective detection of targeted proteins that have clinical importance. PMID:27301208

  11. Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep

    PubMed Central

    Kittelmann, Sandra; Pinares-Patiño, Cesar S.; Seedorf, Henning; Kirk, Michelle R.; Ganesh, Siva; McEwan, John C.; Janssen, Peter H.

    2014-01-01

    The potent greenhouse gas methane (CH4) is produced in the rumens of ruminant animals from hydrogen produced during microbial degradation of ingested feed. The natural animal-to-animal variation in the amount of CH4 emitted and the heritability of this trait offer a means for reducing CH4 emissions by selecting low-CH4 emitting animals for breeding. We demonstrate that differences in rumen microbial community structure are linked to high and low CH4 emissions in sheep. Bacterial community structures in 236 rumen samples from 118 high- and low-CH4 emitting sheep formed gradual transitions between three ruminotypes. Two of these (Q and S) were linked to significantly lower CH4 yields (14.4 and 13.6 g CH4/kg dry matter intake [DMI], respectively) than the third type (H; 15.9 g CH4/kg DMI; p<0.001). Low-CH4 ruminotype Q was associated with a significantly lower ruminal acetate to propionate ratio (3.7±0.4) than S (4.4±0.7; p<0.001) and H (4.3±0.5; p<0.001), and harbored high relative abundances of the propionate-producing Quinella ovalis. Low-CH4 ruminotype S was characterized by lactate- and succinate-producing Fibrobacter spp., Kandleria vitulina, Olsenella spp., Prevotella bryantii, and Sharpea azabuensis. High-CH4 ruminotype H had higher relative abundances of species belonging to Ruminococcus, other Ruminococcaceae, Lachnospiraceae, Catabacteriaceae, Coprococcus, other Clostridiales, Prevotella, other Bacteroidales, and Alphaproteobacteria, many of which are known to form significant amounts of hydrogen. We hypothesize that lower CH4 yields are the result of bacterial communities that ferment ingested feed to relatively less hydrogen, which results in less CH4 being formed. PMID:25078564

  12. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    PubMed Central

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  13. Linked hydrologic and social systems that support resilience of traditional irrigation communities

    NASA Astrophysics Data System (ADS)

    Fernald, A.; Guldan, S.; Boykin, K.; Cibils, A.; Gonzales, M.; Hurd, B.; Lopez, S.; Ochoa, C.; Ortiz, M.; Rivera, J.; Rodriguez, S.; Steele, C.

    2015-01-01

    Southwestern US irrigated landscapes are facing upheaval due to water scarcity and land use conversion associated with climate change, population growth, and changing economics. In the traditionally irrigated valleys of northern New Mexico, these stresses, as well as instances of community longevity in the face of these stresses, are apparent. Human systems have interacted with hydrologic processes over the last 400 years in river-fed irrigated valleys to create linked systems. In this study, we ask if concurrent data from multiple disciplines could show that human-adapted hydrologic and socioeconomic systems have created conditions for resilience. Various types of resiliencies are evident in the communities. Traditional local knowledge about the hydrosocial cycle of community water management and ability to adopt new water management practices is a key response to disturbances such as low water supply from drought. Livestock producers have retained their irrigated land by adapting: changing from sheep to cattle and securing income from outside their livestock operations. Labor-intensive crops decreased as off-farm employment opportunities became available. Hydrologic resilience of the system can be affected by both human and natural elements. We find, for example, that there are multiple hydrologic benefits of traditional irrigation system water seepage: it recharges the groundwater that recharges rivers, supports threatened biodiversity by maintaining riparian vegetation, and ameliorates impacts of climate change by prolonging streamflow hydrographs. Human decisions to transfer water out of agriculture or change irrigation management, as well as natural changes such as long-term drought or climate change, can result in reduced seepage and the benefits it provides. We have worked with the communities to translate the multidisciplinary dimensions of these systems into a common language of causal loop diagrams, which form the basis for modeling future scenarios to

  14. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health.

    PubMed

    Ha, Connie W Y; Lam, Yan Y; Holmes, Andrew J

    2014-11-28

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  15. Oxygen-18 isotope of breath CO2 linking to erythrocytes carbonic anhydrase activity: a biomarker for pre-diabetes and type 2 diabetes

    PubMed Central

    Ghosh, Chiranjit; Banik, Gourab D.; Maity, Abhijit; Som, Suman; Chakraborty, Arpita; Selvan, Chitra; Ghosh, Shibendu; Chowdhury, Subhankar; Pradhan, Manik

    2015-01-01

    Carbonic anhydrase (CA), a well-characterized metalloenzyme, is associated with oxygen-18 ( 18O)-isotopic fractionations of CO2. To investigate how CA activity links the 18O of breath CO2 to pre-diabetes (PD) and type 2 diabetes (T2D) during metabolism, we studied pre- and post-dose CA activities in erythrocytes with simultaneous monitoring of 18O/ 16O-isotope ratios of breath CO2 and thereafter elucidated potential metabolic pathways underlying CA alteration in the pathogenesis of T2D. Here we show that the post-dose CA activity in both T2D and PD was markedly enhanced, whereas the non-diabetic controls (NDC) exhibited a considerable reduction in post-dose CA activity when compared with their basal CA activities. However, T2D and PD exhibited isotopic enrichments of 18O in breath CO2, while a marked depletion of 18O in CO2 was manifested in NDC. Thus, the isotopic enrichments and depletions of 18O in breath CO2 were well correlated with the changes in CA activities for controls, PD and T2D. Our findings suggest the changes in CA activities in erythrocytes may contribute to the pathogenesis of T2D and the breath C 18O 16O regulated by the CA activity as a potential biomarker for non-invasive assessment of T2D, and thus may open a new method for treating T2D. PMID:25633556

  16. A method linking the toxic effects at community-level with contaminant concentrations.

    PubMed

    Wang, Changyou; Su, Rongguo; Zhang, Yong; Liu, Gang

    2016-11-01

    In this study, we developed a method to quantify and link the toxic effects in community-level ecosystems with concentrations of petroleum hydrocarbons. The densities of Platymonas helgolandica var. tsingtaoensis, Isochrysis galbana, and Brachionus plicatilis in single-species tests and customized ecosystems were examined in response to a concentration gradient of petroleum hydrocarbons ranging from 0 to 8.0mgL(-1). A three-population ecological model with interspecies competition-grazing relationships was used to characterize population sizes with concentrations of petroleum hydrocarbons. A threshold concentration of the simplified plankton ecosystem of 0.376mgL(-1) for petroleum hydrocarbons was calculated from the proposed model, which was higher than the no-effect concentration of 0.056mgL(-1) derived from the single-species toxicity tests and the predicted no-effect concentration of 0.076mgL(-1) calculated from the species sensitivity distribution. This finding indicates that interspecies competition and grazing reduced the toxic effect of petroleum hydrocarbons at the community level. The sensitivity analysis for model parameters demonstrates that plankton population biomasses are highly sensitive to filtration rates. Antagonism between interspecies interactions and petroleum hydrocarbon toxicity was attributed to the reduced filtration rate and zooplankton grazing pressure. The proposed method is a simple means to address the concern regarding the impacts of ecological interactions on ecological risk assessments of pollutants. PMID:27348700

  17. Benthic macroinvertebrate and fish communities in Lake Huron are linked to submerged groundwater vents

    USGS Publications Warehouse

    Garrison, Sanders T.; Biddanda, B.A.; Stricker, C.A.; Nold, S.C.

    2011-01-01

    Groundwater can be an important source of nutrients and energy to aquatic ecosystems, but quantifying the inputs and biogeochemical importance remains challenging. A series of submerged groundwater vents in northern Lake Huron were examined to determine the linkage between groundwater nutrients and aquatic food webs. We collected samples of key food-web components from groundwater vent and reference habitats and analyzed them for 13C, 15N, and 34S isotopes. Dissolved inorganic carbon (DIC) in the groundwater was depleted in 13C, while aqueous sulfate was enriched in 34S (mean differences between groundwater and reference sites were -3.9% and +12.0%, respectively). Benthic primary producers, macroinvertebrates, and benthivorous fish had significantly lower ??13C values in groundwater environments, and benthivorous fish were somewhat depleted (-2.5%) in ??34S at groundwater sites compared to reference sites. However, ??15N values were not different between groundwater and reference sites, and pelagic components of the ecosystems (plankton and planktivorous and piscivorous fish) were similar in both ??13C and ??15N. These data suggest benthic metazoan communities surrounding groundwater vents are partially linked to groundwater-derived benthic primary production, while planktivorous and piscivorous communities not directly associated with the benthos do not rely on groundwater nutrients. ?? Inter-Research 2011.

  18. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model.

    PubMed

    Miner, Brooks E; De Meester, Luc; Pfrender, Michael E; Lampert, Winfried; Hairston, Nelson G

    2012-05-22

    How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances. PMID:22298849

  19. A Reemerging Political Space for Linking Person and Community Through Primary Health Care

    PubMed Central

    Bazemore, Andrew; Phillips, Robert L.; Etz, Rebecca S.; Stange, Kurt C.

    2012-01-01

    Objectives. We sought to understand how national policy key informants perceive the value and changing role of primary care in the context of emerging political opportunities. Methods. We conducted 13 semistructured interviews in May 2011 with leaders of federal agencies, think tanks, nonprofits, and quality standard–defining organizations with influence over health care reform policies and implementation. We recorded the interviews and used an editing and immersion–crystallization analysis approach to identify themes. Results. We identified 4 themes: (1) affirmation of primary care as the foundation of a more effective health care system, (2) the patient-centered medical home as a transitional step to foster practice innovation and payment reform, (3) the urgent need for an increased focus on community and population health in primary care, and (4) the ongoing need for advocacy and research efforts to keep primary care on public and policy agendas. Conclusions. Current efforts to reform primary care are only intermediate steps toward a system with a greater focus on community and population health. Transformed and policy-enabled primary care is an essential link between personalized care and population health. PMID:22690969

  20. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

    PubMed Central

    Miner, Brooks E.; De Meester, Luc; Pfrender, Michael E.; Lampert, Winfried; Hairston, Nelson G.

    2012-01-01

    How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances. PMID:22298849

  1. Community Markets for Conservation (COMACO) links biodiversity conservation with sustainable improvements in livelihoods and food production

    PubMed Central

    Lewis, Dale; Bell, Samuel D.; Fay, John; Bothi, Kim L.; Gatere, Lydiah; Kabila, Makando; Mukamba, Mwangala; Matokwani, Edwin; Mushimbalume, Matthews; Moraru, Carmen I.; Lehmann, Johannes; Lassoie, James; Wolfe, David; Lee, David R.; Buck, Louise; Travis, Alexander J.

    2011-01-01

    In the Luangwa Valley, Zambia, persistent poverty and hunger present linked challenges to rural development and biodiversity conservation. Both household coping strategies and larger-scale economic development efforts have caused severe natural resource degradation that limits future economic opportunities and endangers ecosystem services. A model based on a business infrastructure has been developed to promote and maintain sustainable agricultural and natural resource management practices, leading to direct and indirect conservation outcomes. The Community Markets for Conservation (COMACO) model operates primarily with communities surrounding national parks, strengthening conservation benefits produced by these protected areas. COMACO first identifies the least food-secure households and trains them in sustainable agricultural practices that minimize threats to natural resources while meeting household needs. In addition, COMACO identifies people responsible for severe natural resource depletion and trains them to generate alternative income sources. In an effort to maintain compliance with these practices, COMACO provides extension support and access to high-value markets that would otherwise be inaccessible to participants. Because the model is continually evolving via adaptive management, success or failure of the model as a whole is difficult to quantify at this early stage. We therefore test specific hypotheses and present data documenting the stabilization of previously declining wildlife populations; the meeting of thresholds of productivity that give COMACO access to stable, high-value markets and progress toward economic self-sufficiency; and the adoption of sustainable agricultural practices by participants and other community members. Together, these findings describe a unique, business-oriented model for poverty alleviation, food production, and biodiversity conservation. PMID:21873184

  2. Making the links between community structure and individual well-being: community quality of life in Riverdale, Toronto, Canada.

    PubMed

    Raphael, D; Renwick, R; Brown, I; Steinmetz, B; Sehdev, H; Phillips, S

    2001-09-01

    An inquiry into community quality of life was carried out within a framework that recognizes the complex relationship between community structures and individual well-being. Through use of focus groups and key informant interviews, community members, service providers, and elected representatives in a Toronto community considered aspects of their community that affected quality of life. Community members identified strengths of access to amenities, caring and concerned people, community agencies, low-cost housing, and public transportation. Service providers and elected representatives recognized diversity, community agencies and resources, and presence of culturally relevant food stores and services as strengths. At one level, findings were consistent with emerging concepts of social capital. At another level, threats to the community were considered in relation to the hypothesized role neo-liberalism plays in weakening the welfare state. PMID:11439254

  3. Validation of biomarkers of CVD risk from dried blood spots in community-based research: Methodologies and study-specific serum equivalencies

    PubMed Central

    Samuelsson, Laura B.; Hall, Martica H.; McLean, Shakir; Porter, James H.; Berkman, Lisa; Marino, Miguel; Sembajwe, Grace; McDade, Thomas W.; Buxton, Orfeu M.

    2016-01-01

    Objective Dried blood spot (DBS) methodology offers significant advantages over venipuncture in vulnerable populations or large-scale studies, including reduced participant burden and higher response rates. Uncertainty about validity of cardiovascular risk biomarkers remains a barrier to wide-scale use. We determined the validity of DBS-derived biomarkers of CVD risk versus gold-standard assessments, and study-specific, serum-equivalency values for clinical relevance of DBS-derived values. Methods Concurrent venipuncture serum and DBS samples (n=150 adults) were assayed in CLIA-certified and DBS laboratories, respectively. Time controls of DBS standard samples were assayed single-blind along with test samples. Linear regression analyses evaluated DBS-to-serum equivalency values; agreement and bias were assessed via Bland-Altman plots. Results Linear regressions of venipuncture values on DBS-to-serum equivalencies provided R2 values for TC, HDL-C, CRP of 0.484, 0.118, 0.666, respectively. Bland-Altman plots revealed minimal systematic bias between DBS-to-serum and venipuncture values; precision worsened at higher mean values of CRP. Time controls reveal little degradation or change in analyte values for HDL-C and CRP over 30 weeks. Conclusions DBS-assessed biomarkers represent a valid alternative to venipuncture assessments. Large studies using DBS should include study-specific serum-equivalency determinations to optimize individual-level sensitivity, viability of detecting intervention effects, and generalizability in community-level, primary prevention interventions. PMID:26652683

  4. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

    PubMed Central

    Cassman, Noriko A.; Leite, Marcio F. A.; Pan, Yao; de Hollander, Mattias; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-01-01

    Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions. PMID:27020916

  5. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

    NASA Astrophysics Data System (ADS)

    Cassman, Noriko A.; Leite, Marcio F. A.; Pan, Yao; de Hollander, Mattias; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-03-01

    Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.

  6. Analysis Grid for Environments Linked to Obesity (ANGELO) framework to develop community-driven health programmes in an Indigenous community in Canada.

    PubMed

    Willows, Noreen; Dyck Fehderau, David; Raine, Kim D

    2016-09-01

    Indigenous First Nations people in Canada have high chronic disease morbidity resulting in part from enduring social inequities and colonialism. Obesity prevention strategies developed by and for First Nations people are crucial to improving the health status of this group. The research objective was to develop community-relevant strategies to address childhood obesity in a First Nations community. Strategies were derived from an action-based workshop based on the Analysis Grid for Environments Linked to Obesity (ANGELO) framework. Thirteen community members with wide-ranging community representation took part in the workshop. They combined personal knowledge and experience with community-specific and national research to dissect the broad array of environmental factors that influenced childhood obesity in their community. They then developed community-specific action plans focusing on healthy eating and physical activity for children and their families. Actions included increasing awareness of children's health issues among the local population and community leadership, promoting nutrition and physical activity at school, and improving recreation opportunities. Strengthening children's connection to their culture was considered paramount to improving their well-being; thus, workshop participants developed programmes that included elders as teachers and reinforced families' acquaintance with First Nations foods and activities. The research demonstrated that the ANGELO framework is a participatory way to develop community-driven health programmes. It also demonstrated that First Nations people involved in the creation of solutions to health issues in their communities may focus on decolonising approaches such as strengthening their connection to indigenous culture and traditions. External funds were not available to implement programmes and there was no formal follow-up to determine if community members implemented programmes. Future research needs to examine the

  7. Community Engagement in Health-Related Research: A Case Study of a Community-Linked Research Infrastructure, Jefferson County, Arkansas, 2011–2013

    PubMed Central

    Felix, Holly C.; Olson, Mary; Cottoms, Naomi; Bachelder, Ashley; Smith, Johnny; Ford, Tanesha; Dawson, Leah C.; Greene, Paul G.

    2015-01-01

    Background Underrepresentation of racial minorities in research contributes to health inequities. Important factors contributing to low levels of research participation include limited access to health care and research opportunities, lack of perceived relevance, power differences, participant burden, and absence of trust. We describe an enhanced model of community engagement in which we developed a community-linked research infrastructure to involve minorities in research both as participants and as partners engaged in issue selection, study design, and implementation. Community Context We implemented this effort in Jefferson County, Arkansas, which has a predominantly black population, bears a disproportionate burden of chronic disease, and has death rates above state and national averages. Methods Building on existing community–academic partnerships, we engaged new partners and adapted a successful community health worker model to connect community residents to services and relevant research. We formed a community advisory board, a research collaborative, a health registry, and a resource directory. Outcome Newly formed community–academic partnerships resulted in many joint grant submissions and new projects. Community health workers contacted 2,665 black and 913 white community residents from December 2011 through April 2013. Eighty-five percent of blacks and 88% of whites were willing to be re-contacted about research of potential interest. Implementation challenges were addressed by balancing the needs of science with community needs and priorities. Interpretation Our experience indicates investments in community-linked research infrastructure can be fruitful and should be considered by academic health centers when assessing institutional research infrastructure needs. PMID:26203813

  8. Biomarkers in Parkinson's disease: a venture capitalist's perspective.

    PubMed

    Eckstein, Jens W

    2010-10-01

    The emergence of biomarkers linking disease and treatment effects in a clear manner presents an opportunity to change the current drug development paradigm, which could lead to more cost-efficient and higher-quality clinical trials. This has raised the hopes of venture capital investors, who may be able to better navigate the stormy and risky sea of early-stage life science investments, to find a way out of the current funding crisis for novel, nonvalidated drugs and their clinical development. The following survey paints a snapshot of the current perception of biomarkers as a paradigm changer in the eyes of the venture capital community. PMID:20945985

  9. BIOMARKERS DATABASE

    EPA Science Inventory

    This database was developed by assembling and evaluating the literature relevant to human biomarkers. It catalogues and evaluates the usefulness of biomarkers of exposure, susceptibility and effect which may be relevant for a longitudinal cohort study. In addition to describing ...

  10. Maintaining Scientific Community Vocabularies in Drupal through Consumption of Linked Open Data and Web Services

    NASA Astrophysics Data System (ADS)

    Shepherd, A.; Arko, R. A.; Maffei, A. R.; Chandler, C. L.

    2012-12-01

    In the Summer of 2011, a one-year pilot project was funded by the National Science Foundation to build a pre-cruise planning application using the Drupal content management system (CMS). This application will be used to assist the individual operators of research vessels in the UNOLS fleet. A large portion of the operator's pre-cruise process revolves around a questionnaire presented to the principal investigator(PI) that is used to gather information about the nature of their upcoming cruise. The Drupal-based application will be delivered as a distribution for use by any operator of a UNOLS vessel to construct customized questionnaires and provide an interface for the PI to complete this questionnaire at their leisure. A major goal of the project is to develop an application that will require as little programming maintenance as possible after the initial development effort. One of the strategies employed is the reuse of existing controlled vocabularies and linked open data wherever possible for fields of the questionnaire - most notably to populate the concepts of Country, Organization, Port, and Ship. The Rolling Deck to Repository (R2R) program manages controlled vocabularies for these concepts and currently exposes these concepts as linked open data. Furthermore, R2R has identified the authoritative source for pertinent oceanographic community vocabularies as ICES for Ship, UNOLS for Port, IANA for Organization, ISO for Country, ISO for Language, SeaDataNet for Device, FIPS for State, and IHO for Sea Area as described at http://www.rvdata.us/voc. The scope of the terms provided by these sources matches the scope of the operator's needs for these concepts, and so the application is being designed to automatically consume served information about these vocabulary terms to populate and update Drupal taxonomies for use in the questionnaire. Where newer terms are required for a PI to complete a questionnaire (before they appear in the vocabularies), the Drupal

  11. Biomarkers in sepsis.

    PubMed

    Walley, Keith R

    2013-10-01

    There is much enthusiasm and interest in sepsis biomarkers, particularly because sepsis is a highly lethal condition, its diagnosis is challenging, and even simple treatment with antibiotics has led to serious adverse consequences such as emergence of resistant pathogens. Yet development of a sepsis biomarker requires many more steps than simply finding an association between a particular molecule and a clinical state or outcome. Demonstration of improvement of therapeutic practice using receiver-operating characteristic and other analyses is important. Validation in independent, prospective and, preferably, multicenter trials is essential. Many promising candidate sepsis biomarkers have recently been proposed. While procalcitonin (PCT) is currently the most studied sepsis biomarker, evidence of potential value has been found for a wide array of blood biomarkers including proteins, mRNA expression in whole blood or leukocytes, micro-RNAs (miRNA), pathogen and host DNA, pathogen and host genetic variants and metabolomic panels, and even in the novel use of currently available clinical data. While the most common early reports link putative sepsis biomarker levels to severity of illness and outcome (prognostic), this is not anticipated to be their primary use. More important is the distinction between infection and noninfectious inflammatory responses (diagnostic) and the use of sepsis biomarkers to direct therapy (predictive). PMID:23975686

  12. Teachers Learning in the Community: A Field Guide. Connections: Linking Work and Learning Series No. 8.

    ERIC Educational Resources Information Center

    Morales, Dionisia; Haynes, Leslie

    Increasingly, teachers are connecting with people in the community as part of their professional development. Community organizations provide opportunities for teachers to gain a new perspective on what students need to know to be prepared for a global economy. In addition, experiences in the community can help teachers develop integrated…

  13. Links between real and virtual networks: a comparative study of online communities in Japan and Korea.

    PubMed

    Ishii, Kenichi; Ogasahara, Morihiro

    2007-04-01

    The present study explores how online communities affect real-world personal relations based on a cross-cultural survey conducted in Japan and Korea. Findings indicate that the gratifications of online communities moderate the effects of online communities on social participation. Online communities are categorized into a real-group-based community and a virtual-network-based community. The membership of real-group-based online community is positively correlated with social bonding gratification and negatively correlated with information- seeking gratification. Japanese users prefer more virtual-network-based online communities, while their Korean counterparts prefer real-group-based online communities. Korean users are more active in online communities and seek a higher level of socializing gratifications, such as social bonding and making new friends, when compared with their Japanese counterparts. These results indicate that in Korea, personal relations via the online community are closely associated with the real-world personal relations, but this is not the case in Japan. This study suggests that the effects of the Internet are culture-specific and that the online community can serve a different function in different cultural environments. PMID:17474843

  14. Validation of Biomarkers of CVD Risk from Dried Blood Spots in Community-Based Research: Methodologies and Study-Specific Serum Equivalencies.

    PubMed

    Samuelsson, Laura B; Hall, Martica H; McLean, Shakir; Porter, James H; Berkman, Lisa; Marino, Miguel; Sembajwe, Grace; McDade, Thomas W; Buxton, Orfeu M

    2015-01-01

    Dried blood spot (DBS) methodology offers significant advantages over venipuncture in studies of vulnerable populations or large-scale studies, including reduced participant burden and higher response rates. Uncertainty about the validity of cardiovascular disease (CVD) risk biomarkers remains a barrier to wide-scale use. We determined the validity of DBS-derived biomarkers of CVD risk versus gold-standard assessments, and study-specific, serum-equivalency values for clinical relevance of DBS-derived values. Concurrent venipuncture serum and DBS samples (n = 150 adults) were assayed in Clinical Laboratory Improvement Amendments-certified and DBS laboratories, respectively. Time controls of DBS standard samples were assayed single-blind along with test samples. Linear regression analyses evaluated DBS-to-serum equivalency values; agreement and bias were assessed via Bland-Altman plots. Linear regressions of venipuncture values on DBS-to-serum equivalencies provided R(2) values for total cholesterol, high-density lipoprotein cholesterol (HDL-C), and C-reactive protein (CRP) of 0.484, 0.118, and 0.666, respectively. Bland-Altman plots revealed minimal systematic bias between DBS-to-serum and venipuncture values; precision worsened at higher mean values of CRP. Time controls revealed little degradation or change in analyte values for HDL-C and CRP over 30 weeks. We concluded that DBS-assessed biomarkers represent a valid alternative to venipuncture assessments. Large studies using DBS should include study-specific serum-equivalency determinations to optimize individual-level sensitivity, the viability of detecting intervention effects, and generalizability in community-level primary prevention interventions. PMID:26652683

  15. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird–plant network

    PubMed Central

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-01-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird–plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  16. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network.

    PubMed

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-04-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird-plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  17. Responses of Soil Bacterial Communities to Nitrogen Deposition and Precipitation Increment Are Closely Linked with Aboveground Community Variation.

    PubMed

    Li, Hui; Xu, Zhuwen; Yang, Shan; Li, Xiaobin; Top, Eva M; Wang, Ruzhen; Zhang, Yuge; Cai, Jiangping; Yao, Fei; Han, Xingguo; Jiang, Yong

    2016-05-01

    It has been predicted that precipitation and atmospheric nitrogen (N) deposition will increase in northern China; yet, ecosystem responses to the interactive effects of water and N remain largely unknown. In particular, responses of belowground microbial community to projected global change and their potential linkages to aboveground macro-organisms are rarely studied. In this study, we examined the responses of soil bacterial diversity and community composition to increased precipitation and multi-level N deposition in a temperate steppe in Inner Mongolia, China, and explored the diversity linkages between aboveground and belowground communities. It was observed that N addition caused the significant decrease in bacterial alpha-diversity and dramatic changes in community composition. In addition, we documented strong correlations of alpha- and beta-diversity between plant and bacterial communities in response to N addition. It was found that N enriched the so-called copiotrophic bacteria, but reduced the oligotrophic groups, primarily by increasing the soil inorganic N content and carbon availability and decreasing soil pH. We still highlighted that increased precipitation tended to alleviate the effects of N on bacterial diversity and dampen the plant-microbe connections induced by N. The counteractive effects of N addition and increased precipitation imply that even though the ecosystem diversity and function are predicted to be negatively affected by N deposition in the coming decades; the combination with increased precipitation may partially offset this detrimental effect. PMID:26838999

  18. Community-linked maternal death review (CLMDR) to measure and prevent maternal mortality: a pilot study in rural Malawi

    PubMed Central

    Bayley, Olivia; Chapota, Hilda; Kainja, Esther; Phiri, Tambosi; Gondwe, Chelmsford; King, Carina; Nambiar, Bejoy; Mwansambo, Charles; Kazembe, Peter; Costello, Anthony; Rosato, Mikey

    2015-01-01

    Background In Malawi, maternal mortality remains high. Existing maternal death reviews fail to adequately review most deaths, or capture those that occur outside the health system. We assessed the value of community involvement to improve capture and response to community maternal deaths. Methods We designed and piloted a community-linked maternal death review (CLMDR) process in Mchinji District, Malawi, which partnered community and health facility stakeholders to identify and review maternal deaths and generate actions to prevent future deaths. The CLMDR process involved five stages: community verbal autopsy, community and facility review meetings, a public meeting and bimonthly reviews involving both community and facility representatives. Results The CLMDR process was found to be comparable to a previous research-driven surveillance system at identifying deaths in Mchinji District (population 456 500 in 2008). 52 maternal deaths were identified between July 2011 and June 2012, 27 (52%) of which would not have been identified without community involvement. Based on district estimates of population (500 000) and crude birth rate (35 births per 1000 population), the maternal mortality ratio was around 300 maternal deaths per 100 000 live births. Of the 41 cases that started the CLMDR process, 28 (68%) completed all five stages. We found the CLMDR process to increase the quantity of information available and to involve a wider range of stakeholders in maternal death review (MDR). The process resulted in high rates of completion of community-planned actions (82%), and district hospital (67%) and health centre (65%) actions to prevent maternal deaths. Conclusions CLMDR is an important addition to the established forms of MDR. It shows potential as a maternal death surveillance system, and may be applicable to similar contexts with high maternal mortality. PMID:25897028

  19. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    PubMed

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  20. Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure

    PubMed Central

    Haverkamp, Thomas H. A.; Hammer, Øyvind; Jakobsen, Kjetill S.

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  1. Linking community, parenting, and depressive symptom trajectories: testing resilience models of adolescent agency based on race/ethnicity and gender.

    PubMed

    Williams, Amanda L; Merten, Michael J

    2014-09-01

    Family stress models illustrate how communities affect youth outcomes through effects on parents and studies consistently show the enduring effects of early community context. The present study takes a different approach identifying human agency during adolescence as a potentially significant promotive factor mediating the relationship between community, parenting, and mental health. While agency is an important part of resilience, its longitudinal effects are unknown, particularly based on gender and race/ethnicity. The purpose of this research was to model the long-term effects of community structural adversity and social resources as predictors of adolescent depressive symptom trajectories via indirect effects of parental happiness, parent-child relationships, and human agency. Latent growth analyses were conducted with 1,796 participants (53% female; 56% White) across four waves of the National Longitudinal Study of Adolescent Health spanning adolescence (Wave 1) through adulthood (Wave 4). The results identified agency as an important promotive factor during adolescence with long-term mental health benefits, but only for White and male participants. For these individuals, community social resources and the quality of the parent-child relationship were related to higher levels of agency and more positive mental health trajectories. Although community social resources similarly benefitted parenting and agency among females and non-White participants, there were no significant links between agency and depressive symptoms for these youth. The results suggest that agency remains an important, but poorly understood concept and additional work is necessary to continue unpacking its meaning for diverse groups of youth. PMID:24907892

  2. Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

    NASA Astrophysics Data System (ADS)

    Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

    2015-12-01

    Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

  3. The GEOSS Science and Technology Stakeholder Network and Service Suite: Linking S&T Communities and GEOSS

    NASA Astrophysics Data System (ADS)

    Plag, Hans-Peter; Jules-Plag, Shelley

    2015-04-01

    The Global Earth Observation System of Systems (GEOSS) developed by the Group on Earth Observations (GEO) aims to provide practice-relevant knowledge in support of decision making in a wide range of societal benefit areas. Generating this practice-relevant knowledge based on Earth observations, socio-economic data and models often depends on research, and utilization of the societal benefits of EOs requires the involvement of science and research communities. Building a GEOSS responding to the needs of a wide range of users necessitates contributions from many science and technology (S&T) communities. In particular, a strong engagement of science and technology (S&T) communities in both the development and use of GEOSS is necessary to address the complex issues associated with the on-going transition out of the Holocene. S&T support is needed to improve interoperability between global observing, modeling, and information systems; to enable data integration across disciplinary boundaries; to facilitate data sharing, archiving, dissemination, and reanalysis; to optimize the recording of observations, assimilation of data into models, and generation of data products; to enhance the value of observations from individual observing systems through their integration in the SBAs; and to harmonize well-calibrated, highly accurate, stable, sustained in-situ and satellite observations of the same variable recorded by different sensors and different agencies. Consequently, the GEO Work Plan includes several Tasks focusing on outreach to S&T communities, and most of the GEO Community of Practice have a strong S&T component. The GEOSS S&T Stakeholder Network facilitates input from S&T communities to GEO. Infrastructure serving and linking S&T users communities and GEOSS has been developed and is integrated into a GEOSS S&T Service Suite (GSTSS). The GSTSS has several outreach components for the demonstration of GEOSS and its value for S&T communities, and for services supporting

  4. Linking Parent and Community Involvement with Student Achievement: Comparing Principal and Teacher Perceptions of Stakeholder Influence

    ERIC Educational Resources Information Center

    Gordon, Molly F.; Louis, Karen Seashore

    2009-01-01

    Expanding the sources of leadership in schools has been a reform theme since the mid 1980s. Using exploratory factor analysis and regression, we examine the following questions: (1) How does leadership style affect principals' openness to community involvement? (2) Is a principal's openness to community involvement related to student achievement?…

  5. Standing Alone No More: Linking Research to a Writing Course in a Learning Community

    ERIC Educational Resources Information Center

    Rapchak, Marcia; Cipr, Ava

    2015-01-01

    Collaborating with teaching faculty is a well-established method of making library instruction more meaningful and engaging to students, and learning communities provide an excellent opportunity to work closely with both teaching faculty and a cohort of students. A typical learning community brings students together around a similar discipline or…

  6. Linking Community Communication to Conservation of the Maned Wolf in Central Brazil

    ERIC Educational Resources Information Center

    Bizerril, Marcelo Ximenes A.; Soares, Carla Cruz; Santos, Jean Pierre

    2011-01-01

    This article describes the environmental education (EE) program developed in the neighboring community of Serra da Canastra National Park based on a research project focused on the maned wolf conservation. The article assesses three tools used to foster the community's participation in discussing local issues: (1) communal production of a book…

  7. Linking Scholarship and Practice: Community College Leaders, State Mandates, and Leadership Competencies

    ERIC Educational Resources Information Center

    Hebert-Swartzer, Cathleen A.; McNair, Delores E.

    2010-01-01

    To be an effective leader in today's community college requires a sophisticated set of skills that are often learned through on the job training, mentoring, and professional development activities. Using case study methodology, this study examined how community college leaders in California use their skills to implement a state mandate related to…

  8. Exploring Links between Empowerment and Community-Based Arts and Cultural Practices: Perspectives from Barcelona Practitioners

    ERIC Educational Resources Information Center

    Carrasco, Ruben David Fernández; Monferrer, Moisés Carmona; Tarditi, Andrés Di Masso

    2016-01-01

    In this paper, we reflect on the development of community-based arts and cultural (CBAC) practices to promote psychosocial, group/organisational and community changes from the perspective of empowerment. We draw on findings from an initial exploratory phase of an ongoing action-research project in Spain about creative tools that empower artists…

  9. Landscapes for Learning: Growing Children, Youth, Schools, and Communities. Linking Learning with Life.

    ERIC Educational Resources Information Center

    Vander Mey, Brenda J.; McDonald, Sian I.

    This booklet provides information on implementing the Landscapes for Learning (LFL) program, which was conceived to bring children, youths, and communities together to learn about landscaping while beautifying local schools and communities. The booklet begins with a discussion of the concept of environmental stewardship. Described next are the…

  10. School-Linked Service Integration in Action: Lessons Drawn from Seven California Communities.

    ERIC Educational Resources Information Center

    Carreon, Victoria; Jameson, Wendy J.

    State and county initiatives in California have sparked a movement for integration of social services. The practical lessons learned by communities integrating services for children and families were studied and are presented in this report. The study draws on the experiences of seven California communities (Fresno County, Los Angeles County,…

  11. Veterans Coming Home to the Community College: Linking Research to Practice

    ERIC Educational Resources Information Center

    Persky, Karen R.; Oliver, Diane E.

    2011-01-01

    Community colleges must prepare for change as increasing numbers of students who are veterans of the Iraq and Afghanistan Wars use their post-9/11 GI Bill benefits to join the colleges' diverse student bodies. Based on the findings of a mixed methods case study, needs of veterans at the community college are framed and discussed within five major…

  12. Understanding the Link between Social Organization and Crime in Rural Communities

    PubMed Central

    Chilenski, Sarah M.; Syvertsen, Amy K.; Greenberg, Mark T.

    2015-01-01

    Rural communities make up much of America's heartland, yet we know little about their social organization, and how elements of their social organization relate to crime rates. The current study sought to remedy this gap by examining the associations between two measures of social organization – collective efficacy and social trust – with a number of structural community characteristics, local crime rates, and perceptions of safety in a sample of 27 rural and small town communities in two states. Measures of collective efficacy, social trust, and perceived safety, were gathered from key community members in 2006; other measures were drawn from the 2000 Census and FBI Uniform Crime Reporting system. A series of competing hypotheses were tested to examine the relative importance of social trust and collective efficacy in predicting local crime rates. Results do not support the full generalization of the social disorganization model. Correlational analyses showed that neither collective efficacy nor social trust had a direct association with community crime, nor did they mediate the associations between community structural characteristics and crime. However, perceived safety mediated the association between community crime and both measures of social organization. Analyses suggest that social trust may be more important than collective efficacy when understanding the effect of crime on a community's culture in rural areas. Understanding these associations in rural settings can aid decision makers in shaping policies to reduce crime and juvenile delinquency. PMID:26120326

  13. Structured decision making as a framework for linking quantitative decision support to community values

    EPA Science Inventory

    Community-level decisions can have large impacts on production and delivery of ecosystem services, which ultimately affects community well-being. But engaging stakeholders in a process to explore these impacts is a significant challenge. The principles of Structured Decision Ma...

  14. Eco-geophysical imaging of watershed-scale soil patterns links with plant community spatial patterns

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The extent to which soil resource availability, nutrients or 1 moisture, control the structure, function and diversity of plant communities has aroused considerable interest in the past decade, and remains topical in light of global change. Numerous plant communities are controlled either by water o...

  15. Lack of effective communication between communities and hospitals in Uganda: a qualitative exploration of missing links

    PubMed Central

    Rutebemberwa, Elizeus; Ekirapa-Kiracho, Elizabeth; Okui, Olico; Walker, Damien; Mutebi, Aloysius; Pariyo, George

    2009-01-01

    Background Community members are stakeholders in hospitals and have a right to participate in the improvement of quality of services rendered to them. Their views are important because they reflect the perspectives of the general public. This study explored how communities that live around hospitals pass on their views to and receive feedback from the hospitals' management and administration. Methods The study was conducted in eight hospitals and the communities around them. Four of the hospitals were from three districts from eastern Uganda and another four from two districts from western Uganda. Eight key informant interviews (KIIs) were conducted with medical superintendents of the hospitals. A member from each of three hospital management boards was also interviewed. Eight focus group discussions (FGDs) were conducted with health workers from the hospitals. Another eight FGDs (four with men and four with women) were conducted with communities within a five km radius around the hospitals. Four of the FGDs (two with men and two with women) were done in western Uganda and the other four in eastern Uganda. The focus of the KIIs and FGDs was exploring how hospitals communicated with the communities around them. Analysis was by manifest content analysis. Results Whereas health unit management committees were supposed to have community representatives, the representatives never received views from the community nor gave them any feed back from the hospitals. Messages through the mass media like radio were seen to be non specific for action. Views sent through suggestion boxes were seen as individual needs rather than community concerns. Some community members perceived they would be harassed if they complained and had reached a state of resignation preferring instead to endure the problems quietly. Conclusion There is still lack of effective communication between the communities and the hospitals that serve them in Uganda. This deprives the communities of the right to

  16. NABIR Assessment Element, Expanded Rapid, Comprehensive, Lipid Biomarker Analysis for Subsurface, Community Composition and Nutritional/Physiological Status as Monitors of Remediation and Detoxification Effectiveness

    SciTech Connect

    David C. White

    2005-09-14

    NABIR funding at the University of Tennessee Center for Biomarker Analysis (CBA) has led to several key contributions to the investigation of bioremediation of metals and radionuclides. This lab has played an integral part in assessing microbial communities at the field scale at the ORNL FRC (Istok et al., 2004) and two UMTRA sites (Anderson et al., 2003, Chang et al., 2001). Our work over the period of the grant has resulted in 42-peer reviewed publications, 62 presentations (14 of which were international), and one patent pending. Currently CBA has 2 papers in press. The main objectives relating to the field portion of this program were to provide comprehensive biomarker analysis for NABIR collaborators to enhance the understanding of microbial geo-bioprocesses involved in the effective immobilization of metals (We have worked with and published or currently are publishing with 10 groups of NAIBR investigators). The laboratory portion of our research centered on methods development and has led to three major innovations that could result in a systematic way of evaluating sites for potential bioremediation. The first of these is the development of an in situ sampling device (Peacock et al., 2004, Anderson et al., 2003, Istok et al., 2004) for the collection and concentration of microbial biomass. The second is the development of expanded lipid analysis based on the significantly greater sensitivity and selectivity of the LC/MS/MS that allows the analysis of respiratory quinones, diglycerides, sterols, intact phospholipids, poly-hydroxyalkonates, and potentially archaeol, and caldarchaeols from archea. These new analyses are accomplished more rapidly and with increased sensitivities and resolution than in the past (Lytle et al., 2000a, 2000b, 2001a, Geyer et al., 2004). The third advance is the coupling of lipid analysis with 13C enrichment experiments (Lytle et al., 2001b, Geyer et al. 2005). With this technique it is now possible to follow the active portion of

  17. Fine-scale community and genetic structure are tightly linked in species-rich grasslands

    PubMed Central

    Whitlock, Raj; Bilton, Mark C.; Grime, J. Phil; Burke, Terry

    2011-01-01

    Recent evidence indicates that grassland community structure and species diversity are influenced by genetic variation within species. We review what is known regarding the impact of intraspecific diversity on grassland community structure, using an ancient limestone pasture as a focal example. Two genotype-dependent effects appear to modify community structure in this system. First, the abundance of individual constituent species can depend upon the combined influence of direct genetic effects stemming from individuals within the population. Second, the outcome of localized interspecific interactions occurring within the community can depend on the genotypes of participating individuals (indicating indirect genetic effects). Only genotypic interactions are thought to be capable of allowing the long-term coexistence of both genotypes and species. We discuss the implications of these effects for the maintenance of diversity in grasslands. Next, we present new observations indicating that losses of genotypic diversity from each of two species can be predicted by the abundance of other coexisting species within experimental grassland communities. These results suggest genotype-specific responses to abundance in other coexisting species. We conclude that both direct and indirect genetic effects are likely to shape community structure and species coexistence in grasslands, implying tight linkage between fine-scale genetic and community structure. PMID:21444309

  18. Linking DNRA community structure and activity in a shallow lagoonal estuarine system

    PubMed Central

    Song, Bongkeun; Lisa, Jessica A.; Tobias, Craig R.

    2014-01-01

    Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are two nitrate respiration pathways in the microbial nitrogen cycle. Diversity and abundance of denitrifying bacteria have been extensively examined in various ecosystems. However, studies on DNRA bacterial diversity are limited, and the linkage between the structure and activity of DNRA communities has yet to be discovered. We examined the composition, diversity, abundance, and activities of DNRA communities at five sites along a salinity gradient in the New River Estuary, North Carolina, USA, a shallow temporal/lagoonal estuarine system. Sediment slurry incubation experiments with 15N-nitrate were conducted to measure potential DNRA rates, while the abundance of DNRA communities was calculated using quantitative PCR of nrfA genes encoding cytochrome C nitrite reductase, commonly found in DNRA bacteria. A pyrosequencing method targeting nrfA genes was developed using an Ion Torrent sequencer to examine the diversity and composition of DNRA communities within the estuarine sediment community. We found higher levels of nrfA gene abundance and DNRA activities in sediments with higher percent organic content. Pyrosequencing analysis of nrfA genes revealed spatial variation of DNRA communities along the salinity gradient of the New River Estuary. Percent abundance of dominant populations was found to have significant influence on overall activities of DNRA communities. Abundance of dominant DNRA bacteria and organic carbon availability are important regulators of DNRA activities in the eutrophic New River Estuary. PMID:25232351

  19. Linking above and belowground responses to global change at community and ecosystem scales.

    SciTech Connect

    Antoninka, Anita; Wolf, Julie; Bowker, Matt; Classen, Aimee T; JohnsonPhD, Dr Nancy C

    2009-01-01

    Cryptic belowground organisms are difficult to observe and their responses to global changes are not well understood. Nevertheless, there is reason to believe that interactions among above- and belowground communities may mediate ecosystem responses to global change. We used grassland mesocosms to manipulate the abundance of one important group of soil organisms, arbuscular mycorrhizal (AM) fungi, and to study community and ecosystem responses to CO2 and N enrichment. After two growing seasons, biomass responses of plant communities were recorded, and soil community responses were measured using microscopy, phospholipid fatty acids (PLFA) and community-level physiological profiles (CLPP). Ecosystem responses were examined by measuring net primary production (NPP), evapotranspiration, total soil organic matter (SOM), and extractable mineral N. Structural equation modeling was used to examine the causal relationships among treatments and response variables. We found that while CO2 and N tended to directly impact ecosystem functions (evapotranspiration and NPP, respectively), AM fungi indirectly impacted ecosystem functions by strongly influencing the composition of plant and soil communities. For example, the presence of AM fungi had a strong influence on other root and soil fungi and soil bacteria. We found that the mycotrophic status of the dominant plant species in the mesocosms determined whether the presence of AM fungi increased or decreased NPP. Mycotrophic grasses dominated the mesocosm communities during the first growing season, and thus, the mycorrhizal treatments had the highest NPP. In contrast, non-mycotrophic forbs were dominant during the second growing season and thus, the mycorrhizal treatments had the lowest NPP. The composition of the plant community strongly influenced soil N; and the composition of the soil organisms strongly influenced SOM accumulation in the mesocosms. These results show how linkages between above- and belowground communities

  20. Microbial-algal community changes during the latest Permian ecological crisis: Evidence from lipid biomarkers at Cili, South China

    NASA Astrophysics Data System (ADS)

    Luo, Genming; Wang, Yongbiao; Grice, Kliti; Kershaw, Steve; Algeo, Thomas J.; Ruan, Xiaoyan; Yang, Hao; Jia, Chengling; Xie, Shucheng

    2013-06-01

    Microbialites flourished globally immediately following the latest Permian mass extinction. In this study, lipid biomarker records were analyzed in the Cili section (Hunan Province, South China) in order to determine the types of microbes involved in microbialite formation and their response to contemporaneous environmental changes. Various biomarkers were identified in the aliphatic and aromatic fractions using gas chromatography (GC) and GC-mass spectrometry (GC-MS). Low abundance of steranes in the microbialite layer suggests that it did not contain large amounts of algae, in striking contrast to the abundant algal fossils and algal-derived steranes present in the underlying (pre-crisis) skeletal limestone. Although pristine/phytane (Pr/Ph) ratios increased in the microbialite layer, covariation of Pr/Ph with the ratio of low- to high-molecular-weight n-alkanes (C20 -/C20 +) suggests that the former proxy was controlled by microbial (particularly cyanobacterial) inputs rather than by redox conditions. The microbialite also yielded low ratios of hopanes to short-chain n-alkanes (HP/Lalk) and high abundances of C21n-alkylcyclohexane, indicating that, in addition to cyanobacteria, anaerobic bacteria, archaea, and possibly acritarchs flourished in the aftermath of the marine extinction event. The upper part of the thinly bedded micritic limestone overlying the microbialite exhibits a bimodal distribution of n-alkanes as well as increased abundances of extended tricyclic terpanes and steranes, suggesting a return of habitable shallow-marine conditions for eukaryotic algae several hundred thousand years after the latest Permian mass extinction. Increases in the dibenzofuran ratio (i.e., DBF/(DBF + DBT + F)) and in the coronene to phenanthrene ratio (Cor/P) in the skeletal limestone immediately below the microbialite are evidence of enhanced soil erosion rates and wildfire intensity, marking the collapse of terrestrial ecosystems. The terrestrial crisis thus slightly

  1. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

    PubMed Central

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

  2. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

    PubMed

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

  3. Linking with Community To Reclaim Natural Areas for Education: The McLane Elementary School Project.

    ERIC Educational Resources Information Center

    Spencer, Melinda; Smith, Kathy Kurtz

    2002-01-01

    Describes a project in which students, teachers, and the community work to reclaim neglected wetlands and forested areas for use as an environmental study site for interdisciplinary learning. (Author/MM)

  4. Modeling the Biodegradation of Bacterial Community Assembly Linked Antibiotics in River Sediment Using a Deterministic-Stochastic Combined Model.

    PubMed

    Zhang, Wenlong; Li, Yi; Wang, Chao; Wang, Peifang; Hou, Jun; Yu, Zhongbo; Niu, Lihua; Wang, Linqiong; Wang, Jing

    2016-08-16

    To understand the interaction between bacterial community assembly and the assembly linked antibiotics biodegradation, a unique model framework containing a Monod kinetic, a logistic kinetic, and a stochastic item was established to describe the biodegradation of bacterial community assembly linked sulfamethoxazole (SMX) in river sediment. According to the modeling results, both deterministic and stochastic processes driving bacterial population variations played important roles in controlling SMX biodegradation, and the relative importance depended on the in situ concentration of SMX. A threshold concentration of SMX, which was biodegraded in the experimental river sediment depending on different processes, was obtained (i.e., 20 μg/kg). The higher introduced concentration of SMX (>20 μg/kg) was found to promote the acclimation of antibiotic degradation bacteria in microbial community through niche differentiation, which resulted in the specific microbial metabolization of SMX. In contrast, the lower introduced concentration of SMX (<20 μg/kg) was not able to lead to a significant increase of deterministic processes and resulted in the biodegradation of SMX through co-metabolism by the coexisting microorganisms. The developed model can be considered a useful tool for improving the technologies of water environmental protection and remediation. PMID:27428250

  5. Integrating the Environment, the Economy, and Community Health: A Community Health Center’s Initiative to Link Health Benefits to Smart Growth

    PubMed Central

    McAvoy, Peter V.; Driscoll, Mary Beth; Gramling, Benjamin J.

    2004-01-01

    The Sixteenth Street Community Health Center (SSCHC) in Milwaukee, Wis, is making a difference in the livability of surrounding neighborhoods and the overall health of the families it serves. SSCHC is going beyond traditional health care provider models and working to link the environment, the economy, and community health through urban brownfield redevelopment and sustainable land-use planning. In 1997, SSCHC recognized that restoration of local air and water quality and other environmental conditions, coupled with restoring family-supporting jobs in the neighborhood, could have a substantial impact on the overall health of families. Recent events indicate that SSCHC’s pursuit of smart growth strategies has begun to pay off. PMID:15053995

  6. Linking fungal communities to wood density loss after 12 years of log decay.

    PubMed

    Kubartová, Ariana; Ottosson, Elisabet; Stenlid, Jan

    2015-05-01

    Changes in biodiversity might alter decomposition processes and, consequently, carbon and nutrient cycling. We examined fungal diversity and density loss in experimental Norway spruce logs after 12 years of decay in a hemiboreal forest. Between 28 and 50% of the original wood biomass remained, depending on the fungal community composition in the log, operational taxonomic unit (OTU) richness had only a minor effect on the log biomass. Although the communities were OTU rich (190-340 OTUs per log), the majority of OTUs were infrequent or rare; wood degradation therefore depended mostly on the most abundant OTUs and their decomposing abilities. The least decayed logs were characterized by continuous dominance of an earlier colonizer and by high within-log community diversity, which was significantly related to sample variables (position in log, density and moisture). In the most decayed logs, the earlier colonizers were generally replaced by white-rot species able to exploit the highly decomposed wood. The communities were relatively spatially uniform within whole logs, independent of the sample variables, whereas among-log diversity was high. Importance of fungal community composition in decomposition processes should be taken into account when studying and modeling carbon dynamics in forest ecosystems. PMID:25873458

  7. Linking community and disease ecology: the impact of biodiversity on pathogen transmission.

    PubMed

    Roche, Benjamin; Dobson, Andrew P; Guégan, Jean-François; Rohani, Pejman

    2012-10-19

    The increasing number of zoonotic diseases spilling over from a range of wild animal species represents a particular concern for public health, especially in light of the current dramatic trend of biodiversity loss. To understand the ecology of these multi-host pathogens and their response to environmental degradation and species extinctions, it is necessary to develop a theoretical framework that takes into account realistic community assemblages. Here, we present a multi-host species epidemiological model that includes empirically determined patterns of diversity and composition derived from community ecology studies. We use this framework to study the interaction between wildlife diversity and directly transmitted pathogen dynamics. First, we demonstrate that variability in community composition does not affect significantly the intensity of pathogen transmission. We also show that the consequences of community diversity can differentially impact the prevalence of pathogens and the number of infectious individuals. Finally, we show that ecological interactions among host species have a weaker influence on pathogen circulation than inter-species transmission rates. We conclude that integration of a community perspective to study wildlife pathogens is crucial, especially in the context of understanding and predicting infectious disease emergence events. PMID:22966136

  8. Biomarkers for prostate cancer.

    PubMed

    Schiffer, Eric

    2007-12-01

    Novel biomarkers for prostate cancer (PCa) are currently being assessed for utility in PCa diagnosis. This article aims to provide concise information on the current findings that impact prostate cancer research. Results of enzyme-linked immunosorbent assays (ELISA) for single biomarkers, quantitative polymerase chain reaction (PCR)-based assays for DNA/RNA markers will be reviewed in addition to high-throughput proteomic profiling of PCa specimens. The advantages/disadvantages of tissue, blood, urine or seminal plasma as sources for potential biomarkers are discussed emphasizing the consequences for PCa diagnosis. In summary, the majority of promising marker candidates available today needs further validation. Some of the identified markers have the potential to yield novel prognostic tools for PCa, provide novel insights into its pathophysiology, and contribute to the establishment of novel treatment strategies. PMID:17690889

  9. Cross-Scale Variation in Biodiversity-Environment Links Illustrated by Coastal Sandflat Communities

    PubMed Central

    Kraan, Casper; Dormann, Carsten F.; Greenfield, Barry L.; Thrush, Simon F.

    2015-01-01

    Spatial variation in the composition of communities is the product of many biotic and environmental interactions. A neglected factor in the analysis of community distribution patterns is the multi-scale nature of the data, which has implications for understanding ecological processes and the development of conservation and environmental management practice. Drawing on recently established multivariate spatial analyses, we investigate whether including relationships between spatial structure and abiotic variables enable us to better discern patterns of species and communities across scales. Data comprised 1200 macrozoobenthic samples collected over an array of distances (30 cm to 1 km) in three New Zealand harbours, as well as commonly used abiotic variables, such as sediment characteristics and chlorophyll a concentrations, measured at the same scales. Moran’s eigenvector mapping was used to extract spatial scales at which communities were structured. Benthic communities, representing primarily bivalves, polychaetes and crustaceans, were spatially structured at four spatial scales, i.e. >100 m, 50–100 m, 50–15 m, and < 15 m. A broad selection of abiotic variables contributed to the large-scale variation, whereas a more limited set explained part of the fine-scale community structure. Across all scales, less than 30% of the variation in spatial structure was captured by our analysis. The large number of species (48) making up the 10 highest species scores based on redundancy analyses illustrate the variability of species-scale associations. Our results emphasise that abiotic variables and biodiversity are related at all scales investigated and stress the importance of assessing the relationship between environmental variables and the abundance and distribution of biological assemblages across a range of different scales. PMID:26555237

  10. Tuberculosis Beijing strain outbreak in an Israeli Arab rural community linked to an incarcerated immigrant.

    PubMed

    Bishara, H; Rorman, E; Mor, Z; Shechter-Amram, D; Weiler-Ravell, D

    2014-12-01

    A tuberculosis (TB) outbreak with six definite and four probable cases, caused by a Beijing strain isolate, occurred in an Arab rural community in north Israel. Using epidemiological investigation and strain genotyping, we identified the source case as an incarcerated immigrant. This outbreak illustrates how a systematic breakdown in TB prevention and control measures at multiple levels, within prisons and upon exiting prison, can result in rapid, cross-ethnic transmission of TB to a low-risk population. The close social bonds in this rural community and downsizing of the regional TB clinic staff may also have contributed to the magnitude of this outbreak. PMID:25517819

  11. Linking Ready Kids to Ready Schools: "Building Policy on State and Community Successes"

    ERIC Educational Resources Information Center

    W. K. Kellogg Foundation, 2009

    2009-01-01

    More than 200 educators and child advocates from around the country issued a "call to action" during a historic national forum in late March, mobilizing in Washington to develop policies that will link ready kids to ready schools and set America's youngest learners on a path to lifelong achievement. The two-day event in late March--co-sponsored by…

  12. Project Link-Four: Pre-Vocational Education for Adults through Community Linkages.

    ERIC Educational Resources Information Center

    Stedman, Deborah S.

    The Texas adult performance level (APL) project LINK-FOUR implemented a curriculum based on functional competencies at four sites (Austin, Texarkana, Texas City, and Abilene) and formed linkages with local organizations involved in adult vocational education. The concept on which the project was based was that a set of prevocational skills, plus a…

  13. Linking Faculty Development to Community College Student Achievement: A Mixed Methods Approach

    ERIC Educational Resources Information Center

    Elliott, Robert W.; Oliver, Diane E.

    2016-01-01

    Using a mixed methods, multilevel research design, this pilot inquiry explored the relationship between college faculty professional development and the academic achievement of diverse students by coupling two separate links: (a) the effects that professional development activities have on improving teaching strategies, and (b) the effects these…

  14. Applied Scholarship in the Community Service Link: From Classroom Texts to Classroom as Text.

    ERIC Educational Resources Information Center

    Fischer, Ruth Overman

    Students entering the university have to create a space for themselves, not only in the writing classroom, but in their relationships with faculty, other students, and their evolving selves. A curricular support mechanism helps students enlarge their educational process. Such a support system, the Linked Courses Program, has been in operation at…

  15. Biomarkers for antipsychotic therapies.

    PubMed

    Pich, Emilio Merlo; Vargas, Gabriel; Domenici, Enrico

    2012-01-01

    Molecular biomarkers for antipsychotic treatments have been conceptually linked to the measurements of dopamine functions, mostly D(2) receptor occupancy, either by imaging using selective PET/SPECT radioactive tracers or by assessing plasma prolactin levels. A quest for novel biomarkers was recently proposed by various academic, health service, and industrial institutions driven by the need for better treatments of psychoses. In this review we conceptualize biomarkers within the Translational Medicine paradigm whose goal was to provide support to critical decision-making in drug discovery. At first we focused on biomarkers as outcome measure of clinical studies by searching into the database clinicaltrial.gov. The results were somewhat disappointing, showing that out of 1,659 antipsychotic trials only 18 used a biomarker as an outcome measure. Several of these trials targeted plasma lipids as sentinel marker for metabolic adverse effects associated with the use of atypical antipsychotics, while only few studies were aimed to new disease specific biological markers. As an example of a mechanistic biomarker, we described the work done to progress the novel class of glycine transporter inhibitors as putative treatment for negative symptoms of schizophrenia. We also review how large-scale multiplex biological assays were applied to samples from tissues of psychiatric patients, so to learn from changes of numerous analytes (metabolic products, lipids, proteins, RNA transcripts) about the substrates involved in the disease. We concluded that a stringent implementation of these techniques could contribute to the endophenotypic characterization of patients, helping in the identification of key biomarkers to drive personalized medicine and new treatment development. PMID:23129338

  16. Understanding Community College Students' Learning Styles and the Link to Academic Achievement

    ERIC Educational Resources Information Center

    Peters, Kathleen

    2012-01-01

    Learning styles have been an area of interest in educational psychology for many decades. However, community college students have been overlooked in learning styles research. To enhance teacher efficacy and student success, it is important to continue to evaluate the relationship between learning styles and academic achievement. The purpose of…

  17. Roger Tory Peterson Institute Links Interdisciplinary Nature Studies to Increased Community Understanding. Rural Trust Featured Project.

    ERIC Educational Resources Information Center

    Null, Elizabeth Higgins

    The Roger Tory Peterson Institute (Jamestown, New York) has been sparking a regional revival in K-12 nature studies and attracting attention from educators across America. Through summer training sessions and workshops, the Institute introduces multidisciplinary teams of teachers and community members to empirical research techniques for observing…

  18. School Boards: Forging Links to Parents and Community in Small School Districts.

    ERIC Educational Resources Information Center

    Schmuck, Richard A.; Schmuck, Patricia A.

    1992-01-01

    Presents observations of small district school boards based on travels through 21 states. Small communities have faced economic decline, a changing membership of school boards and consolidation, with less representation of professionals and business leaders. Recommended tasks of school boards involve (1) facilitating communication; (2) forming…

  19. Linking Development Benefits to Neighborhoods: A Manual of Community-Based Strategies. Technical Bulletin.

    ERIC Educational Resources Information Center

    Casale, Ellen

    This manual collects experiences of successful linkage programs to demonstrate the promise of linkage and to show its limits and risks. It is intended to help communities assess the capacity of linkage to meet their needs and evaluate the considerable commitment this strategy requires. (In linkage programs, developers who receive community…

  20. Applying the Learning Community Model to Graduate Education: Linking Research and Teaching between Core Courses

    ERIC Educational Resources Information Center

    Romsdahl, Rebecca J.; Hill, Michael J.

    2012-01-01

    In graduate education, there is often a great divide between classroom learning and research endeavors. Using learning community (LC) values and strategies, our goal is to build stronger and more meaningful ties between these two aspects of graduate education so that students see them as complimentary learning rather than separate components. This…

  1. Linked hydrologic and social systems that support resilience of traditional irrigation communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southwestern US irrigated landscapes are facing upheaval due to water scarcity and land use conversion associated with climate change, population growth, and changing economics. In the traditionally irrigated valleys of northern New Mexico, these stresses, as well as instances of community longevity...

  2. Psychological Symptoms Linking Exposure to Community Violence and Academic Functioning in African American Adolescents

    ERIC Educational Resources Information Center

    Busby, Danielle R.; Lambert, Sharon F.; Ialongo, Nicholas S.

    2013-01-01

    African American adolescents are exposed disproportionately to community violence, increasing their risk for emotional and behavioral symptoms that can detract from learning and undermine academic outcomes. The present study examined whether aggressive behavior and depressive and anxious symptoms mediated the association between exposure to…

  3. Linking Student Achievement to Professional Learning Communities in a Juvenile Court School Setting

    ERIC Educational Resources Information Center

    Wyatt, Scott

    2010-01-01

    Purpose: The purpose of the study was to provide verifiable data regarding the impact Professional Learning Communities (PLCs) have on student achievement in the Juvenile Court School (JCS) system. A second purpose was to measure staff perceptions regarding their support and beliefs about the use of PLCs in the JCS setting. Methodology: This…

  4. Exploring Possible Links between Professional Learning Communities and Complex Adaptive Systems

    ERIC Educational Resources Information Center

    Johnson, Eric

    2013-01-01

    Implementation of Professional Learning Communities (PLC), as described by DuFour (2006), has depended upon a balance between teacher buy-in and administrative fiat. The tension between the "bottom-up" character of the former and the "top-down" character of the latter presents a leadership challenge: meeting students' learning…

  5. The Link Between Hepatitis B and Liver Cancer: The Asian American Community

    Cancer.gov

    Dr. Moon Chen, Professor of the Department of Internal Medicine and Associate Director of Cancer Control at the University of California-Davis Comprehensive Cancer Center, speaks about Hepatitis B and Liver Cancer as a more prevalent problem in the Asian American community.

  6. Assessing the bias linked to DNA recovery from biofiltration woodchips for microbial community investigation by fingerprinting.

    PubMed

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2010-01-01

    In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation. PMID:19826809

  7. Using a Community Based Project to Link Teaching and Research: The Bourne Stream Partnership

    ERIC Educational Resources Information Center

    Shah, Anita; Treby, Emma

    2006-01-01

    This paper demonstrates that integrating research into the curriculum can help to enhance the overall student learning experience. The Bourne Stream Partnership is a local community-based project which has provided environmental & geographical science students with the opportunity to work on live projects within a variety of contexts including…

  8. Linking Family Life and Health Professionals, Volunteers, and Family Life Students in a Community Hospice Program.

    ERIC Educational Resources Information Center

    Fruit, Dorothy

    This paper describes the Portage County, Ohio community hospice program, emphasizing the linkages between family life specialists, health professionals, volunteers, and students. Hospice service is defined as a specialized, home-based program for the management of pain and other symptoms of terminal illness, with the family as the unit of care.…

  9. New Song Academy: Linking Education and Community Development To Build Stronger Families and Neighborhoods.

    ERIC Educational Resources Information Center

    Brown, Prudence; Fiester, Leila

    This report describes the New Song Academy, led by New Song Urban Ministries (NSUM), which serves preK-8 children in Baltimore, Maryland, and promotes quality education for urban students through partnerships with families and the community. It operates year-round in six 6-week sessions. Despite the often chaotic nature of children's lives outside…

  10. A Blended Community of Inquiry Approach: Linking Student Engagement and Course Redesign

    ERIC Educational Resources Information Center

    Vaughan, Norman D.

    2010-01-01

    The purpose this article is to describe an institutional initiative created to support faculty engaged in blended course redesign. This Inquiry Through Blended Learning (ITBL) program adapted Garrison, Anderson, and Archer's (2000) Community of Inquiry framework in order to provide faculty participants with a guided inquiry process for discussing…

  11. Natural Resource Service Learning to Link Students, Communities, and the Land

    ERIC Educational Resources Information Center

    Barlow, Rebecca J.

    2013-01-01

    University-based Extension specialists often face the dilemma of scheduling time for both teaching and outreach activities. Service learning projects that give hands-on experience in the application of classroom activities while giving back to the community can bridge this gap. A demonstration forest and service learning techniques were used to…

  12. A 150-year record of ancient DNA, lipid biomarkers and hydrogen isotopes, tracing the microbial-planktonic community succession controlled by (hydro)climatic variability in a tropical lake

    NASA Astrophysics Data System (ADS)

    Smittenberg, Rienk; Yamoah, Kweku; Callac, Nolwenn; Fru, Ernest Chi; Chabangborn, Akkaneewut; Rattray, Jayne; Wohlfarth, Barbara

    2016-04-01

    We investigated the decadal variations in phytoplankton communities, and their response to environmental and climatic conditions, from a ˜150 year long sedimentary archive of Lake Nong Thale Prong (NTP), southern Thailand. We applied a combination of analyses: lipid biomarkers, compound-specific hydrogen isotopes, bulk carbon and nitrogen concentrations and isotopes, environmental SEM, and fossil DNA using qPCR targeted to specific taxa. Past hydrological conditions were reconstructed using the hydrogen isotopic composition of leaf wax n-alkanes. Temperatures were reconstructed using the tetraether-based MBT/CBT index, measured using a new and efficient reverse-phase HPLC-MS method. The climatological data compared well with meteorological data from the last decades. Reconstructed drier and warmer conditions from ˜1857-1916 Common Era (CE) coincided with oligotrophic lake water conditions and dominance of the green algae Botryococcus braunii - evidenced by a combination of both fossil DNA and the occurrence of characteristic botryococcene lipids. A change to higher silica (Si) input ˜1916 CE was related to increased rainfall and lower temperatures concurring with an abrupt takeover by diatom blooms lasting for 50 years - as evidenced by ancient DNA, characteristic highly branched isoprenoid lipids, and SEM. From the 1970s onwards, more eutrophic conditions prevailed, and these were likely caused by increased levels of anthropogenic phosphate (P), aided by stronger lake stratification caused by dryer and warmer conditions. The eutrophic conditions led to increased primary productivity in the lake, consisting again of a Botryococcus sp., although this time not producing botryococcene lipids. Moreover, Cyanobacteria became dominant - again evidenced by ancient DNA and the characteristic C19 alkane. Throughout the record, stratification and primary production could be linked to the intensity of methane cycling, by targeting and quantifying the mcrA gene that is used

  13. Prevention of public health risks linked to bullying: a need for a whole community approach.

    PubMed

    Srabstein, Jorge; Joshi, Paramjit; Due, Pernille; Wright, Joseph; Leventhal, Bennett; Merrick, Joav; Kim, Young-Shin; Silber, Tomas; Kumpulainen, Kirsti; Menvielle, Edgardo; Riibner, Karen

    2008-01-01

    Bullying is a very toxic psychosocial stressor associated with serious health problems and death, affecting both the victims and the bullies. This form of abuse or maltreatment occurs around the world and along the lifespan. Health professionals have the unique responsibility of promoting the development of community initiatives for the prevention of bullying and related health problems. This effort must include ongoing programs with elements of primary, secondary, and tertiary prevention. These programs should be supported and monitored by a public health policy with a strategy aimed at developing a whole community awareness about bullying and the related health risks, prohibiting bullying, and developing emotionally and physically safe environments in schools and workplace settings. Public health policy should mandate the monitoring, detection, and reporting of bullying incidents; provide guidance for school intervention; and offer guidelines for medical consultation. PMID:18714555

  14. Links between Ammonia Oxidizer Community Structure, Abundance, and Nitrification Potential in Acidic Soils ▿ †

    PubMed Central

    Yao, Huaiying; Gao, Yangmei; Nicol, Graeme W.; Campbell, Colin D.; Prosser, James I.; Zhang, Limei; Han, Wenyan; Singh, Brajesh K.

    2011-01-01

    Ammonia oxidation is the first and rate-limiting step of nitrification and is performed by both ammonia-oxidizing archaea (AOA) and bacteria (AOB). However, the environmental drivers controlling the abundance, composition, and activity of AOA and AOB communities are not well characterized, and the relative importance of these two groups in soil nitrification is still debated. Chinese tea orchard soils provide an excellent system for investigating the long-term effects of low pH and nitrogen fertilization strategies. AOA and AOB abundance and community composition were therefore investigated in tea soils and adjacent pine forest soils, using quantitative PCR (qPCR), terminal restriction fragment length polymorphism (T-RFLP) and sequence analysis of respective ammonia monooxygenase (amoA) genes. There was strong evidence that soil pH was an important factor controlling AOB but not AOA abundance, and the ratio of AOA to AOB amoA gene abundance increased with decreasing soil pH in the tea orchard soils. In contrast, T-RFLP analysis suggested that soil pH was a key explanatory variable for both AOA and AOB community structure, but a significant relationship between community abundance and nitrification potential was observed only for AOA. High potential nitrification rates indicated that nitrification was mainly driven by AOA in these acidic soils. Dominant AOA amoA sequences in the highly acidic tea soils were all placed within a specific clade, and one AOA genotype appears to be well adapted to growth in highly acidic soils. Specific AOA and AOB populations dominated in soils at particular pH values and N content, suggesting adaptation to specific niches. PMID:21571885

  15. Student, Home, and School Socio-Demographic Factors: Links to School, Home, and Community Arts Participation

    ERIC Educational Resources Information Center

    Mansour, Marianne; Martin, Andrew J.; Anderson, Michael; Gibson, Robyn; Liem, Gregory Arief D.; Sudmalis, David

    2016-01-01

    This study explored the role of student (e.g., age, language background, gender), home (e.g., parent/caregiver education), and school (e.g., school type, size) socio-demographic factors in students' school (e.g., in-school arts tuition, arts engagement), home (e.g., parent/caregiver-child arts interaction), and community (e.g., arts attendance,…

  16. Analysis of links between groundwater recharge and discharge areas and wetland plant communities distribution in Middle Biebrza Basin, Poland

    NASA Astrophysics Data System (ADS)

    Grygoruk, Mateusz; Batelaan, Okke; Okruszko, Tomasz; Kotowski, Wiktor; Rycharski, Marek; Chormanski, Jaroslaw; Miroslaw-Swiatek, Dorota

    2010-05-01

    Natural evolution of wetlands is strongly dependent on groundwater dynamics, soil aeration and climate. These environmental factors determine the constant development of wetland plant communities and peat forming processes. Depending on spatial distribution of groundwater flow systems and recharge and discharge conditions, shallow groundwater can also be influenced by phreatophytic plants. Such feedback plays an important role in wetland development, especially when landuse or climate changes occur. Thus, understanding the links between dynamics of biotopic and biocenotic relations is crucial for wetland management aimed at the comprehensive set of conservation strategies. Main aim of this study was to review links between valuable wetland plant communities and the groundwater recharge/discharge conditions of particular habitats of Middle Biebrza Basin, Poland. The study area consists of various types of wetland landscapes, of which the dominant are fens. Organogenic top layer is intersected locally by sandy dunes and glaci-fluvial residual plateaus. The northern boundary of the study area is covered with an outwash plateau. A three-dimensional regional groundwater flow model was set up to quantify groundwater system and flow paths. Model calibration involved measured heads of the unconfined organogenic top layer and the underlaying, confined sandy aquifer. Measured thickness of unsaturated zone as well as physical parameters of organogenic layer were taken into account in interpretation of shallow groundwater dynamics. Recharge to groundwater was spatially distributed in accordance to analysis of measured precipitation-groundwater level relationships. Cell-by-cell flow analysis and groundwater exfiltration analysis were applied to map groundwater recharge and discharge areas within the modelled area. Results of groundwater modelling were validated with phytosociologic research combined with remote-sensing based spatial analysis of wetland habitats distribution

  17. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

    PubMed Central

    Muller, Emilie E. L.; Pinel, Nicolás; Laczny, Cédric C.; Hoopmann, Michael R.; Narayanasamy, Shaman; Lebrun, Laura A.; Roume, Hugo; Lin, Jake; May, Patrick; Hicks, Nathan D.; Heintz-Buschart, Anna; Wampach, Linda; Liu, Cindy M.; Price, Lance B.; Gillece, John D.; Guignard, Cédric; Schupp, James M.; Vlassis, Nikos; Baliga, Nitin S.; Moritz, Robert L.; Keim, Paul S.; Wilmes, Paul

    2014-01-01

    Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ. PMID:25424998

  18. Bird community composition linked to human West Nile virus cases along the Colorado front range.

    PubMed

    McKenzie, Valerie J; Goulet, Nicolas E

    2010-12-01

    In the present study, we examined whether bird community composition can predict the annual number of human West Nile virus (WNV) cases on a per county basis in the Colorado Front Range, a region that experienced high numbers of human cases during the early part of the North American epidemic. We analyzed data sets pertaining to birds and human WNV cases from multiple existing databases between the years 2002 and 2008. Based on previous studies that used amplification fractions to compare the relative competence of different bird species, ten bird species that are common in Colorado were selected and categorized as high amplification birds, such as the American Robin (Turdus migratorius), or low amplification birds, such as the American Crow (Corvus brachyrhynchos). A general linear modeling analysis was used with an information theoretic (AIC) model sorting approach to examine which of the models best predicted the number of human WNV cases per county. Candidate models included year as a covariate and one of several bird community descriptors (e.g., richness, diversity, total bird abundance, high amplification abundance, or low amplification abundance). Results demonstrated that high amplification birds were a significant predictor of human WNV cases between 2002 and 2008. Our results suggest that a small subset of the bird community with high amplification fractions may drive the dynamics of human disease risk for West Nile. This study has implications for surveillance of West Nile and may offer insight into disease risk associated with other vector-borne zoonotic diseases. PMID:21125307

  19. Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula angustifolia Mill.

    PubMed

    Emiliani, Giovanni; Mengoni, Alessio; Maida, Isabel; Perrin, Elena; Chiellini, Carolina; Fondi, Marco; Gallo, Eugenia; Gori, Luigi; Maggini, Valentina; Vannacci, Alfredo; Biffi, Sauro; Firenzuoli, Fabio; Fani, Renato

    2014-01-01

    Endophytic bacteria play a crucial role in plant life and are also drawing much attention for their capacity to produce bioactive compounds of relevant biotechnological interest. Here we present the characterisation of the cultivable endophytic bacteria of Lavandula angustifolia Mill.-a species used since antiquity for its therapeutic properties-since the production of bioactive metabolites from medical plants may reside also in the activity of bacterial endophytes through their direct production, PGPR activity on host, and/or elicitation of plant metabolism. Lavender tissues are inhabited by a tissue specific endophytic community dominated by Proteobacteria, highlighting also their difference from the rhizosphere environment where Actinobacteria and Firmicutes are also found. Leaves' endophytic community resulted as the most diverse from the other ecological niches. Overall, the findings reported here suggest: (i) the existence of different entry points for the endophytic community, (ii) its differentiation on the basis of the ecological niche variability, and (iii) a two-step colonization process for roots endophytes. Lastly, many isolates showed a strong inhibition potential against human pathogens and the molecular characterization demonstrated also the presence of not previously described isolates that may constitute a reservoir of bioactive compounds relevant in the field of pathogen control, phytoremediation, and human health. PMID:24971151

  20. [A comprehensive signature biomarker analysis of the in-situ viable biomass, community composition, and nutritional status attributes of deep subsurface microbiota]. Final report

    SciTech Connect

    1998-09-01

    The TAN sites contains subsurface sediment contaminated with trichloroethylene (TC). A suite of microbiological analyses, including ester-linked phospholipid fatty acid (PLFA) analysis, were performed to ascertain the microbial ecology associated with TCE degradation processes. The objective of the PLFA analyses were: (1) to determine the distribution of viable microbes throughout a vertical depth profile through the TCE plume, (2) determine the community composition of the viable extant microbiota and (3) relate the data derived from the PLFA analyses to other measures of the in situ microbiota as well as to the presence of TCE degradative products.

  1. A three-dimensional numerical model for linking community-wide vapour risks

    NASA Astrophysics Data System (ADS)

    Mustafa, Nizar; Mumford, Kevin G.; Gerhard, Jason I.; O'Carroll, Denis M.

    2014-01-01

    A three-dimensional (3D) numerical model that couples contaminant transport in the saturated zone to vapour transport in the vadose zone and vapour intrusion into buildings was developed. Coupling these processes allows the simulation of vapour intrusion, arising from volatilization at the water table, associated with temporally and spatially variable groundwater plumes. In particular, the model was designed to permit, for the first time, 3D simulations of risk at receptors located in the wider community (i.e., kilometre scale) surrounding a contaminated site. The model can account for heterogeneous distributions of permeability, fraction organic carbon, sorption and biodegradation in the vadose and saturated zones. The model formulation, based upon integration of a number of widely accepted models, is presented along with verification and benchmarking tests. In addition, a number of exploratory simulations of benzene and naphthalene transport in a 1000 m long domain (aquifer cross-section: 500 m × 14 m) are presented, which employed conservative assumptions consistent with the development of regulatory guidance. Under these conservative conditions, these simulations demonstrated, for example, that whether houses in the community were predicted to be impacted by groundwater and indoor air concentrations exceeding regulatory standards strongly depended on their distance downgradient from the source and lateral distance from the plume centreline. In addition, this study reveals that the degree of reduction in source concentration (i.e., remediation) required to achieve compliance with standards is less if the risk receptor is in the wider community than at the site boundary. However, these example scenarios suggest that, even considering community receptors, sources with initially high concentrations still required substantial remediation (i.e., > 99% reductions in source concentration). Overall, this work provides insights and a new tool for considering the

  2. A three-dimensional numerical model for linking community-wide vapour risks.

    PubMed

    Mustafa, Nizar; Mumford, Kevin G; Gerhard, Jason I; O'Carroll, Denis M

    2014-01-01

    A three-dimensional (3D) numerical model that couples contaminant transport in the saturated zone to vapour transport in the vadose zone and vapour intrusion into buildings was developed. Coupling these processes allows the simulation of vapour intrusion, arising from volatilization at the water table, associated with temporally and spatially variable groundwater plumes. In particular, the model was designed to permit, for the first time, 3D simulations of risk at receptors located in the wider community (i.e., kilometre scale) surrounding a contaminated site. The model can account for heterogeneous distributions of permeability, fraction organic carbon, sorption and biodegradation in the vadose and saturated zones. The model formulation, based upon integration of a number of widely accepted models, is presented along with verification and benchmarking tests. In addition, a number of exploratory simulations of benzene and naphthalene transport in a 1000 m long domain (aquifer cross-section: 500 m×14 m) are presented, which employed conservative assumptions consistent with the development of regulatory guidance. Under these conservative conditions, these simulations demonstrated, for example, that whether houses in the community were predicted to be impacted by groundwater and indoor air concentrations exceeding regulatory standards strongly depended on their distance downgradient from the source and lateral distance from the plume centreline. In addition, this study reveals that the degree of reduction in source concentration (i.e., remediation) required to achieve compliance with standards is less if the risk receptor is in the wider community than at the site boundary. However, these example scenarios suggest that, even considering community receptors, sources with initially high concentrations still required substantial remediation (i.e., >99% reductions in source concentration). Overall, this work provides insights and a new tool for considering the

  3. Community benefits and health reform: creating new links for public health and not-for-profit hospitals.

    PubMed

    Abbott, Ann L

    2011-01-01

    The Patient Protection and Affordable Care Act (PPACA) put new requirements on not-for-profit (NFP) hospitals to document provision of community benefits, to justify their tax-exempt status. Specific PPACA provisions include requirements that NFP hospitals conduct or participate in a community health needs assessment and work to address the needs identified. Consideration is given to these particular PPACA mandates and to Internal Revenue Service (IRS) actions to implement them. The background of concerns that have been expressed about whether the NFP hospitals' tax exemption should be continued and a brief history of that exemption is noted. Not-for-profit hospitals have resources that the federal government is requiring them to bring to public health improvement, during a time when the public health agencies at the federal and state level continue to experience reductions in funding. Linking of the NFP hospitals' compliance activities with the public health agency community health planning activities will help fulfill its PPACA requirements and the regulatory reporting requirements for the IRS. PMID:21964364

  4. Linking Attitudes, Policy, and Forest Cover Change in Buffer Zone Communities of Chitwan National Park, Nepal.

    PubMed

    Stapp, Jared R; Lilieholm, Robert J; Leahy, Jessica; Upadhaya, Suraj

    2016-06-01

    Deforestation in Nepal threatens the functioning of complex social-ecological systems, including rural populations that depend on forests for subsistence, as well as Nepal's biodiversity and other ecosystem services. Nepal's forests are particularly important to the nation's poorest inhabitants, as many depend upon them for daily survival. Two-thirds of Nepal's population relies on forests for sustenance, and these pressures are likely to increase in the future. This, coupled with high population densities and growth rates, highlights the importance of studying the relationship between human communities, forest cover trends through time, and forest management institutions. Here, we used surveys to explore how household attitudes associated with conservation-related behaviors in two rural communities-one that has experienced significant forest loss, and the other forest gain-compare with forest cover trends as indicated by satellite-derived forest-loss and -regeneration estimates between 2005 and 2013. Results found a significant difference in attitudes in the two areas, perhaps contributing to and reacting from current forest conditions. In both study sites, participation in community forestry strengthened support for conservation, forest conservation-related attitudes aligned with forest cover trends, and a negative relationship was found between economic status and having supportive forest conservation-related attitudes. In addition, on average, respondents were not satisfied with their district forest officers and did not feel that the current political climate in Nepal supported sustainable forestry. These findings are important as Nepal's Master Plan for the Forestry Sector has expired and the country is in the process of structuring a new Forestry Sector Strategy. PMID:26920157

  5. Unusually high food availability in Kaikoura Canyon linked to distinct deep-sea nematode community

    NASA Astrophysics Data System (ADS)

    Leduc, D.; Rowden, A. A.; Nodder, S. D.; Berkenbusch, K.; Probert, P. K.; Hadfield, M. G.

    2014-06-01

    Kaikoura Canyon, on the eastern New Zealand continental margin, is the most productive, non-chemosynthetic deep-sea habitat described to date, with megafaunal biomass 100-fold higher than those of other deep-sea habitats. The present study, which focused on free-living nematodes, provides the first comparison of faunal community structure and diversity between Kaikoura Canyon and nearby open slope habitats. Results show substantially higher food availability in the canyon relative to open slope sediments, which probably reflects greater levels of primary productivity above the canyon, coupled with downwelling and/or topographically-induced channelling, which serves to concentrate surface-derived organic matter along the canyon axis. This high food availability appears to be responsible for the elevated nematode biomass in Kaikoura Canyon, with values exceeding all published nematode biomass data from canyons elsewhere. There was also markedly lower local species diversity of nematodes inside the canyon relative to the open slope habitat, as well as a distinct community structure. The canyon community was dominated by species, such as Sabateria pulchra, which were absent from the open slope and are typically associated with highly eutrophic and/or disturbed environments. The presence of these taxa, as well as the low observed diversity, is likely to reflect the high food availability, and potentially the high levels of physically and biologically induced disturbance within the canyon. Kaikoura Canyon is a relatively small habitat characterised by different environmental conditions that makes a disproportionate contribution to deep-sea diversity in the region, despite its low species richness.

  6. Linking Sediment Microbial Communities to Carbon Cycling in High-Latitude Lakes

    NASA Astrophysics Data System (ADS)

    Emerson, J. B.; Varner, R. K.; Johnson, J. E.; Owusu-Dommey, A.; Binder, M.; Woodcroft, B. J.; Wik, M.; Freitas, N. L.; Boyd, J. A.; Crill, P. M.; Saleska, S. R.; Tyson, G. W.; Rich, V. I.

    2015-12-01

    It is well recognized that thawing permafrost peatlands are likely to provide a positive feedback to climate change via CH4 and CO2 emissions. High-latitude lakes in these landscapes have also been identified as sources of CH4 and CO2 loss to the atmosphere. To investigate microbial contributions to carbon loss from high-latitude lakes, we characterized sediment geochemistry and microbiota via cores collected from deep and shallow regions of two lakes (Inre Harrsjön and Mellersta Harrsjön) in Arctic Sweden in July, 2012. These lakes are within the Stordalen Mire long-term ecological area, a focal site for investigating the impacts of climate change-related permafrost thaw, and the lakes in this area are responsible for ~55% of the CH4 loss from this hydrologically interconnected system. Across 40 samples from 4 to 40 cm deep within four sediment cores, Illumina 16S rRNA gene sequencing revealed that the sedimentary microbiota was dominated by candidate phyla OP9 and OP8 (Atribacteria and Aminicenantes, respectively, including putative fermenters and anaerobic respirers), predicted methanotrophic Gammaproteobacteria, and predicted methanogenic archaea from the Thermoplasmata Group E2 clade. We observed some overlap in community structure with nearby peatlands, which tend to be dominated by methanogens and Acidobacteria. Sediment microbial communities differed significantly between lakes, by overlying lake depth (shallow vs. deep), and by depth within a core, with each trend corresponding to parallel differences in biogeochemical measurements. Overall, our results support the potential for significant microbial controls on carbon cycling in high-latitude lakes associated with thawing permafrost, and ongoing metagenomic analyses of focal samples will yield further insight into the functional potential of these microbial communities and their dominant members.

  7. A methodological framework for linking bioreactor function to microbial communities and environmental conditions.

    PubMed

    de los Reyes, Francis L; Weaver, Joseph E; Wang, Ling

    2015-06-01

    In the continuing quest to relate microbial communities in bioreactors to function and environmental and operational conditions, engineers and biotechnologists have adopted the latest molecular and 'omic methods. Despite the large amounts of data generated, gaining mechanistic insights and using the data for predictive and practical purposes is still a huge challenge. We present a methodological framework that can guide experimental design, and discuss specific issues that can affect how researchers generate and use data to elucidate the relationships. We also identify, in general terms, bioreactor research opportunities that appear promising. PMID:25710123

  8. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

    PubMed Central

    Deng, Jie; Deng, Ye; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Qin, Yujia; Zhou, Jiti; Zhou, Jizhong

    2015-01-01

    Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. coli nagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities

  9. Missing link in community psychiatry: When a patient with schizophrenia was expelled from her home.

    PubMed

    Chen, I-Ming; Wu, Kevin Chien-Chang; Chien, Yi-Ling; Chen, Yu-Hsiang; Lee, Sung-Tai

    2015-06-01

    Treatment and disposition of homeless patients with schizophrenia represent a great challenge in clinical practice. We report a case of this special population, and discuss the development of homelessness, the difficulty in disposition, their utilization of health services, and possible applications of mandatory community treatment in this group of patients. A 51-year-old homeless female was brought to an emergency department for left femur fracture caused by an assault. She was diagnosed with schizophrenia about 20 years ago but received little help from mental health services over the decades. During hospitalization, her psychotic symptoms were only partially responsive to treatment. Her family refused to handle caretaking duties. The social welfare system was mobilized for long-term disposition. Homeless patients with schizophrenia are characterized by family disruption, poor adherence to health care, and multiple emergency visits and hospitalization. We hope this article can provide information about the current mental health policy to medical personnel. It is possible that earlier intervention and better outcome can be achieved by utilizing mandatory community treatment in the future, as well as preventing patients with schizophrenia from losing shelters. PMID:26062968

  10. Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry.

    PubMed

    Fortuna, Ann-Marie; Honeycutt, C Wayne; Vandemark, George; Griffin, Timothy S; Larkin, Robert P; He, Zhongqi; Wienhold, Brian J; Sistani, Karamat R; Albrecht, Stephan L; Woodbury, Bryan L; Torbert, Henry A; Powell, J Mark; Hubbard, Robert K; Eigenberg, Roger A; Wright, Robert J; Alldredge, J Richard; Harsh, James B

    2012-01-01

    Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties. PMID:22218194

  11. Benthic community structure and biomarker responses of the clam Scrobicularia plana in a shallow tidal creek affected by fish farm effluents (Rio San Pedro, SW Spain).

    PubMed

    Silva, Claudio; Mattioli, Mattia; Fabbri, Elena; Yáñez, Eleuterio; Delvalls, T Angel; Martín-Díaz, M Laura

    2012-10-15

    The effects of solid organic wastes from a marine fish farm on sediments were tested using benthic community as ecological indicators and biomarkers in native clam (Scrobicularia plana) as biochemical indicators. The benthic fauna and clam samples were collected in the intertidal sediment in October 2010 from five sites of the Rio San Pedro (RSP) creek, following a gradient of contamination from the aquaculture effluent to the control site. Numbers of species, abundance, richness and Shannon diversity were the biodiversity indicators measured in benthic fauna. Morphological and reproduction status of clams were assessed using the condition factor and gonado-somatic index, respectively. Phase I and Phase II detoxification enzymatic activities (ethoxyresorufin O-deethylase (EROD), glutathione S-transferase (GST)), antioxidant enzymatic activities (glutathione peroxidase (GPX), glutathione reductase (GR)) and oxidative stress parameters (Lipid Peroxidation (LPO) and DNA strand breaks) were measured in clams' digestive gland tissues. In parallel, temperature and salinity in the adjacent water, redox potential, pH and organic matter in sediment, and dissolved oxygen in the interstitial water were measured. The results suggested that RSP showed a spatial gradient characterised by hypoxia/anoxia, reduced potential, acidic conditions and high organic enrichment in sediments at the most contaminated sites. Significant (p<0.05) decrease of biodiversity indicators were observed in the areas impacted by the aquaculture discharges. Biomarkers did not show a clear pattern and of all biochemical responses tested, GPX, DNA damage and LPO were the most sensitive ones and showed significant (p<0.05) increase in the polluted sites. Benthic biodiversity indicators were significantly (p<0.05) positively correlated with pH, redox potential and dissolved oxygen and negatively correlated with organic matter. On the contrary, antioxidant enzymatic responses (GPX) and oxidative stress

  12. Diabetes Connect: Developing a Mobile Health Intervention to Link Diabetes Community Health Workers With Primary Care.

    PubMed

    Cherrington, Andrea L; Agne, April A; Lampkin, Yolanda; Birl, Annie; Shelton, Tanya C; Guzman, Alfredo; Willig, James H

    2015-01-01

    Community health worker (CHW) interventions can help improve diabetes self-management and health outcomes. There is limited evidence on how to effectively integrate CHW programs with primary care efforts. Mobile health technology (mHealth) can connect CHWs to members of the health care team and enhance care. We tested a model for the integration of a CHW-delivered mHealth intervention to improve diabetes self-management. Seventy-two African American patients with diabetes were followed using the mHealth tool. This project partnered an academic institution, a safety-net clinic, and African American churches. The integration of mHealth technology into CHW programs was successfully achieved and readily accepted. PMID:26353025

  13. Linking Environmental Forcing and Trophic Supply to Benthic Communities in the Vercelli Seamount Area (Tyrrhenian Sea)

    PubMed Central

    Covazzi Harriague, Anabella; Bavestrello, Giorgio; Bo, Marzia; Borghini, Mireno; Castellano, Michela; Majorana, Margherita; Massa, Francesco; Montella, Alessandro; Povero, Paolo; Misic, Cristina

    2014-01-01

    Seamounts and their influence on the surrounding environment are currently being extensively debated but, surprisingly, scant information is available for the Mediterranean area. Furthermore, although the deep Tyrrhenian Sea is characterised by a complex bottom morphology and peculiar hydrodynamic features, which would suggest a variable influence on the benthic domain, few studies have been carried out there, especially for soft-bottom macrofaunal assemblages. In order to fill this gap, the structure of the meio-and macrofaunal assemblages of the Vercelli Seamount and the surrounding deep area (northern Tyrrhenian Sea – western Mediterranean) were studied in relation to environmental features. Sediment was collected with a box-corer from the seamount summit and flanks and at two far-field sites in spring 2009, in order to analyse the metazoan communities, the sediment texture and the sedimentary organic matter. At the summit station, the heterogeneity of the habitat, the shallowness of the site and the higher trophic supply (water column phytopigments and macroalgal detritus, for instance) supported a very rich macrofaunal community, with high abundance, biomass and diversity. In fact, its trophic features resembled those observed in coastal environments next to seagrass meadows. At the flank and far-field stations, sediment heterogeneity and depth especially influenced the meiofaunal distribution. From a trophic point of view, the low content of the valuable sedimentary proteins that was found confirmed the general oligotrophy of the Tyrrhenian Sea, and exerted a limiting influence on the abundance and biomass of the assemblages. In this scenario, the rather refractory sedimentary carbohydrates became a food source for metazoans, which increased their abundance and biomass at the stations where the hydrolytic-enzyme-mediated turnover of carbohydrates was faster, highlighting high lability. PMID:25343621

  14. Effects of wetland vs. landscape variables on parasite communities of Rana pipiens: links to anthropogenic factors

    USGS Publications Warehouse

    Schotthoefer, Anna M.; Rohr, Jason R.; Cole, Rebecca A.; Koehler, Anson V.; Johnson, Catherine M.; Johnson, Lucinda B.; Beasley, Val R.

    2011-01-01

    The emergence of several diseases affecting amphibian populations worldwide has prompted investigations into determinants of the occurrence and abundance of parasites in frogs. To understand the spatial scales and identify specific environmental factors that determine risks of parasitism in frogs, helminth communities in metamorphic frogs of the northern leopard frog (Rana pipiens) were examined in relation to wetland and landscape factors at local (1 km) and regional (10 km) spatial extents in an agricultural region of Minnesota (USA) using regression analyses, ordination, and variance partitioning techniques. Greater amounts of forested and woody wetland habitats, shorter distances between woody wetlands, and smaller-sized open water patches in surrounding landscapes were the most consistently positive correlates with the abundances, richness, and diversity of helminths found in the frogs. Wetland and local landscape variables were suggested as most important for larval trematode abundances, whereas local and regional landscape variables appeared most important for adult helminths. As previously reported, the sum concentration of atrazine and its metabolite desethylatrazine, was the strongest predictor of larval trematode communities. In this report, we highlight the additional influences of landscape factors. In particular, our data suggest that anthropogenic activities that have resulted in the loss of the availability and connectivity of suitable habitats in the surrounding landscapes of wetlands are associated with declines in helminth richness and abundance, but that alteration of wetland water quality through eutrophication or pesticide contamination may facilitate the transmission of certain parasite taxa when they are present at wetlands. Although additional research is needed to quantify the negative effects of parasitism on frog populations, efforts to reduce inputs of agrochemicals into wetlands to limit larval trematode infections may be warranted

  15. Linking environmental forcing and trophic supply to benthic communities in the Vercelli Seamount area (Tyrrhenian Sea).

    PubMed

    Covazzi Harriague, Anabella; Bavestrello, Giorgio; Bo, Marzia; Borghini, Mireno; Castellano, Michela; Majorana, Margherita; Massa, Francesco; Montella, Alessandro; Povero, Paolo; Misic, Cristina

    2014-01-01

    Seamounts and their influence on the surrounding environment are currently being extensively debated but, surprisingly, scant information is available for the Mediterranean area. Furthermore, although the deep Tyrrhenian Sea is characterised by a complex bottom morphology and peculiar hydrodynamic features, which would suggest a variable influence on the benthic domain, few studies have been carried out there, especially for soft-bottom macrofaunal assemblages. In order to fill this gap, the structure of the meio-and macrofaunal assemblages of the Vercelli Seamount and the surrounding deep area (northern Tyrrhenian Sea - western Mediterranean) were studied in relation to environmental features. Sediment was collected with a box-corer from the seamount summit and flanks and at two far-field sites in spring 2009, in order to analyse the metazoan communities, the sediment texture and the sedimentary organic matter. At the summit station, the heterogeneity of the habitat, the shallowness of the site and the higher trophic supply (water column phytopigments and macroalgal detritus, for instance) supported a very rich macrofaunal community, with high abundance, biomass and diversity. In fact, its trophic features resembled those observed in coastal environments next to seagrass meadows. At the flank and far-field stations, sediment heterogeneity and depth especially influenced the meiofaunal distribution. From a trophic point of view, the low content of the valuable sedimentary proteins that was found confirmed the general oligotrophy of the Tyrrhenian Sea, and exerted a limiting influence on the abundance and biomass of the assemblages. In this scenario, the rather refractory sedimentary carbohydrates became a food source for metazoans, which increased their abundance and biomass at the stations where the hydrolytic-enzyme-mediated turnover of carbohydrates was faster, highlighting high lability. PMID:25343621

  16. Linking Attitudes, Policy, and Forest Cover Change in Buffer Zone Communities of Chitwan National Park, Nepal

    NASA Astrophysics Data System (ADS)

    Stapp, Jared R.; Lilieholm, Robert J.; Leahy, Jessica; Upadhaya, Suraj

    2016-06-01

    Deforestation in Nepal threatens the functioning of complex social-ecological systems, including rural populations that depend on forests for subsistence, as well as Nepal's biodiversity and other ecosystem services. Nepal's forests are particularly important to the nation's poorest inhabitants, as many depend upon them for daily survival. Two-thirds of Nepal's population relies on forests for sustenance, and these pressures are likely to increase in the future. This, coupled with high population densities and growth rates, highlights the importance of studying the relationship between human communities, forest cover trends through time, and forest management institutions. Here, we used surveys to explore how household attitudes associated with conservation-related behaviors in two rural communities—one that has experienced significant forest loss, and the other forest gain—compare with forest cover trends as indicated by satellite-derived forest-loss and -regeneration estimates between 2005 and 2013. Results found a significant difference in attitudes in the two areas, perhaps contributing to and reacting from current forest conditions. In both study sites, participation in community forestry strengthened support for conservation, forest conservation-related attitudes aligned with forest cover trends, and a negative relationship was found between economic status and having supportive forest conservation-related attitudes. In addition, on average, respondents were not satisfied with their district forest officers and did not feel that the current political climate in Nepal supported sustainable forestry. These findings are important as Nepal's Master Plan for the Forestry Sector has expired and the country is in the process of structuring a new Forestry Sector Strategy.

  17. Determination of neutrophil CD64 expression as a prognostic biomarker in patients with community-acquired pneumonia.

    PubMed

    Burgos, J; Los-Arcos, I; Álvarez de la Sierra, D; Falcó, V; Aguiló, A; Sánchez, I; Almirante, B; Martinez-Gallo, M

    2016-09-01

    The expression of CD64 in neutrophils (nCD64) has shown utility in the diagnosis of sepsis. The aim of this study was to assess the usefulness of nCD64 expression to identify patients with community-acquired pneumonia (CAP) at risk of a poor outcome. A prospective study of nCD64 expression (determined by flow cytometry) in patients with CAP was performed. The sensitivity/specificity of nCD64 in predicting poor outcome [defined as intensive care unit (ICU) admission and/or clinical deterioration after arrival at the emergency department] was calculated. Eighty-three adults with CAP were included; 14.5 % had septic shock, 19.3 % required ICU admission, and 10.8 % presented clinical deterioration after admission. The mean of the median fluorescence intensity (MFI) of nCD64 expression was 1140 (±1097). Patients with nCD64 expression ≥2700 MFI had more clinical deterioration (36.4 vs. 7.2 %, p = 0.015) and more ICU admission (45.5 vs. 14.5 %, p = 0.028). To identify clinical deterioration and ICU admission, nCD64 expression showed a sensitivity of 44.4 and 33.3 % and a specificity of 90.1 and 90.8 %, respectively. The addition of nCD64 expression to the Pneumonia Severity Index and CURB-65 severity scores did not improve the accuracy of predicting these outcomes. Although nCD64 expression is associated with an increased risk of ICU admission or clinical deterioration after admission, its accuracy in predicting these poor outcomes is modest and does not significantly improve the predictive ability of the PSI and CURB-65 severity scores. PMID:27240938

  18. Linking avian communities and avian influenza ecology in southern Africa using epidemiological functional groups

    PubMed Central

    2012-01-01

    The ecology of pathogens, and particularly their emergence in multi-host systems, is complex. New approaches are needed to reduce superficial complexities to a level that still allows scientists to analyse underlying and more fundamental processes. One promising approach for simplification is to use an epidemiological-function classification to describe ecological diversity in a way that relates directly to pathogen dynamics. In this article, we develop and apply the epidemiological functional group (EFG) concept to explore the relationships between wild bird communities and avian influenza virus (AIV) in three ecosystems in southern Africa. Using a two year dataset that combined bird counts and bimonthly sampling for AIV, we allocated each bird species to a set of EFGs that captured two overarching epidemiological functions: the capacity of species to maintain AIV in the system, and their potential to introduce the virus. Comparing AIV prevalence between EFGs suggested that the hypothesis that anseriforms (ducks) and charadriiforms (waders) drive AIV epidemiology cannot entirely explain the high prevalence observed in some EFGs. If anseriforms do play an important role in AIV dynamics in each of the three ecosystems, the role of other species in the local maintenance of AIV cannot be ruled out. The EFG concept thus helped us to identify gaps in knowledge and to highlight understudied bird groups that might play a role in AIV epidemiology. In general, the use of EFGs has potential for generating a range of valuable insights in epidemiology, just as functional group approaches have done in ecology. PMID:23101696

  19. Meeting Report--NASA Radiation Biomarker Workshop

    SciTech Connect

    Straume, Tore; Amundson, Sally A,; Blakely, William F.; Burns, Frederic J.; Chen, Allen; Dainiak, Nicholas; Franklin, Stephen; Leary, Julie A.; Loftus, David J.; Morgan, William F.; Pellmar, Terry C.; Stolc, Viktor; Turteltaub, Kenneth W.; Vaughan, Andrew T.; Vijayakumar, Srinivasan; Wyrobek, Andrew J.

    2008-05-01

    A summary is provided of presentations and discussions from the NASA Radiation Biomarker Workshop held September 27-28, 2007, at NASA Ames Research Center in Mountain View, California. Invited speakers were distinguished scientists representing key sectors of the radiation research community. Speakers addressed recent developments in the biomarker and biotechnology fields that may provide new opportunities for health-related assessment of radiation-exposed individuals, including for long-duration space travel. Topics discussed include the space radiation environment, biomarkers of radiation sensitivity and individual susceptibility, molecular signatures of low-dose responses, multivariate analysis of gene expression, biomarkers in biodefense, biomarkers in radiation oncology, biomarkers and triage following large-scale radiological incidents, integrated and multiple biomarker approaches, advances in whole-genome tiling arrays, advances in mass-spectrometry proteomics, radiation biodosimetry for estimation of cancer risk in a rat skin model, and confounding factors. Summary conclusions are provided at the end of the report.

  20. Using documents to investigate links between implementation and sustainability in a complex community intervention: the PRISM study.

    PubMed

    Willis, Karen; Small, Rhonda; Brown, Stephanie

    2012-10-01

    The increasing imperative to find what works in health services has meant a rise in research trialing interventions deemed 'complex'. While the strength of these interventions comes from taking a 'whole of problem' approach using multiple and inter-linking strategies, ways of examining implementation are under-explored. Building sustainability is an important part of implementing complex intervention research, but this too has received little exploration in the implementation literature. This paper explores issues of implementation and sustainability by examining the case of PRISM (Program of Resources, Information and Support for Mothers), a community randomised trial in Victoria, Australia aimed at improving maternal health and wellbeing. It examines documents placed on the project website. Three groups of documents relating to implementation of the intervention were examined - implementation reports, media reports and community newsletters. Analysing these documents allowed a focus on the 'work' of the intervention - who does the work and what activities comprise the work - in order to examine implementation as it relates to sustainability. Document analysis provides a useful way of considering implementation and sustainability of complex intervention research. It can 'value add' to findings from process evaluation and extend our understanding of an intervention beyond outcome measures. Analysis of the documents in this case provides insights into why sustainability of an intervention may be difficult to achieve during implementation. PMID:22749443

  1. ISOGENIE: Linking geochemistry, isotopic chemistry and microbial dynamics & community composition in a thawing permafrost peatland, Stordalen Mire, Abisco, Sweden.

    NASA Astrophysics Data System (ADS)

    Chanton, J.; Crill, P. M.; Rich, V.; McCalley, C. K.; Hodgkins, S. B.; Tyson, G.; Logan, T.; Wehr, R.; Mondav, R.; Li, C.; Frolking, S.; Saleska, S. R.

    2011-12-01

    As permafrost thaws, increasing CH4 emissions from northern wetlands are likely to cause positive feedback to atmospheric warming. One of the over-arching goals of this project is to connect geochemical processes, particularly focusing on methane production, to underlying microbial population dynamics and genomics. Recent transformative technical advances in both high throughput investigations of microbial communities and high temporal resolution biogeochemical isotope measurements now permit a uniquely comprehensive approach to opening the microbial "black boxes" that impact carbon cycling on global scales. This project links detailed microbial sampling with detailed geochemical and isotopic sampling on seasonal and diel timescales and has an extensive modeling component. Gas exchange is monitored across the wetland gradients in a series of automated chambers and isotopes of emitted and belowground methane and carbon dioxide are measured with a QC laser system. The mire is in a state of partial thaw. With this thaw is an apparent ecological session in wetland community structure and associated changes in organic matter lability, rates of methane production and microbial community. Our group's study sites range from palsa with underlying permanently frozen peat, to recently collapsed and flooded palsa, to flooded palsa colonized by Sphagnum, to flooded eriophorum sites, to sites populated by Carex, to open water lakes. Across this environmental gradient pH ranges from 4 to 6.5. This change is driven by changes in hydrology as the surface of the thawing permafrost subsides and an adjacent lake drains into the mire. Along this environmental gradient, from palsa to Carex, the lability of the peat increases significantly as determined in incubations of peat material and monitoring of methane and carbon dioxide production rates. Coincident with this environmental gradient is a decrease in the apparent fractionation factor between methane and carbon dioxide and methane

  2. Linking Hydro-Meteorological Hazards, Climate and Food Security: an Initiative of International Scientific Community

    NASA Astrophysics Data System (ADS)

    Ismail-Zadeh, A.; Beer, T.

    2013-05-01

    Humans face climatic and hydro-meteorological hazards on different scales in time and space. In particular natural hazards can have disastrous impact in the short term (flood) and in the long term (drought) as they affect human life and health as well as impacting dramatically on the sustainable development of society. They represent a pending danger for vulnerable lifelines, infrastructure and the agricultural systems that depend on the water supply, reservoirs, pipelines, and power plants. Developed countries are affected, but the impact is disproportionate within the developing world. Extreme natural events such as extreme floods or prolonged drought can change the life and economic development of developing nations and stifle their development for decades. The beginning of the XX1st century has been marked by a significant number of natural disasters, such as floods, severe storms, wildfires, hurricanes, and tsunamis. Extreme natural events cause devastation resulting in loss of human life, large environmental damage, and partial or total loss of infrastructure that, in the longer time, will affect the potential for agricultural recovery. Recent catastrophic events of the early 21st century (e.g. floods in Pakistan and Thailand, the 2011 Tohoku earthquake and tsunami) remind us once again that there is a strong coupling between complex solid Earth, oceanic, and atmospheric processes and that even developed countries such as Japan are subject to agricultural declines as a result of disastrous hydro-meteorological events. Scientific community recognizes that communication between the groups of experts of various international organizations dealing with natural hazards and their activity in disaster risk reduction and food security needs to be strengthened. Several international scientific unions and intergovernmental institutions set up a consortium of experts to promote studies of weather, climate and their interaction with agriculture, food and their socio

  3. Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community

    PubMed Central

    Gifford, Scott M.; Sharma, Shalabh; Moran, Mary Ann

    2014-01-01

    For bacterial communities containing hundreds to thousands of distinct populations, connecting functional processes and environmental dynamics at high taxonomic resolution has remained challenging. Here we use the expression of ribosomal proteins (%RP) as a proxy for in situ activity of 200 taxa within 20 metatranscriptomic samples in a coastal ocean time series encompassing both seasonal variability and diel dynamics. %RP patterns grouped the taxa into seven activity clusters with distinct profiles in functional gene expression and correlations with environmental gradients. Clusters 1–3 had their highest potential activity in the winter and fall, and included some of the most active taxa, while Clusters 4–7 had their highest potential activity in the spring and summer. Cluster 1 taxa were characterized by gene expression for motility and complex carbohydrate degradation (dominated by Gammaproteobacteria and Bacteroidetes), and Cluster 2 taxa by transcription of genes for amino acid and aromatic compound metabolism and aerobic anoxygenic phototrophy (Roseobacter). Other activity clusters were enriched in transcripts for proteorhodopsin and methylotrophy (Cluster 4; SAR11 and methylotrophs), photosynthesis and attachment (Clusters 5 and 7; Synechococcus, picoeukaryotes, Verucomicrobia, and Planctomycetes), and sulfur oxidation (Cluster 7; Gammaproteobacteria). The seasonal patterns in activity were overlain, and sometimes obscured, by large differences in %RP over shorter day-night timescales. Seventy-eight taxa, many of them heterotrophs, had a higher %RP activity index during the day than night, indicating a strong diel activity rhythm at this coastal site. Emerging from these taxonomically- and time-resolved estimates of in situ microbial activity are predictions of specific ecological groupings of microbial taxa in a dynamic coastal environment. PMID:24795712

  4. Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in Streamer Biofilm Communities in the Lower Geyser Basin, Yellowstone National Park.

    PubMed

    Schubotz, F; Meyer-Dombard, D R; Bradley, A S; Fredricks, H F; Hinrichs, K-U; Shock, E L; Summons, R E

    2013-11-01

    Detailed analysis of 16S rRNA and intact polar lipids (IPLs) from streamer biofilm communities (SBCs), collected from geochemically similar hot springs in the Lower Geyser Basin, Yellowstone National Park, shows good agreement and affirm that IPLs can be used as reliable markers for the microbial constituents of SBCs. Uncultured Crenarchaea are prominent in SBS, and their IPLs contain both glycosidic and mixed glyco-phospho head groups with tetraether cores, having 0-4 rings. Archaeal IPL contributions increase with increasing temperature and comprise up to one-fourth of the total IPL inventory at >84 °C. At elevated temperatures, bacterial IPLs contain abundant glycosidic glycerol diether lipids. Diether and diacylglycerol (DAG) lipids with aminopentanetetrol and phosphatidylinositol head groups were identified as lipids diagnostic of Aquificales, while DAG glycolipids and glyco-phospholipids containing N-acetylgycosamine as head group were assigned to members of the Thermales. With decreasing temperature and concomitant changes in water chemistry, IPLs typical of phototrophic bacteria, such as mono-, diglycosyl, and sulfoquinovosyl DAG, which are specific for cyanobacteria, increase in abundance, consistent with genomic data from the same samples. Compound-specific stable carbon isotope analysis of IPL breakdown products reveals a large isotopic diversity among SBCs in different hot springs. At two of the hot springs, 'Bison Pool' and Flat Cone, lipids derived from Aquificales are enriched in (13) C relative to biomass and approach values close to dissolved inorganic carbon (DIC) (approximately 0‰), consistent with fractionation during autotrophic carbon fixation via the reversed tricarboxylic acid pathway. At a third site, Octopus Spring, the same Aquificales-diagnostic lipids are 10‰ depleted relative to biomass and resemble stable carbon isotope values of dissolved organic carbon (DOC), indicative of heterotrophy. Other bacterial and archaeal lipids show

  5. Imaging Biomarkers or Biomarker Imaging?

    PubMed Central

    Mitterhauser, Markus; Wadsak, Wolfgang

    2014-01-01

    Since biomarker imaging is traditionally understood as imaging of molecular probes, we highly recommend to avoid any confusion with the previously defined term “imaging biomarkers” and, therefore, only use “molecular probe imaging (MPI)” in that context. Molecular probes (MPs) comprise all kinds of molecules administered to an organism which inherently carry a signalling moiety. This review highlights the basic concepts and differences of molecular probe imaging using specific biomarkers. In particular, PET radiopharmaceuticals are discussed in more detail. Specific radiochemical and radiopharmacological aspects as well as some legal issues are presented. PMID:24967536

  6. Linked Learning in Porterville: Creating Capacity for Innovation and Change through Collaborative Leadership and Community Engagement. Linked Learning Case Study Series

    ERIC Educational Resources Information Center

    Rustique, Elle; Rutherford-Quach, Sara

    2012-01-01

    This case study describes how Porterville Unified School District (PUSD), a rural school district in California's Central Valley, began to fulfill its vision to transform high school and career education through the implementation of Linked Learning. Linked Learning is a state-wide initiative for redesigning large comprehensive high schools into…

  7. Traditional uses of plants in a rural community of Mozambique and possible links with Miombo degradation and harvesting sustainability

    PubMed Central

    2014-01-01

    Background Miombo woodlands play an important role in the livelihood of people living in sub-equatorial African countries, contributing to satisfy basic human needs such as food, medicine, fuelwood and building materials. However, over-exploitation of plant resources and unsustainable harvest practices can potentially degrade forests. The aim of this study was to document the use of Miombo plant products, other than medicinal plants, in local communities, within a wider framework in which we discussed possible links between traditional uses and conservation status of the used species and of the whole Miombo environment. Methods Fieldwork took place in four communities of Muda-Serração, central Mozambique. We conducted semi-structured interviews with 52 informants about their knowledge, use and harvesting practices of useful plants. A survey on local Miombo vegetation was also carried out in order to assess abundance and distribution of useful woody plants cited in the interviews in areas exposed to different exploitation rates. A Conservation Priority index was also applied to rank conservation values of each used woody species. Results Ninety-eight plants cited by the informants were botanically identified. The most relevant general category was represented by food plants (45 species), followed by handicraft plants (38 species) and domestic plants (37 species). Among the 54 woody species observed in vegetation plots, 52% were cited as useful in the interviews. Twenty-six woody species found in ‘natural’ Miombo areas were not found in ‘degraded’ ones: of these, 46% were cited in the interviews (58% in the food category, 50% in the handicraft category, 25% in the domestic category and 8% in the fishing category). Results of conservation ranking showed that 7 woody species deserve conservation priority in the investigated area. Conclusions This study shows that the communities investigated rely heavily on local forest products for their daily subsistence

  8. DOES LOWER SUBJECTIVE SOCIAL STATUS YIELD RISKIER BIOMARKER PROFILES?

    PubMed

    Gersten, Omer; Timiras, Paola S; Boyce, W Thomas

    2015-11-01

    Both objective and, more recently, subjective measures of low social status have been linked to poor health outcomes. It is unclear, however, through which precise physiological mechanisms such standing may influence health, although it has been proposed that those of lower status may have biomarker profiles that are more dysregulated (and hence pose a greater risk for poorer health). The main objective of this study was to investigate whether lower subjective social standing is associated with riskier neuroendocrine biomarker profiles. Data were from the Social Environment and Biomarkers of Aging Study (SEBAS), a nationally representative survey of Taiwanese men and women (ages 54-91) conducted in Taiwan in 2000. Five neuroendocrine markers (cortisol, dehydroepiandrosterone sulphate (DHEAS), adrenaline, noradrenaline and dopamine) were analysed both separately and collectively in an index termed neuroendocrine allostatic load (NAL) in relation to status - both self-reported and as measured through objective socioeconomic status (SES) indicators. For the biomarker DHEAS, some connection was found between its levels and the measures of status, but for the other markers and the NAL index almost no connection was found. The overall negative finding of this paper would be further supported with more and different measures of neuroendocrine system function and a reordering of the subjective social status questions in the survey such that the one probing about status in the community (that has no prompt) was asked before the one probing about status in all of Taiwan (which has a SES prompt). PMID:25287447

  9. Implementation of proteomic biomarkers: making it work

    PubMed Central

    Mischak, Harald; Ioannidis, John PA; Argiles, Angel; Attwood, Teresa K; Bongcam-Rudloff, Erik; Broenstrup, Mark; Charonis, Aristidis; Chrousos, George P; Delles, Christian; Dominiczak, Anna; Dylag, Tomasz; Ehrich, Jochen; Egido, Jesus; Findeisen, Peter; Jankowski, Joachim; Johnson, Robert W; Julien, Bruce A; Lankisch, Tim; Leung, Hing Y; Maahs, David; Magni, Fulvio; Manns, Michael P; Manolis, Efthymios; Mayer, Gert; Navis, Gerjan; Novak, Jan; Ortiz, Alberto; Persson, Frederik; Peter, Karlheinz; Riese, Hans H; Rossing, Peter; Sattar, Naveed; Spasovski, Goce; Thongboonkerd, Visith; Vanholder, Raymond; Schanstra, Joost P; Vlahou, Antonia

    2012-01-01

    While large numbers of proteomic biomarkers have been described, they are generally not implemented in medical practice. We have investigated the reasons for this shortcoming, focusing on hurdles downstream of biomarker verification, and describe major obstacles and possible solutions to ease valid biomarker implementation. Some of the problems lie in suboptimal biomarker discovery and validation, especially lack of validated platforms with well-described performance characteristics to support biomarker qualification. These issues have been acknowledged and are being addressed, raising the hope that valid biomarkers may start accumulating in the foreseeable future. However, successful biomarker discovery and qualification alone does not suffice for successful implementation. Additional challenges include, among others, limited access to appropriate specimens and insufficient funding, the need to validate new biomarker utility in interventional trials, and large communication gaps between the parties involved in implementation. To address this problem, we propose an implementation roadmap. The implementation effort needs to involve a wide variety of stakeholders (clinicians, statisticians, health economists, and representatives of patient groups, health insurance, pharmaceutical companies, biobanks, and regulatory agencies). Knowledgeable panels with adequate representation of all these stakeholders may facilitate biomarker evaluation and guide implementation for the specific context of use. This approach may avoid unwarranted delays or failure to implement potentially useful biomarkers, and may expedite meaningful contributions of the biomarker community to healthcare. PMID:22519700

  10. Linking International Development Actors to Geophysical Infrastructure: Exploring an IRIS Community Role in Bridging a Communications Gap

    NASA Astrophysics Data System (ADS)

    Lerner-Lam, A.; Aster, R.; Beck, S.; Ekstrom, G.; Fisher, K.; Meltzer, A.; Nyblade, A.; Sandvol, E.; Willemann, R.

    2008-12-01

    Over the past quarter century, national investments in high-fidelity digital seismograph networks have resulted in a global infrastructure for real-time in situ earthquake monitoring. Many network operators adhere to community-developed standards, with the result that there are few technical impediments to data sharing and real-time information exchange. Two unanswered questions, however, are whether the existing models of international collaboration will ensure the stability and sustainability of global earthquake monitoring, and whether the participating institutions can work with international development agencies and non- governmental organizations in meeting linked development and natural hazard risk reduction goals. Since the 2004 Indian Ocean tsunami, many of these actors are enlarging their commitments to natural hazard risk reduction and building national technical capacities, among broader programs in poverty alleviation and adaptation to environmental stress. Despite this renewed commitment, international development organizations, with notable exceptions, have been relatively passive in discussions of how the existing earthquake monitoring infrastructure could be leveraged to support risk-reduction programs and meet sustainable development goals. At the same time, the international seismological community - comprising universities and government seismological surveys - has built research and education initiatives such as EarthScope, AfricaArray, and similar programs in China, Europe and South America, that use innovative instrumentation technologies and deployment strategies to enable new science and applications, and promote education and training in critical sectors. Can these developments be combined? Recognizing this communication or knowledge gap, the IRIS International Working Group (IWG) explores the link between the activities of IRIS Members using IRIS facilities and the missions of international development agencies, such as US AID, the World

  11. Regional Approach for Linking Ecosystem Services and Livelihood Strategies Under Climate Change of Pastoral Communities in the Mongolian Steppe Ecosystem

    NASA Astrophysics Data System (ADS)

    Ojima, D. S.; Galvin, K.; Togtohyn, C.

    2012-12-01

    Dramatic changes due to climate and land use dynamics in the Mongolian Plateau affecting ecosystem services and agro-pastoral systems in Mongolia. Recently, market forces and development strategies are affecting land and water resources of the pastoral communities which are being further stressed due to climatic changes. Evaluation of pastoral systems, where humans depend on livestock and grassland ecosystem services, have demonstrated the vulnerability of the social-ecological system to climate change. Current social-ecological changes in ecosystem services are affecting land productivity and carrying capacity, land-atmosphere interactions, water resources, and livelihood strategies. The general trend involves greater intensification of resource exploitation at the expense of traditional patterns of extensive range utilization. Thus we expect climate-land use-land cover relationships to be crucially modified by the social-economic forces. The analysis incorporates information about the social-economic transitions taking place in the region which affect land-use, food security, and ecosystem dynamics. The region of study extends from the Mongolian plateau in Mongolia. Our research indicate that sustainability of pastoral systems in the region needs to integrate the impact of climate change on ecosystem services with socio-economic changes shaping the livelihood strategies of pastoral systems in the region. Adaptation strategies which incorporate integrated analysis of landscape management and livelihood strategies provides a framework which links ecosystem services to critical resource assets. Analysis of the available livelihood assets provides insights to the adaptive capacity of various agents in a region or in a community. Sustainable development pathways which enable the development of these adaptive capacity elements will lead to more effective adaptive management strategies for pastoral land use and herder's living standards. Pastoralists will have the

  12. 14,000 Miles Between Us: Linking Polar Regions and Climate Change Science with Classrooms and Communities Around the World

    NASA Astrophysics Data System (ADS)

    Roop, H. A.

    2011-12-01

    Understanding environmental change in the polar regions is a key research topic for thousands of scientists around the world. Despite the wealth of research and knowledge the scientific community has about these highly sensitive regions, this knowledge is rarely shared directly in classrooms or with the public. In order to increase awareness and engagement in polar science, the West Antarctic Ice Sheet (WAIS) Divide Ice Core Project focused heavily on outreach and education during the 2009-2010 and 2010-2011 field campaigns. With the support of two National Science Foundation-funded outreach projects, including PolarTREC (Teachers and Researchers Exploring and Collaborating) and the Exploratorium's "Ice Stories", thousands of elementary- to college-aged students were direct participants in this Antarctic ice core science. WAIS Divide research was communicated using online journals, short video clips, live webinars from the field, and scientist visits to classrooms. Using the platform of ice core science, and linking the similarities between everyday life at home and in the field, allowed for the effective communication of the excitement and importance of polar science research. Examples of this educational content, classroom ideas, and creative field techniques will help demonstrate the utility of using exciting field science to increase engagement in science and research. Ultimately, by creatively using a model similar to that of the PolarTREC and Ice Stories programs, polar scientists can easily incorporate meaningful education and outreach into their field programs.

  13. Combined use of Daphnia magna in situ bioassays, biomarkers and biological indices to diagnose and identify environmental pressures on invertebrate communities in two Mediterranean urbanized and industrialized rivers (NE Spain).

    PubMed

    Damásio, Joana; Tauler, Romà; Teixidó, Elisabeth; Rieradevall, Maria; Prat, Narcis; Riva, Maria Carmen; Soares, Amadeu M V M; Barata, Carlos

    2008-05-30

    Environmental factors affecting aquatic invertebrate communities were assessed using Daphnia magna in situ bioassays and biological indices based on community assemblages of benthic macroinvertebrates. Investigations were carried out in two heavily industrialized and urbanized river basins from the NE of Spain (Llobregat and Besós). Measures of energy consumption (i.e. algal grazing), and of specific biochemical responses (biomarkers) were conducted on individuals transplanted upstream and downstream from effluent discharges of sewage treatment plants. In both rivers there was a clear deterioration of the ecological water quality parameters and benthic communities towards downstream reaches. In all but one of the 19 locations studied, transplanted organisms were affected in at least one of the five measured responses. In three of them, significant effects were detected in most of the traits considered. Principal Component and Partial Least Square Projections to Latent Structures regression analyses indicated that the measured responses in D. magna in situ bioassays and those of macroinvertebrate assemblages were affected by distinct environmental factors. From up to 20 environmental variables considered, seven of them including habitat degradation, suspended solids, nitrogenous and conductivity related parameters affected macroinvertebrate assemblages. On the other hand, levels of organophosphorus compounds and polycyclic aromatic hydrocarbons were high enough to trigger the responses of D. magna in situ bioassays. These results emphasize the importance of combining biological indices with biomarkers and more generalized and ecologically relevant (grazing) in situ responses to identify ecological effects of effluent discharges from sewage treatment plants in surface waters. PMID:18420289

  14. Aggregated silver nanoparticles based surface-enhanced Raman scattering enzyme-linked immunosorbent assay for ultrasensitive detection of protein biomarkers and small molecules.

    PubMed

    Liang, Jiajie; Liu, Hongwu; Huang, Caihong; Yao, Cuize; Fu, Qiangqiang; Li, Xiuqing; Cao, Donglin; Luo, Zhi; Tang, Yong

    2015-06-01

    Lowering the detection limit is critical to the design of bioassays required for medical diagnostics, environmental monitoring, and food safety regulations. The current sensitivity of standard color-based analyte detection limits the further use of enzyme-linked immunosorbent assays (ELISAs) in research and clinical diagnoses. Here, we demonstrate a novel method that uses the Raman signal as the signal-generating system of an ELISA and combines surface-enhanced Raman scattering (SERS) with silver nanoparticles aggregation for ultrasensitive analyte detection. The enzyme label of the ELISA controls the dissolution of Raman reporter-labeled silver nanoparticles through hydrogen peroxide and generates a strong Raman signal when the analyte is present. Using this assay, prostate-specific antigen (PSA) and the adrenal stimulant ractopamine (Rac) were detected in whole serum and urine at the ultralow concentrations of 10(-9) and 10(-6) ng/mL, respectively. The methodology proposed here could potentially be applied to other molecules detection as well as PSA and Rac. PMID:25928837

  15. Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment.

    PubMed

    Nguyen, Nhu H; Williams, Laura J; Vincent, John B; Stefanski, Artur; Cavender-Bares, Jeannine; Messier, Christian; Paquette, Alain; Gravel, Dominique; Reich, Peter B; Kennedy, Peter G

    2016-08-01

    Exploring the link between above- and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well-recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field-based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant-associated effects on soil fungal communities are largely guild-specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness. PMID:27284759

  16. The missing link.

    PubMed

    Dracup, Kathleen

    2002-06-01

    The uniqueness of nursing research is derived from the philosophical view of the individual as a biopsychosocial being. Nurse scientists are prepared to illuminate the linkages among the biophysiological, psychological, and social domains, and this study is much enhanced by the increasing availability of valid and reliable biomarkers. Researchers need to develop expertise in the use of biomarkers and secure appropriate funding for their use. Missing links may be missing no longer. PMID:12122766

  17. Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone.

    PubMed

    Peay, Kabir G; Kennedy, Peter G; Davies, Stuart J; Tan, Sylvester; Bruns, Thomas D

    2010-01-01

    *Relatively little is known about diversity or structure of tropical ectomycorrhizal communities or their roles in tropical ecosystem dynamics. In this study, we present one of the largest molecular studies to date of an ectomycorrhizal community in lowland dipterocarp rainforest. *We sampled roots from two 0.4 ha sites located across an ecotone within a 52 ha forest dynamics plot. Our plots contained > 500 tree species and > 40 species of ectomycorrhizal host plants. Fungi were identified by sequencing ribosomal RNA genes. *The community was dominated by the Russulales (30 species), Boletales (17), Agaricales (18), Thelephorales (13) and Cantharellales (12). Total species richness appeared comparable to molecular studies of temperate forests. Community structure changed across the ecotone, although it was not possible to separate the role of environmental factors vs host plant preferences. Phylogenetic analyses were consistent with a model of community assembly where habitat associations are influenced by evolutionary conservatism of functional traits within ectomycorrhizal lineages. *Because changes in the ectomycorrhizal fungal community parallel those of the tree community at this site, this study demonstrates the potential link between the distribution of tropical tree diversity and the distribution of tropical ectomycorrhizal diversity in relation to local-scale edaphic variation. PMID:19878464

  18. LINKING EXPOSURES TO INTERNAL DOSES USING BIOMARKERS

    EPA Science Inventory

    Biomonitoring is a useful tool to help assess human exposures/internal doses to chemicals in the environment. This research contributes to EPA's mission to protect human health by understanding what chemicals people are exposed to in their daily environments. In this task, we wil...

  19. Utile or futile: biomarkers in the ICU.

    PubMed

    Balmelli, Cathrin; Drexler, Beatrice; Mueller, Christian

    2011-01-01

    Biomarkers complement other clinical information by proving quantitative data regarding a pathophysiological mechanism that can be used for the early diagnosis of a specific disease, to monitor and guide treatment, and to predict the risk of death or other adverse events. The stronger the link between the information provided by the biomarker and the immediate clinical course of action that we physicians take in response, the higher the clinical utility of the biomarker. This link is weakest for prognostic biomarkers applied in patients with a wide variety of diseases, such as in unselected intensive care unit (ICU) patients. Although the added value on top of current ICU mortality scores seems to be too low to justify clinical use, the observation that hemodynamic cardiac stress and inflammation are present in multiple conditions provides important insights into the pathophysiology of common disorders in the ICU. PMID:21457515

  20. Parasites of flounder (Platichthys flesus L.) from the German Bight, North Sea, and their potential use in biological effects monitoring. C. Pollution effects on the parasite community and a comparison to biomarker responses

    NASA Astrophysics Data System (ADS)

    Schmidt, V.; Zander, S.; Körting, W.; Broeg, K.; von Westernhagen, H.; Dizer, H.; Hansen, P. D.; Skouras, A.; Steinhagen, D.

    2003-10-01

    In the frame of an integrated biological effect monitoring programme, the parasite community of flounder (Platichthys flesus) was investigated at different locations in the German Bight from 1995 to 2000. In order to assess the impact of environmental contamination caused by anthropogenic activities on the parasite community, selected parasitological parameters that displayed significant differences between the sampling sites were subjected to correlation analyses with site-specific contamination and individual pollution loads of their fish hosts. In addition, correlation analyses were conducted with the responses of selected genetic, biochemical, histopathological, physiological and immunological parameters of fish, used as potential biomarkers. In total, 802 flounder were analysed for these parameters. Information on the chemical background at the sampling sites was derived from sediment samples and from 120 samples of blue mussel (Mytilus edulis) tissue, collected at each of the sampling sites. Based on chemical data available from the sediment and blue mussel samples, a pollution gradient could be established between the sampling sites for individual contaminants. The relative abundance of Acanthochondria cornuta, Cucullanus heterochrous and Zoogonoides viviparus, and the community measures species richness and number of heteroxenous species decreased with increasing concentrations of individual heavy metals or hydrocarbons in sediment and blue mussel samples. Most of the parasitological parameters significantly reflected the established site-specific contamination gradient, when data were pooled over all sampling campaigns. Significant correlations were also found with the contamination level of individual flounder. The parasitological parameters included the parasite species Lepeophtheirus pectoralis and Lernaeocera branchialis, which were not correlated to site-specific contamination. Several biomarkers were significantly correlated to the abundance of

  1. Broadening and Deepening the Definition of Outreach Scholarship: Linking Popular Education and Community-Based Participatory Action Research

    ERIC Educational Resources Information Center

    Rai, Kalyani

    2003-01-01

    This paper outlines a Community-based Participatory Action Research model designed and implemented by the University of Wisconsin-Milwaukee School of Continuing Education with two community-based agencies in Milwaukee. In two participatory action learning seminars, research was combined with action to improve the educational experience of…

  2. Creating Links, "Atando Cabitos:" Connecting Parents, Communities, and Future Teachers on the U.S./Mexico Border

    ERIC Educational Resources Information Center

    de la Piedra, Maria Teresa; Munter, Judith Hope; Giron, Hector

    2006-01-01

    This article provides an overview of the conceptual framework and preliminary findings from a compendium of studies on school-university-community partnerships in Latino communities, with a focus on lessons learned on the U.S./Mexico border. The voices of professors, school administrators, and students with whom the co-authors have worked over a…

  3. Improving community development by linking agriculture, nutrition and education: design of a randomised trial of “home-grown” school feeding in Mali

    PubMed Central

    2013-01-01

    Background Providing food through schools has well documented effects in terms of the education, health and nutrition of school children. However, there is limited evidence in terms of the benefits of providing a reliable market for small-holder farmers through “home-grown” school feeding approaches. This study aims to evaluate the impact of school feeding programmes sourced from small-holder farmers on small-holder food security, as well as on school children’s education, health and nutrition in Mali. In addition, this study will examine the links between social accountability and programme performance. Design This is a field experiment planned around the scale-up of the national school feeding programme, involving 116 primary schools in 58 communities in food insecure areas of Mali. The randomly assigned interventions are: 1) a school feeding programme group, including schools and villages where the standard government programme is implemented; 2) a “home-grown” school feeding and social accountability group, including schools and villages where the programme is implemented in addition to training of community based organisations and local government; and 3) the control group, including schools and household from villages where the intervention will be delayed by at least two years, preferably without informing schools and households. Primary outcomes include small-holder farmer income, school participation and learning, and community involvement in the programme. Other outcomes include nutritional status and diet-diversity. The evaluation will follow a mixed method approach, including household, school and village level surveys as well as focus group discussions with small-holder farmers, school children, parents and community members. The impact evaluation will be incorporated within the national monitoring and evaluation (M&E) system strengthening activities that are currently underway in Mali. Baselines surveys are planned for 2012. A monthly

  4. Achieving Synergy: Linking an Internet-Based Inflammatory Bowel Disease Cohort to a Community-Based Inception Cohort and Multicentered Cohort in Inflammatory Bowel Disease

    PubMed Central

    Aldridge, Molly; Cook, Suzanne Follan; Bright, Renee; Mallette, Meaghan; Moniz, Heather; Shah, Samir A; LeLeiko, Neal S; Shapiro, Jason; Sands, Bruce E; Chen, Wenli; Jaeger, Elizabeth; Galanko, Joseph; Long, Millie D; Martin, Christopher F; Sandler, Robert S; Kappelman, Michael D

    2016-01-01

    doctoral degrees, P=.01). In the SHARE cohort, 436 participants enrolled and linked to the Partners cohort. More women (60% vs 50%) linked and those who linked were predominantly white (96%; P<.01). Crohn’s disease patients who linked had lower mean scores on the Harvey-Bradshaw Index (3.6 vs 4.4, P<.01). Ulcerative colitis patients who linked had less extensive disease than those who did not link (45% vs 60%, P<.01). Conclusions Linkage of CCFA Partners with cohorts such as OSCCAR and SHARE may be a cost-effective way to expand the infrastructure for clinical outcomes and translational research. Although linkage is feasible from a technical, legal, and regulatory perspective, participant willingness appears to be a limiting factor. Overcoming this barrier will be needed to generate meaningful sample sizes to conduct studies of biomarkers, natural history, and clinical effectiveness using linked data. PMID:27261008

  5. Linking microbial community structure and function to characterize antibiotic resistant bacteria and antibiotic resistant genes from cattle feces

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is widespread interest in monitoring the development of antibiotic resistant bacteria and antibiotic resistance genes in agriculturally impacted environments, however little is known about the relationships between bacterial community structure, and antibiotic resistance gene profiles. Cattl...

  6. Final Report for Award #0006731. Modeling, Patterning and Evolving Syntrophic Communities that Link Fermentation to Metal Reduction

    SciTech Connect

    Marx, Christopher J.

    2015-07-17

    This project has developed and combined mathematical models, multi-species consortia, and spatially structured environments as an approach for studying metabolic exchange in communities like the ones between fermenters and metal reducers. We have developed novel, broadly-applicable tools for following community dynamics, come to a better understanding of both sugar and lactate-utilization in S. oneidensis, the interactions between carbon and mineral availability, and have a methodology for cell printing to match with spatiotemporal models of consortia metabolism.

  7. Modeling water, ecosystems, economics and culture in traditional acequia irrigation communities of New Mexico and their linked watersheds

    NASA Astrophysics Data System (ADS)

    Fernald, A.; Tidwell, V. C.; Rivera, J.; Rodriguez, S.; Guldan, S.; Steele, C. M.; Ochoa, C. G.; Hurd, B. H.; Ortiz, M.; Boykin, K.; Cibils, A.

    2012-12-01

    Water scarcity, land use conversion, and cultural and ecosystem changes threaten the way of life for traditional irrigation communities of the semi-arid southwestern United States. Nowhere are traditions as strong or potential upheaval as great as in these communities that rely on acequia irrigation systems. Acequias are ancient ditch systems brought from the Iberian Peninsula to the New World over 400 years ago; they are simultaneously gravity flow water delivery systems and shared water governance institutions. Acequias have survived periods of drought and external shocks from changing economics, demographics, and resource uses. Now, climate change and urbanization threaten water availability, ecosystem functions, and the acequia communities themselves. To explore this issue we translated disciplinary understanding into a uniform format of causal loop diagrams to conceptualize the subsystems of the entire acequia-based human-natural system. Four subsystems are identified in this study: hydrology, ecology, land use/economics, and sociocultural. Important linkages between subsystems were revealed as well as variables indicating community cohesion (e.g., total irrigated land, intensity of upland grazing, mutualism). These results will be tested with field data and modeling exercises to capture tipping points for non-sustainability and thresholds for sustainable water use and community longevity.

  8. Linking phytoplankton community size composition with temperature, plankton food web structure and sea-air CO 2 flux

    NASA Astrophysics Data System (ADS)

    Hilligsøe, Karen Marie; Richardson, Katherine; Bendtsen, Jørgen; Sørensen, Lise-Lotte; Nielsen, Torkel Gissel; Lyngsgaard, Maren Moltke

    2011-08-01

    Data collected at open water stations (depth>400 m) in all major ocean basins in 2006-2008 are used to examine the relationship between the size structure of the phytoplankton community (determined by size fractionated chlorophyll filtration), temperature and inorganic nutrient availability. A significant relationship ( p<0.0005) was found between community size structure and temperature, with the importance of large cells in the community decreasing with increase in temperature. Although weaker than the temperature relationship, significant relationships were also noted between community cell size and DIN (nitrate, nitrite and ammonium: p=0.034) and phosphate ( p=0.031) concentrations. When the data were divided into two groups of equal size, representing the samples with the highest and lowest DIN/phosphate concentrations, respectively, no difference could be identified between the slopes of the lines representing the relationship between size structure and temperature. There was, however, a difference in the intercepts between the two groups. If the relationship between size and temperature was only a response to nutrient availability, we would expect that the response would be the strongest in the groups with the lowest nutrient concentrations. These results suggest that, in addition to a nutrient effect, temperature may also directly influence the size structure of phytoplankton communities. The size structure of the phytoplankton community in this study correlated to the magnitude of primary production, export production (determined after Laws et al., 2000) and integrated water column chlorophyll. Significant relationships were also found between mesozooplankton production (determined using the proxy of calanoid+cyclopoid nauplii abundance as a percentage of the total number of these copepods) and both temperature and phytoplankton size, with production being the lowest in the warmest waters where phytoplankton were the smallest. In the North Atlantic, export

  9. Hospital-based community outreach to medically isolated elders. The nurse gerontologist is a key link in this health care delivery system in Wisconsin.

    PubMed

    Haworth, M J

    1993-01-01

    The development of a hospital-based community outreach nursing program has been beneficial for St. Mary's Hospital in several ways. The outreach program has served a community need in that many elderly persons who were previously medically isolated have now been located and linked to the health care delivery system. The outreach program has reinforced the hospital's presence and leadership role in the community through its work with the elderly population. The hospital is seen as being committed to bringing health care services to its elderly neighbors. Through the establishment and coordination of health care services to previously isolated and unconnected elderly persons, there has been a broadened revenue base for hospital operations. The outreach program also supports the mission, philosophy, and objectives of the Daughters of Charity. The efforts of this outreach program have shown that high-quality, accessible, and coordinated care for the elderly population may be obtained using a nurse gerontologist. Efforts to expand the market share of elderly persons by the hospital has continued through the development of other innovative health programs, resources, and services. Hospital administrators need to develop programs and services that effectively utilize limited health care dollars and resources to improve the quality of health care within the community. PMID:8383077

  10. Linking School and Community To Build National Recruitment and Preparation Programs for Teachers of Color: Emerging Leadership Qualities.

    ERIC Educational Resources Information Center

    Hudson, Mildred J.

    1998-01-01

    Discusses the emerging leadership qualities needed to establish and administer programs to recruit and prepare teachers of color. The discussion is derived from experience with the Pathways to Teaching Careers initiative funded by the DeWitt Wallace-Reader's Digest Fund. The importance of linking efforts by educational leaders is stressed. (SLD)

  11. What Can Funders Do to Better Link Science with Decisions? Case Studies of Coastal Communities and Climate Change

    NASA Astrophysics Data System (ADS)

    Matso, Kalle E.; Becker, Mimi L.

    2014-12-01

    Many reports and studies have noted that a significant portion of problem-oriented coastal science does not actually link to decisions. Here, three competitively funded project case studies are studied to determine what funders can and should do to better link science with decisions. The qualitative analysis used for this study indicates that the studied program was seen as being unusually attentive to the issue of linking science to decisions, as opposed to simply generating new knowledge. Nevertheless, much of the data indicate that funders can and should do more. Three ideas figured most prominently in the qualitative data: (1) funders should do more to ensure that the problem itself is defined more thoroughly with people who are envisioned as potential users of the science; (2) funders need to allocate more resources and attention to communicating effectively (with users) throughout the project; and (3) funders need to demand more engagement of users throughout the project. These findings have important implications for how funders review and support science, especially when competitive processes are used. Most importantly, funders should adjust what kind of science they ask for. Secondly, funders need to change who is involved in the review process. Currently, review processes focus on knowledge generation, which means that the reviewers themselves have expertise in that area. Instead, review panels should be balanced between those who focus on knowledge generation and those who focus on linking knowledge to decisions; this is a separate but critical discipline currently left out of the review process.

  12. BIOMARKERS OF REPRODUCTIVE TOXICITY

    EPA Science Inventory

    Identification and verification of anatomical, endocrine, cellular and molecular biomarkers is crucial for successful clinical diagnosis and treatment of toxicity and disease, as well as basic toxicological, epidemiological and other research. Various in situ biomarkers of repro...

  13. Biomarkers in Computational Toxicology

    EPA Science Inventory

    Biomarkers are a means to evaluate chemical exposure and/or the subsequent impacts on toxicity pathways that lead to adverse health outcomes. Computational toxicology can integrate biomarker data with knowledge of exposure, chemistry, biology, pharmacokinetics, toxicology, and e...

  14. A Working Partnership for 1993: Linking Community Colleges and Business. Conference Summary.(Sacramento, California, May 13, 1983).

    ERIC Educational Resources Information Center

    1983

    Summaries are provided of the presentations, discussions, and major conclusions of a conference convened in May 1983 to develop mechanisms for improving the linkages between industry and community colleges in California. Introductory material offers an overview of the conference's goals, employment training in California, and the role of the…

  15. Making Connections: Linking Generalist and Specialist Essentials in Baccalaureate Community/Public Health Nursing Education and Practice.

    ERIC Educational Resources Information Center

    Kaiser, Katherine Laux; Carter, Kimberly Ferren; O'Hare, Patricia A.; Callister, Lynn Clark

    2002-01-01

    Describes the work of a task force to revise public health nursing curriculum that combined the expertise of the American Association of Colleges of Nursing and specialty organizations. Discusses the current state of community/public health nursing and the model used to identify core professional knowledge and values underpinning the curriculum.…

  16. Structures and Strategies for Linking the Higher Education and Employment Communities. Higher Education/CETA Project Monograph.

    ERIC Educational Resources Information Center

    Clark, Donald M.; Rinehart, Richard L.

    A model is presented for establishing or improving cooperative relationships between higher education and the employment community, as part of the American Council on Education's Higher Education/Comprehensive Employment and Training Act (CETA) Project, which was supported by the Fund for the Improvement of Postsecondary Education. Attention is…

  17. Testing the link between community structure and function for ectomycorrhizal fungi involved in a global tripartite symbiosis.

    PubMed

    Walker, Jennifer K M; Cohen, Hannah; Higgins, Logan M; Kennedy, Peter G

    2014-04-01

    Alnus trees associate with ectomycorrhizal (ECM) fungi and nitrogen-fixing Frankia bacteria and, although their ECM fungal communities are uncommonly host specific and species poor, it is unclear whether the functioning of Alnus ECM fungal symbionts differs from that of other ECM hosts. We used exoenzyme root tip assays and molecular identification to test whether ECM fungi on Alnus rubra differed in their ability to access organic phosphorus (P) and nitrogen (N) when compared with ECM fungi on the non-Frankia host Pseudotsuga menziesii. At the community level, potential acid phosphatase (AP) activity of ECM fungal root tips from A. rubra was significantly higher than that from P. menziesii, whereas potential leucine aminopeptidase (LA) activity was significantly lower for A. rubra root tips at one of the two sites. At the individual species level, there was no clear relationship between ECM fungal relative root tip abundance and relative AP or LA enzyme activities on either host. Our results are consistent with the hypothesis that ECM fungal communities associated with Alnus trees have enhanced organic P acquisition abilities relative to non-Frankia ECM hosts. This shift, in combination with the chemical conditions present in Alnus forest soils, may drive the atypical structure of Alnus ECM fungal communities. PMID:24320607

  18. SIMULATION COASTAL PLAIN STREAM FISH COMMUNITY RESPONSE TO NONPOINT SOURCE POLLUTION USING LINKED HYDROLOGIC-ECOLOGICAL MODELS

    EPA Science Inventory

    Nonpoint source pollution is the primary stress in many streams. Characteristic declines in stream fish communities are recognized in streams influenced by nonpoint source pollution, but the processes by which these declines occur are not well understood. Here, predicted time s...

  19. Application of RNA Stable Isotope Probing (SIP) to Link Community Activity with Microorganisms Responsible for Autotrophy in the Subseafloor at Axial Seamount

    NASA Astrophysics Data System (ADS)

    Huber, J. A.; Fortunato, C. S.

    2014-12-01

    The global ocean comprises the Earth's largest biome, with microorganisms playing a dominant biogeochemical role. However, the potential for production of new microbial biomass within the subseafloor is rarely considered in traditional oceanographic paradigms of carbon cycling or microbial food webs. In this study, we used RNA Stable Isotope Probing (RNA SIP) to determine the microbial community composition and genetic repertoire of active subseafloor autotrophs in warm venting fluids from Axial Seamount. RNA is a responsive biomarker because it is a reflection of cellular activity independent of replication, and RNA SIP thus provides access to both the function of a microbial community and the phylogeny of the organisms accountable for key functions. Diffuse fluids were incubated shipboard at 30°C, 55°C, and 80°C with 13DIC and H2. Metatranscriptomic sequencing of both the enriched and non-enriched RNA was carried out from 13C and 12C controls. In addition, filtered fluid samples were preserved in situ for comparative meta -transcriptomic and -genomic analyses. Diverse lineages of bacteria and archaea and accompanying metabolisms were detected in situ, but RNA SIP results show dominance of three different groups of autotrophs active under each experimental condition. At 30°C, members of the Sulfurimonas genus dominated, with genes for hydrogen oxidation, nitrate reduction, and carbon fixation via the rTCA cycle highly expressed. At 55°C, both Caminibacter and Nautilia transcripts were detected for rTCA cycle, hydrogen oxidation, and nitrate reduction. At 80°C, transcripts for hydrogenotrophic methanogenesis mediated by members of Methanocaldococcus were detected. These results suggest the subseafloor hosts various anaerobic chemolithoautotrophs that span a wide temperature range, with hydrogen playing a key role in microbial metabolism. Complementary experiments are currently being carried out on the seafloor with a novel in situ incubator unit to provide

  20. Linking macrobenthic communities structure and zonation patterns on sandy shores: Mapping tool toward management and conservation perspectives in Northern France

    NASA Astrophysics Data System (ADS)

    Rolet, Céline; Spilmont, Nicolas; Dewarumez, Jean-Marie; Luczak, Christophe

    2015-05-01

    In a context of intensifying anthropogenic pressures on sandy shores, the mapping of benthic habitat appears as an essential first step and a fundamental baseline for marine spatial planning, ecosystem-based management and conservation efforts of soft-sediment intertidal areas. Mapping allows representing intertidal habitats that are basically characterised by abiotic (e.g sediments, exposure to waves…) and biotic factors such as macrobenthic communities. Macrobenthic communities are known to show zonation patterns across sandy beaches and many studies highlighted the existence of three biological zones. We tested this general model of a tripartite biological division of the shore at a geographical scale of policy, conservation and management decisions (i.e. Northern France coastline), using multivariate analyses combined with the Direct Field Observation (DFO) method. From the upper to the lower shores, the majority of the beaches exhibited three macrobenthic communities confirming the existence of the tripartite biological division of the shore. Nevertheless, in some cases, two or four zones were found: (1) two zones when the drying zone located on the upper shore was replaced by littoral rock or engineering constructions and (2) four zones on beaches and estuaries where a muddy-sand community occurred from the drift line to the mid shore. The correspondence between this zonation pattern of macrobenthic communities and the EUNIS habitat classification was investigated and the results were mapped to provide a reference state of intertidal soft-sediment beaches and estuaries. Our results showed evidence of the applicability of this EUNIS typology for the beaches and estuaries at a regional scale (Northern France coastline) with a macroecological approach. In order to fulfil the requirements of the European Directives (WFD and MFSD), this mapping appears as a practical tool for any functional study on these coastal ecosystems, for the monitoring of anthropogenic

  1. Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge.

    PubMed

    Westerholm, Maria; Crauwels, Sam; Houtmeyers, Sofie; Meerbergen, Ken; Van Geel, Maarten; Lievens, Bart; Appels, Lise

    2016-10-01

    The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the

  2. Exploring the links between components of coordinated community responses and their impact on contact with intimate partner violence services.

    PubMed

    Klevens, Joanne; Baker, Charlene K; Shelley, Gene A; Ingram, Eben M

    2008-03-01

    In the 1990s, concerns with response fragmentation for intimate partner violence (IPV) led to the promotion of coordinated community responses (CCRs) to prevent and control IPV. Evaluation of CCRs has been limited. A previous evaluation of 10 CCRs funded by the Centers for Disease Control and Prevention showed no overall impact on rates of IPV when compared to matched communities. However, there was great variability in the quality and quantity of CCR efforts between sites and thus potentially different levels of impact. This article establishes the impact of each of the 10 CCRs on women's past-year exposure to IPV and contact with IPV services and explores the associations between specific CCR components and contact with IPV services. PMID:18292374

  3. Benthic–pelagic links and rocky intertidal communities: Bottom-up effects on top-down control?

    PubMed Central

    Menge, Bruce A.; Daley, Bryon A.; Wheeler, Patricia A.; Dahlhoff, Elizabeth; Sanford, Eric; Strub, P. Ted

    1997-01-01

    Insight into the dependence of benthic communities on biological and physical processes in nearshore pelagic environments, long considered a “black box,” has eluded ecologists. In rocky intertidal communities at Oregon coastal sites 80 km apart, differences in abundance of sessile invertebrates, herbivores, carnivores, and macrophytes in the low zone were not readily explained by local scale differences in hydrodynamic or physical conditions (wave forces, surge flow, or air temperature during low tide). Field experiments employing predator and herbivore manipulations and prey transplants suggested top-down (predation, grazing) processes varied positively with bottom-up processes (growth of filter-feeders, prey recruitment), but the basis for these differences was unknown. Shore-based sampling revealed that between-site differences were associated with nearshore oceanographic conditions, including phytoplankton concentration and productivity, particulates, and water temperature during upwelling. Further, samples taken at 19 sites along 380 km of coastline suggested that the differences documented between two sites reflect broader scale gradients of phytoplankton concentration. Among several alternative explanations, a coastal hydrodynamics hypothesis, reflecting mesoscale (tens to hundreds of kilometers) variation in the interaction between offshore currents and winds and continental shelf bathymetry, was inferred to be the primary underlying cause. Satellite imagery and offshore chlorophyll-a samples are consistent with the postulated mechanism. Our results suggest that benthic community dynamics can be coupled to pelagic ecosystems by both trophic and transport linkages. PMID:9405647

  4. Critical tissue residue approach linking accumulated metals in aquatic insects to population and community-level effects

    USGS Publications Warehouse

    Schmidt, Travis S.; Clements, William H.; Zuellig, Robert E.; Mitchell, Katharine A.; Church, Stanley E.; Wanty, Richard B.; San Juan, Carma A.; Adams, Monique; Lamothe, Paul J.

    2011-01-01

    Whole body Zn concentrations in individuals (n = 825) from three aquatic insect taxa (mayflies Rhithrogena spp. and Drunella spp. and the caddisfly Arctopsyche grandis) were used to predict effects on populations and communities (n = 149 samples). Both mayflies accumulated significantly more Zn than the caddisfly. The presence/absence of Drunella spp. most reliably distinguished sites with low and high Zn concentrations; however, population densities of mayflies were more sensitive to increases in accumulated Zn. Critical tissue residues (634 (mu or u)g/g Zn for Drunella spp. and 267 (mu or u)g/g Zn for Rhithrogena spp.) caused a 20% reduction in maximum (90th quantile) mayfly densities. These critical tissue residues were associated with exposure to 7.0 and 3.9 (mu or u)g/L dissolved Zn for Drunella spp. and Rhithrogena spp., respectively. A threshold in a measure of taxonomic completeness (observed/expected) was observed at 5.4 (mu or u)g/L dissolved Zn. Dissolved Zn concentrations associated with critical tissue residues in mayflies were also associated with adverse effects in the aquatic community as a whole. These effects on populations and communities occurred at Zn concentrations below the U.S. EPA hardness-adjusted continuous chronic criterion.

  5. Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm.

    PubMed

    Bartram, Andrea K; Jiang, Xingpeng; Lynch, Michael D J; Masella, Andre P; Nicol, Graeme W; Dushoff, Jonathan; Neufeld, Josh D

    2014-02-01

    Soil pH is an important determinant of microbial community composition and diversity, yet few studies have characterized the specific effects of pH on individual bacterial taxa within bacterial communities, both abundant and rare. We collected composite soil samples over 2 years from an experimentally maintained pH gradient ranging from 4.5 to 7.5 from the Craibstone Experimental Farm (Craibstone, Scotland). Extracted nucleic acids were characterized by bacterial and group-specific denaturing gradient gel electrophoresis and next-generation sequencing of bacterial 16S rRNA genes. Both methods demonstrated comparable and reproducible shifts within higher taxonomic bacterial groups (e.g. Acidobacteria, Alphaproteobacteria, Verrucomicrobia, and Gammaproteobacteria) across the pH gradient. In addition, we used non-negative matrix factorization (NMF) for the first time on 16S rRNA gene data to identify positively interacting (i.e. co-occurring) operational taxonomic unit (OTU) clusters (i.e. 'components'), with abundances that correlated strongly with pH, and sample year to a lesser extent. All OTUs identified by NMF were visualized within principle coordinate analyses of UNIFRAC distances and subjected to taxonomic network analysis (SSUnique), which plotted OTU abundance and similarity against established taxonomies. Most pH-dependent OTUs identified here would not have been identified by previous methodologies for microbial community profiling and were unrelated to known lineages. PMID:24117982

  6. The development and applications of biomarkers

    SciTech Connect

    Normandy, J.; Peeters, J.

    1994-04-15

    This report is a compilation of submitted abstracts of scientific papers presented at the second Department of Energy-supported workshop on the use and applications of biomarkers held in Santa Fe, New Mexico, from April 26--29, 1994. The abstracts present a synopsis of the latest scientific developments in biomarker research and how these developments meet with the practical needs of the occupational physician as well as the industrial hygienist and the health physicist. In addition to considering the practical applications and potential benefits of this promising technology, the potential ethical and legal ramifications of using biomarkers to monitor workers are discussed. The abstracts further present insights on the present benefits that can be derived from using biomarkers as well as a perspective on what further research is required to fully meet the needs of the medical community.

  7. Are Longitudinal Patterns of Bacterial Community Composition and Dissolved Organic Matter Composition Linked Across a River Continuum? (Invited)

    NASA Astrophysics Data System (ADS)

    Mosher, J.; Kaplan, L. A.; Kan, J.; Findlay, R. H.; Podgorski, D. C.; McKenna, A. M.; Branan, T. L.; Griffith, C.

    2013-12-01

    The River Continuum Concept (RCC), an early meta-ecosystem idea, was developed without the benefit of new frontiers in molecular microbial ecology and ultra-high resolution mass spectrometry. We have applied technical advances in these areas to address a hypothesis implicit in the RCC that the upstream legacy of DOM processing contributes to the structure and function of downstream bacterial communities. DOM molecular structure and microbial community structure were measured across river networks within three distinct forested catchments. High-throughput pyrosequencing of bacterial 16S rRNA amplicons and phospholipid fatty acid analysis were used to characterize bacterial communities, and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry characterized the molecular composition of stream water DOM. Total microbial biomass varied among river networks but showed a trend of decreasing biomass in sediment with increasing stream order. There were distinct shifts in bacterial community structure and a trend of decreasing richness was observed traveling downstream in both sediment and epilithic habitats. The bacterial richness in the first order stream sediment habitats was 7728 genera which decreased to 6597 genera in the second order sites and 4867 genera in the third order streams. The richness in the epilithic biofilm habitats was 2830 genera in the first order, 2322 genera in the second order and 1629 genera in the third order sites. Over 45% of the sediment biofilm genera and 37% of the epilithic genera were found in all three orders. In addition to shifts in bacterial richness, we observed a longitudinal shift in bacterial functional-types. In the sediment biofilms, Rhodoplanes spp. (containing rhodopsin pigment) and Bradyrhizobium spp. (nitrogen fixing bacteria) were predominately found in the heavily forested first order streams, while the cyanobacteria Limnothrix spp. was dominant in the second order streams. The third order

  8. Linking a Large-Watershed Hydrogeochemical Model to a Wetland Community-Ecosystem Model to Estimate Plant Invasion Risk in the Coastal Great Lakes Region, USA

    NASA Astrophysics Data System (ADS)

    Currie, W. S.; Bourgeau-Chavez, L. L.; Elgersma, K. J.; French, N. H. F.; Goldberg, D. E.; Hart, S.; Hyndman, D. W.; Kendall, A. D.; Martin, S. L.; Martina, J. P.

    2014-12-01

    In the Laurentian Great Lakes region of the Upper Midwest, USA, agricultural and urban land uses together with high N deposition are contributing to elevated flows of N in rivers and groundwater to coastal wetlands. The functioning of coastal wetlands, which provide a vital link between land and water, are imperative to maintaining the health of the entire Great Lakes Basin. Elevated N inflows are believed to facilitate the spread of large-stature invasive plants (cattails and Phragmites) that reduce biodiversity and have complex effects on other ecosystem services including wetland N retention and C accretion. We enhanced the ILHM (Integrated Landscape Hydrology Model) to simulate the effects of land use on N flows in streams, rivers, and groundwater throughout the Lower Peninsula of Michigan. We used the hydroperiods and N loading rates simulated by ILHM as inputs to the Mondrian model of wetland community-ecosystem processes to estimate invasion risk and other ecosystem services in coastal wetlands around the Michigan coast. Our linked models produced threshold behavior in the success of invasive plants in response to N loading, with the threshold ranging from ca. 8 to 12 g N/m2 y, depending on hydroperiod. Plant invasions increased wetland productivity 3-fold over historically oligotrophic native communities, decreased biodiversity but slightly increased wetland N retention. Regardless of invasion, elevated N loading resulted in significantly enhanced rates of C accretion, providing an important region-wide mechanism of C storage. The linked models predicted a general pattern of greater invasion risk in the southern basins of lakes Michigan and Huron relative to northern areas. The basic mechanisms of invasion have been partially validated in our field mesocosms constructed for this project. The general regional patterns of increased invasion risk have been validated through our field campaigns and remote sensing conducted for this project.

  9. Linking Temporal Changes in Bacterial Community Structures with the Detection and Phylogenetic Analysis of Neutral Metalloprotease Genes in the Sediments of a Hypereutrophic Lake

    PubMed Central

    Tsuboi, Shun; Yamamura, Shigeki; Imai, Akio; Satou, Takayuki; Iwasaki, Kazuhiro

    2014-01-01

    We investigated spatial and temporal variations in bacterial community structures as well as the presence of three functional proteolytic enzyme genes in the sediments of a hypereutrophic freshwater lake in order to acquire an insight into dynamic links between bacterial community structures and proteolytic functions. Bacterial communities determined from 16S rRNA gene clone libraries markedly changed bimonthly, rather than vertically in the sediment cores. The phylum Firmicutes dominated in the 4–6 cm deep sediment layer sample after August in 2007, and this correlated with increases in interstitial ammonium concentrations (p < 0.01). The Firmicutes clones were mostly composed of the genus Bacillus. npr genes encoding neutral metalloprotease, an extracellular protease gene, were detected after the phylum Firmicutes became dominant. The deduced Npr protein sequences from the retrieved npr genes also showed that most of the Npr sequences used in this study were closely related to those of the genus Bacillus, with similarities ranging from 61% to 100%. Synchronous temporal occurrences of the 16S rRNA gene and Npr sequences, both from the genus Bacillus, were positively associated with increases in interstitial ammonium concentrations, which may imply that proteolysis by Npr from the genus Bacillus may contribute to the marked increases observed in ammonium concentrations in the sediments. Our results suggest that sedimentary bacteria may play an important role in the biogeochemical nitrogen cycle of freshwater lakes. PMID:25130992

  10. The Link Between Community-Based Violence and Intimate Partner Violence: the Effect of Crime and Male Aggression on Intimate Partner Violence Against Women.

    PubMed

    Kiss, Ligia; Schraiber, Lilia Blima; Hossain, Mazeda; Watts, Charlotte; Zimmerman, Cathy

    2015-08-01

    Both intimate partner violence (IPV) and community violence are prevalent globally, and each is associated with serious health consequences. However, little is known about their potential links or the possible benefits of coordinated prevention strategies. Using aggregated data on community violence from the São Paulo State Security Department (INFOCRIM) merged with WHO multi-country study on women's health and domestic violence data, random intercept models were created to assess the effect of crime on women's probability of experiencing IPV. The association between IPV and male aggression (measured by women's reports of their partner's fights with other men) was examined using logistic regression models. We found little variation in the likelihood of male IPV perpetration related to neighborhood crime level but did find an increased likelihood of IPV experiences among women whose partners were involved in male-to-male violence. Emerging evidence on violence prevention has suggested some promising avenues for primary prevention that address common risk factors for both perpetration of IPV and male interpersonal violence. Strategies such as early identification and effective treatment of emotional disorders, alcohol abuse prevention and treatment, complex community-based interventions to change gender social norms and social marketing campaigns designed to modify social and cultural norms that support violence may work to prevent simultaneously male-on-male aggression and IPV. Future evaluations of these prevention strategies should simultaneously assess the impact of interventions on IPV and male interpersonal aggression. PMID:26004379

  11. Cancer biomarkers - current perspectives.

    PubMed

    Bhatt, Anant Narayan; Mathur, Rohit; Farooque, Abdullah; Verma, Amit; Dwarakanath, B S

    2010-08-01

    In the recent years, knowledge about cancer biomarkers has increased tremendously providing great opportunities for improving the management of cancer patients by enhancing the efficiency of detection and efficacy of treatment. Recent technological advancement has enabled the examination of many potential biomarkers and renewed interest in developing new biomarkers. Biomarkers of cancer could include a broad range of biochemical entities, such as nucleic acids, proteins, sugars, lipids, and small metabolites, cytogenetic and cytokinetic parameters as well as whole tumour cells found in the body fluid. A comprehensive understanding of the relevance of each biomarker will be very important not only for diagnosing the disease reliably, but also help in the choice of multiple therapeutic alternatives currently available that is likely to benefit the patients. This review provides a brief account on various biomarkers for diagnosis, prognosis and therapeutic purposes, which include markers already in clinical practice as well as various upcoming biomarkers. PMID:20716813

  12. Associations between vitamin K status and hemostatic and inflammatory biomarkers in community-dwelling adults: The multi-ethnic study of atherosclerosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vitamin K is integral to hemostatic function, and in vitro and animal experiments suggest that vitamin K can suppress production of inflammatory cytokines. To test the hypothesis that higher vitamin K status is associated with lower hemostasic activation and inflammation in community-dwelling adults...

  13. Applying Recovery Biomarkers to Calibrate Self-Report Measures of Energy and Protein in the Hispanic Community Health Study/Study of Latinos.

    PubMed

    Mossavar-Rahmani, Yasmin; Shaw, Pamela A; Wong, William W; Sotres-Alvarez, Daniela; Gellman, Marc D; Van Horn, Linda; Stoutenberg, Mark; Daviglus, Martha L; Wylie-Rosett, Judith; Siega-Riz, Anna Maria; Ou, Fang-Shu; Prentice, Ross L

    2015-06-15

    We investigated measurement error in the self-reported diets of US Hispanics/Latinos, who are prone to obesity and related comorbidities, by background (Central American, Cuban, Dominican, Mexican, Puerto Rican, and South American) in 2010-2012. In 477 participants aged 18-74 years, doubly labeled water and urinary nitrogen were used as objective recovery biomarkers of energy and protein intakes. Self-report was captured from two 24-hour dietary recalls. All measures were repeated in a subsample of 98 individuals. We examined the bias of dietary recalls and their associations with participant characteristics using generalized estimating equations. Energy intake was underestimated by 25.3% (men, 21.8%; women, 27.3%), and protein intake was underestimated by 18.5% (men, 14.7%; women, 20.7%). Protein density was overestimated by 10.7% (men, 11.3%; women, 10.1%). Higher body mass index and Hispanic/Latino background were associated with underestimation of energy (P<0.05). For protein intake, higher body mass index, older age, nonsmoking, Spanish speaking, and Hispanic/Latino background were associated with underestimation (P<0.05). Systematic underreporting of energy and protein intakes and overreporting of protein density were found to vary significantly by Hispanic/Latino background. We developed calibration equations that correct for subject-specific error in reporting that can be used to reduce bias in diet-disease association studies. PMID:25995289

  14. Applying Recovery Biomarkers to Calibrate Self-Report Measures of Energy and Protein in the Hispanic Community Health Study/Study of Latinos

    PubMed Central

    Mossavar-Rahmani, Yasmin; Shaw, Pamela A.; Wong, William W.; Sotres-Alvarez, Daniela; Gellman, Marc D.; Van Horn, Linda; Stoutenberg, Mark; Daviglus, Martha L.; Wylie-Rosett, Judith; Siega-Riz, Anna Maria; Ou, Fang-Shu; Prentice, Ross L.

    2015-01-01

    We investigated measurement error in the self-reported diets of US Hispanics/Latinos, who are prone to obesity and related comorbidities, by background (Central American, Cuban, Dominican, Mexican, Puerto Rican, and South American) in 2010–2012. In 477 participants aged 18–74 years, doubly labeled water and urinary nitrogen were used as objective recovery biomarkers of energy and protein intakes. Self-report was captured from two 24-hour dietary recalls. All measures were repeated in a subsample of 98 individuals. We examined the bias of dietary recalls and their associations with participant characteristics using generalized estimating equations. Energy intake was underestimated by 25.3% (men, 21.8%; women, 27.3%), and protein intake was underestimated by 18.5% (men, 14.7%; women, 20.7%). Protein density was overestimated by 10.7% (men, 11.3%; women, 10.1%). Higher body mass index and Hispanic/Latino background were associated with underestimation of energy (P < 0.05). For protein intake, higher body mass index, older age, nonsmoking, Spanish speaking, and Hispanic/Latino background were associated with underestimation (P < 0.05). Systematic underreporting of energy and protein intakes and overreporting of protein density were found to vary significantly by Hispanic/Latino background. We developed calibration equations that correct for subject-specific error in reporting that can be used to reduce bias in diet-disease association studies. PMID:25995289

  15. Characterization of microorganisms responsible for phosphorus removal linking operation performance with microbial community structure at low temperature.

    PubMed

    Zou, Haiming; Lu, Xiwu; Saad, Abualhail

    2014-01-01

    Two enhanced biological phosphorus removal (EBPR) reactors were started up at low temperatures to obtain microorganisms responsible for aerobic and anoxic phosphorus removal, namely polyphosphate-accumulating organisms (PAO) and denitrifying PAO (DPAO), and their operational performance and microbial community were together investigated in the hope of assessment of the effectiveness of the EBPR process at low temperature by combining chemical analysis and microbial community structure evolution based on polymerase chain reaction-denaturing gradient gel electrophoresis. When two reactors reached the steady state after 40 and 80 days for the anaerobic-aerobic (AO) and anaerobic-anoxic (AA) reactor operation in AO and AA modes, respectively, a good ability of anaerobic phosphorus release and aerobic or anoxic phosphorus uptake was present both in these two reactors. During this start-up process, a total of 22 bands were detected in seed, AA and AO sludge samples, including Alpha-, Beta-, Gamma- and Deltaproteobacteria, as well as Chlorobi, Firmicutes, Bacteroidetes and Actinobacteria. Of all the bands, only four bands were present in all the lanes, suggesting that shift in microbial community occurred greatly depending on the electron acceptors in this study. From evolutionary tree, it was found that microorganisms related to DPAO mostly belong to the phylum Betaproteobacteria, while microbes corresponding to PAO were present in several phyla. Overall, the new strategy proposed here was shown to be feasible for the enrichment of PAO and DPAO at low temperature, and may be regarded as a new guidance for the application of EBPR technology to practice, especially in winter. PMID:24701905

  16. Flow regime in a restored wetland determines trophic links and species composition in the aquatic macroinvertebrate community.

    PubMed

    González-Ortegón, E; Walton, M E M; Moghaddam, B; Vilas, C; Prieto, A; Kennedy, H A; Pedro Cañavate, J; Le Vay, L

    2015-01-15

    In a restored wetland (South of Spain), where different flow regimes control water exchange with the adjacent Guadalquivir estuary, the native Palaemon varians coexists with an exotic counterpart species Palaemon macrodactylus. This controlled m\\acrocosm offers an excellent opportunity to investigate how the effects of water management, through different flow regimes, and the presence of a non-native species affect the aquatic community and the trophic niche (by gut contents and C-N isotopic composition) of the native shrimp Palaemon varians. We found that increased water exchange rate (5% day(-1) in mixed ponds vs. 0.1% day(-1) in extensive ponds) modified the aquatic community of this wetland; while extensive ponds are dominated by isopods and amphipods with low presence of P. macrodactylus, mixed ponds presented high biomass of mysids, corixids, copepods and both shrimp species. An estuarine origin of nutrients and primary production might explain seasonal and spatial differences found among ponds of this wetland. A combined analysis of gut contents and isotopic composition of the native and the exotic species showed that: (1) native P. varians is mainly omnivorous (2) while the non-native P. macrodactylus is more zooplanktivorous and (3) a dietary overlap occurred when both species coexist at mixed ponds where a higher water exchange and high abundance of mysids and copepods diversifies the native species' diet. Thus differences in the trophic ecology of both species are clearly explained by water management. This experimental study is a valuable tool for integrated management between river basin and wetlands since it allows quantification of wetland community changes in response to the flow regime. PMID:25242150

  17. Linking benthic community structure to terrestrial runoff and upwelling in the coral reefs of northeastern Hainan Island

    NASA Astrophysics Data System (ADS)

    Li, Xiubao; Wang, Daoru; Huang, Hui; Zhang, Jing; Lian, Jiansheng; Yuan, Xiangcheng; Yang, Jianhui; Zhang, Guoseng

    2015-04-01

    Near-shore coral reefs in northeastern Hainan Island are close to river mouths and aquaculture ponds, and also located at the center of the Qiongdong Upwelling (QDU). However, it is still unclear how terrestrial runoff and upwelling influence the community composition and spatial distribution of the benthos. During three cruises in 2010 and 2011 in Wenchang, northeastern Hainan Island, we determined a subset of environmental parameters in seawater (e.g. temperature, salinity, DO, dissolved inorganic nutrient (DIN), turbidity and transparency) and macroalgal δ15N and investigated the benthic communities (e.g. live coral cover, coral species richness, juvenile coral density, macroalgal cover and coverage of calcified algae) by video transect and visual census techniques at 10 stations (i.e. 1S-6D). The results showed that the QDU has influenced the reef waters in Wenchang. In 2011, the upwelling started in early May, peaked in July and disappeared in September and most upwelling events lasted for 1-2 weeks between May and July. The results also demonstrated that the reef water was nutrient enriched. Stations close to the river mouth and aquaculture ponds had higher levels of DIN and a higher percentage of ammonia in DIN, and there was consistently lower live coral cover, juvenile coral density and higher macroalgal cover. At some stations in this study, live coral cover was negatively correlated with macroalgal cover (i.e. 2S-6D). Live coral cover, species richness, and juvenile coral density all increased with the distance away from the river outlet and decreased with the rise of DIN. These results suggest that terrestrial runoff and upwelling stimulate nutrient enrichment, and that overgrowing macroalgae has an important influence on the coral communities in northeastern Hainan Island.

  18. Biomarker Utility Analysis Using an Exposure-PBPK/PD Model: A Carbaryl Case Study

    EPA Science Inventory

    There are two common biomarkers: markers of exposure and markers of health effects. The strength of the correlation between exposure or effect and a biomarker measurement determines the utility of a biomarker for assessing exposures or risks. In the current study, a linked expo...

  19. Technology Use in Linking Criminal Justice Reentrants to HIV Care in the Community: A Qualitative Formative Research Study

    PubMed Central

    PETERSON, JAMES; COTA, MICHELLE; GRAY, HOLLY; BAZERMAN, LAURI; KUO, IRENE; KURTH, ANN; BECKWITH, CURT

    2014-01-01

    Innovative interventions increasing linkage, adherence and retention in care among HIV-infected persons in the criminal justice system are needed. The authors conducted a qualitative study to investigate technology-based tools to facilitate linkage to community-based care and viral suppression for HIV-infected jail detainees on antiretroviral medications being released to the community. Twenty-four qualitative interviews were conducted in Rhode Island (12) and Washington DC (12) among HIV infected persons recently incarcerated to elicit their perceptions on the use of technology tools to support linkage to HIV care among criminal justice populations. This article discusses participants’ perceptions of the acceptability of technological tools such as (a) a computer-based counseling and (b) text messaging interventions. The participants reported positive experiences when previewing the technology-based tools to facilitate linkage to HIV care and adherence to HIV medications. Successful linkage to care has been shown to improve HIV-associated and non-HIV-associated health outcomes, as well as prevent criminal recidivism and facilitate reentrants’ successful and meaningful transition. These findings can be utilized to inform the implementation of interventions aimed at promoting adherence to antiretroviral medications and linkage to care for HIV-infected persons being released from the correctional setting. PMID:25529057

  20. NET-Works: Linking families, communities and primary care to prevent obesity in preschool-age children☆,☆☆

    PubMed Central

    Sherwood, Nancy E.; French, Simone A.; Veblen-Mortenson, Sara; Crain, A. Lauren; Berge, Jerica; Kunin-Batson, Alicia; Mitchell, Nathan; Senso, Meghan

    2014-01-01

    Obesity prevention in children offers a unique window of opportunity to establish healthful eating and physical activity behaviors to maintain a healthful body weight and avoid the adverse proximal and distal long-term health consequences of obesity. Given that obesity is the result of a complex interaction between biological, behavioral, family-based, and community environmental factors, intervention at multiple levels and across multiple settings is critical for both short- and long-term effectiveness. The Minnesota NET-Works (Now Everybody Together for Amazing and Healthful Kids) study is one of four obesity prevention and/or treatment trials that are part of the Childhood Obesity Prevention and Treatment (COPTR) Consortium. The goal of the NET-Works study is to evaluate an intervention that integrates home, community, primary care and neighborhood strategies to promote healthful eating, activity patterns, and body weight among low income, racially/ethnically diverse preschool-age children. Critical to the success of this intervention is the creation of linkages among the settings to support parents in making home environment and parenting behavior changes to foster healthful child growth. Five hundred racially/ethnically diverse, two–four year old children and their parent or primary caregiver will be randomized to the multi-component intervention or to a usual care comparison group for a three-year period. This paper describes the study design, measurement and intervention protocols, and statistical analysis plan for the NET-Works trial. PMID:24120933

  1. Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

    PubMed Central

    Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

    2012-01-01

    The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

  2. Seasonal Influenza Vaccine Effectiveness in the community (SIVE): protocol for a cohort study exploiting a unique national linked data set

    PubMed Central

    Simpson, Colin; Kavanagh, Kimberley; Robertson, Chris; McMenamin, Jim; Ritchie, Lewis; Sheikh, Aziz

    2012-01-01

    Introduction Seasonal influenza vaccination is recommended for all individuals aged 65 years and over and in individuals younger than 65 years with comorbidities. There is good evidence of vaccine effectiveness (VE) in young healthy individuals but less robust evidence for effectiveness in the populations targeted for influenza vaccination. Undertaking a randomised controlled trial to assess VE is now impractical due to the presence of national vaccination programmes. Quasi-experimental designs offer the potential to advance the evidence base in such scenarios, and the authors have therefore been commissioned to undertake a naturalistic national evaluation of seasonal influenza VE by using data derived from linkage of a number of Scottish health databases. The aim of this study is to examine the effectiveness of the seasonal influenza vaccination in the Scottish population. Methods and analysis A cohort study design will be used pooling data over nine seasons. A primary care database covering 4% of the Scottish population for the period 2000–2009 has been linked to the national database of hospital admissions and the death register and is being linked to the Health Protection Scotland virology database. The primary outcome is VE measured in terms of rate of hospital admissions due to respiratory illness. Multivariable regression will be used to produce estimates of VE adjusted for confounders. The major challenge of this approach is addressing the strong effect of confounding due to vaccinated individuals being systematically different from unvaccinated individuals. Analyses using propensity scores and instrumental variables will be undertaken, and the effect of an unknown confounder will be modelled in a sensitivity analysis to assess the robustness of the estimates. Ethics and dissemination The West of Scotland Research Ethics Committee has classified this project as surveillance. The study findings will be disseminated in peer-reviewed publications and

  3. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

    PubMed Central

    Liu, Jin-Feng; Sun, Xiao-Bo; Yang, Guang-Chao; Mbadinga, Serge M.; Gu, Ji-Dong; Mu, Bo-Zhong

    2015-01-01

    Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs. PMID:25873911

  4. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration.

    PubMed

    Liu, Jin-Feng; Sun, Xiao-Bo; Yang, Guang-Chao; Mbadinga, Serge M; Gu, Ji-Dong; Mu, Bo-Zhong

    2015-01-01

    Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs. PMID:25873911

  5. The Wide and Complex Field of NAFLD Biomarker Research: Trends

    PubMed Central

    Macheiner, Tanja; Kavsek, Barbara; Sargsyan, Karine

    2014-01-01

    Background. Nonalcoholic fatty liver disease is now acknowledged as a complex public health issue linked to sedentary lifestyle, obesity, and related disorders like type 2 diabetes and metabolic syndrome. Aims. We aimed to retrieve its trends out of the huge amount of published data. Therefore, we conducted an extensive literature search to identify possible biomarker and/or biomarker combinations by retrospectively assessing and evaluating common and novel biomarkers to predict progression and prognosis of obesity related liver diseases. Methodology. We analyzed finally 62 articles accounting for 157 cohorts and 45,288 subjects. Results. Despite the various approaches, most cohorts were considerably small and rarely comparable. Also, we found that the same standard parameters were measured rather than novel biomarkers. Diagnostics approaches appeared incomparable. Conclusions. Further collaborative investigations on harmonizing ways of data acquisition and identifying such biomarkers for clinical use are necessary to yield sufficient significant results of potential biomarkers. PMID:27335843

  6. Metagenomic biomarker discovery and explanation

    PubMed Central

    2011-01-01

    This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/. PMID:21702898

  7. Nondestructive biomarkers in ecotoxicology.

    PubMed Central

    Fossi, M C

    1994-01-01

    The aim of this article is to attempt a concise review of the state of the art of the nondestructive biomarkers approach in vertebrates, establishing a consensus on the most useful and sensitive nondestructive biomarker techniques, and proposing research priorities for the development and validation of this promising methodology. The following topics are discussed: the advantages of the use of nondestructive strategies in biomonitoring programs and the research fields in which nondestructive biomarkers can be applied; the biological materials suitable for nondestructive biomarkers and residue analysis in vertebrates; which biomarkers lend themselves to noninvasive techniques; and the validation and implementation strategy of the nondestructive biomarker approach. Examples of applications of this methodology in the hazard assessment of endangered species are also presented. Images Figure 1. C PMID:7713034

  8. Circulating glioma biomarkers

    PubMed Central

    Kros, Johan M.; Mustafa, Dana M.; Dekker, Lennard J.M.; Sillevis Smitt, Peter A.E.; Luider, Theo M.; Zheng, Ping-Pin

    2015-01-01

    Validated biomarkers for patients suffering from gliomas are urgently needed for standardizing measurements of the effects of treatment in daily clinical practice and trials. Circulating body fluids offer easily accessible sources for such markers. This review highlights various categories of tumor-associated circulating biomarkers identified in blood and cerebrospinal fluid of glioma patients, including circulating tumor cells, exosomes, nucleic acids, proteins, and oncometabolites. The validation and potential clinical utility of these biomarkers is briefly discussed. Although many candidate circulating protein biomarkers were reported, none of these have reached the required validation to be introduced for clinical practice. Recent developments in tracing circulating tumor cells and their derivatives as exosomes and circulating nuclear acids may become more successful in providing useful biomarkers. It is to be expected that current technical developments will contribute to the finding and validation of circulating biomarkers. PMID:25253418

  9. Carbon Monoxide Cycling in Hot Spring Microbial Communities and Links to the Composition of the Archean Atmosphere

    NASA Astrophysics Data System (ADS)

    Colman, A. S.; Techtmann, S.; He, B.; Robb, F.

    2010-12-01

    Carbon monoxide (CO) budgets for the Archean atmosphere generally treat the early biosphere as a major sink for CO, thereby preventing the development of a “CO runaway” atmosphere. Indeed, hydrogenogenic carboxydotrophy (CO + H2O → CO2 + H2) is an anaerobic metabolism that appears to be geographically widespread in hydrothermal microbial ecosystems, including those we have studied at hot springs in Uzon Caldera, Kamchatka, Russia. Carboxydotrophs have been isolated that can use CO as sole carbon and energy source in culture medium with headspace CO partial pressures ranging from ≤ 10-4 atm to ≥ 2 atm. In modern environments, this metabolism was thought to depend on CO supplied as a dissolved and free phase constituent of geothermal fluids. Recent dissolved and free phase gas measurements in Uzon hot springs, coupled with rate determinations of CO consumption in hot spring microbial mats, indicate that the supply of CO from volcanic gases is insufficient to meet the needs of the microbial communities in hot spring sediments. Instead, proximal biological production of CO by environmental microbial consortia must be invoked. The plausibility of widespread biogenic production of CO in natural microbial communities is supported by recent pure culture work that has shown small but ecologically significant CO production by certain methanogens and sulfate reducers. In the Archean, leakage to the atmosphere of even a small fraction of the biologically produced CO would have exceeded the volcanic outgassing flux. Biogenic CO production would also have diminished the biospheric sink for atmospheric CO. This would have had a major influence on the chemistry of the Archean atmosphere, possibly enabling CO concentrations to reach percent levels in the atmosphere. Elevated atmospheric CO concentrations in the Archean would have exerted significant pressures on the early biosphere. Futhermore, CO in the Archean atmosphere would have titrated OH radical, influencing the

  10. Phenology of Australian temperate grasslands: linking near-surface phenology to C3/C4 community composition

    NASA Astrophysics Data System (ADS)

    Watson, C. J.

    2015-12-01

    Vegetation phenology is relatively well-studied in northern hemisphere temperate biomes, but limited research has been conducted on phenological drivers and responses in Australian temperate ecosystems. Australian temperate grasslands represent a broad range of plant communities from exotic pastures to native grasslands, but all are important for food security (livestock grazing) and biodiversity retention. Climate predictions for temperate Australia include higher temperatures, altered rainfall frequency/seasonality, increased drought severity and more regular wildfires. The ecosystem response to these climatic factors is unknown, and the need to improve the monitoring of these highly dynamic grassland systems at a landscape scale is acute. The aim of this research is to use high-frequency phenological data to improve the identification of grassland functional types and ultimately use this to improve the inter-annual monitoring of dynamic grassland systems. We use hourly repeat photography and the Green Chromatic Coordinate vegetation index to characterize the vegetative phenology of several native and exotic grassland communities. Monthly vegetation surveys allow us to correlate plant functional groups with indicator features on the phenology profile. C4-dominated grasslands are characterized by a consistent low greenness during winter, the commencement of greening in late spring/early summer and the retention of green vegetation throughout the summer. Exotic C4 grasslands can be distinguished from native ecosystems by their early-spring flush of annual grasses and forbs prior to the primary greening in late spring/early summer. Native C3 grasslands are more variable in response to rainfall and exhibit multiple greening/browning cycles within the year. They tend to green up earlier in the spring and brown off rapidly in response to high temperatures and low rainfall. Exotic C3 grasslands also green up in early spring but exhibit a more traditional unimodal

  11. Are cicadas (Diceroprocta apache) both a "keystone" and a "critical-link" species in lower Colorado River riparian communities?

    USGS Publications Warehouse

    Andersen, Douglas C.

    1994-01-01

    Apache cicada (Homoptera: Cicadidae: Diceroprocta apache Davis) densities were estimated to be 10 individuals/m2 within a closed-canopy stand of Fremont cottonwood (Populus fremontii) and Goodding willow (Salix gooddingii) in a revegetated site adjacent to the Colorado River near Parker, Arizona. Coupled with data drawn from the literature, I estimate that up to 1.3 cm (13 1/m2) of water may be added to the upper soil layers annually through the feeding activities of cicada nymphs. This is equivalent to 12% of the annual precipitation received in the study area. Apache cicadas may have significant effects on ecosystem functioning via effects on water transport and thus act as a critical-link species in this southwest desert riverine ecosystem. Cicadas emerged later within the cottonwood-willow stand than in relatively open saltcedar-mesquite stands; this difference in temporal dynamics would affect their availability to several insectivorous bird species and may help explain the birds' recent declines. Resource managers in this region should be sensitive to the multiple and strong effects that Apache cicadas may have on ecosystem structure and functioning.

  12. The Geisinger MyCode Community Health Initiative: an electronic health record-linked biobank for Precision Medicine research

    PubMed Central

    Carey, David J.; Fetterolf, Samantha N.; Davis, F. Daniel; Faucett, William A.; Kirchner, H. Lester; Mirshahi, Uyenlinh; Murray, Michael F.; Smelser, Diane T.; Gerhard, Glenn S.; Ledbetter, David H.

    2015-01-01

    Purpose Geisinger Health System (GHS) provides an ideal platform for Precision Medicine. Key elements are the integrated health system, stable patient population, and electronic health record (EHR) infrastructure. In 2007 Geisinger launched MyCode®, a system-wide biobanking program to link samples and EHR data for broad research use. Methods Patient-centered input into MyCode® was obtained using participant focus groups. Participation in MyCode® is based on opt-in informed consent and allows recontact, which facilitates collection of data not in the EHR, and, since 2013, the return of clinically actionable results to participants. MyCode® leverages Geisinger’s technology and clinical infrastructure for participant tracking and sample collection. Results MyCode® has a consent rate of >85% with more than 90,000 participants currently, with ongoing enrollment of ~4,000 per month. MyCode® samples have been used to generate molecular data, including high-density genotype and exome sequence data. Genotype and EHR-derived phenotype data replicate previously reported genetic associations. Conclusion The MyCode® project has created resources that enable a new model for translational research that is faster, more flexible, and more cost effective than traditional clinical research approaches. The new model is scalable, and will increase in value as these resources grow and are adopted across multiple research platforms. PMID:26866580

  13. Linking ice core and climate research to the K-12 and broader community in Denali National Park, Alaska

    NASA Astrophysics Data System (ADS)

    Campbell, S. W.; Williams, K.; Marston, L.; Kreutz, K. J.; Osterberg, E. C.; Wake, C. P.

    2013-12-01

    For the past six years, a multi-institution effort has undertaken a broad glaciological and climate research project in Denali National Park. Most recently, two ~208 m long surface to bedrock ice cores were recovered from the Mt. Hunter plateau with supporting geophysical and weather data collected. Twenty two individuals have participated in the field program providing thousands of person-hours towards completing our research goals. Technical and scientific results have been disseminated to the broader scientific community through dozens of professional presentations and six peer-reviewed publications. In addition, we have pursued the development of interactive computer applications that use our results for educational purposes, publically available fact sheets through Denali National Park, and most recently, with assistance from PolarTREC and other affiliations, the development of a children's book and roll-out of K-8 science curriculum based on this project. The K-8 curriculum will provide students with an opportunity to use real scientific data to meet their educational requirements through alternative, interactive, and exciting methods relative to more standard educational programs. Herein, we present examples of this diverse approach towards incorporating polar research into K-12 STEM classrooms.

  14. Direct and indirect costs of co-infection in the wild: Linking gastrointestinal parasite communities, host hematology, and immune function☆

    PubMed Central

    Budischak, Sarah A.; Jolles, Anna E.; Ezenwa, Vanessa O.

    2012-01-01

    Most animals are concurrently infected with multiple parasites, and interactions among these parasites may influence both disease dynamics and host fitness. However, the sublethal costs of parasite infections are difficult to measure and the effects of concomitant infections with multiple parasite species on individual physiology and fitness are poorly described for wild hosts. To understand the direct and indirect physiological costs of co-infection, we investigated the relationships among gastrointestinal parasite richness, species identity, and abundance and host hematological parameters, body condition, and investment in lymphocyte defenses. Using aggregate-scale parasite data from African buffalo (Syncerus caffer), we found few direct or indirect associations between infection and hematology in male hosts, and no significant associations were observed in female hosts or with respect to body condition in either sex. These results suggest that only strong physiological effects are detectable with aggregate-scale parasite data, and that hematological variables may be more sensitive to changes in condition than standard body fat condition indices. Analyses accounting for parasite species identity in female buffalo revealed that different parasites show distinct relationships with host hematology, body condition, and immune investment. However, four of six species-specific associations were obscured when parasites were considered in combination. Overall, fitness-related physiological mediators such as hematological indices may provide assessments of direct and indirect effects of parasite infection, particularly when parasite species identity and community composition are considered. PMID:24533308

  15. Linking the distribution of (210)Po and (210)Pb with plankton community along Line P, Northeast Subarctic Pacific.

    PubMed

    Choi, Hiu Yan; Stewart, Gillian M; Lomas, Michael W; Kelly, Roger P; Moran, S Bradley

    2014-12-01

    Depth profiles of (210)Po and (210)Pb activity and phytoplankton and zooplankton abundance were collected during two cruises along the Canadian time-series Line P in the Northeast Subarctic Pacific (ranging from 48o39 N to 50o00 N and 126o40 W to 145o00 W) in August 2010 and February 2011 to evaluate connections between the planktonic community and distributions of these radionuclides in the upper 500 m of the water column. Statistical analysis indicates that (210)Po is more effectively removed from the surface ocean when large (>0.1 mg ind(-1) dry wt) zooplankton dominate, and is less effectively scavenged when the picoplankton Synechococcus is present at high concentrations (>1 × 10(5) cells ml(-1)). While the zooplankton field data are consistent with previous lab studies and field observations, the phytoplankton results seem to conflict with recent evidence that small cells may contribute significantly to export in other oligotrophic regions. Differences in ecosystem mechanisms between the Subarctic Pacific and other oligotrophic systems that limit the contribution of small cells to sinking flux remain to be identified. PMID:24629375

  16. Linking N2O emission from biochar-amended composting process to the abundance of denitrify (nirK and nosZ) bacteria community.

    PubMed

    Li, Shuqing; Song, Lina; Jin, Yaguo; Liu, Shuwei; Shen, Qirong; Zou, Jianwen

    2016-12-01

    Manure composting has been recognized as an important anthropogenic source of nitrous oxide (N2O) contributing to global warming. However, biochar effect on N2O emissions from manure composting is rarely evaluated, especially by linking it to abundance of denitrifying bacteria community. Results of this study indicated that biochar amendment significantly reduced N2O emissions from manure composting, primarily due to suppression of the nirK gene abundance of denitrifying bacteria. Pearson's correlation analysis showed a significant positive correlation between nirK abundance and N2O fluxes, while a negative correlation between nosZ density and N2O fluxes. Simultaneously, a linear correlation between nirK gene abundance minus nosZ gene abundance with N2O fluxes was also observed. In addition, a statistical model for estimating N2O emissions based on the bacterial denitrifying functional genes was developed and verified to adequately fit the observed emissions. Our results highlighted that biochar amendment would be an alternative strategy for mitigating N2O emissions during manure composting, and the information of related functional bacterial communities could be helpful for understanding the mechanism of N2O emissions. PMID:27207069

  17. A community based approach to linking injection drug users with needed services through pharmacies: An evaluation of a pilot intervention in New York City

    PubMed Central

    Rudolph, AE; Standish, K; Amesty, S; Crawford, ND; Stern, RJ; Badillo, WE; Boyer, A; Brown, D; Ranger, N; Orduna, JM Garcia; Lasenburg, L; Lippek, Sarah; Fuller, CM

    2010-01-01

    Studies suggest that community-based approaches could help pharmacies expand their public health role, particularly pertaining to HIV prevention. Thirteen pharmacies participating in New York’s Expanded Syringe Access Program, which permits non-prescription syringe sales to reduce syringe-sharing among injection drug users (IDUs), were enrolled in an intervention to link IDU syringe customers to medical/social services. Sociodemographics, injection practices, beliefs about and experiences with pharmacy use, and medical/social service utilization were compared among 29 IDUs purchasing syringes from intervention pharmacies and 66 IDUs purchasing syringes from control pharmacies using chi-square tests. Intervention IDUs reported more positive experiences in pharmacies than controls; both groups were receptive to a greater public health pharmacist role. These data provide evidence that CBPR aided in the implementation of a pilot structural intervention to promote understanding of drug use and HIV prevention among pharmacy staff, and facilitated expansion of pharmacy services beyond syringe sales in marginalized, drug-using communities. PMID:20528131

  18. Linking hydrologic, physical and chemical habitat environments for the potential assessment of fish community rehabilitation in a developing city

    NASA Astrophysics Data System (ADS)

    Zhao, C. S.; Yang, S. T.; Liu, C. M.; Dou, T. W.; Yang, Z. L.; Yang, Z. Y.; Liu, X. L.; Xiang, H.; Nie, S. Y.; Zhang, J. L.; Mitrovic, S. M.; Yu, Q.; Lim, R. P.

    2015-04-01

    Aquatic ecological rehabilitation is increasingly attracting considerable public and research attention. An effective method that requires less data and expertise would help in the assessment of rehabilitation potential and in the monitoring of rehabilitation activities as complicated theories and excessive data requirements on assemblage information make many current assessment models expensive and limit their wide use. This paper presents an assessment model for restoration potential which successfully links hydrologic, physical and chemical habitat factors to fish assemblage attributes drawn from monitoring datasets on hydrology, water quality and fish assemblages at a total of 144 sites, where 5084 fish were sampled and tested. In this model three newly developed sub-models, integrated habitat index (IHSI), integrated ecological niche breadth (INB) and integrated ecological niche overlap (INO), are established to study spatial heterogeneity of the restoration potential of fish assemblages based on gradient methods of habitat suitability index and ecological niche models. To reduce uncertainties in the model, as many fish species as possible, including important native fish, were selected as dominant species with monitoring occurring over several seasons to comprehensively select key habitat factors. Furthermore, a detrended correspondence analysis (DCA) was employed prior to a canonical correspondence analysis (CCA) of the data to avoid the "arc effect" in the selection of key habitat factors. Application of the model to data collected at Jinan City, China proved effective reveals that three lower potential regions that should be targeted in future aquatic ecosystem rehabilitation programs. They were well validated by the distribution of two habitat parameters: river width and transparency. River width positively influenced and transparency negatively influenced fish assemblages. The model can be applied for monitoring the effects of fish assemblage restoration

  19. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

    PubMed Central

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-01-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  20. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community.

    PubMed

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-03-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  1. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

    NASA Astrophysics Data System (ADS)

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-05-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbially-mediated processes. Soil amended with biochar has been demonstrated to reduce N2O emissions in the field and in laboratory experiments. Although N2O emission mitigation following soil biochar amendment has been reported frequently the underlying processes and specific role of the nitrogen cycling microbial community in decreasing soil N2O emissions has not been subject of systematic investigation. To investigate the impact of biochar on the microbial community of nitrogen-transforming microorganisms we performed a microcosm study with arable soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature wood derived biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative real-time PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil.

  2. Variations in diatom communities at genus and species levels in peatlands (central China) linked to microhabitats and environmental factors.

    PubMed

    Chen, Xu; Bu, Zhaojun; Stevenson, Mark A; Cao, Yanmin; Zeng, Linghan; Qin, Bo

    2016-10-15

    Peatlands are a specialized type of organic wetlands, fulfilling essential roles as global carbon sinks, headwaters of rivers and biodiversity hotspots. Despite their importance, peatlands are being lost at an alarming rate due to human disturbance and climatic variability. Both the scientific and regulatory communities have focused considerable attention on developing tools for assessing environmental changes in peatlands. Diatoms are widely used in biomonitoring studies of lakes, rivers and streams as they have high abundance, specific ecological preferences and can respond rapidly to environmental change. However, diatom-based assessment studies in peatlands remain limited. The aims of this study were to identify indicator species and genus for three types of habitats (hummocks, hollows and ditch edges) in peatlands (central China), to examine the effects of physiochemical factors on diatom composition at genus and species levels, and to compare the efficiency of species- and genus-level identification in environmental assessment. Our results revealed that hummocks were characterized by drought-tolerant diatoms, while hollows were dominated by species and genus preferring wet conditions. Ditch edges were characterized by diatoms with different life strategies. Depth to water table, redox potential, conductivity and calcium were significant predictors of both genus- and species-level composition. According to ordination analyses, pH was not correlated with species composition while it was a significant factor associated with genus-level composition. Genus-level composition outperformed species composition in describing the response of diatoms to environmental variables. Our results indicate that diatoms can be useful environmental indicators of peatlands, and show that genus-level taxonomic analysis can be a potential tool for assessing environmental change in peatlands. PMID:27289395

  3. Effect of Elevated Salt Concentrations on the Aerobic Granular Sludge Process: Linking Microbial Activity with Microbial Community Structure▿

    PubMed Central

    Bassin, J. P.; Pronk, M.; Muyzer, G.; Kleerebezem, R.; Dezotti, M.; van Loosdrecht, M. C. M.

    2011-01-01

    The long- and short-term effects of salt on biological nitrogen and phosphorus removal processes were studied in an aerobic granular sludge reactor. The microbial community structure was investigated by PCR-denaturing gradient gel electrophoresis (DGGE) on 16S rRNA and amoA genes. PCR products obtained from genomic DNA and from rRNA after reverse transcription were compared to determine the presence of bacteria as well as the metabolically active fraction of bacteria. Fluorescence in situ hybridization (FISH) was used to validate the PCR-based results and to quantify the dominant bacterial populations. The results demonstrated that ammonium removal efficiency was not affected by salt concentrations up to 33 g/liter NaCl. Conversely, a high accumulation of nitrite was observed above 22 g/liter NaCl, which coincided with the disappearance of Nitrospira sp. Phosphorus removal was severely affected by gradual salt increase. No P release or uptake was observed at steady-state operation at 33 g/liter NaCl, exactly when the polyphosphate-accumulating organisms (PAOs), “Candidatus Accumulibacter phosphatis” bacteria, were no longer detected by PCR-DGGE or FISH. Batch experiments confirmed that P removal still could occur at 30 g/liter NaCl, but the long exposure of the biomass to this salinity level was detrimental for PAOs, which were outcompeted by glycogen-accumulating organisms (GAOs) in the bioreactor. GAOs became the dominant microorganisms at increasing salt concentrations, especially at 33 g/liter NaCl. In the comparative analysis of the diversity (DNA-derived pattern) and the activity (cDNA-derived pattern) of the microbial population, the highly metabolically active microorganisms were observed to be those related to ammonia (Nitrosomonas sp.) and phosphate removal (“Candidatus Accumulibacter”). PMID:21926194

  4. Microbial food web mapping: linking carbon cycling and community structure in soils through pyrosequencing enabled stable isotope probing

    SciTech Connect

    Buckley, Daniel H.

    2015-03-15

    Soil represents a massive reservoir of active carbon and climate models vary dramatically in predicting how this carbon will respond to climate change over the coming century. A major cause of uncertainty is that we still have a very limited understand the microorganisms that dominate the soil carbon cycle. The vast majority of soil microbes cannot be cultivated in the laboratory and the diversity of organisms and enzymes that participate in the carbon cycle is staggeringly complex. We have developed a new toolbox for exploring the carbon cycle and the metabolic and ecological characteristics of uncultivated microorganisms. The high-resolution nucleic acid stable isotope probing approach that we have developed makes it possible to characterize microbial carbon cycling dynamics in soil. The approach allows us to track multiple 13C-labeled substrates into thousands of microbial taxa over time. Using this approach we have discovered several major lineages of uncultivated microorganisms that participate in cellulose metabolism and are found widely in soils (including Verrucomicrobia and Chloroflexi, which have not previously been implicated as major players in the soil carbon cycle). Furthermore, isotopic labelling of nucleic acids enables community genomics and permits genome fragment binning for a majority of these cellulolytic microorganisms allowing us to explore the metabolic underpinnings of cellulose degradation. This approach has allowed us to describe unexpected dynamics of carbon metabolism with different microbial taxa exhibiting characteristic patterns of carbon substrate incorporation, indicative of distinct ecological strategies. The data we describe allows us to characterize the activity of novel microorganisms as they occur in the environment and these data provide a basis for understanding how the physiological traits of discrete microorganisms sum to govern the complex responses of the soil carbon cycle.

  5. Translation of neurological biomarkers to clinically relevant platforms.

    PubMed

    Hayes, Ronald L; Robinson, Gillian; Muller, Uwe; Wang, Kevin K W

    2009-01-01

    Like proteomics more generally, neuroproteomics has recently been linked to the discovery of biochemical markers of central nervous system (CNS) injury and disease. Although neuroproteomics has enjoyed considerable success in discovery of candidate biomarkers, there are a number of challenges facing investigators interested in developing clinically useful platforms to assess biomarkers for damage to the CNS. These challenges include intrinsic physiological complications such as the blood-brain barrier. Effective translation of biomarkers to clinical practice also requires development of entirely novel pathways and product development strategies. Drawing from lessons learned from applications of biomarkers to traumatic brain injury, this study outlines major elements of such a pathway. As with other indications, biomarkers can have three major areas of application: (1) drug development; (2) diagnosis and prognosis; (3) patient management. Translation of CNS biomarkers to practical clinical platforms raises a number of integrated elements. Biomarker discovery and initial selection needs to be integrated at the earliest stages with components that will allow systematic prioritization and triage of biomarker candidates. A number of important criteria need to be considered in selecting clinical biomarker candidates. Development of proof of concept assays and their optimization and validation represent an often overlooked feature of biomarker translational research. Initial assay optimization should confirm that assays can detect biomarkers in relevant clinical samples. Since access to human clinical samples is critical to identification of biomarkers relevant to injury and disease as well as for assay development, design of human clinical validation studies is an important component of translational biomarker research platforms. Although these clinical studies share much in common with clinical trials for assessment of drug therapeutic efficacy, there are a number of

  6. Fault2SHA- A European Working group to link faults and Probabilistic Seismic Hazard Assessment communities in Europe

    NASA Astrophysics Data System (ADS)

    Scotti, Oona; Peruzza, Laura

    2016-04-01

    The key questions we ask are: What is the best strategy to fill in the gap in knowledge and know-how in Europe when considering faults in seismic hazard assessments? Are field geologists providing the relevant information for seismic hazard assessment? Are seismic hazard analysts interpreting field data appropriately? Is the full range of uncertainties associated with the characterization of faults correctly understood and propagated in the computations? How can fault-modellers contribute to a better representation of the long-term behaviour of fault-networks in seismic hazard studies? Providing answers to these questions is fundamental, in order to reduce the consequences of future earthquakes and improve the reliability of seismic hazard assessments. An informal working group was thus created at a meeting in Paris in November 2014, partly financed by the Institute of Radioprotection and Nuclear Safety, with the aim to motivate exchanges between field geologists, fault modellers and seismic hazard practitioners. A variety of approaches were presented at the meeting and a clear gap emerged between some field geologists, that are not necessarily familiar with probabilistic seismic hazard assessment methods and needs and practitioners that do not necessarily propagate the "full" uncertainty associated with the characterization of faults. The group thus decided to meet again a year later in Chieti (Italy), to share concepts and ideas through a specific exercise on a test case study. Some solutions emerged but many problems of seismic source characterizations with people working in the field as well as with people tackling models of interacting faults remained. Now, in Wien, we want to open the group and launch a call for the European community at large to contribute to the discussion. The 2016 EGU session Fault2SHA is motivated by such an urgency to increase the number of round tables on this topic and debate on the peculiarities of using faults in seismic hazard

  7. Biomarkers present in asphaltenes

    SciTech Connect

    Philp, R.P.

    1985-01-01

    The significance and distribution of biomarkers in sediments, source rocks and crude oils are well documented in the literature. Little attention has been directed towards the biomarkers that are present in the asphaltene fractions of crude oils and source rock extracts. Asphaltene fractions by definition are insoluble in certain solvents and consist of high molecular components which makes them difficult to analyze by techniques commonly used to characterize the soluble extracts. Asphaltenes are ideally suited for analysis by microscale pyrolysis techniques (py) combined with gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS). Utilization of the multiple ion detection technique in conjunction with the py-GC-MS analyses permits the distribution of the steranes, triterpanes and other biomarker produced by pyrolysis of the asphaltenes to be easily determined. It is proposed in this paper to discuss the pyrolysis of asphaltene from a variety of source rocks and analysis of the biomarkers, released by the pyrolysis. These biomarkers distributions can be used to obtain information on source and maturity of the organic matter in a similar manner to using the soluble biomarkers. It is proposed to discuss the asphaltene biomarker distributions and also to speculate as to why certain biomarkers are present only in the extracts and asphaltenes and not produced by pyrolysis of the kerogens.

  8. Organic biomarker records spanning the last 34,800 years from the southeastern Brazilian upper slope: links between sea surface temperature, displacement of the Brazil Current, and marine productivity

    NASA Astrophysics Data System (ADS)

    Lourenço, Rafael André; de Mahiques, Michel Michaelovitch; Wainer, Ilana Elazari Klein Coaracy; Rosell-Melé, Antoni; Bícego, Márcia Caruso

    2016-06-01

    Collective assessment of marine and terrigenous organic biomarkers was performed on a sediment core spanning the last 34,800 years on the upper slope southeast of Brazil to verify the signatures of climatic variations in sea surface temperature (SST), marine productivity, and the flux of terrigenous material in this region. This evaluation is based on marine and terrigenous proxies including alkenones, chlorins, aliphatic hydrocarbons, n-alcohols, and fatty acids. This first report of organic biomarker data for this region confirms a correlation between SST, changes in terrigenous organic matter flow into the ocean, and marine productivity over the last 34.8 ka as a response to the displacement of the Brazil Current. Conditions prevailing during marine isotopic stage (MIS) 3 may be considered intermediate between the last glacial maximum (LGM) and the Late Holocene. For MIS 2, a period of low relative sea level, it was verified that the lowest SSTs were associated with the LGM and higher marine productivity. SST increased by up to 4.4 °C between the LGM and the Holocene. This reveals synchronicity between SST on the southeastern Brazilian upper slope and the North Atlantic Ocean SST records reported in earlier studies.

  9. Biomarkers in Autism

    PubMed Central

    Goldani, Andre A. S.; Downs, Susan R.; Widjaja, Felicia; Lawton, Brittany; Hendren, Robert L.

    2014-01-01

    Autism spectrum disorders (ASDs) are complex, heterogeneous disorders caused by an interaction between genetic vulnerability and environmental factors. In an effort to better target the underlying roots of ASD for diagnosis and treatment, efforts to identify reliable biomarkers in genetics, neuroimaging, gene expression, and measures of the body’s metabolism are growing. For this article, we review the published studies of potential biomarkers in autism and conclude that while there is increasing promise of finding biomarkers that can help us target treatment, there are none with enough evidence to support routine clinical use unless medical illness is suspected. Promising biomarkers include those for mitochondrial function, oxidative stress, and immune function. Genetic clusters are also suggesting the potential for useful biomarkers. PMID:25161627

  10. Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs

    PubMed Central

    Jahnke, Linda L.; Farmer, Jack D.; Cady, Sherry L.

    2014-01-01

    Abstract The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration. Key Words: Lipid biomarkers—Photosynthesis—Iron—Hot springs—Mars. Astrobiology 14, 502–521. PMID:24886100

  11. Production and early preservation of lipid biomarkers in iron hot springs.

    PubMed

    Parenteau, Mary N; Jahnke, Linda L; Farmer, Jack D; Cady, Sherry L

    2014-06-01

    The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51-54°C, pH 5.5-6.0, and are very high in dissolved Fe(II) at 5.8-5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs--environmental conditions that have been previously identified as highly relevant for Mars exploration. PMID:24886100

  12. Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs

    SciTech Connect

    Parenteau, Mary N.; Jahnke, Linda L.; Farmer, Jack D.; Cady, Sherry L.

    2014-06-01

    The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. Finally, this study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration.

  13. Biomarkers of basic activities of daily living in Alzheimer's disease.

    PubMed

    Hall, James R; Johnson, Leigh A; Barber, Robert C; Vo, Hoa T; Winter, A Scott; O'Bryant, Sid E

    2012-01-01

    Functional impairment is common in Alzheimer's disease (AD) and related to increased caregiver burden and institutionalization. There is a dearth of research investigating the relationship between specific biomarkers and basic activities of daily living (BADLs) such as toileting, feeding, dressing, grooming, bathing, and ambulating. The present study examined the relationship between serum based biomarkers and specific ADLs in a sample of AD patients. Data were collected from 196 participants enrolled in the Texas Alzheimer's Research and Care Consortium Project and diagnosed with AD. BADLs were measured using the Lawton-Brody Physical Self-Maintenance Scale. A panel of 22 biomarkers previously found to be related to AD pathology was used for the analysis. Stepwise regression modeling was used to assess the link between the biomarkers and BADLs. Results were also examined by gender. Nine of the 22 biomarkers were significantly related to BADLs. When stratified by gender, the biomarkers accounted for 32% of the variance in the males and 27% in females. The pattern of significant biomarkers differed by gender with IL 7 and Tenascin C significantly related to BADLs for females and IL 15 significantly related to BADLs for males. The results of this study indicated that a small number of serum based biomarkers are related to BADLs, and these biomarkers differed by gender. PMID:22571981

  14. Impact of biomarker development on drug safety assessment

    SciTech Connect

    Marrer, Estelle; Dieterle, Frank

    2010-03-01

    Drug safety has always been a key aspect of drug development. Recently, the Vioxx case and several cases of serious adverse events being linked to high-profile products have increased the importance of drug safety, especially in the eyes of drug development companies and global regulatory agencies. Safety biomarkers are increasingly being seen as helping to provide the clarity, predictability, and certainty needed to gain confidence in decision making: early-stage projects can be stopped quicker, late-stage projects become less risky. Public and private organizations are investing heavily in terms of time, money and manpower on safety biomarker development. An illustrative and 'door opening' safety biomarker success story is the recent recognition of kidney safety biomarkers for pre-clinical and limited translational contexts by FDA and EMEA. This milestone achieved for kidney biomarkers and the 'know how' acquired is being transferred to other organ toxicities, namely liver, heart, vascular system. New technologies and molecular-based approaches, i.e., molecular pathology as a complement to the classical toolbox, allow promising discoveries in the safety biomarker field. This review will focus on the utility and use of safety biomarkers all along drug development, highlighting the present gaps and opportunities identified in organ toxicity monitoring. A last part will be dedicated to safety biomarker development in general, from identification to diagnostic tests, using the kidney safety biomarkers success as an illustrative example.

  15. Impact of biomarker development on drug safety assessment.

    PubMed

    Marrer, Estelle; Dieterle, Frank

    2010-03-01

    Drug safety has always been a key aspect of drug development. Recently, the Vioxx case and several cases of serious adverse events being linked to high-profile products have increased the importance of drug safety, especially in the eyes of drug development companies and global regulatory agencies. Safety biomarkers are increasingly being seen as helping to provide the clarity, predictability, and certainty needed to gain confidence in decision making: early-stage projects can be stopped quicker, late-stage projects become less risky. Public and private organizations are investing heavily in terms of time, money and manpower on safety biomarker development. An illustrative and "door opening" safety biomarker success story is the recent recognition of kidney safety biomarkers for pre-clinical and limited translational contexts by FDA and EMEA. This milestone achieved for kidney biomarkers and the "know how" acquired is being transferred to other organ toxicities, namely liver, heart, vascular system. New technologies and molecular-based approaches, i.e., molecular pathology as a complement to the classical toolbox, allow promising discoveries in the safety biomarker field. This review will focus on the utility and use of safety biomarkers all along drug development, highlighting the present gaps and opportunities identified in organ toxicity monitoring. A last part will be dedicated to safety biomarker development in general, from identification to diagnostic tests, using the kidney safety biomarkers success as an illustrative example. PMID:20036272

  16. Why commercial broadband satellites absolutely must have laser intersatellite links (ISLs) and how the free-space laser communications community could let them down

    NASA Astrophysics Data System (ADS)

    Freidell, James E.

    1998-05-01

    Large commercial satellite programs needing high bandwidth inter-satellite links (ISLs) are growing rapidly in number. Precious few are visibly maturing. These commercial needs present greater customer diversity and opportunity for free- space laser communications application than the current plans of all the world's governments combined, multiplied manyfold. However, commercial customers generally do not have access to the independent, knowledgeable, but often heterogeneous laser communications expertise upon which government programs have historically relied. Moreover, commercial needs differ substantially from those of governments, particularly in the areas of price sensitivity and assured delivery on schedule and meeting all requirements. And the number of would-be laser ISL terminal suppliers also grows despite little verifiable expertise in actually delivering complete, working space-based laser ISL terminals, regardless of price or performance. Consequently, the opportunity for mistakes, disappointments, and outright failure is intensified. More 'red meatballs' are unfortunately on the horizon and neither customers nor suppliers recognize the warning signs. Is ignorance bliss? Virtually the entire space communications community appears oblivious to emerging terrestrial broadband communications projects which appear better backed with superior management far more attentive to time-to-market and other schedule and business considerations than any space venture. Space systems offer advantages through realizing global network operations not possible terrestrially, yet few promoters recogni the potential. Might these be omens worth capitalizing upon, or perhaps from which escape may be warranted? This paper provides a commercial market status update to that presented in preceding years' papers. Laser ISL applications are reviewed which enable commercial broadband satellite customer opportunities not yet recognized among most in the customer community, despite

  17. Linking community tolerance and structure with low metallic contamination: a field study on 13 biofilms sampled across the Seine river basin.

    PubMed

    Fechner, Lise C; Gourlay-Francé, Catherine; Tusseau-Vuillemin, Marie-Hélène

    2014-03-15

    It is difficult to assess the biological consequences of diffuse water contamination by micropollutants which are present in rivers at low, even sublethal levels. River biofilms, which respond quickly to changes of environmental parameters, are good candidates to acquire knowledge on the response of aquatic organisms to diffuse chemical contamination in the field. The study was designed as an attempt to link biofilm metal tolerance and metallic contamination in a field survey covering 13 different sampling sites in the Seine river basin (north of France) with low contamination levels. Cd and Zn tolerance of heterotrophic communities was assessed using a short-term toxicity test based on β-glucosidase activity. Metal tolerance levels varied between sites but there was no obvious correlation between tolerance and corresponding water contamination levels for Cd and Zn. Indeed, metallic contamination at the sampling sites remained subtle when compared to water quality standards (only two sampling sites had either Zn or both Cu and Zn concentrations exceeding the Environmental Quality Standards set by the EU Water Framework Directive). Yet, multivariate analysis of the data using Partial Least Squares Regression revealed that both metallic and environmental parameters were important variables explaining the variability of metal tolerance levels. Automated Ribosomal Intergenic Spacer Analysis (ARISA) was also performed on both bacterial and eukaryotic biofilm communities from the 13 sampling sites. Multivariate analysis of ARISA fingerprints revealed that biofilms with similar tolerance levels have similar ARISA profiles. Those results confirm that river biofilms are potential indicators of low, diffuse contamination levels of aquatic systems. PMID:24429101

  18. New serological biomarkers of inflammatory bowel disease

    PubMed Central

    Li, Xuhang; Conklin, Laurie; Alex, Philip

    2008-01-01

    Serological biomarkers in inflammatory bowel disease (IBD) are a rapidly expanding list of non-invasive tests for objective assessments of disease activity, early diagnosis, prognosis evaluation and surveillance. This review summarizes both old and new biomarkers in IBD, but focuses on the development and characterization of new serological biomarkers (identified since 2007). These include five new anti-glycan antibodies, anti-chitobioside IgA (ACCA), anti-laminaribioside IgG (ALCA), anti-manobioside IgG (AMCA), and antibodies against chemically synthesized (Σ) two major oligomannose epitopes, Man α-1,3 Man α-1,2 Man (ΣMan3) and Man α-1,3 Man α-1,2 Man α-1,2 Man (ΣMan4). These new biomarkers serve as valuable complementary tools to existing biomarkers not only in differentiating Crohn’s disease (CD), ulcerative colitis (UC), normal and other non-IBD gut diseases, but also in predicting disease involvement (ileum vs colon), IBD risk (as subclinical biomarkers), and disease course (risk of complication and surgery). Interestingly, the prevalence of the antiglycan antibodies, including anti-Saccharomyces cerevisiae antibodies (ASCA), ALCA and AMCA, was found to be associated with single nucleotide polymorphisms (SNPs) of IBD susceptible genes such as NOD2/CARD15, NOD1/CARD4, toll-like receptors (TLR) 2 and 4, and β-defensin-1. Furthermore, a gene dosage effect was observed: anti-glycan positivity became more frequent as the number of NOD2/CARD15 SNPS increased. Other new serum/plasma IBD biomarkers reviewed include ubiquitination factor E4A (UBE4A), CXCL16 (a chemokine), resistin, and apolipoprotein A-IV. This review also discusses the most recent studies in IBD biomarker discovery by the application of new technologies such as proteomics, fourier transform near-infrared spectroscopy, and multiplex enzyme-linked immunosorbent assay (ELISA)’s (with an emphasis on cytokine/chemokine profiling). Finally, the prospects of developing more clinically useful

  19. Incorporating Biomarkers in Studies of Chemoprevention.

    PubMed

    Fabian, Carol J; Kimler, Bruce F

    2016-01-01

    Despite Food and Drug Administration approval of tamoxifen and raloxifene for breast cancer risk reduction and endorsement by multiple agencies, uptake of these drugs for primary prevention in the United States is only 4% for risk eligible women likely to benefit from their use. Side effects coupled with incomplete efficacy and lack of a survival advantage are the likely reasons. This disappointing uptake, after the considerable effort and expense of large Phase III cancer incidence trials required for approval, suggests that a new paradigm is required. Current prevention research is focused on (1) refining risk prediction, (2) exploring behavioral and natural product interventions, and (3) utilizing novel translational trial designs for efficacy. Risk biomarkers will play a central role in refining risk estimates from traditional models and selecting cohorts for prevention trials. Modifiable risk markers called surrogate endpoint or response biomarkers will continue to be used in Phase I and II prevention trials to determine optimal dose or exposure and likely effectiveness from an intervention. The majority of Phase II trials will continue to assess benign breast tissue for response and mechanism of action biomarkers. Co-trials are those in which human and animal cohorts receive the same effective dose and the same tissue biomarkers are assessed for modulation due to the intervention, but then additional animals are allowed to progress to cancer development. These collaborations linking biomarker modulation and cancer prevention may obviate the need for cancer incidence trials for non-prescription interventions. PMID:26987531

  20. Linking Nitrogen-Cycling Microbial Communities to Environmental Fluctuations and Biogeochemical Activity in a Large, Urban Estuary: the San Francisco Bay-Delta

    NASA Astrophysics Data System (ADS)

    Francis, C.

    2015-12-01

    Nitrogen (N) availability is an important factor controlling productivity and thus carbon cycling in estuaries. The fate of N in estuaries depends on the activities of the microbes that carry out the N-cycle, which in turn depend on factors such as organic matter availability, dissolved inorganic N, salinity, oxygen, and temperature. Key microbial N transformations include nitrification (the aerobic oxidation of ammonia to nitrite and nitrate) and denitrification (the anaerobic reduction of nitrate to dinitrogen gas). While denitrification leads to N loss, nitrification is the only link between reduced N (produced by decomposition) and oxidized N (substrates for N loss processes), and both processes are known to produce nitrous oxide (N2O), a potent greenhouse gas. Understanding controls of N-cycling in the San Francisco Bay-Delta (SFBD)—the largest estuary on the west coast of North America—is particularly important, as this urban estuary is massively polluted with N, even compared to classic "eutrophic" systems. Interestingly, the SFBD has been spared the detrimental consequences of nutrient enrichment, largely due to high suspended sediment concentrations (and thus low light penetration) throughout the water column, combined with high grazing pressure. However, the recent "clearing" of SFBD waters due to a sharp decrease in suspended sediments may significantly alter the ecology of the estuary, by increasing phytoplankton growth. Thus, the SFBD may be losing its historical resilience to eutrophication, and may soon be "high-nutrient, low-chlorophyll" no more. Elucidating the environmental factors affecting the community structure, activity, and functioning of N-cycling microbes in SFBD is crucial for determining how changes in turbidity and productivity will be propagated throughout the ecosystem. While substantial ecological research in the SFBD has focused on phytoplankton and food webs, bacterial and archaeal communities have received far less attention

  1. Metabolic products as biomarkers

    USGS Publications Warehouse

    Melancon, M.J.; Alscher, R.; Benson, W.; Kruzynski, G.; Lee, R.F.; Sikka, H.C.; Spies, R.B.

    1992-01-01

    Ideally, endogenous biomarkers would indicate both exposure and environmental effects of toxic chemicals; however, such comprehensive biochemical and physiological indices are currently being developed and, at the present time, are unavailable for use in environmental monitoring programs. Continued work is required to validate the use of biochemical and physiological stress indices as useful components of monitoring programs. Of the compounds discussed only phytochelatins and porphyrins are currently in biomarkers in a useful state; however, glutathione,metallothioneins, stress ethylene, and polyamines are promising as biomarkers in environmental monitoring.

  2. Biomarkers in Severe Asthma.

    PubMed

    Wan, Xiao Chloe; Woodruff, Prescott G

    2016-08-01

    Biomarkers have been critical for studies of disease pathogenesis and the development of new therapies in severe asthma. In particular, biomarkers of type 2 inflammation have proven valuable for endotyping and targeting new biological agents. Because of these successes in understanding and marking type 2 inflammation, lack of knowledge regarding non-type 2 inflammatory mechanisms in asthma will soon be the major obstacle to the development of new treatments and management strategies in severe asthma. Biomarkers can play a role in these investigations as well by providing insight into the underlying biology in human studies of patients with severe asthma. PMID:27401625

  3. Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data

    PubMed Central

    Tosas Auguet, Olga; Betley, Jason R.; Stabler, Richard A.; Patel, Amita; Ioannou, Avgousta; Marbach, Helene; Hearn, Pasco; Aryee, Anna; Goldenberg, Simon D.; Otter, Jonathan A.; Desai, Nergish; Karadag, Tacim; Grundy, Chris; Gaunt, Michael W.; Cooper, Ben S.; Edgeworth, Jonathan D.; Kypraios, Theodore

    2016-01-01

    Background Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation. Methods and Findings This study involved spatial analysis of cross-sectional data linked with all MRSA isolates identified by three National Health Service (NHS) microbiology laboratories between 1 November 2011 and 29 February 2012. The cohort of hospital-based NHS microbiology diagnostic services serves 867,254 usual residents in the Lambeth, Southwark, and Lewisham boroughs in South East London, United Kingdom (UK). Isolates were classified as HA- or CA-MRSA based on whole genome sequencing. All MRSA cases identified over 4 mo within the three-borough catchment area (n = 471) were mapped to small geographies and linked to area-level aggregated socioeconomic and demographic data. Disease mapping and ecological regression models were used to infer the most likely transmission niches for each MRSA genetic classification and to describe the spatial epidemiology of MRSA in relation to social determinants. Specifically, we aimed to identify demographic and socioeconomic population traits that explain cross-area extra variation in HA- and CA-MRSA relative risks following adjustment for hospital attendance data. We explored the potential for associations with

  4. Going retro: Oxidative stress biomarkers in modern redox biology.

    PubMed

    Margaritelis, N V; Cobley, J N; Paschalis, V; Veskoukis, A S; Theodorou, A A; Kyparos, A; Nikolaidis, M G

    2016-09-01

    The field of redox biology is inherently intertwined with oxidative stress biomarkers. Oxidative stress biomarkers have been utilized for many different objectives. Our analysis indicates that oxidative stress biomarkers have several salient applications: (1) diagnosing oxidative stress, (2) pinpointing likely redox components in a physiological or pathological process and (3) estimating the severity, progression and/or regression of a disease. On the contrary, oxidative stress biomarkers do not report on redox signaling. Alternative approaches to gain more mechanistic insights are: (1) measuring molecules that are integrated in pathways linking redox biochemistry with physiology, (2) using the exomarker approach and (3) exploiting -omics techniques. More sophisticated approaches and large trials are needed to establish oxidative stress biomarkers in the clinical setting. PMID:26855421

  5. 2-Furoylglycine as a Candidate Biomarker of Coffee Consumption.

    PubMed

    Heinzmann, Silke S; Holmes, Elaine; Kochhar, Sunil; Nicholson, Jeremy K; Schmitt-Kopplin, Philippe

    2015-09-30

    Specific and sensitive food biomarkers are necessary to support dietary intake assessment and link nutritional habits to potential impact on human health. A multistep nutritional intervention study was conducted to suggest novel biomarkers for coffee consumption. (1)H NMR metabolic profiling combined with multivariate data analysis resolved 2-furoylglycine (2-FG) as a novel putative biomarker for coffee consumption. We relatively quantified 2-FG in the urine of coffee drinkers and investigated its origin, metabolism, and excretion kinetics. When searching for its potential precursors, we found different furan derivatives in coffee products, which are known to get metabolized to 2-FG. Maximal urinary excretion of 2-FG occurred 2 h after consumption (p = 0.0002) and returned to baseline after 24 h (p = 0.74). The biomarker was not excreted after consumption of coffee substitutes such as tea and chicory coffee and might therefore be a promising acute biomarker for the detection of coffee consumption in human urine. PMID:26357997

  6. Hopanoid Biomarker Preservation In Coniform (Phormidium) Stromatolites in Siliceous Thermal Springs, Yellowstone National Park

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Summons, Roger E.; Farmer, Jack D.; Klein, Harold P.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    The microbial communities that characterize modem hydrothermal ecosystems serve as modern analogs to those thought to have dominated early environments on Earth and possibly Mars. The importance of such hydrothermal systems as targets in exploring for an early biosphere on Mars is well established. Such work provides an important basis for the analysis of Martian samples associated with such environments. The surviving molecular structure and isotopic signature of diagnostic lipid biomarkers found as chemical fossils can provide a link between modern bacterially dominated ecosystems and their ancient counterparts. We are interested in the processes involved in the deposition and/or degradation of organic material in moderately thermal, silicifying microbial mats, particularly as this relates to the potential for preservation of some biomarker components known to be more highly resistant to microbial degradation. Several excellent biomarker molecules are associated with the cyanobacteria that dominate these mats, particularly the 2-methylbacteriohopanepolyols (2-MeBHP). These compounds are ubiquitous on Earth and are not easily degraded in nature, a fact documented by their detection in ancient Earth rocks dating back as far as 2,700 Ma.

  7. Biomarker time out.

    PubMed

    Petzold, Axel; Bowser, Robert; Calabresi, Paolo; Zetterberg, Henrik; Uitdehaag, Bernard M J

    2014-10-01

    The advancement of knowledge relies on scientific investigations. The timing between asking a question and data collection defines if a study is prospective or retrospective. Prospective studies look forward from a point in time, are less prone to bias and are considered superior to retrospective studies. This conceptual framework conflicts with the nature of biomarker research. New candidate biomarkers are discovered in a retrospective manner. There are neither resources nor time for prospective testing in all cases. Relevant sources for bias are not covered. Ethical questions arise through the time penalty of an overly dogmatic concept. The timing of sample collection can be separated from testing biomarkers. Therefore the moment of formulating a hypothesis may be after sample collection was completed. A conceptual framework permissive to asking research questions without the obligation to bow to the human concept of calendar time would simplify biomarker research, but will require new safeguards against bias. PMID:24557857

  8. Biomarkers in ALH84001???

    NASA Technical Reports Server (NTRS)

    Treiman, Allen H.

    1999-01-01

    D. McKay and colleagues suggested that four sets of features in ALH84001 were biomarkers, signs of an ancient martian biota that once inhabited the meteorite. Subsequent work has not validated their hypothesis; each suggested biomarker has been found to be ambiguous or immaterial. Nor has their hypothesis been disproved. Rather, it is now one of many hypotheses about the alteration of ALH84001. Additional information is contained in the original extended abstract.

  9. Method validation and preliminary qualification of pharmacodynamic biomarkers employed to evaluate the clinical efficacy of an antisense compound (AEG35156) targeted to the X-linked inhibitor of apoptosis protein XIAP.

    PubMed

    Cummings, J; Ranson, M; Lacasse, E; Ganganagari, J R; St-Jean, M; Jayson, G; Durkin, J; Dive, C

    2006-07-01

    Data are presented on pharmacodynamic (PD) method validation and preliminary clinical qualification of three PD biomarker assays. M65 Elisa, which quantitates different forms of circulating cytokeratin 18 (CK18) as putative surrogate markers of both apoptotic and nonapoptotic tumour cell death, was shown to be highly reproducible: calibration curve linearity r2 = 0.996, mean accuracy > 91% and mean precision < 3%, n = 27. Employing recombinant (r) CK18 and caspase cleaved CK18 (CK18 Asp396 neo-epitope) as external standards, kit to kit reproducibly was < 6% (n = 19). rCK18 was stable in plasma for 4 months at -20 degrees C and -80 degrees C, for 4 weeks at 4 degrees C and had a half-life of 2.3 days at 37 degrees C. Cytokeratin 18 Asp396 NE, the M30 Apoptosense Elisa assay antigen, was stable in plasma for 6 months at -20 degrees C and -80 degrees C, for 3 months at 4 degrees C, while its half-life at 37 degrees C was 3.8 days. Within-day variations in endogenous plasma concentrations of the M30 and M65 antigens were assessed in two predose blood samples collected from a cohort of 15 ovarian cancer patients receiving carboplatin chemotherapy and were shown to be no greater than the variability associated with methods themselves. Between-day fluctuations in circulating levels of the M30 and M65 antigens and in XIAP mRNA levels measured in peripheral blood mononuclear cells by quantitative (q) RT-PCR were evaluated in two predose blood samples collected with a 5- to 7-day gap from 23 patients with advanced cancer enrolled in a phase I trial. The mean variation between the two pretreatment values ranged from 13 to 14 to 25%, respectively, for M65, M30 and qRT-PCR. These data suggest that the M30 and M65 Elisa's and qRT-PCR as PD biomarker assays have favourable performance characteristics for further investigation in clinical trials of anticancer agents which induce tumour apoptosis/necrosis or knockdown of the anti-apoptotic protein XIAP. PMID:16804528

  10. Method validation and preliminary qualification of pharmacodynamic biomarkers employed to evaluate the clinical efficacy of an antisense compound (AEG35156) targeted to the X-linked inhibitor of apoptosis protein XIAP

    PubMed Central

    Cummings, J; Ranson, M; LaCasse, E; Ganganagari, J R; St-Jean, M; Jayson, G; Durkin, J; Dive, C

    2006-01-01

    Data are presented on pharmacodynamic (PD) method validation and preliminary clinical qualification of three PD biomarker assays. M65 Elisa, which quantitates different forms of circulating cytokeratin 18 (CK18) as putative surrogate markers of both apoptotic and nonapoptotic tumour cell death, was shown to be highly reproducible: calibration curve linearity r2=0.996, mean accuracy >91% and mean precision <3%, n=27. Employing recombinant (r) CK18 and caspase cleaved CK18 (CK18 Asp396 neo-epitope) as external standards, kit to kit reproducibly was <6% (n=19). rCK18 was stable in plasma for 4 months at −20°C and −80°C, for 4 weeks at 4°C and had a half-life of 2.3 days at 37°C. Cytokeratin 18 Asp396 NE, the M30 Apoptosense Elisa assay antigen, was stable in plasma for 6 months at −20°C and −80°C, for 3 months at 4°C, while its half-life at 37°C was 3.8 days. Within-day variations in endogenous plasma concentrations of the M30 and M65 antigens were assessed in two predose blood samples collected from a cohort of 15 ovarian cancer patients receiving carboplatin chemotherapy and were shown to be no greater than the variability associated with methods themselves. Between-day fluctuations in circulating levels of the M30 and M65 antigens and in XIAP mRNA levels measured in peripheral blood mononuclear cells by quantitative (q) RT–PCR were evaluated in two predose blood samples collected with a 5- to 7-day gap from 23 patients with advanced cancer enrolled in a phase I trial. The mean variation between the two pretreatment values ranged from 13 to 14 to 25%, respectively, for M65, M30 and qRT–PCR. These data suggest that the M30 and M65 Elisa's and qRT–PCR as PD biomarker assays have favourable performance characteristics for further investigation in clinical trials of anticancer agents which induce tumour apoptosis/necrosis or knockdown of the anti-apoptotic protein XIAP. PMID:16804528

  11. Biomarkers of neurotoxic shellfish poisoning.

    PubMed

    Abraham, Ann; Plakas, Steven M; Flewelling, Leanne J; El Said, Kathleen R; Jester, Edward L E; Granade, Hudson R; White, Kevin D; Dickey, Robert W

    2008-08-01

    Urine specimens from patients diagnosed with neurotoxic shellfish poisoning (NSP) were examined for biomarkers of brevetoxin intoxication. Brevetoxins were concentrated from urine by using solid-phase extraction (SPE), and analyzed by enzyme-linked immunosorbent assay (ELISA) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Urine extracts were fractionated by LC, and fractions analyzed for brevetoxins by ELISA. In subsequent LC-MS/MS analyses, several brevetoxin metabolites of B-type backbone were identified, with elution profiles consistent with those of ELISA. The more abundant brevetoxin metabolites in urine were characterized structurally by LC-MS/MS. With the exception of BTX-3, brevetoxin metabolites in urine differed from those found in shellfish and in shellfish meal remnants. Proposed structures of these major urinary metabolites are methylsulfoxy BTX-3, 27-epoxy BTX-3, and reduced BTX-B5. BTX-3 was found in all specimens examined. BTX-3 concentrations in urine, as determined by LC-MS/MS, correlated well with composite toxin measurements by ELISA (r(2)=0.96). BTX-3 is a useful biomarker for confirmation of clinical diagnosis of NSP. PMID:18582487

  12. Biomarkers and pediatric environmental health.

    PubMed

    Lubin, B; Lewis, R

    1995-09-01

    It is now possible to identify biochemical and/or cellular changes in humans due to exposure to an environmental toxin. These changes are called biomarkers and are currently used in research studies to identify individuals exposed to specific toxic substances. Advances in the field of biomarker technology may have important implications for the detection, prevention, and treatment of certain diseases in children. This technology may enable physicians to screen children who have no clinically detectable illness for evidence of exposure to specific toxins. Such information could lead to implementation of preventive measures and development of new therapeutic strategies. However, several important issues, including potential adverse consequences resulting from the widespread use of this technology, must be considered prior to its utilization within a clinical setting. Leaders of the pediatric and public health communities should recognize the paucity of scientific data in the pediatric environmental health area, and new approaches to this important aspect of child health should be developed. This article will address several of the issues involved in pediatric environmental health and consider questions that should be answered as the potential for technology transfer becomes a reality. PMID:8549501

  13. Etiology of community-acquired pneumonia in a population-based study: Link between etiology and patients characteristics, process-of-care, clinical evolution and outcomes

    PubMed Central

    2012-01-01

    Background The etiologic profile of community-acquired pneumonia (CAP) for each age group could be similar among inpatients and outpatients. This fact brings up the link between etiology of CAP and its clinical evolution and outcome. Furthermore, the majority of pneumonia etiologic studies are based on hospitalized patients, whereas there have been no recent population-based studies encompassing both inpatients and outpatients. Methods To evaluate the etiology of CAP, and the relationship among the different pathogens of CAP to patients characteristics, process-of-care, clinical evolution and outcomes, a prospective population-based study was conducted in Spain from April 1, 2006, to June 30, 2007. Patients (age >18) with CAP were identified through the family physicians and the hospital area. Results A total of 700 patients with etiologic evaluation were included: 276 hospitalized and 424 ambulatory patients. We were able to define the aetiology of pneumonia in 55.7% (390/700). The most frequently isolated organism was S. pneumoniae (170/390, 43.6%), followed by C. burnetti (72/390, 18.5%), M. pneumoniae (62/390, 15.9%), virus as a group (56/390, 14.4%), Chlamydia species (39/390, 106%), and L. pneumophila (17/390, 4.4%). The atypical pathogens and the S. pneumoniae are present in pneumonias of a wide spectrum of severity and age. Patients infected by conventional bacteria were elderly, had a greater hospitalization rate, and higher mortality within 30 days. Conclusions Our study provides information about the etiology of CAP in the general population. The microbiology of CAP remains stable: infections by conventional bacteria result in higher severity, and the S. pneumoniae remains the most important pathogen. However, atypical pathogens could also infect patients in a wide spectrum of severity and age. PMID:22691449

  14. Biomarkers and heart disease.

    PubMed

    Sun, R-R; Lu, L; Liu, M; Cao, Y; Li, X-C; Liu, H; Wang, J; Zhang, P-Y

    2014-10-01

    Heart failure (HF) results from the impaired ability of heart to fill or pump out blood. HF is a common health problem with a multitude of causes and affects ~30 million people worldwide. Since ageing is a major risk factor for HF and as several treatment options are currently available to prolong the patients' survival, the number of affected patients is expected to grow. Even though traditional methods of assessment have been in use for managing HF, these are limited by time consuming and costly subjective interpretation and also by their invasive nature. Comparatively, biomarkers offer an objective and biologically relevant information that in conjunction with the patients' clinical findings provides optimal picture regarding the status of the HF patient and thus helps in diagnosis and prognosis. The current gold standard biomarkers for the diagnosis and prognosis of HF are B-type natriuretic peptide (BNP) and N-terminal proBNP (NT-proBNP). Additional novel biomarkers (e.g., mid-regional pro atrial natriuretic peptide (MR-proANP), mid-regional pro adrenomedullin (MR-proADM), troponins, soluble ST2 (sST2), growth differentiation factor (GDF)-15 and galectin-3) can potentially identify different pathophysiological processes such as myocardial insult, inflammation and remodeling as the causes for the development and progression of HF. Different biomarkers of HF not only reflect the underlying mechanisms/pathways of HF and also its progression and also point specific therapy options. A multi-biomarker approach for personalized medical care is not too far fetched and such approach can greatly enhance diagnosis, prognostication, and therapy guidance for HF. In this review we describe the current status of HF biomarkers in clinical use and in laboratory research and the efforts aimed at the identification of novel biomarkers for HF. PMID:25339488

  15. Mass spectrometry for biomarker development

    SciTech Connect

    Wu, Chaochao; Liu, Tao; Baker, Erin Shammel; Rodland, Karin D.; Smith, Richard D.

    2015-06-19

    Biomarkers potentially play a crucial role in early disease diagnosis, prognosis and targeted therapy. In the past decade, mass spectrometry based proteomics has become increasingly important in biomarker development due to large advances in technology and associated methods. This chapter mainly focuses on the application of broad (e.g. shotgun) proteomics in biomarker discovery and the utility of targeted proteomics in biomarker verification and validation. A range of mass spectrometry methodologies are discussed emphasizing their efficacy in the different stages in biomarker development, with a particular emphasis on blood biomarker development.

  16. Biomarkers: A potential prognostic tool for silicosis

    PubMed Central

    Pandey, Jai Krishna; Agarwal, Deepa

    2012-01-01

    Long-term exposure to respirable dust containing silica leads to pneumoconiosis/silicosis. The disease is irreversible and incurable, and only preventive steps such as job rotation, use of personal protective equipment, etc., remain solutions to the problem. Under such a situation, early diagnosis or prediction may become very useful to control the disease. Biomarkers are biological parameters in blood serum that change their values with deposition of dust in the lung and onset of lung fibrosis. Since these biomarkers can help us to diagnose and in the prognosis of the disease before it is actually diagnosed by the conventional X-ray technique and lung function test used for diagnosis of silicosis. The present paper describes the various types of available biomarkers, their application and usefulness. The paper also suggests that further study of the behavior/level of these biomarkers on a specific subject with time may provide more useful information of a confirmatory nature for prevention of dust-linked diseases. PMID:23776317

  17. Biomarkers: A potential prognostic tool for silicosis.

    PubMed

    Pandey, Jai Krishna; Agarwal, Deepa

    2012-09-01

    Long-term exposure to respirable dust containing silica leads to pneumoconiosis/silicosis. The disease is irreversible and incurable, and only preventive steps such as job rotation, use of personal protective equipment, etc., remain solutions to the problem. Under such a situation, early diagnosis or prediction may become very useful to control the disease. Biomarkers are biological parameters in blood serum that change their values with deposition of dust in the lung and onset of lung fibrosis. Since these biomarkers can help us to diagnose and in the prognosis of the disease before it is actually diagnosed by the conventional X-ray technique and lung function test used for diagnosis of silicosis. The present paper describes the various types of available biomarkers, their application and usefulness. The paper also suggests that further study of the behavior/level of these biomarkers on a specific subject with time may provide more useful information of a confirmatory nature for prevention of dust-linked diseases. PMID:23776317

  18. On comparing heterogeneity across biomarkers

    PubMed Central

    Steininger, Robert J.; Rajaram, Satwik; Girard, Luc; Minna, John D.; Wu, Lani F.; Altschuler, Steven J.

    2015-01-01

    Microscopy reveals complex patterns of cellular heterogeneity that can be biologically informative. However, a limitation of microscopy is that only a small number of biomarkers can typically be monitored simultaneously. Thus, a natural question is whether additional biomarkers provide a deeper characterization of the distribution of cellular states in a population. How much information about a cell’s phenotypic state in one biomarker is gained by knowing its state in another biomarker? Here, we describe a framework for comparing phenotypic states across biomarkers. Our approach overcomes the current limitation of microscopy by not requiring co-staining biomarkers on the same cells; instead we require staining of biomarkers (possibly separately) on a common collection of phenotypically diverse cell lines. We evaluate our approach on two image datasets: 33 oncogenically diverse lung cancer cell lines stained with 7 biomarkers, and 49 less diverse subclones of one lung cancer cell line stained with 12 biomarkers. We first validate our method by comparing it to the “gold standard” of co-staining. We then apply our approach to all pairs of biomarkers and use it to identify biomarkers that yield similar patterns of heterogeneity. The results presented in this work suggest that many biomarkers provide redundant information about heterogeneity. Thus, our approach provides a practical guide for selecting independently informative biomarkers and, more generally, will yield insights into both the connectivity of biological networks and the complexity of the state space of biological systems. PMID:25425168

  19. Lamins as cancer biomarkers.

    PubMed

    Foster, Clare R; Przyborski, Stefan A; Wilson, Robert G; Hutchison, Christopher J

    2010-02-01

    Lamins are multifunctional proteins that are often aberrantly expressed or localized in tumours. Here, we endeavour to assess their uses as cancer biomarkers: to diagnose tumours, analyse cancer characteristics and predict patient survival. It appears that the nature of lamin function in cancer is very complex. Lamin expression can be variable between and even within cancer subtypes, which limits their uses as diagnostic biomarkers. Expression of A-type lamins is a marker of differentiated tumour cells and has been shown to be a marker of good or poor patient survival depending on tumour subtype. Further research into the functions of lamins in cancer cells and the mechanisms that determine its patterns of expression may provide more potential uses of lamins as cancer biomarkers. PMID:20074078

  20. Biomarkers of xenobiotic exposures

    SciTech Connect

    Brewster, M.A.

    1988-07-01

    Direct measurement of xenobiotic (foreign) chemicals is not always feasible as an exposure assessment,--owing to rapid metabolism, sequestration into fatty tissues, or lack of suitable assay methods. Furthermore, suspect exposures often involve complex mixtures of organics. In these circumstances, indirect biomarkers of exposure can be most helpful. This paper reviews four urinary parameters that hold promise as biomarkers of exposure in occupational and environmental settings: glucaric acid (end-product of the glucuronidation pathway), thioethers (end-product of glutathione reaction with electrophilic or alkylating agents), porphyrin pattern (altered with disruption in heme biosynthesis), and the Ames mutagenicity test. 112 references.

  1. Biomarkers in Barrett's esophagus.

    PubMed

    Reid, Brian J; Blount, Patricia L; Rabinovitch, Peter S

    2003-04-01

    This article provides a framework for clinicians who are attempting the difficult task of interpreting the Barrett's biomarker literature with the goal of improving care for their patients. Although many articles. including more that 60 proposed biomarkers, have been published on this subject, only a few describe phase 3 and 4 studies that are of interest to the clinical gastroenterologist (Table 1). For year, dysplasia grade has been the sole means of risk stratification for patients with BE, and it likely will continue to be used in the foreseeable future. The current authors believe that dysplasia classification can be valuable using the team management approach and quality controls described previously. Significant problems, however, have emerged in phase 2 through 4 studies of dysplasia that make it imperative for the Barrett's field to incorporate additional biomarkers as they are validated. These problems include poor reproducibility of dysplasia interpretations, poor predictive value for negative, indefinite, and low-grade dysplasia, and inconsistent results for HGD in different centers, all of which makes it virtually impossible to develop national guidelines for surveillance. Some studies have even suggested that endoscopic biopsy surveillance using dysplasia may not be worthwhile. Currently, flow cytometric tetraploidy and aneuploidy have progressed furthest in biomarker validation (see Table 1). With proper handling, endoscopic biopsy specimens can be shipped to reference laboratories that have the instruments, computer analytic methods, and expertise to reproducibly detect tetraploidy and aneuploidy. The results of phase 4 studies indicate that flow cytometry appears to be useful in detecting a subset of patients who do not have HGD and yet have an increased risk of progression to cancer that cannot be identified by dysplasia grade. For many reasons, the authors anticipate that the number of validated biomarkers will increase substantially in the

  2. Industry perspectives on biomarker qualification.

    PubMed

    Lavezzari, G; Womack, A W

    2016-02-01

    Biomarkers have the potential to expedite drug development, increase patient safety, and optimize clinical response. Yet few have achieved regulatory qualification. A survey was conducted to clarify industry's perspective on biomarker qualification and identify the most promising biomarkers for drug development. The results across toxicities/clinical areas highlight challenges in regulatory qualification, although early prioritization and alignment on an evidentiary standard framework are key factors in facilitating biomarker development and qualification. PMID:26378777

  3. System-wide peripheral biomarker discovery using information theory.

    PubMed

    Alterovitz, Gil; Xiang, Michael; Liu, Jonathan; Chang, Amelia; Ramoni, Marco F

    2008-01-01

    The identification of reliable peripheral biomarkers for clinical diagnosis, patient prognosis, and biological functional studies would allow for access to biological information currently available only through invasive methods. Traditional approaches have so far considered aspects of tissues and biofluid markers independently. Here we introduce an information theoretic framework for biomarker discovery, integrating biofluid and tissue information. This allows us to identify tissue information in peripheral biofluids. We treat tissue-biofluid interactions as an information channel through functional space using 26 proteomes from 45 different sources to determine quantitatively the correspondence of each biofluid for specific tissues via relative entropy calculation of proteomes mapped onto phenotype, function, and drug space. Next, we identify candidate biofluids and biomarkers responsible for functional information transfer (p < 0.01). A total of 851 unique candidate biomarkers proxies were identified. The biomarkers were found to be significant functional tissue proxies compared to random proteins (p < 0.001). This proxy link is found to be further enhanced by filtering the biofluid proteins to include only significant tissue-biofluid information channels and is further validated by gene expression. Furthermore, many of the candidate biomarkers are novel and have yet to be explored. In addition to characterizing proteins and their interactions with a systemic perspective, our work can be used as a roadmap to guide biomedical investigation, from suggesting biofluids for study to constraining the search for biomarkers. This work has applications in disease screening, diagnosis, and protein function studies. PMID:18229689

  4. Salivary Biomarkers in Pediatric Metabolic Disease Research.

    PubMed

    Hartman, Mor-Li; Goodson, J Max; Barake, Roula; Alsmadi, Osama; Al-Mutawa, Sabiha; Ariga, Jitendra; Soparkar, Pramod; Behbehani, Jawad; Behbehani, Kazem

    2016-03-01

    The increasing prevalence of childhood obesity and obesity-related metabolic disorders is now considered a global pandemic. The main goal of the pediatric obesity research community is to identify children who are at risk of becoming obese before their body mass index rises above age norms. To do so, we must identify biomarkers of metabolic health and immunometabolism that can be used for large-scale screening and diagnosis initiatives among at-risk children. Because blood sampling is often unacceptable to both parents and children when there is no direct benefit to the child, as in a community-based research study, there is a clear need for a low-risk, non-invasive sampling strategy. Salivary analysis is now well recognized as a likely candidate for this purpose. In this review, we discuss the physiologic role of saliva and its strengths and limitations as a fluid for biomarker discovery, obesity screening, metabolic disease diagnosis, and response monitoring after interventions. We also describe the current state of the salivary biomarker field as it pertains to metabolic research, with a special emphasis on studies conducted in children and adolescents. Finally, we look forward to technological developments, such as salivary "omics" and point of service diagnostic devices, which have the potential to accelerate the pace of research and discovery in this vitally important field. PMID:27116847

  5. Biomarkers of cell senescence

    DOEpatents

    Dimri, G.P.; Campisi, J.; Peacocke, M.

    1998-08-18

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, {beta}-galactosidase activity is utilized as a means by which cell senescence may be assessed either in vitro cell cultures or in vivo. 1 fig.

  6. Biomarkers of cell senescence

    DOEpatents

    Dirmi, G.P.; Campisi, J.; Peacocke, M.

    1996-02-13

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, {beta}-galactosidase activity is utilized as a means by which cell senescence may be assessed either in in vitro cell cultures or in vivo. 1 fig.

  7. Biomarkers of apoptosis

    PubMed Central

    Ward, T H; Cummings, J; Dean, E; Greystoke, A; Hou, J M; Backen, A; Ranson, M; Dive, C

    2008-01-01

    Within the era of molecularly targeted anticancer agents, it has become increasingly important to provide proof of mechanism as early on as possible in the drug development cycle, especially in the clinic. Selective activation of apoptosis is often cited as one of the major goals of cancer chemotherapy. Thus, the present minireview focuses on a discussion of the pros and cons of a variety of methodological approaches to detect different components of the apoptotic cascade as potential biomarkers of programmed cell death. The bulk of the discussion centres on serological assays utilising the technique of ELISA, since here there is an obvious advantage of sampling multiple time points. Potential biomarkers of apoptosis including circulating tumour cells, cytokeratins and DNA nucleosomes are discussed at length. However, accepting that a single biomarker may not have the power to predict proof of concept and patient outcome, it is clear that in the future more emphasis will be placed on technologies that can analyse panels of biomarkers in small volumes of samples. To this end the increased throughput afforded by multiplex ELISA technologies is discussed. PMID:19238626

  8. Biomarkers of cell senescence

    DOEpatents

    Dirmi, Goberdhan P.; Campisi, Judith; Peacocke, Monica

    1996-01-01

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, .beta.-galactosidase activity is utilized as a means by which cell senescence may be assessed either in in vitro cell cultures or in vivo.

  9. Biomarkers of cell senescence

    DOEpatents

    Dimri, Goberdhan P.; Campisi, Judith; Peacocke, Monica

    1998-01-01

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, .beta.-galactosidase activity is utilized as a means by which cell senescence may be assessed either in vitro cell cultures or in vivo.

  10. Asthma outcomes: Biomarkers

    PubMed Central

    Szefler, Stanley J.; Wenzel, Sally; Brown, Robert; Erzurum, Serpil C.; Fahy, John V.; Hamilton, Robert G.; Hunt, John F.; Kita, Hirohito; Liu, Andrew H.; Panettieri, Reynold A.; Schleimer, Robert P.; Minnicozzi, Michael

    2012-01-01

    Background Measurement of biomarkers has been incorporated within clinical research studies of asthma to characterize the population and associate the disease with environmental and therapeutic effects. Objective National Institutes of Health institutes and federal agencies convened an expert group to propose which biomarkers should be assessed as standardized asthma outcomes in future clinical research studies. Methods We conducted a comprehensive search of the literature to identify studies that developed and/or tested asthma biomarkers. We identified biomarkers relevant to the underlying disease process progression and response to treatment. We classified the biomarkers as either core (required in future studies), supplemental (used according to study aims and standardized), or emerging (requiring validation and standardization). This work was discussed at an National Institutes of Health–organized workshop convened in March 2010 and finalized in September 2011. Results Ten measures were identified; only 1, multiallergen screening to define atopy, is recommended as a core asthma outcome. Complete blood counts to measure total eosinophils, fractional exhaled nitric oxide (Feno), sputum eosinophils, urinary leukotrienes, and total and allergen-specific IgE are recommended as supplemental measures. Measurement of sputum polymorphonuclear leukocytes and other analytes, cortisol measures, airway imaging, breath markers, and system-wide studies (eg, genomics, proteomics) are considered as emerging outcome measures. Conclusion The working group participants propose the use of multiallergen screening in all asthma clinical trials to characterize study populations with respect to atopic status. Blood, sputum, and urine specimens should be stored in biobanks, and standard procedures should be developed to harmonize sample collection for clinical trial biorepositories. PMID:22386512

  11. A Study of the Impacts of Navigational Links, Task Complexity, and Experience with the Older User on Website Usability in a Community College Domain

    ERIC Educational Resources Information Center

    Garrett, Robin Eileen

    2014-01-01

    Community colleges serve a diverse population of learners including many older students counting on the community college for enhanced skills or personal enrichment. Many of these colleges target this population with programs designed specifically to meet the needs and goals of the older adult but may not consider this population when designing a…

  12. Linking Home-Based Child Care and State-Funded Preschool: The Community Connections Preschool Program (Illinois Action for Children). Evaluation Phase 1-Implementation Study

    ERIC Educational Resources Information Center

    Forry, Nicole; Anderson, Rachel; Zaslow, Martha; Chrisler, Alison; Banghart, Patti; Kreader, J. Lee

    2011-01-01

    The Community Connections preschool program (herein referred to as Community Connections) was developed to help prepare children in home-based child care for success in school and in life. It has three goals: (1) to make state prekindergarten classroom experiences available to children in home-based care, (2) to extend classroom learning…

  13. Metrology Standards for Quantitative Imaging Biomarkers.

    PubMed

    Sullivan, Daniel C; Obuchowski, Nancy A; Kessler, Larry G; Raunig, David L; Gatsonis, Constantine; Huang, Erich P; Kondratovich, Marina; McShane, Lisa M; Reeves, Anthony P; Barboriak, Daniel P; Guimaraes, Alexander R; Wahl, Richard L

    2015-12-01

    Although investigators in the imaging community have been active in developing and evaluating quantitative imaging biomarkers (QIBs), the development and implementation of QIBs have been hampered by the inconsistent or incorrect use of terminology or methods for technical performance and statistical concepts. Technical performance is an assessment of how a test performs in reference objects or subjects under controlled conditions. In this article, some of the relevant statistical concepts are reviewed, methods that can be used for evaluating and comparing QIBs are described, and some of the technical performance issues related to imaging biomarkers are discussed. More consistent and correct use of terminology and study design principles will improve clinical research, advance regulatory science, and foster better care for patients who undergo imaging studies. PMID:26267831

  14. Biomarker Modeling of Alzheimer's Disease

    PubMed Central

    Jack, Clifford R; Holtzman, David M

    2014-01-01

    Alzheimer's disease (AD) is a slowly progressing disorder in which pathophysiological abnormalities, detectable in vivo by biomarkers, precede overt clinical symptoms by many years to decades. Five AD biomarkers are sufficiently validated to have been incorporated into clinical diagnostic criteria and commonly used in therapeutic trials. Current AD biomarkers fall into 2 categories: biomarkers of amyloid-β plaques and of tau-related neurodegeneration. Three of the 5 are imaging measures and two are cerebrospinal fluid analytes. AD biomarkers do not evolve in an identical manner but rather in a sequential but temporally overlapping manner. Models of the temporal evolution of AD biomarkers can take the form of plots of biomarker severity (degree of abnormality) vs. time. In this review we discuss several time-dependent models of AD which take into consideration varying age of onset (early vs. late) and the influence of aging and co-occurring brain pathologies that commonly arise in the elderly. PMID:24360540

  15. Frontiers in the Use of Biomarkers of Health in Research on Stress and Aging

    PubMed Central

    Almeida, David M.; Dmitrieva, Natalia O.; Klein, Laura C.

    2010-01-01

    Assessment of biomarkers that reflect objective indicators of physiological processes has become increasingly popular in psychological research on stress and aging. The current article reviews biomarkers of the neuroendocrine and immune systems, including issues related to measurement and normative age-related changes. We also discuss how exposure to stressors can provoke changes in these biomarkers and propose that stressful experiences may accelerate age-related declines in these systems. We recommend that future research examining physical health and aging incorporate dynamic and multivariate methods for assessing links between stressors and biomarkers. PMID:20647348

  16. Clinical applications of imaging biomarkers. Part 1. The neuroradiologist's perspective

    PubMed Central

    Smith, E T S

    2011-01-01

    This article is concerned with the application and usage in clinical practice of techniques of detection and measurement of imaging biomarkers. Some commentaries in the article derive from a literature search and include summaries of recently published material compiled and linked to each other by extensive use of the text contained in the material examined.

  17. Biomarkers for Hepatocellular Carcinoma

    PubMed Central

    Behne, Tara; Copur, M. Sitki

    2012-01-01

    The hepatocellular carcinoma (HCC) is one of the most common malignant tumors and carries a poor survival rate. The management of patients at risk for developing HCC remains challenging. Increased understanding of cancer biology and technological advances have enabled identification of a multitude of pathological, genetic, and molecular events that drive hepatocarcinogenesis leading to discovery of numerous potential biomarkers in this disease. They are currently being aggressively evaluated to establish their value in early diagnosis, optimization of therapy, reducing the emergence of new tumors, and preventing the recurrence after surgical resection or liver transplantation. These markers not only help in prediction of prognosis or recurrence but may also assist in deciding appropriate modality of therapy and may represent novel potential targets for therapeutic interventions. In this paper, a summary of most relevant available data from published papers reporting various tissue and serum biomarkers involved in hepatocellular carcinoma was presented. PMID:22655201

  18. Biomarkers for hepatocellular carcinoma.

    PubMed

    Behne, Tara; Copur, M Sitki

    2012-01-01

    The hepatocellular carcinoma (HCC) is one of the most common malignant tumors and carries a poor survival rate. The management of patients at risk for developing HCC remains challenging. Increased understanding of cancer biology and technological advances have enabled identification of a multitude of pathological, genetic, and molecular events that drive hepatocarcinogenesis leading to discovery of numerous potential biomarkers in this disease. They are currently being aggressively evaluated to establish their value in early diagnosis, optimization of therapy, reducing the emergence of new tumors, and preventing the recurrence after surgical resection or liver transplantation. These markers not only help in prediction of prognosis or recurrence but may also assist in deciding appropriate modality of therapy and may represent novel potential targets for therapeutic interventions. In this paper, a summary of most relevant available data from published papers reporting various tissue and serum biomarkers involved in hepatocellular carcinoma was presented. PMID:22655201

  19. Genetic biomarkers of depression

    PubMed Central

    Tamatam, Anand; Khanum, Farhath; Bawa, Amarinder Singh

    2012-01-01

    Depression is a term that has been used to describe a variety of ailments, ranging from minor to incapacitating. Clinically significant depression, termed as major depression, is a serious condition characterized not only by depressed mood but also by a cluster of somatic, cognitive, and motivational symptoms. Significant research efforts are aimed to understand the neurobiological as well as psychiatric disorders, and the evaluation of treatment of these disorders is still based solely on the assessment of symptoms. In order to identify the biological markers for depression, we have focused on gathering information on different factors responsible for depression including stress, genetic variations, neurotransmitters, and cytokines and chemokines previously suggested to be involved in the pathophysiology of depression. The present review illustrates the potential of biomarker profiling for psychiatric disorders, when conducted in large collections. The review highlighted the biomarker signatures for depression, warranting further investigation. PMID:22754217

  20. Imaging biomarkers in tauopathies.

    PubMed

    Dani, Melanie; Edison, Paul; Brooks, David J

    2016-01-01

    Abnormally aggregated tau protein is central to the pathophysiology of Alzheimer's disease, frontotemporal dementia variants, progressive supranuclear palsy, corticobasal degeneration and chronic traumatic encephalopathy. The post-mortem cortical density of hyperphosphorylated tau tangles correlates with pre-morbid cognitive dysfunction and neuron loss. Selective PET ligands including [18F]THK5117, [18F]THK5351, [18F]AV1451 (T807) and [11C]PBB3 now provide in vivo imaging information about the timing and distribution of tau in the early phases of neurodegenerative diseases. They are potential imaging biomarkers for both supporting diagnosis and tracking disease progression. Here, we discuss the challenges posed in developing selective tau ligands as biomarkers, their state of development and the new clinical information that has been revealed. PMID:26299160

  1. Tear biomarkers for keratoconus.

    PubMed

    Nishtala, Krishnatej; Pahuja, Natasha; Shetty, Rohit; Nuijts, Rudy M M A; Ghosh, Arkasubhra

    2016-01-01

    Keratoconus is a progressive corneal thinning, ectatic condition, which affects vision. Recent advances in corneal topography measurements has helped advance proper diagnosis of this condition and increased research and clinical interests in the disease etiopathogenesis. Considerable progress has been achieved in understanding the progression of the disease and tear fluid has played a major role in the progress. This review discusses the importance of tear fluid as a source of biomarker for keratoconus and how advances in technology have helped map the complexity of tears and thereby molecular readouts of the disease. Expanding knowledge of the tear proteome, lipidome and metabolome opened up new avenues to study keratoconus and to identify probable prognostic or diagnostic biomarkers for the disease. A multidimensional approach of analyzing tear fluid of patients layering on proteomics, lipidomics and metabolomics is necessary in effectively decoding keratoconus and thereby identifying targets for its treatment. PMID:27493978

  2. BIOMARKER LIPIDS IN RED TIDE (GYMNODINIUM BREVE) BLOOMS ALONG THE NORTHWEST FLORIDA COAST

    EPA Science Inventory

    The ability to characterize phytoplankton communities and algal blooms using lipids as biomarkers requires knowledge of their distribution and taxonomic significance. Such an approach would have application, for example, in distinguishing and tracking certain dinoflagellates suc...

  3. Organic Biomarker Preservation in Silica-Rich Hydrothermal Systems with Implications to Mars

    NASA Astrophysics Data System (ADS)

    Jahnke, L. L.; Parenteau, M. N.; Farmer, J. D.

    2016-05-01

    Microbial community structure and preservation of organic matter in siliceous hydrothermal environments is a critical issue given the discovery of hydrothermal vents and silica on Mars. Here we discuss preservation of cyanobacterial biomarker lipid.

  4. Biomarkers of Selenium Status

    PubMed Central

    Combs, Gerald F.

    2015-01-01

    The essential trace element, selenium (Se), has multiple biological activities, which depend on the level of Se intake. Relatively low Se intakes determine the expression of selenoenzymes in which it serves as an essential constituent. Higher intakes have been shown to have anti-tumorigenic potential; and very high Se intakes can produce adverse effects. This hierarchy of biological activities calls for biomarkers informative at different levels of Se exposure. Some Se-biomarkers, such as the selenoproteins and particularly GPX3 and SEPP1, provide information about function directly and are of value in identifying nutritional Se deficiency and tracking responses of deficient individuals to Se-treatment. They are useful under conditions of Se intake within the range of regulated selenoprotein expression, e.g., for humans <55 μg/day and for animals <20 μg/kg diet. Other Se-biomarkers provide information indirectly through inferences based on Se levels of foods, tissues, urine or feces. They can indicate the likelihood of deficiency or adverse effects, but they do not provide direct evidence of either condition. Their value is in providing information about Se status over a wide range of Se intake, particularly from food forms. There is need for additional Se biomarkers particularly for assessing Se status in non-deficient individuals for whom the prospects of cancer risk reduction and adverse effects risk are the primary health considerations. This would include determining whether supranutritional intakes of Se may be required for maximal selenoprotein expression in immune surveillance cells. It would also include developing methods to determine low molecular weight Se-metabolites, i.e., selenoamino acids and methylated Se-metabolites, which to date have not been detectable in biological specimens. Recent analytical advances using tandem liquid chromatography-mass spectrometry suggest prospects for detecting these metabolites. PMID:25835046

  5. Biomarkers in Diabetic Retinopathy.

    PubMed

    Jenkins, Alicia J; Joglekar, Mugdha V; Hardikar, Anandwardhan A; Keech, Anthony C; O'Neal, David N; Januszewski, Andrzej S

    2015-01-01

    There is a global diabetes epidemic correlating with an increase in obesity. This coincidence may lead to a rise in the prevalence of type 2 diabetes. There is also an as yet unexplained increase in the incidence of type 1 diabetes, which is not related to adiposity. Whilst improved diabetes care has substantially improved diabetes outcomes, the disease remains a common cause of working age adult-onset blindness. Diabetic retinopathy is the most frequently occurring complication of diabetes; it is greatly feared by many diabetes patients. There are multiple risk factors and markers for the onset and progression of diabetic retinopathy, yet residual risk remains. Screening for diabetic retinopathy is recommended to facilitate early detection and treatment. Common biomarkers of diabetic retinopathy and its risk in clinical practice today relate to the visualization of the retinal vasculature and measures of glycemia, lipids, blood pressure, body weight, smoking, and pregnancy status. Greater knowledge of novel biomarkers and mediators of diabetic retinopathy, such as those related to inflammation and angiogenesis, has contributed to the development of additional therapeutics, in particular for late-stage retinopathy, including intra-ocular corticosteroids and intravitreal vascular endothelial growth factor inhibitors ('anti-VEGFs') agents. Unfortunately, in spite of a range of treatments (including laser photocoagulation, intraocular steroids, and anti-VEGF agents, and more recently oral fenofibrate, a PPAR-alpha agonist lipid-lowering drug), many patients with diabetic retinopathy do not respond well to current therapeutics. Therefore, more effective treatments for diabetic retinopathy are necessary. New analytical techniques, in particular those related to molecular markers, are accelerating progress in diabetic retinopathy research. Given the increasing incidence and prevalence of diabetes, and the limited capacity of healthcare systems to screen and treat

  6. A photoacoustic immunoassay for biomarker detection.

    PubMed

    Zhao, Yunfei; Cao, Mingfeng; McClelland, John F; Shao, Zengyi; Lu, Meng

    2016-11-15

    Challenges in protein biomarker analysis include insufficient sensitivity for detecting low-abundance biomarkers, poor measurement reproducibility, and the high costs and large footprints of detection systems. To address these issues, a new detection modality was developed for analyzing protein biomarkers based on the plasmon-enhanced photoacoustic (PA) effect. The detection modality employed a heterogeneous immunoassay scheme and used gold nanoparticles (AuNPs) as the signal reporter. Due to their localized plasmon resonance, AuNPs can strongly interact with intensity-modulated laser excitation and generate strong PA signals, which are subsequently sensed and quantified using a microphone. As an example, the performance of the PA immunoassay was evaluated by detecting the human interleukin 8 chemokine. The PA immunoassay provided approximately 143× lower limit of detection (LOD) than observed with the gold standard enzyme-linked immunosorbent assay - a decrease from 23pg/mL to 0.16pg/mL. In addition to the significant performance improvement in terms of the LOD, the PA immunoassay also offers advantages in terms of compatibility with low-cost instruments and the long-term stability of assay results. PMID:27183276

  7. Influence of mussel biological variability on pollution biomarkers.

    PubMed

    González-Fernández, Carmen; Albentosa, Marina; Campillo, Juan A; Viñas, Lucía; Fumega, José; Franco, Angeles; Besada, Victoria; González-Quijano, Amelia; Bellas, Juan

    2015-02-01

    This study deals with the identification and characterization of biological variables that may affect some of the biological responses used as pollution biomarkers. With this aim, during the 2012 mussel survey of the Spanish Marine Pollution monitoring program (SMP), at the North-Atlantic coast, several quantitative and qualitative biological variables were measured (corporal and shell indices, gonadal development and reserves composition). Studied biomarkers were antioxidant enzymatic activities (CAT, GST, GR), lipid peroxidation (LPO) and the physiological rates integrated in the SFG biomarker (CR, AE, RR). Site pollution was considered as the chemical concentration in the whole tissues of mussels. A great geographical variability was observed for the biological variables, which was mainly linked to the differences in food availability along the studied region. An inverse relationship between antioxidant enzymes and the nutritional status of the organism was evidenced, whereas LPO was positively related to nutritional status and, therefore, with higher metabolic costs, with their associated ROS generation. Mussel condition was also inversely related to CR, and therefore to SFG, suggesting that mussels keep an "ecological memory" from the habitat where they have been collected. No overall relationship was observed between pollution and biomarkers, but a significant overall effect of biological variables on both biochemical and physiological biomarkers was evidenced. It was concluded that when a wide range of certain environmental factors, as food availability, coexist in the same monitoring program, it determines a great variability in mussel populations which mask the effect of contaminants on biomarkers. PMID:25483414

  8. Biomarkers in the Diagnosis and Prognosis of Alzheimer's Disease.

    PubMed

    Schaffer, Cole; Sarad, Nakia; DeCrumpe, Ashton; Goswami, Disha; Herrmann, Sara; Morales, Jose; Patel, Parth; Osborne, Jim

    2015-10-01

    Alzheimer's disease (AD) is a neurodegenerative disease that inhibits cognitive functions and has no cure. This report reviews the current diagnostic standards for AD with an emphasis on early diagnosis using the cerebrospinal fluid (CSF) biomarkers amyloid-beta, t-tau, and p-tau and fluorodeoxyglucose positron emission tomography imaging. Abnormal levels of these CSF biomarkers and decreased cerebral uptake of glucose have recently been used in the early diagnosis of AD in experimental studies. These promising biomarkers can be measured using immunoassays performed in singleplex or multiplex formats. Although presently, there are no Food and Drug Administration-approved in vitro diagnostics (IVDs) for early detection of AD, a multiplex immunoassay measuring a panel of promising AD biomarkers in CSF may be a likely IVD candidate for the clinical AD diagnostic market. Specifically, the INNO-BIA AlzBio3 immunoassay kit, performed using bead arrays on the xMAP Luminex analyzer, allows simultaneous quantification of amyloid-beta, t-tau, and p-tau biomarkers. AD biomarkers can also be screened using enzyme-linked immunosorbent assays that are offered as laboratory-developed tests. PMID:25424384

  9. Cancer biomarker discovery and validation

    PubMed Central

    Goossens, Nicolas; Nakagawa, Shigeki; Sun, Xiaochen; Hoshida, Yujin

    2015-01-01

    With the emergence of genomic profiling technologies and selective molecular targeted therapies, biomarkers play an increasingly important role in the clinical management of cancer patients. Single gene/protein or multi-gene “signature”-based assays have been introduced to measure specific molecular pathway deregulations that guide therapeutic decision-making as predictive biomarkers. Genome-based prognostic biomarkers are also available for several cancer types for potential incorporation into clinical prognostic staging systems or practice guidelines. However, there is still a large gap between initial biomarker discovery studies and their clinical translation due to the challenges in the process of cancer biomarker development. In this review we summarize the steps of biomarker development, highlight key issues in successful validation and implementation, and overview representative examples in the oncology field. We also discuss regulatory issues and future perspectives in the era of big data analysis and precision medicine. PMID:26213686

  10. Identification of Serum Biomarkers for Gastric Cancer Diagnosis Using a Human Proteome Microarray.

    PubMed

    Yang, Lina; Wang, Jingfang; Li, Jianfang; Zhang, Hainan; Guo, Shujuan; Yan, Min; Zhu, Zhenggang; Lan, Bin; Ding, Youcheng; Xu, Ming; Li, Wei; Gu, Xiaonian; Qi, Chong; Zhu, Heng; Shao, Zhifeng; Liu, Bingya; Tao, Sheng-Ce

    2016-02-01

    We aimed to globally discover serum biomarkers for diagnosis of gastric cancer (GC). GC serum autoantibodies were discovered and validated using serum samples from independent patient cohorts encompassing 1,401 participants divided into three groups, i.e. healthy, GC patients, and GC-related disease group. To discover biomarkers for GC, the human proteome microarray was first applied to screen specific autoantibodies in a total of 87 serum samples from GC patients and healthy controls. Potential biomarkers were identified via a statistical analysis protocol. Targeted protein microarrays with only the potential biomarkers were constructed and used to validate the candidate biomarkers using 914 samples. To provide further validation, the abundance of autoantibodies specific to the biomarker candidates was analyzed using enzyme-linked immunosorbent assays. Receiver operating characteristic curves were generated to evaluate the diagnostic accuracy of the serum biomarkers. Finally, the efficacy of prognosis efficacy of the final four biomarkers was evaluated by analyzing the clinical records. The final panel of biomarkers consisting of COPS2, CTSF, NT5E, and TERF1 provides high diagnostic power, with 95% sensitivity and 92% specificity to differentiate GC patients from healthy individuals. Prognosis analysis showed that the panel could also serve as independent predictors of the overall GC patient survival. The panel of four serum biomarkers (COPS2, CTSF, NT5E, and TERF1) could serve as a noninvasive diagnostic index for GC, and the combination of them could potentially be used as a predictor of the overall GC survival rate. PMID:26598640

  11. Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers.

    PubMed

    Liu, Rui; Wang, Xiangdong; Aihara, Kazuyuki; Chen, Luonan

    2014-05-01

    Many studies have been carried out for early diagnosis of complex diseases by finding accurate and robust biomarkers specific to respective diseases. In particular, recent rapid advance of high-throughput technologies provides unprecedented rich information to characterize various disease genotypes and phenotypes in a global and also dynamical manner, which significantly accelerates the study of biomarkers from both theoretical and clinical perspectives. Traditionally, molecular biomarkers that distinguish disease samples from normal samples are widely adopted in clinical practices due to their ease of data measurement. However, many of them suffer from low coverage and high false-positive rates or high false-negative rates, which seriously limit their further clinical applications. To overcome those difficulties, network biomarkers (or module biomarkers) attract much attention and also achieve better performance because a network (or subnetwork) is considered to be a more robust form to characterize diseases than individual molecules. But, both molecular biomarkers and network biomarkers mainly distinguish disease samples from normal samples, and they generally cannot ensure to identify predisease samples due to their static nature, thereby lacking ability to early diagnosis. Based on nonlinear dynamical theory and complex network theory, a new concept of dynamical network biomarkers (DNBs, or a dynamical network of biomarkers) has been developed, which is different from traditional static approaches, and the DNB is able to distinguish a predisease state from normal and disease states by even a small number of samples, and therefore has great potential to achieve "real" early diagnosis of complex diseases. In this paper, we comprehensively review the recent advances and developments on molecular biomarkers, network biomarkers, and DNBs in particular, focusing on the biomarkers for early diagnosis of complex diseases considering a small number of samples and high

  12. The microfluidics of the eccrine sweat gland, including biomarker partitioning, transport, and biosensing implications.

    PubMed

    Sonner, Z; Wilder, E; Heikenfeld, J; Kasting, G; Beyette, F; Swaile, D; Sherman, F; Joyce, J; Hagen, J; Kelley-Loughnane, N; Naik, R

    2015-05-01

    Non-invasive and accurate access of biomarkers remains a holy grail of the biomedical community. Human eccrine sweat is a surprisingly biomarker-rich fluid which is gaining increasing attention. This is especially true in applications of continuous bio-monitoring where other biofluids prove more challenging, if not impossible. However, much confusion on the topic exists as the microfluidics of the eccrine sweat gland has never been comprehensively presented and models of biomarker partitioning into sweat are either underdeveloped and/or highly scattered across literature. Reported here are microfluidic models for eccrine sweat generation and flow which are coupled with review of blood-to-sweat biomarker partition pathways, therefore providing insights such as how biomarker concentration changes with sweat flow rate. Additionally, it is shown that both flow rate and biomarker diffusion determine the effective sampling rate of biomarkers at the skin surface (chronological resolution). The discussion covers a broad class of biomarkers including ions (Na(+), Cl(-), K(+), NH4 (+)), small molecules (ethanol, cortisol, urea, and lactate), and even peptides or small proteins (neuropeptides and cytokines). The models are not meant to be exhaustive for all biomarkers, yet collectively serve as a foundational guide for further development of sweat-based diagnostics and for those beginning exploration of new biomarker opportunities in sweat. PMID:26045728

  13. The microfluidics of the eccrine sweat gland, including biomarker partitioning, transport, and biosensing implications

    PubMed Central

    Sonner, Z.; Wilder, E.; Heikenfeld, J.; Kasting, G.; Beyette, F.; Swaile, D.; Sherman, F.; Joyce, J.; Hagen, J.; Kelley-Loughnane, N.; Naik, R.

    2015-01-01

    Non-invasive and accurate access of biomarkers remains a holy grail of the biomedical community. Human eccrine sweat is a surprisingly biomarker-rich fluid which is gaining increasing attention. This is especially true in applications of continuous bio-monitoring where other biofluids prove more challenging, if not impossible. However, much confusion on the topic exists as the microfluidics of the eccrine sweat gland has never been comprehensively presented and models of biomarker partitioning into sweat are either underdeveloped and/or highly scattered across literature. Reported here are microfluidic models for eccrine sweat generation and flow which are coupled with review of blood-to-sweat biomarker partition pathways, therefore providing insights such as how biomarker concentration changes with sweat flow rate. Additionally, it is shown that both flow rate and biomarker diffusion determine the effective sampling rate of biomarkers at the skin surface (chronological resolution). The discussion covers a broad class of biomarkers including ions (Na+, Cl−, K+, NH4+), small molecules (ethanol, cortisol, urea, and lactate), and even peptides or small proteins (neuropeptides and cytokines). The models are not meant to be exhaustive for all biomarkers, yet collectively serve as a foundational guide for further development of sweat-based diagnostics and for those beginning exploration of new biomarker opportunities in sweat. PMID:26045728

  14. Community Partnerships: POWERful Possibilities for Students and Communities.

    PubMed

    Pigza, Jennifer M

    2016-06-01

    This chapter provides a theoretical orientation and practical advice about community partnerships by linking the literature of community engagement with that of leadership. The author introduces the POWERful model for community engagement. PMID:27150904

  15. Biomarker Identification Using Text Mining

    PubMed Central

    Li, Hui; Liu, Chunmei

    2012-01-01

    Identifying molecular biomarkers has become one of the important tasks for scientists to assess the different phenotypic states of cells or organisms correlated to the genotypes of diseases from large-scale biological data. In this paper, we proposed a text-mining-based method to discover biomarkers from PubMed. First, we construct a database based on a dictionary, and then we used a finite state machine to identify the biomarkers. Our method of text mining provides a highly reliable approach to discover the biomarkers in the PubMed database. PMID:23197989

  16. Biomarkers in Prostate Cancer Epidemiology

    PubMed Central

    Verma, Mukesh; Patel, Payal; Verma, Mudit

    2011-01-01

    Understanding the etiology of a disease such as prostate cancer may help in identifying populations at high risk, timely intervention of the disease, and proper treatment. Biomarkers, along with exposure history and clinical data, are useful tools to achieve these goals. Individual risk and population incidence of prostate cancer result from the intervention of genetic susceptibility and exposure. Biochemical, epigenetic, genetic, and imaging biomarkers are used to identify people at high risk for developing prostate cancer. In cancer epidemiology, epigenetic biomarkers offer advantages over other types of biomarkers because they are expressed against a person's genetic background and environmental exposure, and because abnormal events occur early in cancer development, which includes several epigenetic alterations in cancer cells. This article describes different biomarkers that have potential use in studying the epidemiology of prostate cancer. We also discuss the characteristics of an ideal biomarker for prostate cancer, and technologies utilized for biomarker assays. Among epigenetic biomarkers, most reports indicate GSTP1 hypermethylation as the diagnostic marker for prostate cancer; however, NKX2-5, CLSTN1, SPOCK2, SLC16A12, DPYS, and NSE1 also have been reported to be regulated by methylation mechanisms in prostate cancer. Current challenges in utilization of biomarkers in prostate cancer diagnosis and epidemiologic studies and potential solutions also are discussed. PMID:24213111

  17. Serum biomarker panels for diagnosis of gastric cancer

    PubMed Central

    Tong, Weihua; Ye, Fei; He, Liang; Cui, Lifeng; Cui, Miao; Hu, Yuan; Li, Wei; Jiang, Jing; Zhang, David Y; Suo, Jian

    2016-01-01

    Purpose Currently, serum biomarkers that are sufficiently sensitive and specific for early detection and risk classification of gastric adenocarcinomas are not known. In this study, ten serum markers were assessed using the Luminex system and enzyme-linked immunosorbent assay for the diagnosis of gastric cancer and analysis of the relation between prognosis and metastases. Patients and methods A training set consisting of 228 gastric adenocarcinoma and 190 control samples was examined. A Luminex multiplex panel with nine biomarkers, consisting of three proteins discovered through our previous studies and six proteins previously reported to be cancer-associated, was constructed. One additional biomarker was detected using a commercial kit containing EDTA. Logistic regression, random forest (RF), and support vector machine (SVM) were used to identify the panel of discriminatory biomarkers in the training set. After selecting five proteins as candidate biomarkers, multivariate classification analyses were used to identify algorithms for diagnostic biomarker combinations. These algorithms were independently validated using a set of 57 gastric adenocarcinoma and 48 control samples. Results Serum pepsinogen I, serum pepsinogen II, A Disintegrin And Metalloproteinase domain-containing protein 8 (ADAM8), vascular endothelial growth factor (VEGF), and serum IgG to Helicobacter pylori were selected as classifiers in the three algorithms. These algorithms differentiated between the majority of gastric adenocarcinoma and control serum samples in the training/test set with high accuracy (RF 79.0%, SVM 83.8%, logistic regression 76.2%). These algorithms also differentiated the samples in the validation set (accuracy: RF 82.5%, SVM 86.1%, logistic regression 78.7%). Conclusion A panel of combinatorial biomarkers comprising VEGF, ADAM8, IgG to H. pylori, serum pepsinogen I, and pepsinogen II were developed. The use of biomarkers is a less invasive method for the diagnosis of

  18. An Analysis of Actual and Desired Roles of Trustees and Presidents of Community Colleges Linked to Board-President Relationship and Its Impact on College Effectiveness

    ERIC Educational Resources Information Center

    Gilzene, Annette M.

    2009-01-01

    This study's primary purpose was to examine whether or not there were differences in the roles community college boards of trustees and presidents said they currently perform and those they said they should perform. In addition, the study sought to determine whether or not the relationship between trustees and the president impacted the…

  19. Utilizing Paraeducators as Links to Their Communities: A Training Package for Use with Teacher/Paraeducator Teams and in the Pre-Service Training of Teachers.

    ERIC Educational Resources Information Center

    Hermanson, Michael J.; Peterson, Michael D.; Sampson, Marsha; Hoagland, Tina

    To deliver training and continuing education for education personnel in a large rural state, Montana has decentralized its Comprehensive System of Personnel Development (CSPD) by forming five regional councils. The Montana Center on Disabilities developed a statewide training program for using paraeducators as liaisons to communities to enhance…

  20. Linking Service-Learning Opportunities and Domestic Immersion Experiences in US Latino Communities: A Case Study of the "En Nuestra Lengua" Project

    ERIC Educational Resources Information Center

    Tijunelis, Viktorija; Satterfield, Teresa; Benki, Jose R.

    2013-01-01

    We report on the service-learning component of a Spanish-language Saturday school in Ann Arbor, Michigan, for elementary-aged Spanish-language heritage learners and also examine the newly forming Latino community served by this innovative program. The US Spanish-speaking population is growing throughout the country, resulting in greatly increased…

  1. Chiral Biomarkers in Meteorites

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.

    2010-01-01

    The chirality of organic molecules with the asymmetric location of group radicals was discovered in 1848 by Louis Pasteur during his investigations of the rotation of the plane of polarization of light by crystals of sodium ammonium paratartrate. It is well established that the amino acids in proteins are exclusively Levorotary (L-aminos) and the sugars in DNA and RNA are Dextrorotary (D-sugars). This phenomenon of homochirality of biological polymers is a fundamental property of all life known on Earth. Furthermore, abiotic production mechanisms typically yield recemic mixtures (i.e. equal amounts of the two enantiomers). When amino acids were first detected in carbonaceous meteorites, it was concluded that they were racemates. This conclusion was taken as evidence that they were extraterrestrial and produced by abiologically. Subsequent studies by numerous researchers have revealed that many of the amino acids in carbonaceous meteorites exhibit a significant L-excess. The observed chirality is much greater than that produced by any currently known abiotic processes (e.g. Linearly polarized light from neutron stars; Circularly polarized ultraviolet light from faint stars; optically active quartz powders; inclusion polymerization in clay minerals; Vester-Ulbricht hypothesis of parity violations, etc.). This paper compares the measured chirality detected in the amino acids of carbonaceous meteorites with the effect of these diverse abiotic processes. IT is concluded that the levels observed are inconsistent with post-arrival biological contamination or with any of the currently known abiotic production mechanisms. However, they are consistent with ancient biological processes on the meteorite parent body. This paper will consider these chiral biomarkers in view of the detection of possible microfossils found in the Orgueil and Murchison carbonaceous meteorites. Energy dispersive x-ray spectroscopy (EDS) data obtained on these morphological biomarkers will be

  2. Biomarkers in Cervical Cancer

    PubMed Central

    Yim, Eun-Kyoung; Park, Jong-Sup

    2006-01-01

    Cervical cancer, a potentially preventable disease, remains the second most common malignancy in women worldwide. Human papillomavirus (HPV) is the single most important etiological agent in cervical cancer, contributing to neoplastic progression through the action of viral oncoproteins, mainly E6 and E7. Cervical screening programs using Pap smear testing have dramatically improved cervical cancer incidence and reduced deaths, but cervical cancer still remains a global health burden. The biomarker discovery for accurate detection and diagnosis of cervical carcinoma and its malignant precursors (collectively referred to as high-grade cervical disease) represents one of the current challenges in clinical medicine and cytopathology. PMID:19690652

  3. STRESS PROTEINS: POTENTIAL AS MULTITIERED BIOMARKERS

    EPA Science Inventory

    The biomarker concept involves the use of biochemical, cellular, and physiological parameters as diagnostic screening tools in environmental monitoring. lthough biomarkers have been used in a variety of contexts this article deals specifically with the application of biomarkers f...

  4. Biomarkers in cancer screening: a public health perspective.

    PubMed

    Srivastava, Sudhir; Gopal-Srivastava, Rashmi

    2002-08-01

    definitive technology, such as CT scan. The National Cancer Institute's Early Detection Research Network (EDRN) has begun an innovative, investigator-initiated project to improve methods for detecting the biomarkers of cancer cells. The EDRN is a consortium of more than 32 institutions to link discovery of biomarkers to the next steps in the process of developing early detection tests. These discoveries will lead to early clinical validation of tests with improved accuracy and reliability. PMID:12163714

  5. Biomarkers in melanoma.

    PubMed

    Griewank, Klaus G

    2016-01-01

    Malignant melanoma remains the skin cancer with the highest number of mortalities worldwide. While early diagnosis and complete surgical excision remain the best possibility for curing disease, prognosis at the stage of metastasis is still poor. Recent years have brought about considerable advances in terms of understanding the pathogenesis of melanoma and treating advanced disease. The discovery of activating BRAF mutations in around 50% of tumors has led to the introduction of targeted therapies downregulating BRAF signaling output. These have been further refined as combination therapies, which by targeting multiple targets have further improved the clinical outcome. A comparable, potentially even superior therapeutic alternative has been the introduction of immunotherapeutic approaches, including PD-1 and CTLA-4 checkpoint blockade therapies. Despite all genetic knowledge acquired in recent years, a clearly applicable prognostic signature of clinical value has not been established. General prognostic assessment of cutaneous melanoma remains based on clinical and pathological criteria (most importantly tumor thickness). The main challenges lying ahead are to establish a reliable prognostic test effectively determining which tumors will metastasize. Additionally establishing biomarkers which will allow patients to be stratified according to the most promising systemic therapy (immunotherapies and/or BRAF inhibitor therapies) is of utmost importance for patients with metastasized disease. Identifying serum biomarkers enabling disease to be monitored as well as determining tumor properties (i.e. resistance) would also be of great value. While initial results have proven promising, there remains much work to be done. PMID:27467728

  6. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology.

    PubMed

    Roux, F; Bergelson, J

    2016-01-01

    In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity. PMID:27282025

  7. Use of Biomarkers in Oil Spill Risk Assessment in the marine environment

    SciTech Connect

    Anderson, Jack W.; Lee, Richard F.

    2006-12-01

    Numerous molecular, cellular and physiological biomarkers have been used to assess the responses of marine animals to petroleum compounds. To be used in ecological risk assessment after an oil spill, a biomarker response needs to be linked to petroleum exposure and not strongly influenced by internal and external confounding factors. Biomarker responses to petroleum PAH, dominated by alkylated two- and three-ringed aromatics, can be quite different than responses to pyrogenic PAH, dominated by four- and five-ringed aromatics. In many field sites there is a mixture of petrogenic and pyrogenic PAH, along with other contaminant, making it difficult to relate biomarker responses to a particular contaminant class. Biomarkers used to assess marine animal responses in the field include the cytochrome P450 system, heat stress protein, histopathology and bile fluorescent compounds (FAC). Other biomarkers, including DNA/chromosomal damage and phase 2 enzymes, have been shown to respond after laboratory exposure, but more works needs to be done to demonstrate their usefulness in the field. One of the most useful biomarkers of petroleum exposure are the FAC responses in fish, which can be used to distinguish between petrogenic and pyrogenic PAH exposure. Few of the presently used biomarkers are linked to higher order biological effects, e.g toxicity, reproductive failure.

  8. Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress.

    PubMed

    Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; Pieper, Dietmar H; Vilchez-Vargas, Ramiro

    2016-01-01

    Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched. PMID:26850298

  9. Microbial Community Stratification Linked to Utilization of Carbohydrates and Phosphorus Limitation in a Boreal Peatland at Marcell Experimental Forest, Minnesota, USA

    PubMed Central

    Tfaily, Malak M.; Steinweg, J. Megan; Chanton, Patrick; Esson, Kaitlin; Yang, Zamin K.; Chanton, Jeffrey P.; Cooper, William; Schadt, Christopher W.

    2014-01-01

    This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of Acidobacteria and the Syntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of Archaea (primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at

  10. Biomarkers in Alpha-1 Antitrypsin Deficiency Chronic Obstructive Pulmonary Disease.

    PubMed

    Turino, Gerard M; Ma, Shuren; Cantor, Jerome O; Lin, Yong Y

    2016-08-01

    Biomarkers of pathogenesis in chronic obstructive pulmonary disease (COPD) can significantly accelerate drug development. In COPD related to alpha-1 antitrypsin deficiency, the role of neutrophil elastase and its inhibition by alpha-1 antitrypsin protein focused interest on elastin degradation and the development of pulmonary emphysema. Amino acids desmosine and isodesmosine are unique cross-links in mature elastin fibers and can serve as biomarkers of elastin degradation when measured in body fluids. This review gives a perspective on what has been learned by the earliest measurements of desmosine and isodesmosine followed by later studies using methods of increased sensitivity and specificity and the meaning for developing new therapies. Also included are brief statements on the biomarkers fibrinogen, CC-16, and Aa-Val-360 in COPD. PMID:27564670

  11. Stable Isotope Ratios as Biomarkers of Diet for Health Research

    PubMed Central

    O’Brien, Diane M.

    2016-01-01

    Diet is a leading modifiable risk factor for chronic disease, but it remains difficult to measure accurately due to the error and bias inherent in self-reported methods of diet assessment. Consequently there is a pressing need for more objective biomarkers of diet for use in health research. The stable isotope ratios of light elements are a promising set of candidate biomarkers because they vary naturally and reproducibly among foods, and those variations are captured in molecules and tissues with high fidelity. Recent studies have identified valid isotopic measures of short and long-term sugar intake, meat intake, and fish intake in specific populations. These studies provide a strong foundation for validating stable isotopic biomarkers in the general United States population. Approaches to improve specificity for specific foods are needed, for example, by modeling intake using multiple stable isotope ratios, or by isolating and measuring specific molecules linked to foods of interest. PMID:26048703

  12. MOLECULAR CHARACTERIZATION OF MICROBIAL COMMUNITIES IN A JP-4 FUEL CONTAMINATED SOIL

    EPA Science Inventory

    In this study, lipid biomarker characterization of the bacterial and eukaryotic communities was combined with PCR-DGGE analysis of the eubacterial community to evaluate correlation between JP-4 fuel concentration and community structure shifts. Vadose, capillary fringe and satur...

  13. Biomarkers for the differentiation of anemia and their clinical usefulness

    PubMed Central

    Northrop-Clewes, Christine A; Thurnham, David I

    2013-01-01

    The World Health Organization defines anemia as the point at which the amount of hemoglobin in the circulation falls below World Health Organization cutoffs for specific age and sex groups. Anemia is a worldwide problem of complex etiology and is associated with many factors. The purpose of this review was to describe the biomarkers used to identify the nature of anemia in patients and in the community. The important biomarkers are the automated red cell counts, tests for nutritional deficiencies, hemoglobinopathies, and inflammation. Diseases are important potential initiators of anemia, but biomarkers of specific diseases are not included in this review, only the underlying feature common to all disease – namely, inflammation. PMID:23687454

  14. Impact of gravel mining on benthic invertebrate communities in a highly dynamic gravel-bed river: an integrated methodology to link geomorphic disturbances and ecological status

    NASA Astrophysics Data System (ADS)

    Béjar, María; Gibbins, Chris; Vericat, Damià; Batalla, Ramon J.; Buendia, Cristina; Lobera, Gemma

    2014-05-01

    Water and sediments are transported along river channels. Their supply, transport and deposition control river morphology and sedimentary characteristics, which in turn support habitat. Floods disturb river channels naturally although anthropogenic impacts may also contribute. River channel disturbance is considered the main factor affecting the organization of riverine communities and contributes to key ecological processes. In this paper we present an integrated methodology designed to analyze the impacts of in-channel gravel mining on benthic invertebrate communities. The study is conducted in the Upper River Cinca (Southern Pyrenees). A 11 km river reach is being monitored in order to understand the effects of floods and gravel mining on channel morphodynamics and invertebrate communities. The study reach is located in and upland gravel-bed system historically and currently affected by periodical episodes of in-channel sediment mining. This methodology has been developed in the background of the research project MorphSed. An integrated methodology of four components (Co) has been designed and is being implemented: (Co1) acquisition of high resolution imagery to generate topographic models before and after channel disturbances. Floods and in-channel gravel mining are considered natural and anthropogenic disturbances, respectively. Topographic models are obtained by means of combining automated digital photogrammetry (SfM) and optical bathymetric models. Event-scale models are used to assess the spatial extent and magnitude of bed disturbance. (Co2) Invertebrate sampling in 5 representative reaches along the study site. Invertebrate surber samples are providing data to define assemblages and their characteristics (composition, density, distribution, traits). These data is used to assess the spatial extent of channel disturbance impacts on the taxonomic and trait structure of communities. (Co3) Monitoring flow and sediment transport in the upstream and downstream

  15. Imaging Biomarkers in Immunotherapy

    PubMed Central

    Juergens, Rosalyn A.; Zukotynski, Katherine A.; Singnurkar, Amit; Snider, Denis P.; Valliant, John F.; Gulenchyn, Karen Y.

    2016-01-01

    Immune-based therapies have been in use for decades but recent work with immune checkpoint inhibitors has now changed the landscape of cancer treatment as a whole. While these advances are encouraging, clinicians still do not have a consistent biomarker they can rely on that can accurately select patients or monitor response. Molecular imaging technology provides a noninvasive mechanism to evaluate tumors and may be an ideal candidate for these purposes. This review provides an overview of the mechanism of action of varied immunotherapies and the current strategies for monitoring patients with imaging. We then describe some of the key researches in the preclinical and clinical literature on the current uses of molecular imaging of the immune system and cancer. PMID:26949344

  16. Biomarkers for lymphoma

    DOEpatents

    Zangar, Richard C.; Varnum, Susan M.

    2014-09-02

    A biomarker, method, test kit, and diagnostic system for detecting the presence of lymphoma in a person are disclosed. The lymphoma may be Hodgkin's lymphoma or non-Hodgkin's lymphoma. The person may be a high-risk subject. In one embodiment, a plasma sample from a person is obtained. The level of at least one protein listed in Table S3 in the plasma sample is measured. The level of at least one protein in the plasma sample is compared with the level in a normal or healthy subject. The lymphoma is diagnosed based upon the level of the at least one protein in the plasma sample in comparison to the normal or healthy level.

  17. [Biomarkers: "Found in translation"].

    PubMed

    Lockhart, Brian P; Walther, Bernard

    2009-04-01

    Despite continued increase in global Pharma R & D expenditure, the number of innovative drugs obtaining market approval has declined since 1994. The pharmaceutical industry is now entering a crucial juncture where increasing rates of attrition in clinical drug development as well as increasing development timelines are impacted by external factors such as intense regulatory pricing and safety pressures, increasing sales erosion due to generics, as well as exponential increases in the costs of bringing a drug to market. Despite these difficulties, numerous opportunities exist such as multiple unmet medical needs, the increasing incidence of certain diseases such as Alzheimer's disease, cancer, diabetes and obesity due to demographic changes, as well as the emergence of evolving markets such as China, India, and Eastern Europe. Consequently, Pharma is now responding to this challenge by improving both the productivity and the innovation in its drug discovery and development pipelines. In this regard, the advent of new technologies and expertise such as genomics, proteomics, structural biology, and molecular informatics in an integrated systems biology approach also provides a powerful opportunity for Pharma to address some of these difficulties. The key features behind this new strategy imply a discovery process based on an improved understanding of the molecular mechanism of diseases and drugs, translational research that places the patient at the center of the research process, and the application of biomarkers throughout the discovery and development phases. Moreover, new paradigms are required to improve target validation and develop more predictive cellular and animal models of human pathologies, a greater capacity in informatics-based analysis, and, consequently, a greater access to the vast sources of accumulating biological data and its integrated analysis. In the present review, we will address some of these issues and in particular emphasize how the

  18. Link Analysis

    NASA Astrophysics Data System (ADS)

    Donoho, Steve

    Link analysis is a collection of techniques that operate on data that can be represented as nodes and links. This chapter surveys a variety of techniques including subgraph matching, finding cliques and K-plexes, maximizing spread of influence, visualization, finding hubs and authorities, and combining with traditional techniques (classification, clustering, etc). It also surveys applications including social network analysis, viral marketing, Internet search, fraud detection, and crime prevention.

  19. Biomarker Discovery for Heterogeneous Diseases

    PubMed Central

    Wallstrom, Garrick; Anderson, Karen S.; LaBaer, Joshua

    2013-01-01

    Background Modern genomic and proteomic studies reveal that many diseases are heterogeneous, comprising multiple different subtypes. The common notion that one biomarker can be predictive for all patients may need to be replaced by an understanding that each subtype has its own set of unique biomarkers, affecting how discovery studies are designed and analyzed. Methods We used Monte Carlo simulation to measure and compare the performance of eight selection methods with homogeneous and heterogeneous diseases using both single-stage and two-stage designs. We also applied the selection methods in an actual proteomic biomarker screening study of heterogeneous breast cancer cases. Results Different selection methods were optimal and more than 2-fold larger sample sizes were needed for heterogeneous diseases compared with homogeneous diseases. We also found that for larger studies, two-stage designs can achieve nearly the same statistical power as single-stage designs at significantly reduced cost. Conclusions We found that disease heterogeneity profoundly affected biomarker performance. We report sample size requirements and provide guidance on the design and analysis of biomarker discovery studies for both homogeneous and heterogeneous diseases. Impact We have shown that studies to identify biomarkers for the early detection of heterogeneous disease require different statistical selection methods and larger sample sizes than if the disease were homogeneous. These findings provide a methodological platform for biomarker discovery of heterogeneous diseases. PMID:23462916

  20. Novel Biomarkers of Acute Kidney Injury After Contrast Coronary Angiography.

    PubMed

    Connolly, M; McEneaney, D; Menown, Ian; Morgan, N; Harbinson, M

    2015-01-01

    Acute kidney injury (AKI), defined as a rise in serum creatinine of greater than 25% from baseline measured at 48 hours after renal insult, may follow iodinated contrast coronary angiography. Termed contrast-induced nephropathy, it can result in considerable morbidity and mortality. Measurement of serum creatinine as a functional biomarker of glomerular filtration rate is widely used for detection of AKI, but it lacks sensitivity for the early diagnosis of AKI (typically rising 24 hours after functional loss) and, as a solely functional marker of glomerular filtration rate, is unable to differentiate among the various causes of AKI. These intrinsic limitations to creatinine measurement and the recognition that improved clinical outcomes are linked to a more timely diagnosis of AKI, has led investigators to search for novel biomarkers of "early" kidney injury. Several studies have investigated the utility of renal injury biomarkers in a variety of clinical settings including angiography/percutaneous coronary intervention, coronary artery bypass graft surgery, sepsis in intensive care patients, and pediatric cardiac surgery. In this article, we discuss the use of iodinated contrast for coronary procedures and the risk factors for contrast-induced nephropathy, followed by a review the potential diagnostic utility of several novel biomarkers of early AKI in the clinical settings of coronary angiography/percutaneous coronary intervention. In particular, we discuss neutrophil gelatinase associated lipocalin in depth. If validated, such biomarkers would facilitate earlier AKI diagnosis and improve clinical outcomes. PMID:25699983

  1. Biomarkers of cardiovascular stress in obstructive sleep apnea.

    PubMed

    Maeder, Micha T; Mueller, Christian; Schoch, Otto D; Ammann, Peter; Rickli, Hans

    2016-09-01

    Obstructive sleep apnea (OSA) is a common sleep-related breathing disorder associated with "cardiovascular stress", i.e. cardiovascular risk factors, cardiovascular diseases, and an increased risk of heart failure, stroke, and death. Experimental and clinical studies have characterized potential underlying mechanisms including biventricular dysfunction, atherosclerosis, and arrhythmia. Assessment of these cardiovascular features of OSA requires a spectrum of clinical tools including ECG, echocardiography, exercise testing, and angiography. In contrast to many cardiovascular diseases, the role of blood biomarkers to characterize cardiovascular function and cardiovascular risk in OSA is poorly defined. In the present review we summarize the available data on biomarkers potentially providing information on cardiovascular features in OSA patients without overt cardiovascular disease. The vast majority of studies on biomarkers of cardiovascular stress in OSA evaluated B-type natriuretic peptide (BNP)/N-terminal-B-type natriuretic peptide (NT-proBNP), and cardiac troponins (cTn). Although some studies found significant associations between these cardiac biomarkers and the presence and severity of OSA, data remain conflicting. Also, the detailed pathophysiological mechanisms underlying the link between OSA and hemodynamic cardiac stress (BNP/NT-proBNP) and cardiomyocyte damage (cTn) are poorly understood. Major research efforts are required to establish the clinical role of cardiovascular biomarkers in patients with OSA. PMID:27380998

  2. Buds from the tree of life: linking compartmentalized prokaryotes and eukaryotes by a non-hyperthermophile common ancestor and implications for understanding Archaean microbial communities

    NASA Astrophysics Data System (ADS)

    Fuerst, John A.; Nisbet, Euan G.

    2004-07-01

    The origin of the first nucleated eukaryote and the nature of the last common ancestor of the three domains of life are major questions in the evolutionary biology of cellular life on Earth, the solutions to which may be linked. Planctomycetes are unusual compartmentalized bacteria that include a membrane-bounded nucleoid. The possibility that they constitute a very deep branch of the domain Bacteria suggests a model for the evolution of the three domains of life from a last common ancestor that was a mesophile or moderate thermophile with a compartmentalized eukaryote-like cell plan. Planctomycetes and some members of the domain Archaea may have retained cell compartmentalization present in an original eukaryote-like last common ancestor of the three domains of life. The implications of this model for possible habitats of the early evolution of domains of cellular life and for interpretation of geological evidence relating to those habitats and the early emergence of life are examined here.

  3. Biomarkers as tracers for life on early earth and Mars

    NASA Technical Reports Server (NTRS)

    Simoneit, B. R.; Summons, R. E.; Jahnke, L. L.

    1998-01-01

    Biomarkers in geological samples are products derived from biochemical (natural product) precursors by reductive and oxidative processes (e.g., cholestanes from cholesterol). Generally, lipids, pigments and biomembranes are preserved best over longer geological times and labile compounds such as amino acids, sugars, etc. are useful biomarkers for recent times. Thus, the detailed characterization of biomarker compositions permits the assessment of the major contributing species of extinct and/or extant life. In the case of the early Earth, work has progressed to elucidate molecular structure and carbon isotropic signals preserved in ancient sedimentary rocks. In addition, the combination of bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems permits the modeling of the nature, behavior and preservation potential of primitive microbial communities. This approach uses combined molecular and isotopic analyses to characterize lipids produced by cultured bacteria (representative of ancient strains) and to test a variety of culture conditions which affect their biosynthesis. On considering Mars, the biomarkers from lipids and biopolymers would be expected to be preserved best if life flourished there during its early history (3.5-4 x 10(9) yr ago). Both oxidized and reduced products would be expected. This is based on the inferred occurrence of hydrothermal activity during that time with the concomitant preservation of biochemically-derived organic matter. Both known biomarkers (i.e., as elucidated for early terrestrial samples and for primitive terrestrial microbiota) and novel, potentially unknown compounds should be characterized.

  4. Inflammatory Biomarkers of Birth Asphyxia.

    PubMed

    Chalak, Lina F

    2016-09-01

    Although therapies in addition to whole-body cooling are being developed to treat the neonate at risk for hypoxic-ischemic encephalopathy, we have no quickly measured serum inflammatory or neuronal biomarkers to acutely and accurately identify brain injury or to follow the efficacy of therapy. This review covers inflammatory serum biomarkers in the setting of birth asphyxia that can help assess the degree or severity of encephalopathy at birth and neurodevelopmental outcomes. These biomarkers still need to be independently validated in large cohorts before they are ready for clinical implementation in practice. PMID:27524450

  5. Urinary Biomarkers of Brain Diseases

    PubMed Central

    An, Manxia; Gao, Youhe

    2016-01-01

    Biomarkers are the measurable changes associated with a physiological or pathophysiological process. Unlike blood, urine is not subject to homeostatic mechanisms. Therefore, greater fluctuations could occur in urine than in blood, better reflecting the changes in human body. The roadmap of urine biomarker era was proposed. Although urine analysis has been attempted for clinical diagnosis, and urine has been monitored during the progression of many diseases, particularly urinary system diseases, whether urine can reflect brain disease status remains uncertain. As some biomarkers of brain diseases can be detected in the body fluids such as cerebrospinal fluid and blood, there is a possibility that urine also contain biomarkers of brain diseases. This review summarizes the clues of brain diseases reflected in the urine proteome and metabolome. PMID:26751805

  6. A Robust Biomarker

    NASA Technical Reports Server (NTRS)

    Westall, F.; Steele, A.; Toporski, J.; Walsh, M. M.; Allen, C. C.; Guidry, S.; McKay, D. S.; Gibson, E. K.; Chafetz, H. S.

    2000-01-01

    containing fossil biofilm, including the 3.5 b.y..-old carbonaceous cherts from South Africa and Australia. As a result of the unique compositional, structural and "mineralisable" properties of bacterial polymer and biofilms, we conclude that bacterial polymers and biofilms constitute a robust and reliable biomarker for life on Earth and could be a potential biomarker for extraterrestrial life.

  7. Biomarker in archaeological soils

    NASA Astrophysics Data System (ADS)

    Wiedner, Katja; Glaser, Bruno; Schneeweiß, Jens

    2015-04-01

    The use of biomarkers in an archaeological context allow deeper insights into the understanding of anthropogenic (dark) earth formation and from an archaeological point of view, a completely new perspective on cultivation practices in the historic past. During an archaeological excavation of a Slavic settlement (10th/11th C. A.D.) in Brünkendorf (Wendland region in Northern Germany), a thick black soil (Nordic Dark Earth) was discovered that resembled the famous terra preta phenomenon. For the humid tropics, terra preta could act as model for sustainable agricultural practices and as example for long-term CO2-sequestration into terrestrial ecosystems. The question was whether this Nordic Dark Earth had similar properties and genesis as the famous Amazonian Dark Earth in order to find a model for sustainable agricultural practices and long term CO2-sequestration in temperate zones. For this purpose, a multi-analytical approach was used to characterize the sandy-textured Nordic Dark Earth in comparison to less anthropogenically influenced soils in the adjacent area in respect of ecological conditions (e.g. amino sugar), input materials (faeces) and the presence of stable soil organic matter (black carbon). Amino sugar analyses showed that Nordic Dark Earth contained higher amounts of microbial residues being dominated by soil fungi. Faecal biomarkers such as stanols and bile acids indicated animal manure from omnivores and herbivores but also human excrements. Black carbon content of about 30 Mg ha-1 in the Nordic Dark Earth was about four times higher compared to the adjacent soil and in the same order of magnitude compared to terra preta. Our data strongly suggest parallels to anthropogenic soil formation in Amazonia and in Europe by input of organic wastes, faecal material and charred organic matter. An obvious difference was that in terra preta input of human-derived faecal material dominated while in NDE human-derived faecal material played only a minor role

  8. Translational progress on tumor biomarkers

    PubMed Central

    Guo, Hongwei; Zhou, Xiaolin; Lu, Yi; Xie, Liye; Chen, Qian; Keller, Evan T; Liu, Qian; Zhou, Qinghua; Zhang, Jian

    2015-01-01

    There is an urgent need to apply basic research achievements to the clinic. In particular, mechanistic studies should be developed by bench researchers, depending upon clinical demands, in order to improve the survival and quality of life of cancer patients. To date, translational medicine has been addressed in cancer biology, particularly in the identification and characterization of novel tumor biomarkers. This review focuses on the recent achievements and clinical application prospects in tumor biomarkers based on translational medicine. PMID:26557902

  9. Linking microbial comunity composition and soil processes in acalifornia annual grassland and mixed-conifer forest

    SciTech Connect

    Balser, T.C.; Firestone, M.K.

    2003-07-21

    To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbon dioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO2 production and soil NH4+ concentration, while microbial community characteristics correlated with N2O production, nitrification potential, gross N-mineralization, and soil NO3 concentration, independent of environmental controllers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes, particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology.

  10. Linking Environmental Exposure with Public Health: Dichlorodiphenyltrichloroethane Extracted from Soils and Water of Recently Exposed Communities of Selected Locations in Zambia

    PubMed Central

    Sipilanyambe Munyinda, Nosiku; Michelo, Charles; Sichilongo, Kwenga

    2015-01-01

    Background. In 2000, a Zambian private mining company reintroduced the use of dichlorodiphenyltrichloroethane (DDT) to control malaria in two districts. From 2000 to 2010, DDT had been applied in homes without any studies conducted to ascertain its fate in the environment. We aimed to quantify the presence of DDT and its metabolites in the soil and water around communities where it was recently used. Methods. We collected superficial soil and water samples from drinking sources of three study areas. DDT was extracted by QuEChERS method and solid phase extraction for soils and water, respectively. Analysis was by gas chromatography-mass spectrometry. A revalidated method with limits of detection ranging from 0.034 to 0.04 ppb was used. Results. Median levels of total DDT were found at 100.4 (IQR 90.9–110) and 725.4 ng/L (IQR 540–774.5) for soils and water, respectively. No DDT above detection limits was detected in the reference area. These results are clinically significant given the persistent characteristics of DDT. Conclusion. DDT presence in these media suggests possible limitations in the environmental safeguards during IRS. Such occurrence could have potential effects on humans, especially children; hence, there is a need to further examine possible associations between this exposure and humans. PMID:26579199

  11. Protein biomarkers of periodontitis in saliva.

    PubMed

    Taylor, John J

    2014-01-01

    Periodontitis is a chronic inflammatory condition of the tissues that surround and support the teeth and is initiated by inappropriate and excessive immune responses to bacteria in subgingival dental plaque leading to loss of the integrity of the periodontium, compromised tooth function, and eventually tooth loss. Periodontitis is an economically important disease as it is time-consuming and expensive to treat. Periodontitis has a worldwide prevalence of 5-15% and the prevalence of severe disease in western populations has increased in recent decades. Furthermore, periodontitis is more common in smokers, in obesity, in people with diabetes, and in heart disease patients although the pathogenic processes underpinning these links are, as yet, poorly understood. Diagnosis and monitoring of periodontitis rely on traditional clinical examinations which are inadequate to predict patient susceptibility, disease activity, and response to treatment. Studies of the immunopathogenesis of periodontitis and analysis of mediators in saliva have allowed the identification of many potentially useful biomarkers. Convenient measurement of these biomarkers using chairside analytical devices could form the basis for diagnostic tests which will aid the clinician and the patient in periodontitis management; this review will summarise this field and will identify the experimental, technical, and clinical issues that remain to be addressed before such tests can be implemented. PMID:24944840

  12. Exploring biomarkers in head and neck cancer.

    PubMed

    Langer, Corey J

    2012-08-15

    Personalized medicine based on predictive markers linked to drug response, it is hoped, will lead to improvements in outcomes and avoidance of unnecessary treatment in squamous cell carcinoma of the head and neck (SCCHN). Recent research has shown that expression of ERCC1 may predict resistance to treatment with platinum agents. Future testing for this marker may help select the optimal type of chemotherapy. Infection with human papillomavirus (HPV) is associated with less aggressive disease and better prognosis in locally advanced SCCHN treated with chemoradiation or radiation alone; HPV-positive patients may ultimately benefit from less intensive, less toxic therapy. K-RAS mutations, occurring in about 40% of colorectal cancers and associated with lack of benefit from epidermal growth factor receptor (EGFR) antibodies in this disease, are found in <5% of SCCHN patients, making routine testing for K-RAS mutations unwarranted at this time. Virtually all head and neck tumors overexpress EGFR, which limits the usefulness of EGFR expression as a marker for treatment selection. Although the incidence of EGFR tyrosine kinase domain mutations is very rare, a better understanding of the role of EGFR mutations, expression, amplification, and downstream effects in SCCHN may help define the role of EGFR in this setting. These observations caution against extrapolating results obtained with biomarkers in other types of cancer to SCCHN. Validation of each biomarker in the context of SCCHN clinical trials will be required before a specific marker can be incorporated into daily practice. PMID:22281752

  13. Evaluating Biomarkers in Melanoma

    PubMed Central

    Karagiannis, Panagiotis; Fittall, Matthew; Karagiannis, Sophia N.

    2015-01-01

    The incidence of cutaneous melanoma has more than doubled over the last decades making it one of the fastest rising cancers worldwide. Improved awareness and early detection of malignant moles now permit earlier diagnosis aiming to decrease the likelihood of recurrence. However, it is difficult to identify those patients initially diagnosed with localized melanoma who subsequently develop metastatic disease. For this group, prognosis remains poor and clinical outcomes are variable and challenging to predict. Considerable efforts have focused on the search for novel prognostic tools, with numerous markers evaluated in the circulation and in tumor lesions. The most reliable predictors of patient outcome are the clinical and histological features of the primary tumor such as Breslow thickness, ulceration status, and mitotic rate. Elevated serum levels of the enzyme lactate dehydrogenase, likely to indicate active metastatic disease, are also routinely used to monitor patients. The emergence of novel immune and checkpoint antibody treatments for melanoma and increasing appreciation of key roles of the immune system in promoting or halting cancer progression have focused attention to immunological biomarkers. Validation of the most promising of these may have clinical applications in assisting prognosis, assessing endpoints in therapy, and monitoring responses during treatment. PMID:25667918

  14. Neuroimmune biomarkers in schizophrenia.

    PubMed

    Tomasik, Jakub; Rahmoune, Hassan; Guest, Paul C; Bahn, Sabine

    2016-09-01

    Schizophrenia is a heterogeneous psychiatric disorder with a broad spectrum of clinical and biological manifestations. Due to the lack of objective tests, the accurate diagnosis and selection of effective treatments for schizophrenia remains challenging. Numerous technologies have been employed in search of schizophrenia biomarkers. These studies have suggested that neuroinflammatory processes may play a role in schizophrenia pathogenesis, at least in a subgroup of patients. The evidence indicates alterations in both pro- and anti-inflammatory molecules in the central nervous system, which have also been found in peripheral tissues and may correlate with schizophrenia symptoms. In line with these findings, certain immunomodulatory interventions have shown beneficial effects on psychotic symptoms in schizophrenia patients, in particular those with distinct immune signatures. In this review, we evaluate these findings and their potential for more targeted drug interventions and the development of companion diagnostics. Although currently no validated markers exist for schizophrenia patient stratification or the prediction of treatment efficacy, we propose that utilisation of inflammatory markers for diagnostic and theranostic purposes may lead to novel therapeutic approaches and deliver more effective care for schizophrenia patients. PMID:25124519

  15. Linked Systems.

    ERIC Educational Resources Information Center

    Association of Research Libraries, Washington, DC.

    Three papers are compiled here for research library directors: (1) "Background: Open Systems Interconnection," in which David F. Bishop provides fundamental background information to explain the concept of the emerging technology of linked systems and open systems interconnection--i.e., an agreed upon standard set of conventions or rules that,…

  16. Regional Approach for Managing for Resilience Linking Ecosystem Services and Livelihood Strategies for Agro-Pastoral Communities in the Mongolian Steppe Ecosystem

    NASA Astrophysics Data System (ADS)

    Ojima, D. S.; Togtohyn, C.; Qi, J.; Galvin, K.

    2011-12-01

    Dramatic changes due to climate and land use dynamics in the Mongolian Plateau are affecting ecosystem services and agro-pastoral livelihoods in Mongolia and China. Recently, evaluation of pastoral systems, where humans depend on livestock and grassland ecosystem services, have demonstrated the vulnerability of the social-ecological system to climate change. Current social-ecological changes in ecosystem services are affecting land productivity and carrying capacity, land-atmosphere interactions, water resources, and livelihood strategies. Regional dust events, changes in hydrological cycle, and land use changes contribute to changing interactions between ecosystem and landscape processes which then affect social-ecological systems. The general trend involves greater intensification of resource exploitation at the expense of traditional patterns of extensive range utilization. Thus we expect climate-land use-land cover relationships to be crucially modified by the socio-economic forces. The analysis incorporates information of the socio-economic transitions taking place in the region which affect land-use, food security, and ecosystem dynamics. The region of study extends from the Mongolian plateau in Mongolia and China to the fertile northeast China plain. Sustainability of agro-pastoral systems in the region needs to integrate the impact of climate change on ecosystem services with socio-economic changes shaping the livelihood strategies of pastoral systems in the region. Adaptation strategies which incorporate landscape management provides a potential framework to link ecosystem services across space and time more effectively to meet the needs of agro-pastoral land use, herd quality, and herder's living standards. Under appropriate adaptation strategies agro-pastoralists will have the opportunity to utilize seasonal resources and enhance their ability to process and manufacture products from the available ecosystem services in these dynamic social

  17. The use of biomarkers to trace carbon transformations and input in soils

    NASA Astrophysics Data System (ADS)

    Jansen, Boris; Kalbitz, Karsten

    2015-04-01

    Tracing the origin of soil organic matter is an important tool to unravel mechanisms that lead to (de)stabilization of organic carbon in soil systems. To this end biomarkers, i.e. (groups of) specific molecules that can be linked to (groups of) specific plant species or plant parts are often used. A good example is the use of suberin and cutin as biomarkers to distinguish organic matter with a root origin from organic matter with a leaf origin. However, the use of biomarkers to trace the origin of soil organic matter is also subject of fierce scientific debate. On the one extreme end there are those colleagues who see biomarkers as a cure-all solution to all organic matter tracing problems. On the other end of the spectrum there are experts who claim that the concept of biomarkers is so intrinsically flawed that it can never yield meaningful information about carbon transformations except in the most specific cases. We believe that neither vision is correct. In our presentation we discuss the merits and drawbacks of using biomarkers to trace root versus leaf derived organic matter in soils. For this we use a 1-year incubation experiment with fine root and leaf material of six temperate tree species as a case study. We discuss the abundance, or lack thereof, of root and leaf derived biomarkers and the development of their concentration over time. Specifically, we found that the specificity of root and leaf specific biomarkers depended strongly on the amount and diversity of studied species. For instance, four molecules were identified to be leaf biomarkers for some species, while serving as root biomarkers for others. This could result in serious misjudgment of root and leaf specific biomarkers if the boundary conditions, including species of interest, are not well known. On the other hand, our results show that cutin and suberin derived biomarkers can indeed be successfully used to distinguish root from leaf input in certain situations, such as an ecosystem

  18. Phytoplankton Diversity and Geologically Relevant Carbon: Using metagenomics to determine phytoplankton biomarker production

    NASA Astrophysics Data System (ADS)

    Kodner, R. B.; Armbrust, E.

    2008-12-01

    Phytoplankton play an important role in the global carbon cycle, on short and long time scales. On long time scales, organic carbon, especially recalcitrant forms of biomass such as lipids, can be preserved and thus sequestered in sediments and rocks on geologic time scales. If the preserved lipids have some taxonomic specificity, they can be used as fossil biomarkers to characterize the community of organisms that contributed to ancient carbon sinks. Currently, it is not well understood how well the complex mixture of organic compounds preserved in geological carbon sinks represents the original community that produced those molecules or how the diversity of organism in a community is reflected in the lipid biomarkers they collectively synthesize. We have begun to investigate these questions by characterizing lipid biomarker production in modern phytoplankton communities with metagenomic data sets. Here we evaluate the information on community biomarker biosynthesis gathered from this type of data set using sterols as a case study. We have identified genes involved in sterol biosynthesis in a number of metagenomes and placed these genes in a phylogenetic context using a method designed to deal with short metagenomic sequences. The degree of taxonomic diversity of biomarker production measured with gene sequences can be more specific than lipid analysis alone.

  19. Temporal Trends in Syngenetic Lipid Biomarker Signals from Proterozoic Sedimentary Organic Matter

    NASA Astrophysics Data System (ADS)

    Love, G. D.; Li, C.; Summons, R. E.

    2008-12-01

    The development of continuous-flow catalytic hydropyrolysis (HyPy) for reproducible recovery of biomarker lipid skeletons covalently-bound within kerogen has proved to be an important analytical breakthrough for ancient lipid biomarker research. The parallel analyses of free (solvent-extractable) and kerogen-bound biomarkers affords more confidence that we have correctly identified syngenetic compounds. Combining HyPy with detailed biomarker product analyzes using metastable reaction monitoring-gas chromatography mass spectrometry (MRM-GC-MS) allows detection of a large suite of biomarker compounds which are usually too low in abundance to be analyzed in detail using conventional GC-MS. Here we compare free and bound lipid biomarker records generated from Paleoproterozoic (ca. 1.7 Ga) to Late Ediacaran age (ca. 542 Ma) strata from marine basins from North and South China, Australia and Oman. Fundamental changes in eukaryotic community structure are evident after the Sturtian glaciation (ca. 713 Ma) from distinctive sterane distributions. In particular, radiations in basal animals (sponges) and chlorophyte microalgae are first apparent in Huqf sedimentary rocks from South Oman Salt Basin. Marine microbial communities were not globally homogenous in contemporaneous Proterozoic settings from comparison of biomarker profiles and this could reflect differences in ocean chemistry, affecting nutrient supply, from basin to basin.

  20. Deep biomarkers of human aging: Application of deep neural networks to biomarker development

    PubMed Central

    Putin, Evgeny; Mamoshina, Polina; Aliper, Alexander; Korzinkin, Mikhail; Moskalev, Alexey; Kolosov, Alexey; Ostrovskiy, Alexander; Cantor, Charles; Vijg, Jan; Zhavoronkov, Alex

    2016-01-01

    One of the major impediments in human aging research is the absence of a comprehensive and actionable set of biomarkers that may be targeted and measured to track the effectiveness of therapeutic interventions. In this study, we designed a modular ensemble of 21 deep neural networks (DNNs) of varying depth, structure and optimization to predict human chronological age using a basic blood test. To train the DNNs, we used over 60,000 samples from common blood biochemistry and cell count tests from routine health exams performed by a single laboratory and linked to chronological age and sex. The best performing DNN in the ensemble demonstrated 81.5 % epsilon-accuracy r = 0.90 with R2 = 0.80 and MAE = 6.07 years in predicting chronological age within a 10 year frame, while the entire ensemble achieved 83.5% epsilon-accuracy r = 0.91 with R2 = 0.82 and MAE = 5.55 years. The ensemble also identified the 5 most important markers for predicting human chronological age: albumin, glucose, alkaline phosphatase, urea and erythrocytes. To allow for public testing and evaluate real-life performance of the predictor, we developed an online system available at http://www.aging.ai. The ensemble approach may facilitate integration of multi-modal data linked to chronological age and sex that may lead to simple, minimally invasive, and affordable methods of tracking integrated biomarkers of aging in humans and performing cross-species feature importance analysis. PMID:27191382

  1. Deep biomarkers of human aging: Application of deep neural networks to biomarker development.

    PubMed

    Putin, Evgeny; Mamoshina, Polina; Aliper, Alexander; Korzinkin, Mikhail; Moskalev, Alexey; Kolosov, Alexey; Ostrovskiy, Alexander; Cantor, Charles; Vijg, Jan; Zhavoronkov, Alex

    2016-05-01

    One of the major impediments in human aging research is the absence of a comprehensive and actionable set of biomarkers that may be targeted and measured to track the effectiveness of therapeutic interventions. In this study, we designed a modular ensemble of 21 deep neural networks (DNNs) of varying depth, structure and optimization to predict human chronological age using a basic blood test. To train the DNNs, we used over 60,000 samples from common blood biochemistry and cell count tests from routine health exams performed by a single laboratory and linked to chronological age and sex. The best performing DNN in the ensemble demonstrated 81.5 % epsilon-accuracy r = 0.90 with R(2) = 0.80 and MAE = 6.07 years in predicting chronological age within a 10 year frame, while the entire ensemble achieved 83.5% epsilon-accuracy r = 0.91 with R(2) = 0.82 and MAE = 5.55 years. The ensemble also identified the 5 most important markers for predicting human chronological age: albumin, glucose, alkaline phosphatase, urea and erythrocytes. To allow for public testing and evaluate real-life performance of the predictor, we developed an online system available at http://www.aging.ai. The ensemble approach may facilitate integration of multi-modal data linked to chronological age and sex that may lead to simple, minimally invasive, and affordable methods of tracking integrated biomarkers of aging in humans and performing cross-species feature importance analysis. PMID:27191382

  2. Linking Human Health and Livestock Health: A “One-Health” Platform for Integrated Analysis of Human Health, Livestock Health, and Economic Welfare in Livestock Dependent Communities

    PubMed Central

    Thumbi, S. M.; Njenga, M. Kariuki; Marsh, Thomas L.; Noh, Susan; Otiang, Elkanah; Munyua, Peninah; Ochieng, Linus; Ogola, Eric; Yoder, Jonathan; Audi, Allan; Montgomery, Joel M.; Bigogo, Godfrey; Breiman, Robert F.; Palmer, Guy H.; McElwain, Terry F.

    2015-01-01

    Background For most rural households in sub-Saharan Africa, healthy livestock play a key role in averting the burden associated with zoonotic diseases, and in meeting household nutritional and socio-economic needs. However, there is limited understanding of the complex nutritional, socio-economic, and zoonotic pathways that link livestock health to human health and welfare. Here we describe a platform for integrated human health, animal health and economic welfare analysis designed to address this challenge. We provide baseline epidemiological data on disease syndromes in humans and the animals they keep, and provide examples of relationships between human health, animal health and household socio-economic status. Method We designed a study to obtain syndromic disease data in animals along with economic and behavioral information for 1500 rural households in Western Kenya already participating in a human syndromic disease surveillance study. Data collection started in February 2013, and each household is visited bi-weekly and data on four human syndromes (fever, jaundice, diarrhea and respiratory illness) and nine animal syndromes (death, respiratory, reproductive, musculoskeletal, nervous, urogenital, digestive, udder disorders, and skin disorders in cattle, sheep, goats and chickens) are collected. Additionally, data from a comprehensive socio-economic survey is collected every 3 months in each of the study households. Findings Data from the first year of study showed 93% of the households owned at least one form of livestock (55%, 19%, 41% and 88% own cattle, sheep, goats and chickens respectively). Digestive disorders, mainly diarrhea episodes, were the most common syndromes observed in cattle, goats and sheep, accounting for 56% of all livestock syndromes, followed by respiratory illnesses (18%). In humans, respiratory illnesses accounted for 54% of all illnesses reported, followed by acute febrile illnesses (40%) and diarrhea illnesses (5%). While controlling

  3. Biomarkers and Microbial Fossils In Antarctic Rocks

    NASA Astrophysics Data System (ADS)

    Wierzchos, J.; Ascaso, C.

    Lithobiontic microbial communities living within Antarctic rocks are an example of survival in an extremely cold and dry environment. Any unfavourable change in ex- ternal conditions can result in the death and disappearance of microscopic organisms, and this may be followed by the appearance of trace biomarkers and microbial fossils. The extinction of these microorganisms in some zones of the Ross Desert, probably provoked by the hostile environment, might be considered a good terrestrial analogue of the first stage of the disappearance of possible life on early Mars. Granite samples from maritime Antarctica (Granite Harbour) and sandstone rocks from the continental Ross Desert were collected with the aim of searching for biomarkers and microbial fossils at the microscopic level of observation. To this end, a novel in situ applica- tion of scanning electron microscopy with backscattered electron imaging was com- bined with the simultaneous use of X-ray energy dispersive spectroscopy techniques. Our findings confirm the existence of inorganic biomarkers in the form of physico- chemically bioweathered minerals within the granitic rocks. The presence of Fe-rich diagenetic minerals, such as iron hydroxide nanocrystals and biogenic clays around chasmoendolithic hyphae and bacterial cells was also observed. Others biomarkers, including inorganic deposits such as calcium oxalates and silica accumulations, are clear signs of endolithic microorganism activity. The interior of the sandstone rocks (Ross Desert, Mt. Fleming) reveal the presence of microbial fossils of algae and other endolithic microorganisms. These microbial fossils, detected for the first time within Antarctic rocks, contain well preserved and morphologically distinguishable relics of ultrastructural cytoplasm elements, such as cell walls, chloroplast membranes, and oc- casionally, pyrenoids and traces of organic matter. These structures are similar to those observed in live cells also found in Antarctic

  4. Leaf Litter Mixtures Alter Microbial Community Development: Mechanisms for Non-Additive Effects in Litter Decomposition

    PubMed Central

    Chapman, Samantha K.; Newman, Gregory S.; Hart, Stephen C.; Schweitzer, Jennifer A.; Koch, George W.

    2013-01-01

    To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate. PMID:23658639

  5. Analytical Aspects of the Implementation of Biomarkers in Clinical Transplantation.

    PubMed

    Shipkova, Maria; López, Olga Millán; Picard, Nicolas; Noceti, Ofelia; Sommerer, Claudia; Christians, Uwe; Wieland, Eberhard

    2016-04-01

    In response to the urgent need for new reliable biomarkers to complement the guidance of the immunosuppressive therapy, a huge number of biomarker candidates to be implemented in clinical practice have been introduced to the transplant community. This includes a diverse range of molecules with very different molecular weights, chemical and physical properties, ex vivo stabilities, in vivo kinetic behaviors, and levels of similarity to other molecules, etc. In addition, a large body of different analytical techniques and assay protocols can be used to measure biomarkers. Sometimes, a complex software-based data evaluation is a prerequisite for appropriate interpretation of the results and for their reporting. Although some analytical procedures are of great value for research purposes, they may be too complex for implementation in a clinical setting. Whereas the proof of "fitness for purpose" is appropriate for validation of biomarker assays used in exploratory drug development studies, a higher level of analytical validation must be achieved and eventually advanced analytical performance might be necessary before diagnostic application in transplantation medicine. A high level of consistency of results between laboratories and between methods (if applicable) should be obtained and maintained to make biomarkers effective instruments in support of therapeutic decisions. This overview focuses on preanalytical and analytical aspects to be considered for the implementation of new biomarkers for adjusting immunosuppression in a clinical setting and highlights critical points to be addressed on the way to make them suitable as diagnostic tools. These include but are not limited to appropriate method validation, standardization, education, automation, and commercialization. PMID:26418704

  6. The Uganda Newborn Study (UNEST): an effectiveness study on improving newborn health and survival in rural Uganda through a community-based intervention linked to health facilities - study protocol for a cluster randomized controlled trial

    PubMed Central

    2012-01-01

    Background Reducing neonatal-related deaths is one of the major bottlenecks to achieving Millennium Development Goal 4. Studies in Asia and South America have shown that neonatal mortality can be reduced through community-based interventions, but these have not been adapted to scalable intervention packages for sub-Saharan Africa where the culture, health system and policy environment is different. In Uganda, health outcomes are poor for both mothers and newborn babies. Policy opportunities for neonatal health include the new national Health Sector Strategic Plan, which now prioritizes newborn health including use of a community model through Village Health Teams (VHT). The aim of the present study is to adapt, develop and cost an integrated maternal-newborn care package that links community and facility care, and to evaluate its effect on maternal and neonatal practices in order to inform policy and scale-up in Uganda. Methods/Design Through formative research around evidence-based practices, and dialogue with policy and technical advisers, we constructed a home-based neonatal care package implemented by the responsible VHT member, effectively a Community Health Worker (CHW). This CHW was trained to identify pregnant women and make five home visits - two before and three just after birth - so that linkages will be made to facility care and targeted messages for home-care and care-seeking delivered. The project is improving care in health units to provide standardized care for the mother and the newborn in both intervention and comparison areas. The study is taking place in a new Demographic Surveillance Site in two rural districts, Iganga and Mayuge, in Uganda. It is a two-arm cluster randomized controlled design with 31 intervention and 32 control areas (villages). The comparison parishes receive the standard care already being provided by the district, but to the intervention villages are added a system for CHWs to visit the mother five times in her home during

  7. Biomarkers in acute heart failure.

    PubMed

    Mallick, Aditi; Januzzi, James L

    2015-06-01

    The care of patients with acutely decompensated heart failure is being reshaped by the availability and understanding of several novel and emerging heart failure biomarkers. The gold standard biomarkers in heart failure are B-type natriuretic peptide and N-terminal pro-B-type natriuretic peptide, which play an important role in the diagnosis, prognosis, and management of acute decompensated heart failure. Novel biomarkers that are increasingly involved in the processes of myocardial injury, neurohormonal activation, and ventricular remodeling are showing promise in improving diagnosis and prognosis among patients with acute decompensated heart failure. These include midregional proatrial natriuretic peptide, soluble ST2, galectin-3, highly-sensitive troponin, and midregional proadrenomedullin. There has also been an emergence of biomarkers for evaluation of acute decompensated heart failure that assist in the differential diagnosis of dyspnea, such as procalcitonin (for identification of acute pneumonia), as well as markers that predict complications of acute decompensated heart failure, such as renal injury markers. In this article, we will review the pathophysiology and usefulness of established and emerging biomarkers for the clinical diagnosis, prognosis, and management of acute decompensated heart failure. PMID:25911167

  8. Biomarkers in traumatic brain injury: a review.

    PubMed

    Toman, Emma; Harrisson, S; Belli, T

    2016-04-01

    Biomarkers allow physiological processes to be monitored, in both health and injury. Multiple attempts have been made to use biomarkers in traumatic brain injury (TBI). Identification of such biomarkers could allow improved understanding of the pathological processes involved in TBI, diagnosis, prognostication and development of novel therapies. This review article aims to cover both established and emerging TBI biomarkers along with their benefits and limitations. It then discusses the potential value of TBI biomarkers to military, civilian and sporting populations and the future hopes for developing a role for biomarkers in head injury management. PMID:26527607

  9. DMS-prefiltered mass spectrometry for the detection of biomarkers

    NASA Astrophysics Data System (ADS)

    Coy, Stephen L.; Krylov, Evgeny V.; Nazarov, Erkinjon G.

    2008-04-01

    Technologies based on Differential Mobility Spectrometry (DMS) are ideally matched to rapid, sensitive, and selective detection of chemicals like biomarkers. Biomarkers linked to exposure to radiation, exposure to CWA's, exposure to toxic materials (TICs and TIMs) and to specific diseases are being examined in a number of laboratories. Screening for these types of exposure can be improved in accuracy and greatly speeded up by using DMS-MS instead of slower techniques like LC-MS and GC-MS. We have performed an extensive series of tests with nanospray-DMS-mass spectroscopy and standalone nanospray-DMS obtaining extensive information on chemistry and detectivity. DMS-MS systems implemented with low-resolution, low-cost, portable mass-spectrometry systems are very promising. Lowresolution mass spectrometry alone would be inadequate for the task, but with DMS pre-filtration to suppress interferences, can be quite effective, even for quantitative measurement. Bio-fluids and digests are well suited to ionization by electrospray and detection by mass-spectrometry, but signals from critical markers are overwhelmed by chemical noise from unrelated species, making essential quantitative analysis impossible. Sionex and collaborators have presented data using DMS to suppress chemical noise, allowing detection of cancer biomarkers in 10,000-fold excess of normal products 1,2. In addition, a linear dynamic range of approximately 2,000 has been demonstrated with accurate quantitation 3. We will review the range of possible applications and present new data on DMS-MS biomarker detection.

  10. Quantitative Imaging Biomarkers of NAFLD

    PubMed Central

    Kinner, Sonja; Reeder, Scott B.

    2016-01-01

    Conventional imaging modalities, including ultrasonography (US), computed tomography (CT), and magnetic resonance (MR), play an important role in the diagnosis and management of patients with nonalcoholic fatty liver disease (NAFLD) by allowing noninvasive diagnosis of hepatic steatosis. However, conventional imaging modalities are limited as biomarkers of NAFLD for various reasons. Multi-parametric quantitative MRI techniques overcome many of the shortcomings of conventional imaging and allow comprehensive and objective evaluation of NAFLD. MRI can provide unconfounded biomarkers of hepatic fat, iron, and fibrosis in a single examination—a virtual biopsy has become a clinical reality. In this article, we will review the utility and limitation of conventional US, CT, and MR imaging for the diagnosis NAFLD. Recent advances in imaging biomarkers of NAFLD are also discussed with an emphasis in multi-parametric quantitative MRI. PMID:26848588

  11. Quantitative Imaging Biomarkers of NAFLD.

    PubMed

    Kinner, Sonja; Reeder, Scott B; Yokoo, Takeshi

    2016-05-01

    Conventional imaging modalities, including ultrasonography (US), computed tomography (CT), and magnetic resonance (MR), play an important role in the diagnosis and management of patients with nonalcoholic fatty liver disease (NAFLD) by allowing noninvasive diagnosis of hepatic steatosis. However, conventional imaging modalities are limited as biomarkers of NAFLD for various reasons. Multi-parametric quantitative MRI techniques overcome many of the shortcomings of conventional imaging and allow comprehensive and objective evaluation of NAFLD. MRI can provide unconfounded biomarkers of hepatic fat, iron, and fibrosis in a single examination-a virtual biopsy has become a clinical reality. In this article, we will review the utility and limitation of conventional US, CT, and MR imaging for the diagnosis NAFLD. Recent advances in imaging biomarkers of NAFLD are also discussed with an emphasis in multi-parametric quantitative MRI. PMID:26848588

  12. Linked Ocean Data

    NASA Astrophysics Data System (ADS)

    Leadbetter, Adam; Arko, Robert; Chandler, Cynthia; Shepherd, Adam

    2014-05-01

    Data repositories. The benefits of this approach include: increased interoperability between the metadata created by projects; improved data discovery as users of SeaDataNet, R2R and BCO-DMO terms can find data using labels with which they are familiar both standard tools and newly developed custom tools may be used to explore the data; and using standards means the custom tools are easier to develop Linked Data is a concept which has been in existence for nearly a decade, and has a simple set of formal best practices associated with it. Linked Data is increasingly being seen as a driver of the next generation of "community science" activities. While many data providers in the oceanographic domain may be unaware of Linked Data, they may also be providing it at one of its lower levels. Here we have shown that it is possible to deliver the highest standard of Linked Oceanographic Data, and some of the benefits of the approach.

  13. Molecular Biomarkers: their significance and application in marine pollution monitoring.

    PubMed

    Sarkar, A; Ray, D; Shrivastava, Amulya N; Sarker, Subhodeep

    2006-05-01

    This paper presents an overview of the significance of the use of molecular biomarkers as diagnostic and prognostic tools for marine pollution monitoring. In order to assess the impact of highly persistent pollutants such as polychlorinated biphenyls (PCB), polychlorinated dibenzo-dioxins (PCDD), polychlorinated dibenzo-furans (PCDF), polynuclear aromatic hydrocarbons (PAH), tributyltin (TBT) and other toxic metals on the marine ecosystem a suite of biomarkers are being extensively used worldwide. Among the various types of biomarkers, the following have received special attention: cytochrome P4501A induction, DNA integrity, acetylcholinesterase activity and metallothionein induction. These biomarkers are being used to evaluate exposure of various species of sentinel marine organisms (e.g. mussels, clams, oysters, snails, fishes, etc.) to and the effect of various contaminants (organic xenobiotics and metals) using different molecular approaches [biochemical assays, enzyme linked immuno-sorbent assays (ELISA), spectrophotometric, fluorometric measurement, differential pulsed polarography, liquid chromatography, atomic absorption spectrometry]. The induction of the biotransformation enzyme, cytochrome P4501A in fishes (Callionymus lyra, Limanda limanda, Serranus sp., Mullus barbatus) and mussels (Dreissena polymorpha) by various xenobiotic contaminants such as PCBs, PAHs, PCDs is used as a biomarker of exposure to such organic pollutants. The induction of cytochrome P4501A is involved in chemical carcinogenesis through catalysis of the covalent bonding of organic contaminants to a DNA strand leading to formation of DNA adduct. Measurement of the induction of cytochrome P4501A in terms of EROD (7-ethoxy resorufin O-deethylase) activity is successfully used as a potential biomarker of exposure to xenobiotic contaminants in marine pollution monitoring. In order to assess the impact of neurotoxic compounds on marine environment the evaluation of acetylcholinesterase

  14. Scaling up Learning Communities: The Experience of Six Community Colleges

    ERIC Educational Resources Information Center

    Visher, Mary G.; Schneider, Emily; Wathington, Heather; Collado, Herbert

    2010-01-01

    The Learning Communities Demonstration is a large-scale, random assignment evaluation of learning community programs at six community colleges. During the first year of the demonstration, all six colleges expanded their learning community programs and, in the process, faced similar challenges in selecting courses to link, recruiting and supporting…

  15. Microbial communities responsible for fixation of CO2 revealed by using mcrA, cbbM, cbbL, fthfs, fefe-hydrogenase genes as molecular biomarkers in petroleum reservoirs of different temperatures

    NASA Astrophysics Data System (ADS)

    Liu, J.-F.; Mbadinga, S. M.; Sun, X.-B.; Yang, G.-C.; Yang, S.-Z.; Gu, J.-D.; Mu, B.-Z.

    2015-01-01

    Sequestration of CO2 in oil reservoir is one of the feasible options for mitigating atmospheric CO2 building up. The in situ bioconversion of sequestrated CO2 to methane by microorganisms inhabiting oil reservoirs is feasible. To evaluate the potential of in situ microbial fixation and conversion of CO2 into CH4 in oil reservoirs, a comprehensive molecular survey was performed to reveal microbial communities inhabiting four oil reservoirs with different temperatures by analysis of functional genes involved in the biochemical pathways of CO2 fixation and CH4 synthesis (cbbM, cbbL, fthfs, [FeFe]-hydrogenase encoding gene, and mcrA). A rich diversity of these functional genes was found in all the samples with both high and low temperatures and they were affiliated to members of the Proteobacteria (cbbL and cbbM, fthfs), Firmicutes and Actinobacteria (fthfs), uncultured bacteria ([FeFe]-hydrogenase), and Methanomirobiales, Methanobacteriales and Methanosarcinales (mcrA). The predominant methanogens were all identified to be hydrogenotrophic CO2-reducing physiological types. These results showed that functional microbial communities capable of microbial fixation and bioconversion of CO2 into methane inhabit widely in oil reservoirs, which is helpful to microbial recycling of sequestrated CO2 to further new energy in oil reservoirs.

  16. Interpretation of fish biomarker data for identification, classification, risk assessment and testing of endocrine disrupting chemicals.

    PubMed

    Dang, ZhiChao

    2016-01-01

    Chemical induced changes in fish biomarkers vitellogenin (VTG), secondary sex characteristics (SSC), and sex ratio indicate modes/mechanisms of action (MOAs) of EAS (estrogen, androgen and steroidogenesis) pathways. These biomarkers could be used for defining MOAs and the causal link between MOAs and adverse effects in fish for the identification of endocrine disrupting chemicals (EDCs). This paper compiled data sets of 150 chemicals for VTG, 57 chemicals for SSC and 38 chemicals for sex ratio in fathead minnow, medaka and zebrafish. It showed 1) changes in fish biomarkers can indicate the MOAs as anticipated; 2) in addition to EAS pathways, chemicals with non-EAS pathways induced changes in fish biomarkers; 3) responses of fish biomarkers did not always follow the anticipated patterns of EAS pathways. These responses may result from the interaction of chemical-induced multiple MOAs and confounding factors like fish diet, infection, culture conditions, general toxicity and stress response. The complex response of fish biomarkers to a chemical of interest requires EDC testing at multiple biological levels. Interpretation of fish biomarker data should be combined with relevant information at different biological levels, which is critical for defining chemical specific MOAs. The utility of fish biomarker data for identification, classification, PBT assessment, risk assessment, and testing of EDCs in the regulatory context was discussed. This paper emphasizes the importance of fish biomarker data in the regulatory context, a weight of evidence approach for the interpretation of fish biomarker data and the need for defining levels of evidence for the identification of EDCs. PMID:27155823

  17. Prisoner's Dilemma on community networks

    NASA Astrophysics Data System (ADS)

    Chen, Xiaojie; Fu, Feng; Wang, Long

    2007-05-01

    We introduce a community network model which exhibits scale-free property and study the evolutionary Prisoner's Dilemma game (PDG) on this network model. It is found that the frequency of cooperators decreases with the increment of the average degree kbar from the simulation results. And reducing inter-community links can promote cooperation when we keep the total links (including inner-community and inter-community links) unchanged. It is also shown that the heterogeneity of networks does not always enhance cooperation and the pattern of links among all the vertices under a given degree-distribution plays a crucial role in the dominance of cooperation in the network model.

  18. Oncometabolites: linking altered metabolism with cancer

    PubMed Central

    Yang, Ming; Soga, Tomoyoshi; Pollard, Patrick J.

    2013-01-01

    The discovery of cancer-associated mutations in genes encoding key metabolic enzymes has provided a direct link between altered metabolism and cancer. Advances in mass spectrometry and nuclear magnetic resonance technologies have facilitated high-resolution metabolite profiling of cells and tumors and identified the accumulation of metabolites associated with specific gene defects. Here we review the potential roles of such “oncometabolites” in tumor evolution and as clinical biomarkers for the detection of cancers characterized by metabolic dysregulation. PMID:23999438

  19. Biomarkers associated with checkpoint inhibitors.

    PubMed

    Manson, G; Norwood, J; Marabelle, A; Kohrt, H; Houot, R

    2016-07-01

    Checkpoint inhibitors (CPI), namely anti-CTLA4 and anti-PD1/PD-L1 antibodies, demonstrated efficacy across multiple types of cancer. However, only subgroups of patients respond to these therapies. Additionally, CPI can induce severe immune-related adverse events (irAE). Biomarkers that predict efficacy and toxicity may help define the patients who may benefit the most from these costly and potentially toxic therapies. In this study, we review the main biomarkers that have been associated with the efficacy (pharmacodynamics and clinical benefit) and the toxicity (irAE) of CPIs in patients. PMID:27122549

  20. Breast cancer and protein biomarkers

    PubMed Central

    Gam, Lay-Harn

    2012-01-01

    Breast cancer is a healthcare concern of women worldwide. Despite procedures being available for diagnosis, prognosis and treatment of breast cancer, researchers are working intensively on the disease in order to improve the life quality of breast cancer patients. At present, there is no single treatment known to bring a definite cure for breast cancer. One of the possible solutions for combating breast cancer is through identification of reliable protein biomarkers that can be effectively used for early detection, prognosis and treatments of the cancer. Therefore, the task of identification of biomarkers for breast cancer has become the focus of many researchers worldwide. PMID:24520539

  1. Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation.

    PubMed

    Kalra, Hina; Simpson, Richard J; Ji, Hong; Aikawa, Elena; Altevogt, Peter; Askenase, Philip; Bond, Vincent C; Borràs, Francesc E; Breakefield, Xandra; Budnik, Vivian; Buzas, Edit; Camussi, Giovanni; Clayton, Aled; Cocucci, Emanuele; Falcon-Perez, Juan M; Gabrielsson, Susanne; Gho, Yong Song; Gupta, Dwijendra; Harsha, H C; Hendrix, An; Hill, Andrew F; Inal, Jameel M; Jenster, Guido; Krämer-Albers, Eva-Maria; Lim, Sai Kiang; Llorente, Alicia; Lötvall, Jan; Marcilla, Antonio; Mincheva-Nilsson, Lucia; Nazarenko, Irina; Nieuwland, Rienk; Nolte-'t Hoen, Esther N M; Pandey, Akhilesh; Patel, Tushar; Piper, Melissa G; Pluchino, Stefano; Prasad, T S Keshava; Rajendran, Lawrence; Raposo, Graca; Record, Michel; Reid, Gavin E; Sánchez-Madrid, Francisco; Schiffelers, Raymond M; Siljander, Pia; Stensballe, Allan; Stoorvogel, Willem; Taylor, Douglas; Thery, Clotilde; Valadi, Hadi; van Balkom, Bas W M; Vázquez, Jesús; Vidal, Michel; Wauben, Marca H M; Yáñez-Mó, María; Zoeller, Margot; Mathivanan, Suresh

    2012-01-01

    Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field. PMID:23271954

  2. Vesiclepedia: A Compendium for Extracellular Vesicles with Continuous Community Annotation

    PubMed Central

    Kalra, Hina; Simpson, Richard J.; Ji, Hong; Aikawa, Elena; Altevogt, Peter; Askenase, Philip; Bond, Vincent C.; Borràs, Francesc E.; Breakefield, Xandra; Budnik, Vivian; Buzas, Edit; Camussi, Giovanni; Clayton, Aled; Cocucci, Emanuele; Falcon-Perez, Juan M.; Gabrielsson, Susanne; Gho, Yong Song; Gupta, Dwijendra; Harsha, H. C.; Hendrix, An; Hill, Andrew F.; Inal, Jameel M.; Jenster, Guido; Krämer-Albers, Eva-Maria; Lim, Sai Kiang; Llorente, Alicia; Lötvall, Jan; Marcilla, Antonio; Mincheva-Nilsson, Lucia; Nazarenko, Irina; Nieuwland, Rienk; Nolte-'t Hoen, Esther N. M.; Pandey, Akhilesh; Patel, Tushar; Piper, Melissa G.; Pluchino, Stefano; Prasad, T. S. Keshava; Rajendran, Lawrence; Raposo, Graca; Record, Michel; Reid, Gavin E.; Sánchez-Madrid, Francisco; Schiffelers, Raymond M.; Siljander, Pia; Stensballe, Allan; Stoorvogel, Willem; Taylor, Douglas; Thery, Clotilde; Valadi, Hadi; van Balkom, Bas W. M.; Vázquez, Jesús; Vidal, Michel; Wauben, Marca H. M.; Yáñez-Mó, María; Zoeller, Margot; Mathivanan, Suresh

    2012-01-01

    Extracellular vesicles (EVs) are membraneous vesicles released by a variety of cells into their microenvironment. Recent studies have elucidated the role of EVs in intercellular communication, pathogenesis, drug, vaccine and gene-vector delivery, and as possible reservoirs of biomarkers. These findings have generated immense interest, along with an exponential increase in molecular data pertaining to EVs. Here, we describe Vesiclepedia, a manually curated compendium of molecular data (lipid, RNA, and protein) identified in different classes of EVs from more than 300 independent studies published over the past several years. Even though databases are indispensable resources for the scientific community, recent studies have shown that more than 50% of the databases are not regularly updated. In addition, more than 20% of the database links are inactive. To prevent such database and link decay, we have initiated a continuous community annotation project with the active involvement of EV researchers. The EV research community can set a gold standard in data sharing with Vesiclepedia, which could evolve as a primary resource for the field. PMID:23271954

  3. Diagnostic gene expression biomarkers of coral thermal stress.

    PubMed

    Kenkel, C D; Sheridan, C; Leal, M C; Bhagooli, R; Castillo, K D; Kurata, N; McGinty, E; Goulet, T L; Matz, M V

    2014-07-01

    Gene expression biomarkers can enable rapid assessment of physiological conditions in situ, providing a valuable tool for reef managers interested in linking organism physiology with large-scale climatic conditions. Here, we assessed the ability of quantitative PCR (qPCR)-based gene expression biomarkers to evaluate (i) the immediate cellular stress response (CSR) of Porites astreoides to incremental thermal stress and (ii) the magnitude of CSR and cellular homeostasis response (CHR) during a natural bleaching event. Expression levels largely scaled with treatment temperature, with the strongest responses occurring in heat-shock proteins. This is the first demonstration of a 'tiered' CSR in a coral, where the magnitude of expression change is proportional to stress intensity. Analysis of a natural bleaching event revealed no signature of an acute CSR in normal or bleached corals, indicating that the bleaching stressor(s) had abated by the day of sampling. Another long-term stress CHR-based indicator assay was significantly elevated in bleached corals, although assay values overall were low, suggesting good prospects for recovery. This study represents the first step in linking variation in gene expression biomarkers to stress tolerance and bleaching thresholds in situ by quantifying the severity of ongoing thermal stress and its accumulated long-term impacts. PMID:24354729

  4. Reconceptualizing the Linked Courses Model

    ERIC Educational Resources Information Center

    Baxter, Mary

    2008-01-01

    To help students meet the demands of society, the University of Houston is using the framework of learning communities and constructivism to create a cross-disciplinary approach to teaching to provide media-rich thematically linked courses to engage a diverse student population. A case study investigated three semesters of thematically linked…

  5. BIOMARKERS: HOPES AND CHALLENGES IN THE PATH FROM DISCOVERY TO CLINICAL PRACTICE

    PubMed Central

    Frangogiannis, Nikolaos G

    2015-01-01

    Biomarkers are objectively measured indicators of normal or pathological processes that may be helpful in diagnosis, staging, monitoring treatment, or prognostic evaluation of a disease. Although development of genomic, metabolomic and proteomic technologies has contributed to an explosion in identification of candidate analytes, validation remains expensive and challenging, and successful introduction of new biomarkers to clinical practice occurs at a very slow pace. The goal of this introductory overview is to provide the context for a series of review manuscripts published in the special issue on biomarkers. The promises and challenges of biomarker discovery are highlighted. Discovery and implementation of transformative new biomarkers in clinical practice requires close collaborations between scientists, clinicians and industry. High throughput technologies can identify a myriad of promising candidates but cannot predict their clinical value. In addition to rapid effective and systematic approaches for clinical validation, there is a need to study and establish links between the purported biomarker and the pathophysiologic basis of the disease of interest. Biomarkers are most informative when they provide insights into activation of specific pathways, thus serving as windows into the molecular basis of the disease. PMID:22424424

  6. Biomarkers to guide clinical therapeutics in rheumatology?

    PubMed Central

    Robinson, William H.; Mao, Rong

    2016-01-01

    Purpose of review The use of biomarkers in rheumatology can help identify disease risk, improve diagnosis and prognosis, target therapy, assess response to treatment, and further our understanding of the underlying pathogenesis of disease. Here, we discuss the recent advances in biomarkers for rheumatic disorders, existing impediments to progress in this field, and the potential of biomarkers to enable precision medicine and thereby transform rheumatology. Recent findings Although significant challenges remain, progress continues to be made in biomarker discovery and development for rheumatic diseases. The use of next-generation technologies, including large-scale sequencing, proteomic technologies, metabolomic technologies, mass cytometry, and other single-cell analysis and multianalyte analysis technologies, has yielded a slew of new candidate biomarkers. Nevertheless, these biomarkers still require rigorous validation and have yet to make their way into clinical practice and therapeutic development. This review focuses on advances in the biomarker field in the last 12 months as well as the challenges that remain. Summary Better biomarkers, ideally mechanistic ones, are needed to guide clinical decision making in rheumatology. Although the use of next-generation techniques for biomarker discovery is making headway, it is imperative that the roadblocks in our search for new biomarkers are overcome to enable identification of biomarkers with greater diagnostic and predictive utility. Identification of biomarkers with robust diagnostic and predictive utility would enable precision medicine in rheumatology. PMID:26720904

  7. New Developments in Biomarkers for Atopic Dermatitis

    PubMed Central

    Thijs, Judith L.; van Seggelen, Wouter; Bruijnzeel-Koomen, Carla; de Bruin-Weller, Marjolein; Hijnen, DirkJan

    2015-01-01

    The application of biomarkers in medicine is evolving. Biomarkers do not only give us a better understanding of pathogenesis, but also increase treatment efficacy and safety, further enabling more precise clinical care. This paper focuses on the current use of biomarkers in atopic dermatitis, new developments and future perspectives. Biomarkers can be used for many different purposes, including the objective determination of disease severity, confirmation of clinical diagnosis, and to predict response to treatment. In atopic dermatitis, many biomarkers have been investigated as a marker for disease severity. Currently serum thymus and activation-regulated chemokine (TARC) is the superior biomarker for assessing disease severity. However, we have recently shown that the use of a panel of serum biomarkers is more suitable for assessing disease severity than an individual biomarker. In this overview, we will discuss alternative sources for biomarkers, such as saliva and capillary blood, which can increase the user friendliness of biomarkers in atopic dermatitis (AD). Both methods offer simple, non-invasive and cost effective alternatives to venous blood. This provides great translational and clinical potential. Biomarkers will play an increasingly important role in AD research and personalized medicine. The use of biomarkers will enhance the efficacy of AD treatment by facilitating the individualization of therapy targeting the patients’ specific biological signature and also by providing tools for predicting and monitoring of therapeutic response. PMID:26239250

  8. Transatlantic link

    NASA Astrophysics Data System (ADS)

    (left) European Geophysical Society (EGS) President Rolf Meissner at AGU Headquarters with (center) Executive Director Fred Spilhaus and (right) Foreign Secretary Juan Roederer. Meissner attended the meeting of AGU's Committee on International Participation (CIP) on February 26, 1988. At that meeting, specific ways of fostering close links between AGU and EGS were discussed.A few weeks later, Roederer and AGU staff, working with EGS Secretary-General Arne Richter at the EGS meeting in Bologna, Italy, March 21-25, planned details of the establishment of an AGU office in Europe. The Copernicus Gesellschaft, a new entity located on the premises of the Max Planck Institute for Aeronomy in Lindau, Federal Republic of Germany, will provide the administrative staff and handle logistics.

  9. Using artificial neural network tools to analyze microbial biomarker data

    SciTech Connect

    Brandt, C.C.; Schryver, J.C.; Almeida, J.S.; Pfiffner, S.M.; Palumbo, A.V.

    2004-03-17

    A major challenge in the successful implementation of bioremediation is understanding the structure of the indigenous microbial community and how this structure is affected by environmental conditions. Culture-independent approaches that use biomolecular markers have become the key to comparative microbial community analysis. However, the analysis of biomarkers from environmental samples typically generates a large number of measurements. The large number and complex nonlinear relationships among these measurements makes conventional linear statistical analysis of the data difficult. New data analysis tools are needed to help understand these data. We adapted artificial neural network (ANN) tools for relating changes in microbial biomarkers to geochemistry. ANNs are nonlinear pattern recognition methods that can learn from experience to improve their performance. We have successfully applied these techniques to the analysis of membrane lipids and nucleic acid biomarker data from both laboratory and field studies. Although ANNs typically outperform linear data analysis techniques, the user must be aware of several considerations and issues to ensure that analysis results are not misleading: (1) Overfitting, especially in small sample size data sets; (2) Model selection; (3) Interpretation of analysis results; and (4) Availability of tools (code). This poster summarizes approaches for addressing each of these issues. The objectives are: (1) Develop new nonlinear data analysis tools for relating microbial biomolecular markers to geochemical conditions; (2) Apply these nonlinear tools to field and laboratory studies relevant to the NABIR Program; and (3) Provide these tools and guidance in their use to other researchers.

  10. BIOMARKERS OF DIESEL EXHAUST PARTICLES

    EPA Science Inventory

    The objective of this project is to examine the detectability of some chemical components of diesel exhaust particles (DEP) in human urine following controlled human diesel exposures (IRB-approved). Ultimately, and upon validation, we propose to apply these components as biomarke...

  11. Toxicogenomic Biomarkers for Liver Toxicity

    PubMed Central

    Kiyosawa, Naoki; Ando, Yosuke; Manabe, Sunao; Yamoto, Takashi

    2009-01-01

    Toxicogenomics (TGx) is a widely used technique in the preclinical stage of drug development to investigate the molecular mechanisms of toxicity. A number of candidate TGx biomarkers have now been identified and are utilized for both assessing and predicting toxicities. Further accumulation of novel TGx biomarkers will lead to more efficient, appropriate and cost effective drug risk assessment, reinforcing the paradigm of the conventional toxicology system with a more profound understanding of the molecular mechanisms of drug-induced toxicity. In this paper, we overview some practical strategies as well as obstacles for identifying and utilizing TGx biomarkers based on microarray analysis. Since clinical hepatotoxicity is one of the major causes of drug development attrition, the liver has been the best documented target organ for TGx studies to date, and we therefore focused on information from liver TGx studies. In this review, we summarize the current resources in the literature in regard to TGx studies of the liver, from which toxicologists could extract potential TGx biomarker gene sets for better hepatotoxicity risk assessment. PMID:22271975

  12. Novel Biomarkers for Renal Diseases? None for the Moment (but One).

    PubMed

    Gentile, Giorgio; Remuzzi, Giuseppe

    2016-08-01

    Recent years have witnessed the unprecedented development and integration of genomics, epigenetics, transcriptomics, proteomics, and metabolomics, as well as a growing interest in novel single biomarkers and process-specific biomarker panels in human renal diseases. In a scenario currently dominated by kidney biopsy and established biomarkers such as serum creatinine, albuminuria, and proteinuria, novel biomarkers could potentially provide vital diagnostic and prognostic information and help to predict response to treatment in several clinical settings, including acute kidney injury, renal transplant, autosomal dominant polycystic kidney disease, and glomerulopathies. However, it is still uncertain whether and to what extent novel biomarkers will succeed in this difficult task. To date, they have generally failed to provide relevant information over and above what is already granted by established, cheap, and easily available biomarkers such as proteinuria, while the complexity and costs of these technology platforms are an important obstacle to their wide adoption. On the other hand, the successful implementation of anti-phospholipase A2 receptor antibodies as a diagnostic and prognostic biomarker of membranous nephropathy, as well as the huge number of ongoing collaborative efforts worldwide, should induce the nephrology community to be rather optimistic about a potential breakthrough in the management of kidney diseases over the next few decades. PMID:26950928

  13. The potential role of biomarkers in predicting gestational diabetes.

    PubMed

    Brink, Huguette S; van der Lely, Aart Jan; van der Linden, Joke

    2016-09-01

    Gestational diabetes (GD) is a frequent complication during pregnancy and is associated with maternal and neonatal complications. It is suggested that a disturbing environment for the foetus, such as impaired glucose metabolism during intrauterine life, may result in enduring epigenetic changes leading to increased disease risk in adult life. Hence, early prediction of GD is vital. Current risk prediction models are based on maternal and clinical parameters, lacking a strong predictive value. Adipokines are mainly produced by adipocytes and suggested to be a link between obesity and its cardiovascular complications. Various adipokines, including adiponectin, leptin and TNF&, have shown to be dysregulated in GD. This review aims to outline biomarkers potentially associated with the pathophysiology of GD and discuss the role of integrating predictive biomarkers in current clinical risk prediction models, in order to enhance the identification of those at risk. PMID:27492245

  14. Biomarkers of (osteo)arthritis

    PubMed Central

    Mobasheri, Ali; Henrotin, Yves

    2015-01-01

    Abstract Arthritic diseases are a major cause of disability and morbidity, and cause an enormous burden for health and social care systems globally. Osteoarthritis (OA) is the most common form of arthritis. The key risk factors for the development of OA are age, obesity, joint trauma or instability. Metabolic and endocrine diseases can also contribute to the pathogenesis of OA. There is accumulating evidence to suggest that OA is a whole-organ disease that is influenced by systemic mediators, inflammaging, innate immunity and the low-grade inflammation induced by metabolic syndrome. Although all joint tissues are implicated in disease progression in OA, articular cartilage has received the most attention in the context of aging, injury and disease. There is increasing emphasis on the early detection of OA as it has the capacity to target and treat the disease more effectively. Indeed it has been suggested that this is the era of “personalized prevention” for OA. However, the development of strategies for the prevention of OA require new and sensitive biomarker tools that can detect the disease in its molecular and pre-radiographic stage, before structural and functional alterations in cartilage integrity have occurred. There is also evidence to support a role for biomarkers in OA drug discovery, specifically the development of disease modifying osteoarthritis drugs. This Special Issue of Biomarkers is dedicated to recent progress in the field of OA biomarkers. The papers in this Special Issue review the current state-of-the-art and discuss the utility of OA biomarkers as diagnostic and prognostic tools. PMID:26954784

  15. Biomarkers of (osteo)arthritis.

    PubMed

    Mobasheri, Ali; Henrotin, Yves

    2015-12-01

    Arthritic diseases are a major cause of disability and morbidity, and cause an enormous burden for health and social care systems globally. Osteoarthritis (OA) is the most common form of arthritis. The key risk factors for the development of OA are age, obesity, joint trauma or instability. Metabolic and endocrine diseases can also contribute to the pathogenesis of OA. There is accumulating evidence to suggest that OA is a whole-organ disease that is influenced by systemic mediators, inflammaging, innate immunity and the low-grade inflammation induced by metabolic syndrome. Although all joint tissues are implicated in disease progression in OA, articular cartilage has received the most attention in the context of aging, injury and disease. There is increasing emphasis on the early detection of OA as it has the capacity to target and treat the disease more effectively. Indeed it has been suggested that this is the era of "personalized prevention" for OA. However, the development of strategies for the prevention of OA require new and sensitive biomarker tools that can detect the disease in its molecular and pre-radiographic stage, before structural and functional alterations in cartilage integrity have occurred. There is also evidence to support a role for biomarkers in OA drug discovery, specifically the development of disease modifying osteoarthritis drugs. This Special Issue of Biomarkers is dedicated to recent progress in the field of OA biomarkers. The papers in this Special Issue review the current state-of-the-art and discuss the utility of OA biomarkers as diagnostic and prognostic tools. PMID:26954784

  16. Systems biology and biomarker discovery

    SciTech Connect

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  17. DNA Methylation as a Biomarker for Preeclampsia

    SciTech Connect

    Anderson, Cindy M.; Ralph, Jody L.; Wright, Michelle L.; Linggi, Bryan E.; Ohm, Joyce E.

    2014-10-01

    Background: Preeclampsia contributes significantly to pregnancy-associated morbidity and mortality as well as future risk of cardiovascular disease in mother and offspring, and preeclampsia in offspring. The lack of reliable methods for early detection limits the opportunities for prevention, diagnosis, and timely treatment. Purpose: The purpose of this study was to explore distinct DNA methylation patterns associated with preeclampsia in both maternal cells and fetal-derived tissue that represent potential biomarkers to predict future preeclampsia and inheritance in children. Method: A convenience sample of nulliparous women (N = 55) in the first trimester of pregnancy was recruited for this prospective study. Genome-wide DNA methylation was quantified in first-trimester maternal peripheral white blood cells and placental chorionic tissue from normotensive women and those with preeclampsia (n = 6/group). Results: Late-onset preeclampsia developed in 12.7% of women. Significant differences in DNA methylation were identified in 207 individual linked cytosine and guanine (CpG) sites in maternal white blood cells collected in the first trimester (132 sites with gain and 75 sites with loss of methylation), which were common to approximately 75% of the differentially methylated CpG sites identified in chorionic tissue of fetal origin. Conclusion: This study is the first to identify maternal epigenetic targets and common targets in fetal-derived tissue that represent putative biomarkers for early detection and heritable risk of preeclampsia. Findings may pave the way for diagnosis of preeclampsia prior to its clinical presentation and acute damaging effects, and the potential for prevention of the detrimental long-term sequelae.

  18. Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas

    PubMed Central

    2014-01-01

    Background The majority of genetic biomarkers for human cancers are defined by statistical screening of high-throughput genomics data. While a large number of genetic biomarkers have been proposed for diagnostic and prognostic applications, only a small number have been applied in the clinic. Similarly, the use of proteomics methods for the discovery of cancer biomarkers is increasing. The emerging field of proteogenomics seeks to enrich the value of genomics and proteomics approaches by studying the intersection of genomics and proteomics data. This task is challenging due to the complex nature of transcriptional and translation regulatory mechanisms and the disparities between genomic and proteomic data from the same samples. In this study, we have examined tumor antigens as potential biomarkers for breast cancer using genomics and proteomics data from previously reported laser capture microdissected ER+ tumor samples. Results We applied proteogenomic analyses to study the genetic aberrations of 32 tumor antigens determined in the proteomic data. We found that tumor antigens that are aberrantly expressed at the genetic level and expressed at the protein level, are likely involved in perturbing pathways directly linked to the hallmarks of cancer. The results found by proteogenomic analysis of the 32 tumor antigens studied here, capture largely the same pathway irregularities as those elucidated from large-scale screening of genomics analyses, where several thousands of genes are often found to be perturbed. Conclusion Tumor antigens are a group of proteins recognized by the cells of the immune system. Specifically, they are recognized in tumor cells where they are present in larger than usual amounts, or are physiochemically altered to a degree at which they no longer resemble native human proteins. This proteogenomic analysis of 32 tumor antigens suggests that tumor antigens have the potential to be highly specific biomarkers for different cancers. PMID:25521819

  19. Biomarkers in connective tissue disease-associated interstitial lung disease.

    PubMed

    Bonella, Francesco; Costabel, Ulrich

    2014-04-01

    This article reviews major biomarkers in serum and bronchoalveolar lavage fluid (BALF) with respect to their diagnostic and prognostic value in connective tissue disease-associated interstitial lung disease (CTD-ILD). In some CTD such as systemic sclerosis (SSc), the incidence of ILD is up to two-third of patients, and currently ILD represents the leading cause of death in SSc. Because of the extremely variable incidence and outcome of ILD in CTD, progress in the discovery and validation of biomarkers for diagnosis, prognosis, patients' subtyping, response to treatment, or as surrogate endpoints in clinical trials is extremely important. In contrast to idiopathic interstitial pneumonias, autoantibodies play a crucial role as biomarkers in CTD-ILD because their presence is strictly linked to the pathogenesis and tissue damage. Patterns of autoantibodies, for instance, anticitrullinated peptide antibodies in rheumatoid arthritis or aminoacyl-tRNA synthetases (ARS) in polymyositis/dermatomyositis, have been found to correlate with the presence and occasionally with the course of ILD in CTD. Besides autoantibodies, an increase in serum or BALF of a biomarker of pulmonary origin may be able to predict or reflect the development of fibrosis, the impairment of lung function, and ideally also the prognosis. Promising biomarkers are lung epithelium-derived proteins such as KL-6 (Krebs von den Lungen-6), SP-D (surfactant protein-D), SP-A (surfactant protein-A), YKL-40 (chitinase-3-like protein 1 [CHI3L1] or cytokines such as CCL18 [chemokine (C-C) motif ligand 18]). In the future, genetic/epigenetic markers, such as human leukocyte antigen (HLA) haplotypes, single nucleotide polymorphisms, and micro-RNA, may help to identify subtypes of patients with different needs of management and treatment strategies. PMID:24668534

  20. Biomarkers for nutrient intake with focus on alternative sampling techniques.

    PubMed

    Holen, T; Norheim, F; Gundersen, T E; Mitry, P; Linseisen, J; Iversen, P O; Drevon, C A

    2016-01-01

    Biomarkers of nutrient intake or nutrient status are important objective measures of foods/nutrients as one of the most important environmental factors people are exposed to. It is very difficult to obtain accurate data on individual food intake, and there is a large variation of nutrient composition of foods consumed in a population. Thus, it is difficult to obtain precise measures of exposure to different nutrients and thereby be able to understand the relationship between diet, health, and disease. This is the background for investing considerable resources in studying biomarkers of nutrients believed to be important in our foods. Modern technology with high sensitivity and specificity concerning many nutrient biomarkers has allowed an interesting development with analyses of very small amounts of blood or tissue material. In combination with non-professional collection of blood by finger-pricking and collection on filters or sticks, this may make collection of samples and analyses of biomarkers much more available for scientists as well as health professionals and even lay people in particular in relation to the marked trend of self-monitoring of body functions linked to mobile phone technology. Assuming standard operating procedures are used for collection, drying, transport, extraction, and analysis of samples, it turns out that many analytes of nutritional interest can be measured like metabolites, drugs, lipids, vitamins, minerals, and many types of peptides and proteins. The advantage of this alternative sampling technology is that non-professionals can collect, dry, and mail the samples; the samples can often be stored under room temperature in a dry atmosphere, requiring small amounts of blood. Another promising area is the potential relation between the microbiome and biomarkers that may be measured in feces as well as in blood. PMID:27551313

  1. Community Connections: Intergenerational Links in Art Education

    ERIC Educational Resources Information Center

    La Porte, Angela M., Ed.

    2004-01-01

    Intergenerational programs have become widespread since the mid-20th century, emphasizing "activities that increase cooperation and exchange between any two generations. Typically, they involve interaction between young and old in which there is a sharing of skills, knowledge, and experience" (Newman, 1986, p. 6). They developed in response to…

  2. Biomarkers in translational research of Alzheimer's disease.

    PubMed

    Tarawneh, Rawan; Holtzman, David M

    2010-01-01

    The identification and characterization of amyloid-beta (Abeta) and tau as the main pathological substrates of Alzheimer's disease (AD) have driven many efforts in search for suitable biomarkers for AD. In the last decade, research in this area has focused on developing a better understanding of the principles that govern protein deposition, mechanisms that link aggregation to toxicity and neuronal death, and a better understanding of protein dynamics in brain tissue, interstitial fluid and CSF. While Abeta and tau represent the two key pathological mediators of disease, other aspects of this multifaceted disease (e.g. oxidative stress, calcium-mediated toxicity, and neuroinflammation) are being unraveled, with the hope to develop a more comprehensive approach in exploring disease mechanisms. This has not only expanded possible areas for disease-modifying therapies, but has also allowed the introduction of novel, and potentially useful, fluid and radiological markers for the presence and progression of AD pathology. There is no doubt that the identification of several fluid and imaging biomarkers that can reliably detect the early stages of AD will have great implications in the design of clinical trials, in the selection of homogenous research populations, and in the assessment of disease outcomes. Markers with good diagnostic specificity will aid researchers in differentiating individuals with preclinical and probable AD from individuals who do not have AD pathology or have other dementing disorders. Markers that change with disease progression may offer utility in assessing the rates of disease progression and the efficacy of potential therapeutic agents on AD pathology. For both of these purposes, CSF Abeta42, amyloid imaging, and CSF tau appear to be very good markers of the presence of AD pathology as well as predictive of who will progress from MCI to AD. Volumetric MRI is also good at separating individuals with MCI and AD from controls and is predictive of

  3. Biofilms as "Connectors" for Oral and Systems Medicine: A New Opportunity for Biomarkers, Molecular Targets, and Bacterial Eradication.

    PubMed

    Sintim, Herman O; Gürsoy, Ulvi Kahraman

    2016-01-01

    Oral health and systems medicine are intimately related but have remained, sadly, as isolated knowledge communities for decades. Are there veritable connector knowledge domains that can usefully link them together on the critical path to biomarker research and "one health"? In this context, it is noteworthy that bacteria form surface-attached communities on most biological surfaces, including the oral cavity. Biofilm-forming bacteria contribute to periodontal diseases and recent evidences point to roles of these bacteria in systemic diseases as well, with cardiovascular diseases, obesity, and cancer as notable examples. Interestingly, the combined mass of microorganisms such as bacteria are so large that when we combine all plants and animals on earth, the total biomass of bacteria is still bigger. They literally do colonize everywhere, not only soil and water but our skin, digestive tract, and even oral cavity are colonized by bacteria. Hence efforts to delineate biofilm formation mechanisms of oral bacteria and microorganisms and the development of small molecules to inhibit biofilm formation in the oral cavity is very timely for both diagnostics and therapeutics. Research on biofilms can benefit both oral and systems medicine. Here, we examine, review, and synthesize new knowledge on the current understanding of oral biofilm formation, the small molecule targets that can inhibit biofilm formation in the mouth. We suggest new directions for both oral and systems medicine, using various omics technologies such as SILAC and RNAseq, that could yield deeper insights, biomarkers, and molecular targets to design small molecules that selectively aim at eradication of pathogenic oral bacteria. Ultimately, devising new ways to control and eradicate bacteria in biofilms will open up novel diagnostic and therapeutic avenues for oral and systemic diseases alike. PMID:26583256

  4. Biofilms as “Connectors” for Oral and Systems Medicine: A New Opportunity for Biomarkers, Molecular Targets, and Bacterial Eradication

    PubMed Central

    Gürsoy, Ulvi Kahraman

    2016-01-01

    Abstract Oral health and systems medicine are intimately related but have remained, sadly, as isolated knowledge communities for decades. Are there veritable connector knowledge domains that can usefully link them together on the critical path to biomarker research and “one health”? In this context, it is noteworthy that bacteria form surface-attached communities on most biological surfaces, including the oral cavity. Biofilm-forming bacteria contribute to periodontal diseases and recent evidences point to roles of these bacteria in systemic diseases as well, with cardiovascular diseases, obesity, and cancer as notable examples. Interestingly, the combined mass of microorganisms such as bacteria are so large that when we combine all plants and animals on earth, the total biomass of bacteria is still bigger. They literally do colonize everywhere, not only soil and water but our skin, digestive tract, and even oral cavity are colonized by bacteria. Hence efforts to delineate biofilm formation mechanisms of oral bacteria and microorganisms and the development of small molecules to inhibit biofilm formation in the oral cavity is very timely for both diagnostics and therapeutics. Research on biofilms can benefit both oral and systems medicine. Here, we examine, review, and synthesize new knowledge on the current understanding of oral biofilm formation, the small molecule targets that can inhibit biofilm formation in the mouth. We suggest new directions for both oral and systems medicine, using various omics technologies such as SILAC and RNAseq, that could yield deeper insights, biomarkers, and molecular targets to design small molecules that selectively aim at eradication of pathogenic oral bacteria. Ultimately, devising new ways to control and eradicate bacteria in biofilms will open up novel diagnostic and therapeutic avenues for oral and systemic diseases alike. PMID:26583256

  5. Salivary Biomarkers in the Control of Mosquito-Borne Diseases

    PubMed Central

    Doucoure, Souleymane; Drame, Papa Makhtar

    2015-01-01

    Vector control remains the most effective measure to prevent the transmission of mosquito-borne diseases. However, the classical entomo-parasitological methods used to evaluate the human exposure to mosquito bites and the effectiveness of control strategies are indirect, labor intensive, and lack sensitivity in low exposure/transmission areas. Therefore, they are limited in their accuracy and widespread use. Studying the human antibody response against the mosquito salivary proteins has provided new biomarkers for a direct and accurate evaluation of the human exposure to mosquito bites, at community and individual levels. In this review, we discuss the development, applications and limits of these biomarkers applied to Aedes- and Anopheles-borne diseases. PMID:26593952

  6. Biomarker and Carbon Isotope Signals from Leaf to Terrestrial Archive

    NASA Astrophysics Data System (ADS)

    Freeman, K. H.

    2012-12-01

    Biomarker and isotopic signatures of terrestrial organic matter are increasingly used to discern organic matter provenance in transport systems as well as to reconstruct environmental conditions of ancient landscapes. Such tools help scholars evaluate river transport and the influence of climate on terrestrial biomass and soil carbon, the largest reduced carbon inventories within the global surface environment. These signals reflect isotopic fractionation during photosynthesis and the abundance and composition of plant lipids, which are ultimately influenced by plant community, ecosystem structure and climate. Case studies and literature data for plants, biomarkers, litter carbon and soil organic matter refine the framework for evaluating and interpreting ancient terrestrial environments. Such studies reveal isotopic and biomarker patterns primarily track woody cover and moisture gradients in ancient landscapes. This emerging approach is currently limited by a lack of supporting and critical information about carbon isotopic differences between lipids and leaves, which appear to vary with environment as well as plant type. Environmental reconstructions and carbon-cycle studies are also limited by incomplete understanding of carbon isotopic relationships between modern litter, mineral soil, leaf waxes, and ancient archives of these properties. The net imprint of diagenesis on bulk carbon archives can potentially be constrained with companion biomarker studies, provided biomass production, litter delivery and lipid isotopic characteristics are constrained. Soil organic matter isotopic diagenesis is not fully understood, especially on geologic timescales, but appears to vary with both climate and ecosystem properties. This presentation will highlight recent findings and current knowledge gaps in understanding biomarker and ancient soil organic carbon as landscape tracers of past vegetation and climate.

  7. Biomarkers of PTSD: military applications and considerations

    PubMed Central

    Lehrner, Amy; Yehuda, Rachel

    2014-01-01

    Background Although there are no established biomarkers for posttraumatic stress disorder (PTSD) as yet, biological investigations of PTSD have made progress identifying the pathophysiology of PTSD. Given the biological and clinical complexity of PTSD, it is increasingly unlikely that a single biomarker of disease will be identified. Rather, investigations will more likely identify different biomarkers that indicate the presence of clinically significant PTSD symptoms, associate with risk for PTSD following trauma exposure, and predict or identify recovery. While there has been much interest in PTSD biomarkers, there has been less discussion of their potential clinical applications, and of the social, legal, and ethical implications of such biomarkers. Objective This article will discuss possible applications of PTSD biomarkers, including the social, legal, and ethical implications of such biomarkers, with an emphasis on military applications. Method Literature on applications of PTSD biomarkers and on potential ethical and legal implications will be reviewed. Results Biologically informed research findings hold promise for prevention, assessment, treatment planning, and the development of prophylactic and treatment interventions. As with any biological indicator of disorder, there are potentially positive and negative clinical, social, legal, and ethical consequences of using such biomarkers. Conclusions Potential clinical applications of PTSD biomarkers hold promise for clinicians, patients, and employers. The search for biomarkers of PTSD should occur in tandem with an interdisciplinary discussion regarding the potential implications of applying biological findings in clinical and employment settings. PMID:25206945

  8. Parasite communities of the deep-sea fish Alepocephalus rostratus Risso, 1820 in the Balearic Sea (NW Mediterranean) along the slope and relationships with enzymatic biomarkers and health indicators

    NASA Astrophysics Data System (ADS)

    Pérez-i-García, D.; Constenla, M.; Padrós, F.; Soler-Membrives, A.; Solé, M.; Carrassón, M.

    2015-05-01

    This study examines the parasite communities of Alepocephalus rostratus and its influence on some fish biochemical markers and histological alterations. A. rostratus constitutes the second most important fish species, in terms of biomass, inhabiting the deep slope of the Catalan Sea (Balearic Sea, NW Mediterranean). The study revealed eight different parasite species in this host: one coccidian, one digenean, one monogenean, one cestode and four nematodes. The parasite fauna of A. rostratus was partially dominated by larval forms (four of the seven metazoan taxa found), which combined with low species richness corresponds to a parasite fauna pattern more typical of bathypelagic fish species rather than demersal ones. The larval tetraphyllideans and cucullanid nematodes were the predominant species. In relation to depth, differences in abundance of the nematodes Cucullaninae gen. sp. and Hysterothylacium aduncum were found, probably due to the dietary shift in the fish host at greater depth. Thus, Cucullaninae gen. sp. and H. aduncum could be regarded as indicators for discriminating populations of A. rostratus in relation to depth in NW Mediterranean waters. Of the biochemical markers examined, acetylcholinesterase (AChE) and lactate dehydrogenase (LDH) activities and lipid peroxidation (LP) levels, only LP showed significant differences between depths. A positive relationship was found between AChE activity and Tetraphyllidea fam. gen. sp., Anisakis physeteris and H. aduncum abundance and a negative one with the abundance of Cucullaninae gen. sp. LDH showed a positive relationship with the abundance of the parasites Paracyclocotyla cherbonnieri and Tetraphyllidea fam. gen. sp. At cyto-histological level, coccidians were detected in the pyloric caeca with a prevalence of 90% in Barcelona, but in the rest of organs almost no alterations were detected. The restricted macroplanktonic diet of A. rostratus, that maintains it distant from the sea-floor for longer periods

  9. Equity in development and access to health services in the Wild Coast of South Africa: the community view through four linked cross-sectional studies between 1997 and 2007

    PubMed Central

    2011-01-01

    Background After election in 1994, the South African government implemented national and regional programmes, such as the Wild Coast Spatial Development Initiative (SDI), to provoke economic growth and to decrease inequities. CIET measured development in the Wild Coast region across four linked cross-sectional surveys (1997-2007). The 2007 survey was an opportunity to look at inequities since the original 1997 baseline, and how such inequities affect access to health care. Methods The 2000, 2004 and 2007 follow-up surveys revisited the communities of the 1997 baseline. Household-level multivariate analysis looked at development indicators and access to health in the context of inequities such as household crowding, access to protected sources of water, house roof construction, main food item purchased, and perception of community empowerment. Individual multivariate models accounted for age, sex, education and income earning opportunities. Results Overall access to protected sources of water increased since the baseline (from 20% in 1997 to 50% in 2007), yet households made of mud and grass, and households who bought basics as their main food item were still less likely to have protected sources of water. The most vulnerable, such as those with less education and less water and food security, were also less likely to have worked for wages leaving them with little chance of improving their standard of living (less education OR 0.59, 95%CI 0.37-0.94; less water security OR 0.67, 95%CI 0.48-0.93; less food security OR 0.43, 95%CI 0.29-0.64). People with less income were more likely to visit government services (among men OR 0.28, 95%CI 0.13-0.59; among women OR 0.33, 95%CI 0.20-0.54), reporting decision factors of cost and distance; users of private clinics sought out better service and medication. Lower food security and poorer house construction was also associated with women visiting government rather than private health services. Women with some formal education

  10. Translational Biomarkers of Neurotoxicity: A Health and Environmental Sciences Institute Perspective on The Way Forward

    EPA Science Inventory

    Neurotoxicity has been linked to a number of common drugs and chemicals, yet efficient and accurate methods to detect it are lacking. There is a need for more sensitive and specific biomarkers of neurotoxicity that can help diagnose and predict neurotoxicity that are relevant acr...

  11. Biosecurity--The Bio-Link Project.

    ERIC Educational Resources Information Center

    Johnson, Elaine A.

    2002-01-01

    Describes Bio-Link, the Advanced Technological Education (ATE) Center for Biotechnology established with funding from the National Science Foundation (NSF). Reports that Bio-Link, headquartered at City College of San Francisco, has created a national network and resource base for community colleges, industry, and others interested in biotechnology…

  12. Vaginal biogenic amines: biomarkers of bacterial vaginosis or precursors to vaginal dysbiosis?

    PubMed Central

    Nelson, Tiffanie M.; Borgogna, Joanna-Lynn C.; Brotman, Rebecca M.; Ravel, Jacques; Walk, Seth T.; Yeoman, Carl J.

    2015-01-01

    Bacterial vaginosis (BV) is the most common vaginal disorder among reproductive age women. One clinical indicator of BV is a “fishy” odor. This odor has been associated with increases in several biogenic amines (BAs) that may serve as important biomarkers. Within the vagina, BA production has been linked to various vaginal taxa, yet their genetic capability to synthesize BAs is unknown. Using a bioinformatics approach, we show that relatively few vaginal taxa are predicted to be capable of producing BAs. Many of these taxa (Dialister, Prevotella, Parvimonas, Megasphaera, Peptostreptococcus, and Veillonella spp.) are more abundant in the vaginal microbial community state type (CST) IV, which is depleted in lactobacilli. Several of the major Lactobacillus species (L. crispatus, L. jensenii, and L. gasseri) were identified as possessing gene sequences for proteins predicted to be capable of putrescine production. Finally, we show in a small cross sectional study of 37 women that the BAs putrescine, cadaverine and tyramine are significantly higher in CST IV over CSTs I and III. These data support the hypothesis that BA production is conducted by few vaginal taxa and may be important to the outgrowth of BV-associated (vaginal dysbiosis) vaginal bacteria. PMID:26483694

  13. Clinical biomarkers of angiogenesis inhibition

    PubMed Central

    Brown, Aaron P.; Citrin, Deborah E.; Camphausen, Kevin A.

    2009-01-01

    Introduction An expanding understanding of the importance of angiogenesis in oncology and the development of numerous angiogenesis inhibitors are driving the search for biomarkers of angiogenesis. We review currently available candidate biomarkers and surrogate markers of anti-angiogenic agent effect. Discussion A number of invasive, minimally invasive, and non-invasive tools are described with their potential benefits and limitations. Diverse markers can evaluate tumor tissue or biological fluids, or specialized imaging modalities. Conclusions The inclusion of these markers into clinical trials may provide insight into appropriate dosing for desired biological effects, appropriate timing of additional therapy, prediction of individual response to an agent, insight into the interaction of chemotherapy and radiation following exposure to these agents, and perhaps most importantly, a better understanding of the complex nature of angiogenesis in human tumors. While many markers have potential for clinical use, it is not yet clear which marker or combination of markers will prove most useful. PMID:18414993

  14. [Biomarkers for chronic inflammatory diseases].

    PubMed

    Holzinger, D; Föll, D

    2015-12-01

    Inflammatory disorders of childhood, such as juvenile idiopathic arthritis (JIA) and inflammatory bowel disease (IBD) are a challenge for laboratory diagnostics. Firstly, the classical inflammatory markers, such as C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) often inadequately reflect disease activity but on the other hand there are few specific biomarkers that can be helpful in managing these diseases. Acute phase proteins reflect the systemic inflammatory response insufficiently as their increase is only the indirect result of local inflammatory processes. Modern inflammation diagnostics aim to reflect these local processes and to allow precise monitoring of disease activity. Experimental biomarkers, such as S100 proteins can detect subclinical inflammatory activity. In addition, established laboratory parameters exist for JIA [antinuclear antibodies (ANA), rheumatoid factor (RF), antibodies against cyclic citrullinated peptide (anti-CCP)] and for chronic IBD (fecal calprotectin) that are useful in the treatment of these diseases. PMID:26608264

  15. Biomarkers in Colorectal Cancer Screening.

    PubMed

    Nguyen, Minhhuyen T; Weinberg, David S

    2016-08-01

    Colorectal cancer (CRC) is the third most common cause of cancer death in men and women in the United States. The main goals of screening are to prevent carcinogenesis (via adenoma detection and removal) and detect cancer at an early, curable stage. CRC mortality is steadily dropping in the United States, partly because of greater screening utilization. However, nearly 1 in 3 average-risk people are not up to date with standard CRC screening recommendations. This review surveys a wide range of CRC biomarkers in various stages of development, which may offer attractive risk stratification tools; a few have reached the commercial stage. If widely accepted, these tools may contribute to shift CRC screening practices away from 1-step colonoscopy to a 2-step risk stratification process of predictive biomarker measurements followed by colonoscopy for lower-risk patients with a positive result. Such strategies could potentially increase the rate of CRC screening. PMID:27496118

  16. Biomarkers of immunotoxicity in man.

    PubMed

    Descotes, J; Nicolas, B;