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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. Biomarkers in Pediatric Community-Acquired Pneumonia

    PubMed Central

    Principi, Nicola; Esposito, Susanna

    2017-01-01

    Community-acquired pneumonia (CAP) is an infectious disease caused by bacteria, viruses, or a combination of these infectious agents. The severity of the clinical manifestations of CAP varies significantly. Consequently, both the differentiation of viral from bacterial CAP cases and the accurate assessment and prediction of disease severity are critical for effectively managing individuals with CAP. To solve questionable cases, several biomarkers indicating the etiology and severity of CAP have been studied. Unfortunately, only a few studies have examined the roles of these biomarkers in pediatric practice. The main aim of this paper is to detail current knowledge regarding the use of biomarkers to diagnose and treat CAP in children, analyzing the most recently published relevant studies. Despite several attempts, the etiologic diagnosis of pediatric CAP and the estimation of the potential outcome remain unsolved problems in most cases. Among traditional biomarkers, procalcitonin (PCT) appears to be the most effective for both selecting bacterial cases and evaluating the severity. However, a precise cut-off separating bacterial from viral and mild from severe cases has not been defined. The three-host protein assay based on C-reactive protein (CRP), tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), plasma interferon-γ protein-10 (IP-10), and micro-array-based whole genome expression arrays might offer more advantages in comparison with former biomarkers. However, further studies are needed before the routine use of those presently in development can be recommended. PMID:28218726

  6. Influence of Inter-Community Link Strength on Community Networks

    NASA Astrophysics Data System (ADS)

    Peng, Qian-Jin; Zhao, Ming; Zhang, Hai-Feng

    2013-09-01

    This paper mainly discusses how the strength of inter-community links affects the synchronization state of the whole network and the individual community. It is found, when the inter-community link number is neither too small nor too large and the overall coupling strength takes right values, there will be an optimal inter-community link strength value, in which the community networks are in a balance region where the individual community is maximally independent, while the information transmission remains effective among different communities. Combining the result of this paper and that of the number of inter-community links, it is easy to help us find the most effective community networks.

  7. 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

  8. Link prediction based on local community properties

    NASA Astrophysics Data System (ADS)

    Yang, Xu-Hua; Zhang, Hai-Feng; Ling, Fei; Cheng, Zhi; Weng, Guo-Qing; Huang, Yu-Jiao

    2016-09-01

    The link prediction algorithm is one of the key technologies to reveal the inherent rule of network evolution. This paper proposes a novel link prediction algorithm based on the properties of the local community, which is composed of the common neighbor nodes of any two nodes in the network and the links between these nodes. By referring to the node degree and the condition of assortativity or disassortativity in a network, we comprehensively consider the effect of the shortest path and edge clustering coefficient within the local community on node similarity. We numerically show the proposed method provide good link prediction results.

  9. UniPep - a database for human N-linked glycosites: a resource for biomarker discovery

    PubMed Central

    Zhang, Hui; Loriaux, Paul; Eng, Jimmy; Campbell, David; Keller, Andrew; Moss, Pat; Bonneau, Richard; Zhang, Ning; Zhou, Yong; Wollscheid, Bernd; Cooke, Kelly; Yi, Eugene C; Lee, Hookeun; Peskind, Elaine R; Zhang, Jing; Smith, Richard D; Aebersold, Ruedi

    2006-01-01

    There has been considerable recent interest in proteomic analyses of plasma for the purpose of discovering biomarkers. Profiling N-linked glycopeptides is a particularly promising method because the population of N-linked glycosites represents the proteomes of plasma, the cell surface, and secreted proteins at very low redundancy and provides a compelling link between the tissue and plasma proteomes. Here, we describe UniPep - a database of human N-linked glycosites - as a resource for biomarker discovery. PMID:16901351

  10. Evolutionary link community structure discovery in dynamic weighted networks

    NASA Astrophysics Data System (ADS)

    Liu, Qiang; Liu, Caihong; Wang, Jiajia; Wang, Xiang; Zhou, Bin; Zou, Peng

    2017-01-01

    Traditional community detection methods are often restricted in static network analysis. In fact, most of networks in real world obviously show dynamic characteristics with time passing. In this paper, we design a link community structure discovery algorithm in dynamic weighted networks, which can not only reveal the evolutionary link community structure, but also detect overlapping communities by mapping link communities to node communities. Meanwhile, our algorithm can also get the hierarchical structure of link communities by tuning a parameter. The proposed algorithm is based on weighted edge fitness and weighted partition density so as to determine whether to add a link to a community and whether to merge two communities to form a new link community. Experiments on both synthetic and real world networks demonstrate the proposed algorithm can detect evolutionary link community structure in dynamic weighted networks effectively.

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

    PubMed

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

    2015-03-02

    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.

  13. 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.

  14. 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

  15. 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

  16. Serum glycoprotein-derived N- and O-linked glycans as cancer biomarkers

    PubMed Central

    Lan, Ying; Hao, Cui; Zeng, Xuan; He, Yanli; Zeng, Pengjiao; Guo, Zhihua; Zhang, Lijuan

    2016-01-01

    Early detection of cancer is the key to improving survival. Since most clinically used serum cancer biomarkers are either glycoproteins or glycan structures that can be recognized by specific monoclonal antibodies, developing glycan structure-based biomarkers from human serum/plasma glycoproteins through mass spectrometry (MS) analysis are active research field during the past decades. Numerous studies have shown that changes in serum/plasma glycan structures occur during cancer initiation, progression, and treatment. This review describes N- and O-linked glycan structures identified from serum/plasma glycoprotein (s) by MS analysis with focus on alterations associated with different types of human cancers. The global changes in serum N- and O-linked glycan structures, especially the glycans that are not made by cancer cells such as B lymphocyte-derived IgG and liver-synthesized haptoglobin and α1 acid glycoprotein, suggest that glycans might be the long sought diagnostic biomarkers associated with system malfunction in the blood circulation of cancer patients. Therefore, N- and O-linked glycan structures have great potential to serve as cancer diagnosis, prognosis, and treatment monitoring biomarkers to facilitate personalized medicine. PMID:27904760

  17. 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.

  18. 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…

  19. 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…

  20. 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…

  1. 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.

  2. Measurement of inflammatory biomarkers in synovial tissue extracts by enzyme-linked immunosorbent assay.

    PubMed

    Rosengren, Sanna; Firestein, Gary S; Boyle, David L

    2003-11-01

    We developed methods for measuring inflammatory biomarkers (cytokines, chemokines, and metalloproteinases) in synovial biopsy specimens from patients with rheumatoid arthritis (RA) and osteoarthritis (OA). Soluble extracts of synovial fragments were prepared with mild detergent and analyzed by enzyme-linked immunosorbent assay (ELISA) for interleukin 1beta (IL-1beta), IL-6, IL-8, tumor necrosis factor alpha (TNF-alpha), and matrix metalloproteinase 3. The optimal detergent was 0.1% Igepal CA-630, which interfered minimally with ELISA detection but extracted 80% of IL-6 from synovial tissue. Upon spiking, 81 to 107% of added biomarkers could be recovered. To determine within-tissue variability, multiple biopsy specimens from each RA synovial extract were analyzed individually. A resulting coefficient of variation of 35 to 62% indicated that six biopsy specimens per synovial extract would result in a sampling error of < or = 25%. Preliminary power analysis suggested that 8 to 15 patients per group would suffice to observe a threefold difference before and after treatment in a serial biopsy clinical study. The previously described significant differences in IL-1beta, IL-6, IL-8, and TNF-alpha levels between RA and OA could be detected, thereby validating the use of synovial extracts for biomarker analysis in arthritis. These methods allow monitoring of biomarker protein levels in synovial tissue and could potentially be applied to early-phase clinical trials to provide a preliminary estimate of drug efficacy.

  3. Active semi-supervised community detection based on must-link and cannot-link constraints.

    PubMed

    Cheng, Jianjun; Leng, Mingwei; Li, Longjie; Zhou, Hanhai; Chen, Xiaoyun

    2014-01-01

    Community structure detection is of great importance because it can help in discovering the relationship between the function and the topology structure of a network. Many community detection algorithms have been proposed, but how to incorporate the prior knowledge in the detection process remains a challenging problem. In this paper, we propose a semi-supervised community detection algorithm, which makes full utilization of the must-link and cannot-link constraints to guide the process of community detection and thereby extracts high-quality community structures from networks. To acquire the high-quality must-link and cannot-link constraints, we also propose a semi-supervised component generation algorithm based on active learning, which actively selects nodes with maximum utility for the proposed semi-supervised community detection algorithm step by step, and then generates the must-link and cannot-link constraints by accessing a noiseless oracle. Extensive experiments were carried out, and the experimental results show that the introduction of active learning into the problem of community detection makes a success. Our proposed method can extract high-quality community structures from networks, and significantly outperforms other comparison methods.

  4. 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…

  5. 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,…

  6. 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…

  7. Collaborative Links with the Community: Lessons from Exemplary Secondary Schools.

    ERIC Educational Resources Information Center

    Wilson, Bruce L.; Rossman, Gretchen B.

    1986-01-01

    A review of the Department of Education's Secondary Schools Recognition Program shows that exemplary secondary schools often have formed collaborative links with their communities. The five ways schools do this are: recruiting volunteers, aggressive public relations, attracting financial resources, school members volunteering in the community, and…

  8. 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…

  9. Home-School Links: Networking the Learning Community.

    ERIC Educational Resources Information Center

    1996

    The topic of networking the learning community with home-school links is addressed in four papers: "Internet Access via School: Expectations of Students and Parents" (Roy Crotty); "The School Library as Community Information Gateway" (Megan Perry); "Rural Access to the Internet" (Ken Eustace); and "NetDay '96:…

  10. Biomarker reconstruction of phytoplankton productivity and community structure changes in the Japan Sea over the last 166 ka

    NASA Astrophysics Data System (ADS)

    Xing, L.; Zhang, R.; Liu, Y.; Zhang, H.; Shi, X.; Zhao, M.

    2009-12-01

    Glacial/interglacial changes in surface hydrography and sea level caused the drastic variations of ocean circulation and ecosystem structure in the Japan Sea. Previous reconstructions of ecosystem structure using microfossils revealed increases in productivity and a shift from calcareous to siliceous plankton during the last two glacial to interglacial transitions. Muti-biomarkers are analyzed to further study the changes in productivity and phytoplankton community structure in the Japan Sea over the last 166 ka. The following biomarkers are used as productivity proxies: brassicasterol for diatoms, C37:2+C37:3 alkenones for coccolithophorids, dinosterol for dinoflagellates, cholesterol for zooplankton. The reconstructed SST oscillated between 3.8 and 21.5°C with maximum values during MIS 5.3 and minimum values during MIS 6. During the last 166 ka, the content of brassicasterol varied between 15.7 ng/g and 5552 ng/g, dinosterol between 8.9 and 1297 ng/g, alkenones between 24.5 and 20179 ng/g, their total contents (as an indicator of marine organic matter) varied between 45.9 and 23354.5 ng/g. The content of n-alkanols (C28OH+C30OH+C32OH) ( as a proxy for terrestrial organic matter input) ranged from 569 to 17504 ng/g. The marine organic matter to terrestrial organic matter ratio varied between 0.03 and 2.64. Biomarker records indicate high content values occurred during both glacial periods and interglacial periods, but the ratios of marine to terrestrial organic matter were generally higher during interglacial periods. High biomarker contents during interglacials are interpreted to be caused by high productivity, whereas high contents during glacials were related to better preservation of organic matters due to euxinic conditions. In contrast to previous results, our biomarker records reveal a shift from a diatom-dominated phytoplankton community during the glacials to a coccolithophorid-dominated community during the interglacials. The glacial decrease in

  11. 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.

  12. 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.

  13. Linking pediatric primary care obesity management to community programs.

    PubMed

    Ariza, Adolfo J; Hartman, Jennifer; Grodecki, Jennifer; Clavier, Alejandro; Ghaey, Kamala; Elsner, Mary; Moore, Chantal; Reina, Olga Ochoa; Binns, Helen J

    2013-01-01

    Guidelines for obesity management in primary care call for linking to community services. The Promoting Health Project (PHP) was a multi-component, practice-based intervention aimed at improving care of obese children, including referrals to community services. Promoting Health Project staff identified and interviewed representatives of 40 nutrition or physical activity services/programs. Quality improvement (QI) teams at three practices worked to improve overweight/obesity identification and care and implement practice-to-community connections that used the information gathered from the programs/ services. A practice community coordinator (PCC) facilitated interactions between practices, community programs and families. Researchers tracked patients referred, PCC to family interactions, and time spent. They surveyed parents of referred patients and interviewed key clinicians. Forty-six patients participated in programs. Substantial efforts were necessary to create smooth referral systems. Family motivation was perceived as a limiting factor in program attendance. Clinicians were satisfied with systems established. Effectively linking practitioners to community programs requires the use of additional resources.

  14. Linking community size structure and ecosystem functioning using metabolic theory.

    PubMed

    Yvon-Durocher, Gabriel; Allen, Andrew P

    2012-11-05

    Understanding how biogeochemical cycles relate to the structure of ecological communities is a central research question in ecology. Here we approach this problem by focusing on body size, which is an easily measured species trait that has a pervasive influence on multiple aspects of community structure and ecosystem functioning. We test the predictions of a model derived from metabolic theory using data on ecosystem metabolism and community size structure. These data were collected as part of an aquatic mesocosm experiment that was designed to simulate future environmental warming. Our analyses demonstrate significant linkages between community size structure and ecosystem functioning, and the effects of warming on these links. Specifically, we show that carbon fluxes were significantly influenced by seasonal variation in temperature, and yielded activation energies remarkably similar to those predicted based on the temperature dependencies of individual-level photosynthesis and respiration. We also show that community size structure significantly influenced fluxes of ecosystem respiration and gross primary production, particularly at the annual time-scale. Assessing size structure and the factors that control it, both empirically and theoretically, therefore promises to aid in understanding links between individual organisms and biogeochemical cycles, and in predicting the responses of key ecosystem functions to future environmental change.

  15. Inflammatory biomarkers as predictors of hospitalization and death in community-dwelling older adults.

    PubMed

    Salanitro, Amanda H; Ritchie, Christine S; Hovater, Martha; Roth, David L; Sawyer, Patricia; Locher, Julie L; Bodner, Eric; Brown, Cynthia J; Allman, Richard M

    2012-01-01

    Individuals with multimorbidity may be at increased risk of hospitalization and death. Comorbidity indexes do not capture severity of illness or healthcare utilization; however, inflammation biomarkers that are not disease-specific may predict hospitalization and death in older adults. We sought to predict hospitalization and mortality of older adults using inflammation biomarkers. From a prospective, observational study, 370 community-dwelling adults 65 years or older from central Alabama participated in an in-home assessment and provided fasting blood samples for inflammation biomarker testing in 2004. We calculated an inflammation summary score (range 0-4), one point each for low albumin, high C-reactive protein, low cholesterol, and high interleukin-6. Utilizing Cox proportional hazards models, inflammation summary scores were used to predicted time to hospitalization and death during a 4-year follow up period. The mean age was 73.7 (±5.9 yrs), and 53 (14%) participants had summary scores of 3 or 4. The rates of dying were significantly increased for participants with inflammation summary scores of 2, 3, or 4 (hazard ratio (HR) 2.22, 2.78, and 7.55, respectively; p<0.05). An inflammation summary score of 4 significantly predicted hospitalization (HR 5.92, p<0.05). Community-dwelling older adults with biomarkers positive for inflammation had increased rates of being hospitalized or dying during the follow up period. Assessment of the individual contribution of particular inflammation biomarkers in the prediction of health outcomes in older populations and the development of validated summary scores to predict morbidity and mortality are needed.

  16. 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.

  17. 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

  18. An electronic medical record-linked biorepository to identify novel biomarkers for atherosclerotic cardiovascular disease

    PubMed Central

    Ye, Zi; Kalloo, Fara S; Dalenberg, Angela K.; Kullo, Iftikhar J

    2013-01-01

    Background: Atherosclerotic vascular disease (AVD), a leading cause of morbidity and mortality, is increasing in prevalence in the developing world. We describe an approach to establish a biorepository linked to medical records with the eventual goal of facilitating discovery of biomarkers for AVD. Methods: The Vascular Disease Biorepository at Mayo Clinic was established to archive DNA, plasma, and serum from patients with suspected AVD. AVD phenotypes, relevant risk factors and comorbid conditions were ascertained by electronic medical record (EMR)-based electronic algorithms that included diagnosis and procedure codes, laboratory data and text searches to ascertain medication use. Results: Up to December 2012, 8800 patients referred for vascular ultrasound examination and non-invasive lower extremity arterial evaluation were approached, of whom 5268 consented. The mean age of the initial 2182 patients recruited was 70.4 ± 11.2 years, 62.6% were men and 97.6% were whites. The prevalences of AVD phenotypes were: carotid artery stenosis 48%, abdominal aortic aneurysm 21% and peripheral arterial disease 38%. Positive predictive values for electronic phenotyping algorithms were>0.90 for cases (and>0.95 for controls) for each AVD phenotype, using manual review of the EMR as the gold standard. The prevalences of risk factors and comorbidities were as follows: hypertension 78%, diabetes 29%, dyslipidemia 73%, smoking 70%, coronary heart disease 37%, heart failure 12%, cerebrovascular disease 20% and chronic kidney disease 19%. Conclusions: Our study demonstrates the feasibility of establishing a biorepository of plasma, serum and DNA, with relatively rapid annotation of clinical variables using EMR-based algorithms. PMID:24689004

  19. Links between plant community composition, soil organic matter quality and microbial communities in contrasting tundra habitats.

    PubMed

    Eskelinen, Anu; Stark, Sari; Männistö, Minna

    2009-08-01

    Plant communities, soil organic matter and microbial communities are predicted to be interlinked and to exhibit concordant patterns along major environmental gradients. We investigated the relationships between plant functional type composition, soil organic matter quality and decomposer community composition, and how these are related to major environmental variation in non-acid and acid soils derived from calcareous versus siliceous bedrocks, respectively. We analysed vegetation, organic matter and microbial community compositions from five non-acidic and five acidic heath sites in alpine tundra in northern Europe. Sequential organic matter fractionation was used to characterize organic matter quality and phospholipid fatty acid analysis to detect major variation in decomposer communities. Non-acidic and acidic heaths differed substantially in vegetation composition, and these disparities were associated with congruent shifts in soil organic matter and microbial communities. A high proportion of forbs in the vegetation was positively associated with low C:N and high soluble N:phenolics ratios in soil organic matter, and a high proportion of bacteria in the microbial community. On the contrary, dwarf shrub-rich vegetation was associated with high C:N and low soluble N:phenolics ratios, and a high proportion of fungi in the microbial community. Our study demonstrates a strong link between the plant community composition, soil organic matter quality, and microbial community composition, and that differences in one compartment are paralleled by changes in others. Variation in the forb-shrub gradient of vegetation may largely dictate variations in the chemical quality of organic matter and decomposer communities in tundra ecosystems. Soil pH, through its direct and indirect effects on plant and microbial communities, seems to function as an ultimate environmental driver that gives rise to and amplifies the interactions between above- and belowground systems.

  20. Community-based knowledge transfer and exchange: Helping community-based organizations link research to action

    PubMed Central

    2010-01-01

    Background Community-based organizations (CBOs) are important stakeholders in health systems and are increasingly called upon to use research evidence to inform their advocacy, program planning, and service delivery efforts. CBOs increasingly turn to community-based research (CBR) given its participatory focus and emphasis on linking research to action. In order to further facilitate the use of research evidence by CBOs, we have developed a strategy for community-based knowledge transfer and exchange (KTE) that helps CBOs more effectively link research evidence to action. We developed the strategy by: outlining the primary characteristics of CBOs and why they are important stakeholders in health systems; describing the concepts and methods for CBR and for KTE; comparing the efforts of CBR to link research evidence to action to those discussed in the KTE literature; and using the comparison to develop a framework for community-based KTE that builds on both the strengths of CBR and existing KTE frameworks. Discussion We find that CBR is particularly effective at fostering a climate for using research evidence and producing research evidence relevant to CBOs through community participation. However, CBOs are not always as engaged in activities to link research evidence to action on a larger scale or to evaluate these efforts. Therefore, our strategy for community-based KTE focuses on: an expanded model of 'linkage and exchange' (i.e., producers and users of researchers engaging in a process of asking and answering questions together); a greater emphasis on both producing and disseminating systematic reviews that address topics of interest to CBOs; developing a large-scale evidence service consisting of both 'push' efforts and efforts to facilitate 'pull' that highlight actionable messages from community relevant systematic reviews in a user-friendly way; and rigorous evaluations of efforts for linking research evidence to action. Summary Through this type of strategy

  1. Biomarkers of Delirium in a Low-Risk Community-Acquired Pneumonia-Induced Sepsis.

    PubMed

    Tomasi, Cristiane Damiani; Vuolo, Francieli; Generoso, Jaqueline; Soares, Márcio; Barichello, Tatiana; Quevedo, João; Ritter, Cristiane; Dal-Pizzol, Felipe

    2017-01-01

    There are different theories about the pathophysiology of sepsis-associated encephalopathy (SAE), and the majority of our knowledge was derived from critically ill patients. 7In less severe sepsis, it is probable that neuroinflammation can be a major aspect of SAE development. We hypothesized that in non-severe septic patients, blood biomarkers of inflammation, endothelial activation, coagulation, and brain function would be different when compared to patients with and without brain dysfunction. A total of 30 patients presenting with community-acquired pneumonia (CAP)-induced sepsis were included of which 10 (33 %) developed SAE. Eight medical patients admitted to the general ward, except due to sepsis or infection, which developed delirium were included as delirium, non-sepsis group. From all measured biomarkers, only brain-derived neurotrophic factor (BDNF), regulated upon activation normal T cell expressed, and presumably secreted (RANTES), and interleukin (IL)-10 where significantly different when compared to SAE and sepsis groups. In addition, SAE patients presented higher levels of BDNF, vascular cellular adhesion molecule-1 (VCAM-1), intercellular adhesion molecule-1 (ICAM-1), platelet-derived growth factor (PDGF)-AB/BB and RANTES when compared to delirium patients. In conclusion, the profile of biomarkers differs between SAE, sepsis, and delirium patients, suggesting that pathways related to SAE are different from delirium and from sepsis itself.

  2. Microphytobenthos biomass and community composition studied by pigment biomarkers: importance and fate in the carbon cycle of a tidal flat

    NASA Astrophysics Data System (ADS)

    Barranguet, C.; Herman, P. M. J.; Sinke, J. J.

    1997-12-01

    Microphytobenthos biomass and community composition were studied by the use of pigment biomarkers during one year at a tidal flat located in the Westerschelde (SW Netherlands). Benthic microphytes appeared to be an important carbon source in the Westerschelde, especially in the central part of the flat with a mean biomass as high as 65 mg Chl a m -2 in the superficial 1 mm of sediment. Diatoms (fucoxanthin, Chl c) dominated the population during both spring and autumn blooms. In summer microphytobenthic biomass decreased, and diatoms coexisted with Cyanobacteria (zeaxanthin) and Euglenophyceae (Chl b, zeaxanthin and lutein). The shift in the community composition may possibly be linked with the decrease in silicon concentration in the overlying water. The degradation and recycling of microphytobenthic biomass was assessed by the study of degraded chlorophyll pigments, and pigments in deeper sediment layers. The fate of microphytobenthos appears to include rapid bacterial degradation in spring, episodic grazing by benthic animals in surface layers of sediments in the centre of the flat, and export by resuspension in sediments more exposed to currents.

  3. Multiple Inflammatory Biomarkers in Relation to Cardiovascular Events and Mortality in the Community

    PubMed Central

    Schnabel, Renate B.; Yin, Xiaoyan; Larson, Martin G.; Yamamoto, Jennifer F.; Fontes, João D.; Kathiresan, Sekar; Rong, Jian; Levy, Daniel; Keaney, John F.; Wang, Thomas J.; Murabito, Joanne M.; Vasan, Ramachandran S.; Benjamin, Emelia J.

    2013-01-01

    Objective Evidence suggests that chronic low-grade inflammation and oxidative stress are related to cardiovascular disease (CVD) and mortality. Approach and Results We examined 11 established and novel biomarkers representing inflammation and oxidative stress (C-reactive protein [CRP], fibrinogen, interleukin-6, intercellular adhesion molecule-1 [ICAM-1], lipoprotein-associated phospholipase A2 (mass and activity), monocyte chemoattractant protein-1, myeloperoxidase, CD40 ligand, P-selectin, tumor necrosis factor receptor II [TNFRII]) in relation to incident major CVD and mortality in the community. We studied 3035 participants (mean age 61±9 years, 53% women). During follow-up (median 8.9 years), 253 participants experienced a CVD event and 343 died. CRP (hazard ratios [HR] reported per standard deviation ln-transformed biomarker, 1.18, 95% confidence interval [CI] 1.02-1.35; nominal P=0.02) and TNFRII (HR 1.15, 95% CI; 1.01-1.32; nominal P=0.04) were retained in multivariable-adjusted models for major CVD, but were not significant after adjustment for multiple testing. The biomarkers related to mortality were TNFRII (HR 1.33, 95% CI: 1.19-1.49; P<0.0001); ICAM-1 (HR 1.24, 95% CI: 1.12-1.37; P<0.0001), and interleukin-6 (HR 1.25, 95% CI: 1.12-1.39; P<0.0001). The addition of these markers to the model including traditional risk factors increased discrimination and reclassification for risk of death (P<0.0001), but not for CVD. Conclusions Of 11 biomarkers, TNFRII was associated nominally with incident major CVD, and significantly with all-cause mortality, which renders it an interesting target for future research. The combination of TNFRII with CRP in relation to CVD and with interleukin-6 to mortality increased the predictive ability in addition to CVD risk factors for total mortality but not for incident CVD. PMID:23640499

  4. Cytokines and Chemokines as Biomarkers of Community-Acquired Bacterial Infection

    PubMed Central

    Lawrence, David A.; Andersen, Nancy; Beran, Ondřej; Marešová, Vilma

    2013-01-01

    Routinely used biomarkers of bacterial etiology of infection, such as C-reactive protein and procalcitonin, have limited usefulness for evaluation of infections since their expression is enhanced by a number of different conditions. Therefore, several inflammatory cytokines and chemokines were analyzed with sera from patients hospitalized for moderate bacterial and viral infectious diseases. In total, 57 subjects were enrolled: 21 patients with community-acquired bacterial infections, 26 patients with viral infections, and 10 healthy subjects (control cohorts). The laboratory analyses were performed using Luminex technology, and the following molecules were examined: IL-1Ra, IL-2, IL-4, IL-6, IL-8, TNF-α, INF-γ, MIP-1β, and MCP-1. Bacterial etiology of infection was associated with significantly (P < 0.001) elevated serum concentrations of IL-1Ra, IL-2, IL-6, and TNF-α in comparison to levels observed in the sera of patients with viral infections. In the patients with bacterial infections, IL-1Ra and IL-8 demonstrated positive correlation with C-reactive protein, whereas, IL-1Ra, TNF-α, and MCP-1 correlated with procalcitonin. Furthermore, elevated levels of IL-1Ra, IL-6, and TNF-α decreased within 3 days of antibiotic therapy to levels observed in control subjects. The results show IL-1Ra as a potential useful biomarker of community-acquired bacterial infection. PMID:23690657

  5. Cytokines and chemokines as biomarkers of community-acquired bacterial infection.

    PubMed

    Holub, Michal; Lawrence, David A; Andersen, Nancy; Davidová, Alžběta; Beran, Ondřej; Marešová, Vilma; Chalupa, Pavel

    2013-01-01

    Routinely used biomarkers of bacterial etiology of infection, such as C-reactive protein and procalcitonin, have limited usefulness for evaluation of infections since their expression is enhanced by a number of different conditions. Therefore, several inflammatory cytokines and chemokines were analyzed with sera from patients hospitalized for moderate bacterial and viral infectious diseases. In total, 57 subjects were enrolled: 21 patients with community-acquired bacterial infections, 26 patients with viral infections, and 10 healthy subjects (control cohorts). The laboratory analyses were performed using Luminex technology, and the following molecules were examined: IL-1Ra, IL-2, IL-4, IL-6, IL-8, TNF- α , INF- γ , MIP-1 β , and MCP-1. Bacterial etiology of infection was associated with significantly (P < 0.001) elevated serum concentrations of IL-1Ra, IL-2, IL-6, and TNF- α in comparison to levels observed in the sera of patients with viral infections. In the patients with bacterial infections, IL-1Ra and IL-8 demonstrated positive correlation with C-reactive protein, whereas, IL-1Ra, TNF- α , and MCP-1 correlated with procalcitonin. Furthermore, elevated levels of IL-1Ra, IL-6, and TNF- α decreased within 3 days of antibiotic therapy to levels observed in control subjects. The results show IL-1Ra as a potential useful biomarker of community-acquired bacterial infection.

  6. IDBD: infectious disease biomarker database.

    PubMed

    Yang, In Seok; Ryu, Chunsun; Cho, Ki Joon; Kim, Jin Kwang; Ong, Swee Hoe; Mitchell, Wayne P; Kim, Bong Su; Oh, Hee-Bok; Kim, Kyung Hyun

    2008-01-01

    Biomarkers enable early diagnosis, guide molecularly targeted therapy and monitor the activity and therapeutic responses across a variety of diseases. Despite intensified interest and research, however, the overall rate of development of novel biomarkers has been falling. Moreover, no solution is yet available that efficiently retrieves and processes biomarker information pertaining to infectious diseases. Infectious Disease Biomarker Database (IDBD) is one of the first efforts to build an easily accessible and comprehensive literature-derived database covering known infectious disease biomarkers. IDBD is a community annotation database, utilizing collaborative Web 2.0 features, providing a convenient user interface to input and revise data online. It allows users to link infectious diseases or pathogens to protein, gene or carbohydrate biomarkers through the use of search tools. It supports various types of data searches and application tools to analyze sequence and structure features of potential and validated biomarkers. Currently, IDBD integrates 611 biomarkers for 66 infectious diseases and 70 pathogens. It is publicly accessible at http://biomarker.cdc.go.kr and http://biomarker.korea.ac.kr.

  7. 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.

  8. Putative link between Staphylococcus aureus bacteriophage serotype and community association.

    PubMed

    Mohamed, D H; Saberesheikh, S; Kearns, A M; Saunders, N A

    2012-07-01

    Methicillin-resistant Staphylococcus aureus (MRSA) from humans can be broadly separated into 3 groups: healthcare-associated (HA), community-associated (CA), and livestock-associated (LA) MRSA. Initially based on epidemiological features, division into these classes is becoming increasingly problematic. The sequencing of S. aureus genomes has highlighted variations in their accessory components, which likely account for differences in pathogenicity and epidemicity. In particular, temperate bacteriophages have been regarded as key players in bacterial pathogenesis. Bacteriophage-associated Panton-Valentine leukocidin genes (luk-PV) are regarded as epidemiological markers of the CA-MRSA due to their high prevalence in CA strains. This paper describes the development and application of a partial composite S. aureus virulence-associated gene microarray. Epidemic, pandemic, and sporadic lineages of UK HA and CA S. aureus were compared. Phage structural genes linked with CA isolates were identified and in silico analysis revealed these to be correlated with phage serogroup. CA strains predominantly carried a PVL-associated phage either of the A or Fb serogroup, whilst HA strains predominantly carried serogroup Fa or B phages. We speculate that carriage of a serogroup A/Fb PVL-associated phage rather than the luk-PV genes specifically is correlated with CA status.

  9. Heterogeneity of neuroanatomical patterns in prodromal Alzheimer's disease: links to cognition, progression and biomarkers.

    PubMed

    Dong, Aoyan; Toledo, Jon B; Honnorat, Nicolas; Doshi, Jimit; Varol, Erdem; Sotiras, Aristeidis; Wolk, David; Trojanowski, John Q; Davatzikos, Christos

    2016-12-20

    Individuals with mild cognitive impairment and Alzheimer's disease clinical diagnoses can display significant phenotypic heterogeneity. This variability likely reflects underlying genetic, environmental and neuropathological differences. Characterizing this heterogeneity is important for precision diagnostics, personalized predictions, and recruitment of relatively homogeneous sets of patients into clinical trials. In this study, we apply state-of-the-art semi-supervised machine learning methods to the Alzheimer's disease Neuroimaging cohort (ADNI) to elucidate the heterogeneity of neuroanatomical differences between subjects with mild cognitive impairment (n = 530) and Alzheimer's disease (n = 314) and cognitively normal individuals (n = 399), thereby adding to an increasing literature aiming to establish neuroanatomical and neuropathological (e.g. amyloid and tau deposition) dimensions in Alzheimer's disease and its prodromal stages. These dimensional approaches aim to provide surrogate measures of heterogeneous underlying pathologic processes leading to cognitive impairment. We relate these neuroimaging patterns to cerebrospinal fluid biomarkers, white matter hyperintensities, cognitive and clinical measures, and longitudinal trajectories. We identified four such atrophy patterns: (i) individuals with largely normal neuroanatomical profiles, who also turned out to have the least abnormal cognitive and cerebrospinal fluid biomarker profiles and the slowest clinical progression during follow-up; (ii) individuals with classical Alzheimer's disease neuroanatomical, cognitive, cerebrospinal fluid biomarkers and clinical profile, who presented the fastest clinical progression; (iii) individuals with a diffuse pattern of atrophy with relatively less pronounced involvement of the medial temporal lobe, abnormal cerebrospinal fluid amyloid-β1-42 values, and proportionally greater executive impairment; and (iv) individuals with notably focal involvement of the medial

  10. 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…

  11. Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities.

    PubMed

    Helb, Danica A; Tetteh, Kevin K A; Felgner, Philip L; Skinner, Jeff; Hubbard, Alan; Arinaitwe, Emmanuel; Mayanja-Kizza, Harriet; Ssewanyana, Isaac; Kamya, Moses R; Beeson, James G; Tappero, Jordan; Smith, David L; Crompton, Peter D; Rosenthal, Philip J; Dorsey, Grant; Drakeley, Christopher J; Greenhouse, Bryan

    2015-08-11

    Tools to reliably measure Plasmodium falciparum (Pf) exposure in individuals and communities are needed to guide and evaluate malaria control interventions. Serologic assays can potentially produce precise exposure estimates at low cost; however, current approaches based on responses to a few characterized antigens are not designed to estimate exposure in individuals. Pf-specific antibody responses differ by antigen, suggesting that selection of antigens with defined kinetic profiles will improve estimates of Pf exposure. To identify novel serologic biomarkers of malaria exposure, we evaluated responses to 856 Pf antigens by protein microarray in 186 Ugandan children, for whom detailed Pf exposure data were available. Using data-adaptive statistical methods, we identified combinations of antibody responses that maximized information on an individual's recent exposure. Responses to three novel Pf antigens accurately classified whether an individual had been infected within the last 30, 90, or 365 d (cross-validated area under the curve = 0.86-0.93), whereas responses to six antigens accurately estimated an individual's malaria incidence in the prior year. Cross-validated incidence predictions for individuals in different communities provided accurate stratification of exposure between populations and suggest that precise estimates of community exposure can be obtained from sampling a small subset of that community. In addition, serologic incidence predictions from cross-sectional samples characterized heterogeneity within a community similarly to 1 y of continuous passive surveillance. Development of simple ELISA-based assays derived from the successful selection strategy outlined here offers the potential to generate rich epidemiologic surveillance data that will be widely accessible to malaria control programs.

  12. Teaching Inquiry with Linked Classes and Learning Communities

    ERIC Educational Resources Information Center

    Piercey, Victor; Cullen, Roxanne

    2017-01-01

    In order to improve problem-solving dispositions, a section of an inquiry-based math sequence for first-year business students was linked with a section of our general education English sequence. We describe how the linked classes worked and compare some preliminary results from linked and unlinked sections of the math sequence.

  13. Temporal organization of phytoplankton communities linked to physical forcing.

    PubMed

    Winder, Monika; Hunter, Deborah A

    2008-05-01

    The performance of individual phytoplankton species is strongly governed by the thermal stratification's impact on vertical mixing within the water column, which alters the position of phytoplankton relative to nutrients and light. The present study documents shifts in phytoplankton structure and vertical positioning that have accompanied intensified long-term stratification in a natural ecosystem. Ordination analysis is used to extract gradients in phytoplankton composition in Lake Tahoe, an extremely nutrient-poor lake, over a 23-year period of records. Community structure in the 1980s was associated most strongly with resource availability (low nitrogen to phosphorus ratios, deeper euphotic zone depth), while intensified stratification dominated the phytoplankton structure since the late 1990s. Within diatoms, small-sized cells increased with reduced mixing, suggesting that suppressed turbulence provides them with a competitive advantage over large-sized cells. Among the morphologically diverse chlorophytes, filamentous and coenobial forms were favored under intensified stratification. The selection for small-sized diatoms is accompanied by a shoaling trend in their vertical position in the water column. In contrast, the motile flagellates displayed a deeper vertical positioning in recent years, indicating that optimal growth conditions shifted likely due to reduced upwelling of nutrients. As the thermal stratification of lakes and oceans is strongly linked to climate variables, the present study confirms that climate warming will alter phytoplankton structure and dynamics largely through effects on nutrient availability and sinking velocities. Intensified stratification should favor the expansion of small-sized species and species with the capability of buoyancy regulation, which may alter primary productivity, nutrient recycling, and higher trophic productivity.

  14. 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…

  15. Discovering link communities in complex networks by an integer programming model and a genetic algorithm.

    PubMed

    Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

    2013-01-01

    Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks.

  16. 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…

  17. 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.

  18. Instructional Technology as Link between University and Community.

    ERIC Educational Resources Information Center

    Rossett, Allison

    1981-01-01

    Examines the proclaimed dichotomy between real and unreal, theory and practice, actual and idealized notions of community needs and university attitudes with regard to training, and describes how San Diego State University's Educational Technology program attempts simultaneously to educate graduate students and serve its community. (Author/MER)

  19. Methylglyoxal in diabetes: link to treatment, glycaemic control and biomarkers of complications.

    PubMed

    Beisswenger, Paul J

    2014-04-01

    Diabetic complications are major health problems worldwide, with the cost of caring for diabetes rising to US$245 billion in 2012 in the U.S.A. alone. It is widely recognized that non-enzymatic glycation in diabetes is a major cause of damage and dysfunction of key vascular cells. MG (methylglyoxal) is directly toxic to tissues, and is a major precursor of AGEs (advanced glycation end-products). Various propensities to diabetic complications are seen among individuals with diabetes, with accelerated rates occurring in some individuals with modest hyperglycaemia, while others never progress in spite of poor glycaemic control over many years. Since production and detoxification of MG is ultimately controlled by enzymatic mechanisms, both genetic and environmental factors could regulate tissue glycation and potentially account for these variable complication rates. Activation of pathways that determine MG levels occurs in susceptible patients, indicting an important role in pathogenesis. MG leads to formation of specific AGEs, which are likely to predict propensity to diabetic complications. We have shown recently that three specific plasma AGE biomarkers [MG-H1 (MG-derived hydroimidazolones), CEL (Nε-carboxyethyl-lysine) and CML (Nε-carboxymethyl-lysine)] predict biopsy-documented fast DN (diabetic nephropathy) progression. Since two of the predictive biomarkers are MG end-products, these outcomes support a role for MG in the development of DN. Our studies on MG and its end-products have also shown anti-complication effects of the drug metformin, which binds and inactivates MG, thus reducing MG-related AGEs. We have also shown that reducing post-meal glucose decreases MG levels, as well as levels of MG-related AGEs. Our clinical outcome studies have been based on the novel concept that the unique glycation products that we can measure reflect the activity of specific chemical pathways that are selectively activated by hyperglycaemia in patients that are inherently

  20. Bile acid aspiration associated with lung chemical profile linked to other biomarkers of injury after lung transplantation.

    PubMed

    Neujahr, D C; Uppal, K; Force, S D; Fernandez, F; Lawrence, C; Pickens, A; Bag, R; Lockard, C; Kirk, A D; Tran, V; Lee, K; Jones, D P; Park, Y

    2014-04-01

    Aspiration of gastrointestinal contents has been linked to worse outcomes following lung transplantation but uncertainty exists about underlying mechanisms. We applied high-resolution metabolomics of bronchoalveolar lavage fluid (BALF) in patients with episodic aspiration (defined by bile acids in the BALF) to identify potential metabolic changes associated with aspiration. Paired samples, one with bile acids and another without, from 29 stable lung transplant patients were studied. Liquid chromatography coupled to high-resolution mass spectroscopy was used to interrogate metabolomic contents of these samples. Data were obtained for 7068 ions representing intermediary metabolites, environmental agents and chemicals associated with microbial colonization. A substantial number (2302) differed between bile acid positive and negative samples when analyzed by false discovery rate at q = 0.01. These included pathways associated with microbial metabolism. Hierarchical cluster analysis defined clusters of chemicals associated with bile acid aspiration that were correlated to previously reported biomarkers of lung injury including T cell granzyme B level and the chemoattractants CXCL9 and CXCL10. These data specifically link bile acids presence in lung allografts to inflammatory pathways known to segregate with worsening allograft outcome, and provide additional mechanistic insight into the association between reflux and lung allograft injury.

  1. A pH Indicator-linked Immunosorbent assay following direct amplification strategy for colorimetric detection of protein biomarkers.

    PubMed

    Shao, Fengying; Jiao, Lei; Miao, Luyang; Wei, Qin; Li, He

    2017-04-15

    A new pH indicator-linked immunosorbent assay (PILISA) reached pg/mL sensitivity based on pH indicator molecules loaded carbon nitride nanosheets as signal enhancer has been developed for colorimetric detection of protein biomarkers. As the secondary antibody binds to the carbon nitride nanosheets, the carbon nitride nanosheets and pH indicator complex as the signal amplification platform for colour change by detecting absorbance of pH indicator. The colour change was resulted from the releasing of pH indicator molecules from carbon nitride nanosheets triggered by alkali solution (AS). In this novel PILISA, the intensity absorbance of pH indicator is proportional to the concentration of the disease marker. The outstanding detection performance of the PILISA can be attributed to the following reasons: (1) ultrathin carbon nitride nanosheets with a larger surface area could adsorb abundant phenolphthalein (PP) molecules through hydrophobic interactions as well as the resulted PP anions can be free easily released into aqueous solution, leading to an obvious allochroic response; (2) the signal intensity is precisely determined by the amount of PP molecules loading onto the carbon nitride nanosheets surface, which ensures simple, low-cost and stable colorimetric detection. As expected, this new PILISA method offered an enzyme-free approach followed enzyme-linked immunosorbent assay format, which showed great promising potential as an innovative robust assay method for practical clinical applications.

  2. Sediment biomarker, bacterial community characterization of high arsenic aquifers in Jianghan Plain, China

    NASA Astrophysics Data System (ADS)

    Ye, Hengpeng; Yang, Zeyu; Wu, Xiang; Wang, Jingwen; Du, Dongyun; Cai, Jian; Lv, Kangle; Chen, Huiyun; Mei, Jingkun; Chen, Mengqi; Du, Hong

    2017-02-01

    Representative biomarkers (e.g., n-alkanes), diversity and microbial community in the aquifers contaminated by high concentration of arsenic (As) in different sediment depth (0–30 m) in Jianghan Plain, Hubei, China, were analyzed to investigate the potential mechanism of As enrichment in groundwater. The concentration of As was abundant in top soil and sand, but not in clay. The analysis of the distribution of n-alkanes, CPI values, and wax to total n-alkane ratio (Wax(n)%) indicated that the organic matter (OM) from fresh terrestrial plants were abundant in the shallow sediment. However, n-alkanes have suffered from significant biodegradation from the depth of 16 m to 30 m. The deposition of fresh terrestrial derived organic matters may facilitate the release of As from sediment to groundwater in the sediment of 0–16 m. However, the petroleum derived organic matters may do the favor to the release of As in the deeper section of borehole (16 m to 30 m). The 16S rRNA gene sequences identification indicated that Acidobacteria, Actinomycetes and Hydrogenophaga are abundant in the sediments with high arsenic. Therefore, microbes and organic matters from different sources may play important roles in arsenic mobilization in the aquifers of the study area.

  3. Sediment biomarker, bacterial community characterization of high arsenic aquifers in Jianghan Plain, China

    PubMed Central

    Ye, Hengpeng; Yang, Zeyu; Wu, Xiang; Wang, Jingwen; Du, Dongyun; Cai, Jian; Lv, Kangle; Chen, Huiyun; Mei, Jingkun; Chen, Mengqi; Du, Hong

    2017-01-01

    Representative biomarkers (e.g., n-alkanes), diversity and microbial community in the aquifers contaminated by high concentration of arsenic (As) in different sediment depth (0–30 m) in Jianghan Plain, Hubei, China, were analyzed to investigate the potential mechanism of As enrichment in groundwater. The concentration of As was abundant in top soil and sand, but not in clay. The analysis of the distribution of n-alkanes, CPI values, and wax to total n-alkane ratio (Wax(n)%) indicated that the organic matter (OM) from fresh terrestrial plants were abundant in the shallow sediment. However, n-alkanes have suffered from significant biodegradation from the depth of 16 m to 30 m. The deposition of fresh terrestrial derived organic matters may facilitate the release of As from sediment to groundwater in the sediment of 0–16 m. However, the petroleum derived organic matters may do the favor to the release of As in the deeper section of borehole (16 m to 30 m). The 16S rRNA gene sequences identification indicated that Acidobacteria, Actinomycetes and Hydrogenophaga are abundant in the sediments with high arsenic. Therefore, microbes and organic matters from different sources may play important roles in arsenic mobilization in the aquifers of the study area. PMID:28165031

  4. 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...

  5. 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.

  6. 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

  7. 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

  8. Community Involvement: Linking Parents and Non-Parents.

    ERIC Educational Resources Information Center

    Kenner, Lynn; Gribbin, Randall

    1992-01-01

    To ensure the success of its enrichment activities program, a Texas elementary school formed principal assistants committees (PACs) comprised of highly diverse community volunteer coordinators. In the PAC program, parents, nonparents, and educators work together, sharing problems and solutions while supporting each others' efforts. Sidebars list…

  9. Lifelong Career Development Handbook: Linking Community Services for Disabled Adults.

    ERIC Educational Resources Information Center

    Brolin, Donn E.; And Others

    Designed for use by those who work with the disabled, this handbook explains and provides procedures for implementing the Lifelong Career Development (LCD) Model. (Designed for implementation at the community college level, the LCD model provides a competency-based approach to meeting the career development needs of disabled people and provides…

  10. 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

  11. A Tiered Model for Linking Students to the Community

    ERIC Educational Resources Information Center

    Meyer, Laura Landry; Gerard, Jean M.; Sturm, Michael R.; Wooldridge, Deborah G.

    2016-01-01

    A tiered practice model (introductory, pre-internship, and internship) embedded in the curriculum facilitates community engagement and creates relevance for students as they pursue a professional identity in Human Development and Family Studies. The tiered model integrates high-impact teaching practices (HIP) and student engagement pedagogies…

  12. 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…

  13. 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…

  14. 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…

  15. 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.

  16. 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.

  17. 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

  18. Linking microbial community structure and microbial processes: an empirical and conceptual overview.

    PubMed

    Bier, Raven L; Bernhardt, Emily S; Boot, Claudia M; Graham, Emily B; Hall, Edward K; Lennon, Jay T; Nemergut, Diana R; Osborne, Brooke B; Ruiz-González, Clara; Schimel, Joshua P; Waldrop, Mark P; Wallenstein, Matthew D

    2015-10-01

    A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009-13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

  19. Linking microbial community structure and microbial processes: An empirical and conceptual overview

    USGS Publications Warehouse

    Bier, R.L.; Bernhardt, E.S.;; Boot, C.M.; Graham, E.B.;; Hall, E.K.; Lennon, J.T.; Nemergut, D.R.; Osborne, B.B.; Ruiz-Gonzalez, C.; Schimel, J.P.; Waldrop, Mark P.; Wallenstein, M.D.

    2015-01-01

    A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

  20. 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.

  1. Links between plant and rhizoplane bacterial communities in grassland soils, characterized using molecular techniques.

    PubMed

    Nunan, Naoise; Daniell, Timothy J; Singh, Brajesh K; Papert, Artemis; McNicol, James W; Prosser, James I

    2005-11-01

    Molecular analysis of grassland rhizosphere soil has demonstrated complex and diverse bacterial communities, with resultant difficulties in detecting links between plant and bacterial communities. These studies have, however, analyzed "bulk" rhizosphere soil, rather than rhizoplane communities, which interact most closely with plants through utilization of root exudates. The aim of this study was to test the hypothesis that plant species was a major driver for bacterial rhizoplane community composition on individual plant roots. DNA extracted from individual roots was used to determine plant identity, by analysis of the plastid tRNA leucine (trnL) UAA gene intron, and plant-related bacterial communities. Bacterial communities were characterized by analysis of PCR-amplified 16S rRNA genes using two fingerprinting methods: terminal restriction fragment length polymorphisms (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). Links between plant and bacterial rhizoplane communities could not be detected by visual examination of T-RFLP patterns or DGGE banding profiles. Statistical analysis of fingerprint patterns did not reveal a relationship between bacterial community composition and plant species but did demonstrate an influence of plant community composition. The data also indicated that topography and other, uncharacterized, environmental factors are important in driving bacterial community composition in grassland soils. T-RFLP had greater potential resolving power than DGGE, but findings from the two methods were not significantly different.

  2. 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.

  3. Virtual community consultation? Using the literature and weblogs to link community perspectives and health technology assessment

    PubMed Central

    Street, Jackie M.; Braunack‐Mayer, Annette J.; Facey, Karen; Ashcroft, Richard E.; Hiller, Janet E.

    2008-01-01

    Abstract Background  Community views, expressed in social impact assessments and collected through community consultation, should play an important role in health technology assessment (HTA). Yet HTA methodologists have been slow to include outcomes of these forms of inquiry in analyses, in part because collecting community views is time‐consuming and resource intensive. Objective  To explore how community views sourced from published studies, grey literature and informal internet web pages can inform HTA. Methods  A technology reviewed by Adelaide HTA in 2004 was selected: retinal photography for detection of diabetic retinopathy. Published literature, ‘grey’ literature and informal web pages were searched to examine the availability of evidence about service community and user community views with respect to this technology. Particular efforts were made to source evidence relating to rural, remote and Aboriginal populations. Results  We found that journal articles, reports from the grey literature and informal internet web pages (including blogs and discussion forums) can provide valuable insight into community views. Although there was little empirical evidence relating to the experience of diabetes and diabetes management in rural, remote and Aboriginal communities, there were indications that some evidence may be transferable from other populations. Conclusions  Community perspectives on selected health technologies can be gauged from available resources in published and grey literature and perspectives collected in this way can provide insight into whether the introduction of the technology would be acceptable to the community. The limitations of this approach are discussed. PMID:18430153

  4. 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.

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

    PubMed Central

    Mueller, Rebecca C; Paula, Fabiana S; Mirza, Babur S; Rodrigues, Jorge LM; Nüsslein, Klaus; Bohannan, Brendan JM

    2014-01-01

    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

  6. 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.

  7. Evaluation of uncertainties associated with the determination of community drug use through the measurement of sewage drug biomarkers.

    PubMed

    Castiglioni, Sara; Bijlsma, Lubertus; Covaci, Adrian; Emke, Erik; Hernández, Félix; Reid, Malcolm; Ort, Christoph; Thomas, Kevin V; van Nuijs, Alexander L N; de Voogt, Pim; Zuccato, Ettore

    2013-02-05

    The aim of this study was to integrally address the uncertainty associated with all the steps used to estimate community drug consumption through the chemical analysis of sewage biomarkers of illicit drugs. Uncertainty has been evaluated for sampling, chemical analysis, stability of drug biomarkers in sewage, back-calculation of drug use (specific case of cocaine), and estimation of population size in a catchment using data collected from a recent Europe-wide investigation and from the available literature. The quality of sampling protocols and analytical measurements has been evaluated by analyzing standardized questionnaires collected from 19 sewage treatments plants (STPs) and the results of an interlaboratory study (ILS), respectively. Extensive reviews of the available literature have been used to evaluate stability of drug biomarkers in sewage and the uncertainty related to back-calculation of cocaine use. Different methods for estimating population size in a catchment have been compared and the variability among the collected data was very high (7-55%). A reasonable strategy to reduce uncertainty was therefore to choose the most reliable estimation case by case. In the other cases, the highest uncertainties are related to the analysis of sewage drug biomarkers (uncertainty as relative standard deviation; RSD: 6-26% from ILS) and to the back-calculation of cocaine use (uncertainty; RSD: 26%). Uncertainty can be kept below 10% in the remaining steps, if specific requirements outlined in this work are considered. For each step, a best practice protocol has been suggested and discussed to reduce and keep to a minimum the uncertainty of the entire procedure and to improve the reliability of the estimates of drug use.

  8. 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.

  9. Cold-spotting: linking primary care and public health to create communities of solution.

    PubMed

    Westfall, John M

    2013-01-01

    By providing enhanced primary care and social services to patients with high utilization of expensive emergency and hospital care, there is evidence that their health can improve and their costs can be lowered. This type of "hot-spotting" improves the care of individual patients. It may be that these patients live in communities with disintegrated social determinants of health, little community support, and poor access to primary care. These "cold spots" in the community may be amenable to interventions targeted at linking primary care and public health at broader community and population levels. Building local communities of solution that address the individual and population may help decrease these cold spots, thereby eliminating the hot spots as well.

  10. 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.

  11. 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.

  12. Linking Classes: Learning Communities, "High" Culture, and the Working Class Student

    ERIC Educational Resources Information Center

    Rodriguez, Ginger G.; Buczinsky, Christopher

    2013-01-01

    How do you teach the humanities to working class students living in the shadow of a BP oil refinery? Calumet College uses freshman learning communities that link humanities, social justice, and English composition classes to provide a foundation for college success to predominantly first-generation students who are often underprepared for…

  13. Social Networks: A Link between Psychiatric Epidemiology and Community Mental Health.

    ERIC Educational Resources Information Center

    Llamas, Robert; And Others

    1981-01-01

    Examines the concept of social network as a mediating construct linking psychiatric epidemiology and community mental health. Presents a selective review of studies investigating the structural and interactional features of the social networks of psychiatrically impaired persons. Implications of results are discussed. (Author)

  14. 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.

  15. Biomarkers in Veterinary Medicine.

    PubMed

    Myers, Michael J; Smith, Emily R; Turfle, Phillip G

    2017-02-08

    This article summarizes the relevant definitions related to biomarkers; reviews the general processes related to biomarker discovery and ultimate acceptance and use; and finally summarizes and reviews, to the extent possible, examples of the types of biomarkers used in animal species within veterinary clinical practice and human and veterinary drug development. We highlight opportunities for collaboration and coordination of research within the veterinary community and leveraging of resources from human medicine to support biomarker discovery and validation efforts for veterinary medicine.

  16. 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

  17. 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

  18. Chip-based Reversed-phase Liquid Chromatography-Mass Spectrometry of Permethylated N-linked Glycans: a Potential Methodology for Cancer-biomarker Discovery

    PubMed Central

    Alley, William R.; Madera, Milan; Mechref, Yehia; Novotny, Milos V.

    2010-01-01

    The study of protein glycosylation in biological fluids and tissues has substantial medical importance, as changes in glycan structures have now been associated with a number of diseases. Quantification of glycomic-profile changes is becoming increasingly important in the search for disease biomarkers. Here, we report a highly reproducible combination of a glycomic sample preparation/solid-phase derivatization of glycoprotein-derived N-linked glycans with their subsequent microchip-based separation and mass-spectrometric (MS) measurements. Following our previously-described reductive β-elimination for O-linked glycans with ammonia-borane complex to reduce N-linked structures, the N-linked alditol structures are effectively methylated in dimethylformamide medium to avoid artefacts in MS measurements. Reversed-phase microfluidic liquid chromatography (LC) of methylated N-linked oligosaccharide alditols resolved some closely related structures into regular retention increments, aiding in their structural assignments. Optimized LC gradients, together with nanospray MS, have been applied here in the quantitative measurements of N-linked glycans in blood serum, distinguishing breast cancer patients from control individuals. PMID:20491449

  19. 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

  20. Stable Isotope Probing: Linking Functional Activity to Specific Members of Microbial Communities

    SciTech Connect

    Kreuzer-Martin, Helen W.

    2007-03-12

    Abstract Linking organisms or groups of organisms to specific functions within natural environments is a fundamental challenge in microbial ecology. Advances in technology for manipulating and analyzing nucleic acids have made it possible to characterize the members of microbial communities without the intervention of laboratory culturing. Results from such studies have shown that the vast majority of soil organisms have never been cultured, highlighting the risks of culture-based approaches in community analysis. The development of culture-independent techniques for following the flow of substrates through microbial communities therefore represents an important advance. These techniques, collectively known as stable isotope probing (SIP), involve introducing a stable isotope-labeled substrate into a microbial community and following the fate of the substrate by detecting the appearance of the isotope in diagnostic molecules such as fatty acids and nucleic acids. The molecules in which the isotope label appears provide identifying information about the organism that incorporated the substrate. SIP allows direct observations of substrate assimilation in minimally disturbed communities, and thus represents an exciting new tool for linking microbial identity and function. The use of lipids or nucleic acids as the diagnostic molecule brings different strengths and weaknesses to the experimental approach, and necessitates the use of significantly different instrumentation and analytical techniques. This mini-review provides an overview of the lipid and nucleic acid approaches, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.

  1. 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.

  2. Step 5: Has Clearly Defined Policies, Procedures for Collaboration, Consultation, Links to Community Resources

    PubMed Central

    Salt, Karen

    2007-01-01

    Step 5 of the Ten Steps of Mother-Friendly Care ensures that the hospital, birth center, or home birth service has clearly defined policies and procedures for collaborating and consulting with other maternity services and for linking the mother and baby to appropriate community services during both the prenatal and the postpartum periods. The rationales and evidence in support of this step are presented. PMID:18523674

  3. Linking Returning Veterans in Rural Community Colleges to Mental Health Care

    DTIC Science & Technology

    2014-01-01

    with mental health problems to care in order to promote successful re-integration into a productive, civilian life. One reintegration domain that is...student veterans ’ mental health needs as they reintegrate and attend two-year community colleges. A concurrent challenge is that many returning student...Linking these suffering student veterans to quality care is critical to their educational success on the new GI bill and their successful re

  4. 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

  5. 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.

  6. Link community detection by non-negative matrix factorization with multi-step similarities

    NASA Astrophysics Data System (ADS)

    Tang, Xianchao; Yang, Guoqing; Xu, Tao; Feng, Xia; Wang, Xiao; Li, Qiannan; Liu, Yanbei

    2016-11-01

    Uncovering community structures is a fundamental and important problem in analyzing the complex networks. While most of the methods focus on identifying node communities, recent works show the intuitions and advantages of detecting link communities in networks. In this paper, we propose a non-negative matrix factorization (NMF) based method to detect the link community structures. Traditional NMF-based methods mainly consider the adjacency matrix as the representation of network topology, while the adjacency matrix only shows the relationship between immediate neighbor nodes, which does not take the relationship between non-neighbor nodes into consideration. This may greatly reduce the information contained in the network topology, and thus leads to unsatisfactory results. Here, we address this by introducing multi-step similarities using the graph random walk approach so that the similarities between non-neighbor nodes can be captured. Meanwhile, in order to reduce impact caused by self-similarities (similarities between nodes themselves) and increase importance gained from similarities between other different nodes, we add a penalty term to our objective function. Then an efficient optimization scheme for the objective function is derived. Finally, we test the proposed method on both synthetic and real networks. Experimental results demonstrate the effectiveness of the proposed approach.

  7. 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.

  8. 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.

  9. Association of Elevated Amyloid Levels With Cognition and Biomarkers in Cognitively Normal People From the Community

    PubMed Central

    Petersen, Ronald C.; Wiste, Heather J.; Weigand, Stephen D.; Rocca, Walter A.; Roberts, Rosebud O.; Mielke, Michelle M.; Lowe, Val J.; Knopman, David S.; Pankratz, Vernon S.; Machulda, Mary M.; Geda, Yonas E.; Jack, Clifford R.

    2015-01-01

    IMPORTANCE The role of amyloid in the progression of Alzheimer disease (AD) pathophysiology is of central interest to the design of randomized clinical trials. The presence of amyloid has become a prerequisite for enrollment in several secondary prevention trials for AD, yet the precise effect of elevated amyloid levels on subsequent clinical and biomarker events is less certain. OBJECTIVE To explore the effect of elevated amyloid levels on subsequent changes in cognition and biomarkers. DESIGN, SETTING, AND PARTICIPANTS A total of 564 cognitively normal individuals (median age, 78 years) from the Mayo Clinic Study of Aging, a population-based longitudinal study in Olmsted County, Minnesota, with serial cognitive data were selected for this study. The data used in this study were collected from January 12, 2006, to January 9, 2014. Individuals included in this study had undergone magnetic resonance imaging, fluorodeoxyglucose positron emission tomography (FDG-PET), and Pittsburgh Compound B (PiB) PET at baseline were not cognitively impaired at baseline and had at least 1 clinical follow-up. A subset of 286 individuals also underwent serial imaging. Elevated amyloid level was defined as a standardized uptake value ratio of greater than 1.5 on PiB PET. Associations with baseline amyloid status and baseline and longitudinal change in clinical and imaging measures were evaluated after adjusting for age and hippocampal volume. APOE4 effects were also evaluated. MAIN OUTCOMES AND MEASURES Cognitive measures of memory, language, attention/executive function, visuospatial skills, PiB levels, hippocampal and ventricular volumes, and FDG-PET measures. RESULTS At baseline, 179 (31.7%) individuals with elevated amyloid levels had poorer cognition in all domains measured, reduced hippocampal volume, and greater FDG-PET hypometabolism. Elevated amyloid levels at baseline were associated with a greater rate of cognitive decline in all domains (0.04 to 0.09 z score units per year

  10. APPLICATION OF PHOTOPIGMENT BIOMARKERS FOR QUANTIFYING MICROALGAL COMMUNITY COMPOSITION AND IN SITU GROWTH RATES. (R828677)

    EPA Science Inventory

    In estuarine waters, phytoplankton are exposed to rapidly changing conditions that may affect community structure and function. In this study we determined the effects of mixing, turbidity, and limiting nutrient (N) additions on natural phytoplankton growth rates and algal gro...

  11. APPLICATION OF PHOTOPIGMENT BIOMARKERS FOR QUANTIFYING MICROALGAL COMMUNITY COMPOSITION AND IN SITU GROWTH RATES. (R826938)

    EPA Science Inventory

    In estuarine waters, phytoplankton are exposed to rapidly changing conditions that may affect community structure and function. In this study we determined the effects of mixing, turbidity, and limiting nutrient (N) additions on natural phytoplankton growth rates and algal gro...

  12. 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

  13. Bacterial community dynamics are linked to patterns of coral heat tolerance.

    PubMed

    Ziegler, Maren; Seneca, Francois O; Yum, Lauren K; Palumbi, Stephen R; Voolstra, Christian R

    2017-02-10

    Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked.

  14. Bacterial community dynamics are linked to patterns of coral heat tolerance

    PubMed Central

    Ziegler, Maren; Seneca, Francois O.; Yum, Lauren K.; Palumbi, Stephen R.; Voolstra, Christian R.

    2017-01-01

    Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked. PMID:28186132

  15. Bacterial community dynamics are linked to patterns of coral heat tolerance

    NASA Astrophysics Data System (ADS)

    Ziegler, Maren; Seneca, Francois O.; Yum, Lauren K.; Palumbi, Stephen R.; Voolstra, Christian R.

    2017-02-01

    Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked.

  16. 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.

  17. 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

  18. Linking Wildfire and Climate as Drivers of Plant Species and Community-level Change

    NASA Astrophysics Data System (ADS)

    Newingham, B. A.; Hudak, A. T.; Bright, B. C.

    2015-12-01

    Plant species distributions and community shifts after fire are affected by burn severity, elevation, aspect, and climate. However, little empirical data exists on long-term (decadal) recovery after fire across these interacting factors, limiting understanding of fire regime characteristics and climate in post-fire community trajectories. We examined plant species and community responses a decade after fire across five fires in ponderosa pine, dry mixed coniferous, and moist mixed coniferous forests across the western USA. Using field data, we determined changes in plant communities one and ten years post-fire across gradients of burn severity, elevation, and aspect. Existing published work has shown that plant species distributions can be accurately predicted from physiologically relevant climate variables using non-parametric Random Forests models; such models have also been linked to projected climate profiles in 2030, 2060, and 2090 generated from three commonly used general circulation models (GCMs). We explore the possibility that fire and climate are coupled drivers affecting plant species distributions. Climate change may not manifest as a slow shift in plant species distributions, but as sudden, localized events tied to changing fire and other disturbance regimes.

  19. Assessing the Year 1 Effort: A Process Evaluation of Linking Institutional Networks to Community and Kinship Systems.

    ERIC Educational Resources Information Center

    Kelly, Eileen

    Linking Institutional Networks to Community and Kinship Systems (LINCKS) is a three year research and demonstration project undertaken by the Washington, D.C. Parent Child Center, Cardozo High School, and the American Institutes for Research to show how communities can work together to better develop their young parent families. The project's…

  20. Linking participants in school-based sport programs to community clubs.

    PubMed

    Eime, Rochelle M; Payne, Warren R

    2009-03-01

    A decline in youth (12-25 years) participation in sport and physical activity has been reported. School programs that are delivered within schools by external agencies are a key strategy to promote participation in sport and physical activity. It is important that there is a transfer for participants from school-based sport to community opportunities. This study explored the structural links between participation programs conducted in schools and participation in community-based sporting clubs. The study in Victoria, Australia, involved a survey of 49 State Sports Governing Organisations (SSGOs), focus group discussions with 15 representatives from eight of these bodies, in-depth analysis of one school-based sports program that involved the coordinator from the SSGO, three teachers, four parents and one teacher/parent from six participating schools. A majority of SSGOs (59.1%) reported delivering programs within school settings; however they acknowledged that this structure does not represent an efficient or effective way to develop community-level club sports participation and club membership. Facilitators and barriers for transferring participation in school-based sport programs to sustained participation and membership in community club sport are discussed. It is recommended that sports organisations tailor their school-based programs using recognised health promotion planning principles (including community engagement) rather than continuing their current 'one-size-fits-all' approach. This will assist SSGOs and clubs to develop sustainable participation programs and increase club membership. It is recognised that such a change will have significant resource implications due to increased demands on time and human resources.

  1. Two different bacterial community types are linked with the low-methane emission trait in sheep.

    PubMed

    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.

  2. Links Among Warming, Fungal Communities, and Carbon Fluxes in Boreal Forest Ecosystems

    NASA Astrophysics Data System (ADS)

    Allison, S. D.; Czimczik, C. I.; Treseder, K. K.

    2006-12-01

    Microbial responses to climate change could drive positive feedbacks to the carbon cycle, particularly in high latitude ecosystems. We used molecular and enzymatic approaches to determine whether fungal communities changed in response to experimental warming in boreal forest ecosystems. We also measured the flux and 14C signature of soil respiration from warmed and unwarmed soils to link microbial responses with the carbon cycle. In an early-successional site recovering from a 1999 fire, warming significantly increased the activities of cellulose- and chitin-degrading enzymes by 17% and 30%, respectively. In a second site dominated by mature black spruce trees, the activity of the chitin-degrading enzyme declined significantly by 24%. However, warming did not affect soil CO2 fluxes in either site, or the source of soil respiration as measured by 14C isotopic analyses in the mature forest site. Together, these results suggest that warming does alter fungal community composition and potentially carbon substrate utilization. However, the total amount and 14C age of microbially-respired carbon does not change. Despite shifts in fungal community composition, ecosystem processes driven by microbial activity may be resistant to climate warming in these well-drained boreal ecosystems.

  3. 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

  4. 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

  5. Links between the structure of an Antarctic shallow-water community and ice-scour frequency.

    PubMed

    Brown, Kirsty M; Fraser, Keiron P P; Barnes, David K A; Peck, Lloyd S

    2004-09-01

    Ice is a major structuring force in marine and freshwater environments at high latitudes. Although recovery from scouring has been quantified in time, the frequency of scouring in the Antarctic has not. We placed grids of markers at 9-17 m depth at two sites, to study ice-scouring over 2 years at Adelaide island (Antarctic Peninsula). We quantified the time scale of scour frequencies, and linked this to community mortality, age and diversity. Markers were hit from zero to at least three times in 2 years. At the least disturbed site (South Cove) 24% of markers were destroyed per year, whereas in North Cove 60% of markers were destroyed. There were significant differences in scouring frequency between our two sites: a given area in North Cove was on average hit twice as often as one in South Cove. Compared with near shore environments elsewhere, faunas of both sites were characteristic of high disturbance regimes, exhibiting low percent cover, diversity, ages and a high proportion of pioneers. Aspects of the encrusting communities studied reflected the differences between site disturbance regimes. North Cove was scoured twice as often, and bryozoan communities there had half the number of species, two-thirds the space occupation and twice the mortality level of those in South Cove. Maximum age in North Cove bryozoans was also half that in South Cove. Although there are natural disturbance events that rival ice-scouring in either frequency or catastrophic power at lower latitudes, none do both nor across such a wide depth range. We suggest that ice scour effects on polar benthos are even more significant than the same magnitude of disturbance at lower latitudes as recovery rates of high latitude communities are very slow. Climate warming seems likely to increase iceloading of near shore polar waters, so that some of the world's most intensely disturbed faunas may soon suffer even more disturbance.

  6. Circulating biomarkers in renal cell carcinoma: the link between microRNAs and extracellular vesicles, where are we now?

    PubMed Central

    Teixeira, Ana L; Dias, Francisca; Gomes, Mónica; Fernandes, Mara

    2014-01-01

    Renal cell carcinoma (RCC) is a lethal urological cancer, with incidence and mortality rates increasing by 2-3% per decade. The lack of standard screening tests contributes to the fact that one-third of patients are diagnosed with locally invasive or metastatic disease. Moreover, 20-40% of RCC patients submitted to surgical nephrectomy will develop metastasis. MicroRNAs (miRNAs) are small non-coding RNAs responsible for gene regulation at a post-transcriptional level. It is accepted that they are deregulated in cancer and can influence tumor development. Thus, miRNAs are promising RCC biomarkers, since they can be detected using non-invasive methods. They are highly stable and easier to quantify in circulating biofluids. The elevated miRNA stability in circulating samples may be the consequence of their capacity to circulate inside of extracellular microvesicles (EMVs), for example, the exosomes. The EMVs are bilayered membrane vesicles secreted by all cell types. They can be released in the interstitial space or into circulating biofluids, which allows the travelling, binding and entrance of these vesicles in receptor cells. This type of cell communication can shuttle bioactive molecules between cells, allowing the horizontal transference of genetic material. In this review, we focus on circulating miRNAs (miR-210, miR-1233, miR-221, miR-15a, miR-451, miR-508, miR-378) in the biofluids of RCC patients and attempt to establish the diagnostic and prognostic accuracy, their synergic effects, and the pathways involved in RCC biology. PMID:28326253

  7. 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.

  8. 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

  9. 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.

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

    PubMed

    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

    2011-08-23

    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.

  11. 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

  12. The role of volatile metabolites in microbial communities of the lSS higher plant link

    NASA Astrophysics Data System (ADS)

    Tirranen, L. S.; Gitelson, I. I.

    The possibility of controlling the microbial community composition through metabolites produced by microbes has been considered. Basing on the comparative analysis of the experimental data we have revealed the greater contribution of volatile metabolites to microbial interaction than non-volatile. Investigations proved that the interaction between microorganisms through extracted volatile materials is a widespread phenomenon peculiar to many microorganisms. Most cultures inhibited each other's growth, in a number of cases displayed bactericidal action. Stimulatory action occurred 6 - 8 times rarely. The individuality of affect on studied test-cultures growth and the spectrum of microbial resistance to volatile metabolites have been revealed. Based on the comparative cluster analysis of these spectra from 100 studied cultures we have revealed that studied organisms produce a complex of volatile metabolites including 82 inhibiting and 52 stimulating. It was found that excretion of volatile metabolites of studied microorganisms depended upon the culture age, concentration of nutrient medium separate components and volatile by-products excreted by other microorganisms. The production can be increased or decreased by volatile by-products of other microbes. This is related to strain features and the culture age. The prospects of using these regulating metabolites can be defined by the "range", specificity and safety for other members of the microbial community in insufficient concentrations. Volatile metabolites of either plants and microorganisms or other system links - humans and technological equipment installed inside the closed ecosystem - can influence the formation of microbial communities, gas composition of the system atmosphere and state of the plants through the atmosphere. Special experiments showed that volatile microorganism metabolites could accumulate in the environment, dissolve in atmospheric water and maintain their biological activity for many days

  13. 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.

  14. Mass spectrometry assay as an alternative to the enzyme-linked immunosorbent assay test for biomarker quantitation in ecotoxicology: application to vitellogenin in Crustacea (Gammarus fossarum).

    PubMed

    Simon, Romain; Jubeaux, Guillaume; Chaumot, Arnaud; Lemoine, Jérôme; Geffard, Olivier; Salvador, Arnaud

    2010-07-30

    Vitellogenin (Vg) is a widespread biomarker for measuring exposure to endocrine disruptors. Vg quantification is usually done by using the ELISA test (enzyme-linked immunosorbent assay). Since this test is specific to a target protein, it can rarely be used with other species due to low cross-reactivity across species. Therefore alternative analytical methods have to be considered as the development of a specific and sensitive ELISA test for each new target is time-consuming and may prove unsuccessful. This paper focuses on the development of a quantitative assay by liquid chromatography tandem mass spectrometry (LC-MS/MS) of vitelogenin in an invertebrate (Gammarus fossarum) for which no ELISA kit is available. The linearity of the method was within the concentration range 2.5-25,000pg/mL and the limit of detection was estimated at 0.75pg/mL of Vg. This method has been demonstrated to be an alternative to existing immunological methods for quantifying Vg in invertebrates due to its greater sensitivity, specificity and reproducibility (intra- and inter-assay below 15%). This assay was applied for Vg determination in female G. fossarum following exposure to a known endocrine disruptor, methyl farnesoate, in crustaceans. The availability of a quantitative G. fossarum LC-MS/MS assay should open the way for further studies to evaluate xenoestrogen effects in aquatic male G. fossarum.

  15. 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.

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

    PubMed

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

    2016-03-29

    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.

  17. Linking service-learning with community-based participatory research: an interprofessional course for health professional students.

    PubMed

    Marcus, Marianne T; Taylor, Wendell C; Hormann, Mark D; Walker, Thomas; Carroll, Deidra

    2011-01-01

    Service-learning is a valued strategy for educating health professionals. Linking service-learning with community-based participatory research (CBPR) engages students with community stakeholders and faculty in a collaborative process to bring about social change and improved health. The purpose of this paper is to describe a strategy for involving interprofessional students in ongoing faculty CBPR in an underserved community. The process includes the design and implementation of a course that combines weekly seminars with field experiences in the targeted community, emphasizing community assessment, and working with community members to find solutions to health problems. Nursing, public health, and medical students were recruited to the initial course, and offered the opportunity to meet objectives of required components of their disciplinary curriculum. Community members became actively involved in educating students while working to solve identified health problems. Important principles of CBPR--trust, collaboration, excellence in science, and ethics--are emphasized throughout the initiative. This course is now a regular offering for interprofessional students, providing valuable learning experiences for students, faculty, and the community. Ongoing faculty CBPR continues a trusting community-academic relationship and gives the community a voice in the solution for health problems.

  18. 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

  19. Community Services and Continuing Education in the Next Decade: Linking to Institutional Priorities.

    ERIC Educational Resources Information Center

    Myran, Gunder A.

    1989-01-01

    Discusses ways in which community services/continuing education practitioners can strengthen relations with community college presidents by emphasizing institutional and presidential priorities. Considers two options for community services in the coming "instructional effectiveness era": assuming institutional leadership for lifelong…

  20. Association of Cardiometabolic Genes with Arsenic Metabolism Biomarkers in American Indian Communities: The Strong Heart Family Study (SHFS)

    PubMed Central

    Balakrishnan, Poojitha; Vaidya, Dhananjay; Franceschini, Nora; Voruganti, V. Saroja; Gribble, Matthew O.; Haack, Karin; Laston, Sandra; Umans, Jason G.; Francesconi, Kevin A.; Goessler, Walter; North, Kari E.; Lee, Elisa; Yracheta, Joseph; Best, Lyle G.; MacCluer, Jean W.; Kent, Jack; Cole, Shelley A.; Navas-Acien, Ana

    2016-01-01

    VS, Gribble MO, Haack K, Laston S, Umans JG, Francesconi KA, Goessler W, North KE, Lee E, Yracheta J, Best LG, MacCluer JW, Kent J Jr., Cole SA, Navas-Acien A. 2017. Association of cardiometabolic genes with arsenic metabolism biomarkers in American Indian communities: the Strong Heart Family Study (SHFS). Environ Health Perspect 125:15–22; http://dx.doi.org/10.1289/EHP251 PMID:27352405

  1. Connecting the Dots: Progress toward the Integration of School Reform, School-Linked Services, Parent Involvement and Community Schools.

    ERIC Educational Resources Information Center

    Lawson, Hal; Briar-Lawson, Katharine

    This report describes the outcomes of research that investigated school reform, school-linked services, parent involvement, and community school programs in schools in 36 states. Results found that services were often added on to school sites without any intent to integrate them with school reform; teachers were not directly involved in services;…

  2. 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

  3. HUMAN BIOMONITORING TO LINK ENVIRONMENTAL EXPOSURE TO BIOLOGICALLY RELEVANT DOSE

    EPA Science Inventory

    The abstract and presentation on Human Biomonitoring to Link Environmental Exposure to Biologically Relevant Dose describes the use of biomarkers of exposure, biomarkers of current health state, and biomarker measurements. The abstract and presentation focuses on how biomarkers ...

  4. Rural Student Entrepreneurs: Linking Commerce and Community. (Benefits)[Squared]: The Exponential Results of Linking School Improvement and Community Development, Issue Number Three.

    ERIC Educational Resources Information Center

    Boethel, Martha

    In many rural areas, both communities and schools are threatened by decreasing population and changing economic conditions. To boost both the local economy and student achievement, a growing number of rural schools are turning to entrepreneurial education. In school entrepreneurship programs, students create small businesses under the guidance of…

  5. Objectively-Measured Sedentary Time and Cardiometabolic Biomarkers in U.S. Hispanic/Latino Adults: The Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

    PubMed Central

    Qi, Qibin; Strizich, Garrett; Merchant, Gina; Sotres-Alvarez, Daniela; Buelna, Christina; Castañeda, Sheila F.; Gallo, Linda C.; Cai, Jianwen; Gellman, Marc D.; Isasi, Carmen R.; Moncrieft, Ashley E.; Sanchez-Johnsen, Lisa; Schneiderman, Neil; Kaplan, Robert C.

    2015-01-01

    Background Sedentary behavior is recognized as a distinct construct from lack of moderate-vigorous physical activity and is associated with deleterious health outcomes. Previous studies have primarily relied on self-reported data, while data on the relationship between objectively-measured sedentary time and cardiometabolic biomarkers are sparse, especially among U.S. Hispanics/Latinos. Methods and Results We examined associations of objectively-measured sedentary time (via Actical accelerometers for 7 days) and multiple cardiometabolic biomarkers among 12,083 participants, aged 18–74 years, from the Hispanic Community Health Study/Study of Latinos. Hispanics/Latinos of diverse backgrounds (Central American, Cuban, Dominican, Mexican, Puerto Rican, and South American) were recruited from 4 U.S. cities between 2008 and 2011. Sedentary time (<100 counts/minute) was standardized to 16-hour/day of wear time. The mean sedentary time was 11.9 hours/day (74% of accelerometer wear time). After adjustment for moderate-vigorous physical activity and confounding variables, prolonged sedentary time was associated with decreased high-density lipoprotein (HDL)-cholesterol (P=0.04), and increased triglycerides, 2-hour glucose, fasting insulin and HOMA-IR (all P<0.0001). These associations were generally consistent across age, sex, Hispanic/Latino backgrounds, and physical activity levels. Even among individuals meeting physical activity guidelines, sedentary time was detrimentally associated with several cardiometabolic biomarkers (diastolic blood pressure, HDL-cholesterol, fasting and 2-hour glucose, fasting insulin and HOMA-IR; all P<0.05). Conclusions Our large population-based, objectively-derived data showed deleterious associations between sedentary time and cardiometabolic biomarkers, independent of physical activity, in U.S. Hispanics/Latinos. Our findings emphasize the importance of reducing sedentary behavior for the prevention of cardiometabolic diseases, even in

  6. Inflammation biomarkers in blood as mortality predictors in community-acquired pneumonia admitted patients: Importance of comparison with neutrophil count percentage or neutrophil-lymphocyte ratio

    PubMed Central

    Curbelo, Jose; Luquero Bueno, Sergio; Galván-Román, José María; Ortega-Gómez, Mara; Rajas, Olga; Fernández-Jiménez, Guillermo; Vega-Piris, Lorena; Rodríguez-Salvanes, Francisco; Arnalich, Belén; Díaz, Ana; Costa, Ramón; de la Fuente, Hortensia; Lancho, Ángel; Suárez, Carmen; Ancochea, Julio

    2017-01-01

    Introduction The increase and persistence of inflammation in community-acquired pneumonia (CAP) patients can lead to higher mortality. Biomarkers capable of measuring this inadequate inflammatory response are likely candidates to be related with a bad outcome. We investigated the association between concentrations of several inflammatory markers and mortality of CAP patients. Material and methods This was a prospective study of hospitalised CAP patients in a Spanish university hospital. Blood tests upon admittance and in the early-stage evolution (72–120 hours) were carried out, where C-reactive protein, procalcitonin, proadrenomedullin, copeptin, white blood cell, Lymphocyte Count Percentage (LCP), Neutrophil Count Percentage (NCP) and Neutrophil/Lymphocyte Ratio (NLR) were measured. The outcome variable was mortality at 30 and 90 days. Statistical analysis included logistic regression, ROC analysis and area-under-curve test. Results 154 hospitalised CAP patients were included. Patients who died during follow-up had higher levels of procalcitonin, copeptin, proadrenomedullin, lower levels of LCP, and higher of NCP and NLR. Remarkably, multivariate analysis showed a relationship between NCP and mortality, regardless of age, severity of CAP and comorbidities. AUC analysis showed that NLR and NCP at admittance and during early-stage evolution achieved a good diagnostic power. ROC test for NCP and NLR were similar to those of the novel serum biomarkers analysed. Conclusions NLR and NCP, are promising candidate predictors of mortality for hospitalised CAP patients, and both are cheaper, easier to perform, and at least as reliable as the new serum biomarkers. Future implementation of new biomarkers would require comparison not only with classic inflammatory parameters like White Blood Cell count but also with NLR and NCP. PMID:28301543

  7. MicroRNA-19b is a potential biomarker of increased myocardial collagen cross-linking in patients with aortic stenosis and heart failure

    PubMed Central

    Beaumont, Javier; López, Begoña; Ravassa, Susana; Hermida, Nerea; José, Gorka San; Gallego, Idoia; Valencia, Félix; Gómez-Doblas, Juan José; de Teresa, Eduardo; Díez, Javier; González, Arantxa

    2017-01-01

    This study analyzed the potential associations of 7 myocardial fibrosis-related microRNAs with the quality of the collagen network (e.g., the degree of collagen fibril cross-linking or CCL) and the enzyme lysyl oxidase (LOX) responsible for CCL in 28 patients with severe aortic stenosis (AS) of whom 46% had a diagnosis of chronic heart failure (HF). MicroRNA expression was analyzed in myocardial and blood samples. From the studied microRNAs only miR-19b presented a direct correlation (p < 0.05) between serum and myocardium. Compared to controls both myocardial and serum miR-19b were reduced (p < 0.01) in AS patients. In addition, miR-19b was reduced in the myocardium (p < 0.01) and serum (p < 0.05) of patients with HF compared to patients without HF. Myocardial and serum miR-19b were inversely correlated (p < 0.05) with LOX, CCL and LV stiffness in AS patients. In in vitro studies miR-19b inhibition increased (p < 0.05) connective tissue growth factor protein and LOX protein expression in human fibroblasts. In conclusion, decreased miR-19b may be involved in myocardial LOX up-regulation and excessive CCL, and consequently increased LV stiffness in AS patients, namely in those with HF. Serum miR-19b can be a biomarker of these alterations of the myocardial collagen network in AS patients, particularly in patients with HF. PMID:28091585

  8. Urinary Biomarkers KIM-1 and NGAL for Detection of Chronic Kidney Disease of Uncertain Etiology (CKDu) among Agricultural Communities in Sri Lanka

    PubMed Central

    Mohammed Abdul, Khaja Shameem; Eakanayake, Eakanayake M. D. V.; Jayasinghe, Sudheera Sammanthi; Jayasumana, Channa; Asanthi, Hewa Bandulage; Perera, Hettiarachigae S. D.; Chaminda, Gamage G. Tushara; Chandana, Ediriweera P. S.; Siribaddana, Sisira H.

    2016-01-01

    Chronic Kidney Disease of uncertain etiology (CKDu) is an emerging epidemic among farming communities in rural Sri Lanka. Victims do not exhibit common causative factors, however, histopathological studies revealed that CKDu is a tubulointerstitial disease. Urine albumin or albumin-creatinine ratio is still being used as a traditional diagnostic tool to identify CKDu, but accuracy and prevalence data generated are questionable. Urinary biomarkers have been used in similar nephropathy and are widely recognised for their sensitivity, specificity and accuracy in determining CKDu and early renal injury. However, these biomarkers have never been used in diagnosing CKDu in Sri Lanka. Male farmers (n = 1734) were recruited from 4 regions in Sri Lanka i.e. Matara and Nuwara Eliya (farming locations with no CKDu prevalence) and two CKDu emerging locations from Hambantota District in Southern Sri Lanka; Angunakolapelessa (EL1) and Bandagiriya (EL2). Albuminuria (ACR ≥ 30mg/g); serum creatinine based estimation of glomerular filtration rate (eGFR); creatinine normalized urinary kidney injury molecule (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) were measured. Fourteen new CKDu cases (18%) from EL1 and nine CKDu cases (9%) from EL2 were recognized for the first time from EL1, EL2 locations, which were previously considered as non-endemic of the disease and associated with persistent albuminuria (ACR ≥ 30mg/g Cr). No CKDu cases were identified in non-endemic study locations in Matara (CM) and Nuwara Eliya (CN). Analysis of urinary biomarkers showed urinary KIM-1 and NGAL were significantly higher in new CKDu cases in EL1 and EL2. However, we also reported significantly higher KIM-1 and NGAL in apparently healthy farmers in EL 1 and EL 2 with comparison to both control groups. These observations may indicate possible early renal damage in absence of persistent albuminuria and potential capabilities of urinary KIM-1 and NGAL in early detection of renal injury

  9. Urinary Biomarkers KIM-1 and NGAL for Detection of Chronic Kidney Disease of Uncertain Etiology (CKDu) among Agricultural Communities in Sri Lanka.

    PubMed

    De Silva, Pallagae Mangala C S; Mohammed Abdul, Khaja Shameem; Eakanayake, Eakanayake M D V; Jayasinghe, Sudheera Sammanthi; Jayasumana, Channa; Asanthi, Hewa Bandulage; Perera, Hettiarachigae S D; Chaminda, Gamage G Tushara; Chandana, Ediriweera P S; Siribaddana, Sisira H

    2016-09-01

    Chronic Kidney Disease of uncertain etiology (CKDu) is an emerging epidemic among farming communities in rural Sri Lanka. Victims do not exhibit common causative factors, however, histopathological studies revealed that CKDu is a tubulointerstitial disease. Urine albumin or albumin-creatinine ratio is still being used as a traditional diagnostic tool to identify CKDu, but accuracy and prevalence data generated are questionable. Urinary biomarkers have been used in similar nephropathy and are widely recognised for their sensitivity, specificity and accuracy in determining CKDu and early renal injury. However, these biomarkers have never been used in diagnosing CKDu in Sri Lanka. Male farmers (n = 1734) were recruited from 4 regions in Sri Lanka i.e. Matara and Nuwara Eliya (farming locations with no CKDu prevalence) and two CKDu emerging locations from Hambantota District in Southern Sri Lanka; Angunakolapelessa (EL1) and Bandagiriya (EL2). Albuminuria (ACR ≥ 30mg/g); serum creatinine based estimation of glomerular filtration rate (eGFR); creatinine normalized urinary kidney injury molecule (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) were measured. Fourteen new CKDu cases (18%) from EL1 and nine CKDu cases (9%) from EL2 were recognized for the first time from EL1, EL2 locations, which were previously considered as non-endemic of the disease and associated with persistent albuminuria (ACR ≥ 30mg/g Cr). No CKDu cases were identified in non-endemic study locations in Matara (CM) and Nuwara Eliya (CN). Analysis of urinary biomarkers showed urinary KIM-1 and NGAL were significantly higher in new CKDu cases in EL1 and EL2. However, we also reported significantly higher KIM-1 and NGAL in apparently healthy farmers in EL 1 and EL 2 with comparison to both control groups. These observations may indicate possible early renal damage in absence of persistent albuminuria and potential capabilities of urinary KIM-1 and NGAL in early detection of renal injury

  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. Linking leaf veins to growth and mortality rates: an example from a subtropical tree community.

    PubMed

    Iida, Yoshiko; Sun, I-Fang; Price, Charles A; Chen, Chien-Teh; Chen, Zueng-Sang; Chiang, Jyh-Min; Huang, Chun-Lin; Swenson, Nathan G

    2016-09-01

    A fundamental goal in ecology is to link variation in species function to performance, but functional trait-performance investigations have had mixed success. This indicates that less commonly measured functional traits may more clearly elucidate trait-performance relationships. Despite the potential importance of leaf vein traits, which are expected to be related to resource delivery rates and photosynthetic capacity, there are few studies, which examine associations between these traits and demographic performance in communities. Here, we examined the associations between species traits including leaf venation traits and demographic rates (Relative Growth Rate, RGR and mortality) as well as the spatial distributions of traits along soil environment for 54 co-occurring species in a subtropical forest. Size-related changes in demographic rates were estimated using a hierarchical Bayesian approach. Next, Kendall's rank correlations were quantified between traits and estimated demographic rates at a given size and between traits and species-average soil environment. Species with denser venation, smaller areoles, less succulent, or thinner leaves showed higher RGR for a wide range of size classes. Species with leaves of denser veins, larger area, cheaper construction costs or thinner, or low-density wood were associated with high mortality rates only in small size classes. Lastly, contrary to our expectations, acquisitive traits were not related to resource-rich edaphic conditions. This study shows that leaf vein traits are weakly, but significantly related to tree demographic performance together with other species traits. Because leaf traits associated with an acquisitive strategy such as denser venation, less succulence, and thinner leaves showed higher growth rate, but similar leaf traits were not associated with mortality, different pathways may shape species growth and survival. This study suggests that we are still not measuring some of key traits related to

  12. 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.

  13. Bridging the Gap: Linking Co-Curricular Activities to Student Learning Outcomes in Community College Students

    ERIC Educational Resources Information Center

    Storey, Katie Lauren

    2010-01-01

    This study investigated the extent to which participation in co-curricular events enhances the achievement of student-learning outcomes in community college students. One community college in Illinois--Chicago Metropolitan Area Community College (CMACC), a pseudonym--was selected to research based on its robust co-curricular activity programming.…

  14. 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…

  15. 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.

  16. Using biomarkers in wastewater to monitor community drug use: a conceptual approach for dealing with new psychoactive substances.

    PubMed

    Reid, Malcolm J; Baz-Lomba, J A; Ryu, Yeonsuk; Thomas, Kevin V

    2014-07-15

    Data obtained from the analysis of wastewater from large-scale sewage treatment plants has been successfully applied to study trends in the use of classical illicit drugs such as cocaine, but the dynamic nature of the new psychoactive substances (NPS) market presents a unique set of challenges to epidemiologists. In an attempt to overcome some of the challenges, this paper presents a framework whereby a collection of tools and alternative data-sources can be used to support the design and implementation of wastewater-based studies on NPS use. Within this framework the most likely and most suitable biomarkers for a given NPS are predicted via in-silico metabolism, biotransformation and sorption models. Subsequent detection and confirmation of the biomarkers in samples of wastewater are addressed via high-resolution mass spectrometry (HRMS). The proposed framework is applied to a set of test substances including synthetic cannabinoids and cathinones. In general, the in-silico models predict that transformation via N-dealkylation and hydroxylation is likely for these compounds, and that adsorption is expected to be significant for cannabinoids in wastewater. Screening via HRMS is discussed with examples from the literature, and common-fragment searching and mass-defect filtering are successfully performed on test samples such that spectral noise is removed to leave only the information that is most likely to be related to the NPS biomarkers. HRMS screening is also applied to a set of pissoir-sourced wastewater samples and a total of 48 pharmaceuticals and drugs including 1-(2-methoxyphenyl)piperazine (oMeOPP) are identified. The framework outlined in this paper can provide an excellent means of maximizing the chances of success when identifying and detecting biomarkers of NPS in wastewater.

  17. 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

    2014-04-07

    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.

  18. 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

  19. Using Faculty Learning Communities to Link FYE and High-Risk Core Courses: A Pilot Study

    ERIC Educational Resources Information Center

    Cuevas, Mo; Campbell, Kendra; Lowery-Hart, Russell D.; Mallard, Jessica; Andersen, Amy

    2013-01-01

    Can success rates in a gateway course be improved by linking it to a college success course? This article describes the results of a pilot study that linked a first-year biology course that had a high drop-out and failure rate to a college success course that included study skills. The proposal to link courses came from the work of a faculty…

  20. From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks

    PubMed Central

    Cannistraci, Carlo Vittorio; Alanis-Lobato, Gregorio; Ravasi, Timothy

    2013-01-01

    Growth and remodelling impact the network topology of complex systems, yet a general theory explaining how new links arise between existing nodes has been lacking, and little is known about the topological properties that facilitate link-prediction. Here we investigate the extent to which the connectivity evolution of a network might be predicted by mere topological features. We show how a link/community-based strategy triggers substantial prediction improvements because it accounts for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP). We observe that LCP networks are mainly formed by weak interactions and characterise heterogeneous and dynamic systems that use self-organisation as a major adaptation strategy. These systems seem designed for global delivery of information and processing via multiple local modules. Conversely, non-LCP networks have steady architectures formed by strong interactions, and seem designed for systems in which information/energy storage is crucial. PMID:23563395

  1. 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.

  2. 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.

  3. Linking Returning Veterans in Rural Community Colleges to Mental Health Care

    DTIC Science & Technology

    2013-01-01

    that is feasible in the community  college  setting and acceptable to this  student  veteran population and their families.  The survey portion of the...partnership with  student  Veterans and  representatives from these community  colleges .     15. SUBJECT TERMS Community, college , student , depression, PTSD...little has been done to address student veterans’ mental health needs as they reintegrate and attend two-year community colleges . A concurrent challenge

  4. Deep analyses of the associations of a series of biomarkers with insulin resistance, metabolic syndrome, and diabetes risk in nondiabetic middle-aged and elderly individuals: results from a Chinese community-based study

    PubMed Central

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

    2016-01-01

    Objective The current study was designed to perform deep analyses of the associations of biomarkers, including high-sensitivity C-reactive protein (hs-CRP), N-terminal prohormone of brain natriuretic peptide (NT-proBNP), and homocysteine (Hcy), with insulin resistance (IR), metabolic syndrome (MetS), and diabetes risk and evaluate the abilities of biomarkers to identify IR, MetS, and diabetes risk in Chinese community-dwelling middle-aged and elderly residents. Participants and methods A total of 396 participants older than 45 years underwent physical examinations and laboratory analyses following standardized protocol. Results Serum hs-CRP concentrations were able to identify MetS, Chinese diabetes risk score (CDRS) ≥4, high-density lipoprotein-cholesterol (HDL-c) <0.9/1.0 mmol/L, and HDL-c <1.0/1.3 mmol/L (P<0.05 for all). Serum NT-proBNP concentrations were able to identify homeostasis model assessment of IR >1.5, CDRS ≥4, overweight, and blood pressure (BP) ≥140/90 mmHg (P<0.05 for all). Serum Hcy concentrations were able to identify CDRS ≥4, general obesity, overweight, and BP ≥140/90 mmHg (P<0.05 for all). Serum hs-CRP concentrations were independently associated with MetS as well as HDL-c <1.0/1.3 mmol/L and HDL-c <0.9/1.0 mmol/L (P<0.05 for all). Serum NT-proBNP concentrations were independently associated with BP ≥140/90 mmHg (P<0.05). Serum Hcy concentrations were independently associated with CDRS ≥4 (P<0.05). Conclusion Serum HDL-c levels were the major determinant of the associations between serum hs-CRP levels and MetS and the key link between inflammation and MetS. There was no other association of these biomarkers with IR, MetS, and diabetes risk after full adjustment. PMID:27822025

  5. 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

  6. 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…

  7. Linking Community Context to Quality of Parenting: A Study of Rural Families.

    ERIC Educational Resources Information Center

    Simons, Ronald L.; And Others

    1997-01-01

    Iowa study of 207 nonmetropolitan White female-headed families (each a divorced mother, an adolescent in grade 8-9, and a sibling) found that mothers' ineffective parenting styles were related to community disorganization, both directly and indirectly via negative events, lack of social support, and depression. Community disorganization was highly…

  8. 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…

  9. 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?…

  10. Lessons from Linking Community Education and Social-Work Philosophies and Practices.

    ERIC Educational Resources Information Center

    Ward, Carolyn M. Siemens

    2001-01-01

    Both community education and social work from a settlement house perspective focus on empowerment, problem solving, and increasing participation in lifelong learning. Both fields debate narrow versus broader methods. Collaborative university-community approaches show how their combined philosophies and practices offer reform possibilities. (SK)

  11. 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...

  12. 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...

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

    PubMed

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

    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.

  14. 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…

  15. 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…

  16. 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.

  17. 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

  18. Advanced primary care in San Antonio: linking practice and community strategies to improve health.

    PubMed

    Ferrer, Robert L; Gonzalez Schlenker, Carolina; Lozano Romero, Raquel; Poursani, Ramin; Bazaldua, Oralia; Davidson, DeWayne; Ann Gonzales, Melissa; Dehoyos, Janie; Castilla, Martha; Corona, Betty A; Tysinger, James; Alsip, Bryan; Trejo, Jonathan; Jaén, Carlos Roberto

    2013-01-01

    Improving health among people living in poverty often transcends narrowly focused illness care. Meaningful success is unlikely without confronting the complex social origins of illness. We describe an emerging community of solution to improve health outcomes for a population of 6000 San Antonio, Texas, residents enrolled in a county health care program. The community of solution comprises a county health system, a family medicine residency program, a metropolitan public health department, and local nonprofit organizations and businesses. Community-based activities responding to the needs of individuals and their neighborhoods are driven by a cohort of promotores (community health workers) whose mission encompasses change at both the individual and community levels. Centered on patients' functional goals, promotores mobilize family and community resources and consider what community-level action will address the social determinants of health. On the clinical side, care teams implement population-based risk assessment and nurse care management with a focus on care transitions as well as other measures to meet the needs of patients with high morbidity and high use of health care. Population-based outcome metrics include reductions in hospitalizations, emergency department and urgent care visits, and the associated charges. Promotores also assess patients' progress along the trajectory of their selected functional goals.

  19. Psychological symptoms linking exposure to community violence and academic functioning in African American adolescents.

    PubMed

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

    2013-02-01

    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 community violence and academic functioning, and if the indirect effects of community violence on academic functioning differed for boys and girls, in a community sample of urban African American adolescents (N = 491; 46.6 % female). Structural equation modeling was used to examine the indirect effect of exposure to community violence in grade 6 on grade 8 academic functioning. Results revealed that aggression in grade 7 mediated the association between grade 6 exposure to community violence and grade 8 academic functioning. There were no indirect effects through depressive and anxious symptoms, and gender did not moderate the indirect effect. Findings highlight the importance of targeting aggressive behavior for youth exposed to community violence to not only improve their behavioral adjustment but also their academic functioning. Implications for future research are discussed.

  20. 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.

  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 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)

  3. 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

  4. Predator community composition is linked to soil carbon retention across a human land use gradient.

    PubMed

    Schmitz, Oswald J; Buchkowski, Robert W; Smith, Jeffrey R; Telthorst, Mark; Rosenblatt, Adam E

    2017-03-08

    Soil carbon (C) storage is a major component of the carbon cycle. Consensus holds that soil C uptake and storage is regulated by plant-microbe-soil interactions. However, the contribution of animals in aboveground food webs to this process has been overlooked. Using insights from prior long-term experimentation in an old-field ecosystem and mathematical modeling, we predicted that the amount of soil C retention within a field should increase with the proportion of active hunting predators comprising the aboveground community of active hunting and sit-and-wait predators. This comes about because predators with different hunting modes have different cascading effects on plants. Our test of the prediction revealed that the composition of the arthropod predator community and associated cascading effects on the plant community explained 41% of variation in soil C retention among 15 old-fields across a human land use gradient. We also evaluated the potential for several other candidate factors to explain variation in soil C retention among fields, independent of among-field variation in the predator community. These included live plant biomass, insect herbivore community composition, soil arthropod decomposer community composition, degree of land use development around the fields, field age, and soil texture. None of these candidate variables significantly explained soil C retention among the fields. The study offers a generalizable understanding of the pathways through which arthropod predator community composition can contribute to old-field ecosystem carbon storage. This insight helps support ongoing efforts to understand and manage the effects of anthropogenic land use change on soil C storage. This article is protected by copyright. All rights reserved.

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

    PubMed Central

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

    2012-01-01

    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

  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.

  7. Linking plant communities on land and at sea: The effects of Posidonia oceanica wrack on the structure of dune vegetation

    NASA Astrophysics Data System (ADS)

    Del Vecchio, Silvia; Jucker, Tommaso; Carboni, Marta; Acosta, Alicia T. R.

    2017-01-01

    Although terrestrial and marine ecosystems are often perceived as clearly distinct, in coastal areas biological communities on land and at sea are in fact intimately linked. One way in which terrestrial and marine systems interact is through the accumulation of seagrass wrack on beaches, which plays an important role as a nutrient input in coastal dune food webs. Here we test whether accumulated beach-cast wrack also influences the structure and diversity of coastal dune plant communities. Relying on a database of 572 vegetation surveys distributed across the island of Sardinia, we used mixed-effects models to compare the vegetation cover and species richness of plant communities exposed to different amounts of Posidonia oceanica beach-cast wrack. We found that beaches which receive high amounts of P. oceanica wrack have considerably greater vegetation cover (10% on average) than those with fewer deposits. The positive relationship between beach-cast wrack and vegetation cover was especially strong in nearshore plant communities, becoming progressively weaker along the habitat zonation. A similar pattern was found for species richness: beaches with high levels of accumulated wrack had more diverse drift line and foredune plant communities, while habitats further away from the shoreline were unaffected. Our study is the first to present evidence suggesting that activities which reduce wrack accumulation on beaches - either through direct removal of deposits or by causing P. oceanica seabeds to decline - can have effects on both the structure and diversity of coastal dune plant communities. Effective management of Mediterranean coastal dune ecosystems will require developing clear strategies for the removal and relocation of accumulated beach-cast wrack.

  8. Lost in translation: the question of evidence linking community-based arts and health promotion.

    PubMed

    Putland, Christine

    2008-03-01

    Reflecting a wider preoccupation with 'evidence-based-policy', the effectiveness of community-based arts practice designed to promote individual and community level health and well-being is in the spotlight. Evidence is said to remain elusive despite the proliferation of initiatives and government investment. Responses to this issue can broadly be characterized as health perspectives (calling for more scientific approaches to evaluation research that go beyond anecdote and opinion) and arts perspectives (concerned about reductive measures and narrowly prescribed social outcomes). This article seeks to advance an intersectoral dialogue by highlighting the tensions within present approaches and canvassing alternative frameworks.

  9. Service-Learning Linking Family Child Care Providers, Community Partners, and Preservice Professionals

    ERIC Educational Resources Information Center

    Garner, Pamela W.; Parker, Tameka S.

    2016-01-01

    This article describes the implementation of a service-learning project, which was infused into a child development course. The project linked family child care providers, their licensing agency, and 39 preservice teachers in a joint effort to develop a parent handbook to be used by the providers in their child care businesses and to support…

  10. 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…

  11. 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…

  12. 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…

  13. Louisiana's Ventilator Assisted Care Program: Case Management Services to Link Tertiary with Community-Based Care.

    ERIC Educational Resources Information Center

    Kirkhart, Kathryn A.; And Others

    1988-01-01

    The Ventilator Assisted Care Program provides centralized case management services to ventilator-using youths and their families in Louisiana. Case managers develop individualized, comprehensive plans to be implemented locally using community resources; plans are based on needs identified by tertiary care providers and family members and are…

  14. 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…

  15. A Blended Faculty Community of Inquiry: Linking Leadership, Course Redesign, and Evaluation

    ERIC Educational Resources Information Center

    Vaughan, Norman; Garrison, Randy

    2006-01-01

    This article describes an institutional course redesign initiative in terms of leadership, support, and preliminary findings, based on the Inquiry Through Blended Learning (ITBL) program created to support faculty engaging in blended course redesign. Garrison, Anderson, and Archer's (2000) Community of Inquiry framework has been adapted to a…

  16. 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…

  17. 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…

  18. 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…

  19. 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...

  20. 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…

  1. 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.

  2. 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.…

  3. 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…

  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. 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.

  6. Linking Educators' Professional Development to Workplace/Community Learning Experiences. TeachNET Educational Brief.

    ERIC Educational Resources Information Center

    Sargent, Thomas A.

    Mindful of the need for quality professional development and its characteristics, large numbers of educators are self-selecting to participate in workplace/community learning (WCL) experiences. Viewed as an alternative to less desirable forms of traditional professional development, WCL displays characteristics of high-quality professional…

  7. Linking molecular biomarkers with higher level condition indicators to identify effects of copper exposures on the endangered delta smelt (Hypomesus transpacificus).

    PubMed

    Connon, Richard E; Beggel, Sebastian; D'Abronzo, Leandro S; Geist, Juergen P; Pfeiff, Janice; Loguinov, Alexander V; Vulpe, Christopher D; Werner, Inge

    2011-02-01

    The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin estuary (CA, USA), and considered an indicator of ecosystem health. Copper is a contaminant of concern in Californian waterways that may affect the development and survival of this endangered species. The experimental combination of molecular biomarkers with higher level effects may allow for interpretation of responses in a functional context that can be used to predict detrimental outcomes caused by exposure. A delta smelt microarray was developed and applied to screen for candidate molecular biomarkers that may be used in monitoring programs. Functional classifications of microarray responses were used along with quantitative polymerase chain reaction determining effects upon neuromuscular, digestive, and immune responses in Cu-exposed delta smelt. Differences in sensitivity were measured between juveniles and larvae (median lethal concentration = 25.2 and 80.4 µg/L Cu(2+), respectively). Swimming velocity declined with higher exposure concentrations in a dose-dependent manner (r =  -0.911, p < 0.05), though was not statistically significant to controls. Genes encoding for aspartoacylase, hemopexin, α-actin, and calcium regulation proteins were significantly affected by exposure and were functionally interpreted with measured swimming responses. Effects on digestion were measured by upregulation of chitinase and downregulation of amylase, whereas downregulation of tumor necrosis factor indicated a probable compromised immune system. Results from this study, and many others, support the use of functionally characterized molecular biomarkers to assess effects of contaminants in field scenarios. We thus propose that to attribute environmental relevance to molecular biomarkers, research should concentrate on their application in field studies with the aim of assisting monitoring programs.

  8. Associations between dietary patterns and flow cytometry-measured biomarkers of inflammation and cellular activation in the Atherosclerosis Risk in Communities (ARIC) Carotid Artery MRI Study

    PubMed Central

    Nettleton, Jennifer A.; Matijevic, Nena; Follis, Jack L.; Folsom, Aaron R.; Boerwinkle, Eric

    2010-01-01

    Background Specific foods and overall dietary patterns are associated with soluble biomarkers of systemic inflammation and endothelial activation. However, no large epidemiological studies have evaluated relationships between such dietary factors and cell-specific markers of activation and inflammation as measured by flow cytometry. Methods Cell aggregates and multiple platelet and leukocyte markers were quantified by flow cytometry in fresh whole blood from 1,101 white adults participating in the Carotid Artery MRI study, a subset of the larger Atherosclerosis Risk in Communities (ARIC) study. Two dietary patterns (“Healthy” and “Western”) were empirically-derived via principal components analysis using data collected by food frequency questionnaire. Cross-sectional associations between dietary patterns and flow cytometry-measured biomarkers were evaluated, adjusting for demographics and lifestyle factors, including medications use. Results After multivariable adjustment, monocyte lipopolysaccharide receptor (CD14), monocyte toll-like receptor-2, and platelet glycoprotein IIb (CD41) showed inverse associations with the Healthy dietary pattern (p = 0.01, 0.04, and 0.01, respectively). In contrast, the Western dietary pattern was positively associated with CD41 and platelet-granulocyte aggregates (p = 0.01 and 0.04, respectively). Independent of other dietary factors, alcohol consumption was inversely associated with levels of pan leukocyte marker (CD45), P-selectin (CD62P) on PLA1 and on PLA2 platelets, and platelet-monocyte, platelet-granulocyte, and platelet-lymphocyte aggregates. Conclusion Dietary patterns and alcohol intake were each cross-sectionally associated with select markers of cellular activation and inflammation measured by flow cytometry. These data are consistent with the hypothesis that holistic measures of dietary intake are associated with inflammation. PMID:20537646

  9. The Mediating Role of Social Support in the Community Environment--Psychological Distress Link among Low-Income African American Women

    ERIC Educational Resources Information Center

    Lin, Jielu; Thompson, Martie P.; Kaslow, Nadine J.

    2009-01-01

    Living in a disordered community is negatively associated with psychological well-being. We investigated the role of social support in the link between community environment and psychological distress in a sample of 152 African American women from low socioeconomic backgrounds in a large metropolitan southeastern city. Structural equation modeling…

  10. A thready affair: linking fungal diversity and community dynamics to terrestrial decomposition processes.

    PubMed

    van der Wal, Annemieke; Geydan, Thomas D; Kuyper, Thomas W; de Boer, Wietse

    2013-07-01

    Filamentous fungi are critical to the decomposition of terrestrial organic matter and, consequently, in the global carbon cycle. In particular, their contribution to degradation of recalcitrant lignocellulose complexes has been widely studied. In this review, we focus on the functioning of terrestrial fungal decomposers and examine the factors that affect their activities and community dynamics. In relation to this, impacts of global warming and increased N deposition are discussed. We also address the contribution of fungal decomposer studies to the development of general community ecological concepts such as diversity-functioning relationships, succession, priority effects and home-field advantage. Finally, we indicate several research directions that will lead to a more complete understanding of the ecological roles of terrestrial decomposer fungi such as their importance in turnover of rhizodeposits, the consequences of interactions with other organisms and niche differentiation.

  11. Linking Community Hospital Initiatives With Osteopathic Medical Students' Quality Improvement Training: A Pilot Program.

    PubMed

    Brannan, Grace D; Russ, Ronald; Winemiller, Terry R; Mast, Eric

    2016-01-01

    Quality improvement (QI) continues to be a health care challenge, and the literature indicates that osteopathic medical students need more training. To qualify for portions of managed care reimbursement, hospitals are required to meet measures intended to improve quality of care and patient satisfaction, which may be challenging for small community hospitals with limited resources. Because osteopathic medical training is grounded on community hospital experiences, an opportunity exists to align the outcomes needs of hospitals and QI training needs of students. In this pilot program, 3 sponsoring hospitals recruited and mentored 1 osteopathic medical student each through a QI project. A mentor at each hospital identified a project that was important to the hospital's patient care QI goals. This pilot program provided osteopathic medical students with hands-on QI training, created opportunities for interprofessional collaboration, and contributed to hospital initiatives to improve patient outcomes.

  12. 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,…

  13. 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

  14. Linking Returning Veterans in Rural Community Colleges to Mental Health Care

    DTIC Science & Technology

    2015-01-01

    focus groups are ongoing. Analyses from the survey indicate that psychiatric distress is prevalent in the sample of veterans: 32% depression , 23...Community, college, student, depression , PTSD, mental health 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 51 19a...pursuits, and educational activities, a significant percentage have difficulty because they suffer with TBI, PTSD, depression , and substance misuse and do

  15. 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

  16. 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.

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

    PubMed Central

    Emiliani, Giovanni; 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

  18. 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

  19. Linking river flow regimes to riparian plant guilds: a community-wide modeling approach.

    PubMed

    Lytle, David A; Merritt, David M; Tonkin, Jonathan D; Olden, Julian D; Reynolds, Lindsay V

    2017-03-06

    Modeling riparian plant dynamics along rivers is complicated by the fact that plants have different edaphic and hydrologic requirements at different life-stages. With intensifying human demands for water and continued human alteration of rivers, there is a growing need for predicting responses of vegetation to flow alteration, including responses related to climate change and river flow management. We developed a coupled structured population model that coombines stage-specific responses of plant guilds with specific attributes of river hydrologic regime. The model uses information on the vital rates of guilds as they relate to different hydrologic conditions (flood, drought, and baseflow), but deliberately omits biotic interactions from the structure ("interaction neutral"). Our intent was to: 1) consolidate key vital rates concerning plant population dynamics and to incorporate these data into a quantitative framework, 2) determine whether complex plant stand dynamics, including biotic interactions, can be predicted from basic vital rates and river hydrology, and 3) project how altered flow regimes might affect riparian communities. We illustrated the approach using five flow-response guilds that encompass much of the river floodplain community: hydroriparian tree, xeroriparian shrub, hydroriparian shrub, mesoriparian meadow, and desert shrub. We also developed novel network-based tools for predicting community-wide effects of climate-driven shifts and deliberately altered flow regimes. The model recovered known patterns of hydroriparian tree vs. xeroriparian shrub dominance, including the relative proportion of these two guilds as a function of river flow modification. By simulating flow alteration scenarios ranging from increased drought to shifts in flood timing, the model predicted that mature hydroriparian forest should be most abundant near the observed natural flow regime. Multiguild sensitivity analysis identified substantial network connectivity (many

  20. 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

  1. 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

  2. Hospital and Community Ampicillin-Resistant Enterococcus faecium Are Evolutionarily Closely Linked but Have Diversified through Niche Adaptation

    PubMed Central

    de Regt, Marieke J. A.; van Schaik, Willem; van Luit-Asbroek, Miranda; Dekker, Huberta A. T.; van Duijkeren, Engeline; Koning, Catherina J. M.; Bonten, Marc J. M.; Willems, Rob J. L.

    2012-01-01

    Background Ampicillin-resistant Enterococcus faecium (ARE) has emerged as a nosocomial pathogen. Here, we quantified ARE carriage in different community sources and determined genetic relatedness with hospital ARE. Methods and Results ARE was recovered from rectal swabs of 24 of 79 (30%) dogs, 11 of 85 (13%) cats and 0 of 42 horses and from 3 of 40 (8%) faecal samples of non-hospitalized humans receiving amoxicillin. Multi-locus Sequence Typing revealed 21 sequence types (STs), including 5 STs frequently associated with hospital-acquired infections. Genes previously found to be enriched in hospital ARE, such as IS16, orf903, orf905, orf907, were highly prevalent in community ARE (≥79%), while genes with a proposed role in pathogenesis, such as esp, hyl and ecbA, were found rarely (≤5%) in community isolates. Comparative genome analysis of 2 representative dog isolates revealed that the dog strain of ST192 was evolutionarily closely linked to two previously sequenced hospital ARE, but had, based on gene content, more genes in common with the other, evolutionarily more distantly related, dog strain (ST266). Conclusion ARE were detected in dogs, cats and sporadically in healthy humans, with evolutionary linkage to hospital ARE. Yet, their accessory genome has diversified, probably as a result of niche adaptation. PMID:22363425

  3. Linking Climate Change Science and Adaptation Policy at the Community Scale through Anticipatory Governance: A Review of Concepts with Application to Arizona Communities (Invited)

    NASA Astrophysics Data System (ADS)

    White, D. D.; Quay, R.; Ferguson, D. B.; Buizer, J. L.; Guido, Z.; Chhetri, N.

    2013-12-01

    Scientific consensus and certainty varies regarding the link between climate change, specific natural hazards and extreme events, and local and regional impacts. Despite these uncertainties, it is necessary to apply the best available scientific knowledge to anticipate a range of possible futures, develop mitigation and adaptation strategies, and monitor changes to build resilience. While there is widespread recognition of the need to improve the linkages between climate science information and public policy for adaptation at the community scale, there are significant challenges to this goal. Many community outreach and engagement efforts, for instance, operate using a one-size-fits-all approach. Recent research has shown this to be problematic for local governments. Public policy occurs in a cycle that includes problem understanding, planning and policy approval, and implementation, with ongoing policy refinement through multiple such cycles. One promising approach to incorporating scientific knowledge with uncertainty into public policy is an anticipatory governance approach. Anticipatory governance employs a continual cycle of anticipation (understanding), planning, monitoring, and adaptation (policy choice and implementation). The types of information needed in each of these phases will be different given the nature of each activity and the unique needs of each community. It is highly unlikely that all local governments will be in the same phase of climate adaptation with the same unique needs at the same time and thus a uniform approach to providing scientific information will only be effective for a discrete group of communities at any given point in time. A key concept for the effective integration of scientific information into public discourse is that such information must be salient, credible, and legitimate. Assuming a scientific institution has established credibility with engaged communities, maximizing the effectiveness of climate science requires

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. Dimensions of Oppositionality in a Brazilian Community Sample: Testing the DSM-5 Proposal and Etiological Links

    PubMed Central

    Krieger, Fernanda Valle; Polanczyk, Guilherme Vanoni; Goodman, Robert; Rohde, Luis Augusto; Graeff-Martins, Ana Soledade; Salum, Giovanni; Gadelha, Ary; Pan, Pedro; Stahl, Daniel; Stringaris, Argyris

    2013-01-01

    Objective Investigating dimensions of oppositional symptoms may help to explain heterogeneity of etiology and outcomes for mental disorders across development and provide further empirical justification for the DSM-5–proposed modifications of oppositional defiant disorder (ODD). However, dimensions of oppositionality have not previously been tested in samples outside Europe or the United States. In this study, we used a large Brazilian community sample to compare the fit of different models for dimensions of oppositional symptoms; to examine the association of psychiatric diagnoses and symptoms with dimensions of oppositionality; and to examine the associations between dimensions of oppositionality and parental history of mental disorders. Method A Brazilian community sample of 2,512 children 6 through 12 years old were investigated in this study. Confirmatory factorial analyses were performed to compare the fit of alternative models, followed by linear and logistic regression analyses of associations with psychiatric diagnosis and parental history of psychopathology. Results A three-factor model with irritable, headstrong, and hurtful dimensions fitted best. The irritable dimension showed a strong association with emotional disorders in the child (p<.001) and history of depression (p<.01) and suicidality (p<.05) in the mother. The headstrong dimension was uniquely associated with attention-deficit/hyperactivity disorder (ADHD) in the child (p<.001) and with maternal history of ADHD symptoms (p<.05). The hurtful dimension was specifically associated with conduct disorder (p< .05). Conclusions Our findings from a large community sample of Brazilian children support a distinction between dimensions of oppositionality consistent with current DSM-5 recommendations and provide further evidence for etiological distinctions between these dimensions. PMID:23582870

  9. 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

  10. [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.

  11. Phenotypic constraints and community structure: linking trade-offs within and among species.

    PubMed

    Angert, Amy L; Kimball, Sarah; Peterson, Megan; Huxman, Travis E; Venable, David L

    2014-11-01

    Trade-offs are central to many topics in biology, from the evolution of life histories to ecological mechanisms of species coexistence. Trade-offs observed among species may reflect pervasive constraints on phenotypes that are achievable given biophysical and resource limitations. If so, then among-species trade-offs should be consistent with trade-offs within species. Alternatively, trait variation among co-occurring species may reflect historical contingencies during community assembly rather than within-species constraints. Here, we test whether a key trade-off between relative growth rate (RGR) and water-use efficiency (WUE) among Sonoran Desert winter annual plants is apparent within four species representing different strategies in the system. We grew progeny of maternal families from multiple populations in a greenhouse common garden. One species, Pectocarya recurvata, displayed the expected RGR-WUE trade-off among families within populations. For other species, although RGR and WUE often varied clinally among populations, among-family variation within populations was lacking, implicating a role for past selection on these traits. Our results suggest that a combination of limited genetic variation in single traits and negative trait correlations could pose constraints on the evolution of a high-RGR and high-WUE phenotype within species, providing a microevolutionary explanation for phenotypes that influence community-level patterns of abundance and coexistence.

  12. 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.

  13. Community-based carbon sequestration in East Africa: Linking science and sustainability

    NASA Astrophysics Data System (ADS)

    Hultman, N. E.

    2004-12-01

    International agreements on climate change have set the stage for an expanding market for greenhouse gas emissions reduction credits. Projects that can generate credits for trading are diverse, but one of the more controversial types involve biological carbon sequestration. For several reasons, most of the activity on these "sinks" projects has been in Latin America and Southeast Asia. Yet people in sub-saharan Africa could benefit from properly implemented projects. This poster will discuss estimates of the potential and risks of such projects in East Africa, and will describe in detail a case study located in central Tanzania and now part of the World Bank's BioCarbon Fund portfolio. Understanding climate variability and risk can effectively link international agreements on climate change, local realities of individual projects, and the characteristics of targeted ecosystems.

  14. Diabetes Connect: Developing a Mobile Health Intervention to Link Diabetes Community Health Workers with Primary Care

    PubMed Central

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

    2016-01-01

    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 healthcare 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

  15. 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

  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. 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

  18. 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.

  19. A tale of two chitons: is habitat specialisation linked to distinct associated bacterial communities?

    PubMed

    Duperron, Sébastien; Pottier, Marie-Anne; Léger, Nelly; Gaudron, Sylvie M; Puillandre, Nicolas; Le Prieur, Stéphanie; Sigwart, Julia D; Ravaux, Juliette; Zbinden, Magali

    2013-03-01

    Although most chitons (Mollusca: Polyplacophora) are shallow-water molluscs, diverse species also occur in deep-sea habitats. We investigated the feeding strategies of two species, Leptochiton boucheti and Nierstraszella lineata, recovered on sunken wood sampled in the western Pacific, close to the Vanuatu Islands. The two species display distinctly different associations with bacterial partners. Leptochiton boucheti harbours Mollicutes in regions of its gut epithelium and has no abundant bacterium associated with its gill. Nierstraszella lineata displays no dense gut-associated bacteria, but harbours bacterial filaments attached to its gill epithelium, related to the Deltaproteobacteria symbionts found in gills of the wood-eating limpet Pectinodonta sp. Stable carbon and nitrogen isotope signatures and an absence of cellulolytic activity give evidence against a direct wood-feeding diet; both species are secondary consumers within the wood food web. We suggest that the distinct associations with bacterial partners are linked to niche specialisations of the two species. Nierstraszella lineata is in a taxonomic family restricted to sunken wood and is possibly adapted to more anoxic conditions thanks to its gill-associated bacteria. Leptochiton boucheti is phylogenetically more proximate to an ancestral form not specialised on wood and may itself be more of a generalist; this observation is congruent with its association with Mollicutes, a bacterial clade comprising gut-associated bacteria occurring in several metazoan phyla.

  20. Community Theories of Change: Linking Environmental Justice to Sustainability through Stakeholder Perceptions in Milwaukee (WI, USA)

    PubMed Central

    Hornik, Kaitlyn; Cutts, Bethany; Greenlee, Andrew

    2016-01-01

    Environmental justice and sustainability are compatible lenses, yet action toward equity is often missing from urban sustainability initiatives. This study aims to assess the cohesion of these frameworks in practice. To do this, we parse individuals’ theories of change, or how they identify and propose to resolve environmental injustices in the pursuit of sustainability. We posit that these theories of change are comprised of three main components: (1) perceived environmental benefits and burdens; (2) the causal pathways of environmental and social injustice; and (3) visions for positive change. Drawing from 35 stakeholder interviews in Milwaukee (WI, USA) we examine individual and institutional perspectives on environmental and social change and their links to the production of injustice. Our findings reveal that participants do not distinguish between environmental and social injustices. Instead, both social and environmental factors are implicated in injustice. Furthermore, we identify two mental maps for how social and economic change reproduce injustice. These findings suggest the need to reorient how urban injustice is considered and make efforts to acknowledge how a diversity of operational theories of change could either be divisive or could bring environmental justice and sustainability initiatives together. PMID:27706068

  1. Community Theories of Change: Linking Environmental Justice to Sustainability through Stakeholder Perceptions in Milwaukee, (WI, USA).

    PubMed

    Hornik, Kaitlyn; Cutts, Bethany; Greenlee, Andrew

    2016-09-30

    Environmental justice and sustainability are compatible lenses, yet action toward equity is often missing from urban sustainability initiatives. This study aims to assess the cohesion of these frameworks in practice. To do this, we parse individuals' theories of change, or how they identify and propose to resolve environmental injustices in the pursuit of sustainability. We posit that these theories of change are comprised of three main components: (1) perceived environmental benefits and burdens; (2) the causal pathways of environmental and social injustice; and (3) visions for positive change. Drawing from 35 stakeholder interviews in Milwaukee (WI, USA) we examine individual and institutional perspectives on environmental and social change and their links to the production of injustice. Our findings reveal that participants do not distinguish between environmental and social injustices. Instead, both social and environmental factors are implicated in injustice. Furthermore, we identify two mental maps for how social and economic change reproduce injustice. These findings suggest the need to reorient how urban injustice is considered and make efforts to acknowledge how a diversity of operational theories of change could either be divisive or could bring environmental justice and sustainability initiatives together.

  2. 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

  3. Linking internal and external bacterial community control gives mechanistic framework for pelagic virus‐to‐bacteria ratios

    PubMed Central

    Pree, Bernadette; Thingstad, T. Frede

    2016-01-01

    Summary For more than 25 years, virus‐to‐bacteria ratios (VBR) have been measured and interpreted as indicators of the importance of viruses in aquatic ecosystems, yet a generally accepted theory for understanding mechanisms controlling VBR is still lacking. Assuming that the denominator (total bacterial abundance) is primarily predator controlled, while viral lysis compensates for host growth rates exceeding this grazing loss, the numerator (viral abundance) reflects activity differences between prokaryotic hosts. VBR is then a ratio between mechanisms generating structure within the bacterial community and interactions between different plankton functional types controlling bacterial community size. We here show how these arguments can be formalized by combining a recently published model for co‐evolutionary host‐virus interactions, with a previously published “minimum” model for the microbial food web. The result is a framework where viral lysis links bacterial diversity to microbial food web structure and function, creating relationships between different levels of organization that are strongly modified by organism‐level properties such as cost of resistance. PMID:27231817

  4. 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.

  5. 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

  6. Building Capacity for Earthquake Monitoring: Linking Regional Networks with the Global Community

    NASA Astrophysics Data System (ADS)

    Willemann, R. J.; Lerner-Lam, A.

    2006-12-01

    Installing or upgrading a seismic monitoring network is often among the mitigation efforts after earthquake disasters, and this is happening in response to the events both in Sumatra during December 2004 and in Pakistan during October 2005. These networks can yield improved hazard assessment, more resilient buildings where they are most needed, and emergency relief directed more quickly to the worst hit areas after the next large earthquake. Several commercial organizations are well prepared for the fleeting opportunity to provide the instruments that comprise a seismic network, including sensors, data loggers, telemetry stations, and the computers and software required for the network center. But seismic monitoring requires more than hardware and software, no matter how advanced. A well-trained staff is required to select appropriate and mutually compatible components, install and maintain telemetered stations, manage and archive data, and perform the analyses that actually yield the intended benefits. Monitoring is more effective when network operators cooperate with a larger community through free and open exchange of data, sharing information about working practices, and international collaboration in research. As an academic consortium, a facility operator and a founding member of the International Federation of Digital Seismographic Networks, IRIS has access to a broad range of expertise with the skills that are required to help design, install, and operate a seismic network and earthquake analysis center, and stimulate the core training for the professional teams required to establish and maintain these facilities. But delivering expertise quickly when and where it is unexpectedly in demand requires advance planning and coordination in order to respond to the needs of organizations that are building a seismic network, either with tight time constraints imposed by the budget cycles of aid agencies following a disastrous earthquake, or as part of more informed

  7. 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

  8. 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

  9. 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

  10. 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…

  11. Applying recovery biomarkers to calibrate self-report measures of sodium and potassium in the Hispanic Community Health Study/Study of Latinos.

    PubMed

    Mossavar-Rahmani, Y; Sotres-Alvarez, D; Wong, W W; Loria, C M; Gellman, M D; Van Horn, L; Alderman, M H; Beasley, J M; Lora, C M; Siega-Riz, A M; Kaplan, R C; Shaw, P A

    2017-02-16

    Measurement error in assessment of sodium and potassium intake obscures associations with health outcomes. The level of this error in a diverse US Hispanic/Latino population is unknown. We investigated the measurement error in self-reported dietary intake of sodium and potassium and examined differences by background (Central American, Cuban, Dominican, Mexican, Puerto Rican and South American). In 2010-2012, we studied 447 participants aged 18-74 years from four communities (Miami, Bronx, Chicago and San Diego), obtaining objective 24-h urinary sodium and potassium excretion measures. Self-report was captured from two interviewer-administered 24-h dietary recalls. Twenty percent of the sample repeated the study. We examined bias in self-reported sodium and potassium from diet and the association of mismeasurement with participant characteristics. Linear regression relating self-report with objective measures was used to develop calibration equations. Self-report underestimated sodium intake by 19.8% and 20.8% and potassium intake by 1.3% and 4.6% in men and women, respectively. Sodium intake underestimation varied by Hispanic/Latino background (P<0.05) and was associated with higher body mass index (BMI). Potassium intake underestimation was associated with higher BMI, lower restaurant score (indicating lower consumption of foods prepared away from home and/or eaten outside the home) and supplement use. The R(2) was 19.7% and 25.0% for the sodium and potassium calibration models, respectively, increasing to 59.5 and 61.7% after adjusting for within-person variability in each biomarker. These calibration equations, corrected for subject-specific reporting error, have the potential to reduce bias in diet-disease associations within this largest cohort of Hispanics in the United States.Journal of Human Hypertension advance online publication, 16 February 2017; doi:10.1038/jhh.2016.98.

  12. 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

  13. 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.

  14. 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

  15. Biomarkers in pediatrics: children as biomarker orphans.

    PubMed

    Savage, William J; Everett, Allen D

    2010-12-01

    Biomarkers have enormous potential to improve patient care by establishing tests of diagnosis, prognosis, and treatment effects. Successfully translating a biomarker from discovery to clinical application demands high-quality discovery research and high-quality clinical studies for biomarker validation; however, there are additional challenges that face biomarker research in pediatrics. There are also additional characteristics of pediatric medicine that make biomarker research especially needed. This review focuses on the fundamentals of biomarkers, the additional considerations needed for applying biomarker research to children, and recommendations for advancing pediatric biomarker research.

  16. Analysis of bacterial core communities in the central Baltic by comparative RNA-DNA-based fingerprinting provides links to structure-function relationships.

    PubMed

    Brettar, Ingrid; Christen, Richard; Höfle, Manfred G

    2012-01-01

    Understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.

  17. Linking social, ecological, and physical science to advance natural and nature-based protection for coastal communities.

    PubMed

    Arkema, Katie K; Griffin, Robert; Maldonado, Sergio; Silver, Jessica; Suckale, Jenny; Guerry, Anne D

    2017-03-30

    Interest in the role that ecosystems play in reducing the impacts of coastal hazards has grown dramatically. Yet the magnitude and nature of their effects are highly context dependent, making it difficult to know under what conditions coastal habitats, such as saltmarshes, reefs, and forests, are likely to be effective for saving lives and protecting property. We operationalize the concept of natural and nature-based solutions for coastal protection by adopting an ecosystem services framework that propagates the outcome of a management action through ecosystems to societal benefits. We review the literature on the basis of the steps in this framework, considering not only the supply of coastal protection provided by ecosystems but also the demand for protective services from beneficiaries. We recommend further attention to (1) biophysical processes beyond wave attenuation, (2) the combined effects of multiple habitat types (e.g., reefs, vegetation), (3) marginal values and expected damage functions, and, in particular, (4) community dependence on ecosystems for coastal protection and co-benefits. We apply our approach to two case studies to illustrate how estimates of multiple benefits and losses can inform restoration and development decisions. Finally, we discuss frontiers for linking social, ecological, and physical science to advance natural and nature-based solutions to coastal protection.

  18. The Pseudomonas community in metal-contaminated sediments as revealed by quantitative PCR: a link with metal bioavailability.

    PubMed

    Roosa, Stéphanie; Wauven, Corinne Vander; Billon, Gabriel; Matthijs, Sandra; Wattiez, Ruddy; Gillan, David C

    2014-10-01

    Pseudomonas bacteria are ubiquitous Gram-negative and aerobic microorganisms that are known to harbor metal resistance mechanisms such as efflux pumps and intracellular redox enzymes. Specific Pseudomonas bacteria have been quantified in some metal-contaminated environments, but the entire Pseudomonas population has been poorly investigated under these conditions, and the link with metal bioavailability was not previously examined. In the present study, quantitative PCR and cell cultivation were used to monitor and characterize the Pseudomonas population at 4 different sediment sites contaminated with various levels of metals. At the same time, total metals and metal bioavailability (as estimated using an HCl 1 m extraction) were measured. It was found that the total level of Pseudomonas, as determined by qPCR using two different genes (oprI and the 16S rRNA gene), was positively and significantly correlated with total and HCl-extractable Cu, Co, Ni, Pb and Zn, with high correlation coefficients (>0.8). Metal-contaminated sediments featured isolates of the Pseudomonas putida, Pseudomonas fluorescens, Pseudomonas lutea and Pseudomonas aeruginosa groups, with other bacterial genera such as Mycobacterium, Klebsiella and Methylobacterium. It is concluded that Pseudomonas bacteria do proliferate in metal-contaminated sediments, but are still part of a complex community.

  19. 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

  20. 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).

  1. 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.

  2. Biomarker qualification via public-private partnerships.

    PubMed

    Eck, S L; Paul, S M

    2010-01-01

    Biomarkers linked to patient outcomes (safety and efficacy) have an increasingly important role in drug development. Consequently, validation and qualification of such biomarkers are essential, often requiring large data sets from well-controlled randomized clinical trials. In the December 2009 issue of Clinical Pharmacology & Therapeutics, investigators utilizing data from four pharmaceutical companies and working under the auspices of the Biomarkers Consortium described the utility of adiponectin as an early predictor of glycemic control in diabetic patients taking peroxisome proliferator-activated receptor (PPAR) agonists. This work illustrates the advantages of large public-private partnerships for biomarker qualification.

  3. Biomarkers for Heart Failure in Asia.

    PubMed

    Richards, Arthur Mark

    2015-10-01

    Contributions from the Asian biomedical community to knowledge of biomarkers in heart failure have grown rapidly since 2000. Japan has made world-leading contributions in the discovery and application of cardiac natriuretic peptides as biomarkers in heart failure, but there has been rapid growth in reports from China. Contributions also come from Taiwan, South Korea, Singapore, and Hong Kong. Centers in Asia have established clinical cohorts providing powerful platforms for the discovery and validation of biomarkers in heart failure. This century, Asian enquiry into biomarkers in heart failure will include peptides, cytokines, metabolites, nucleic acids, and other analytes.

  4. [Biomarkers of Alzheimer disease].

    PubMed

    Rachel, Wojciech; Grela, Agatha; Zyss, Tomasz; Zieba, Andrzej; Piekoszewski, Wojciech

    2014-01-01

    Cognitive impairment is one of the most abundant age-related psychiatric disorders. The outcome of cognitive impairment in Alzheimer's disease has both individual (the patients and their families) and socio-economic effects. The prevalence of Alzheimer's disease doubles after the age of 65 years, every 4.5 years. An etiologically heterogenic group of disorders related to aging as well as genetic and environmental interactions probably underlie the impairment in Alzheimer's disease. Those factors cause the degeneration of brain tissue which leads to significant cognitive dysfunction. There are two main hypotheses that are linked to the process of neurodegeneration: (i) amyloid cascade and (ii) the role of secretases and dysfunction of mitochondria. From the therapeutic standpoint it is crucial to get an early diagnosis and start with an adequate treatment. The undeniable progress in the field of biomarker research should lead to a better understanding of the early stages of the disorder. So far, the best recognised and described biomarkers of Alzheimer's disease, which can be detected in both cerebrospinal fluid and blood, are: beta-amyloid, tau-protein and phosphorylated tau-protein (phospho-tau). The article discusses the usefulness of the known biomarkers of Alzheimer's disease in early diagnosis.

  5. Impacts of organic and inorganic fertilizers on nitrification in a cold climate soil are linked to the bacterial ammonia oxidizer community.

    PubMed

    Fan, Fenliang; Yang, Qianbao; Li, Zhaojun; Wei, Dan; Cui, Xi'an; Liang, Yongchao

    2011-11-01

    The microbiology underpinning soil nitrogen cycling in northeast China remains poorly understood. These agricultural systems are typified by widely contrasting temperature, ranging from -40 to 38°C. In a long-term site in this region, the impacts of mineral and organic fertilizer amendments on potential nitrification rate (PNR) were determined. PNR was found to be suppressed by long-term mineral fertilizer treatment but enhanced by manure treatment. The abundance and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities were assessed using quantitative polymerase chain reaction and denaturing gradient gel electrophoresis techniques. The abundance of AOA was reduced by all fertilizer treatments, while the opposite response was measured for AOB, leading to a six- to 60-fold reduction in AOA/AOB ratio. The community structure of AOA exhibited little variation across fertilization treatments, whereas the structure of the AOB community was highly responsive. PNR was correlated with community structure of AOB rather than that of AOA. Variation in the community structure of AOB was linked to soil pH, total carbon, and nitrogen contents induced by different long-term fertilization regimes. The results suggest that manure amendment establishes conditions which select for an AOB community type which recovers mineral fertilizer-suppressed soil nitrification.

  6. 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

  7. How perceptions of community environment influence health behaviours: using the Analysis Grid for Environments Linked to Obesity Framework as a mechanism for exploration

    PubMed Central

    Nieuwendyk, L. M.; Belon, A. P.; Vallianatos, H.; Raine, K. D.; Schopflocher, D.; Spence, J. C.; Plotnikoff, R. C.; Nykiforuk, C. I.

    2016-01-01

    Abstract Introduction: Overweight and obesity are influenced by a complex interplay of individual and environmental factors that affect physical activity and healthy eating. Nevertheless, little has been reported on people’s perceptions of those factors. Addressing this critical gap and community partner needs, this study explored how people perceived the influence of micro- and macroenvironmental factors on physical activity and healthy eating. Methods: Community partners wanted the study results in a format that would be readily and easily used by local decision makers. We used photovoice to engage 35 community members across four municipalities in Alberta, Canada, and to share their narratives about their physical activity and healthy eating. A combination of inductive and deductive analysis categorized data by environmental level (micro vs. macro) and type (physical, political, economic, and sociocultural), guided by the Analysis Grid for Environments Linked to Obesity Framework. Results: Participants conceptualized health-influencing factors more broadly than physical activity and healthy eating to include “community social health.” Participants spoke most often about the influence of the microenvironment (n = 792 ANGELO Framework coding tallies) on their physical activity, healthy eating and community social health in comparison to the macroenvironment (n = 93). Photovoice results provided a visual narrative to community partners and decision makers about how people’s ability to make healthy choices can be limited by macroenvironmental forces beyond their control. Conclusion: Focussing future research on macro- and microenvironmental influences and localized community social health can inform practice by providing strategies on how to implement healthy changes within communities, while ensuring that research and interventions echo diverse people’s perceptions. PMID:27670920

  8. Links between soil microbial communities and plant traits in a species-rich grassland under long-term climate change.

    PubMed

    Sayer, Emma J; Oliver, Anna E; Fridley, Jason D; Askew, Andrew P; Mills, Robert T E; Grime, J Philip

    2017-02-01

    Climate change can influence soil microorganisms directly by altering their growth and activity but also indirectly via effects on the vegetation, which modifies the availability of resources. Direct impacts of climate change on soil microorganisms can occur rapidly, whereas indirect effects mediated by shifts in plant community composition are not immediately apparent and likely to increase over time. We used molecular fingerprinting of bacterial and fungal communities in the soil to investigate the effects of 17 years of temperature and rainfall manipulations in a species-rich grassland near Buxton, UK. We compared shifts in microbial community structure to changes in plant species composition and key plant traits across 78 microsites within plots subjected to winter heating, rainfall supplementation, or summer drought. We observed marked shifts in soil fungal and bacterial community structure in response to chronic summer drought. Importantly, although dominant microbial taxa were largely unaffected by drought, there were substantial changes in the abundances of subordinate fungal and bacterial taxa. In contrast to short-term studies that report high resistance of soil fungi to drought, we observed substantial losses of fungal taxa in the summer drought treatments. There was moderate concordance between soil microbial communities and plant species composition within microsites. Vector fitting of community-weighted mean plant traits to ordinations of soil bacterial and fungal communities showed that shifts in soil microbial community structure were related to plant traits representing the quality of resources available to soil microorganisms: the construction cost of leaf material, foliar carbon-to-nitrogen ratios, and leaf dry matter content. Thus, our study provides evidence that climate change could affect soil microbial communities indirectly via changes in plant inputs and highlights the importance of considering long-term climate change effects, especially

  9. 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

  10. Community.

    ERIC Educational Resources Information Center

    Grauer, Kit, Ed.

    1995-01-01

    Art in context of community is the theme of this newsletter. The theme is introduced in an editorial "Community-Enlarging the Definition" (Kit Grauer). Related articles include: (1) "The Children's Bridge is not Destroyed: Heart in the Middle of the World" (Emil Robert Tanay); (2) "Making Bridges: The Sock Doll…

  11. 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

  12. 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.

  13. A generic operational strategy to qualify translational safety biomarkers.

    PubMed

    Matheis, Katja; Laurie, David; Andriamandroso, Christiane; Arber, Nadir; Badimon, Lina; Benain, Xavier; Bendjama, Kaïdre; Clavier, Isabelle; Colman, Peter; Firat, Hüseyin; Goepfert, Jens; Hall, Steve; Joos, Thomas; Kraus, Sarah; Kretschmer, Axel; Merz, Michael; Padro, Teresa; Planatscher, Hannes; Rossi, Annamaria; Schneiderhan-Marra, Nicole; Schuppe-Koistinen, Ina; Thomann, Peter; Vidal, Jean-Marc; Molac, Béatrice

    2011-07-01

    The importance of using translational safety biomarkers that can predict, detect and monitor drug-induced toxicity during human trials is becoming increasingly recognized. However, suitable processes to qualify biomarkers in clinical studies have not yet been established. There is a need to define clear scientific guidelines to link biomarkers to clinical processes and clinical endpoints. To help define the operational approach for the qualification of safety biomarkers the IMI SAFE-T consortium has established a generic qualification strategy for new translational safety biomarkers that will allow early identification, assessment and management of drug-induced injuries throughout R&D.

  14. Linking Microbial Community, Environmental Variables, and Methanogenesis in Anaerobic Biogas Digesters of Chemically Enhanced Primary Treatment Sludge.

    PubMed

    Ju, Feng; Lau, Frankie; Zhang, Tong

    2017-04-04

    Understanding the influences of biotic and abiotic factors on microbial community structure and methanogenesis are important for its engineering and ecological significance. In this study, four biogas digesters were supplied with the same inoculum and feeding sludge but operated at different sludge retention time (7 to 16 days) and organic loading rates for 90 days to determine the relative influence of biotic and environmental factors on the microbial community assembly and methanogenic performance. Despite different operational parameters, all digester communities were dominated by Bacteroidales, Clostridiales, and Thermotogales and followed the same trend of population dynamics over time. Network and multivariate analyses suggest that deterministic factors, including microbial competition (involving Bacteroidales spp.), niche differentiation (e.g., within Clostridiales spp.), and periodic microbial immigration (from feed sludge), are the key drivers of microbial community assembly and dynamics. A yet-to-be-cultured phylotype of Bacteroidales (GenBank ID: GU389558.1 ) is implicated as a strong competitor for carbohydrates. Moreover, biogas-producing rate and methane content were significantly related with the abundances of functional populations rather than any operational or physicochemical parameter, revealing microbiological mediation of methanogenesis. Combined, this study enriches our understandings of biological and environmental drivers of microbial community assembly and performance in anaerobic digesters.

  15. 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.

  16. Linking optimal foraging behavior to bird community structure in an urban-desert landscape: field experiments with artificial food patches.

    PubMed

    Shochat, Eyal; Lerman, Susannah B; Katti, Madhusudan; Lewis, David B

    2004-08-01

    Urban bird communities exhibit high population densities and low species diversity, yet mechanisms behind these patterns remain largely untested. We present results from experimental studies of behavioral mechanisms underlying these patterns and provide a test of foraging theory applied to urban bird communities. We measured foraging decisions at artificial food patches to assess how urban habitats differ from wildlands in predation risk, missed-opportunity cost, competition, and metabolic cost. By manipulating seed trays, we compared leftover seed (giving-up density) in urban and desert habitats in Arizona. Deserts exhibited higher predation risk than urban habitats. Only desert birds quit patches earlier when increasing the missed-opportunity cost. House finches and house sparrows coexist by trading off travel cost against foraging efficiency. In exclusion experiments, urban doves were more efficient foragers than passerines. Providing water decreased digestive costs only in the desert. At the population level, reduced predation and higher resource abundance drive the increased densities in cities. At the community level, the decline in diversity may involve exclusion of native species by highly efficient urban specialists. Competitive interactions play significant roles in structuring urban bird communities. Our results indicate the importance and potential of mechanistic approaches for future urban bird community studies.

  17. Biomarkers and surrogate end points for fit-for-purpose development and regulatory evaluation of new drugs.

    PubMed

    Wagner, J A; Williams, S A; Webster, C J

    2007-01-01

    A consistent framework for the acceptance and qualification of biomarkers for regulatory use is needed to facilitate innovative and efficient research and subsequent application of biomarkers in drug development. One key activity is biomarker qualification, a graded, "fit-for-purpose" evidentiary process linking a biomarker with biology and clinical end points. A biomarker consortium model will distribute cost and risk, and drive efficient execution of research and ultimately regulatory acceptance of biomarkers for specific indications.

  18. 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

  19. Linking microbial community structure and function to seasonal differences in soil moisture and temperature in a Chihuahuan desert grassland.

    PubMed

    Bell, Colin W; Acosta-Martinez, Veronica; McIntyre, Nancy E; Cox, Stephen; Tissue, David T; Zak, John C

    2009-11-01

    Global and regional climate models predict higher air temperature and less frequent, but larger precipitation events in arid regions within the next century. While many studies have addressed the impact of variable climate in arid ecosystems on plant growth and physiological responses, fewer studies have addressed soil microbial community responses to seasonal shifts in precipitation and temperature in arid ecosystems. This study examined the impact of a wet (2004), average (2005), and dry (2006) year on subsequent responses of soil microbial community structure, function, and linkages, as well as soil edaphic and nutrient characteristics in a mid-elevation desert grassland in the Chihuahuan Desert. Microbial community structure was classified as bacterial (Gram-negative, Gram-positive, and actinomycetes) and fungal (saprophytic fungi and arbuscular mycorrhiza) categories using (fatty acid methyl ester) techniques. Carbon substrate use and enzymic activity was used to characterize microbial community function annually and seasonally (summer and winter). The relationship between saprophytic fungal community structure and function remained consistent across season independent of the magnitude or frequency of precipitation within any given year. Carbon utilization by fungi in the cooler winter exceeded use in the warmer summer each year suggesting that soil temperature, rather than soil moisture, strongly influenced fungal carbon use and structure and function dynamics. The structure/function relationship for AM fungi and soil bacteria notably changed across season. Moreover, the abundance of Gram-positive bacteria was lower in the winter compared to Gram-negative bacteria. Bacterial carbon use, however, was highest in the summer and lower during the winter. Enzyme activities did not respond to either annual or seasonal differences in the magnitude or timing of precipitation. Specific structural components of the soil microbiota community became uncoupled from total

  20. Culturally and linguistically diverse (CALD) families dealing with dementia: an examination of the experiences and perceptions of multicultural community link workers.

    PubMed

    Boughtwood, Desiree; Shanley, Chris; Adams, Jon; Santalucia, Yvonne; Kyriazopoulos, Helena; Pond, Dimity; Rowland, Jeffery

    2011-12-01

    Dementia is a chronic illness involving increasing levels of care, often provided by family members, particularly in culturally and linguistically diverse (CALD) communities. Multicultural community link workers are often the primary service providers assisting families to access health and welfare services and as such have extensive experience of, and possess in-depth knowledge about, CALD family care-giving for dementia. While research has been undertaken on dementia in CALD communities, this research has not focused on the experiences and perceptions of these multicultural workers with regards to CALD family care-giving. In response to this gap in the research, this paper presents the results of an empirical investigation of multicultural workers' perspectives with regard to the cultural traditions informing CALD family care-giving, CALD families' understandings of the term 'carer' and family arrangements regarding care. Due to their close relationship and knowledge of families, multicultural workers can offer an important perspective that is invaluable in informing the provision of carer education and support within CALD communities.

  1. 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.

  2. Milk fat biomarkers and cardiometabolic disease

    PubMed Central

    Risérus, Ulf; Marklund, Matti

    2017-01-01

    Purpose of review Dairy is a major food group with potential impact on cardiometabolic health. Self-reported dairy intake has limitations that can partly be avoided by using biomarkers. This review aims to summarize the evidence of odd-chain saturated fatty acids (OCFAs), that is, pentadecanoic acid (C15 : 0) and heptadecanoic acid (17 : 0), as biomarkers of dairy fat intake. In addition, the associations of OCFA biomarkers with cardiometabolic disease will be overviewed. Recent findings Adipose tissue 15 : 0 is the preferred biomarker but also circulating 15 : 0, and to a weaker extent 17 : 0, reflects both habitual and changes in dairy intake. Whereas results from studies assessing cardiovascular outcomes are inconsistent, OCFA biomarkers are overall associated with lower diabetes risk. Residual confounding should however be considered until interventional data and mechanisms are available. Although OCFA biomarkers mainly reflect dairy fat intake, recently proposed endogenous synthesis and metabolism do motivate further research. Summary Taking into account the study population diet and limitations of OCFA biomarkers, both adipose and circulating levels of 15 : 0, in particular, are useful for estimating total dairy fat intake. OCFA biomarkers are overall not linked to cardiovascular disease risk, but a possible beneficial role of dairy foods in diabetes prevention warrant further study. PMID:27906713

  3. 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...

  4. 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.…

  5. 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…

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. Amphidromy Links a Newly Documented Fish Community of Continental Australian Streams, to Oceanic Islands of the West Pacific

    PubMed Central

    Thuesen, Paul A.; Ebner, Brendan C.; Larson, Helen; Keith, Philippe; Silcock, Rebecca M.; Prince, Jason; Russell, David J.

    2011-01-01

    Background Indo-Pacific high island streams experience extreme hydrological variation, and are characterised by freshwater fish species with an amphidromous life history. Amphidromy is a likely adaptation for colonisation of island streams following stochastic events that lead to local extirpation. In the Wet Tropics of north-eastern Australia, steep coastal mountain streams share similar physical characteristics to island systems. These streams are poorly surveyed, but may provide suitable habitat for amphidromous species. However, due to their ephemeral nature, common non-diadromous freshwater species of continental Australia are unlikely to persist. Consequently, we hypothesise that coastal Wet Tropics streams are faunally more similar, to distant Pacific island communities, than to nearby faunas of large continental rivers. Methods/Principal Findings Surveys of coastal Wet Tropics streams recorded 26 species, 10 of which are first records for Australia, with three species undescribed. This fish community is unique in an Australian context in that it contains mostly amphidromous species, including sicydiine gobies of the genera Sicyopterus, Sicyopus, Smilosicyopus and Stiphodon. Species presence/absence data of coastal Wet Tropics streams were compared to both Wet Tropics river networks and Pacific island faunas. ANOSIM indicated the fish fauna of north-eastern Australian coastal streams were more similar to distant Pacific islands (R = 0.76), than to nearby continental rivers (R = 0.98). Main Conclusions/Significance Coastal Wet Tropics streams are faunally more similar to distant Pacific islands (79% of species shared), than to nearby continental fauna due to two factors. First, coastal Wet Tropics streams lack many non-diadromous freshwater fish which are common in nearby large rivers. Second, many amphidromous species found in coastal Wet Tropics streams and Indo-Pacific islands remain absent from large rivers of the Wet Tropics. The evolutionary and

  15. 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.

  16. A Changing Europe: The Maturation of the European Community and How It Will Affect the Trans-Atlantic Link

    DTIC Science & Technology

    1990-04-01

    to the two Germanies agreeing to cohabitate without the official sanction of matrimony and hoping I that as time passes their common-law marriage will...intent can be realized and what hindrances U there are to US involvement in Europe. 3 52 R. Hornick, "The Peace Dividend: Myth and Reality," Tim 12 Feb...Summer 1988. I Hornick, R. "The Peace Dividend: Myth and Reality." Time 12 February 1990, p. 22. Howe, Robert. The European Community’s 1992 Plan

  17. Defining Pesticide Biomarkers

    EPA Pesticide Factsheets

    Biomarkers are measurable substances or characteristics in the human body that can be used to monitor the presence of a chemical in the body, biological responses or harm to health. This Web page describes categories of biomarkers and provides examples.

  18. 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...

  19. 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...

  20. Technology use in linking criminal justice reentrants to HIV care in the community: a qualitative formative research study.

    PubMed

    Peterson, James; Cota, Michelle; Gray, Holly; Bazerman, Lauri; Kuo, Irene; Kurth, Ann; Beckwith, Curt

    2015-01-01

    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. The authors conducted 24 qualitative interview-12 in Rhode Island and 12 in Washington, DC-among recently incarcerated HIV-infected persons 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 used 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.

  1. 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

  2. Linking patients with community resources: use of a free YMCA membership among low-income black women.

    PubMed

    Greaney, Mary L; Askew, Sandy; Foley, Perry; Wallington, Sherrie F; Bennett, Gary G

    2016-08-02

    Given the increasing interest in expanding obesity prevention efforts to cover community-based programs, we examined whether individuals would access a YMCA for physical activity promotion. We provided a no-cost 12-month YMCA membership to socioeconomically disadvantaged black women who were randomized to the intervention arm of a weight gain prevention trial (n = 91). Analyses examined associations of membership activation and use with baseline psychosocial, contextual, health-related, and sociodemographic factors. Many participants (70.3 %) activated their memberships; however, use was low (42.2 % had no subsequent visits, 46.9 % had one to ten visits). There were no predictors of membership activation, but individuals living below/borderline the federal poverty line were more likely to use the center (1+ visits), as were those who met physical activity guidelines at baseline. More comprehensive and intensive interventions may be necessary to promote use of community resources-even when provided free-among high-risk populations of women with obesity that live in rural areas of the USA.

  3. Microbial community structure and activity linked to contrasting biogeochemical gradients in bog and fen environments of the Glacial Lake Agassiz Peatland.

    PubMed

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

    2012-10-01

    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.

  4. 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...

  5. Reappraising the link between peritraumatic dissociation and PTSD symptom severity: evidence from a longitudinal study of community violence survivors.

    PubMed

    Marshall, Grant N; Schell, Terry L

    2002-11-01

    Cross-lagged panel analysis of longitudinal data collected from young adult survivors of community violence was used to examine the relationship between recall of peritraumatic dissociation and posttraumatic stress disorder (PTSD) symptom severity. Recollections of peritraumatic dissociation assessed within days of exposure differed from recollections measured at 3- and 12-month follow-up interviews. Peritraumatic dissociation was highly correlated with PTSD symptoms within each wave of data collection. Baseline recollections of peritraumatic dissociation were not predictive of follow-up PTSD symptom severity after controlling for baseline PTSD symptom severity. This pattern of results replicates previous work demonstrating a correlation between peritraumatic dissociation and subsequent symptom severity. However, findings are not consistent with the prevailing view that peritraumatic dissociation leads to increased PTSD symptom severity.

  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. Development of imaging biomarkers and generation of big data.

    PubMed

    Alberich-Bayarri, Ángel; Hernández-Navarro, Rafael; Ruiz-Martínez, Enrique; García-Castro, Fabio; García-Juan, David; Martí-Bonmatí, Luis

    2017-02-21

    Several image processing algorithms have emerged to cover unmet clinical needs but their application to radiological routine with a clear clinical impact is still not straightforward. Moving from local to big infrastructures, such as Medical Imaging Biobanks (millions of studies), or even more, Federations of Medical Imaging Biobanks (in some cases totaling to hundreds of millions of studies) require the integration of automated pipelines for fast analysis of pooled data to extract clinically relevant conclusions, not uniquely linked to medical imaging, but in combination to other information such as genetic profiling. A general strategy for the development of imaging biomarkers and their integration in the cloud for the quantitative management and exploitation in large databases is herein presented. The proposed platform has been successfully launched and is being validated nowadays among the early adopters' community of radiologists, clinicians, and medical imaging researchers.

  8. Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation.

    PubMed

    Cohen Freue, Gabriela V; Meredith, Anna; Smith, Derek; Bergman, Axel; Sasaki, Mayu; Lam, Karen K Y; Hollander, Zsuzsanna; Opushneva, Nina; Takhar, Mandeep; Lin, David; Wilson-McManus, Janet; Balshaw, Robert; Keown, Paul A; Borchers, Christoph H; McManus, Bruce; Ng, Raymond T; McMaster, W Robert

    2013-04-01

    Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac

  9. Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation

    PubMed Central

    Cohen Freue, Gabriela V.; Meredith, Anna; Smith, Derek; Bergman, Axel; Sasaki, Mayu; Lam, Karen K. Y.; Hollander, Zsuzsanna; Opushneva, Nina; Takhar, Mandeep; Lin, David; Wilson-McManus, Janet; Balshaw, Robert; Keown, Paul A.; Borchers, Christoph H.; McManus, Bruce; Ng, Raymond T.; McMaster, W. Robert

    2013-01-01

    Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac

  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. 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

  12. 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.

  13. Outbreak of viral hepatitis B in a rural community in India linked to inadequately sterilized needles and syringes.

    PubMed Central

    Singh, J.; Bhatia, R.; Gandhi, J. C.; Kaswekar, A. P.; Khare, S.; Patel, S. B.; Oza, V. B.; Jain, D. C.; Sokhey, J.

    1998-01-01

    In India, virtually all outbreaks of viral hepatitis are considered to be due to faeco-orally transmitted hepatitis E virus. Recently, a cluster of 15 cases of viral hepatitis B was found in three villages in Gujarat State. The cases were epidemiologically linked to the use of inadequately sterilized needles and syringes by a local unqualified medical practitioner. The outbreak evolved slowly over a period of 3 months and was marked by a high case fatality rate (46.7%), probably because of concurrent infection with hepatitis D virus (HDV) or sexually transmitted infections. But for the many fatalities within 2-3 weeks of the onset of illness, the outbreak would have gone unnoticed. The findings emphasize the importance of inadequately sterilized needles and syringes in the transmission of viral hepatitis B in India, the need to strengthen the routine surveillance system, and to organize an education campaign targeting all health care workers including private practitioners, especially those working in rural areas, as well as the public at large, to take all possible measures to prevent this often fatal infection. PMID:9615501

  14. 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.

  15. Microbial community structure of a heavy fuel oil-degrading marine consortium: linking microbial dynamics with polycyclic aromatic hydrocarbon utilization.

    PubMed

    Vila, Joaquim; María Nieto, José; Mertens, Jelle; Springael, Dirk; Grifoll, Magdalena

    2010-08-01

    A marine microbial consortium obtained from a beach contaminated by the Prestige oil spill proved highly efficient in removing the different hydrocarbon families present in this heavy fuel oil. Seawater cultures showed a complete removal of all the linear and branched alkanes, an extensive attack on three to five-ring polycyclic aromatic hydrocarbons [PAHs; including anthracene, fluoranthene, pyrene, benzo(a)anthracene, chrysene, and benzo(a)pyrene] (30-100%), and a considerable depletion of their alkyl derivatives. Community dynamics analysis revealed that Alcanivorax species, known alkane degraders, predominated in the initial stages. This was followed by an increase in Alphaproteobacteria (i.e. Maricaulis, Roseovarius), which coincided with the depletion of low molecular PAHs. Finally, these were succeeded by Gammaproteobacteria (mainly Marinobacter and Methylophaga), which were involved in the degradation of the high molecular-weight PAHs. The role of these populations in the removal of the specific components was confirmed by the analysis of subcultures established using the aliphatic or the aromatic fraction of the fuel oil, or single PAHs, as carbon sources. The genus Marinobacter seemed to play a major role in the degradation of a variety of hydrocarbons, as several members of this group were isolated from the different enrichment cultures and grew on plates with hexadecane or single PAHs as sole carbon sources.

  16. Psychotic experiences are linked to cannabis use in adolescents in the community because of common underlying environmental risk factors.

    PubMed

    Shakoor, Sania; Zavos, Helena M S; McGuire, Philip; Cardno, Alastair G; Freeman, Daniel; Ronald, Angelica

    2015-06-30

    Cannabis users are more likely to have psychotic experiences (PEs). The degree to which these associations are driven by genetic or environmental influences in adolescence is unknown. This study estimated the genetic and environmental contributions to the relationship between cannabis use and PEs. Specific PEs were measured in a community-based twin sample (4830 16-year-old pairs) using self-reports and parent-reports. Adolescents reported on ever using cannabis. Multivariate liability threshold structural equation model-fitting was conducted. Cannabis use was significantly correlated with PEs. Modest heritability (37%), common environmental influences (55%) and unique environment (8%) were found for cannabis use. For PEs, modest heritability (27-54%), unique environmental influences (E=12-50%) and little common environmental influences (11-20%), with the exception of parent-rated Negative Symptoms (42%), were reported. Environmental influences explained all of the covariation between cannabis use and paranoia, cognitive disorganization and parent-rated negative symptoms (bivariate common environment=69-100%, bivariate unique environment=28-31%), whilst the relationship between cannabis use and hallucinations indicated familial influences. Cannabis use explains 2-5% of variance in positive, cognitive, and negative PEs. Cannabis use and psychotic experience co-occur due to environmental factors. Focus on specific environments may reveal why adolescent cannabis use and psychotic experiences tend to 'travel together'.

  17. 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.

  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. 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.

  20. Determination of microbial biomass and its community structure from the distribution of phospholipid ester-linked fatty acids in sediments of Hiroshima Bay and its adjacent bays

    NASA Astrophysics Data System (ADS)

    Rajendran, N.; Matsuda, O.; Imamura, N.; Urushigawa, Y.

    1992-05-01

    Phospholipid ester-linked fatty acid (PLFA) composition in sediment samples collected from 20 sampling stations of Hiroshima Bay and its adjacent bays are reported. Thirty-one individual fatty acids were identified in the sediments which comprised of saturated, monounsaturated, polyunsaturated and branched fatty acids. A majority of these fatty acids are characteristic of aerobic and anaerobic bacteria especially sulphate-reducing bacteria. PLFA profiles in the sediments varied among the stations indicating the differences in the contributing microbial communities. The calculated biomass also varied from 0·3 × 10 7 to 2·6 × 10 7 cells g -1 dry weight sediment. The shift in microbial community structure within the study area is understood from the seven clusters obtained by the similarity analysis of PLFA composition. The results of environmental parameters revealed the existence of both oxic and anoxic conditions in the study area and the PLFA composition in sediments is discussed in relation to these environmental parameters. Low concentrations of polyunsaturated fatty acids (PUFA) determined in sediments, characteristic of microeukaryotes, could be attributed to the existing environmental conditions and pollution in the study area. Small quantities of long chain fatty acids in sediments indicated that the terrestrial input is low.

  1. A link between gut community metabolism and pathogenesis: molecular hydrogen-stimulated glucarate catabolism aids Salmonella virulence.

    PubMed

    Lamichhane-Khadka, Reena; Benoit, Stéphane L; Maier, Susan E; Maier, Robert J

    2013-12-04

    Glucarate, an oxidized product of glucose, is a major serum organic acid in humans. Still, its role as a carbon source for a pathogen colonizing hosts has not been studied. We detected high-level expression of a potential glucarate permease encoding gene gudT when Salmonella enterica serovar Typhimurium are exposed to hydrogen gas (H(2)), a gaseous by-product of gut commensal metabolism. A gudT strain of Salmonella is deficient in glucarate-dependent growth, however, it can still use other monosaccharides, such as glucose or galactose. Complementation of the gudT mutant with a plasmid harbouring gudT restored glucarate-dependent growth to wild-type (WT) levels. The gudT mutant exhibits attenuated virulence: the mean time of death for mice inoculated with WT strain was 2 days earlier than for mice inoculated with the gudT strain. At 4 days postinoculation, liver and spleen homogenates from mice inoculated with a gudT strain contained significantly fewer viable Salmonella than homogenates from animals inoculated with the parent. The parent strain grew well H(2)-dependently in a minimal medium with amino acids and glucarate provided as the sole carbon sources, whereas the gudT strain achieved approximately 30% of the parent strain's yield. Glucarate-mediated growth of a mutant strain unable to produce H(2) was stimulated by H(2) addition, presumably owing to the positive transcriptional response to H(2). Gut microbiota-produced molecular hydrogen apparently signals Salmonella to catabolize an alternative carbon source available in the host. Our results link a gut microbiome-produced diffusible metabolite to augmenting bacterial pathogenesis.

  2. 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

  3. A link between gut community metabolism and pathogenesis: molecular hydrogen-stimulated glucarate catabolism aids Salmonella virulence

    PubMed Central

    Lamichhane-Khadka, Reena; Benoit, Stéphane L.; Maier, Susan E.; Maier, Robert J.

    2013-01-01

    Glucarate, an oxidized product of glucose, is a major serum organic acid in humans. Still, its role as a carbon source for a pathogen colonizing hosts has not been studied. We detected high-level expression of a potential glucarate permease encoding gene gudT when Salmonella enterica serovar Typhimurium are exposed to hydrogen gas (H2), a gaseous by-product of gut commensal metabolism. A gudT strain of Salmonella is deficient in glucarate-dependent growth, however, it can still use other monosaccharides, such as glucose or galactose. Complementation of the gudT mutant with a plasmid harbouring gudT restored glucarate-dependent growth to wild-type (WT) levels. The gudT mutant exhibits attenuated virulence: the mean time of death for mice inoculated with WT strain was 2 days earlier than for mice inoculated with the gudT strain. At 4 days postinoculation, liver and spleen homogenates from mice inoculated with a gudT strain contained significantly fewer viable Salmonella than homogenates from animals inoculated with the parent. The parent strain grew well H2-dependently in a minimal medium with amino acids and glucarate provided as the sole carbon sources, whereas the gudT strain achieved approximately 30% of the parent strain's yield. Glucarate-mediated growth of a mutant strain unable to produce H2 was stimulated by H2 addition, presumably owing to the positive transcriptional response to H2. Gut microbiota-produced molecular hydrogen apparently signals Salmonella to catabolize an alternative carbon source available in the host. Our results link a gut microbiome-produced diffusible metabolite to augmenting bacterial pathogenesis. PMID:24307595

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Biomarkers in clinical medicine.

    PubMed

    Chen, Xiao-He; Huang, Shuwen; Kerr, David

    2011-01-01

    Biomarkers have been used in clinical medicine for decades. With the rise of genomics and other advances in molecular biology, biomarker studies have entered a whole new era and hold promise for early diagnosis and effective treatment of many diseases. A biomarker is a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes or pharmacologic responses to a therapeutic intervention (1). They can be classified into five categories based on their application in different disease stages: 1) antecedent biomarkers to identify the risk of developing an illness, 2) screening biomarkers to screen for subclinical disease, 3) diagnostic biomarkers to recognize overt disease, 4) staging biomarkers to categorise disease severity, and 5) prognostic biomarkers to predict future disease course, including recurrence, response to therapy, and monitoring efficacy of therapy (1). Biomarkers can indicate a variety of health or disease characteristics, including the level or type of exposure to an environmental factor, genetic susceptibility, genetic responses to environmental exposures, markers of subclinical or clinical disease, or indicators of response to therapy. This chapter will focus on how these biomarkers have been used in preventive medicine, diagnostics, therapeutics and prognostics, as well as public health and their current status in clinical practice.

  9. Validation and clinical utility of prostate cancer biomarkers

    PubMed Central

    Scher, Howard I.; Morris, Michael J.; Larson, Steven; Heller, Glenn

    2013-01-01

    To improve future drug development and patient management for patients with castration-resistant prostate cancer (CRPC), surrogate biomarkers that are linked to relevant outcomes are urgently needed. A biomarker must be measurable, reproducible, linked to relevant clinical outcomes, and demonstrate utility. This is a rapidly evolving area, with recent trials in CRPC incorporating the detection of circulating tumour cells (CTCs), imaging, and patient-reported outcome biomarkers. We discuss the framework for the development of biomarkers for CRPC, including different categories and contexts of use. We also highlight the requirements of analytical validation, the sequence of trials needed for clinical validation and regulatory approval, and the future outlook for imaging and CTC biomarkers. PMID:23459624

  10. Effectiveness of a school-community linked program on physical activity levels and health-related quality of life for adolescent girls

    PubMed Central

    2014-01-01

    Background This study evaluated the effectiveness of a school-community program on Health-Related Quality of Life (HRQoL; the primary outcome), physical activity (PA), and potential mediators of PA among adolescent girls living in low-socioeconomic rural/regional settings. Method The study was a cluster-randomized controlled trial. Twelve communities with the requisite sports clubs and facilities were paired according to relevant criteria; one of each pair was randomly assigned to the intervention or control condition. Eight schools per condition were randomly selected from these communities and the intervention was conducted over one school year (2011). Female students in grades 7–9 in intervention schools participated in two 6-session PA units – a sport unit (football or tennis) and a recreational unit (leisure centre-based). These were incorporated into physical education (PE) curriculum and linked to PA opportunities for participation outside school. Students were surveyed at baseline and endpoint, self-reporting impact on primary and secondary outcome measures (HRQoL, PA) and PA mediators (e.g. self-efficacy). Linear mixed models for two-group (intervention, control) and three-group (completers, non-completers, control) analyses were conducted with baseline value, age and BMI as covariates, group as a fixed effect and school as random cluster effect. Results Participants completing baseline and endpoint measures included: 358 intervention (baseline response rate 33.7%, retention rate 61.3%) and 256 control (14.1% and 84.0%). Adjustment for age and BMI made no substantive difference to outcomes, and there were no cluster effects. For HRQoL, after adjustment for baseline scores, the intervention group showed significantly higher scores on all three PedsQL scores (physical functioning: M ± SE = 83.9 ± 0.7, p = .005; psychosocial: 79.9 ± 0.8, p = .001; total score: 81.3 ± 0.7, p = .001) than the control group (80.9 ± 0

  11. 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

  12. 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

  13. 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

  14. Biomarkers for Parkinson's disease.

    PubMed

    Sherer, Todd B

    2011-04-20

    Biomarkers for detecting the early stages of Parkinson's disease (PD) could accelerate development of new treatments. Such biomarkers could be used to identify individuals at risk for developing PD, to improve early diagnosis, to track disease progression with precision, and to test the efficacy of new treatments. Although some progress has been made, there are many challenges associated with developing biomarkers for detecting PD in its earliest stages.

  15. The Biomarker Guide

    NASA Astrophysics Data System (ADS)

    Peters, K. E.; Walters, C. C.; Moldowan, J. M.

    2005-01-01

    Biomarkers are compounds found in crude oil with structures inherited from once-living organisms. They persist in oil spills, refinery products and archaeological artifacts, and can be used to identify the origin, geological age and environmental conditions prevalent during their formation and alteration. These two volumes will be an invaluable resource for geologists, petroleum geochemists, biogeochemists, environmental and forensic scientists, natural product chemists and archaeologists. The first of two volumes of The Biomarker Guide discusses the origins of biomarkers and introduces basic chemical principles relevant to their study. It goes on to discuss analytical techniques, and the applications of biomarkers in environmental and archaeological problems.

  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. Description of an integrated framework for building linkages among primary care clinics and community organizations for the prevention of type 2 diabetes: emerging themes from the CC-Link study.

    PubMed

    Ackermann, Ronald T

    2010-06-01

    Strong clinic-community linkages are pivotal for the success of preventive services that combine clinical and community resources. Unfortunately, there has been limited guidance for how clinical and community groups can partner to improve self-care and prevention for chronic conditions. This manuscript describes the development and implementation of an integrated framework to guide clinic-community linkages for the prevention of type 2 diabetes in an ongoing randomized effectiveness trial known as Clinical-Community Linkages to Prevent Diabetes (CC-Link) study. This study involves 10 primary care practices in a metropolitan area of the Midwest US. The study provided each practice location with technical assistance to select, implement, evaluate and refine different strategies to identify and address pre-diabetes using a clinic-community linkage. Sites were also randomized to receive either direct or indirect involvement by a community liaison/expert from the YMCA of Greater Indianapolis. Early implementation of the CC-Link Framework has underscored the importance of strong leadership and partnership synergy, and it uncovered several examples of how linkages can be designed to make the most of partner strengths. This success is promising, and an evaluation of the effectiveness of these efforts to improve lifestyle behaviours of adults with prediabetes is now underway.

  18. 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

  19. The relationship between grip strength and muscle mass (MM), inflammatory biomarkers and physical performance in community-dwelling very old persons.

    PubMed

    Legrand, D; Adriaensen, W; Vaes, B; Matheï, C; Wallemacq, P; Degryse, J

    2013-01-01

    The main consequence of the loss of MM and muscle strength is limitations of physical performance and disability in older people. It is unclear whether a decline in functional capacity results from the loss of MM and/or the qualitative impairment of the muscle tissue. The aim of our research was to investigate the relationship between physical performance and grip strength, inflammatory markers and MM in a population of community-dwelling very old persons. This study is a cross-sectional analysis within the BELFRAIL-study, a cohort study of subjects aged 80 years and older (n=567). MM was assessed by bioelectrical impedance. Interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) concentrations were determined on fasting blood samples. Logistic regression analysis was build using a low physical performance level evaluated according to Short Physical Performance Battery (SPPB) (dependent variable) and grip strength, pro-inflammatory status and MM (independent variables) adjusted for age and for the total number of chronic diseases. Low SPPB scores were associated with grip strength scores for women (OR 0.86 (95% CI 0.77-0.96)), and for men (OR 0.89 (95% CI 0.81-0.96)). The relationships between low SPPB and MM or inflammatory profile were not significant. Our results show that low physical performance remains associated with low grip strength even after considering other risk factors for sarcopenia in the oldest old and support the hypothesis that low muscle strength is a better indicator than low MM. The role of an inflammatory component in the age-related loss of muscle strength and function could not be confirmed.

  20. 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

    2016-10-01

    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.

  1. An Integrated Approach to Falls Prevention: A Model for Linking Clinical and Community Interventions through the Massachusetts Prevention and Wellness Trust Fund

    PubMed Central

    Coe, Laura J.; St. John, Julie Ann; Hariprasad, Santhi; Shankar, Kalpana N.; MacCulloch, Patricia A.; Bettano, Amy L.; Zotter, Jean

    2017-01-01

    Older adult falls continue to be a public health priority across the United States—Massachusetts (MA) being no exception. The MA Prevention and Wellness Trust Fund (PWTF) program within the MA Department of Public Health aims to reduce the physical and economic burdens of chronic health conditions by linking evidence-based clinical care with community intervention programs. The PWTF partnerships that focused on older adult falls prevention integrated the Centers for Disease Control and Prevention’s Stopping Elderly Accidents, Death and Injuries toolkit into clinical settings. Partnerships also offer referrals for home safety assessments, Tai Chi, and Matter of Balance programs. This paper describes the PWTF program implementation process involving 49 MA organizations, while highlighting the successes achieved and lessons learned. With the unprecedented expansion of the U.S. Medicare beneficiary population, and the escalating incidence of falls, widespread adoption of effective prevention strategies will become increasingly important for both public health and for controlling healthcare costs. The lessons learned from this PWTF initiative offer insights and recommendations for future falls prevention program development and implementation. PMID:28321393

  2. School-Linked Services.

    ERIC Educational Resources Information Center

    Family Resource Coalition, Chicago, IL.

    Noting that educating children requires commitment and resources from the whole community as well as the schools, this document explores school-based collaborations with social services and family programs to improve students' performance. The document first provides a rationale for school-linked programs, then describes the School-Linked Services…

  3. 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.

  4. Respiratory Toxicity Biomarkers

    EPA Science Inventory

    The advancement in high throughput genomic, proteomic and metabolomic techniques have accelerated pace of lung biomarker discovery. A recent growth in the discovery of new lung toxicity/disease biomarkers have led to significant advances in our understanding of pathological proce...

  5. 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.

  6. 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.

  7. 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

  8. Biomarkers in Parkinson's disease.

    PubMed

    Morgan, John C; Mehta, Shyamal H; Sethi, Kapil D

    2010-11-01

    Biomarkers are objectively measured characteristics that are indicators of normal biological processes, pathogenic processes, or responses to therapeutic interventions. To date, clinical assessment remains the gold standard in the diagnosis of Parkinson's disease (PD) and clinical rating scales are well established as the gold standard for tracking progression of PD. Researchers have identified numerous potential biomarkers that may aid in the differential diagnosis of PD and/or tracking disease progression. Clinical, genetic, blood and cerebrospinal fluid (proteomics, transcriptomics, metabolomics), and neuroimaging biomarkers may provide useful tools in the diagnosis of PD and in measuring disease progression and response to therapies. Some potential biomarkers are inexpensive and do not require much technical expertise, whereas others are expensive or require specialized equipment and technical skills. Many potential biomarkers in PD show great promise; however, they need to be assessed for their sensitivity and specificity over time in large and varied samples of patients with and without PD.

  9. Biomarkers of Reflux Disease.

    PubMed

    Kia, Leila; Pandolfino, John E; Kahrilas, Peter J

    2016-06-01

    Gastroesophageal reflux disease (GERD) encompasses an array of disorders unified by the reflux of gastric contents. Because there are many potential disease manifestations, esophageal and extraesophageal, there is no single biomarker of the entire disease spectrum; a set of GERD biomarkers that each quantifies specific aspects of GERD-related pathology might be needed. We review recent reports of biomarkers of GERD, specifically in relation to endoscopically negative esophageal disease and excluding conventional pH-impedance monitoring. We consider histopathologic biomarkers, baseline impedance, and serologic assays to determine that most markers are based on manifestations of impaired esophageal mucosal integrity, which is based on increased ionic and molecular permeability, and/or destruction of tight junctions. Impaired mucosal integrity quantified by baseline mucosal impedance, proteolytic fragments of junctional proteins, or histopathologic features has emerged as a promising GERD biomarker.

  10. 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.

  11. [Biomarkers in Alzheimer's disease].

    PubMed

    García-Ribas, G; López-Sendón Moreno, J L; García-Caldentey, J

    2014-04-01

    The new diagnostic criteria for Alzheimer's disease (AD) include brain imaging and cerebrospinal fluid (CSF) biomarkers, with the aim of increasing the certainty of whether a patient has an ongoing AD neuropathologic process or not. Three CSF biomarkers, Aß42, total tau, and phosphorylated tau, reflect the core pathological features of AD. It is already known that these pathological processes of AD starts decades before the first symptoms, so these biomarkers may provide means of early disease detection. At least three stages of AD could be identified: preclinical AD, mild cognitive impairment due to AD, and dementia due to AD. In this review, we aim to summarize the CSF biomarker data available for each of these stages. We also review the actual research on blood-based biomarkers. Recent studies on healthy elderly subjects and on carriers of dominantly inherited AD mutations have also found biomarker changes that allow separate groups in these preclinical stages. These studies may aid for segregate populations in clinical trials and objectively evaluate if there are changes over the pathological processes of AD. Limits to widespread use of CSF biomarkers, apart from the invasive nature of the process itself, is the higher coefficient of variation for the analyses between centres. It requires strict pre-analytical and analytical procedures that may make feasible multi-centre studies and global cut-off points for the different stages of AD.

  12. Commentary: statistics for biomarkers.

    PubMed

    Lovell, David P

    2012-05-01

    This short commentary discusses Biomarkers' requirements for the reporting of statistical analyses in submitted papers. It is expected that submitters will follow the general instructions of the journal, the more detailed guidance given by the International Committee of Medical Journal Editors, the specific guidelines developed by the EQUATOR network, and those of various specialist groups. Biomarkers expects that the study design and subsequent statistical analyses are clearly reported and that the data reported can be made available for independent assessment. The journal recognizes that there is continuing debate about different approaches to statistical science. Biomarkers appreciates that the field continues to develop rapidly and encourages the use of new methodologies.

  13. 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.; Huggett, Robert J.; Kimerle, Richard A.; Mehrle, Paul M.=; Bergman, Harold L.

    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.

  14. 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.

  15. Seasonality, risk factors and burden of community-acquired pneumonia in COPD patients: a population database study using linked health care records

    PubMed Central

    Williams, Nicholas P; Coombs, Ngaire A; Johnson, Matthew J; Josephs, Lynn K; Rigge, Lucy A; Staples, Karl J; Thomas, Mike; Wilkinson, Tom MA

    2017-01-01

    Background Community-acquired pneumonia (CAP) is more common in patients with COPD than in the adult general population, with studies of hospitalized CAP patients consistently reporting COPD as a frequent comorbidity. However, despite an increasing recognition of its importance, large studies evaluating the incidence patterns over time, risk factors and burden of CAP in COPD are currently lacking. Methods A retrospective observational study using a large UK-based database of linked primary and secondary care records was conducted. Patients with a diagnosis of COPD aged ≥40 years were followed up for 5 years from January 1, 2010. CAP and exacerbation episodes were identified from hospital discharge data and primary care coding records, and rates were calculated per month, adjusting for mortality, and displayed over time. In addition, baseline factors predicting future risk of CAP and hospital admission with CAP were identified. Results A total of 14,513 COPD patients were identified: 13.4% (n=1,938) had ≥1 CAP episode, of whom 18.8% suffered from recurrent (≥2) CAP. Highest rates of both CAP and exacerbations were seen in winter. A greater proportion of frequent, compared to infrequent, exacerbators experienced recurrent CAP (5.1% versus 2.0%, respectively, P<0.001); 75.6% of CAP episodes were associated with hospital admission compared to 22.1% of exacerbations. Older age and increasing grade of airflow limitation were independently associated with increased odds of CAP and hospital admission with CAP. Other independent predictors of future CAP included lower body mass index, inhaled corticosteroid use, prior frequent exacerbations and comorbidities, including ischemic heart disease and diabetes. Conclusion CAP in COPD demonstrates clear seasonal patterns, with patient characteristics predictive of the odds of future CAP and hospital admission with CAP. Highlighting this burden of COPD-associated CAP during the winter period informs us of the likely triggers

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. II. Species sensitivity distributions based on biomarkers and whole organism responses for integrated impact and risk assessment criteria.

    PubMed

    Sanni, Steinar; Lyng, Emily; Pampanin, Daniela M; Smit, Mathijs G D

    2016-12-26

    The aim of this paper is to bridge gaps between biomarker and whole organism responses related to oil based offshore discharges. These biomarker bridges will facilitate acceptance criteria for biomarker data linked to environmental risk assessment and translate biomarker results to higher order effects. Biomarker based species sensitivity distributions (SSDbiomarkers) have been constructed for relevant groups of biomarkers based on laboratory data from oil exposures. SSD curves express the fraction of species responding to different types of biomarkers. They have been connected to SSDs for whole organism responses (WORs) constructed in order to relate the SSDbiomarkers to animal fitness parameters that are commonly used in environmental risk assessment. The resulting SSD curves show that biomarkers and WORs can be linked through their potentially affected fraction of species (PAF) distributions, enhancing the capability to monitor field parameters with better correlation to impact and risk assessment criteria and providing improved chemical/biological integration.

  1. Biomarkers for neuromyelitis optica.

    PubMed

    Chang, Kuo-Hsuan; Ro, Long-Sun; Lyu, Rong-Kuo; Chen, Chiung-Mei

    2015-02-02

    Neuromyelitis optica (NMO) is an acquired, heterogeneous inflammatory disorder, which is characterized by recurrent optic neuritis and longitudinally extensive spinal cord lesions. The discovery of the serum autoantibody marker, anti-aquaporin 4 (anti-AQP4) antibody, revolutionizes our understanding of pathogenesis of NMO. In addition to anti-AQP4 antibody, other biomarkers for NMO are also reported. These candidate biomarkers are particularly involved in T helper (Th)17 and astrocytic damages, which play a critical role in the development of NMO lesions. Among them, IL-6 in the peripheral blood is associated with anti-AQP4 antibody production. Glial fibrillary acidic protein (GFAP) in CSF demonstrates good correlations with clinical severity of NMO relapses. Detecting these useful biomarkers may be useful in the diagnosis and evaluation of disease activity of NMO. Development of compounds targeting these biomarkers may provide novel therapeutic strategies for NMO. This article will review the related biomarker studies in NMO and discuss the potential therapeutics targeting these biomarkers.

  2. Methodological and analytic considerations for blood biomarkers.

    PubMed

    Christenson, Robert H; Duh, Show-Hong

    2012-01-01

    Biomarkers typically evolve from a research setting to use in clinical care as evidence for their independent contribution to patient management accumulates. This evidence relies heavily on knowledge of the preanalytical, analytical, and postanalytical characteristics of the biomarker's measurement. For the preanalytical phase, considerations such specimen type, acceptable anticoagulants for blood samples, biologic variation and stability of the biomarker under various conditions are key. The analytical phase entails critical details for development and maintenance of assays having performance characteristics that are "fit for service" for the clinical application at hand. Often, these characteristics describe the ability to measure minute quantities in the biologic matrix used for measurement. Although techniques such as mass spectrometry are used effectively for biomarker discovery, routine quantification often relies on use of immunoassays; early in development, the most common immunoassay used is the enzyme-linked immunosorbent assay format. As biomarkers evolve successfully, they will be adapted to large main laboratory platforms or, depending on the need for speed, point-of-care devices. Users must pay particular attention to performance parameters of assays they are considering for clinical implementation. These parameters include the limit of blank, a term used to describe the limit of analytical noise for an assay; limit of detection, which describes the lowest concentration that can reliably be discriminated from analytical noise; and perhaps most importantly, the limit of quantitation, which is the lowest concentration at which a biomarker can be reliably measured within some predefined specifications for total analytical error that is based on clinical requirements of the test. The postanalytical phase involves reporting biomarker values, which includes reporting units, any normalization factors, and interpretation. Standardization, a process that

  3. Upcoming biomarkers for the diagnosis of Kawasaki disease: A review.

    PubMed

    Parthasarathy, Pavithra; Agarwal, Arnav; Chawla, Karan; Tofighi, Taraneh; Mondal, Tapas K

    2015-11-01

    Kawasaki disease (KD) is a major cause of acquired heart disease among children and increases the risk of myocardial infarction. While the biochemical basis of the disease is unclear, the evidence suggests interplay between a microbial infection and a genetic predisposition in the development of the disease. Diagnosis of KD based on clinical observation is not completely reliable and is problematic due to the time-sensitive nature of the disease. Hence, identification of inflammatory, proteomic, and genetic biomarkers may assist in earlier and more effective diagnosis and treatment. This review of observational studies and clinical trials analyzes biomarkers in recent research that may be used to establish a gold standard test for KD diagnosis. 65 articles in the literature are assessed to investigate these new biomarkers in addition to biomarkers presently in use. ESR≥40mm/h, leukocyte count ≥16∗10(9)/L and increased WBC count are together suggestive of the presence of KD. Among proteomic biomarkers, elevated NT-proBNP and differing levels of several other proteomic biomarkers such as iNOS in monocytes and neutrophils have been observed in KD patients. Genetic polymorphisms of six HLA class I genes have also been linked with the disease, alongside MICA alleles A4 and A5.1. The results suggest that NT-proBNP is currently a very promising biomarker for future investigation; further research is warranted to allow for accurate and early detection of the disease using this biomarker.

  4. The link in Linking

    PubMed Central

    Caldwell, Jane C; Chiale, Pablo A; Gonzalez, Mario D; Baranchuk, Adrian

    2013-01-01

    We present 2 cases of the slow-fast form of AVNRT with initially narrow QRS complexes followed by sudden unexpected transition to persistently wide QRS complexes due to aberrant intraventricular conduction. Introduction of a properly timed extrastimulus in one case and critical oscillations in cycle length due to short-long coupling in the second case set the stage for the initial bundle branch block. However, persistence of the aberrancy pattern once the initial event abated was maintained by the "linking" phenomenon. Delayed, retrograde concealed activation from the contralateral bundle branch perpetuated the initial bundle branch block. PMID:23840106

  5. The link in Linking.

    PubMed

    Caldwell, Jane C; Chiale, Pablo A; Gonzalez, Mario D; Baranchuk, Adrian

    2013-05-01

    We present 2 cases of the slow-fast form of AVNRT with initially narrow QRS complexes followed by sudden unexpected transition to persistently wide QRS complexes due to aberrant intraventricular conduction. Introduction of a properly timed extrastimulus in one case and critical oscillations in cycle length due to short-long coupling in the second case set the stage for the initial bundle branch block. However, persistence of the aberrancy pattern once the initial event abated was maintained by the "linking" phenomenon. Delayed, retrograde concealed activation from the contralateral bundle branch perpetuated the initial bundle branch block.

  6. Kidney biomarkers in cirrhosis.

    PubMed

    Francoz, Claire; Nadim, Mitra K; Durand, François

    2016-10-01

    Impaired renal function due to acute kidney injury (AKI) and/or chronic kidney diseases (CKD) is frequent in cirrhosis. Recurrent episodes of AKI may occur in end-stage cirrhosis. Differential diagnosis between functional (prerenal and hepatorenal syndrome) and acute tubular necrosis (ATN) is crucial. The concept that AKI and CKD represent a continuum rather than distinct entities, is now emerging. Not all patients with AKI have a potential for full recovery. Precise evaluation of kidney function and identification of kidney changes in patients with cirrhosis is central in predicting reversibility. This review examines current biomarkers for assessing renal function and identifying the cause and mechanisms of impaired renal function. When CKD is suspected, clearance of exogenous markers is the reference to assess glomerular filtration rate, as creatinine is inaccurate and cystatin C needs further evaluation. Recent biomarkers may help differentiate ATN from hepatorenal syndrome. Neutrophil gelatinase-associated lipocalin has been the most extensively studied biomarker yet, however, there are no clear-cut values that differentiate each of these conditions. Studies comparing ATN and hepatorenal syndrome in cirrhosis, do not include a gold standard. Combinations of innovative biomarkers are attractive to identify patients justifying simultaneous liver and kidney transplantation. Accurate biomarkers of underlying CKD are lacking and kidney biopsy is often contraindicated in this population. Urinary microRNAs are attractive although not definitely validated. Efforts should be made to develop biomarkers of kidney fibrosis, a common and irreversible feature of CKD, whatever the cause. Biomarkers of maladaptative repair leading to irreversible changes and CKD after AKI are also promising.

  7. Lung Cancer Biomarkers.

    PubMed

    I, Hoseok; Cho, Je-Yoel

    2015-01-01

    Lung cancer is the most frequently occurring cancer in the world and continually leads in mortality among cancers. The overall 5-year survival rate for lung cancer has risen only 4% (from 12% to 16%) over the past 4 decades, and late diagnosis is a major obstacle in improving lung cancer prognosis. Survival of patients undergoing lung resection is greater than 80%, suggesting that early detection and diagnosis of cancers before they become inoperable and lethal will greatly improve mortality. Lung cancer biomarkers can be used for screening, detection, diagnosis, prognosis, prediction, stratification, therapy response monitoring, and so on. This review focuses on noninvasive diagnostic and prognostic biomarkers. For that purpose, our discussion in this review will focus on biological fluid-based biomarkers. The body fluids include blood (serum or plasma), sputum, saliva, BAL, pleural effusion, and VOC. Since it is rich in different cellular and molecular elements and is one of the most convenient and routine clinical procedures, serum or plasma is the main source for the development and validation of many noninvasive biomarkers. In terms of molecular aspects, the most widely validated ones are proteins, some of which are used in the clinical sector, though in limited accessory purposes. We will also discuss the lung cancer (protein) biomarkers in clinical trials and currently in the validation phase with hundreds of samples. After proteins, we will discuss microRNAs, methylated DNA, and circulating tumor cells, which are being vigorously developed and validated as potential lung cancer biomarkers. The main aim of this review is to provide researchers and clinicians with an understanding of the potential noninvasive lung cancer biomarkers in biological fluids that have recently been discovered.

  8. Linking Changes to Intraspecific Trait Diversity to Community Functional Diversity and Biomass in Response to Snow and Nitrogen Addition Within an Inner Mongolian Grassland

    PubMed Central

    Mao, Wei; Felton, Andrew J.; Zhang, Tonghui

    2017-01-01

    In recent years, both the intraspecific and interspecific functional diversity (FD) of plant communities have been studied with new approaches to improve an understanding about the mechanisms underlying plant species coexistence. Yet, little is known about how global change drivers will impact intraspecific FD and trait overlap among species, and in particular how this may scale to impacts on community level FD and ecosystem functioning. To address this uncertainty, we assessed the direct and indirect responses of specific leaf area (SLA) among both dominant annual and subordinate perennial species to the independent and interactive effects of nitrogen and snow addition within the Inner Mongnolian steppe. More specifically, we investigated the consequences for these responses on plant community FD, trait overlap and biomass. Nitrogen addition increased the biomass of the dominant annual species and as a result increased total community biomass. This occurred despite concurrent decreases in the biomass of subordinate perennial species. Nitrogen addition also increased intraspecific FD and trait overlap of both annual species and perennial species, and consequently increased the degree of trait overlap in SLA at the community level. However, snow addition did not significantly impact intraspecific FD and trait overlap of SLA for perennial species, but increased intraspecific FD and trait overlap of annual species, of which scaled to changes in community level FD. We found that the responses of the dominant annual species to nitrogen and snow additions were generally more sensitive than the subordinate perennial species within the inner Mongolian grassland communities of our study. As a consequence of this sensitivity, the responses of the dominant species largely drove impacts to community FD, trait overlap and community biomass. In total, our study demonstrates that the responses of dominant species in a community to environmental change may drive the initial

  9. Linking biochemical properties of particles to particle-attached and free-living bacterial community structure along the particle density gradient from freshwater to open ocean

    NASA Astrophysics Data System (ADS)

    Zhang, Yao; Xiao, Wei; Jiao, Nianzhi

    2016-08-01

    To test the hypothesis that particle composition has a stronger influence on the community structure of particle-attached than free-living bacteria, elemental (C/N, δ13C, and δ15N) and chemical composition of particles and the size-fractionated bacterial community composition were examined along the particle density gradient from the Pearl River to the open basin in the South China Sea. Microbial communities were collected at the three size fractions of 0.2-0.8, 0.8-3, and >3 µm, and the community composition was analyzed using high-throughput sequencing of the 16S rRNA gene (V3-V4 regions). Multivariate analysis evaluating the similarities of bacterial community composition and chemical composition of particles revealed their general consistent spatial variations along the particle density gradient from freshwater to the sea basin. However, compositions of particulate organic matter were more strongly related to the free living than to the particle-attached bacterial community composition, which was composed of relatively abundant anaerobic bacteria and those taxa preferring low-oxygen conditions. This latter result might be caused by low-oxygen microzones in particles. Community network models further revealed tighter interactions within the particle-attached than in free-living bacterial communities, suggesting that a relatively confined space in particles is more favorable for interactions within the community. These analyses indicated that particle microniche properties might be important in shaping particle-attached community structure. In contrast, particulate organic matter compositions significantly influenced the free-living bacterial community probably through the release of labile or semilabile organic matter from particles contributing to the bioavailability of dissolved organic carbon.

  10. Biomarkers of sepsis.

    PubMed

    Faix, James D

    2013-01-01

    Sepsis is an unusual systemic reaction to what is sometimes an otherwise ordinary infection, and it probably represents a pattern of response by the immune system to injury. A hyper-inflammatory response is followed by an immunosuppressive phase during which multiple organ dysfunction is present and the patient is susceptible to nosocomial infection. Biomarkers to diagnose sepsis may allow early intervention which, although primarily supportive, can reduce the risk of death. Although lactate is currently the most commonly used biomarker to identify sepsis, other biomarkers may help to enhance lactate's effectiveness; these include markers of the hyper-inflammatory phase of sepsis, such as pro-inflammatory cytokines and chemokines; proteins such as C-reactive protein and procalcitonin which are synthesized in response to infection and inflammation; and markers of neutrophil and monocyte activation. Recently, markers of the immunosuppressive phase of sepsis, such as anti-inflammatory cytokines, and alterations of the cell surface markers of monocytes and lymphocytes have been examined. Combinations of pro- and anti-inflammatory biomarkers in a multi-marker panel may help identify patients who are developing severe sepsis before organ dysfunction has advanced too far. Combined with innovative approaches to treatment that target the immunosuppressive phase, these biomarkers may help to reduce the mortality rate associated with severe sepsis which, despite advances in supportive measures, remains high.

  11. Biomarkers intersect with the exposome.

    PubMed

    Rappaport, Stephen M

    2012-09-01

    The exposome concept promotes use of omic tools for discovering biomarkers of exposure and biomarkers of disease in studies of diseased and healthy populations. A two-stage scheme is presented for profiling omic features in serum to discover molecular biomarkers and then for applying these biomarkers in follow-up studies. The initial component, referred to as an exposome-wide-association study (EWAS), employs metabolomics and proteomics to interrogate the serum exposome and, ultimately, to identify, validate and differentiate biomarkers of exposure and biomarkers of disease. Follow-up studies employ knowledge-driven designs to explore disease causality, prevention, diagnosis, prognosis and treatment.

  12. Linking Classroom and Community: A Theoretical Alignment of Service Learning and a Human-Centered Design Methodology in Contemporary Communication Design Education

    ERIC Educational Resources Information Center

    Bowie, Anneli; Cassim, Fatima

    2016-01-01

    The current emphasis on social responsibility and community collaboration within higher education has led to an increased drive to include service learning in the curriculum. With its emphasis on mutually beneficial collaborations, service learning can be meaningful for both students and the community, but is challenging to manage successfully.…

  13. 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…

  14. Education and Community: The Collaborative Solution. Proceedings of the International Conference Linking Research and Practice (Toronto, Ontario, Canada, March 3-5, 1994).

    ERIC Educational Resources Information Center

    Lawton, Stephen B., Ed.; Tanenzapt, Elaine, Ed.; Townsend, Richard G., Ed.

    These proceedings are divided into two sections that explore collaboration between schools and communities. In Part I, the first four papers, analytic frameworks are described that provide different perspectives on collaboration. In Part II, descriptions of concrete programs and advice for developing better school-community relations are offered.…

  15. 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…

  16. The use and misuse of biomarkers in ecotoxicology.

    PubMed

    Forbes, Valery E; Palmqvist, Annemette; Bach, Lis

    2006-01-01

    Substantial efforts have been devoted to developing and applying biomarkers for use in ecotoxicology. These efforts have resulted partly from a desire for early warning indicators that respond before measurable effects on individuals and populations occur and partly as an aid to identifying the causes of observed population- and community-level effects. Whereas older biomarkers focused on measures of organism physiology or biochemistry, advances in molecular biology are extending the biomarker philosophy to the level of the genes (i.e., ecotoxicogenomics). However, the extent to which biomarkers are able to provide unambiguous and ecologically relevant indicators of exposure to or effects of toxicants remains highly controversial. In the present paper, we briefly discuss the application of biomarkers in ecotoxicology and ecological risk assessment, and we provide examples of how they have been applied. We conclude that although biomarkers can be helpful for gaining insight regarding the mechanisms causing observed effects of chemicals on whole-organism performance and may, in some cases, provide useful indicators of exposure, individual biomarker responses should not be expected to provide useful predictions of relevant ecological effects--and probably not even predictions of whole-organism effects. Suites of biomarkers are only likely to provide increased predictability if they can be used in a comprehensive mechanistic model that integrates them into a measure of fitness. Until this can be achieved, biomarkers may be useful for hypothesis generation in carefully controlled experiments. However, because the aims of environmental monitoring and ecological risk assessment are to detect and/or predict adverse chemical impacts on populations, communities, and ecosystems, we should be focusing our efforts on improving methods to do this directly. This will involve developing and testing models of appropriate complexity that can describe real-world systems at multiple

  17. Nanoparticles: potential biomarker harvesters.

    PubMed

    Geho, David H; Jones, Clinton D; Petricoin, Emanuel F; Liotta, Lance A

    2006-02-01

    A previously untapped bank of information resides within the low molecular weight proteomic fraction of blood. Intensive efforts are underway to harness this information so that it can be used for early diagnosis of diseases such as cancer. The physicochemical malleability and high surface areas of nanoparticle surfaces make them ideal candidates for developing biomarker harvesting platforms. Given the variety of engineering strategies afforded through nanoparticle technologies, a significant goal is to tailor nanoparticle surfaces to selectively bind a subset of biomarkers, sequestering them for later study using high sensitivity proteomic tests. To date, applications of nanoparticles have largely focused on imaging systems and drug delivery vectors. As such, biomarker harvesting is an underutilized application of nanoparticle technology and is an area of nanotechnology research that will likely undergo substantial growth.

  18. On comparing heterogeneity across biomarkers.

    PubMed

    Steininger, Robert J; Rajaram, Satwik; Girard, Luc; Minna, John D; Wu, Lani F; Altschuler, Steven J

    2015-06-01

    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 costaining 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 costaining. 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.

  19. The NINDS Parkinson's disease biomarkers program: The Ninds Parkinson's Disease Biomarkers Program

    SciTech Connect

    Rosenthal, Liana S.; Drake, Daniel; Alcalay, Roy N.; Babcock, Debra; Bowman, F. DuBois; Chen-Plotkin, Alice; Dawson, Ted M.; Dewey, Richard B.; German, Dwight C.; Huang, Xuemei; Landin, Barry; McAuliffe, Matthew; Petyuk, Vladislav A.; Scherzer, Clemens R.; Hillaire-Clarke, Coryse St.; Sieber, Beth-Anne; Sutherland, Margaret; Tarn, Chi; West, Andrew; Vaillancourt, David; Zhang, Jing; Gwinn, Katrina

    2015-10-07

    Background: Neuroprotection for Parkinson Disease (PD) remains elusive. Biomarkers hold the promise of removing roadblocks to therapy development. The National Institute of Neurological Disorders and Stroke (NINDS) has therefore established the Parkinson’s Disease Biomarkers Program (PDBP) to promote discovery of biomarkers for use in phase II-III clinical trials in PD. Methods: The PDBP facilitates biomarker development to improve neuroprotective clinical trial design, essential for advancing therapeutics for PD. To date, eleven consortium projects in the PDBP are focused on the development of clinical and laboratory-based PD biomarkers for diagnosis, progression tracking, and/or the prediction of prognosis. Seven of these projects also provide detailed longitudinal data and biospecimens from PD patients and controls, as a resource for all PD researchers. Standardized operating procedures and pooled reference samples have been created in order to allow cross-project comparisons and assessment of batch effects. A web-based Data Management Resource facilitates rapid sharing of data and biosamples across the entire PD research community for additional biomarker projects. Results: Here we describe the PDBP, highlight standard operating procedures for the collection of biospecimens and data, and provide an interim report with quality control analysis on the first 1082 participants and 1033 samples with quality control analysis collected as of October 2014. Conclusions: By making samples and data available to academics and industry, encouraging the adoption of existing standards, and providing a resource which complements existing programs, the PDBP will accelerate the pace of PD biomarker research, with the goal of improving diagnostic methods and treatment.

  20. Biomarkers in Parkinson's disease: Advances and strategies.

    PubMed

    Delenclos, Marion; Jones, Daryl R; McLean, Pamela J; Uitti, Ryan J

    2016-01-01

    Parkinson's disease (PD) is a neurodegenerative disorder characterized by progressive motor disturbances and affects more than 1% of the worldwide population. Despite considerable progress in understanding PD pathophysiology, including genetic and biochemical causes, diagnostic approaches lack accuracy and interventions are restricted to symptomatic treatments. PD is a complex syndrome with different clinical subtypes and a wide variability in disorder course. In order to deliver better clinical management of PD patients and discovery of novel therapies, there is an urgent need to find sensitive, specific, and reliable biomarkers. The development of biomarkers will not only help the scientific community to identify populations at risk, but also facilitate clinical diagnosis. Furthermore, these tools could monitor progression, which could ultimately deliver personalized therapeutic strategies. The field of biomarker discovery in PD has attracted significant attention and there have been numerous contributions in recent years. Although none of the parameters have been validated for clinical practice, some candidates hold promise. This review summarizes recent advances in the development of PD biomarkers and discusses new strategies for their utilization.

  1. Biomarkers in Parkinson's disease: Advances and strategies

    PubMed Central

    Delenclos, Marion; Jones, Daryl R.; McLean, Pamela J.; Uitti, Ryan J.

    2016-01-01

    Parkinson's disease (PD) is a neurodegenerative disorder characterized by progressive motor disturbances and affects more than 1% of the worldwide population. Despite considerable progress in understanding PD pathophysiology, including genetic and biochemical causes, diagnostic approaches lack accuracy and interventions are restricted to symptomatic treatments. PD is a complex syndrome with different clinical subtypes and a wide variability in disorder course. In order to deliver better clinical management of PD patients and discovery of novel therapies, there is an urgent need to find sensitive, specific, and reliable biomarkers. The development of biomarkers will not only help the scientific community to identify populations at risk, but also facilitate clinical diagnosis. Furthermore, these tools could monitor progression, which could ultimately deliver personalized therapeutic strategies. The field of biomarker discovery in PD has attracted significant attention and there have been numerous contributions in recent years. Although none of the parameters have been validated for clinical practice, some candidates hold promise. This review summarizes recent advances in the development of PD biomarkers and discusses new strategies for their utilization. PMID:26439946

  2. Link direction for link prediction

    NASA Astrophysics Data System (ADS)

    Shang, Ke-ke; Small, Michael; Yan, Wei-sheng

    2017-03-01

    Almost all previous studies on link prediction have focused on using the properties of the network to predict the existence of links between pairs of nodes. Unfortunately, previous methods rarely consider the role of link direction for link prediction. In fact, many real-world complex networks are directed and ignoring the link direction will mean overlooking important information. In this study, we propose a phase-dynamic algorithm of the directed network nodes to analyse the role of link directions and demonstrate that the bi-directional links and the one-directional links have different roles in link prediction and network structure formation. From this, we propose new directional prediction methods and use six real networks to test our algorithms. In real networks, we find that compared to a pair of nodes which are connected by a one-directional link, a pair of nodes which are connected by a bi-directional link always have higher probabilities to connect to the common neighbours with only bi-directional links (or conversely by one-directional links). We suggest that, in the real networks, the bi-directional links will generally be more informative for link prediction and network structure formation. In addition, we propose a new directional randomized algorithm to demonstrate that the direction of the links plays a significant role in link prediction and network structure formation.

  3. [Biomarkers for anorexia nervosa].

    PubMed

    Sjøgren, Jan Magnus

    2017-01-16

    Biomarkers for anorexia nervosa (AN) which reflect the pathophysiology and relate to the aetiology of the disease, are warranted and could bring us one step closer to targeted treatment of AN. Some leads may be found in the biochemistry which often is found disturbed in AN, although normalization in many aspects is seen at recovery from undernutrition. Recent genome-wide association studies support that genetic factors play a role in the pathophysiology of AN, of which some are independent of BMI-related mechanisms. In this review, an update on blood-based biomarkers of AN is presented.

  4. Lung Cancer Biomarkers.

    PubMed

    Villalobos, Pamela; Wistuba, Ignacio I

    2017-02-01

    The molecular characterization of lung cancer has changed the classification and treatment of these tumors, becoming an essential component of pathologic diagnosis and oncologic therapy decisions. Through the recognition of novel biomarkers, such as epidermal growth factor receptor mutations and anaplastic lymphoma kinase translocations, it is possible to identify subsets of patients who benefit from targeted molecular therapies. The success of targeted anticancer therapies and new immunotherapy approaches has created a new paradigm of personalized therapy and has led to accelerated development of new drugs for lung cancer treatment. This article focuses on clinically relevant cancer biomarkers as targets for therapy and potential new targets for drug development.

  5. Biomarkers for systemic lupus erythematosus.

    PubMed

    Ahearn, Joseph M; Liu, Chau-Ching; Kao, Amy H; Manzi, Susan

    2012-04-01

    The urgent need for lupus biomarkers was demonstrated in September 2011 during a Workshop sponsored by the Food and Drug Administration: Potential Biomarkers Predictive of Disease Flare. After 2 days of discussion and more than 2 dozen presentations from thought leaders in both industry and academia, it became apparent that highly sought biomarkers to predict lupus flare have not yet been identified. Even short of the elusive biomarker of flare, few biomarkers for systemic lupus erythematosus (SLE) diagnosis, monitoring, and stratification have been validated and employed for making clinical decisions. This lack of reliable, specific biomarkers for SLE hampers proper clinical management of patients with SLE and impedes development of new lupus therapeutics. As such, the intensity of investigation to identify lupus biomarkers is climbing a steep trajectory, lending cautious optimism that a validated panel of biomarkers for lupus diagnosis, monitoring, stratification, and prediction of flare may soon be in hand.

  6. Prognostic Biomarkers in Ovarian Cancer

    PubMed Central

    Huang, Jie; Hu, Wei; Sood, Anil K

    2014-01-01

    Epithelial ovarian cancer (EOC) remains the most lethal gynecological malignancy despite several decades of progress in diagnosis and treatment. Taking advantage of the robust development of discovery and utility of prognostic biomarkers, clinicians and researchers are developing personalized and targeted treatment strategies. This review encompasses recently discovered biomarkers of ovarian cancer, the utility of published prognostic biomarkers for EOC (especially biomarkers related to angiogenesis and key signaling pathways), and their integration into clinical practice. PMID:22045356

  7. Tracking Biocultural Pathways to Health Disparities: The Value of Biomarkers

    PubMed Central

    Worthman, Carol M.; Costello, E. Jane

    2009-01-01

    Background Cultural factors and biomarkers are emerging emphases in social epidemiology that readily ally with human biology and anthropology. Persistent health challenges and disparities have established biocultural roots, and environment plays an integral role in physical development and function that form the bases of population health. Biomarkers have proven to be valuable tools for investigating biocultural bases of health disparities. Aims We apply recent insights from biology to consider how culture gets under the skin and evaluate the construct of embodiment. We analyze contrasting biomarker models and applications, and propose an integrated model for biomarkers. Three examples from the Great Smoky Mountains Study (GSMS) illustrate these points. Subjects and methods The longitudinal developmental epidemiological GSMS comprises a population-based sample of 1420 children with repeated measures including mental and physical health, life events, household conditions, and biomarkers for pubertal development and allostatic load. Results Analyses using biomarkers resolved competing explanations for links between puberty and depression, identified gender differences in stress at puberty, and revealed interactive effects of birthweight and postnatal adversity on risk for depression at puberty in girls. Conclusion An integrated biomarker model can both enrich epidemiology and illuminate biocultural pathways in population health. PMID:19381986

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. BluePen Biomarkers LLC: integrated biomarker solutions.

    PubMed

    Blair, Ian A; Mesaros, Clementina; Lilley, Patrick; Nunez, Matthew

    2016-06-01

    BluePen Biomarkers provides a unique comprehensive multi-omics biomarker discovery and validation platform. We can quantify, integrate and analyze genomics, proteomics, metabolomics and lipidomics biomarkers, alongside clinical data, demographics and other phenotypic data. A unique bio-inspired signal processing analytic approach is used that has the proven ability to identify biomarkers in a wide variety of diseases. The resulting biomarkers can be used for diagnosis, prognosis, mechanistic studies and predicting treatment response, in contexts from core research through clinical trials. BluePen Biomarkers provides an additional groundbreaking research goal: identifying surrogate biomarkers from different modalities. This not only provides new biological insights, but enables least invasive, least-cost tests that meet or exceed the predictive quality of current tests.

  13. Biomarkers in chronic adult hydrocephalus

    PubMed Central

    Tarnaris, Andrew; Watkins, Laurence D; Kitchen, Neil D

    2006-01-01

    Awareness of the importance of chronic adult hydrocephalus has been raised again with the recent emergence of epidemiological studies. It is estimated that between 5 and 10% of patients suffering from dementia might, in fact, have chronic hydrocephalus. Although, surgical diversion of the cerebrospinal fluid (CSF) represents the only known procedure able to treat the symptoms of this condition, the selection of surgical patients has always been problematic. In the last 40 years, we have become wiser in using appropriate diagnostic tests for the selection of these patients; however, the area of biological markers has so far been overlooked in this condition, in contrast to that for other neurodegenerative disorders and dementias. Biomarkers are biological substances that may be used to indicate either the onset or the presence, and the progression of a clinical condition, being closely linked to its pathophysiology. In such a setting they might assist in the more appropriate selection of patients for shunt surgery. In this article, we have reviewed research carried out in the last 25 years regarding the identification of serum and CSF biomarkers for chronic hydrocephalus, discussed the potential for each one, and finally discussed the limitations for use, as well as future directions and possibilities in this field. It is concluded that tumour-necrosis factor, tau protein, lactate, sulfatide and neurofilament triple protein are the most promising CSF markers for chronic hydrocephalus. At present however, none of these meet the criteria required to justify a change clinical practice. In the future, collaborative multi-centre projects will be needed to obtain more substantial data that overcome the problems that arise from small individual and uncoordinated studies. PMID:17020616

  14. 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.

  15. Biomarkers of Inflammatory Bowel Disease

    PubMed Central

    Fengming, Yi; Jianbing, Wu

    2014-01-01

    Inflammatory bowel disease (IBD) is a chronic disease mostly involved with intestine with unknown etiology. Diagnosis, evaluation of severity, and prognosis are still present as challenges for physicians. An ideal biomarker with the characters such as simple, easy to perform, noninvasive or microinvasive, cheap, rapid, and reproducible is helpful for patients and clinicians. Currently biomarkers applied in clinic include CRP, ESR, pANCA, ASCA, and fecal calprotectin. However, they are far from ideal. Lots of studies are focused on seeking for ideal biomarker for IBD. Herein, the paper reviewed recent researches on biomarkers of IBD to get advances of biomarkers in inflammatory bowel disease. PMID:24963213

  16. Forging Links.

    ERIC Educational Resources Information Center

    Stewig, John Warren

    Blacksmiths and their craft have changed with the times, and as times change for teachers, they too should be forgers of links. Teacher-to-teacher links should extend beyond the faculty lounge to support systems and active groups of individuals concerned about each other. Another personal link can be made by developing a grade level, system-wide…

  17. Evaluating many treatments and biomarkers in oncology: a new design.

    PubMed

    Kaplan, Richard; Maughan, Timothy; Crook, Angela; Fisher, David; Wilson, Richard; Brown, Louise; Parmar, Mahesh

    2013-12-20

    There is a pressing need for more-efficient trial designs for biomarker-stratified clinical trials. We suggest a new approach to trial design that links novel treatment evaluation with the concurrent evaluation of a biomarker within a confirmatory phase II/III trial setting. We describe a new protocol using this approach in advanced colorectal cancer called FOCUS4. The protocol will ultimately answer three research questions for a number of treatments and biomarkers: (1) After a period of first-line chemotherapy, do targeted novel therapies provide signals of activity in different biomarker-defined populations? (2) If so, do these definitively improve outcomes? (3) Is evidence of activity restricted to the biomarker-defined groups? The protocol randomizes novel agents against placebo concurrently across a number of different biomarker-defined population-enriched cohorts: BRAF mutation; activated AKT pathway: PI3K mutation/absolute PTEN loss tumors; KRAS and NRAS mutations; and wild type at all the mentioned genes. Within each biomarker-defined population, the trial uses a multistaged approach with flexibility to adapt in response to planned interim analyses for lack of activity. FOCUS4 is the first test of a protocol that assigns all patients with metastatic colorectal cancer to one of a number of parallel population-enriched, biomarker-stratified randomized trials. Using this approach allows questions regarding efficacy and safety of multiple novel therapies to be answered in a relatively quick and efficient manner, while also allowing for the assessment of biomarkers to help target treatment.

  18. Mapping ethical and social aspects of cancer biomarkers.

    PubMed

    Blanchard, Anne

    2016-12-25

    Cancer biomarkers represent a revolutionary advance toward personalised cancer treatment, promising therapies that are tailored to subgroups of patients sharing similar generic traits. Notwithstanding the optimism driving this development, biomarkers also present an array of social and ethical questions, as witnessed in sporadic debates across different literatures. This review article seeks to consolidate these debates in a mapping of the complex terrain of ethical and social aspects of cancer biomarker research. This mapping was undertaken from the vantage point offered by a working cancer biomarker research centre called the Centre for Cancer Biomarkers (CCBIO) in Norway, according to a dialectic move between the literature and discussions with researchers and practitioners in the laboratory. Starting in the lab, we found that, with the exception of some classical bioethical dilemmas, researchers regarded many issues relative to the ethos of the biomarker community; how the complexity and uncertainty characterising biomarker research influence their scientific norms of quality. Such challenges to the ethos of cancer research remain largely implicit, outside the scope of formal bioethical enquiry, yet form the basis for other social and ethical issues. Indeed, looking out from the lab we see how questions of complexity, uncertainty and quality contribute to debates around social and global justice; undermining policies for the prioritisation of care, framing the stratification of those patients worthy of treatment, and limiting global access to this highly sophisticated research. We go on to discuss biomarker research within the culturally-constructed 'war on cancer' and highlight an important tension between the expectations of 'magic bullets' and the complexity and uncertainty faced in the lab. We conclude by arguing, with researchers in the CCBIO, for greater reflexivity and humility in cancer biomarker research and policy.

  19. 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.

  20. 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...

  1. 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.

  2. 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…

  3. 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…

  4. Inflammatory Biomarkers in Osteoarthritis

    PubMed Central

    Daghestani, Hikmat N.; Kraus, Virginia B.

    2015-01-01

    Summary Osteoarthritis (OA) is highly prevalent and a leading cause of disability worldwide. Despite the global burden of OA, diagnostic tests and treatments for the molecular or early subclinical stages are still not available for clinical use. In recent years, there has been a large shift in the understanding of OA as a “wear and tear” disease to an inflammatory disease. This has been demonstrated through various studies using MRI, ultrasound, histochemistry, and biomarkers. It would of great value to be able to readily identify subclinical and/or sub-acute inflammation, particularly in such a way as to be appropriate for a clinical setting. Here we review several types of biomarkers associated with OA in human studies that point to a role of inflammation in OA. PMID:26521734

  5. 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

  6. Biomarkers for PTSD

    DTIC Science & Technology

    2012-07-01

    smaller dentate/ CA3 hippocampal subfield volumes, lower ambient cortisol levels, and greater cortisol suppression following dexamethasone...administration. It is also predicted that lower neuropeptide Y levels will be associated with smaller Dentate/ CA3 volumes, and that APO E4 polymorphisms will be...associated with smaller Dentate/ CA3 volumes. 5 BODY: The Biomarkers for PTSD study is in the implementation phase. In year 2 of the grant

  7. Stemina biomarker discovery.

    PubMed

    Cezar, Gabriela G; Donley, Elizabeth L R

    2008-09-01

    Stemina Biomarker Discovery was established in 2006 to commercialize technology developed by Dr Gabriela Cezar at the University of Wisconsin (WI, USA). Stemina's cell-based assays arise from the strategic convergence of two cutting edge technologies: metabolomics and human embryonic stem (hES) cells. Stemina analyzes the small molecules secreted by hES cells and differentiated cell types such as neural and heart cells derived from hES cells by liquid chromatography mass spectrometry at its state-of-the-art facilities in Madison, WI, USA. Stemina's first technology platform has identified a dynamic set of small molecules in the extracellular secretome of hES cells secreted in response to exposure to a library of known teratogens. Alterations to small molecules in the biochemical pathway(s) of hES cells are mapped in silico to identify biomarkers of toxicity for drug screening and development in an all human system. These small human molecules may then be translated in vivo as biomarkers of toxic response and disease.

  8. Biomarker Discovery in Animal Health and Disease: The Application of Post-Genomic Technologies

    PubMed Central

    Moore, Rowan E.; Kirwan, Jennifer; Doherty, Mary K.; Whitfield, Phillip D.

    2007-01-01

    Summary: The causes of many important diseases in animals are complex and multifactorial, which present unique challenges. Biomarkers indicate the presence or extent of a biological process, which is directly linked to the clinical manifestations and outcome of a particular disease. Identifying biomarkers or biomarker profiles will be an important step towards disease characterization and management of disease in animals. The emergence of post-genomic technologies has led to the development of strategies aimed at identifying specific and sensitive biomarkers from the thousands of molecules present in a tissue or biological fluid. This review will summarize the current developments in biomarker discovery and will focus on the role of transcriptomics, proteomics and metabolomics in biomarker discovery for animal health and disease. PMID:19662203

  9. 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

  10. 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.

  11. Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

    PubMed Central

    Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; 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

  12. 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

  13. Parkinson's disease biomarkers program brain imaging repository.

    PubMed

    Ofori, Edward; Du, Guangwei; Babcock, Debra; Huang, Xuemei; Vaillancourt, David E

    2016-01-01

    The Parkinson's Disease Biomarkers Program (PDBP) is a multi-site study designed to identify Parkinson's disease (PD) biomarkers that can be used to improve the understanding of PD pathophysiology and to develop tools that provide novel measures to evaluate PD clinical trials. The PDBP consortium comprises numerous individual projects of which two are specifically geared to the development of brain imaging markers for diagnosis, progression, and prognosis of PD or related disorders. All study data from PD patients, atypical Parkinsonian patients, patients with essential tremor, and healthy controls collected from the sites are integrated in the PDBP database and will be publically available. All subjects are asked to submit blood samples, and undergo a battery of clinical evaluations that cover motor, cognitive, and other background information. In addition, a subset of subjects contributed cerebrospinal fluid samples. A restricted access, web-based Data Management Resource facilitates rapid sharing of data and biosamples across the entire PD research community. The PDBP consortium is a useful resource for research and collaboration aimed at the discovery of biomarkers and their use in understanding the pathophysiology of PD.

  14. Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA.

    PubMed

    Lin, Xueju; Tfaily, Malak M; Steinweg, J Megan; Chanton, Patrick; Esson, Kaitlin; Yang, Zamin K; Chanton, Jeffrey P; Cooper, William; Schadt, Christopher W; Kostka, Joel E

    2014-06-01

    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

  15. 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

  16. 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

  17. Qualification of biomarkers for drug development in organ transplantation.

    PubMed

    Burckart, Gilbert J; Amur, Shashi; Goodsaid, Federico M; Lesko, Lawrence J; Frueh, Felix W; Huang, Shiew-Mei; Cavaille-Coll, Marc W

    2008-02-01

    The drug development process is dependent upon having established end points for measuring drug efficacy and adverse effects. New drug development in organ transplantation suffers from having end points which are either outdated or which do not serve the purpose of addressing the current critical drug therapy problems. Numerous biomarkers have been examined in organ transplantation, but almost all would be classified as exploratory for drug development purposes. Some of the possible pathways out of this dilemma include investigator- or consortium-initiated research that would qualify the biomarkers as either probable or known valid biomarkers, help in identification of new end points in transplantation and their associated biomarkers, co-development of a new biomarker and drug for transplantation and the use of new clinical trial design methods which facilitate enriched or stratified transplant patient populations. With new biomarkers and new study design methodologies for drug development, improvement in the drug development process for transplantation is a real possibility that the transplant clinical and research community can help to bring about.

  18. 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.

  19. 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

  20. Biomarkers of Irritable Bowel Syndrome

    PubMed Central

    Kim, Jae Hak; Lin, Eugenia; Pimentel, Mark

    2017-01-01

    Traditionally, irritable bowel syndrome (IBS) has not been regarded as an organic disease, and the pathophysiology of IBS is heterogeneous. Currently, the diagnosis of IBS is based upon the Rome diagnostic criteria. The performance of these criteria is only modest in predicting IBS, and moreover their validation is lacking. Additionally, as functional symptoms are common in the general population, healthy controls or volunteers are difficult to define and there is currently no definition of “normal” in the Rome criteria. Due to the weaknesses of the current diagnostic criteria, patients and doctors expect new gold standard diagnostic tools. Various etiologic mechanisms result in potential biomarkers. The focus of this research has been to find non-invasive biomarkers from serum, breath gas, and fecal materials. Though biomarkers should be based on biological and pathogenic processes, most biomarkers for IBS have been developed to identify organic diseases and therefore eliminate IBS. To date, these types of biomarkers for IBS have been disappointing. The purposes of developing biomarkers include improvement of diagnosis, differentiation from other organic diseases, and discrimination of IBS subtypes. A true mechanistic biomarker would make it possible to rule in IBS, rather than to rule out other organic diseases. New serologic biomarkers for diarrhea-predominant IBS have been introduced based on the pathophysiologic findings from a rat model and validation in a large-scale clinical trial. Further investigations of abnormal organic findings from each subtype of IBS would enable the development of new, simple subtype-specific biomarkers. PMID:27817184

  1. Molecular Biomarkers of Knee Pathology.

    PubMed

    Cuellar, Vanessa; Strauss, Eric

    2017-01-01

    The identification of biomarkers has become increasingly important in our fundamental understanding of the molecular basis for disease and subsequently in the advancement of modern medicine. Biomarkers have been identified in a plethora of normal and pathologic conditions and are most often found in blood, tissue, or synovial fluid. Orthopaedic research has more recently focused on biomarkers of cartilage and joint diseases, with an emphasis on understanding the molecular underpinnings of their pathophysiology. This article focuses on the biomarkers identified to date in several select knee pathologies and how further research can contribute to new diagnostic tools and targeted therapeutics.

  2. Screening and Identification of APOC1 as a Novel Potential Biomarker for Differentiate of Mycoplasma pneumoniae in Children

    PubMed Central

    Li, Jieqiong; Sun, Lin; Xu, Fang; Qi, Hui; Shen, Chen; Jiao, Weiwei; Xiao, Jing; Li, Qinjing; Xu, Baoping; Shen, Adong

    2016-01-01

    Background: Although Mycoplasma pneumoniae (MP) is a common cause of community-acquired pneumonia (CAP) in children, the currently used diagnostic methods are not optimal. Proteomics is increasingly being used to study the biomarkers of infectious diseases. Methods: Label-free quantitative proteomics and liquid chromatography-mass/mass spectrometry were used to analyze the fold change of protein expression in plasma of children with MP pneumonia (MPP), infectious disease control (IDC), and healthy control (HC) groups. Selected proteins that can distinguish MPP from HC and IDC were further validated by enzyme-linked immunosorbent assay (ELISA). Results: After multivariate analyses, 27 potential plasma biomarkers were identified to be expressed differently among child MPP, HC, and IDC groups. Among these proteins, SERPINA3, APOC1, ANXA6, KNTC1, and CFLAR were selected for ELISA verification. SERPINA3, APOC1, and CFLAR levels were significantly different among the three groups and the ratios were consistent with the trends of proteomics results. A comparison of MPP patients and HC showed APOC1 had the largest area under the curve (AUC) of 0.853, with 77.6% sensitivity and 81.1% specificity. When APOC1 levels were compared between MPP and IDC patients, it also showed a relatively high AUC of 0.882, with 77.6% sensitivity and 85.3% specificity. Conclusion: APOC1 is a potential biomarker for the rapid and noninvasive diagnosis of MPP in children. The present finding may offer new insights into the pathogenesis and biomarker selection of MPP in children. PMID:28018301

  3. 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

  4. 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...

  5. 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.

  6. A xandarellid artiopodan from Morocco – a middle Cambrian link between soft-bodied euarthropod communities in North Africa and South China

    PubMed Central

    Ortega-Hernández, Javier; Azizi, Abdelfattah; Hearing, Thomas W.; Harvey, Thomas H. P.; Edgecombe, Gregory D.; Hafid, Ahmid; El Hariri, Khadija

    2017-01-01

    Xandarellida is a well-defined clade of Lower Palaeozoic non-biomineralized artiopodans that is exclusively known from the early Cambrian (Stage 3) Chengjiang biota of South China. Here we describe a new member of this group, Xandarella mauretanica sp. nov., from the middle Cambrian (Stage 5) Tatelt Formation of Morocco, making this the first non-trilobite Cambrian euarthropod known from North Africa. X. mauretanica sp. nov. represents the youngest occurrence of Xandarellida – extending its stratigraphic range by approximately 10 million years – and expands the palaeobiogeographic distribution of the group to the high southern palaeolatitudes of West Gondwana. The new species provides insights into the lightly sclerotized ventral anatomy of Xandarellida, and offers stratigraphically older evidence for a palaeobiogeographic connection between Burgess Shale-type euarthropod communities in North Africa and South China, relative to the (Tremadocian) Fezouata biota. PMID:28211461

  7. A xandarellid artiopodan from Morocco - a middle Cambrian link between soft-bodied euarthropod communities in North Africa and South China.

    PubMed

    Ortega-Hernández, Javier; Azizi, Abdelfattah; Hearing, Thomas W; Harvey, Thomas H P; Edgecombe, Gregory D; Hafid, Ahmid; El Hariri, Khadija

    2017-02-17

    Xandarellida is a well-defined clade of Lower Palaeozoic non-biomineralized artiopodans that is exclusively known from the early Cambrian (Stage 3) Chengjiang biota of South China. Here we describe a new member of this group, Xandarella mauretanica sp. nov., from the middle Cambrian (Stage 5) Tatelt Formation of Morocco, making this the first non-trilobite Cambrian euarthropod known from North Africa. X. mauretanica sp. nov. represents the youngest occurrence of Xandarellida - extending its stratigraphic range by approximately 10 million years - and expands the palaeobiogeographic distribution of the group to the high southern palaeolatitudes of West Gondwana. The new species provides insights into the lightly sclerotized ventral anatomy of Xandarellida, and offers stratigraphically older evidence for a palaeobiogeographic connection between Burgess Shale-type euarthropod communities in North Africa and South China, relative to the (Tremadocian) Fezouata biota.

  8. A xandarellid artiopodan from Morocco – a middle Cambrian link between soft-bodied euarthropod communities in North Africa and South China

    NASA Astrophysics Data System (ADS)

    Ortega-Hernández, Javier; Azizi, Abdelfattah; Hearing, Thomas W.; Harvey, Thomas H. P.; Edgecombe, Gregory D.; Hafid, Ahmid; El Hariri, Khadija

    2017-02-01

    Xandarellida is a well-defined clade of Lower Palaeozoic non-biomineralized artiopodans that is exclusively known from the early Cambrian (Stage 3) Chengjiang biota of South China. Here we describe a new member of this group, Xandarella mauretanica sp. nov., from the middle Cambrian (Stage 5) Tatelt Formation of Morocco, making this the first non-trilobite Cambrian euarthropod known from North Africa. X. mauretanica sp. nov. represents the youngest occurrence of Xandarellida – extending its stratigraphic range by approximately 10 million years – and expands the palaeobiogeographic distribution of the group to the high southern palaeolatitudes of West Gondwana. The new species provides insights into the lightly sclerotized ventral anatomy of Xandarellida, and offers stratigraphically older evidence for a palaeobiogeographic connection between Burgess Shale-type euarthropod communities in North Africa and South China, relative to the (Tremadocian) Fezouata biota.

  9. 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.

  10. Biomarkers of tobacco smoke exposure.

    PubMed

    Mattes, William; Yang, Xi; Orr, Michael S; Richter, Patricia; Mendrick, Donna L

    2014-01-01

    Diseases and death caused by exposure to tobacco smoke have become the single most serious preventable public health concern. Thus, biomarkers that can monitor tobacco exposure and health effects can play a critical role in tobacco product regulation and public health policy. Biomarkers of exposure to tobacco toxicants are well established and have been used in population studies to establish public policy regarding exposure to second-hand smoke, an example being the nicotine metabolite cotinine, which can be measured in urine. Biomarkers of biological response to tobacco smoking range from those indicative of inflammation to mRNA and microRNA patterns related to tobacco use and/or disease state. Biomarkers identifying individuals with an increased risk for a pathological response to tobacco have also been described. The challenge for any novel technology or biomarker is its translation to clinical and/or regulatory application, a process that requires first technical validation of the assay and then careful consideration of the context the biomarker assay may be used in the regulatory setting. Nonetheless, the current efforts to investigate new biomarker of tobacco smoke exposure promise to offer powerful new tools in addressing the health hazards of tobacco product use. This review will examine such biomarkers, albeit with a focus on those related to cigarette smoking.

  11. 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.

  12. Emerging biomarkers in psoriatic arthritis.

    PubMed

    Paek, So Yeon; Han, Ling; Weiland, Matthew; Lu, Chuan-Jian; McKinnon, Kathleen; Zhou, Li; Lim, Henry W; Elder, James T; Mi, Qing-Sheng

    2015-12-01

    Psoriasis is an immune-mediated skin disease which affects 2-4% of the worldwide population. Approximately 20-30% of patients with psoriasis develop psoriatic arthritis (PsA), a frequently destructive and disabling condition. As skin manifestations precede joint symptoms in nearly all patients with PsA, identification of biomarkers for early prediction of joint damage is an important clinical need. Because not all patients with PsA respond to treatment in the same fashion, identification of biomarkers capable of predicting therapeutic response is also imperative. Here, we review existing literature and discuss current investigations to identify potential biomarkers for PsA disease activity, with particular emphasis on microRNAs as novel markers of interest. Serum (soluble) biomarkers, peripheral osteoclast precursor as cellular biomarkers, and genetic loci associated with skin and joint disease are also reviewed.

  13. Stable Isotope Ratios as Biomarkers of Diet for Health Research.

    PubMed

    O'Brien, Diane M

    2015-01-01

    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 US 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.

  14. 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

  15. 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

  16. Food and Nutrition Insecurity in Selected Rural Communities of KwaZulu-Natal, South Africa—Linking Human Nutrition and Agriculture

    PubMed Central

    Govender, Laurencia; Pillay, Kirthee; Siwela, Muthulisi; Modi, Albert; Mabhaudhi, Tafadzwanashe

    2016-01-01

    Lack of access to nutritious and balanced diets remains a major impediment to the health and well-being of people living in rural areas. The study utilizes a qualitative systematic approach to conduct an environmental scan and review of scientific literature of studies conducted in South Africa, specifically KwaZulu-Natal (KZN). Availability and access to nutritious, diverse and balanced diets were identified as key constraints for achieving food and nutrition security as well as for human health and well-being. This has led to both under- and over-nutrition, with the former, in particular stunting, affecting children under 5 years. A high incidence of over-nutrition, both overweight and obesity, was observed among black African females. In South Africa, poor people rely mostly on social grants and cannot afford a balanced diet. Under these circumstances, agriculture could be used to increase availability and access to diverse and nutritious foods for the attainment of a balanced diet. The wider use of traditional vegetable crops and pulses could improve availability and access to healthy and locally available alternatives. The promotion of household and community food gardens, and the use of nutrient dense crops with low levels of water use, i.e., high nutritional water productivity, offers prospects for addressing malnutrition in poor rural areas. PMID:28036008

  17. Effort-reward imbalance at work and driving anger in an Australian community sample: is there a link between work stress and road rage?

    PubMed

    Hoggan, Benjamin L; Dollard, Maureen F

    2007-11-01

    Both workplace stress and road rage are reported to be on the increase. This study examined the effort-reward imbalance (ERI) model of work stress and its relationship with general anger and driving anger in a community sample of 130 Australian workers. It also examined international differences in driving anger, with Australian motorists reporting lower levels of driving anger than American motorists but higher levels than British motorists. Hierarchical multiple regressions confirmed ERI increased driving anger via the mediating variables of general anger and overcommitment; individuals suffering ERI may develop increased general anger or overcommitment, in turn increasing propensity to experience driving anger. Regressions also showed that overcommitment (but not general anger) moderated the effect of ERI on driving anger; ERI has a greater influence on increasing driving anger in individuals with high overcommitment at work. The results have considerable implications for the safety and emotional health of individuals who perceive an imbalance between their efforts and rewards at work, and overcommitted individuals may be at greater risk. The wider implications of the relationship between work stress, emotional well-being and driving anger in employees, along with the potential of driver education interventions, are discussed as public health issues.

  18. Food and Nutrition Insecurity in Selected Rural Communities of KwaZulu-Natal, South Africa-Linking Human Nutrition and Agriculture.

    PubMed

    Govender, Laurencia; Pillay, Kirthee; Siwela, Muthulisi; Modi, Albert; Mabhaudhi, Tafadzwanashe

    2016-12-27

    Lack of access to nutritious and balanced diets remains a major impediment to the health and well-being of people living in rural areas. The study utilizes a qualitative systematic approach to conduct an environmental scan and review of scientific literature of studies conducted in South Africa, specifically KwaZulu-Natal (KZN). Availability and access to nutritious, diverse and balanced diets were identified as key constraints for achieving food and nutrition security as well as for human health and well-being. This has led to both under- and over-nutrition, with the former, in particular stunting, affecting children under 5 years. A high incidence of over-nutrition, both overweight and obesity, was observed among black African females. In South Africa, poor people rely mostly on social grants and cannot afford a balanced diet. Under these circumstances, agriculture could be used to increase availability and access to diverse and nutritious foods for the attainment of a balanced diet. The wider use of traditional vegetable crops and pulses could improve availability and access to healthy and locally available alternatives. The promotion of household and community food gardens, and the use of nutrient dense crops with low levels of water use, i.e., high nutritional water productivity, offers prospects for addressing malnutrition in poor rural areas.

  19. 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.

  20. Molecular biomarkers of neurodegeneration.

    PubMed

    Höglund, Kina; Salter, Hugh

    2013-11-01

    Neuronal dysfunction and degeneration are central events of a number of major diseases with significant unmet need. Neuronal dysfunction may not necessarily be the result of cell death, but may also be due to synaptic damage leading to impaired neuronal cell signaling or long-term potentiation. Once degeneration occurs, it is unclear whether axonal or synaptic loss comes first or whether this precedes neuronal cell death. In this review we summarize the pathophysiology of four major neurodegenerative diseases; Alzheimer's disease, Parkinson's disease, multiple sclerosis and amyotrophic lateral sclerosis (Lou Gehrig's disease) For each of these diseases, we describe how biochemical biomarkers are currently understood in relation to the pathophysiology and in terms of neuronal biology, and we discuss the clinical and diagnostic utility of these potential tools, which are at present limited. We discuss how markers may be used to drive drug development and clinical practice.

  1. Inflammatory biomarkers for AMD.

    PubMed

    Stanton, Chloe M; Wright, Alan F

    2014-01-01

    Age-related macular degeneration (AMD) is the leading cause of blindness worldwide, affecting an estimated 50 million individuals aged over 65 years.Environmental and genetic risk-factors implicate chronic inflammation in the etiology of AMD, contributing to the formation of drusen, retinal pigment epithelial cell dysfunction and photoreceptor cell death. Consistent with a role for chronic inflammation in AMD pathogenesis, several inflammatory mediators, including complement components, chemokines and cytokines, are elevated at both the local and systemic levels in AMD patients. These mediators have diverse roles in the alternative complement pathway, including recruitment of inflammatory cells, activation of the inflammasome, promotion of neovascularisation and in the resolution of inflammation. The utility of inflammatory biomarkers in assessing individual risk and progression of the disease is controversial. However, understanding the role of these inflammatory mediators in AMD onset, progression and response to treatment may increase our knowledge of disease pathogenesis and provide novel therapeutic options in the future.

  2. 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

  3. Community and Virtual Community.

    ERIC Educational Resources Information Center

    Ellis, David; Oldridge, Rachel; Vasconcelos, Ana

    2004-01-01

    Presents a literature review that covers the following topics related to virtual communities: (1) information and virtual community; (2) virtual communities and communities of practice; (3) virtual communities and virtual arenas, including virtual community networks; and (4) networked virtual communities. (Contains 175 references.) (MES)

  4. 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

  5. Systematic Review of Biomarkers To Monitor Therapeutic Response in Leishmaniasis

    PubMed Central

    Kip, Anke E.; Balasegaram, Manica; Beijnen, Jos H.; Schellens, Jan H. M.; de Vries, Peter J.

    2014-01-01

    Recently, there has been a renewed interest in the development of new drugs for the treatment of leishmaniasis. This has spurred the need for pharmacodynamic markers to monitor and compare therapies specifically for visceral leishmaniasis, in which the primary recrudescence of parasites is a particularly long-term event that remains difficult to predict. We performed a systematic review of studies evaluating biomarkers in human patients with visceral, cutaneous, and post-kala-azar dermal leishmaniasis, which yielded a total of 170 studies in which 53 potential pharmacodynamic biomarkers were identified. In conclusion, the large majority of these biomarkers constituted universal indirect markers of activation and subsequent waning of cellular immunity and therefore lacked specificity. Macrophage-related markers demonstrate favorable sensitivity and times to normalcy, but more evidence is required to establish a link between these markers and clinical outcome. Most promising are the markers directly related to the parasite burden, but future effort should be focused on optimization of molecular or antigenic targets to increase the sensitivity of these markers. In general, future research should focus on the longitudinal evaluation of the pharmacodynamic biomarkers during treatment, with an emphasis on the correlation of studied biomarkers and clinical parameters. PMID:25367913

  6. Ethical Issues in Measuring Biomarkers in Children’s Environmental Health

    PubMed Central

    Sly, Peter D.; Eskenazi, Brenda; Pronczuk, Jenny; Šrám, Radim; Diaz-Barriga, Fernando; Machin, Diego Gonzalez; Carpenter, David O.; Surdu, Simona; Meslin, Eric M.

    2009-01-01

    Background Studying the impact of environmental exposures is important in children because they are more vulnerable to adverse effects on growth, development, and health. Assessing exposure in children is difficult, and measuring biomarkers is potentially useful. Research measuring biomarkers in children raises a number of ethical issues, some of which relate to children as research subjects and some of which are specific to biomarker research. Objective As an international group with experience in pediatric research, biomarkers, and the ethics of research in children, we highlight the ethical issues of undertaking biomarker research in children in these environments. Discussion Significant issues include undertaking research in vulnerable communities, especially in developing countries; managing community expectations; obtaining appropriate consent to conduct the research; the potential conflicts of obtaining permission from an ethics review board in an economically developed country to perform research in a community that may have different cultural values; returning research results to participants and communities when the researchers are uncertain of how to interpret the results; and the conflicting ethical obligations of maintaining participant confidentiality when information about harm or illegal activities mandate reporting to authorities. Conclusion None of these challenges are insurmountable and all deserve discussion. Pediatric biomarker research is necessary for advancing child health. PMID:19672395

  7. 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.

  8. Can Molecular Biomarkers Change the Paradigm of Pancreatic Cancer Prognosis?

    PubMed Central

    Garcia-Foncillas, Jesus

    2016-01-01

    Pancreatic ductal adenocarcinoma is one of the most lethal types of tumour, and its incidence is rising worldwide. Although survival can be improved when these tumours are detected at an early stage, this cancer is usually asymptomatic, and the disease only becomes apparent after metastasis. The only prognostic biomarker approved by the FDA to date is carbohydrate antigen 19-9 (CA19-9); however, the specificity of this biomarker has been called into question, and diagnosis is usually based on clinical parameters. Tumour size, degree of differentiation, lymph node status, presence of distant metastasis at diagnosis, protein levels of KI-67 or C-reactive protein, and mutational status of P53, KRAS, or BRCA2 are the most useful biomarkers in clinical practice. In addition to these, recent translational research has provided evidence of new biomarkers based on different molecules involved in endoplasmic reticulum stress, epithelial-to-mesenchymal transition, and noncoding RNA panels, especially microRNAs and long noncoding RNAs. These new prospects open new paths to tumour detection using minimally or noninvasive techniques such as liquid biopsies. To find sensitive and specific biomarkers to manage these patients constitutes a challenge for the research community and for public health policies. PMID:27689078

  9. Development of Parkinson's disease biomarkers.

    PubMed

    Prakash, Kumar M; Tan, Eng-King

    2010-12-01

    Parkinson's disease (PD) is the most common neurodegenerative movement disorder, affecting over 6 million people worldwide. It is anticipated that the number of affected individuals may increase significantly in the most populous nations by 2030. During the past 20 years, much progress has been made in identifying and assessing various potential clinical, biochemical, imaging and genetic biomarkers for PD. Despite the wealth of information, development of a validated biomarker for PD is still ongoing. It is hoped that reliable and well-validated biomarkers will provide critical clues to assist in the diagnosis and management of Parkinson's disease patients in the near future.

  10. Urinary Biomarkers for Prostate Cancer.

    PubMed

    Tosoian, Jeffrey J; Ross, Ashley E; Sokoll, Lori J; Partin, Alan W; Pavlovich, Christian P

    2016-02-01

    In light of the overdiagnosis and overtreatment associated with widespread prostate-specific antigen-based screening, controversy persists surrounding the detection and diagnosis of prostate cancer (PCa). Given its anatomic proximity to the prostate, urine has been proposed as a noninvasive substrate for prostatic biomarkers. With greater understanding of the molecular pathways of carcinogenesis and significant technological advances, the breadth of potential biomarkers is substantial. In this review, the authors aim to provide an evidence-based assessment of current and emerging urinary biomarkers used in the detection and prognostication of PCa and high-grade PCa, with particular attention on clinically relevant findings.

  11. 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

  12. Microbial community dynamics and biodegradation of polycyclic aromatic hydrocarbons in polluted marine sediments in Hong Kong.

    PubMed

    Wang, Y F; Tam, N F Y

    2011-01-01

    Dynamics of microbial community and biodegradation of polycyclic aromatic hydrocarbons (PAHs) in polluted marine sediments, artificially spiked with a mixture of PAHs (fluorene, phenanthrene, fluoranthene and pyrene), were examined for a period of 60 days. Microbial communities were characterised by bacterial counts, ester-linked fatty acid methyl ester (EL-FAME) analysis and denaturing gradient gel electrophoresis (DGGE). A noted reduction in species diversity occurred only in the high PAH level treatment at onset. Both EL-FAME and DGGE demonstrated a marked shift in microbial community, in all the PAH level treatments, afterwards, with increases in the number of fatty acid degraders, the relative abundance of fatty acid biomarkers for gram-negative bacteria and a decrease in species diversity. The shift was also accompanied by the significant decrease in PAH concentrations. By the end of the experiment, diversity indices, based on both approaches, recovered when PAH concentrations declined to their background levels, except in the high PAH level treatment.

  13. 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

  14. 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.

  15. 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

  16. Biomarkers in localized prostate cancer.

    PubMed

    Ferro, Matteo; Buonerba, Carlo; Terracciano, Daniela; Lucarelli, Giuseppe; Cosimato, Vincenzo; Bottero, Danilo; Deliu, Victor M; Ditonno, Pasquale; Perdonà, Sisto; Autorino, Riccardo; Coman, Ioman; De Placido, Sabino; Di Lorenzo, Giuseppe; De Cobelli, Ottavio

    2016-02-01

    Biomarkers can improve prostate cancer diagnosis and treatment. Accuracy of prostate-specific antigen (PSA) for early diagnosis of prostate cancer is not satisfactory, as it is an organ- but not cancer-specific biomarker, and it can be improved by using models that incorporate PSA along with other test results, such as prostate cancer antigen 3, the molecular forms of PSA (proPSA, benign PSA and intact PSA), as well as kallikreins. Recent reports suggest that new tools may be provided by metabolomic studies as shown by preliminary data on sarcosine. Additional molecular biomarkers have been identified by the use of genomics, proteomics and metabolomics. We review the most relevant biomarkers for early diagnosis and management of localized prostate cancer.

  17. 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

  18. Biomarkers of satiation and satiety.

    PubMed

    de Graaf, Cees; Blom, Wendy A M; Smeets, Paul A M; Stafleu, Annette; Hendriks, Henk F J

    2004-06-01

    This review's objective is to give a critical summary of studies that focused on physiologic measures relating to subjectively rated appetite, actual food intake, or both. Biomarkers of satiation and satiety may be used as a tool for assessing the satiating efficiency of foods and for understanding the regulation of food intake and energy balance. We made a distinction between biomarkers of satiation or meal termination and those of meal initiation related to satiety and between markers in the brain [central nervous system (CNS)] and those related to signals from the periphery to the CNS. Various studies showed that physicochemical measures related to stomach distension and blood concentrations of cholecystokinin and glucagon-like peptide 1 are peripheral biomarkers associated with meal termination. CNS biomarkers related to meal termination identified by functional magnetic resonance imaging and positron emission tomography are indicators of neural activity related to sensory-specific satiety. These measures cannot yet serve as a tool for assessing the satiating effect of foods, because they are not yet feasible. CNS biomarkers related to satiety are not yet specific enough to serve as biomarkers, although they can distinguish between extreme hunger and fullness. Three currently available biomarkers for satiety are decreases in blood glucose in the short term (<5 min), which have been shown to be involved in meal initiation; leptin changes during longer-term (>2-4 d) negative energy balance; and ghrelin concentrations, which have been implicated in both short-term and long-term energy balance. The next challenge in this research area is to identify food ingredients that have an effect on biomarkers of satiation, satiety, or both. These ingredients may help consumers to maintain their energy intake at a level consistent with a healthy body weight.

  19. Targeted proteomic strategy for clinical biomarker discovery.

    PubMed

    Schiess, Ralph; Wollscheid, Bernd; Aebersold, Ruedi

    2009-02-01

    The high complexity and large dynamic range of blood plasma proteins currently prohibit the sensitive and high-throughput profiling of disease and control plasma proteome sample sets large enough to reliably detect disease indicating differences. To circumvent these technological limitations we describe here a new two-stage strategy for the mass spectrometry (MS) assisted discovery, verification and validation of disease biomarkers. In an initial discovery phase N-linked glycoproteins with distinguishable expression patterns in primary normal and diseased tissue are detected and identified. In the second step the proteins identified in the initial phase are subjected to targeted MS analysis in plasma samples, using the highly sensitive and specific selected reaction monitoring (SRM) technology. Since glycosylated proteins, such as those secreted or shed from the cell surface are likely to reside and persist in blood, the two-stage strategy is focused on the quantification of tissue derived glycoproteins in plasma. The focus on the N-glycoproteome not only reduces the complexity of the analytes, but also targets an information-rich subproteome which is relevant for remote sensing of diseases in the plasma. The N-glycoprotein based biomarker discovery and validation workflow reviewed here allows for the robust identification of protein candidate panels that can finally be selectively monitored in the blood plasma at high sensitivity in a reliable, non-invasive and quantitative fashion.

  20. 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

  1. Biomarkers of opiate use.

    PubMed

    Stefanidou, M; Athanaselis, S; Spiliopoulou, C; Dona, A; Maravelias, C

    2010-11-01

    The interpretation of toxicological findings is critical for the thorough investigation of the use and abuse of psychoactive substances. A positive analytical result for a sample taken could usually result in criminal proceedings and a punitive outcome for the defendant whose sample was analysed. The detection of markers of illicit opiate misuse is important both in the management of substance misuse and in the postmortem identification of illicit opiate use. The aim of this study was to emphasise the role of opiate biomarkers available at the laboratory and in the clinical environment. Urine remains the biological tool of choice for qualitative detection of illicit drug use in a clinical setting, while quantitative accuracy remains strictly the domain of blood. Accurate interpretation of the screening tests within a clinical setting alongside other relevant information remains the key to the usefulness of any test. Moreover, the finding of a morphine/codeine concentration ratio in blood exceeding unity is a strong evidence that the person had used heroin, as opposed to having taken a prescription analgesic drug containing codeine.

  2. BIOMARKERS for CHRONIC FATIGUE

    PubMed Central

    Broderick, Gordon; Fletcher, Mary Ann

    2012-01-01

    Fatigue that persists for 6 months or more is termed chronic fatigue. Chronic fatigue (CF) in combination with a minimum of 4 of 8 symptoms and the absence of diseases that could explain these symptoms, constitute the case definition for chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME). Inflammation, immune system activation, autonomic dysfunction, impaired functioning in the hypothalamic-pituitary-adrenal axis, and neuroendocrine dysregulation have all been suggested as root causes of fatigue. The identification of objective markers consistently associated with CFS/ME is an important goal in relation to diagnosis and treatment, as the current case definitions are based entirely on physical signs and symptoms. This review is focused on the recent literature related to biomarkers for fatigue associated with CFS/ME and, for comparison, those associated with other diseases. These markers are distributed across several of the body’s core regulatory systems. A complex construct of symptoms emerges from alterations and/or dysfunctions in the nervous, endocrine and immune systems. We propose that new insight will depend on our ability to develop and deploy an integrative profiling of CFS/ME pathogenesis at the molecular level. Until such a molecular signature is obtained efforts to develop effective treatments will continue to be severely limited. PMID:22732129

  3. 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

  4. 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

  5. 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.

  6. Global standardization measurement of cerebral spinal fluid for Alzheimer's disease: an update from the Alzheimer's Association Global Biomarkers Consortium.

    PubMed

    Carrillo, Maria C; Blennow, Kaj; Soares, Holly; Lewczuk, Piotr; Mattsson, Niklas; Oberoi, Pankaj; Umek, Robert; Vandijck, Manu; Salamone, Salvatore; Bittner, Tobias; Shaw, Leslie M; Stephenson, Diane; Bain, Lisa; Zetterberg, Henrik

    2013-03-01

    Recognizing that international collaboration is critical for the acceleration of biomarker standardization efforts and the efficient development of improved diagnosis and therapy, the Alzheimer's Association created the Global Biomarkers Standardization Consortium (GBSC) in 2010. The consortium brings together representatives of academic centers, industry, and the regulatory community with the common goal of developing internationally accepted common reference standards and reference methods for the assessment of cerebrospinal fluid (CSF) amyloid β42 (Aβ42) and tau biomarkers. Such standards are essential to ensure that analytical measurements are reproducible and consistent across multiple laboratories and across multiple kit manufacturers. Analytical harmonization for CSF Aβ42 and tau will help reduce confusion in the AD community regarding the absolute values associated with the clinical interpretation of CSF biomarker results and enable worldwide comparison of CSF biomarker results across AD clinical studies.

  7. Biomarkers of peat-forming plants and their signal in tidal flat sediments of the german bight

    NASA Astrophysics Data System (ADS)

    Wöstmann, R.; Köller, C.; Rullkötter, J.

    2003-04-01

    Induced by the Holocene sea level rise a number of different peat layers developed in the surface of today´s Wadden Sea of NW Germany. Furthermore, lipid analysis of Wadden Sea sediments showed a significant component of terrestrial organic matter derived from erosion of peat layers in this highly dynamic area. In order to characterise these peats and their remnants in tidal flat sediments in a paleochemotaxonomical way, recent plant material as well as different types of peats were selected for biomarker investigation. Recent plant material was linked paleochemotaxonomically to deposited peats and Wadden Sea sediments by means of selected biomarkers. A significant variation of the n-alkane distribution pattern between raised bog plants and fen plants was detected. The raised bog plants showed an n-alkane maximum at n-C31, the fen plants at n-C27 and n-C29. This is in agreement with results of the botanical and geochemical analysis of different types of Holocene peat layers in this area. In the selected Wadden Sea sediment core the n-alkane distribution showed an odd over even carbon number predominance with maxima at n-C27, n-C29 or n-C31, indicating an origin from different peat types. In addition, pentacyclic triterpenoids are characteristic biomarkers for bog and fen plant communities. Their distribution patterns and total amounts allow a clear distinction between raised-bog-forming plants and fen-peat-forming plants. Whereas all analysed fen-peat-forming plants were barren of triterpenoids, raised-bog-forming plants like Erica tetralix contain triterpenoids at a level of more than 10% of the total lipid extract. All other bog-forming plants also contain high amounts of triterpenoids like a-amyrin, ß-amyrin, friedelin, lupeol, multiflorenon and taraxerol. However, individual triterpenoids are not plant-specific biomarkers because of possible diagenetic effects. When triterpenoids are found in fen peats they are due to the influence of non-peat-forming plant

  8. 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.

  9. Statistical considerations when analyzing biomarker data.

    PubMed

    Beam, Craig A

    2015-11-01

    Biomarkers have become, and will continue to become, increasingly important to clinical immunology research. Yet, biomarkers often present new problems and raise new statistical and study design issues to scientists working in clinical immunology. In this paper I discuss statistical considerations related to the important biomarker problems of: 1) The design and analysis of clinical studies which seek to determine whether changes from baseline in a biomarker are associated with changes in a metabolic outcome; 2) The conditions that are required for a biomarker to be considered a "surrogate"; 3) Considerations that arise when analyzing whether or not a predictive biomarker could act as a surrogate endpoint; 4) Biomarker timing relative to the clinical endpoint; 5) The problem of analyzing studies that measure many biomarkers from few subjects; and, 6) The use of statistical models when analyzing biomarker data arising from count data.

  10. 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

  11. Proteome Screening of Pleural Effusions Identifies Galectin 1 as a Diagnostic Biomarker and Highlights Several Prognostic Biomarkers for Malignant Mesothelioma*

    PubMed Central

    Mundt, Filip; Johansson, Henrik J.; Forshed, Jenny; Arslan, Sertaç; Metintas, Muzaffer; Dobra, Katalin; Lehtiö, Janne; Hjerpe, Anders

    2014-01-01

    Malignant mesothelioma is an aggressive asbestos-induced cancer, and affected patients have a median survival of approximately one year after diagnosis. It is often difficult to reach a conclusive diagnosis, and ancillary measurements of soluble biomarkers could increase diagnostic accuracy. Unfortunately, few soluble mesothelioma biomarkers are suitable for clinical application. Here we screened the effusion proteomes of mesothelioma and lung adenocarcinoma patients to identify novel soluble mesothelioma biomarkers. We performed quantitative mass-spectrometry-based proteomics using isobaric tags for quantification and used narrow-range immobilized pH gradient/high-resolution isoelectric focusing (pH 4–4.25) prior to analysis by means of nano liquid chromatography coupled to MS/MS. More than 1,300 proteins were identified in pleural effusions from patients with malignant mesothelioma (n = 6), lung adenocarcinoma (n = 6), or benign mesotheliosis (n = 7). Data are available via ProteomeXchange with identifier PXD000531. The identified proteins included a set of known mesothelioma markers and proteins that regulate hallmarks of cancer such as invasion, angiogenesis, and immune evasion, plus several new candidate proteins. Seven candidates (aldo-keto reductase 1B10, apolipoprotein C-I, galectin 1, myosin-VIIb, superoxide dismutase 2, tenascin C, and thrombospondin 1) were validated by enzyme-linked immunosorbent assays in a larger group of patients with mesothelioma (n = 37) or metastatic carcinomas (n = 25) and in effusions from patients with benign, reactive conditions (n = 16). Galectin 1 was identified as overexpressed in effusions from lung adenocarcinoma relative to mesothelioma and was validated as an excellent predictor for metastatic carcinomas against malignant mesothelioma. Galectin 1, aldo-keto reductase 1B10, and apolipoprotein C-I were all identified as potential prognostic biomarkers for malignant mesothelioma. This analysis of the effusion proteome

  12. 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…

  13. Calprotectin as a Biomarker for Melioidosis Disease Progression and Management.

    PubMed

    Natesan, Mohan; Corea, Enoka; Krishnananthasivam, Shivankari; Sathkumara, Harindra Darshana; Dankmeyer, Jennifer L; Dyas, Beverly K; Amemiya, Kei; De Silva, Aruna Dharshan; Ulrich, Robert G

    2017-04-01

    Melioidosis is a neglected tropical disease that is caused by the bacterium Burkholderia pseudomallei and is underreported in many countries where the disease is endemic. A long and costly administration of antibiotics is needed to clear infections, and there is an unmet need for biomarkers to guide antibiotic treatment and increase the number of patients that complete therapy. We identified calprotectin as a lead biomarker of B. pseudomallei infections and examined correlations between this serum protein and the antibiotic treatment outcomes of patients with melioidosis. Serum levels of calprotectin and C-reactive protein were significantly higher in patients with melioidosis and nonmelioidosis sepsis than in healthy controls. Median calprotectin levels were higher in patients with melioidosis than in those with nonmelioidosis sepsis, whereas C-reactive protein levels were similar in both groups. Notably, intensive intravenous antibiotic treatment of patients with melioidosis resulted in lower levels of calprotectin and C-reactive protein (P < 0.0001), coinciding with recovery. The median percent reduction of calprotectin and C-reactive protein was 71% for both biomarkers after antibacterial therapy. In contrast, we found no significant differences in calreticulin levels between the two melioidosis treatment phases. Thus, reductions in serum calprotectin levels were linked to therapeutic responses to antibiotics. Our results suggest that calprotectin may be a sensitive indicator of melioidosis disease activity and illustrate the potential utility of this biomarker in guiding the duration of antibiotic therapy.

  14. 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.

  15. Systems Biology Approaches for Discovering Biomarkers for Traumatic Brain Injury

    PubMed Central

    Feala, Jacob D.; AbdulHameed, Mohamed Diwan M.; Yu, Chenggang; Dutta, Bhaskar; Yu, Xueping; Schmid, Kara; Dave, Jitendra; Tortella, Frank

    2013-01-01

    Abstract The rate of traumatic brain injury (TBI) in service members with wartime injuries has risen rapidly in recent years, and complex, variable links have emerged between TBI and long-term neurological disorders. The multifactorial nature of TBI secondary cellular response has confounded attempts to find cellular biomarkers for its diagnosis and prognosis or for guiding therapy for brain injury. One possibility is to apply emerging systems biology strategies to holistically probe and analyze the complex interweaving molecular pathways and networks that mediate the secondary cellular response through computational models that integrate these diverse data sets. Here, we review available systems biology strategies, databases, and tools. In addition, we describe opportunities for applying this methodology to existing TBI data sets to identify new biomarker candidates and gain insights about the underlying molecular mechanisms of TBI response. As an exemplar, we apply network and pathway analysis to a manually compiled list of 32 protein biomarker candidates from the literature, recover known TBI-related mechanisms, and generate hypothetical new biomarker candidates. PMID:23510232

  16. 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.

  17. Circulating Biomarkers in Bladder Cancer

    PubMed Central

    Nandagopal, Lakshminarayanan; Sonpavde, Guru

    2016-01-01

    Bladder cancer is a molecularly heterogeneous disease characterized by multiple unmet needs in the realm of diagnosis, clinical staging, monitoring and therapy. There is an urgent need to develop precision medicine for advanced urothelial carcinoma. Given the difficulty of serial analyses of metastatic tumor tissue to identify resistance and new therapeutic targets, development of non-invasive monitoring using circulating molecular biomarkers is critically important. Although the development of circulating biomarkers for the management of bladder cancer is in its infancy and may currently suffer from lower sensitivity of detection, they have inherent advantages owing to non-invasiveness. Additionally, circulating molecular alterations may capture tumor heterogeneity without the sampling bias of tissue biopsy. This review describes the accumulating data to support further development of circulating biomarkers including circulating tumor cells, cell-free circulating tumor (ct)-DNA, RNA, micro-RNA and proteomics to improve the management of bladder cancer. PMID:28035318

  18. 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

  19. 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

  20. Translational implications of inflammatory biomarkers and cytokine networks in psychoneuroimmunology.

    PubMed

    Yan, Qing

    2012-01-01

    Developments in psychoneuroimmunology (PNI) need to be translated into personalized medicine to achieve better clinical outcomes. One of the most critical steps in this translational process is to identify systemic biomarkers for better diagnosis and treatment. Applications of systems biology approaches in PNI would enable the insights into the correlations among various systems and different levels for the identification of the basic elements of the psychophysiological framework. Among the potential PNI biomarkers, inflammatory markers deserve special attention as they play a pivotal role linking various health conditions and disorders. The elucidation of inflammatory markers, cytokine networks, and immune-brain-behavior interactions may help establish PNI profiles for the identification of potential targets for personalized interventions in at risk populations. The understanding of the general systemic pathways among different disorders may contribute to the transition from the disease-centered medicine to patient-centered medicine. Integrative strategies targeting these factors and pathways would be useful for the prevention and treatment of a spectrum of diseases that share the common links. Examples of the translational implications of potential PNI biomarkers and networks in diseases including depression, Alzheimer's disease, obesity, cardiovascular disease, stroke, and HIV are discussed in details.

  1. 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 mea