WorldWideScience

Sample records for approach identifies research

  1. One Health approach to identify research needs in bovine and human babesioses: workshop report

    OpenAIRE

    McElwain Terry F; Cochran Matt H; Bent Stephen J; Bowers Edwin J; Hewitt David G; Ortega-Santos Alfonso; Teel Pete D; Duhaime Roberta A; Ugstad Paul O; Messenger Matthew T; Hillman Robert; Almazán Consuelo; Wagner Gale G; Miller Ryan S; Wikel Stephen K

    2010-01-01

    Abstract Background Babesia are emerging health threats to humans and animals in the United States. A collaborative effort of multiple disciplines to attain optimal health for people, animals and our environment, otherwise known as the One Health concept, was taken during a research workshop held in April 2009 to identify gaps in scientific knowledge regarding babesioses. The impetus for this analysis was the increased risk for outbreaks of bovine babesiosis, also known as Texas cattle fever,...

  2. One Health approach to identify research needs in bovine and human babesioses: workshop report

    Directory of Open Access Journals (Sweden)

    McElwain Terry F

    2010-04-01

    Full Text Available Abstract Background Babesia are emerging health threats to humans and animals in the United States. A collaborative effort of multiple disciplines to attain optimal health for people, animals and our environment, otherwise known as the One Health concept, was taken during a research workshop held in April 2009 to identify gaps in scientific knowledge regarding babesioses. The impetus for this analysis was the increased risk for outbreaks of bovine babesiosis, also known as Texas cattle fever, associated with the re-infestation of the U.S. by cattle fever ticks. Results The involvement of wildlife in the ecology of cattle fever ticks jeopardizes the ability of state and federal agencies to keep the national herd free of Texas cattle fever. Similarly, there has been a progressive increase in the number of cases of human babesiosis over the past 25 years due to an increase in the white-tailed deer population. Human babesiosis due to cattle-associated Babesia divergens and Babesia divergens-like organisms have begun to appear in residents of the United States. Research needs for human and bovine babesioses were identified and are presented herein. Conclusions The translation of this research is expected to provide veterinary and public health systems with the tools to mitigate the impact of bovine and human babesioses. However, economic, political, and social commitments are urgently required, including increased national funding for animal and human Babesia research, to prevent the re-establishment of cattle fever ticks and the increasing problem of human babesiosis in the United States.

  3. 78 FR 20672 - Literature Review ApproachIdentifying Research Needs for Assessing Safe Use of High Intakes of...

    Science.gov (United States)

    2013-04-05

    ... HUMAN SERVICES National Institutes of Health Literature Review Approach ``Identifying Research Needs for... Assessing Safe Use of High Intakes of Folic Acid,'' for review of the pertinent literature. The document is... discussion at the workshop. As background for the workshop, a literature review document on these...

  4. An operational research approach to identify cardiac surgery patients at risk of severe post-operative bleeding.

    Science.gov (United States)

    Reddy, Brian; Pagel, Christina; Vuylsteke, Alain; Gerrard, Caroline; Nashef, Sam; Utley, Martin

    2011-09-01

    Severe post-operative bleeding can lead to adverse outcomes for cardiac surgery patients and is a relatively common complication of cardiac surgery. One of the most effective drugs to prevent such bleeding, aprotinin, has been withdrawn from the market due to concerns over its safety. Alternative prophylactic drugs which can be given to patients to prevent bleeding can result in significant side effects and are expensive. For this reason it is difficult to make a clinical or economic case for administering these drugs to all cardiac surgery patients, and the prevailing view is that their use should be targeted at patients considered to be at relatively high risk of post-operative bleeding. However, there is currently no objective method for identifying such patients. Over the past 7 years, a team of clinicians and researchers at Papworth Hospital has collected data concerning post-operative blood loss for each cardiac surgery patient, totalling 11,592 consecutive records. They approached a team of operational researchers (MU, ACP, BR) with extensive experience of developing clinical risk models with the aim of devising a risk stratification scheme that could potentially be used to identify a cohort of higher risk patients. Such patients could be treated with the available prophylactic drugs or recruited to studies to evaluate new interventions. This paper is intended to describe the Operational Research process adopted in the development of this scheme. A concise description of the scheme and its clinical interpretation is published elsewhere.

  5. Identifying food proteins with allergenic potential: evolution of approaches to safety assessment and research to provide additional tools.

    Science.gov (United States)

    Ladics, Gregory S; Selgrade, MaryJane K

    2009-08-01

    A safety assessment process exists for genetically engineered crops that includes the evaluation of the expressed protein for allergenic potential. The objectives of this evaluation are twofold: (1) to protect allergic consumers from exposure to known allergenic or cross-reactive proteins, and (2) protect the general population from risks associated with the introduction of genes encoding proteins that are likely to become food allergens. The first systematic approach to address these concerns was formulated by Metcalfe et al. [Metcalfe, D.D., Astwood, J.D., Townsend, R., Sampson, H.A., Taylor, S.L., and Fuchs, R.L. 1996. Assessment of the allergenic potential of foods from genetically engineered crop plants. Crit. Rev. Food Sci. Nutr. 36(5), 165-186.] and subsequently Food and Agriculture Organization of the United Nations/World Health Organization (FAO/WHO) [FAO/WHO, 2001. Evaluation of allergenicity of genetically modified foods. Report of a Joint FAO/WHO Expert Consultation on Allergenicity of Foods Derived from Biotechnology. January 22-25, 2001. Rome, Italy]. More recently, Codex [Codex Alimentarius Commission, 2003. Alinorm 03/34: Joint FAO/WHO Food Standard Programme, Codex Alimentarius Commission, Twenty-Fifth Session, Rome, Italy, 30 June-5 July, 2003. Appendix III, Guideline for the conduct of food safety assessment of foods derived from recombinant-DNA plants, and Appendix IV, Annex on the assessment of possible allergenicity. pp. 47-60], noting that no single factor is recognized as an identifier for protein allergenicity, suggested a weight of evidence approach be conducted that takes into account a variety of factors and approaches for an overall assessment of allergenic potential. These various recommendations are based on what is known about allergens, including the history of exposure and safety of the gene(s) source; amino acid sequence identity to human allergens; stability to pepsin digestion in vitro; protein abundance in the crop and

  6. Identifying Geographic Clusters: A Network Analytic Approach

    CERN Document Server

    Catini, Roberto; Penner, Orion; Riccaboni, Massimo

    2015-01-01

    In recent years there has been a growing interest in the role of networks and clusters in the global economy. Despite being a popular research topic in economics, sociology and urban studies, geographical clustering of human activity has often studied been by means of predetermined geographical units such as administrative divisions and metropolitan areas. This approach is intrinsically time invariant and it does not allow one to differentiate between different activities. Our goal in this paper is to present a new methodology for identifying clusters, that can be applied to different empirical settings. We use a graph approach based on k-shell decomposition to analyze world biomedical research clusters based on PubMed scientific publications. We identify research institutions and locate their activities in geographical clusters. Leading areas of scientific production and their top performing research institutions are consistently identified at different geographic scales.

  7. Urinary Metabolomics Identifies a Molecular Correlate of Interstitial Cystitis/Bladder Pain Syndrome in a Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP Research Network Cohort

    Directory of Open Access Journals (Sweden)

    Kaveri S. Parker

    2016-05-01

    Full Text Available Interstitial cystitis/bladder pain syndrome (IC/BPS is a poorly understood syndrome affecting up to 6.5% of adult women in the U.S. The lack of broadly accepted objective laboratory markers for this condition hampers efforts to diagnose and treat this condition. To identify biochemical markers for IC/BPS, we applied mass spectrometry-based global metabolite profiling to urine specimens from a cohort of female IC/BPS subjects from the Multidisciplinary Approach to the Study of Chronic Pelvic Pain (MAPP Research Network. These analyses identified multiple metabolites capable of discriminating IC/BPS and control subjects. Of these candidate markers, etiocholan-3α-ol-17-one sulfate (Etio-S, a sulfoconjugated 5-β reduced isomer of testosterone, distinguished female IC/BPS and control subjects with a sensitivity and specificity >90%. Among IC/BPS subjects, urinary Etio-S levels are correlated with elevated symptom scores (symptoms, pelvic pain, and number of painful body sites and could resolve high- from low-symptom IC/BPS subgroups. Etio-S-associated biochemical changes persisted through 3–6 months of longitudinal follow up. These results raise the possibility that an underlying biochemical abnormality contributes to symptoms in patients with severe IC/BPS.

  8. NIH Researchers Identify OCD Risk Gene

    Science.gov (United States)

    ... News From NIH NIH Researchers Identify OCD Risk Gene Past Issues / Summer 2006 Table of Contents For ... and Alcoholism (NIAAA) have identified a previously unknown gene variant that doubles an individual's risk for obsessive- ...

  9. A new approach for identifying metabolic biomakers

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ The idea of finding a single metabolite biomarker that can unambiguously diagnose a disease is a beguiling one, but unfortunately not currently supported by reality. Although researchers have reported the discovery of a whole range of potential biomarkers for numerous diseases, they often don't stand up to closer scrutiny. But now, by combining together a whole range of different analytical and statistical techniques, a team of Chinese and German chemists may just have improved the chances of detecting a proper biomarker.

  10. Researchers Develop Method to Identify Sparticles in Big Bang Conditions

    CERN Multimedia

    2008-01-01

    Three Northeastern University researchers have proposed a new approach for the highly anticipated discovery of supersymmetric particles, often called sparticles. The methodology, which was published in the December 21 issue of the Physical Review Letters, is based on identifying the hierarchical mass patterns of sparticles, which are assumed to exist in a new class of particle physics theories beyond the Standard Model.

  11. Identifying MMORPG Bots: A Traffic Analysis Approach

    Directory of Open Access Journals (Sweden)

    Wen-Chin Chen

    2008-11-01

    Full Text Available Massively multiplayer online role playing games (MMORPGs have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1 the regularity in the release time of client commands, 2 the trend and magnitude of traffic burstiness in multiple time scales, and 3 the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  12. Identifying MMORPG Bots: A Traffic Analysis Approach

    Science.gov (United States)

    Chen, Kuan-Ta; Jiang, Jhih-Wei; Huang, Polly; Chu, Hao-Hua; Lei, Chin-Laung; Chen, Wen-Chin

    2008-12-01

    Massively multiplayer online role playing games (MMORPGs) have become extremely popular among network gamers. Despite their success, one of MMORPG's greatest challenges is the increasing use of game bots, that is, autoplaying game clients. The use of game bots is considered unsportsmanlike and is therefore forbidden. To keep games in order, game police, played by actual human players, often patrol game zones and question suspicious players. This practice, however, is labor-intensive and ineffective. To address this problem, we analyze the traffic generated by human players versus game bots and propose general solutions to identify game bots. Taking Ragnarok Online as our subject, we study the traffic generated by human players and game bots. We find that their traffic is distinguishable by 1) the regularity in the release time of client commands, 2) the trend and magnitude of traffic burstiness in multiple time scales, and 3) the sensitivity to different network conditions. Based on these findings, we propose four strategies and two ensemble schemes to identify bots. Finally, we discuss the robustness of the proposed methods against countermeasures of bot developers, and consider a number of possible ways to manage the increasingly serious bot problem.

  13. An approach to identify urban groundwater recharge

    Directory of Open Access Journals (Sweden)

    E. Vázquez-Suñé

    2010-10-01

    Full Text Available Evaluating the proportion in which waters from different origins are mixed in a given water sample is relevant for many hydrogeological problems, such as quantifying total recharge, assessing groundwater pollution risks, or managing water resources. Our work is motivated by urban hydrogeology, where waters with different chemical signature can be identified (losses from water supply and sewage networks, infiltration from surface runoff and other water bodies, lateral aquifers inflows, .... The relative contribution of different sources to total recharge can be quantified by means of solute mass balances, but application is hindered by the large number of potential origins. Hence, the need to incorporate data from a large number of conservative species, the uncertainty in sources concentrations and measurement errors. We present a methodology to compute mixing ratios and end-members composition, which consists of (i Identification of potential recharge sources, (ii Selection of tracers, (iii Characterization of the hydrochemical composition of potential recharge sources and mixed water samples, and (iv Computation of mixing ratios and reevaluation of end-members. The analysis performed in a data set from samples of the Barcelona city aquifers suggests that the main contributors to total recharge are the water supply network losses (22%, the sewage network losses (30%, rainfall, concentrated in the non-urbanized areas (17%, from runoff infiltration (20%, and the Besòs River (11%. Regarding species, halogens (chloride, fluoride and bromide, sulfate, total nitrogen, and stable isotopes (18O, 2H, and 34S behaved quite conservatively. Boron, residual alkalinity, EDTA and Zn did not. Yet, including these species in the computations did not affect significantly the proportion estimations.

  14. An approach to identify urban groundwater recharge

    Directory of Open Access Journals (Sweden)

    E. Vázquez-Suñé

    2010-04-01

    Full Text Available Evaluating the proportion in which waters from different origins are mixed in a given water sample is relevant for many hydrogeological problems, such as quantifying total recharge, assessing groundwater pollution risks, or managing water resources. Our work is motivated by urban hydrogeology, where waters with different chemical signature can be identified (losses from water supply and sewage networks, infiltration from surface runoff and other water bodies, lateral aquifers inflows, .... The relative contribution of different sources to total recharge can be quantified by means of solute mass balances, but application is hindered by the large number of potential origins. Hence, the need to incorporate data from a large number of conservative species, the uncertainty in sources concentrations and measurement errors. We present a methodology to compute mixing ratios and end-members composition, which consists of (i Identification of potential recharge sources, (ii Selection of tracers, (iii Characterization of the hydrochemical composition of potential recharge sources and mixed water samples, and (iv Computation of mixing ratios and reevaluation of end-members. The analysis performed in a data set from samples of the Barcelona city aquifers suggests that the main contributors to total recharge are the water supply network losses (22%, the sewage network losses (30%, rainfall, concentrated in the non-urbanized areas (17%, from runoff infiltration (20%, and the Besòs River (11%. Regarding species, halogens (chloride, fluoride and bromide, sulfate, total nitrogen, and stable isotopes (18O2H, and 34S behaved quite conservatively. Boron, residual alkalinity, EDTA and Zn did not. Yet, including these species in the computations did not affect significantly the proportion estimations.

  15. Experimental approaches to identify small RNAs and their diverse roles in bacteria--what we have learnt in one decade of MicA research.

    Science.gov (United States)

    Van Puyvelde, Sandra; Vanderleyden, Jozef; De Keersmaecker, Sigrid C J

    2015-10-01

    Nowadays the identification of small RNAs (sRNAs) and characterization of their role within regulatory networks takes a prominent place in deciphering complex bacterial phenotypes. Compared to the study of other components of bacterial cells, this is a relatively new but fast-growing research field. Although reports on new sRNAs appear regularly, some sRNAs are already subject of research for a longer time. One of such sRNAs is MicA, a sRNA best described for its role in outer membrane remodeling, but probably having a much broader function than anticipated. An overview of what we have learnt from MicA led to the conclusion that even for this well-described sRNA, we still do not have the overall picture. More general, the story of MicA might become an experimental lead for unraveling the many sRNAs with unknown functions. In this review, three important topics in the sRNA field are covered, exemplified from the perspective of MicA: (i) identification of new sRNAs, (ii) target identification and unraveling the biological function, (iii) structural analysis. The complex mechanisms of action of MicA deliver some original insights in the sRNA field which includes the existence of dimer formation or simultaneous cis and trans regulation, and might further inspire the understanding of the function of other sRNAs.

  16. Contemporary Approaches for Identifying Rare Bone Disease Causing Genes

    Institute of Scientific and Technical Information of China (English)

    Charles R.Farber; Thomas L.Clemens

    2013-01-01

    Recent improvements in the speed and accuracy of DNA sequencing, together with increasingly sophisti-cated mathematical approaches for annotating gene networks, have revolutionized the field of human genetics and made these once time consuming approaches assessable to most investigators. In the field of bone research, a particularly active area of gene discovery has occurred in patients with rare bone disorders such as osteogenesis imperfecta (OI) that are caused by mutations in single genes. In this perspective, we highlight some of these technological advances and describe how they have been used to identify the genetic determinants underlying two previously unexplained cases of OI. The widespread availability of advanced methods for DNA sequencing and bioinformatics analysis can be expected to greatly facilitate identification of novel gene networks that normally function to control bone formation and maintenance.

  17. New approach for identifying boundary characteristics using transmissibility

    Science.gov (United States)

    Joo, Kyung-Hoon; Min, Dongwoo; Kim, Jun-Gu; Kang, Yeon June

    2017-04-01

    A novel approach is proposed for identifying boundary properties as a response model using transmissibility. This approach differs from those proposed in previous studies dealing with frequency response functions (FRFs) for joint identification. Transmissibility includes only response data, unlike FRFs that include force measurements. The boundary properties can be estimated by comparing the characteristics of the components under the free condition and connected to boundary conditions. When analyzing the components assembled compactly in the system for setting the shaker or measuring the impact force exerted on the component correctly, the proposed method could reduce the errors caused by an incorrectly measured force. The derived equation is verified using a discrete multiple degrees of freedom system with single boundary and multiple boundary conditions and by application to a beam, which is the simplest continuous structural form to validate the feasibility of the theory. The transmissibility defined by the apparent mass matrix is used for verifying the derived equation for identifying the boundary properties in the discrete system. However, when applying the equation to practical cases, as is the purpose of this research, the transmissibility matrix should be defined using only the response data. For this purpose, the accelerance matrix is modified slightly to the response matrix using the input as a unit force. This transmissibility matrix composed of response data is used for validating the equation in a continuous system. Furthermore, the effects of measurement noise are also investigated to assess the robustness of the method for application under practical conditions. Consequently, the proposed method could show reliable results by properly extracting the boundary properties in both cases. In many practical cases, this research is expected to contribute toward identifying the boundary properties in a complex system more conveniently compared to the method

  18. A Narrative Approach to Research

    Science.gov (United States)

    Bell, Anne

    2003-01-01

    In this paper I present a narrative approach to environmental education research. This approach evolved through a dynamic interplay between research questions, theory, experience, conversation, and reflection. I situate the approach with respect to narrative inquiry and clarify the key conceptual metaphors underpinning my study, including…

  19. Researchers Identify Early Sign of Pancreatic Cancer

    Science.gov (United States)

    ... be detected before the disease is diagnosed.” The researchers utilized blood samples collected years earlier from 1,500 people participating in large health-tracking studies. They analyzed the samples for more than ...

  20. Covert Flow Graph Approach to Identifying Covert Channels

    OpenAIRE

    XiangMei Song; ShiGuang Ju

    2011-01-01

    In this paper, the approach for identifying covert channels using a graph structure called Covert Flow Graph is introduced. Firstly, the construction of Covert Flow Graph which can offer information flows of the system for covert channel detection is proposed, and the search and judge algorithm used to identify covert channels in Covert Flow Graph is given. Secondly, an example file system analysis using Covert Flow Graph approach is provided, and the analysis result is compared with that of ...

  1. Novel approaches to identify protective malaria vaccine candidates

    Directory of Open Access Journals (Sweden)

    Wan Ni eChia

    2014-11-01

    Full Text Available Efforts to develop vaccines against malaria have been the focus of substantial research activities for decades. Several categories of candidate vaccines are currently being developed for protection against malaria, based on antigens corresponding to the pre-erythrocytic, blood-stage or sexual stages of the parasite. Long lasting sterile protection from Plasmodium falciparum sporozoite challenge has been observed in human following vaccination with whole parasite formulations, clearly demonstrating that a protective immune response targeting predominantly the pre-erythrocytic stages can develop against malaria. However, most of vaccine candidates currently being investigated, which are mostly subunits vaccines, have not been able to induce substantial (>50% protection thus far. This is due to the fact that the antigens responsible for protection against the different parasite stages are still yet to be known and relevant correlates of protection have remained elusive. For a vaccine to be developed in a timely manner, novel approaches are required. In this article, we review the novel approaches that have been developed to identify the antigens for the development of an effective malaria vaccine.

  2. Identifying the "Truly Disadvantaged": A Comprehensive Biosocial Approach

    Science.gov (United States)

    Barnes, J. C.; Beaver, Kevin M.; Connolly, Eric J.; Schwartz, Joseph A.

    2016-01-01

    There has been significant interest in examining the developmental factors that predispose individuals to chronic criminal offending. This body of research has identified some social-environmental risk factors as potentially important. At the same time, the research producing these results has generally failed to employ genetically sensitive…

  3. A predictive approach to identify genes differentially expressed

    Science.gov (United States)

    Saraiva, Erlandson F.; Louzada, Francisco; Milan, Luís A.; Meira, Silvana; Cobre, Juliana

    2012-10-01

    The main objective of gene expression data analysis is to identify genes that present significant changes in expression levels between a treatment and a control biological condition. In this paper, we propose a Bayesian approach to identify genes differentially expressed calculating credibility intervals from predictive densities which are constructed using sampled mean treatment effect from all genes in study excluding the treatment effect of genes previously identified with statistical evidence for difference. We compare our Bayesian approach with the standard ones based on the use of the t-test and modified t-tests via a simulation study, using small sample sizes which are common in gene expression data analysis. Results obtained indicate that the proposed approach performs better than standard ones, especially for cases with mean differences and increases in treatment variance in relation to control variance. We also apply the methodologies to a publicly available data set on Escherichia coli bacteria.

  4. Covert Flow Graph Approach to Identifying Covert Channels

    Directory of Open Access Journals (Sweden)

    XiangMei Song

    2011-12-01

    Full Text Available In this paper, the approach for identifying covert channels using a graph structure called Covert Flow Graph is introduced. Firstly, the construction of Covert Flow Graph which can offer information flows of the system for covert channel detection is proposed, and the search and judge algorithm used to identify covert channels in Covert Flow Graph is given. Secondly, an example file system analysis using Covert Flow Graph approach is provided, and the analysis result is compared with that of Shared Resource Matrix and Covert Flow Tree method. Finally, the comparison between Covert Flow Graph approach and other two methods is discussed. Different from previous methods, Covert Flow Graph approach provides a deep insight for system’s information flows, and gives an effective algorithm for covert channel identification.

  5. A Computer Vision Approach to Identify Einstein Rings and Arcs

    Science.gov (United States)

    Lee, Chien-Hsiu

    2017-03-01

    Einstein rings are rare gems of strong lensing phenomena; the ring images can be used to probe the underlying lens gravitational potential at every position angles, tightly constraining the lens mass profile. In addition, the magnified images also enable us to probe high-z galaxies with enhanced resolution and signal-to-noise ratios. However, only a handful of Einstein rings have been reported, either from serendipitous discoveries or or visual inspections of hundred thousands of massive galaxies or galaxy clusters. In the era of large sky surveys, an automated approach to identify ring pattern in the big data to come is in high demand. Here, we present an Einstein ring recognition approach based on computer vision techniques. The workhorse is the circle Hough transform that recognise circular patterns or arcs in the images. We propose a two-tier approach by first pre-selecting massive galaxies associated with multiple blue objects as possible lens, than use Hough transform to identify circular pattern. As a proof-of-concept, we apply our approach to SDSS, with a high completeness, albeit with low purity. We also apply our approach to other lenses in DES, HSC-SSP, and UltraVISTA survey, illustrating the versatility of our approach.

  6. Similarity transformation approach to identifiability analysis of nonlinear compartmental models.

    Science.gov (United States)

    Vajda, S; Godfrey, K R; Rabitz, H

    1989-04-01

    Through use of the local state isomorphism theorem instead of the algebraic equivalence theorem of linear systems theory, the similarity transformation approach is extended to nonlinear models, resulting in finitely verifiable sufficient and necessary conditions for global and local identifiability. The approach requires testing of certain controllability and observability conditions, but in many practical examples these conditions prove very easy to verify. In principle the method also involves nonlinear state variable transformations, but in all of the examples presented in the paper the transformations turn out to be linear. The method is applied to an unidentifiable nonlinear model and a locally identifiable nonlinear model, and these are the first nonlinear models other than bilinear models where the reason for lack of global identifiability is nontrivial. The method is also applied to two models with Michaelis-Menten elimination kinetics, both of considerable importance in pharmacokinetics, and for both of which the complicated nature of the algebraic equations arising from the Taylor series approach has hitherto defeated attempts to establish identifiability results for specific input functions.

  7. Identifying Subgroups among Hardcore Smokers: a Latent Profile Approach

    NARCIS (Netherlands)

    Bommelé, J.; Kleinjan, M.; Schoenmakers, T.M.; Eijnden, R. van den; Mheen, D. van de

    2015-01-01

    Introduction: Hardcore smokers are smokers who have little to no intention to quit. Previous research suggests that there are distinct subgroups among hardcore smokers and that these subgroups vary in the perceived pros and cons of smoking and quitting. Identifying these subgroups could help to deve

  8. A statistical approach to identify candidate cues for nestmate recognition

    DEFF Research Database (Denmark)

    van Zweden, Jelle; Pontieri, Luigi; Pedersen, Jes Søe

    2014-01-01

    normalization, centroid,and distance calculation is most diagnostic to discriminate between NMR cues andother compounds. We find that using a “global centroid” instead of a “colony centroid”significantly improves the analysis. One reason may be that this new approach, unlikeprevious ones, provides...... than forF. exsecta, possibly due to less than ideal datasets. Nonetheless, some compound setsperformed better than others, showing that this approach can be used to identify candidatecompounds to be tested in bio-assays, and eventually crack the sophisticated code thatgoverns nestmate recognition....

  9. A Function-First Approach to Identifying Formulaic Language in Academic Writing

    Science.gov (United States)

    Durrant, Philip; Mathews-Aydinli, Julie

    2011-01-01

    There is currently much interest in creating pedagogically-oriented descriptions of formulaic language. Research in this area has typically taken what we call a "form-first" approach, in which formulas are identified as the most frequent recurrent forms in a relevant corpus. While this research continues to yield valuable results, the present…

  10. Identifying acute coronary syndrome patients approaching end-of-life.

    Directory of Open Access Journals (Sweden)

    Stephen Fenning

    Full Text Available BACKGROUND: Acute coronary syndrome (ACS is common in patients approaching the end-of-life (EoL, but these patients rarely receive palliative care. We compared the utility of a palliative care prognostic tool (Gold Standards Framework (GSF and the Global Registry of Acute Coronary Events (GRACE score, to help identify patients approaching EoL. METHODS AND FINDINGS: 172 unselected consecutive patients with confirmed ACS admitted over an eight-week period were assessed using prognostic tools and followed up for 12 months. GSF criteria identified 40 (23% patients suitable for EoL care while GRACE identified 32 (19% patients with ≥ 10% risk of death within 6 months. Patients meeting GSF criteria were older (p = 0.006, had more comorbidities (1.6 ± 0.7 vs. 1.2 ± 0.9, p = 0.007, more frequent hospitalisations before (p = 0.001 and after (0.0001 their index admission, and were more likely to die during follow-up (GSF+ 20% vs GSF- 7%, p = 0.03. GRACE score was predictive of 12-month mortality (C-statistic 0.75 and this was improved by the addition of previous hospital admissions and previous history of stroke (C-statistic 0.88. CONCLUSIONS: This study has highlighted a potentially large number of ACS patients eligible for EoL care. GSF or GRACE could be used in the hospital setting to help identify these patients. GSF identifies ACS patients with more comorbidity and at increased risk of hospital readmission.

  11. Reverse Pathway Genetic Approach Identifies Epistasis in Autism Spectrum Disorders

    Science.gov (United States)

    Traglia, Michela; Tsang, Kathryn; Bearden, Carrie E.; Rauen, Katherine A.

    2017-01-01

    Although gene-gene interaction, or epistasis, plays a large role in complex traits in model organisms, genome-wide by genome-wide searches for two-way interaction have limited power in human studies. We thus used knowledge of a biological pathway in order to identify a contribution of epistasis to autism spectrum disorders (ASDs) in humans, a reverse-pathway genetic approach. Based on previous observation of increased ASD symptoms in Mendelian disorders of the Ras/MAPK pathway (RASopathies), we showed that common SNPs in RASopathy genes show enrichment for association signal in GWAS (P = 0.02). We then screened genome-wide for interactors with RASopathy gene SNPs and showed strong enrichment in ASD-affected individuals (P < 2.2 x 10−16), with a number of pairwise interactions meeting genome-wide criteria for significance. Finally, we utilized quantitative measures of ASD symptoms in RASopathy-affected individuals to perform modifier mapping via GWAS. One top region overlapped between these independent approaches, and we showed dysregulation of a gene in this region, GPR141, in a RASopathy neural cell line. We thus used orthogonal approaches to provide strong evidence for a contribution of epistasis to ASDs, confirm a role for the Ras/MAPK pathway in idiopathic ASDs, and to identify a convergent candidate gene that may interact with the Ras/MAPK pathway. PMID:28076348

  12. Engaging basic scientists in translational research: identifying opportunities, overcoming obstacles

    Directory of Open Access Journals (Sweden)

    Hobin Jennifer A

    2012-04-01

    Full Text Available Abstract This report is based on the Federation of American Societies for Experimental Biology’s symposium, “Engaging basic Scientists in Translational Research: Identifying Opportunities, Overcoming Obstacles,” held in Chevy Chase, MD, March 24–25, 2011. Meeting participants examined the benefits of engaging basic scientists in translational research, the challenges to their participation in translational research, and the roles that research institutions, funding organizations, professional societies, and scientific publishers can play to address these challenges.

  13. A Sensitivity Analysis Approach to Identify Key Environmental Performance Factors

    Directory of Open Access Journals (Sweden)

    Xi Yu

    2014-01-01

    Full Text Available Life cycle assessment (LCA is widely used in design phase to reduce the product’s environmental impacts through the whole product life cycle (PLC during the last two decades. The traditional LCA is restricted to assessing the environmental impacts of a product and the results cannot reflect the effects of changes within the life cycle. In order to improve the quality of ecodesign, it is a growing need to develop an approach which can reflect the changes between the design parameters and product’s environmental impacts. A sensitivity analysis approach based on LCA and ecodesign is proposed in this paper. The key environmental performance factors which have significant influence on the products’ environmental impacts can be identified by analyzing the relationship between environmental impacts and the design parameters. Users without much environmental knowledge can use this approach to determine which design parameter should be first considered when (redesigning a product. A printed circuit board (PCB case study is conducted; eight design parameters are chosen to be analyzed by our approach. The result shows that the carbon dioxide emission during the PCB manufacture is highly sensitive to the area of PCB panel.

  14. An Efficient Approach for Identifying Stable Lobes with Discretization Method

    Directory of Open Access Journals (Sweden)

    Baohai Wu

    2013-01-01

    Full Text Available This paper presents a new approach for quick identification of chatter stability lobes with discretization method. Firstly, three different kinds of stability regions are defined: absolute stable region, valid region, and invalid region. Secondly, while identifying the chatter stability lobes, three different regions within the chatter stability lobes are identified with relatively large time intervals. Thirdly, stability boundary within the valid regions is finely calculated to get exact chatter stability lobes. The proposed method only needs to test a small portion of spindle speed and cutting depth set; about 89% computation time is savedcompared with full discretization method. It spends only about10 minutes to get exact chatter stability lobes. Since, based on discretization method, the proposed method can be used for different immersion cutting including low immersion cutting process, the proposed method can be directly implemented in the workshop to promote machining parameters selection efficiency.

  15. Systems approaches in osteoarthritis: Identifying routes to novel diagnostic and therapeutic strategies.

    Science.gov (United States)

    Mueller, Alan J; Peffers, Mandy J; Proctor, Carole J; Clegg, Peter D

    2017-03-20

    Systems orientated research offers the possibility of identifying novel therapeutic targets and relevant diagnostic markers for complex diseases such as osteoarthritis. This review demonstrates that the osteoarthritis research community has been slow to incorporate systems orientated approaches into research studies, although a number of key studies reveal novel insights into the regulatory mechanisms that contribute both to joint tissue homeostasis and its dysfunction. The review introduces both top-down and bottom-up approaches employed in the study of osteoarthritis. A holistic and multiscale approach, where clinical measurements may predict dysregulation and progression of joint degeneration, should be a key objective in future research. The review concludes with suggestions for further research and emerging trends not least of which is the coupled development of diagnostic tests and therapeutics as part of a concerted effort by the osteoarthritis research community to meet clinical needs. This article is protected by copyright. All rights reserved.

  16. Research to Identify Effective Antifungal Agents, 1993 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Schreck, Carl

    1993-10-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990, 1991, and 1992). The objectives of the present study were to select and evaluate candidate fungicides.

  17. Identifying and Researching Market Opportunities for New High Technology Products.

    Science.gov (United States)

    Dunstan, Peter

    Using a product called the synchro-pulse welder as a case study example, this paper discusses the activities of CSIRO (Commonwealth Scientific and Industrial Research Organisation) in identifying and marketing new high-technology products. A general discussion of CSIRO's market research plans includes two goals to be attained within the next 5…

  18. The Baby TALK Model: An Innovative Approach to Identifying High-Risk Children and Families

    Science.gov (United States)

    Villalpando, Aimee Hilado; Leow, Christine; Hornstein, John

    2012-01-01

    This research report examines the Baby TALK model, an innovative early childhood intervention approach used to identify, recruit, and serve young children who are at-risk for developmental delays, mental health needs, and/or school failure, and their families. The report begins with a description of the model. This description is followed by an…

  19. Identifying Appropriate Quantitative Study Designs for Library Research

    Directory of Open Access Journals (Sweden)

    Diane Lorenzetti

    2007-03-01

    Full Text Available This paper is concerned with the identification of quantitative study designs suitable for library research. Identifying a researchable question and selecting a research method best suited to it are key to the successful design and execution of any research project. Each research situation is unique, and each researcher must find the method that best suits both their situation and the question at hand. Following a brief discussion of issues related to question development, the author outlines a checklist that may assist the process of selecting study designs for quantitative research projects. When faced with options in terms of study design selection, pragmatic issues such as expertise, funding, time, and access to participants may influence this decision‐making process.

  20. An action research approach to curriculum development

    Directory of Open Access Journals (Sweden)

    Phil Riding

    1995-01-01

    Full Text Available Action research has been used in many areas where an understanding of complex social situations has been sought in order to improve the quality of life. Among these are industrial, health and community work settings. Kurt Lewin, often cited as the originator of action research, used the methodology in his work with people affected by post- war social problems. Action research approaches to educational research were adopted in the late 60s and early 70s by the ‘teacher- researcher’ movement in the secondary education sector. This sought to bring the practising classroom teacher into the research process as the most effective person to identify problems and to find solutions.We believe that an action research approach can contribute very positively to activity within the tertiary sector concerned with teaching quality issues, and with national Teaching Quality Assessment initiatives. As 'reflective practitioners', we can achieve greater ownership of the evaluative process by becoming systematically self-assessing, alongside, and feeding into, external assessment processes.

  1. Identifying Pathogenicity Islands in Bacterial Pathogenomics Using Computational Approaches

    Directory of Open Access Journals (Sweden)

    Dongsheng Che

    2014-01-01

    Full Text Available High-throughput sequencing technologies have made it possible to study bacteria through analyzing their genome sequences. For instance, comparative genome sequence analyses can reveal the phenomenon such as gene loss, gene gain, or gene exchange in a genome. By analyzing pathogenic bacterial genomes, we can discover that pathogenic genomic regions in many pathogenic bacteria are horizontally transferred from other bacteria, and these regions are also known as pathogenicity islands (PAIs. PAIs have some detectable properties, such as having different genomic signatures than the rest of the host genomes, and containing mobility genes so that they can be integrated into the host genome. In this review, we will discuss various pathogenicity island-associated features and current computational approaches for the identification of PAIs. Existing pathogenicity island databases and related computational resources will also be discussed, so that researchers may find it to be useful for the studies of bacterial evolution and pathogenicity mechanisms.

  2. PROCESS OF IDENTIFYING COMPETENCIES BASED ON A FUNCTIONAL APPROACH

    Directory of Open Access Journals (Sweden)

    NAOUFAL SEFIANI

    2012-01-01

    Full Text Available To cope with fast change of the technological and organizational context, managers need tools to help them to improve competence management. Our contribution aims at supporting the task of competence identification that is considered as the first step of the management process. The proposed identification involves tree stages.The first stage concerns the research of competences based on a functional approach. The second stage is to define a typology of the component of competence (characterization and the third stage to define the core competencies of competence (prioritization. The application of the method in an industrial case in the logisticsfield confirms the possibility of using the “principle of solution” to provide a dynamic process for the identification of requisite competencies.

  3. Bioinformatics Approaches for Human Gut Microbiome Research

    Directory of Open Access Journals (Sweden)

    Zhijun Zheng

    2016-07-01

    Full Text Available The human microbiome has received much attention because many studies have reported that the human gut microbiome is associated with several diseases. The very large datasets that are produced by these kinds of studies means that bioinformatics approaches are crucial for their analysis. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also summarized the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our understanding of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and monitoring.

  4. Systematically Identifying Relevant Research: Case Study on Child Protection Social Workers' Resilience

    Science.gov (United States)

    McFadden, Paula; Taylor, Brian J.; Campbell, Anne; McQuilkin, Janice

    2012-01-01

    Context: The development of a consolidated knowledge base for social work requires rigorous approaches to identifying relevant research. Method: The quality of 10 databases and a web search engine were appraised by systematically searching for research articles on resilience and burnout in child protection social workers. Results: Applied Social…

  5. Identifying perinatal risk factors for infant maltreatment: an ecological approach

    Directory of Open Access Journals (Sweden)

    Hallisey Elaine J

    2006-12-01

    Full Text Available Abstract Background Child maltreatment and its consequences are a persistent problem throughout the world. Public health workers, human services officials, and others are interested in new and efficient ways to determine which geographic areas to target for intervention programs and resources. To improve assessment efforts, selected perinatal factors were examined, both individually and in various combinations, to determine if they are associated with increased risk of infant maltreatment. State of Georgia birth records and abuse and neglect data were analyzed using an area-based, ecological approach with the census tract as a surrogate for the community. Cartographic visualization suggested some correlation exists between risk factors and child maltreatment, so bivariate and multivariate regression were performed. The presence of spatial autocorrelation precluded the use of traditional ordinary least squares regression, therefore a spatial regression model coupled with maximum likelihood estimation was employed. Results Results indicate that all individual factors or their combinations are significantly associated with increased risk of infant maltreatment. The set of perinatal risk factors that best predicts infant maltreatment rates are: mother smoked during pregnancy, families with three or more siblings, maternal age less than 20 years, births to unmarried mothers, Medicaid beneficiaries, and inadequate prenatal care. Conclusion This model enables public health to take a proactive stance, to reasonably predict areas where poor outcomes are likely to occur, and to therefore more efficiently allocate resources. U.S. states that routinely collect the variables the National Center for Health Statistics (NCHS defines for birth certificates can easily identify areas that are at high risk for infant maltreatment. The authors recommend that agencies charged with reducing child maltreatment target communities that demonstrate the perinatal risks

  6. Computational Approaches to Vestibular Research

    Science.gov (United States)

    Ross, Muriel D.; Wade, Charles E. (Technical Monitor)

    1994-01-01

    The Biocomputation Center at NASA Ames Research Center is dedicated to a union between computational, experimental and theoretical approaches to the study of neuroscience and of life sciences in general. The current emphasis is on computer reconstruction and visualization of vestibular macular architecture in three-dimensions (3-D), and on mathematical modeling and computer simulation of neural activity in the functioning system. Our methods are being used to interpret the influence of spaceflight on mammalian vestibular maculas in a model system, that of the adult Sprague-Dawley rat. More than twenty 3-D reconstructions of type I and type II hair cells and their afferents have been completed by digitization of contours traced from serial sections photographed in a transmission electron microscope. This labor-intensive method has now been replace d by a semiautomated method developed in the Biocomputation Center in which conventional photography is eliminated. All viewing, storage and manipulation of original data is done using Silicon Graphics workstations. Recent improvements to the software include a new mesh generation method for connecting contours. This method will permit the investigator to describe any surface, regardless of complexity, including highly branched structures such as are routinely found in neurons. This same mesh can be used for 3-D, finite volume simulation of synapse activation and voltage spread on neuronal surfaces visualized via the reconstruction process. These simulations help the investigator interpret the relationship between neuroarchitecture and physiology, and are of assistance in determining which experiments will best test theoretical interpretations. Data are also used to develop abstract, 3-D models that dynamically display neuronal activity ongoing in the system. Finally, the same data can be used to visualize the neural tissue in a virtual environment. Our exhibit will depict capabilities of our computational approaches and

  7. Reverse Vaccinology: An Approach for Identifying Leptospiral Vaccine Candidates

    Science.gov (United States)

    Dellagostin, Odir A.; Grassmann, André A.; Rizzi, Caroline; Schuch, Rodrigo A.; Jorge, Sérgio; Oliveira, Thais L.; McBride, Alan J. A.; Hartwig, Daiane D.

    2017-01-01

    Leptospirosis is a major public health problem with an incidence of over one million human cases each year. It is a globally distributed, zoonotic disease and is associated with significant economic losses in farm animals. Leptospirosis is caused by pathogenic Leptospira spp. that can infect a wide range of domestic and wild animals. Given the inability to control the cycle of transmission among animals and humans, there is an urgent demand for a new vaccine. Inactivated whole-cell vaccines (bacterins) are routinely used in livestock and domestic animals, however, protection is serovar-restricted and short-term only. To overcome these limitations, efforts have focused on the development of recombinant vaccines, with partial success. Reverse vaccinology (RV) has been successfully applied to many infectious diseases. A growing number of leptospiral genome sequences are now available in public databases, providing an opportunity to search for prospective vaccine antigens using RV. Several promising leptospiral antigens were identified using this approach, although only a few have been characterized and evaluated in animal models. In this review, we summarize the use of RV for leptospirosis and discuss the need for potential improvements for the successful development of a new vaccine towards reducing the burden of human and animal leptospirosis. PMID:28098813

  8. Reverse Vaccinology: An Approach for Identifying Leptospiral Vaccine Candidates

    Directory of Open Access Journals (Sweden)

    Odir A. Dellagostin

    2017-01-01

    Full Text Available Leptospirosis is a major public health problem with an incidence of over one million human cases each year. It is a globally distributed, zoonotic disease and is associated with significant economic losses in farm animals. Leptospirosis is caused by pathogenic Leptospira spp. that can infect a wide range of domestic and wild animals. Given the inability to control the cycle of transmission among animals and humans, there is an urgent demand for a new vaccine. Inactivated whole-cell vaccines (bacterins are routinely used in livestock and domestic animals, however, protection is serovar-restricted and short-term only. To overcome these limitations, efforts have focused on the development of recombinant vaccines, with partial success. Reverse vaccinology (RV has been successfully applied to many infectious diseases. A growing number of leptospiral genome sequences are now available in public databases, providing an opportunity to search for prospective vaccine antigens using RV. Several promising leptospiral antigens were identified using this approach, although only a few have been characterized and evaluated in animal models. In this review, we summarize the use of RV for leptospirosis and discuss the need for potential improvements for the successful development of a new vaccine towards reducing the burden of human and animal leptospirosis.

  9. Research to Identify Effective Antifungal Agents, 1992 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Schreck, Carl

    1993-03-01

    This study is a continuation of ``Research to Identify Effective Antifungal Agents'' sponsored by Bonneville Power Administration (Schreck et al. 1990 and Schreck et al. 1991). The objectives of the present study were to select and evaluate up to 10 candidate fungicides.

  10. A practical guideline for identifying research intent with projects that collect private, identifiable health information.

    Science.gov (United States)

    Amdur, Robert J; Speers, Marjorie A

    2003-06-01

    Radiation oncologists frequently engage in activities that involve the collection and analysis of data from medical records. Access to health information is an ethical issue because, if not done according to appropriate guidelines, it constitutes an invasion of privacy or breach in confidentiality. To protect patients for the social harm that may result from medical record review, our society has established laws and regulations that apply to projects that require medical record review. A major branch point in the guidelines for such projects is whether private information will be collected for research or nonresearch purposes. However, a problem with discussing privacy protection in terms of a research versus nonresearch model is that it is difficult to make this distinction for many kinds of projects. The purpose of this paper is to establish a practical guideline that can be used to decide if a project that involves analysis of private, identifiable medical information should be considered research from the regulatory standpoint.

  11. Bioinformatics approaches for identifying new therapeutic bioactive peptides in food

    Directory of Open Access Journals (Sweden)

    Nora Khaldi

    2012-10-01

    Full Text Available ABSTRACT:The traditional methods for mining foods for bioactive peptides are tedious and long. Similar to the drug industry, the length of time to identify and deliver a commercial health ingredient that reduces disease symptoms can take anything between 5 to 10 years. Reducing this time and effort is crucial in order to create new commercially viable products with clear and important health benefits. In the past few years, bioinformatics, the science that brings together fast computational biology, and efficient genome mining, is appearing as the long awaited solution to this problem. By quickly mining food genomes for characteristics of certain food therapeutic ingredients, researchers can potentially find new ones in a matter of a few weeks. Yet, surprisingly, very little success has been achieved so far using bioinformatics in mining for food bioactives.The absence of food specific bioinformatic mining tools, the slow integration of both experimental mining and bioinformatics, and the important difference between different experimental platforms are some of the reasons for the slow progress of bioinformatics in the field of functional food and more specifically in bioactive peptide discovery.In this paper I discuss some methods that could be easily translated, using a rational peptide bioinformatics design, to food bioactive peptide mining. I highlight the need for an integrated food peptide database. I also discuss how to better integrate experimental work with bioinformatics in order to improve the mining of food for bioactive peptides, therefore achieving a higher success rates.

  12. Identifying predictors of physics item difficulty: A linear regression approach

    Science.gov (United States)

    Mesic, Vanes; Muratovic, Hasnija

    2011-06-01

    Large-scale assessments of student achievement in physics are often approached with an intention to discriminate students based on the attained level of their physics competencies. Therefore, for purposes of test design, it is important that items display an acceptable discriminatory behavior. To that end, it is recommended to avoid extraordinary difficult and very easy items. Knowing the factors that influence physics item difficulty makes it possible to model the item difficulty even before the first pilot study is conducted. Thus, by identifying predictors of physics item difficulty, we can improve the test-design process. Furthermore, we get additional qualitative feedback regarding the basic aspects of student cognitive achievement in physics that are directly responsible for the obtained, quantitative test results. In this study, we conducted a secondary analysis of data that came from two large-scale assessments of student physics achievement at the end of compulsory education in Bosnia and Herzegovina. Foremost, we explored the concept of “physics competence” and performed a content analysis of 123 physics items that were included within the above-mentioned assessments. Thereafter, an item database was created. Items were described by variables which reflect some basic cognitive aspects of physics competence. For each of the assessments, Rasch item difficulties were calculated in separate analyses. In order to make the item difficulties from different assessments comparable, a virtual test equating procedure had to be implemented. Finally, a regression model of physics item difficulty was created. It has been shown that 61.2% of item difficulty variance can be explained by factors which reflect the automaticity, complexity, and modality of the knowledge structure that is relevant for generating the most probable correct solution, as well as by the divergence of required thinking and interference effects between intuitive and formal physics knowledge

  13. Moving Beyond the Systems Approach in SCM and Logistics Research

    DEFF Research Database (Denmark)

    Nilsson, Fredrik; Gammelgaard, Britta

    2012-01-01

    Purpose – The purpose of this paper is to provide a paradigmatic reflection on theoretical approaches recently identified in logistics and supply chain management (SCM); namely complex adaptive systems and complexity thinking, and to compare it to the dominant approach in logistics and SCM research......, namely the systems approach. By analyzing the basic assumptions of the three approaches, SCM and logistics researchers are guided in their choice of research approaches which increases their awareness of the consequences different approaches have on theory and practice. Design...... to the dominant approach in SCM and logistics research, the systems approach, it is concluded that the underlying assumptions of complex adaptive systems and complexity thinking are more appropriate than systems approach for contemporary challenges of organizational complexity in SCM and logistics. It is found...

  14. Constructing New Theory for Identifying Students with Emotional Disturbance: A Constructivist Approach to Grounded Theory

    OpenAIRE

    2012-01-01

    A grounded theory study that examined how practitioners in a county alternative and correctional education setting identify youth with emotional and behavioral difficulties for special education services provides an exemplar for a constructivist approach to grounded theory methodology. Discussion focuses on how a constructivist orientation to grounded theory methodology informed research decisions, shaped the development of the emergent grounded theory, and prompted a way of thinking about da...

  15. An Approach to Identify and Characterize a Subunit Candidate Shigella Vaccine Antigen.

    Science.gov (United States)

    Pore, Debasis; Chakrabarti, Manoj K

    2016-01-01

    Shigellosis remains a serious issue throughout the developing countries, particularly in children under the age of 5. Numerous strategies have been tested to develop vaccines targeting shigellosis; unfortunately despite several years of extensive research, no safe, effective, and inexpensive vaccine against shigellosis is available so far. Here, we illustrate in detail an approach to identify and establish immunogenic outer membrane proteins from Shigella flexneri 2a as subunit vaccine candidates.

  16. DNA enrichment approaches to identify unauthorized genetically modified organisms (GMOs).

    Science.gov (United States)

    Arulandhu, Alfred J; van Dijk, Jeroen P; Dobnik, David; Holst-Jensen, Arne; Shi, Jianxin; Zel, Jana; Kok, Esther J

    2016-07-01

    With the increased global production of different genetically modified (GM) plant varieties, chances increase that unauthorized GM organisms (UGMOs) may enter the food chain. At the same time, the detection of UGMOs is a challenging task because of the limited sequence information that will generally be available. PCR-based methods are available to detect and quantify known UGMOs in specific cases. If this approach is not feasible, DNA enrichment of the unknown adjacent sequences of known GMO elements is one way to detect the presence of UGMOs in a food or feed product. These enrichment approaches are also known as chromosome walking or gene walking (GW). In recent years, enrichment approaches have been coupled with next generation sequencing (NGS) analysis and implemented in, amongst others, the medical and microbiological fields. The present review will provide an overview of these approaches and an evaluation of their applicability in the identification of UGMOs in complex food or feed samples.

  17. Research Priorities for Fertility and Conception Research as Identified by Multidisciplinary Health Care Practitioners and Researchers.

    Science.gov (United States)

    Moran, Lisa J; Spencer, Laura; Russell, Darryl L; Hull, Mary Louise; Robertson, Sarah A; Varcoe, Tamara J; Davies, Michael J; Brown, Hannah M; Rodgers, Raymond J

    2016-01-13

    The Robinson Research Institute of the University of Adelaide convened a multidisciplinary group of n = 33 clinicians, researchers and representatives of government organisations on the 2 October 2014 for a workshop entitled "Promoting fertility and healthy conception. How do we generate greater reproductive health awareness?" The key aim of the workshop was to assess the body of knowledge that informs clinical practice and government policy, and to identify questions and additional information needed by health practitioners and government representatives working in the field of reproductive health and to frame future research and policy. The workshop identified topics that fell mostly into three categories: lifestyle-related, societal and biological factors. The lifestyle topics included nutrition and diet, exercise, obesity, shift work and other factors deemed to be modifiable at the level of the individual. The societal topics included discussions of matters that are structural, and resistant to change by individuals, including specific ethical issues, social disadvantage, government and educational policies. The biological factors are intrinsic physical states of the individual, and included many factors where there is a dense body of scientific knowledge which may not be readily accessible in less academic language. This workshop thus provided an opportunity to identify further actions that could be undertaken to meet the needs of diverse organisations and groups of professionals with an interest in human fertility. Since so many factors in our social and biological environment can impact fertility and preconception health, it is imperative to involve many disciplines or levels of government or societal organisations that have not traditionally been involved in this area.

  18. Research Priorities for Fertility and Conception Research as Identified by Multidisciplinary Health Care Practitioners and Researchers

    Directory of Open Access Journals (Sweden)

    Lisa J. Moran

    2016-01-01

    Full Text Available The Robinson Research Institute of the University of Adelaide convened a multidisciplinary group of n = 33 clinicians, researchers and representatives of government organisations on the 2 October 2014 for a workshop entitled “Promoting fertility and healthy conception. How do we generate greater reproductive health awareness?” The key aim of the workshop was to assess the body of knowledge that informs clinical practice and government policy, and to identify questions and additional information needed by health practitioners and government representatives working in the field of reproductive health and to frame future research and policy. The workshop identified topics that fell mostly into three categories: lifestyle-related, societal and biological factors. The lifestyle topics included nutrition and diet, exercise, obesity, shift work and other factors deemed to be modifiable at the level of the individual. The societal topics included discussions of matters that are structural, and resistant to change by individuals, including specific ethical issues, social disadvantage, government and educational policies. The biological factors are intrinsic physical states of the individual, and included many factors where there is a dense body of scientific knowledge which may not be readily accessible in less academic language. This workshop thus provided an opportunity to identify further actions that could be undertaken to meet the needs of diverse organisations and groups of professionals with an interest in human fertility. Since so many factors in our social and biological environment can impact fertility and preconception health, it is imperative to involve many disciplines or levels of government or societal organisations that have not traditionally been involved in this area.

  19. A comparison of approaches for finding minimum identifying codes on graphs

    Science.gov (United States)

    Horan, Victoria; Adachi, Steve; Bak, Stanley

    2016-05-01

    In order to formulate mathematical conjectures likely to be true, a number of base cases must be determined. However, many combinatorial problems are NP-hard and the computational complexity makes this research approach difficult using a standard brute force approach on a typical computer. One sample problem explored is that of finding a minimum identifying code. To work around the computational issues, a variety of methods are explored and consist of a parallel computing approach using MATLAB, an adiabatic quantum optimization approach using a D-Wave quantum annealing processor, and lastly using satisfiability modulo theory (SMT) and corresponding SMT solvers. Each of these methods requires the problem to be formulated in a unique manner. In this paper, we address the challenges of computing solutions to this NP-hard problem with respect to each of these methods.

  20. Constructing New Theory for Identifying Students with Emotional Disturbance: A Constructivist Approach to Grounded Theory

    Directory of Open Access Journals (Sweden)

    Dori Barnett

    2012-06-01

    Full Text Available A grounded theory study that examined how practitioners in a county alternative and correctional education setting identify youth with emotional and behavioral difficulties for special education services provides an exemplar for a constructivist approach to grounded theory methodology. Discussion focuses on how a constructivist orientation to grounded theory methodology informed research decisions, shaped the development of the emergent grounded theory, and prompted a way of thinking about data collection and analysis. Implications for future research directions and policy and practice in the field of special and alternative education are discussed.

  1. Identifying Effective Methods of Instruction for Adult Emergent Readers through Community-Based Research

    Science.gov (United States)

    Blackmer, Rachel; Hayes-Harb, Rachel

    2016-01-01

    We present a community-based research project aimed at identifying effective methods and materials for teaching English literacy skills to adult English as a second language emergent readers. We conducted a quasi-experimental study whereby we evaluated the efficacy of two approaches, one based on current practices at the English Skills Learning…

  2. A Community-Based Approach to Identifying Influential Spreaders

    Directory of Open Access Journals (Sweden)

    Zhiying Zhao

    2015-04-01

    Full Text Available Identifying influential spreaders in complex networks has a significant impact on understanding and control of spreading process in networks. In this paper, we introduce a new centrality index to identify influential spreaders in a network based on the community structure of the network. The community-based centrality (CbC considers both the number and sizes of communities that are directly linked by a node. We discuss correlations between CbC and other classical centrality indices. Based on simulations of the single source of infection with the Susceptible-Infected-Recovered (SIR model, we find that CbC can help to identify some critical influential nodes that other indices cannot find. We also investigate the stability of CbC.

  3. An Approach for Identifying Benefit Segments among Prospective College Students.

    Science.gov (United States)

    Miller, Patrick; And Others

    1990-01-01

    A study investigated the importance to 578 applicants of various benefits offered by a moderately selective private university. Applicants rated the institution on 43 academic, social, financial, religious, and curricular attributes. The objective was to test the efficacy of one approach to college market segmentation. Results support the utility…

  4. Research Methodology: A Practitioner Approach

    Science.gov (United States)

    Singh, Sukhpal; Chana, Inderveer; Singh, Maninder

    2015-01-01

    The ultimate goal of scientific research is publication so as to showcase the research outcomes. Scientists, starting as graduate students, are measured primarily not by their dexterity in laboratory manipulations, not by their innate knowledge of either broad or narrow scientific subjects, and certainly not by their wit or charm; they are…

  5. cgaTOH: extended approach for identifying tracts of homozygosity.

    Directory of Open Access Journals (Sweden)

    Li Zhang

    Full Text Available Identification of disease variants via homozygosity mapping and investigation of the effects of genome-wide homozygosity regions on traits of biomedical importance have been widely applied recently. Nonetheless, the existing methods and algorithms to identify long tracts of homozygosity (TOH are not able to provide efficient and rigorous regions for further downstream association investigation. We expanded current methods to identify TOHs by defining "surrogate-TOH", a region covering a cluster of TOHs with specific characteristics. Our defined surrogate-TOH includes cTOH, viz a common TOH region where at least ten TOHs present; gTOH, whereby a group of highly overlapping TOHs share proximal boundaries; and aTOH, which are allelically-matched TOHs. Searching for gTOH and aTOH was based on a repeated binary spectral clustering algorithm, where a hierarchy of clusters is created and represented by a TOH cluster tree. Based on the proposed method of identifying different species of surrogate-TOH, our cgaTOH software was developed. The software provides an intuitive and interactive visualization tool for better investigation of the high-throughput output with special interactive navigation rings, which will find its applicability in both conventional association studies and more sophisticated downstream analyses. NCBI genome map viewer is incorporated into the system. Moreover, we discuss the choice of implementing appropriate empirical ranges of critical parameters by applying to disease models. This method identifies various patterned clusters of SNPs demonstrating extended homozygosity, thus one can observe different aspects of the multi-faceted characteristics of TOHs.

  6. 76 FR 44593 - Identifying the Center for Drug Evaluation and Research's Science and Research Needs...

    Science.gov (United States)

    2011-07-26

    ... Science and Research Needs; Availability of a Draft Report; Request for Comments AGENCY: Food and Drug... announcing the availability of a draft report entitled ``Identifying CDER's Science and Research Needs... efforts. Through external communication of the science and research needs outlined in the report,...

  7. Identifying Priorities for International Arctic Research and Policy

    Science.gov (United States)

    Rachold, V.; Hik, D.; Barr, S.

    2015-12-01

    Participants. This paper presents an overview of IASC´s efforts and achievements in terms of identifying Arctic research priorities and providing scientific expertise to policy makers and people who live in or near the Arctic.

  8. Videoethnographic approaches to audience research

    DEFF Research Database (Denmark)

    Wildermuth, Norbert

      In my paper I will explore the methodological uses and epistemological consequences of videoethnography in audience studies. With reference to research done on young people and their media appropriations in Recife (Brazil), in December 2005, I will argue for the creative integration of video...... recordings in doing mediaethnographic audience research. Moreover, I will discuss the use and potentials of hypermedia in presenting the results of ethnographic audience research. Based on recent conceptualisations and theories of hypermodality and multimodal ethnography (Lemke, 2002; Idema, 2003; Dicks......'. Finally, considerations regarding a planned hypermediated presentation of my research project in Recife, will be related to the experiences made with video as tool of mediaethnographic investigation and analysis. How the potential of non-sequentiality enshrined in hypermedia applications can...

  9. A novel pattern mining approach for identifying cognitive activity in EEG based functional brain networks.

    Science.gov (United States)

    Thilaga, M; Vijayalakshmi, R; Nadarajan, R; Nandagopal, D

    2016-06-01

    The complex nature of neuronal interactions of the human brain has posed many challenges to the research community. To explore the underlying mechanisms of neuronal activity of cohesive brain regions during different cognitive activities, many innovative mathematical and computational models are required. This paper presents a novel Common Functional Pattern Mining approach to demonstrate the similar patterns of interactions due to common behavior of certain brain regions. The electrode sites of EEG-based functional brain network are modeled as a set of transactions and node-based complex network measures as itemsets. These itemsets are transformed into a graph data structure called Functional Pattern Graph. By mining this Functional Pattern Graph, the common functional patterns due to specific brain functioning can be identified. The empirical analyses show the efficiency of the proposed approach in identifying the extent to which the electrode sites (transactions) are similar during various cognitive load states.

  10. Quantitative and qualitative approaches to identifying migration chronology in a continental migrant

    Science.gov (United States)

    Beatty, William S.; Kesler, Dylan C.; Webb, Elisabeth B.; Raedeke, Andrew H.; Naylor, Luke W.; Humburg, Dale D.

    2013-01-01

    The degree to which extrinsic factors influence migration chronology in North American waterfowl has not been quantified, particularly for dabbling ducks. Previous studies have examined waterfowl migration using various methods, however, quantitative approaches to define avian migration chronology over broad spatio-temporal scales are limited, and the implications for using different approaches have not been assessed. We used movement data from 19 female adult mallards (Anas platyrhynchos) equipped with solar-powered global positioning system satellite transmitters to evaluate two individual level approaches for quantifying migration chronology. The first approach defined migration based on individual movements among geopolitical boundaries (state, provincial, international), whereas the second method modeled net displacement as a function of time using nonlinear models. Differences in migration chronologies identified by each of the approaches were examined with analysis of variance. The geopolitical method identified mean autumn migration midpoints at 15 November 2010 and 13 November 2011, whereas the net displacement method identified midpoints at 15 November 2010 and 14 November 2011. The mean midpoints for spring migration were 3 April 2011 and 20 March 2012 using the geopolitical method and 31 March 2011 and 22 March 2012 using the net displacement method. The duration, initiation date, midpoint, and termination date for both autumn and spring migration did not differ between the two individual level approaches. Although we did not detect differences in migration parameters between the different approaches, the net displacement metric offers broad potential to address questions in movement ecology for migrating species. Ultimately, an objective definition of migration chronology will allow researchers to obtain a comprehensive understanding of the extrinsic factors that drive migration at the individual and population levels. As a result, targeted

  11. Quantitative and qualitative approaches to identifying migration chronology in a continental migrant.

    Science.gov (United States)

    Beatty, William S; Kesler, Dylan C; Webb, Elisabeth B; Raedeke, Andrew H; Naylor, Luke W; Humburg, Dale D

    2013-01-01

    The degree to which extrinsic factors influence migration chronology in North American waterfowl has not been quantified, particularly for dabbling ducks. Previous studies have examined waterfowl migration using various methods, however, quantitative approaches to define avian migration chronology over broad spatio-temporal scales are limited, and the implications for using different approaches have not been assessed. We used movement data from 19 female adult mallards (Anas platyrhynchos) equipped with solar-powered global positioning system satellite transmitters to evaluate two individual level approaches for quantifying migration chronology. The first approach defined migration based on individual movements among geopolitical boundaries (state, provincial, international), whereas the second method modeled net displacement as a function of time using nonlinear models. Differences in migration chronologies identified by each of the approaches were examined with analysis of variance. The geopolitical method identified mean autumn migration midpoints at 15 November 2010 and 13 November 2011, whereas the net displacement method identified midpoints at 15 November 2010 and 14 November 2011. The mean midpoints for spring migration were 3 April 2011 and 20 March 2012 using the geopolitical method and 31 March 2011 and 22 March 2012 using the net displacement method. The duration, initiation date, midpoint, and termination date for both autumn and spring migration did not differ between the two individual level approaches. Although we did not detect differences in migration parameters between the different approaches, the net displacement metric offers broad potential to address questions in movement ecology for migrating species. Ultimately, an objective definition of migration chronology will allow researchers to obtain a comprehensive understanding of the extrinsic factors that drive migration at the individual and population levels. As a result, targeted

  12. Quantitative and qualitative approaches to identifying migration chronology in a continental migrant.

    Directory of Open Access Journals (Sweden)

    William S Beatty

    Full Text Available The degree to which extrinsic factors influence migration chronology in North American waterfowl has not been quantified, particularly for dabbling ducks. Previous studies have examined waterfowl migration using various methods, however, quantitative approaches to define avian migration chronology over broad spatio-temporal scales are limited, and the implications for using different approaches have not been assessed. We used movement data from 19 female adult mallards (Anas platyrhynchos equipped with solar-powered global positioning system satellite transmitters to evaluate two individual level approaches for quantifying migration chronology. The first approach defined migration based on individual movements among geopolitical boundaries (state, provincial, international, whereas the second method modeled net displacement as a function of time using nonlinear models. Differences in migration chronologies identified by each of the approaches were examined with analysis of variance. The geopolitical method identified mean autumn migration midpoints at 15 November 2010 and 13 November 2011, whereas the net displacement method identified midpoints at 15 November 2010 and 14 November 2011. The mean midpoints for spring migration were 3 April 2011 and 20 March 2012 using the geopolitical method and 31 March 2011 and 22 March 2012 using the net displacement method. The duration, initiation date, midpoint, and termination date for both autumn and spring migration did not differ between the two individual level approaches. Although we did not detect differences in migration parameters between the different approaches, the net displacement metric offers broad potential to address questions in movement ecology for migrating species. Ultimately, an objective definition of migration chronology will allow researchers to obtain a comprehensive understanding of the extrinsic factors that drive migration at the individual and population levels. As a result

  13. Computational approaches to identify functional genetic variants in cancer genomes

    DEFF Research Database (Denmark)

    Gonzalez-Perez, Abel; Mustonen, Ville; Reva, Boris;

    2013-01-01

    The International Cancer Genome Consortium (ICGC) aims to catalog genomic abnormalities in tumors from 50 different cancer types. Genome sequencing reveals hundreds to thousands of somatic mutations in each tumor but only a minority of these drive tumor progression. We present the result of discu...... of discussions within the ICGC on how to address the challenge of identifying mutations that contribute to oncogenesis, tumor maintenance or response to therapy, and recommend computational techniques to annotate somatic variants and predict their impact on cancer phenotype....

  14. A Maximum Entropy Approach to Identifying Sentence Boundaries

    CERN Document Server

    Reynar, J C; Reynar, Jeffrey C.; Ratnaparkhi, Adwait

    1997-01-01

    We present a trainable model for identifying sentence boundaries in raw text. Given a corpus annotated with sentence boundaries, our model learns to classify each occurrence of ., ?, and ! as either a valid or invalid sentence boundary. The training procedure requires no hand-crafted rules, lexica, part-of-speech tags, or domain-specific information. The model can therefore be trained easily on any genre of English, and should be trainable on any other Roman-alphabet language. Performance is comparable to or better than the performance of similar systems, but we emphasize the simplicity of retraining for new domains.

  15. Research fronts analysis : A bibliometric to identify emerging fields of research

    Science.gov (United States)

    Miwa, Sayaka; Ando, Satoko

    Research fronts analysis identifies emerging areas of research through observing co-clustering in highly-cited papers. This article introduces the concept of research fronts analysis, explains its methodology and provides case examples. It also demonstrates developing research fronts in Japan by looking at the past winners of Thomson Reuters Research Fronts Awards. Research front analysis is currently being used by the Japanese government to determine new trends in science and technology. Information professionals can also utilize this bibliometric as a research evaluation tool.

  16. Three Approaches to Evaluation Research.

    Science.gov (United States)

    Rafter, David O.

    1984-01-01

    Three common evaluation models are the scientific, interactive, and hybrid. A study of evaluation projects mandated by the Wisconsin legislature revealed that the hybrid model was most effective in achieving policy planning and policy control utilization, the interactive approach provided aid to individual utilization, and the scientific approach…

  17. Nanotechnology-based approaches in anticancer research.

    Science.gov (United States)

    Jabir, Nasimudeen R; Tabrez, Shams; Ashraf, Ghulam Md; Shakil, Shazi; Damanhouri, Ghazi A; Kamal, Mohammad A

    2012-01-01

    Cancer is a highly complex disease to understand, because it entails multiple cellular physiological systems. The most common cancer treatments are restricted to chemotherapy, radiation and surgery. Moreover, the early recognition and treatment of cancer remains a technological bottleneck. There is an urgent need to develop new and innovative technologies that could help to delineate tumor margins, identify residual tumor cells and micrometastases, and determine whether a tumor has been completely removed or not. Nanotechnology has witnessed significant progress in the past few decades, and its effect is widespread nowadays in every field. Nanoparticles can be modified in numerous ways to prolong circulation, enhance drug localization, increase drug efficacy, and potentially decrease chances of multidrug resistance by the use of nanotechnology. Recently, research in the field of cancer nanotechnology has made remarkable advances. The present review summarizes the application of various nanotechnology-based approaches towards the diagnostics and therapeutics of cancer.

  18. An approach to identify issues affecting ERP implementation in Indian SMEs

    Directory of Open Access Journals (Sweden)

    Rana Basu

    2012-06-01

    Full Text Available Purpose: The purpose of this paper is to present the findings of a study which is based on the results of a comprehensive compilation of literature and subsequent analysis of ERP implementation success issues in context to Indian Small and Medium scale Enterprises (SME’s. This paper attempts to explore the existing literature and highlight those issues on ERP implementation and further to this the researchers applied TOPSIS (Technique for order preference by similarity to ideal solution method to prioritize issues affecting successful implementation of ERP. Design/methodology/approach: Based on the literature review certain issues leading to successful ERP implementation have been identified and to identify key issues Pareto Analysis (80-20 Rule have been applied. Further to extraction of key issues a survey based on TOPSIS was carried out in Indian small and medium scale enterprises. Findings: Based on review of literature 25 issues have been identified and further Pareto analysis has been done to extract key issues which is further prioritized by applying Topsis method. Research limitations/implications: Beside those identified issues there may be other issues that need to be explored. There is scope to enhance this study by taking into consideration different type of industries and by extending number of respondents. Practical implications: By identifying key issues for SMEs, managers can better prioritize issues to make implementation process smooth without disruption. ERP vendors can take inputs from this study to change their implementation approach while targeting small scale enterprises. Originality/value: There is no published literature available which followed a similar approach in identification of the critical issues affecting ERP in small and mid-sized companies in India or in any developing economy.

  19. Experimental design research approaches, perspectives, applications

    CERN Document Server

    Stanković, Tino; Štorga, Mario

    2016-01-01

    This book presents a new, multidisciplinary perspective on and paradigm for integrative experimental design research. It addresses various perspectives on methods, analysis and overall research approach, and how they can be synthesized to advance understanding of design. It explores the foundations of experimental approaches and their utility in this domain, and brings together analytical approaches to promote an integrated understanding. The book also investigates where these approaches lead to and how they link design research more fully with other disciplines (e.g. psychology, cognition, sociology, computer science, management). Above all, the book emphasizes the integrative nature of design research in terms of the methods, theories, and units of study—from the individual to the organizational level. Although this approach offers many advantages, it has inherently led to a situation in current research practice where methods are diverging and integration between individual, team and organizational under...

  20. A Black feminist approach to nursing research.

    Science.gov (United States)

    Barbee, E L

    1994-10-01

    Despite the presence of a body of Black feminist literature, the growing body of nursing literature on feminism and the feminist approach to research remains narrowly focused on White feminist concerns. By essentially ignoring the realities of Black women, nursing has reproduced the errors of previous White feminists. This article demonstrates the relevance of the Black feminist approach to nursing by applying it in combination with general feminist research principles and anthropological theory in research concerned with low-income Black women's experiences with dysphoria and depression. The findings of the research suggest that a combination approach more clearly illuminates how context effects dysphoria in poor Black women.

  1. Identifying prognostic features by bottom-up approach and correlating to drug repositioning.

    Directory of Open Access Journals (Sweden)

    Wei Li

    Full Text Available Traditionally top-down method was used to identify prognostic features in cancer research. That is to say, differentially expressed genes usually in cancer versus normal were identified to see if they possess survival prediction power. The problem is that prognostic features identified from one set of patient samples can rarely be transferred to other datasets. We apply bottom-up approach in this study: survival correlated or clinical stage correlated genes were selected first and prioritized by their network topology additionally, then a small set of features can be used as a prognostic signature.Gene expression profiles of a cohort of 221 hepatocellular carcinoma (HCC patients were used as a training set, 'bottom-up' approach was applied to discover gene-expression signatures associated with survival in both tumor and adjacent non-tumor tissues, and compared with 'top-down' approach. The results were validated in a second cohort of 82 patients which was used as a testing set.Two sets of gene signatures separately identified in tumor and adjacent non-tumor tissues by bottom-up approach were developed in the training cohort. These two signatures were associated with overall survival times of HCC patients and the robustness of each was validated in the testing set, and each predictive performance was better than gene expression signatures reported previously. Moreover, genes in these two prognosis signature gave some indications for drug-repositioning on HCC. Some approved drugs targeting these markers have the alternative indications on hepatocellular carcinoma.Using the bottom-up approach, we have developed two prognostic gene signatures with a limited number of genes that associated with overall survival times of patients with HCC. Furthermore, prognostic markers in these two signatures have the potential to be therapeutic targets.

  2. A Novel Approach for Identify Small and Capital Handwritten Letter

    Directory of Open Access Journals (Sweden)

    Ekta Tiwari

    2012-06-01

    Full Text Available A handwritten character is represented as a sequence of strokes whose features are extracted and classified. Although the off-line and on-line character recognition techniques have different approaches, they share a lot of common problems and solutions. The printed documents available in the form of books, papers, magazines, etc. are scanned using standard scanners which produce an image of the scanned document. The preprocessed image is segmented using an algorithm which decomposes the scanned text into paragraphs using special space detection technique and then the paragraphs into lines using vertical histograms, and lines into words using horizontal histograms, and words into character image glyphs using horizontal histograms. Each image glyph is comprised of 24x24 pixels. Thus a database of character image glyphs is created out of the segmentation phase. The various features that are considered for classification are the character height, character width, the number of horizontal lines (long and short, image centroid and special dots. we proposed extracted features were passed to a Support Vector Machine (SVM where the characters are classified by Supervised Learning Algorithm. These classes are mapped onto for recognition. Then the text is reconstructed using fonts.

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

    Science.gov (United States)

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

    2016-01-01

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

  4. An optimized Leave One Out approach to efficiently identify outliers

    Science.gov (United States)

    Biagi, L.; Caldera, S.; Perego, D.

    2012-04-01

    Least squares are a well established and very popular statistical toolbox in geomatics. Particularly, LS are applied to routinely adjust geodetic networks in the cases both of classical surveys and of modern GNSS permanent networks, both at the local and at the global spatial scale. The linearized functional model between the observables and a vector of unknowns parameters is given. A vector of N observations and its apriori covariance is available. Typically, the observations vector can be decomposed into n subvectors, internally correlated but reciprocally uncorrelated. This happens, for example, when double differences are built from undifferenced observations and are processed to estimate the network coordinates of a GNSS session. Note that when all the observations are independent, n=N: this is for example the case of the adjustment of a levelling network. LS provide the estimates of the parameters, the observables, the residuals and of the a posteriori variance. The testing of the initial hypotheses, the rejection of outliers and the estimation of accuracies and reliabilities can be performed at different levels of significance and power. However, LS are not robust. The a posteriori estimation of the variance can be biased by one unmodelled outlier in the observations. In some case, the unmodelled bias is spread into all the residuals and its identification is difficult. A possible solution to this problem is given by the so called Leave One Out (LOO) approach. A particular subvector can be excluded from the adjustment, whose results are used to check the residuals of the excluded subvector. Clearly, the check is more robust, because a bias in the subvector does not affect the adjustment results. The process can be iterated on all the subvectors. LOO is robust but can be very slow, when n adjustments are performed. An optimized LLO algorithm has been studied. The usual LS adjustment on all the observations is performed to obtain a 'batch' result. The

  5. A landscape ecology approach identifies important drivers of urban biodiversity.

    Science.gov (United States)

    Turrini, Tabea; Knop, Eva

    2015-04-01

    Cities are growing rapidly worldwide, yet a mechanistic understanding of the impact of urbanization on biodiversity is lacking. We assessed the impact of urbanization on arthropod diversity (species richness and evenness) and abundance in a study of six cities and nearby intensively managed agricultural areas. Within the urban ecosystem, we disentangled the relative importance of two key landscape factors affecting biodiversity, namely the amount of vegetated area and patch isolation. To do so, we a priori selected sites that independently varied in the amount of vegetated area in the surrounding landscape at the 500-m scale and patch isolation at the 100-m scale, and we hold local patch characteristics constant. As indicator groups, we used bugs, beetles, leafhoppers, and spiders. Compared to intensively managed agricultural ecosystems, urban ecosystems supported a higher abundance of most indicator groups, a higher number of bug species, and a lower evenness of bug and beetle species. Within cities, a high amount of vegetated area increased species richness and abundance of most arthropod groups, whereas evenness showed no clear pattern. Patch isolation played only a limited role in urban ecosystems, which contrasts findings from agro-ecological studies. Our results show that urban areas can harbor a similar arthropod diversity and abundance compared to intensively managed agricultural ecosystems. Further, negative consequences of urbanization on arthropod diversity can be mitigated by providing sufficient vegetated space in the urban area, while patch connectivity is less important in an urban context. This highlights the need for applying a landscape ecological approach to understand the mechanisms shaping urban biodiversity and underlines the potential of appropriate urban planning for mitigating biodiversity loss.

  6. Design and Implementation of Collaborative Research Approaches

    Science.gov (United States)

    Venti, Mike W.; Berger, David E.

    2009-01-01

    This poster reviews the collarborative research approaches that NASA has been designing and implementing for the Integrated Vehicle Health Management (IVHM) Project. The inputs for the technical plan are reviewed, the Research Test and Integration Plan (RTIP) WIKI, is used to create and propose a multi-themed and multi-partner research testing opportunities. The outputs are testing opportunities.

  7. Research on consistency of identifying solitary pulmonary masses with CT

    Institute of Scientific and Technical Information of China (English)

    Qiuping Wang; Gang Niu; Yun Zhang; Yongqian Qiang; Zicheng Li; Youmin Guo

    2008-01-01

    Objective:To research on consistency of identifying solitary pulmonary masses with CT.Methods:Three observers with different working backgrounds in imaging diagnosis individually interpreted the same group images of solitary pulmonary mass, by 12 indexes of objective signs.The differences in interpretation resulted in ante- and post-interpretations were assessed by the x2 test.The agreement of two interpretations from the same observer was confirmed with the kappa test.A double-blind method was adopted for analysis.Results:The agreement rates of ante- and post-interpreting from the three observers were respectively 82.65%(486/588) 80.27%(472/588) and 84.86% (499/588) while their interpreting results were generally accordant without significant difference(x2 = 4.975, df= 2,P = 0.083) however there was difference between the observer 2 and observer 3(x2 = 4.875, df= 1, P = 0.027).There were five indexes with k > 0.40 of ante- and post-interpreting results of the three observers, including clarity of nodule borderline, presence of sentus, uniformity of density, existence of cavity and calcification in pathological region, among them, the agreement rate of interpreting borderline and cavity was higher(k > 0.07); the blood vessel convergence poorer(0 < k ≤ 0.40); the other six CT signs of interpretation were slightly different.Conclusion:The ability to identify solitary pulmonary mass was inconsistent, and needs to be improved further.

  8. Flight Test Approach to Adaptive Control Research

    Science.gov (United States)

    Pavlock, Kate Maureen; Less, James L.; Larson, David Nils

    2011-01-01

    The National Aeronautics and Space Administration s Dryden Flight Research Center completed flight testing of adaptive controls research on a full-scale F-18 testbed. The validation of adaptive controls has the potential to enhance safety in the presence of adverse conditions such as structural damage or control surface failures. This paper describes the research interface architecture, risk mitigations, flight test approach and lessons learned of adaptive controls research.

  9. USING QUALITATIVE APPROACH IN SPECIAL EDUCATION RESEARCH

    OpenAIRE

    Natasa GALEVSKA

    1998-01-01

    The text deals with some methodological problems in special education research. The limits of purely positivistic, quantitative, experimental research in the area of special education lately are overcome with the use of qualitative approach. Qualitative research are flexibly designed. The data are descriptive and collected in natural setting. Characteristics of the qualitative research make them more appropriate for investigation of the phenomena in special education, considering the small nu...

  10. Enfoques metodológicos para identificar y caracterizar la investigación mexicana en química en bases de datos bibliográficas Methodological approaches to identify and describe Mexican chemistry research in bibliographic databases

    Directory of Open Access Journals (Sweden)

    Yoscelina Hernández García

    2013-04-01

    Full Text Available Las distintas visiones que dan las diferentes fuentes de información con respecto a un campo de investigación en particular es un fenómeno conocido en los estudios bibliométricos y cienciométricos. El presente artículo tiene por propósito entender el impacto de las fuentes de información en la identificación y la caracterización de un campo científico en un contexto particular: la química en México. No se trata de comparar la producción científica en este campo extraída de varias bases de datos bibliográficas, sino de partir de una metodología original que consiste en construir estrategias de búsqueda adecuadas para cada fuente y procesos de normalización, análisis y visualización de los resultados, mostrar que la definición del campo científico estudiado depende de las fuentes de información usadas. Se usaron fuentes nacionales e internacionales especializadas, o relacionadas con las ciencias químicas, así como recursos multidisciplinarios, a saber Web of Science (WoS, Chemical Abstracts Service (CAS, PERIÓDICA y CAB Abstracts (CAB en el periodo de 2000-2004. Los resultados apuntan al impacto de las especificidades de la estructura de cada base de datos en los resultados de las búsquedas; en PERIÓDICA, la producción se concentra en 37 revistas (44% mientras que los trabajos en revistas internacionales se encuentran repartidas en un total de 1559 publicaciones (WoS, 188 (CAB y 1640 (CAS.The varying visions of a particular research field in diverse information sources are a recognized phenomenon in bibliometric and scientometric studies. The purpose of this paper is to provide an understanding of the impact of using distinct information sources for the identification and description of a scientific field in a specific context, in this instance the field of chemistry in Mexico. We use both international and national sources specializing in or related to chemistry, as well as suitable multidisciplinary services

  11. Identifying overlapping and hierarchical thematic structures in networks of scholarly papers: a comparison of three approaches.

    Science.gov (United States)

    Havemann, Frank; Gläser, Jochen; Heinz, Michael; Struck, Alexander

    2012-01-01

    The aim of this paper is to introduce and assess three algorithms for the identification of overlapping thematic structures in networks of papers. We implemented three recently proposed approaches to the identification of overlapping and hierarchical substructures in graphs and applied the corresponding algorithms to a network of 492 information-science papers coupled via their cited sources. The thematic substructures obtained and overlaps produced by the three hierarchical cluster algorithms were compared to a content-based categorisation, which we based on the interpretation of titles, abstracts, and keywords. We defined sets of papers dealing with three topics located on different levels of aggregation: h-index, webometrics, and bibliometrics. We identified these topics with branches in the dendrograms produced by the three cluster algorithms and compared the overlapping topics they detected with one another and with the three predefined paper sets. We discuss the advantages and drawbacks of applying the three approaches to paper networks in research fields.

  12. Identifying overlapping and hierarchical thematic structures in networks of scholarly papers: a comparison of three approaches.

    Directory of Open Access Journals (Sweden)

    Frank Havemann

    Full Text Available The aim of this paper is to introduce and assess three algorithms for the identification of overlapping thematic structures in networks of papers. We implemented three recently proposed approaches to the identification of overlapping and hierarchical substructures in graphs and applied the corresponding algorithms to a network of 492 information-science papers coupled via their cited sources. The thematic substructures obtained and overlaps produced by the three hierarchical cluster algorithms were compared to a content-based categorisation, which we based on the interpretation of titles, abstracts, and keywords. We defined sets of papers dealing with three topics located on different levels of aggregation: h-index, webometrics, and bibliometrics. We identified these topics with branches in the dendrograms produced by the three cluster algorithms and compared the overlapping topics they detected with one another and with the three predefined paper sets. We discuss the advantages and drawbacks of applying the three approaches to paper networks in research fields.

  13. Identifying Overlapping and Hierarchical Thematic Structures in Networks of Scholarly Papers: A Comparison of Three Approaches

    CERN Document Server

    Havemann, Frank; Heinz, Michael; Struck, Alexander

    2011-01-01

    We implemented three recently proposed approaches to the identification of overlapping and hierarchical substructures in graphs and applied the corresponding algorithms to a network of 492 information-science papers coupled via their cited sources. The thematic substructures obtained and overlaps produced by the three hierarchical cluster algorithms were compared to a content-based categorisation, which we based on the interpretation of titles and keywords. We defined sets of papers dealing with three topics located on different levels of aggregation: h-index, webometrics, and bibliometrics. We identified these topics with branches in the dendrograms produced by the three cluster algorithms and compared the overlapping topics they detected with one another and with the three pre-defined paper sets. We discuss the advantages and drawbacks of applying the three approaches to paper networks in research fields.

  14. Identifying the Critical Links in Road Transportation Networks: Centrality-based approach utilizing structural properties

    Energy Technology Data Exchange (ETDEWEB)

    Chinthavali, Supriya [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-04-01

    Surface transportation road networks share structural properties similar to other complex networks (e.g., social networks, information networks, biological networks, and so on). This research investigates the structural properties of road networks for any possible correlation with the traffic characteristics such as link flows those determined independently. Additionally, we define a criticality index for the links of the road network that identifies the relative importance in the network. We tested our hypotheses with two sample road networks. Results show that, correlation exists between the link flows and centrality measures of a link of the road (dual graph approach is followed) and the criticality index is found to be effective for one test network to identify the vulnerable nodes.

  15. Identifying comorbid depression and disruptive behavior disorders: comparison of two approaches used in adolescent studies.

    Science.gov (United States)

    Vander Stoep, Ann; Adrian, Molly C; Rhew, Isaac C; McCauley, Elizabeth; Herting, Jerald R; Kraemer, Helena C

    2012-07-01

    Interest in commonly co-occurring depression and disruptive behavior disorders in children has yielded a small body of research that estimates the prevalence of this comorbid condition and compares children with the comorbid condition and children with depression or disruptive behavior disorders alone with respect to antecedents and outcomes. Prior studies have used one of two different approaches to measure comorbid disorders: (1) meeting criteria for two DSM or ICD diagnoses or (2) scoring .5 SD above the mean or higher on two dimensional scales. This study compares two snapshots of comorbidity taken simultaneously in the same sample with each of the measurement approaches. The Developmental Pathways Project administered structured diagnostic interviews as well as dimensional scales to a community-based sample of 521 11-12 year olds to assess depression and disruptive behavior disorders. Clinical caseness indicators of children identified as "comorbid" by each method were examined concurrently and 3-years later. Cross-classification of adolescents via the two approaches revealed low agreement. When other indicators of caseness, including functional impairment, need for services, and clinical elevations on other symptom scales were examined, adolescents identified as comorbid via dimensional scales only were similar to those who were identified as comorbid via DSM-IV diagnostic criteria. Findings suggest that when relying solely on DSM diagnostic criteria for comorbid depression and disruptive behavior disorders, many adolescents with significant impairment will be overlooked. Findings also suggest that lower dimensional scale thresholds can be set when comorbid conditions, rather than single forms of psychopathology, are being identified.

  16. TCGA researchers identify 4 subtypes of stomach cancer

    Science.gov (United States)

    Stomach cancers fall into four distinct molecular subtypes, researchers with The Cancer Genome Atlas (TCGA) Network have found. Scientists report that this discovery could change how researchers think about developing treatments for stomach cancer, also c

  17. Flight Approach to Adaptive Control Research

    Science.gov (United States)

    Pavlock, Kate Maureen; Less, James L.; Larson, David Nils

    2011-01-01

    The National Aeronautics and Space Administration's Dryden Flight Research Center completed flight testing of adaptive controls research on a full-scale F-18 testbed. The testbed served as a full-scale vehicle to test and validate adaptive flight control research addressing technical challenges involved with reducing risk to enable safe flight in the presence of adverse conditions such as structural damage or control surface failures. This paper describes the research interface architecture, risk mitigations, flight test approach and lessons learned of adaptive controls research.

  18. Identifying the barriers to conducting outcomes research in integrative health care clinic settings - a qualitative study

    Directory of Open Access Journals (Sweden)

    Findlay-Reece Barbara

    2010-01-01

    Full Text Available Abstract Background Integrative health care (IHC is an interdisciplinary blending of conventional medicine and complementary and alternative medicine (CAM with the purpose of enhancing patients' health. In 2006, we designed a study to assess outcomes that are relevant to people using such care. However, we faced major challenges in conducting this study and hypothesized that this might be due to the lack of a research climate in these clinics. To investigate these challenges, we initiated a further study in 2008, to explore the reasons why IHC clinics are not conducting outcomes research and to identify strategies for conducting successful in-house outcomes research programs. The results of the latter study are reported here. Methods A total of 25 qualitative interviews were conducted with key participants from 19 IHC clinics across Canada. Basic content analysis was used to identify key themes from the transcribed interviews. Results Barriers identified by participants fell into four categories: organizational culture, organizational resources, organizational environment and logistical challenges. Cultural challenges relate to the philosophy of IHC, organizational leadership and practitioner attitudes and beliefs. Participants also identified significant issues relating to their organization's lack of resources such as funding, compensation, infrastructure and partnerships/linkages. Environmental challenges such as the nature of a clinic's patient population and logistical issues such as the actual implementation of a research program and the applicability of research data also posed challenges to the conduct of research. Embedded research leadership, integration of personal and professional values about research, alignment of research activities and clinical workflow processes are some of the factors identified by participants that support IHC clinics' ability to conduct outcomes research. Conclusions Assessing and enhancing the broader

  19. Identifying functional reorganization of spelling networks: An Individual Peak Probability Comparison Approach.

    Directory of Open Access Journals (Sweden)

    Jeremy Joseph Purcell

    2013-12-01

    Full Text Available Previous research has shown that damage to the neural substrates of orthographic processing can lead to functional reorganization during reading (Tsapkini et al., 2011; in this research we ask if the same is true for spelling. To examine the functional reorganization of spelling networks we present a novel three-stage Individual Peak Probability Comparison (IPPC analysis approach for comparing the activation patterns obtained during fMRI of spelling in a single brain-damaged individual with dysgraphia to those obtained in a set of non-impaired control participants. The first analysis stage characterizes the convergence in activations across non-impaired control participants by applying a technique typically used for characterizing activations across studies: Activation Likelihood Estimate (ALE (Turkeltaub et al., 2002. This method was used to identify locations that have a high likelihood of yielding activation peaks in the non-impaired participants. The second stage provides a characterization of the degree to which the brain-damaged individual’s activations correspond to the group pattern identified in Stage 1. This involves performing a Mahalanobis distance statistics analysis (Tsapkini et al., 2011 that compares each of a control group’s peak activation locations to the nearest peak generated by the brain-damaged individual. The third stage evaluates the extent to which the brain-damaged individual’s peaks are atypical relative to the range of individual variation among the control participants. This IPPC analysis allows for a quantifiable, statistically sound method for comparing an individual’s activation pattern to the patterns observed in a control group and, thus, provides a valuable tool for identifying functional reorganization in a brain-damaged individual with impaired spelling. Furthermore, this approach can be applied more generally to compare any individual’s activation pattern with that of a set of other individuals.

  20. Identifying functional reorganization of spelling networks: an individual peak probability comparison approach.

    Science.gov (United States)

    Purcell, Jeremy J; Rapp, Brenda

    2013-01-01

    Previous research has shown that damage to the neural substrates of orthographic processing can lead to functional reorganization during reading (Tsapkini et al., 2011); in this research we ask if the same is true for spelling. To examine the functional reorganization of spelling networks we present a novel three-stage Individual Peak Probability Comparison (IPPC) analysis approach for comparing the activation patterns obtained during fMRI of spelling in a single brain-damaged individual with dysgraphia to those obtained in a set of non-impaired control participants. The first analysis stage characterizes the convergence in activations across non-impaired control participants by applying a technique typically used for characterizing activations across studies: Activation Likelihood Estimate (ALE) (Turkeltaub et al., 2002). This method was used to identify locations that have a high likelihood of yielding activation peaks in the non-impaired participants. The second stage provides a characterization of the degree to which the brain-damaged individual's activations correspond to the group pattern identified in Stage 1. This involves performing a Mahalanobis distance statistics analysis (Tsapkini et al., 2011) that compares each of a control group's peak activation locations to the nearest peak generated by the brain-damaged individual. The third stage evaluates the extent to which the brain-damaged individual's peaks are atypical relative to the range of individual variation among the control participants. This IPPC analysis allows for a quantifiable, statistically sound method for comparing an individual's activation pattern to the patterns observed in a control group and, thus, provides a valuable tool for identifying functional reorganization in a brain-damaged individual with impaired spelling. Furthermore, this approach can be applied more generally to compare any individual's activation pattern with that of a set of other individuals.

  1. Narrative Inquiry: A Spiritual and Liberating Approach to Research

    Science.gov (United States)

    Bruce, Elizabeth McIsaac

    2008-01-01

    This article identifies various research characteristics of narrative inquiry including its holistic and creative approach and its emphases on experience, relationships and participation, subjectivity and consciousness-raising, commitment and resistance, ethical action, and claiming voice and power. The author suggests that these characteristics…

  2. Identifying Research Priorities for School Improvement in the Developing World

    Science.gov (United States)

    Read, Robyn; Fernandez-Hermosilla, Magdalena; Anderson, Stephen; Mundy, Karen

    2016-01-01

    This paper discusses a research agenda setting project conducted for an international non-governmental organization which aims to help create a regionally relevant, high-quality knowledge base on key education issues of policy and practice. Specifically, we illustrate how our team adapted the Child Health and Nutrition Research Initiative (CHRNI)…

  3. Gene-based Association Approach Identify Genes Across Stress Traits in Fruit Flies

    DEFF Research Database (Denmark)

    Rohde, Palle Duun; Edwards, Stefan McKinnon; Sarup, Pernille Merete;

    approach grouping variants accordingly to gene position, thus lowering the number of statistical tests performed and increasing the probability of identifying genes with small to moderate effects. Using this approach we identify numerous genes associated with different types of stresses in Drosophila...

  4. A systematic approach for identifying and presenting mechanistic evidence in human health assessments

    Science.gov (United States)

    Kushman, Mary E.; Kraft, Andrew D.; Guyton, Kathryn Z.; Chiu, Weihsueh A.; Makris, Susan L.; Rusyn, Ivan

    2013-01-01

    Clear documentation of literature search and presentation methodologies can improve transparency in chemical hazard assessments. We sought to improve clarity for the scientific support for cancer mechanisms of action using a systematic approach to literature retrieval, selection, and presentation of studies. The general question was “What are the mechanisms by which a chemical may cause carcinogenicity in the target tissue?” Di(2-ethylhexyl)phthalate was used as a case study chemical with a complex database of >3,000 publications. Relevant mechanistic events were identified from published reviews. The PubMed search strategy included relevant synonyms and wildcards for DEHP and its metabolites, mechanistic events, and species of interest. Tiered exclusion/inclusion criteria for study pertinence were defined, and applied to the retrieved literature. Manual curation was conducted for mechanistic events with large literature databases. Literature trees documented identification and selection of the literature evidence. The selected studies were summarized in evidence tables accompanied by succinct narratives. Primary publications were deposited into the Health and Environmental Research Online (http://hero.epa.gov/) database and identified by pertinence criteria and key terms to permit organized retrieval. This approach contributes to human health assessment by effectively managing a large volume of literature, improving transparency, and facilitating subsequent synthesis of information across studies. PMID:23959061

  5. A non-target approach to identify disinfection byproducts of structurally similar sulfonamide antibiotics.

    Science.gov (United States)

    Wang, Mian; Helbling, Damian E

    2016-10-01

    There is growing concern over the formation of new types of disinfection byproducts (DBPs) from pharmaceuticals and other emerging contaminants during drinking water production. Free chlorine is a widely used disinfectant that reacts non-selectively with organic molecules to form a variety of byproducts. In this research, we aimed to investigate the DBPs formed from three structurally similar sulfonamide antibiotics (sulfamethoxazole, sulfathiazole, and sulfadimethoxine) to determine how chemical structure influences the types of chlorination reactions observed. We conducted free chlorination experiments and developed a non-target approach to extract masses from the experimental dataset that represent the masses of candidate DBPs. Structures were assigned to the candidate DBPs based on analytical data and knowledge of chlorine chemistry. Confidence levels were assigned to each proposed structure according to conventions in the field. In total, 11, 12, and 15 DBP structures were proposed for sulfamethoxazole, sulfathiazole, and sulfadimethoxine, respectively. The structures of the products suggest a variety of reaction types including chlorine substitution, SC cleavage, SN hydrolysis, desulfonation, oxidation/hydroxylation, and conjugation reactions. Some reaction types were common to all of the sulfonamide antibiotics, but unique reaction types were also observed for each sulfonamide antibiotic suggesting that selective prediction of DBP structures of other sulfonamide antibiotics based on chemical structure is unlikely to be possible based on these data alone. This research offers an approach to comprehensively identify DBPs of organic molecules and fills in much needed data on the formation of specific DBPs from three environmentally relevant sulfonamide antibiotics.

  6. Proteomic approaches in research of cyanobacterial photosynthesis.

    Science.gov (United States)

    Battchikova, Natalia; Angeleri, Martina; Aro, Eva-Mari

    2015-10-01

    Oxygenic photosynthesis in cyanobacteria, algae, and plants is carried out by a fabulous pigment-protein machinery that is amazingly complicated in structure and function. Many different approaches have been undertaken to characterize the most important aspects of photosynthesis, and proteomics has become the essential component in this research. Here we describe various methods which have been used in proteomic research of cyanobacteria, and demonstrate how proteomics is implemented into on-going studies of photosynthesis in cyanobacterial cells.

  7. Identifying reasons for failure in biomedical research and publishing

    Directory of Open Access Journals (Sweden)

    D. Bousfield

    2009-07-01

    Full Text Available The regular assessment of Brazilian scientific output means that individual university departments need to constantly improve the quantity and quality of their scientific output. A significant proportion of this output involves the work of Master’s and Doctoral students, but getting this work published in a suitable journal can often prove to be a challenge. Although students’ lack of fluency in English is a contributing factor, many of the problems observed have an early origin in the formulation of the research problem and its relevance to current research trends in the international literature. In short, more time needs to be spent in the library and less in the laboratory, and more effort needs to be made in teaching students basic research skills such as the effective use of bibliographic databases like PubMed, Web of Science and Scopus.

  8. Identifying the critical financial ratios for stocks evaluation: A fuzzy delphi approach

    Science.gov (United States)

    Mokhtar, Mazura; Shuib, Adibah; Mohamad, Daud

    2014-12-01

    Stocks evaluation has always been an interesting and challenging problem for both researchers and practitioners. Generally, the evaluation can be made based on a set of financial ratios. Nevertheless, there are a variety of financial ratios that can be considered and if all ratios in the set are placed into the evaluation process, data collection would be more difficult and time consuming. Thus, the objective of this paper is to identify the most important financial ratios upon which to focus in order to evaluate the stock's performance. For this purpose, a survey was carried out using an approach which is based on an expert judgement, namely the Fuzzy Delphi Method (FDM). The results of this study indicated that return on equity, return on assets, net profit margin, operating profit margin, earnings per share and debt to equity are the most important ratios.

  9. Identifying Risk and Protective Factors in Recidivist Juvenile Offenders: A Decision Tree Approach

    Science.gov (United States)

    Ortega-Campos, Elena; García-García, Juan; Gil-Fenoy, Maria José; Zaldívar-Basurto, Flor

    2016-01-01

    Research on juvenile justice aims to identify profiles of risk and protective factors in juvenile offenders. This paper presents a study of profiles of risk factors that influence young offenders toward committing sanctionable antisocial behavior (S-ASB). Decision tree analysis is used as a multivariate approach to the phenomenon of repeated sanctionable antisocial behavior in juvenile offenders in Spain. The study sample was made up of the set of juveniles who were charged in a court case in the Juvenile Court of Almeria (Spain). The period of study of recidivism was two years from the baseline. The object of study is presented, through the implementation of a decision tree. Two profiles of risk and protective factors are found. Risk factors associated with higher rates of recidivism are antisocial peers, age at baseline S-ASB, problems in school and criminality in family members. PMID:27611313

  10. An interdisciplinary approach to identify adaptation strategies that enhance flood resilience and urban liveability

    DEFF Research Database (Denmark)

    Rogers, B. C.; Bertram, N.; Gunn, Alex;

    This paper provides guidance on how to identify and design the most suitable climate adaptation strategies for enhancing the liveability and flood resilience of urban catchments. It presents findings from a case study of Elwood, a coastal Melbourne suburb regularly affected by flooding....... The research integrates social science, architecture and environmental engineering to co-develop technical, design and policy solutions that respond to the local community’s vision for the future and are robust under a range of future climate, population and urban development scenarios. The paper shows...... that ensuring a city’s flood resilience involves a range of measures to retreat from, adapt to and defend against flooding; this necessarily requires an integrated approach and interdisciplinary expertise to develop adaptation pathways that are grounded in community aspirations and priorities, inspired by novel...

  11. Human Trafficking in Ethiopia: A Scoping Review to Identify Gaps in Service Delivery, Research, and Policy.

    Science.gov (United States)

    Beck, Dana C; Choi, Kristen R; Munro-Kramer, Michelle L; Lori, Jody R

    2016-03-31

    The purpose of this review is to integrate evidence on human trafficking in Ethiopia and identify gaps and recommendations for service delivery, research and training, and policy. A scoping literature review approach was used to systematically search nursing, medical, psychological, law, and international databases and synthesize information on a complex, understudied topic. The search yielded 826 articles, and 39 met the predetermined criteria for inclusion in the review. Trafficking in Ethiopia has occurred internally and externally in the form of adult and child labor and sex trafficking. There were also some reports of organ trafficking and other closely related human rights violations, such as child marriage, child soldiering, and exploitative intercountry adoption. Risk factors for trafficking included push factors (poverty, political instability, economic problems, and gender discrimination) and pull factors (demand for cheap labor). Trafficking was associated with poor health and economic outcomes for victims. Key recommendations for service delivery, research and training, and policy are identified, including establishing comprehensive services for survivor rehabilitation and reintegration, conducting quantitative health outcomes research, and reforming policy around migration and trafficking. Implementing the recommendations identified by this review will allow policy makers, researchers, and practitioners to take meaningful steps toward confronting human trafficking in Ethiopia.

  12. Sourcing Program: To identify outstanding women and ethnic minorities in research and research management

    Energy Technology Data Exchange (ETDEWEB)

    Nissen, S.H.

    1991-08-01

    To meet the challenges of the changing demographics and a projected shortage of technically trained workers in the 21st century, Lawrence Livermore National (LLNL) is increasing its commitment to develop a diverse work force with the abilities to carry out the Laboratory's missions. In addition to the recruitment programs already established at LLNL, a sourcing program to identify outstanding women and minorities in research and research management was initiated in the summer of 1990. A research methodology, time table, selection criteria, and data generation strategy were designed and implemented for this program. Through extensive contacts with R D facilities, women's and minority professional organizations, national research councils, technical professional societies and universities, other sourcing programs were investigated and evaluated and a network of contacts and resources was developed. This report describes the design and implementation of the sourcing program targeting outstanding women and minorities in science and engineering. It details the investigation and evaluation of sourcing programs in other R D facilities and provides information regarding methods and sources used to identify potential candidates. Conclusions and recommendations are presented. 10 refs., 5 tabs.

  13. A Framework for Rigorously Identifying Research Gaps in Qualitative Literature Reviews

    DEFF Research Database (Denmark)

    Müller-Bloch, Christoph; Kranz, Johann

    2015-01-01

    Identifying research gaps is a fundamental goal of literature reviewing. While it is widely acknowledged that literature reviews should identify research gaps, there are no methodological guidelines for how to identify research gaps in qualitative literature reviews ensuring rigor and replicabili...

  14. Identifying inhibitory compounds in lignocellulosic biomass hydrolysates using an exometabolomics approach

    NARCIS (Netherlands)

    Y. Zha; J.A. Westerhuis; B. Muilwijk; K.M. Overkamp; B.M. Nijmeijer; L. Coulier; A.K. Smilde; P.J. Punt

    2014-01-01

    BACKGROUND: Inhibitors are formed that reduce the fermentation performance of fermenting yeast during the pretreatment process of lignocellulosic biomass. An exometabolomics approach was applied to systematically identify inhibitors in lignocellulosic biomass hydrolysates. RESULTS: We studied the co

  15. Identifying inhibitory compounds in lignocellulosic biomass hydrolysates using an exometabolomics approach

    NARCIS (Netherlands)

    Zha, Y.; Westerhuis, J.A.; Muilwijk, B.; Overkamp, K.M.; Nijmeijer, B.M.; Coulier, L.; Smilde, A.K.; Punt, P.J.

    2014-01-01

    Background: Inhibitors are formed that reduce the fermentation performance of fermenting yeast during the pretreatment process of lignocellulosic biomass. An exometabolomics approach was applied to systematically identify inhibitors in lignocellulosic biomass hydrolysates.Results: We studied the com

  16. Integrative screening approach identifies regulators of polyploidization and targets for acute megakaryocytic leukemia

    Science.gov (United States)

    Wen, Qiang; Goldenson, Benjamin; Silver, Serena J.; Schenone, Monica; Dancik, Vladimir; Huang, Zan; Wang, Ling-Zhi; Lewis, Timothy; An, W. Frank; Li, Xiaoyu; Bray, Mark-Anthony; Thiollier, Clarisse; Diebold, Lauren; Gilles, Laure; Vokes, Martha S.; Moore, Christopher B.; Bliss-Moreau, Meghan; VerPlank, Lynn; Tolliday, Nicola J.; Mishra, Rama; Vemula, Sasidhar; Shi, Jianjian; Wei, Lei; Kapur, Reuben; Lopez, Cécile K.; Gerby, Bastien; Ballerini, Paola; Pflumio, Francoise; Gilliland, D. Gary; Goldberg, Liat; Birger, Yehudit; Izraeli, Shai; Gamis, Alan S.; Smith, Franklin O.; Woods, William G.; Taub, Jeffrey; Scherer, Christina A.; Bradner, James; Goh, Boon-Cher; Mercher, Thomas; Carpenter, Anne E.; Gould, Robert J.; Clemons, Paul A.; Carr, Steven A.; Root, David E.; Schreiber, Stuart L.; Stern, Andrew M.; Crispino, John D.

    2012-01-01

    Summary The mechanism by which cells decide to skip mitosis to become polyploid is largely undefined. Here we used a high-content image-based screen to identify small-molecule probes that induce polyploidization of megakaryocytic leukemia cells and serve as perturbagens to help understand this process. We found that dimethylfasudil (diMF, H-1152P) selectively increased polyploidization, mature cell-surface marker expression, and apoptosis of malignant megakaryocytes. A broadly applicable, highly integrated target identification approach employing proteomic and shRNA screening revealed that a major target of diMF is Aurora A kinase (AURKA), which has not been studied extensively in megakaryocytes. Moreover, we discovered that MLN8237 (Alisertib), a selective inhibitor of AURKA, induced polyploidization and expression of mature megakaryocyte markers in AMKL blasts and displayed potent anti-AMKL activity in vivo. This research provides the rationale to support clinical trials of MLN8237 and other inducers of polyploidization in AMKL. Finally, we have identified five networks of kinases that regulate the switch to polyploidy. PMID:22863010

  17. Identifying creative research accomplishments: Methodology and results for nanotechnology and human genetics

    NARCIS (Netherlands)

    Heinze, Thomas; Shapira, Philip; Senker, Jacqueline; Kuhlmann, Stefan

    2007-01-01

    Motivated by concerns about the organizational and institutional conditions that foster research creativity in science, we focus on how creative research can be defined, operationalized, and empirically identified. A functional typology of research creativity is proposed encompassing theoretical, me

  18. The interdisciplinary approach in community interpreting research

    OpenAIRE

    Vargas Urpi, Mireia

    2011-01-01

    Community interpreting is a complex activity that has been studied from many different angles. Based on a review of the literature, this paper aims to highlight the importance of an interdisciplinary approach in community interpreting research, as well as the close relationship between the theoretical and methodological frameworks that have been used to date. As a prospective study and by describing theories applied from five different fields (i.e. anthropology, sociology, applied linguistics...

  19. Arts-Based Research: Trojan Horses and Shibboleths. The Liabilities of a Hybrid Research Approach. "What Hath Eisner Wrought?"

    Science.gov (United States)

    Pariser, David

    2009-01-01

    The term "arts-based research" has been debated for some time now. In an article strongly in favor of this approach Bean (2007) identifies three species: "Research on the arts (italics in the original) (art history, visual and cultural studies, media studies etc.)...Research for the arts, refers to research into applied techniques, materials and…

  20. An algorithmic calibration approach to identify globally optimal parameters for constraining the DayCent model

    Energy Technology Data Exchange (ETDEWEB)

    Rafique, Rashid; Kumar, Sandeep; Luo, Yiqi; Kiely, Gerard; Asrar, Ghassem R.

    2015-02-01

    he accurate calibration of complex biogeochemical models is essential for the robust estimation of soil greenhouse gases (GHG) as well as other environmental conditions and parameters that are used in research and policy decisions. DayCent is a popular biogeochemical model used both nationally and internationally for this purpose. Despite DayCent’s popularity, its complex parameter estimation is often based on experts’ knowledge which is somewhat subjective. In this study we used the inverse modelling parameter estimation software (PEST), to calibrate the DayCent model based on sensitivity and identifi- ability analysis. Using previously published N2 O and crop yield data as a basis of our calibration approach, we found that half of the 140 parameters used in this study were the primary drivers of calibration dif- ferences (i.e. the most sensitive) and the remaining parameters could not be identified given the data set and parameter ranges we used in this study. The post calibration results showed improvement over the pre-calibration parameter set based on, a decrease in residual differences 79% for N2O fluxes and 84% for crop yield, and an increase in coefficient of determination 63% for N2O fluxes and 72% for corn yield. The results of our study suggest that future studies need to better characterize germination tem- perature, number of degree-days and temperature dependency of plant growth; these processes were highly sensitive and could not be adequately constrained by the data used in our study. Furthermore, the sensitivity and identifiability analysis was helpful in providing deeper insight for important processes and associated parameters that can lead to further improvement in calibration of DayCent model.

  1. Shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity.

    Directory of Open Access Journals (Sweden)

    J R Managbanag

    Full Text Available BACKGROUND: Identification of genes that modulate longevity is a major focus of aging-related research and an area of intense public interest. In addition to facilitating an improved understanding of the basic mechanisms of aging, such genes represent potential targets for therapeutic intervention in multiple age-associated diseases, including cancer, heart disease, diabetes, and neurodegenerative disorders. To date, however, targeted efforts at identifying longevity-associated genes have been limited by a lack of predictive power, and useful algorithms for candidate gene-identification have also been lacking. METHODOLOGY/PRINCIPAL FINDINGS: We have utilized a shortest-path network analysis to identify novel genes that modulate longevity in Saccharomyces cerevisiae. Based on a set of previously reported genes associated with increased life span, we applied a shortest-path network algorithm to a pre-existing protein-protein interaction dataset in order to construct a shortest-path longevity network. To validate this network, the replicative aging potential of 88 single-gene deletion strains corresponding to predicted components of the shortest-path longevity network was determined. Here we report that the single-gene deletion strains identified by our shortest-path longevity analysis are significantly enriched for mutations conferring either increased or decreased replicative life span, relative to a randomly selected set of 564 single-gene deletion strains or to the current data set available for the entire haploid deletion collection. Further, we report the identification of previously unknown longevity genes, several of which function in a conserved longevity pathway believed to mediate life span extension in response to dietary restriction. CONCLUSIONS/SIGNIFICANCE: This work demonstrates that shortest-path network analysis is a useful approach toward identifying genetic determinants of longevity and represents the first application of

  2. Using mixed methods to identify and answer clinically relevant research questions.

    Science.gov (United States)

    Shneerson, Catherine L; Gale, Nicola K

    2015-06-01

    The need for mixed methods research in answering health care questions is becoming increasingly recognized because of the complexity of factors that affect health outcomes. In this article, we argue for the value of using a qualitatively driven mixed method approach for identifying and answering clinically relevant research questions. This argument is illustrated by findings from a study on the self-management practices of cancer survivors and the exploration of one particular clinically relevant finding about higher uptake of self-management in cancer survivors who had received chemotherapy treatment compared with those who have not. A cross-sectional study generated findings that formed the basis for the qualitative study, by informing the purposive sampling strategy and generating new qualitative research questions. Using a quantitative research component to supplement a qualitative study can enhance the generalizability and clinical relevance of the findings and produce detailed, contextualized, and rich answers to research questions that would be unachievable through quantitative or qualitative methods alone.

  3. Identifying research priorities on infections in older adults: proceedings of an interdisciplinary workshop

    Directory of Open Access Journals (Sweden)

    Lohfeld Lynne

    2001-08-01

    Full Text Available Abstract Background Infections pose a substantial burden to the health of older adults. In this report, we describe the proceedings of a workshop to formulate and prioritize research questions about infections in older adults using an interdisciplinary approach. Methods Researchers from four sectors (basic science, clinical sciences, health services and epidemiology/determinants of health and representatives from various Canadian local, provincial, and federal stakeholder groups were invited to a two-day workshop. Five multi-disciplinary groups and stakeholders from each of three healthcare settings (long term, acute care and community discussed research priorities for each of the settings. Five to ten research questions were identified for each setting. Results The research questions proposed ranged from risk factors and outcomes for different infections to the effect of nutrition on infection and the role of alternative and complementary medicine in treating infections. Health service issues included barriers to immunization, prolongation of hospital length of stay by infection, use of care paths for managing infections, and decision-making in determining the site of care for individuals with infections. Clinical questions included risk factor assessment for infection, the effectiveness of preventative strategies, and technology evaluation. Epidemiologic issues included the challenge of achieving a better understanding of respiratory infections in the community and determining the prevalence of colonization with multi-resistant bacteria. Conclusions The questions are of direct relevance to researchers in a wide variety of fields. Bringing together a multi-disciplinary group of researchers to frame and prioritize research questions about aging is feasible, participants valued the opinions of people working in other areas.

  4. Computational Approaches for Mining GRO-Seq Data to Identify and Characterize Active Enhancers.

    Science.gov (United States)

    Nagari, Anusha; Murakami, Shino; Malladi, Venkat S; Kraus, W Lee

    2017-01-01

    Transcriptional enhancers are DNA regulatory elements that are bound by transcription factors and act to positively regulate the expression of nearby or distally located target genes. Enhancers have many features that have been discovered using genomic analyses. Recent studies have shown that active enhancers recruit RNA polymerase II (Pol II) and are transcribed, producing enhancer RNAs (eRNAs). GRO-seq, a method for identifying the location and orientation of all actively transcribing RNA polymerases across the genome, is a powerful approach for monitoring nascent enhancer transcription. Furthermore, the unique pattern of enhancer transcription can be used to identify enhancers in the absence of any information about the underlying transcription factors. Here, we describe the computational approaches required to identify and analyze active enhancers using GRO-seq data, including data pre-processing, alignment, and transcript calling. In addition, we describe protocols and computational pipelines for mining GRO-seq data to identify active enhancers, as well as known transcription factor binding sites that are transcribed. Furthermore, we discuss approaches for integrating GRO-seq-based enhancer data with other genomic data, including target gene expression and function. Finally, we describe molecular biology assays that can be used to confirm and explore further the function of enhancers that have been identified using genomic assays. Together, these approaches should allow the user to identify and explore the features and biological functions of new cell type-specific enhancers.

  5. Using Community-Based Participatory Research to Prevent HIV Disparities: Assumptions and Opportunities Identified by The Latino Partnership

    Science.gov (United States)

    Rhodes, Scott D.; Duck, Stacy; Alonzo, Jorge; Daniel-Ulloa, Jason; Aronson, Robert E.

    2013-01-01

    Background HIV disproportionately affects vulnerable populations in the United States (US), including recently arrived immigrant Latinos. However, the current arsenal of effective approaches to increase adherence to risk-reduction strategies and treatment within Latino populations remains insufficient. Methods Our community-based participatory research (CBPR) partnership blends multiple perspectives of community members, organizational representatives, local business leaders, and academic researchers to explore and intervene on HIV risk within Latino populations. We used CBPR to develop, implement, and evaluate two interventions that were found to be efficacious. Results We identified seven assumptions of CBPR as an approach to research, including more authentic study designs, stronger measurement, and improved quality of knowledge gained; increased community capacity to tackle other health disparities; the need to focus on community priorities; increased participation and retention rates; more successful interventions; reduced generalizability; and increased sustainability. Conclusions Despite the advancement of CBPR as an approach to research, key assumptions remain. Further research is needed to compare CBPR to other more traditional approaches to research. Such research would move us from assuming the value of CBPR to identifying its actual value in health disparity reduction. After all, communities carrying disproportionate burden of HIV, including immigrant Latino communities, deserve the best science possible. PMID:23673883

  6. Identifying medication error chains from critical incident reports: a new analytic approach.

    Science.gov (United States)

    Huckels-Baumgart, Saskia; Manser, Tanja

    2014-10-01

    Research into the distribution of medication errors usually focuses on isolated stages within the medication use process. Our study aimed to provide a novel process-oriented approach to medication incident analysis focusing on medication error chains. Our study was conducted across a 900-bed teaching hospital in Switzerland. All reported 1,591 medication errors 2009-2012 were categorized using the Medication Error Index NCC MERP and the WHO Classification for Patient Safety Methodology. In order to identify medication error chains, each reported medication incident was allocated to the relevant stage of the hospital medication use process. Only 25.8% of the reported medication errors were detected before they propagated through the medication use process. The majority of medication errors (74.2%) formed an error chain encompassing two or more stages. The most frequent error chain comprised preparation up to and including medication administration (45.2%). "Non-consideration of documentation/prescribing" during the drug preparation was the most frequent contributor for "wrong dose" during the administration of medication. Medication error chains provide important insights for detecting and stopping medication errors before they reach the patient. Existing and new safety barriers need to be extended to interrupt error chains and to improve patient safety.

  7. What influences motivation in Physical Education? A multilevel approach for identifying climate determinants of achievement motivation

    Directory of Open Access Journals (Sweden)

    Benjamin Niederkofler

    2015-03-01

    Full Text Available The present research tested the longitudinal and hierarchical influences of students’ climate perception on the development of achievement motives in Physical Education (PE. Students from Switzerland (N = 919; 45 classes; 50.1% female, age: M = 13.2, SD = 0.6 responded to the questionnaire. Perceived climate was measured using the German LASSO scales (Von Saldern & Littig, 1987, namely teacher care, classmate cooperativeness and satisfaction with teaching. To assess sport specific achievement motives (Hope of Success, HS; Fear of Failure, FF, we used a validated German scale from Elbe, Wenhold, and Müller (2005. Multilevel analysis revealed a link between perceived climate on change of students’ motivation in PE. The investigation also identified factors determining motivation decline caused by the classroom environment and teachers. Moreover, results showed significant gender effects on both motives and a significant impact of individual teacher care on the HS. This was also found for individual and aggregated satisfaction with teaching. The latter was significant for FF on both levels. Interestingly, teacher care showed inhibitory effects on both achievement motives. These findings suggest that students in PE may have unique behaviour which requires a different teaching approach than in normal classroom. This describes a specific learning environment in PE classes. Results are discussed based on students’ unique needs and gender effects.

  8. Towards a community effort to identify ethical principles for research in hydrology

    Science.gov (United States)

    Montanari, Alberto

    2010-05-01

    The hydrological community in Europe is growing rapidly in both size and, more importantly, scientific relevance and integrity. The Hydrological Sciences (HS) Division of EGU actively is promoting the above development by identifying research targets, stimulating the involvement of young scientists and managing a scientific open access journal based on a public peer review process. The management of the Division itself and the organisation of the General Assembly are carried out transparently, with the aim to seek an improved involvement of top and young scientists, with a bottom up approach. I believe the HS community is animated by a strong enthusiasm which, however, is not adequately supported by economical funding. In my opinion this is a major problem which HS should consider and discuss. The relevance of the societal and environmental problems dealt with by hydrologists, in a professional way and with exceptional scientific skills, is without doubt and therefore the limited amount of funding is not justified in practice. In my opinion, in order to refine the structure of the HS community, and promote its visibility, we should formally identify HS ethical principles for research in environmental science. The principles should highlight the role of hydrology as well as the ethical and scientific solidity of the HS community. Establishing ethical principles is even more important in view of the transparent approach HS is adopting for reviewing and publishing contributions and in view of the increasing need to transparently prove how public funding for research is administered. Establishing ethical principles for hydrology is not a trivial task. Hydrology is characterised by a relevant uncertainty in data, models and parameters. Hydrology is also relying on a large variety of approaches, ranging from statistical to physically based. The purpose of this poster is to present a collection of ethical principles for scientific research presented by the literature and

  9. Alternative approaches to research in physical therapy: positivism and phenomenology.

    Science.gov (United States)

    Shepard, K F; Jensen, G M; Schmoll, B J; Hack, L M; Gwyer, J

    1993-02-01

    This article presents philosophical approaches to research in physical therapy. A comparison is made to demonstrate how the research purpose, research design, research methods, and research data differ when one approaches research from the philosophical perspective of positivism (predominantly quantitative) as compared with the philosophical perspective of phenomenology (predominantly qualitative). Differences between the two approaches are highlighted by examples from research articles published in Physical Therapy. The authors urge physical therapy researchers to become familiar with the tenets, rigor, and knowledge gained from the use of both approaches in order to increase their options in conducting research relevant to the practice of physical therapy.

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

    Science.gov (United States)

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

    2010-12-01

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

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

    Science.gov (United States)

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

    2013-01-01

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

  12. A Research Agenda for Identifying and Developing Required Competencies in Software Engineering

    Directory of Open Access Journals (Sweden)

    Yvonne Sedelmaier

    2013-04-01

    Full Text Available 0 0 1 130 820 Hochschule Coburg 6 1 949 14.0 96 Normal 0 21 false false false DE JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Normale Tabelle"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman";} Various issues make learning and teaching software engineering a challenge for both students and instructors. Since there are no standard curricula and no cookbook recipes for successful software engineering, it is fairly hard to figure out which specific topics and competencies should be learned or acquired by a particular group of students. Furthermore, it is not clear which particular didactic approaches might work well for a specific topic and a particular group of students. This contribution presents a research agenda that aims at identifying relevant competencies and environmental constraints as well as their effect on learning and teaching software engineering. To that end, an experimental approach will be taken. As a distinctive feature, this approach iteratively introduces additional or modified didactical methods into existing courses and carefully evaluates their appropriateness. Thus, it continuously improves these methods.

  13. An operational modal analysis approach based on parametrically identified multivariable transmissibilities

    Science.gov (United States)

    Devriendt, Christof; De Sitter, Gert; Guillaume, Patrick

    2010-07-01

    In this contribution the approach to identify modal parameters from output-only (scalar) transmissibility measurements [C. Devriendt, P. Guillaume, The use of transmissibility measurements in output-only modal analysis, Mechanical Systems and Signal Processing 21 (7) (2007) 2689-2696] is generalized to multivariable transmissibilities. In general, the poles that are identified from (scalar as well as multivariable) transmissibility measurements do not correspond with the system's poles. However, by combining transmissibility measurements under different loading conditions, it is shown in this paper how model parameters can be identified from multivariable transmissibility measurements.

  14. CONFERENCE CHEVREUL Nutrition research: the industrial approach

    Directory of Open Access Journals (Sweden)

    Korver Onno

    2000-01-01

    Full Text Available The goal of nutrition research in an industrial setting is the marketing of products. Since consumers cannot see from the product whether it is healthy, communication to the consumer about the nutritional and health values of the products is essential. Industrial nutrition research therefore has to provide the scientific dossier to underpin the claims and other communication on and around the product as well as the scientific basis for the communication. These two lines are illustrated in figure 1. For scientific audiences the steps to collect the scientific evidence are obvious: first screening for new ideas on the basis of scientific developments and business options, then identifying ingredients that can deliver the health benefit, followed by mechanistic and bioavailability studies and finally human intervention trials. The communication line is less obvious for most scientifically oriented audiences. Experience has shown that an information cascade has to be followed: during the execution of the research work close contact with academic experts (a true dialogue is essential, when the research data are available information of a wide selection of health professionals (e.g. physicians, dieticians, science journalists is taking place and only after this step communication to the consumer starts. The communication with the scientific experts (the first step of the cascade obviously has to be in the hands of the nutrition research group of the industry involved. In Unilever this is the Unilever Nutrition Centre based in Vlaardingen in the Netherlands. Their role in the scientific dialogue is outlined in figure 2. The fact that the “Medaille Chevreul” has been awarded twice to members of the Unilever Nutrition Centre in the last two decades, illustrates that the UNC is considered to be a group with a truly scientific tradition.

  15. Identifying Core Mobile Learning Faculty Competencies Based Integrated Approach: A Delphi Study

    Science.gov (United States)

    Elbarbary, Rafik Said

    2015-01-01

    This study is based on the integrated approach as a concept framework to identify, categorize, and rank a key component of mobile learning core competencies for Egyptian faculty members in higher education. The field investigation framework used four rounds Delphi technique to determine the importance rate of each component of core competencies…

  16. Identifying bioaccumulative halogenated organic compounds using a nontargeted analytical approach: seabirds as sentinels.

    Directory of Open Access Journals (Sweden)

    Christopher J Millow

    Full Text Available Persistent organic pollutants (POPs are typically monitored via targeted mass spectrometry, which potentially identifies only a fraction of the contaminants actually present in environmental samples. With new anthropogenic compounds continuously introduced to the environment, novel and proactive approaches that provide a comprehensive alternative to targeted methods are needed in order to more completely characterize the diversity of known and unknown compounds likely to cause adverse effects. Nontargeted mass spectrometry attempts to extensively screen for compounds, providing a feasible approach for identifying contaminants that warrant future monitoring. We employed a nontargeted analytical method using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC/TOF-MS to characterize halogenated organic compounds (HOCs in California Black skimmer (Rynchops niger eggs. Our study identified 111 HOCs; 84 of these compounds were regularly detected via targeted approaches, while 27 were classified as typically unmonitored or unknown. Typically unmonitored compounds of note in bird eggs included tris(4-chlorophenylmethane (TCPM, tris(4-chlorophenylmethanol (TCPMOH, triclosan, permethrin, heptachloro-1'-methyl-1,2'-bipyrrole (MBP, as well as four halogenated unknown compounds that could not be identified through database searching or the literature. The presence of these compounds in Black skimmer eggs suggests they are persistent, bioaccumulative, potentially biomagnifying, and maternally transferring. Our results highlight the utility and importance of employing nontargeted analytical tools to assess true contaminant burdens in organisms, as well as to demonstrate the value in using environmental sentinels to proactively identify novel contaminants.

  17. International mobility technology research: a Delphi study to identify challenges and compensatory strategies.

    Science.gov (United States)

    Jefferds, Alexandra N; Pearlman, Jon L; Wee, Joy; Cooper, Rory A

    2011-01-01

    We sought to identify logistical and ethical challenges to performing wheelchair-related research in low- and middle-income countries and to generate a list of compensatory strategies to address these challenges. Thirteen individuals with experience in the field participated in an online Delphi study. The surveys asked participants to identify research challenges, suggest strategies to address the selected challenges, and critique each other's strategies. Participants identified challenges in the use of research techniques, compensation for participation that does not result coercion, oral and written translation materials, funding for research, collaboration with local professionals, and "respect for persons." Effective international mobility research requires time, cultural sensitivity, collaboration, and careful planning. An understanding of these requirements can allow researchers to anticipate and compensate for common pitfalls of their work, thus making the research more productive and beneficial to subjects. Future research is required to verify the general effectiveness of compensatory strategies.

  18. Methodological approaches in the research of organizational culture

    Directory of Open Access Journals (Sweden)

    Janićijević Nebojša

    2011-01-01

    Full Text Available In the thirty-years-long research of organizational culture, two mutually opposed methodological approaches have emerged: objectivistic quantitative and subjectivistic-qualitative. These two approaches are based on opposite ontological and epistemological assumptions: they include different types of research, and use opposite, quantitative vs. qualitative, methods of research. Each of the methodological approaches has its advantages and disadvantages. For this reason a hybrid approach emerges as a legitimate choice in organizational culture research methodology. It combines elements of both subjectivistic and objectivistic methodological approaches, according to the goals, content, and context of the research and preferences of the researcher himself/herself. Since it is possible to combine the two principal methodological approaches in various ways, there are several possible hybrid methodologies in organizational culture research. After the review of objectivistic quantitative and subjectivistic-qualitative methodological approaches, one of possible hybrid approaches in the research of organizational culture is presented in this paper.

  19. Molecular biology approaches in bioadhesion research

    Directory of Open Access Journals (Sweden)

    Marcelo Rodrigues

    2014-07-01

    Full Text Available The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1 generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2 setting up a BLAST search facility, (3 perform an in situ hybridization screen, and (4 functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.

  20. Identifying and Quantifying Cultural Factors That Matter to the IT Workforce: An Approach Based on Automated Content Analysis

    DEFF Research Database (Denmark)

    Schmiedel, Theresa; Müller, Oliver; Debortoli, Stefan;

    2016-01-01

    builds on 112,610 online reviews of Fortune 500 IT companies collected from Glassdoor, an online platform on which current and former employees can anonymously review companies and their management. We perform an automated content analysis to identify cultural factors that employees emphasize...... of culture and the success of companies, the validity of this approach is often discussed and researchers call for new ways of studying culture. Therefore, our research goal is to present an alternative approach to culture analysis for examining which cultural factors matter to the IT workforce. Our study...... in their reviews. Through a regression analysis on numerical employee satisfaction ratings, we find that a culture of learning and performance orientation contributes to employee motivation, while a culture of assertiveness and gender inegalitarianism has a strong negative influence on employees’ satisfaction...

  1. A model-based approach to identify binding sites in CLIP-Seq data.

    Directory of Open Access Journals (Sweden)

    Tao Wang

    Full Text Available Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq has made it possible to identify the targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present a novel model-based approach (MiClip to identify high-confidence protein-RNA binding sites from CLIP-seq datasets. This approach assigns a probability score for each potential binding site to help prioritize subsequent validation experiments. The MiClip algorithm has been tested in both HITS-CLIP and PAR-CLIP datasets. In the HITS-CLIP dataset, the signal/noise ratios of miRNA seed motif enrichment produced by the MiClip approach are between 17% and 301% higher than those by the ad hoc method for the top 10 most enriched miRNAs. In the PAR-CLIP dataset, the MiClip approach can identify ∼50% more validated binding targets than the original ad hoc method and two recently published methods. To facilitate the application of the algorithm, we have released an R package, MiClip (http://cran.r-project.org/web/packages/MiClip/index.html, and a public web-based graphical user interface software (http://galaxy.qbrc.org/tool_runner?tool_id=mi_clip for customized analysis.

  2. Candidate fire blight resistance genes in Malus identified with the use of genomic tools and approaches

    Science.gov (United States)

    The goal of this research is to utilize current advances in Rosaceae genomics to identify DNA markers for use in marker-assisted selection of durable resistance to fire blight. Candidate fire blight resistance genes were selected and ranked based upon differential expression after inoculation with ...

  3. A cellular genetics approach identifies gene-drug interactions and pinpoints drug toxicity pathway nodes

    Directory of Open Access Journals (Sweden)

    Oscar Takeo Suzuki

    2014-08-01

    Full Text Available New approaches to toxicity testing have incorporated high-throughput screening across a broad-range of in vitro assays to identify potential key events in response to chemical or drug treatment. To date, these approaches have primarily utilized repurposed drug discovery assays. In this study, we describe an approach that combines in vitro screening with genetic approaches for the experimental identification of genes and pathways involved in chemical or drug toxicity. Primary embryonic fibroblasts isolated from 32 genetically-characterized inbred mouse strains were treated in concentration-response format with 65 compounds, including pharmaceutical drugs, environmental chemicals, and compounds with known modes-of-action. Integrated cellular responses were measured at 24 and 72 hours using high-content imaging and included cell loss, membrane permeability, mitochondrial function, and apoptosis. Genetic association analysis of cross-strain differences in the cellular responses resulted in a collection of candidate loci potentially underlying the variable strain response to each chemical. As a demonstration of the approach, one candidate gene involved in rotenone sensitivity, Cybb, was experimentally validated in vitro and in vivo. Pathway analysis on the combined list of candidate loci across all chemicals identified a number of over-connected nodes that may serve as core regulatory points in toxicity pathways.

  4. Your name is not good enough: introducing the ORCID researcher identifier at Imperial College London

    Directory of Open Access Journals (Sweden)

    Torsten Reimer

    2015-11-01

    Full Text Available The ORCID researcher identifier ensures that research outputs can always reliably be traced back to their authors. ORCID also makes it possible to automate the sharing of research information, thereby increasing data quality, reducing duplication of effort for academics and saving institutions money. In 2014, Imperial College London created ORCID identifiers (iDs for academic and research staff. This article discusses the implementation project in the context of the role of ORCID in the global scholarly communications system. It shows how ORCID can be used to automate reporting, help with research data publication and support open access (OA.

  5. FRIGA, A New Approach To Identify Isotopes and Hypernuclei In N-Body Transport Models

    CERN Document Server

    Fèvre, A Le; Aichelin, J; Hartnack, Ch; Kireyev, V; Bratkovskaya, E

    2015-01-01

    We present a new algorithm to identify fragments in computer simulations of relativistic heavy ion collisions. It is based on the simulated annealing technique and can be applied to n-body transport models like the Quantum Molecular Dynamics. This new approach is able to predict isotope yields as well as hyper-nucleus production. In order to illustrate its predicting power, we confront this new method to experimental data, and show the sensitivity on the parameters which govern the cluster formation.

  6. New Research Approach to Rebuild Sport Facilities

    Directory of Open Access Journals (Sweden)

    Gaetano Raiola

    2011-01-01

    Full Text Available Problem statement: The game court of team sport, part of Sport Centre of Arturo Collana, was closed after structural accident in 2006 and the local administration is now designing the rebuilding of it. For this reason, it has already allocated economical resource to study a partial reconstruction of it to reutilize actual structure. The problem is how can satisfy the customers according to suggesting the old and new solutions. Approach: The aim is to recognize expected demand about the real choice of customers with the proposal for a various architectural aspects. A survey was carries out by using statistical model to correlate a demand of multi game sport relating to various hypotheses, already designed with a different solution. A sample of 100 customers that have submitted questionnaire with the specific parameters about the architecture and engine was taken to apply the qualitative research method to the market research. Results and Conclusion: The result of this study concludes that it is not possible to the partially construct but it is useful the plenty reconstruction of game court. The local organization of Coni (Italian National Olympic Committee designed a new project according to a specific parameter that follows the same characteristic of old game court without searching the other engineer and architectural solutions. Thus the question is a mix of engine and architectural aspects, economical and functional elements of it. The data showed association between demand of multisport and new architectonical hypothesis and the association between demand of single sport and old architectural structure. The percentage of multi sport demand is higher than single sport and this orientation has to follow to design a new sport facilities.

  7. Self-Directed Learning and Schooling: Identifying Pertinent Theories and Illustrative Research.

    Science.gov (United States)

    Skager, Rodney

    1979-01-01

    Six theoretical positions on human learning are identified as relevant to the development of self-direction: modeling; reinforcement; curiosity motivation; competency motivation; attribution theory and personal causation; and humanism. Four approaches to educational practice associated with self-direction are identified: experimental learning;…

  8. A cognitive approach to research and education

    NARCIS (Netherlands)

    Guney, A.

    2009-01-01

    What do we mean by research? How could we explain it in terms of a semantic network? Do we need to make research to learn? Is it necessary for our own education as a researcher? Does it make a substantial contribution to educating ourselves? Do researchers need teaching to improve their research. W

  9. Identifying and assessing the application of ecosystem services approaches in environmental policies and decision making.

    Science.gov (United States)

    Van Wensem, Joke; Calow, Peter; Dollacker, Annik; Maltby, Lorraine; Olander, Lydia; Tuvendal, Magnus; Van Houtven, George

    2017-01-01

    The presumption is that ecosystem services (ES) approaches provide a better basis for environmental decision making than do other approaches because they make explicit the connection between human well-being and ecosystem structures and processes. However, the existing literature does not provide a precise description of ES approaches for environmental policy and decision making, nor does it assess whether these applications will make a difference in terms of changing decisions and improving outcomes. We describe 3 criteria that can be used to identify whether and to what extent ES approaches are being applied: 1) connect impacts all the way from ecosystem changes to human well-being, 2) consider all relevant ES affected by the decision, and 3) consider and compare the changes in well-being of different stakeholders. As a demonstration, we then analyze retrospectively whether and how the criteria were met in different decision-making contexts. For this assessment, we have developed an analysis format that describes the type of policy, the relevant scales, the decisions or questions, the decision maker, and the underlying documents. This format includes a general judgment of how far the 3 ES criteria have been applied. It shows that the criteria can be applied to many different decision-making processes, ranging from the supranational to the local scale and to different parts of decision-making processes. In conclusion we suggest these criteria could be used for assessments of the extent to which ES approaches have been and should be applied, what benefits and challenges arise, and whether using ES approaches made a difference in the decision-making process, decisions made, or outcomes of those decisions. Results from such studies could inform future use and development of ES approaches, draw attention to where the greatest benefits and challenges are, and help to target integration of ES approaches into policies, where they can be most effective. Integr Environ

  10. Identifying Patients in the Acute Psychiatric Hospital Who May Benefit From a Palliative Care Approach.

    Science.gov (United States)

    Burton, M Caroline; Warren, Mark; Cha, Stephen S; Stevens, Maria; Blommer, Megan; Kung, Simon; Lapid, Maria I

    2016-04-01

    Identifying patients who will benefit from a palliative care approach is the first critical step in integrating palliative with curative therapy. Criteria are established that identify hospitalized medical patients who are near end of life, yet there are no criteria with respect to hospitalized patients with psychiatric disorders. The records of 276 consecutive patients admitted to a dedicated inpatient psychiatric unit were reviewed to identify prognostic criteria predictive of mortality. Mortality predictors were 2 or more admissions in the past year (P = .0114) and older age (P = .0006). Twenty-two percent of patients met National Hospice and Palliative Care Organization noncancer criteria for dementia. Palliative care intervention should be considered when treating inpatients with psychiatric disorders, especially older patients who have a previous hospitalization or history of dementia.

  11. Big data as a new approach in emergency medicine research

    Institute of Scientific and Technical Information of China (English)

    Ho Ting Wong; QianYin; Ying Qi Guo; Kristen Murray; Dong Hau Zhou; Diana Slade

    2015-01-01

    Big data is a hot topic in the academic sector, and healthcare researchers are definitely not an exception. This article aims to provide a showcase in emergency medicine research to demonstrate the advantages of conducting such research using big data. Big data is a new and cost-effective research approach, and emergency medicine researchers could benefit from using this approach and by doing so producing high-quality research at a faster pace.

  12. Big data as a new approach in emergency medicine research

    Directory of Open Access Journals (Sweden)

    Ho Ting Wong

    2015-08-01

    Full Text Available Big data is a hot topic in the academic sector, and healthcare researchers are definitely not an exception. This article aims to provide a showcase in emergency medicine research to demonstrate the advantages of conducting such research using big data. Big data is a new and cost-effective research approach, and emergency medicine researchers could benefit from using this approach and by doing so producing high-quality research at a faster pace.

  13. Complementary Approaches to Existing Target Based Drug Discovery for Identifying Novel Drug Targets

    Directory of Open Access Journals (Sweden)

    Suhas Vasaikar

    2016-11-01

    Full Text Available In the past decade, it was observed that the relationship between the emerging New Molecular Entities and the quantum of R&D investment has not been favorable. There might be numerous reasons but few studies stress the introduction of target based drug discovery approach as one of the factors. Although a number of drugs have been developed with an emphasis on a single protein target, yet identification of valid target is complex. The approach focuses on an in vitro single target, which overlooks the complexity of cell and makes process of validation drug targets uncertain. Thus, it is imperative to search for alternatives rather than looking at success stories of target-based drug discovery. It would be beneficial if the drugs were developed to target multiple components. New approaches like reverse engineering and translational research need to take into account both system and target-based approach. This review evaluates the strengths and limitations of known drug discovery approaches and proposes alternative approaches for increasing efficiency against treatment.

  14. Quantifying complexity in translational research: an integrated approach

    Science.gov (United States)

    Munoz, David A.; Nembhard, Harriet Black; Kraschnewski, Jennifer L.

    2014-01-01

    Purpose This article quantifies complexity in translational research. The impact of major operational steps and technical requirements (TR) is calculated with respect to their ability to accelerate moving new discoveries into clinical practice. Design/Methodology/Approach A three-phase integrated Quality Function Deployment (QFD) and Analytic Hierarchy Process (AHP) method was used to quantify complexity in translational research. A case study in obesity was used to usability. Findings Generally, the evidence generated was valuable for understanding various components in translational research. Particularly, we found that collaboration networks, multidisciplinary team capacity and community engagement are crucial for translating new discoveries into practice. Research limitations/implications As the method is mainly based on subjective opinion, some argue that the results may be biased. However, a consistency ratio is calculated and used as a guide to subjectivity. Alternatively, a larger sample may be incorporated to reduce bias. Practical implications The integrated QFD-AHP framework provides evidence that could be helpful to generate agreement, develop guidelines, allocate resources wisely, identify benchmarks and enhance collaboration among similar projects. Originality/value Current conceptual models in translational research provide little or no clue to assess complexity. The proposed method aimed to fill this gap. Additionally, the literature review includes various features that have not been explored in translational research. PMID:25417380

  15. Translational informatics approach for identifying the functional molecular communicators linking coronary artery disease, infection and inflammation.

    Science.gov (United States)

    Sharma, Ankit; Ghatge, Madankumar; Mundkur, Lakshmi; Vangala, Rajani Kanth

    2016-05-01

    Translational informatics approaches are required for the integration of diverse and accumulating data to enable the administration of effective translational medicine specifically in complex diseases such as coronary artery disease (CAD). In the current study, a novel approach for elucidating the association between infection, inflammation and CAD was used. Genes for CAD were collected from the CAD‑gene database and those for infection and inflammation were collected from the UniProt database. The cytomegalovirus (CMV)‑induced genes were identified from the literature and the CAD‑associated clinical phenotypes were obtained from the Unified Medical Language System. A total of 55 gene ontologies (GO) termed functional communicator ontologies were identified in the gene sets linking clinical phenotypes in the diseasome network. The network topology analysis suggested that important functions including viral entry, cell adhesion, apoptosis, inflammatory and immune responses networked with clinical phenotypes. Microarray data was extracted from the Gene Expression Omnibus (dataset: GSE48060) for highly networked disease myocardial infarction. Further analysis of differentially expressed genes and their GO terms suggested that CMV infection may trigger a xenobiotic response, oxidative stress, inflammation and immune modulation. Notably, the current study identified γ‑glutamyl transferase (GGT)‑5 as a potential biomarker with an odds ratio of 1.947, which increased to 2.561 following the addition of CMV and CMV‑neutralizing antibody (CMV‑NA) titers. The C‑statistics increased from 0.530 for conventional risk factors (CRFs) to 0.711 for GGT in combination with the above mentioned infections and CRFs. Therefore, the translational informatics approach used in the current study identified a potential molecular mechanism for CMV infection in CAD, and a potential biomarker for risk prediction.

  16. Personal identifiers in medical research networks: evaluation of the personal identifier generator in the Competence Network Paediatric Oncology and Haematology

    Directory of Open Access Journals (Sweden)

    Pommerening, Klaus

    2006-06-01

    Full Text Available The Society for Paediatric Oncology and Haematology (GPOH and the corresponding Competence Network Paediatric Oncology and Haematology conduct various clinical trials. The comprehensive analysis requires reliable identification of the recruited patients. Therefore, a personal identifier (PID generator is used to assign unambiguous, pseudonymous, non-reversible PIDs to participants in those trials. We tested the matching algorithm of the PID generator using a configuration specific to the GPOH. False data was used to verify the correct processing of PID requests (functionality tests, while test data was used to evaluate the matching outcome. We also assigned PIDs to more than 44,000 data records from the German Childhood Cancer Registry (GCCR and assessed the status of the associated patient list which contains the PIDs, partly encrypted data items and information on the PID generation process for each data record. All the functionality tests showed the expected results. Neither 14,915 test data records nor the GCCR data records yielded any homonyms. Six synonyms were found in the test data, due to erroneous birth dates, and 22 synonyms were found when the GCCR data was run against the actual patient list of 2579 records. In the resulting patient list of 45,693 entries, duplicate record submissions were found for about 7% of all listed patients, while more frequent submissions occurred in less than 1% of cases. The synonym error rate depends mainly on the quality of the input data and on the frequency of multiple submissions. Depending on the requirements on maximally tolerable synonym and homonym error rates, additional measures for securing input data quality might be necessary. The results demonstrate that the PID generator is an appropriate tool for reliably identifying trial participants in medical research networks.

  17. Teacher Professional Development Approach:Action Research

    Institute of Scientific and Technical Information of China (English)

    LIU Yang

    2013-01-01

    Theory and practice, researchers and practitioners are usually isolated in traditional education research, so much so that the research results can not solve the problems that teachers encounter in their teaching practice. As a new mode, action research provides a bridge linking theory and teaching practice as well as a way to promote teacher development.

  18. A systems medicine research approach for studying alcohol addiction.

    Science.gov (United States)

    Spanagel, Rainer; Durstewitz, Daniel; Hansson, Anita; Heinz, Andreas; Kiefer, Falk; Köhr, Georg; Matthäus, Franziska; Nöthen, Markus M; Noori, Hamid R; Obermayer, Klaus; Rietschel, Marcella; Schloss, Patrick; Scholz, Henrike; Schumann, Gunter; Smolka, Michael; Sommer, Wolfgang; Vengeliene, Valentina; Walter, Henrik; Wurst, Wolfgang; Zimmermann, Uli S; Stringer, Sven; Smits, Yannick; Derks, Eske M

    2013-11-01

    According to the World Health Organization, about 2 billion people drink alcohol. Excessive alcohol consumption can result in alcohol addiction, which is one of the most prevalent neuropsychiatric diseases afflicting our society today. Prevention and intervention of alcohol binging in adolescents and treatment of alcoholism are major unmet challenges affecting our health-care system and society alike. Our newly formed German SysMedAlcoholism consortium is using a new systems medicine approach and intends (1) to define individual neurobehavioral risk profiles in adolescents that are predictive of alcohol use disorders later in life and (2) to identify new pharmacological targets and molecules for the treatment of alcoholism. To achieve these goals, we will use omics-information from epigenomics, genetics transcriptomics, neurodynamics, global neurochemical connectomes and neuroimaging (IMAGEN; Schumann et al. ) to feed mathematical prediction modules provided by two Bernstein Centers for Computational Neurosciences (Berlin and Heidelberg/Mannheim), the results of which will subsequently be functionally validated in independent clinical samples and appropriate animal models. This approach will lead to new early intervention strategies and identify innovative molecules for relapse prevention that will be tested in experimental human studies. This research program will ultimately help in consolidating addiction research clusters in Germany that can effectively conduct large clinical trials, implement early intervention strategies and impact political and healthcare decision makers.

  19. Removing the College Involvement "Research Asterisk": Identifying and Rethinking Predictors of American Indian College Student Involvement

    Science.gov (United States)

    Garland, John L.

    2010-01-01

    The purpose of this study was to identify campus environmental predictors of American Indian college student involvement. The American Indian research asterisk, or not including American Indian data, has prevailed over student development research for decades. As a result, student affairs professionals have been limited in their ability to develop…

  20. Improving accuracy for identifying related PubMed queries by an integrated approach.

    Science.gov (United States)

    Lu, Zhiyong; Wilbur, W John

    2009-10-01

    PubMed is the most widely used tool for searching biomedical literature online. As with many other online search tools, a user often types a series of multiple related queries before retrieving satisfactory results to fulfill a single information need. Meanwhile, it is also a common phenomenon to see a user type queries on unrelated topics in a single session. In order to study PubMed users' search strategies, it is necessary to be able to automatically separate unrelated queries and group together related queries. Here, we report a novel approach combining both lexical and contextual analyses for segmenting PubMed query sessions and identifying related queries and compare its performance with the previous approach based solely on concept mapping. We experimented with our integrated approach on sample data consisting of 1539 pairs of consecutive user queries in 351 user sessions. The prediction results of 1396 pairs agreed with the gold-standard annotations, achieving an overall accuracy of 90.7%. This demonstrates that our approach is significantly better than the previously published method. By applying this approach to a one day query log of PubMed, we found that a significant proportion of information needs involved more than one PubMed query, and that most of the consecutive queries for the same information need are lexically related. Finally, the proposed PubMed distance is shown to be an accurate and meaningful measure for determining the contextual similarity between biological terms. The integrated approach can play a critical role in handling real-world PubMed query log data as is demonstrated in our experiments.

  1. Identifying western yellow-billed cuckoo breeding habitat with a dual modelling approach

    Science.gov (United States)

    Johnson, Matthew J.; Hatten, James R.; Holmes, Jennifer A.; Shafroth, Patrick B.

    2017-01-01

    The western population of the yellow-billed cuckoo (Coccyzus americanus) was recently listed as threatened under the federal Endangered Species Act. Yellow-billed cuckoo conservation efforts require the identification of features and area requirements associated with high quality, riparian forest habitat at spatial scales that range from nest microhabitat to landscape, as well as lower-suitability areas that can be enhanced or restored. Spatially explicit models inform conservation efforts by increasing ecological understanding of a target species, especially at landscape scales. Previous yellow-billed cuckoo modelling efforts derived plant-community maps from aerial photography, an expensive and oftentimes inconsistent approach. Satellite models can remotely map vegetation features (e.g., vegetation density, heterogeneity in vegetation density or structure) across large areas with near perfect repeatability, but they usually cannot identify plant communities. We used aerial photos and satellite imagery, and a hierarchical spatial scale approach, to identify yellow-billed cuckoo breeding habitat along the Lower Colorado River and its tributaries. Aerial-photo and satellite models identified several key features associated with yellow-billed cuckoo breeding locations: (1) a 4.5 ha core area of dense cottonwood-willow vegetation, (2) a large native, heterogeneously dense forest (72 ha) around the core area, and (3) moderately rough topography. The odds of yellow-billed cuckoo occurrence decreased rapidly as the amount of tamarisk cover increased or when cottonwood-willow vegetation was limited. We achieved model accuracies of 75–80% in the project area the following year after updating the imagery and location data. The two model types had very similar probability maps, largely predicting the same areas as high quality habitat. While each model provided unique information, a dual-modelling approach provided a more complete picture of yellow-billed cuckoo habitat

  2. A multi-criteria decision making approach to identify a vaccine formulation.

    Science.gov (United States)

    Dewé, Walthère; Durand, Christelle; Marion, Sandie; Oostvogels, Lidia; Devaster, Jeanne-Marie; Fourneau, Marc

    2016-01-01

    This article illustrates the use of a multi-criteria decision making approach, based on desirability functions, to identify an appropriate adjuvant composition for an influenza vaccine to be used in elderly. The proposed adjuvant system contained two main elements: monophosphoryl lipid and α-tocopherol with squalene in an oil/water emulsion. The objective was to elicit a stronger immune response while maintaining an acceptable reactogenicity and safety profile. The study design, the statistical models, the choice of the desirability functions, the computation of the overall desirability index, and the assessment of the robustness of the ranking are all detailed in this manuscript.

  3. The Research Journey: A "Lonely Planet" Approach

    Science.gov (United States)

    Mackenzie, Noella M.; Ling, Lorraine M.

    2009-01-01

    In this article the authors discuss the impact of research on a neophyte researcher and the research supervisor. The methodology which is applied throughout this article is autoethnographic narrative. It represents retrospective reflection on the part of the authors and thus to some extent is about retrospective meaning making. It centres upon the…

  4. Research on the Theory of Communicative Approach

    Institute of Scientific and Technical Information of China (English)

    Wang Changxue

    2014-01-01

    As speaking and listening are the two basic and essential skills in English learning,the communicative approach which focus on the learners’communicative competence take a very significant status. This paper aims to review and analyze the communicative approach and promote it to apply in the English teaching class.

  5. Bacterial vaginosis: identifying research gaps proceedings of a workshop sponsored by DHHS/NIH/NIAID.

    Science.gov (United States)

    Marrazzo, Jeanne M; Martin, David H; Watts, D Heather; Schulte, Joann; Sobel, Jack D; Hillier, Sharon L; Deal, Carolyn; Fredricks, David N

    2010-12-01

    The microbiota of the human vagina can affect the health of women, their fetuses, and newborns. Bacterial vaginosis (BV) is the most prevalent form of vaginal infection in women of reproductive age, affecting 8% to 23%, and is the most common etiology of vaginal symptoms prompting women to seek medical care. While traditional cultivation has identified numerous BV-associated bacteria involved in these processes, recent advances in molecular biology have facilitated the detection and identification of bacteria without cultivation, some of which have not previously been described or well characterized. A more complete understanding of vaginal microbial populations resulting from the adoption of molecular tools may lead to better strategies to maintain healthy vaginal microbial communities-thus enhancing women's health-and will create opportunities to explore the role of novel bacteria in reproductive tract diseases. On November 19-20, 2008, the NIH convened a workshop of experts in the field of research and clinical practice related to BV in order to discuss how these new advances should be interpreted and applied to research in progress and collaborations between relevant disciplines. This paper summarizes the presentations of this workshop and outlines general recommendations arising from the related discussions. Future studies of BV and its associated adverse outcomes should determine if specific combinations of organisms are more pathogenic than others, and causally associated with different adverse events. Moreover, determination of causality will depend not only on more precise categorization of the vaginal microbiota, but also on variations in the host environment that may be associated with changes in bacterial communities over time. In this report, we offer suggestions and recommendations that we hope will facilitate conduct of consistent approaches to collaborative efforts towards advancing our understanding of the vaginal microbiota and its impact on human

  6. A New Tool for Identifying Research Standards and Evaluating Research Performance

    Science.gov (United States)

    Bacon, Donald R.; Paul, Pallab; Stewart, Kim A.; Mukhopadhyay, Kausiki

    2012-01-01

    Much has been written about the evaluation of faculty research productivity in promotion and tenure decisions, including many articles that seek to determine the rank of various marketing journals. Yet how faculty evaluators combine journal quality, quantity, and author contribution to form judgments of a scholar's performance is unclear. A…

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

    Science.gov (United States)

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

    2015-01-01

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

  8. Identifying ligands at orphan GPCRs: current status using structure-based approaches.

    Science.gov (United States)

    Ngo, Tony; Kufareva, Irina; Coleman, James Lj; Graham, Robert M; Abagyan, Ruben; Smith, Nicola J

    2016-10-01

    GPCRs are the most successful pharmaceutical targets in history. Nevertheless, the pharmacology of many GPCRs remains inaccessible as their endogenous or exogenous modulators have not been discovered. Tools that explore the physiological functions and pharmacological potential of these 'orphan' GPCRs, whether they are endogenous and/or surrogate ligands, are therefore of paramount importance. Rates of receptor deorphanization determined by traditional reverse pharmacology methods have slowed, indicating a need for the development of more sophisticated and efficient ligand screening approaches. Here, we discuss the use of structure-based ligand discovery approaches to identify small molecule modulators for exploring the function of orphan GPCRs. These studies have been buoyed by the growing number of GPCR crystal structures solved in the past decade, providing a broad range of template structures for homology modelling of orphans. This review discusses the methods used to establish the appropriate signalling assays to test orphan receptor activity and provides current examples of structure-based methods used to identify ligands of orphan GPCRs. Linked Articles This article is part of a themed section on Molecular Pharmacology of G Protein-Coupled Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v173.20/issuetoc.

  9. Complexity and interdisciplinary approaches to environmental research

    Science.gov (United States)

    Kammen, Daniel M.

    2013-03-01

    The launch of volume 8 of Environmental Research Letters (ERL) comes at a critical time in terms of innovations and exciting areas of science, but particularly in the areas linking environmental research and action. The most recent climate change Conference of the Parties meeting (COP), in Doha in December 2012, has now come and gone. As has been dissected in the press, very little was accomplished. Some will see this as a failure, as I do, and others will reasonably enough note that this meeting, the 18th such COP was1 never intended to be a milestone moment. The current plan, in fact, is for a 'post-Kyoto' international climate agreement to be adopted only at the COP20 summit in December 2015. As we lead up to COP20, and potentially other regional or national approaches to climate protection, innovations in science, innovations in policy tools, and political commitment must come together. The science of climate change only continues to get clearer and clearer, and bleaker [1]. Later this year the IPCC will release its Fifth Assessment Report, AR5. The draft versions are out for review now. ERL has published a number of papers on climate change science, mitigation and adaptation, but one area where the world needs a particular focus is on the nexus of science and action. A summary of the Intergovernmental Panel on Climate Change's findings from the first assessment report (FAR; 1990) to the latest report is presented in figure 1. This graphic is specifically not about the scientific record alone. What is most important about this figure is the juxtaposition of the language of science and the language of ... language. Figure 1. Figure 1. A superposition of the state of climate science in three key data sets, and the dates of the first, second, third and fourth assessment reports (FAR, SAR, TAR, and AR4, respectively) plotted as vertical lines. On the right are the key statements from each of these reports, along with the conclusion of the Special Report on

  10. Direct and heterologous approaches to identify the LET-756/FGF interactome

    Directory of Open Access Journals (Sweden)

    Birnbaum Daniel

    2006-05-01

    Full Text Available Abstract Background Fibroblast growth factors (FGFs are multifunctional proteins that play important roles in cell communication, proliferation and differentiation. However, many aspects of their activities are not well defined. LET-756, one of the two C. elegans FGFs, is expressed throughout development and is essential for worm development. It is both expressed in the nucleus and secreted. Results To identify nuclear factors associated with LET-756, we used three approaches. First, we screened a two-hybrid cDNA library derived from mixed stages worms and from a normalized library, using LET-756 as bait. This direct approach allowed the identification of several binding partners that play various roles in the nucleus/nucleolus, such as PAL-1, a transcription regulator, or RPS-16, a component of the small ribosomal subunit. The interactions were validated by co-immunoprecipitation and determination of their site of occurrence in mammalian cells. Second, because patterns of protein interactions may be conserved throughout species, we searched for orthologs of known mammalian interactors and measured binary interaction with these predicted candidates. We found KIN-3 and KIN-10, the orthologs of CK2α and CK2β, as new partners of LET-756. Third, following the assumption that recognition motifs mediating protein interaction may be conserved between species, we screened a two-hybrid cDNA human library using LET-756 as bait. Among the few FGF partners detected was 14-3-3β. In support of this interaction we showed that the two 14-3-3β orthologous proteins, FTT-1 and FTT-2/PAR-5, interacted with LET-756. Conclusion We have conducted the first extensive search for LET-756 interactors using a multi-directional approach and established the first interaction map of LET-756/FGF with other FGF binding proteins from other species. The interactors identified play various roles in developmental process or basic biochemical events such as ribosome biogenesis.

  11. A recursive network approach can identify constitutive regulatory circuits in gene expression data

    Science.gov (United States)

    Blasi, Monica Francesca; Casorelli, Ida; Colosimo, Alfredo; Blasi, Francesco Simone; Bignami, Margherita; Giuliani, Alessandro

    2005-03-01

    The activity of the cell is often coordinated by the organisation of proteins into regulatory circuits that share a common function. Genome-wide expression profiles might contain important information on these circuits. Current approaches for the analysis of gene expression data include clustering the individual expression measurements and relating them to biological functions as well as modelling and simulation of gene regulation processes by additional computer tools. The identification of the regulative programmes from microarray experiments is limited, however, by the intrinsic difficulty of linear methods to detect low-variance signals and by the sensitivity of the different approaches. Here we face the problem of recognising invariant patterns of correlations among gene expression reminiscent of regulation circuits. We demonstrate that a recursive neural network approach can identify genetic regulation circuits from expression data for ribosomal and genome stability genes. The proposed method, by greatly enhancing the sensitivity of microarray studies, allows the identification of important aspects of genetic regulation networks and might be useful for the discrimination of the different players involved in regulation circuits. Our results suggest that the constitutive regulatory networks involved in the generic organisation of the cell display a high degree of clustering depending on a modular architecture.

  12. Evaluation of approaches to identify the targets of cellular immunity on a proteome-wide scale.

    Directory of Open Access Journals (Sweden)

    Fernanda C Cardoso

    Full Text Available BACKGROUND: Vaccine development against malaria and other complex diseases remains a challenge for the scientific community. The recent elucidation of the genome, proteome and transcriptome of many of these complex pathogens provides the basis for rational vaccine design by identifying, on a proteome-wide scale, novel target antigens that are recognized by T cells and antibodies from exposed individuals. However, there is currently no algorithm to effectively identify important target antigens from genome sequence data; this is especially challenging for T cell targets. Furthermore, for some of these pathogens, such as Plasmodium, protein expression using conventional platforms has been problematic but cell-free in vitro transcription translation (IVTT strategies have recently proved successful. Herein, we report a novel approach for proteome-wide scale identification of the antigenic targets of T cell responses using IVTT products. PRINCIPAL FINDINGS: We conducted a series of in vitro and in vivo experiments using IVTT proteins either unpurified, absorbed to carboxylated polybeads, or affinity purified through nickel resin or magnetic beads. In vitro studies in humans using CMV, EBV, and Influenza A virus proteins showed antigen-specific cytokine production in ELIspot and Cytometric Bead Array assays with cells stimulated with purified or unpurified IVTT antigens. In vitro and in vivo studies in mice immunized with the Plasmodium yoelii circumsporozoite DNA vaccine with or without IVTT protein boost showed antigen-specific cytokine production using purified IVTT antigens only. Overall, the nickel resin method of IVTT antigen purification proved optimal in both human and murine systems. CONCLUSIONS: This work provides proof of concept for the potential of high-throughput approaches to identify T cell targets of complex parasitic, viral or bacterial pathogens from genomic sequence data, for rational vaccine development against emerging and re

  13. A sequence-based approach to identify reference genes for gene expression analysis

    Directory of Open Access Journals (Sweden)

    Chari Raj

    2010-08-01

    Full Text Available Abstract Background An important consideration when analyzing both microarray and quantitative PCR expression data is the selection of appropriate genes as endogenous controls or reference genes. This step is especially critical when identifying genes differentially expressed between datasets. Moreover, reference genes suitable in one context (e.g. lung cancer may not be suitable in another (e.g. breast cancer. Currently, the main approach to identify reference genes involves the mining of expression microarray data for highly expressed and relatively constant transcripts across a sample set. A caveat here is the requirement for transcript normalization prior to analysis, and measurements obtained are relative, not absolute. Alternatively, as sequencing-based technologies provide digital quantitative output, absolute quantification ensues, and reference gene identification becomes more accurate. Methods Serial analysis of gene expression (SAGE profiles of non-malignant and malignant lung samples were compared using a permutation test to identify the most stably expressed genes across all samples. Subsequently, the specificity of the reference genes was evaluated across multiple tissue types, their constancy of expression was assessed using quantitative RT-PCR (qPCR, and their impact on differential expression analysis of microarray data was evaluated. Results We show that (i conventional references genes such as ACTB and GAPDH are highly variable between cancerous and non-cancerous samples, (ii reference genes identified for lung cancer do not perform well for other cancer types (breast and brain, (iii reference genes identified through SAGE show low variability using qPCR in a different cohort of samples, and (iv normalization of a lung cancer gene expression microarray dataset with or without our reference genes, yields different results for differential gene expression and subsequent analyses. Specifically, key established pathways in lung

  14. Vygotskian Approaches to Second Language Research.

    Science.gov (United States)

    Lantolf, James P., Ed.; Appel, Gabriela, Ed.

    The collection of essays on aspects of Vygotskian theory focuses on the theory's application to research on second language learning. Articles include: "Theoretical Framework: An Introduction to Vygotskian Perspectives on Second Language Research" (James P. Lantolf, Gabriela Appel); Collective Scaffolding in Second Language…

  15. Using the Pyramid Approach to Teaching Marketing Research.

    Science.gov (United States)

    Peltier, James W.; Westfall, John; Ainscough, Thomas L.

    2001-01-01

    Underscores the need for teaching marketing research skills at the secondary level and shows how marketing research fits into marketing education. Provides an example of how to use the pyramid approach to research, which involves review of secondary sources, key informant interviews, focus groups, and quantitative research. (Author/JOW)

  16. An affinity pull-down approach to identify the plant cyclic nucleotide interactome

    KAUST Repository

    Donaldson, Lara Elizabeth

    2013-09-03

    Cyclic nucleotides (CNs) are intracellular second messengers that play an important role in mediating physiological responses to environmental and developmental signals, in species ranging from bacteria to humans. In response to these signals, CNs are synthesized by nucleotidyl cyclases and then act by binding to and altering the activity of downstream target proteins known as cyclic nucleotide-binding proteins (CNBPs). A number of CNBPs have been identified across kingdoms including transcription factors, protein kinases, phosphodiesterases, and channels, all of which harbor conserved CN-binding domains. In plants however, few CNBPs have been identified as homology searches fail to return plant sequences with significant matches to known CNBPs. Recently, affinity pull-down techniques have been successfully used to identify CNBPs in animals and have provided new insights into CN signaling. The application of these techniques to plants has not yet been extensively explored and offers an alternative approach toward the unbiased discovery of novel CNBP candidates in plants. Here, an affinity pull-down technique for the identification of the plant CN interactome is presented. In summary, the method involves an extraction of plant proteins which is incubated with a CN-bait, followed by a series of increasingly stringent elutions that eliminates proteins in a sequential manner according to their affinity to the bait. The eluted and bait-bound proteins are separated by one-dimensional gel electrophoresis, excised, and digested with trypsin after which the resultant peptides are identified by mass spectrometry - techniques that are commonplace in proteomics experiments. The discovery of plant CNBPs promises to provide valuable insight into the mechanism of CN signal transduction in plants. © Springer Science+Business Media New York 2013.

  17. Toward a Personalized Approach in Prebiotics Research

    Directory of Open Access Journals (Sweden)

    Moul Dey

    2017-01-01

    Full Text Available Recent characterization of the human microbiome and its influences on health have led to dramatic conceptual shifts in dietary bioactives research. Prebiotic foods that include many dietary fibers and resistant starches are perceived as beneficial for maintaining a healthy gut microbiota. This article brings forward some current perspectives in prebiotic research to discuss why reporting of individual variations in response to interventions will be important to discern suitability of prebiotics as a disease prevention tool.

  18. Toward a Personalized Approach in Prebiotics Research

    Science.gov (United States)

    Dey, Moul

    2017-01-01

    Recent characterization of the human microbiome and its influences on health have led to dramatic conceptual shifts in dietary bioactives research. Prebiotic foods that include many dietary fibers and resistant starches are perceived as beneficial for maintaining a healthy gut microbiota. This article brings forward some current perspectives in prebiotic research to discuss why reporting of individual variations in response to interventions will be important to discern suitability of prebiotics as a disease prevention tool. PMID:28134778

  19. Persistent Identifiers for Field Expeditions: A Next Step for the US Oceanographic Research Fleet

    Science.gov (United States)

    Arko, Robert; Carbotte, Suzanne; Chandler, Cynthia; Smith, Shawn; Stocks, Karen

    2016-04-01

    Oceanographic research cruises are complex affairs, typically requiring an extensive effort to secure the funding, plan the experiment, and mobilize the field party. Yet cruises are not typically published online as first-class digital objects with persistent, citable identifiers linked to the scientific literature. The Rolling Deck to Repository (R2R; info@rvdata.us) program maintains a master catalog of oceanographic cruises for the United States research fleet, currently documenting over 6,000 expeditions on 37 active and retired vessels. In 2015, R2R started routinely publishing a Digital Object Identifier (DOI) for each completed cruise. Cruise DOIs, in turn, are linked to related persistent identifiers where available including the Open Researcher and Contributor ID (ORCID) for members of the science party, the International Geo Sample Number (IGSN) for physical specimens collected during the cruise, the Open Funder Registry (FundRef) codes that supported the experiment, and additional DOIs for datasets, journal articles, and other products resulting from the cruise. Publishing a persistent identifier for each field expedition will facilitate interoperability between the many different repositories that hold research products from cruises; will provide credit to the investigators who secured the funding and carried out the experiment; and will facilitate the gathering of fleet-wide altmetrics that demonstrate the broad impact of oceanographic research.

  20. Critical research needs for identifying future changes in Gulf coral reef ecosystems

    KAUST Repository

    Feary, David A.

    2013-07-01

    Expert opinion was assessed to identify current knowledge gaps in determining future changes in Arabian/Persian Gulf (thereafter \\'Gulf\\') coral reefs. Thirty-one participants submitted 71 research questions that were peer-assessed in terms of scientific importance (i.e., filled a knowledge gap and was a research priority) and efficiency in resource use (i.e., was highly feasible and ecologically broad). Ten research questions, in six major research areas, were highly important for both understanding Gulf coral reef ecosystems and also an efficient use of limited research resources. These questions mirrored global evaluations of the importance of understanding and evaluating biodiversity, determining the potential impacts of climate change, the role of anthropogenic impacts in structuring coral reef communities, and economically evaluating coral reef communities. These questions provide guidance for future research on coral reef ecosystems within the Gulf, and enhance the potential for assessment and management of future changes in this globally significant region. © 2013 Elsevier Ltd.

  1. Critical research needs for identifying future changes in Gulf coral reef ecosystems.

    Science.gov (United States)

    Feary, David A; Burt, John A; Bauman, Andrew G; Al Hazeem, Shaker; Abdel-Moati, Mohamed A; Al-Khalifa, Khalifa A; Anderson, Donald M; Amos, Carl; Baker, Andrew; Bartholomew, Aaron; Bento, Rita; Cavalcante, Geórgenes H; Chen, Chaolun Allen; Coles, Steve L; Dab, Koosha; Fowler, Ashley M; George, David; Grandcourt, Edwin; Hill, Ross; John, David M; Jones, David A; Keshavmurthy, Shashank; Mahmoud, Huda; Moradi Och Tapeh, Mahdi; Mostafavi, Pargol Ghavam; Naser, Humood; Pichon, Michel; Purkis, Sam; Riegl, Bernhard; Samimi-Namin, Kaveh; Sheppard, Charles; Vajed Samiei, Jahangir; Voolstra, Christian R; Wiedenmann, Joerg

    2013-07-30

    Expert opinion was assessed to identify current knowledge gaps in determining future changes in Arabian/Persian Gulf (thereafter 'Gulf') coral reefs. Thirty-one participants submitted 71 research questions that were peer-assessed in terms of scientific importance (i.e., filled a knowledge gap and was a research priority) and efficiency in resource use (i.e., was highly feasible and ecologically broad). Ten research questions, in six major research areas, were highly important for both understanding Gulf coral reef ecosystems and also an efficient use of limited research resources. These questions mirrored global evaluations of the importance of understanding and evaluating biodiversity, determining the potential impacts of climate change, the role of anthropogenic impacts in structuring coral reef communities, and economically evaluating coral reef communities. These questions provide guidance for future research on coral reef ecosystems within the Gulf, and enhance the potential for assessment and management of future changes in this globally significant region.

  2. Health Research and Millennium Development Goals: Identifying the Gap From Public Health Perspective.

    Science.gov (United States)

    El Lawindi, Mona I; Galal, Yasmine S; Khairy, Walaa A

    2015-08-23

    Assessing the research output within the universities could provide an effective means for tracking the Millennium Development Goals (MDGs) progress. This analytical database study was designed to assess the trend of research theses conducted by the Public Health Department (PHD), Faculty of Medicine, Cairo University during the period 1990 to 2014 as related to the: MDGS, Faculty and department research priority plans and to identify the discrepancies between researchers' priorities versus national and international research priorities. A manual search of the theses was done at the Postgraduate Library using a specially designed checklist to chart adherence of each thesis to: MDGs, Faculty and department research plans (RPs). The theses' profile showed that the highest research output was for addressing the MDGS followed by the PHD and Faculty RPs. Compliance to MDGs 5 and 6 was obvious, whereas; MDGs 2, 3, and 7 were not represented at all after year 2000. No significant difference was found between PH theses addressing the Faculty RPs and those which were not before and after 2010. A significantly lower percent of PH theses was fulfilling the PHD research priorities compared to those which were not after 2010. This study showed a definite decline in research output tackling the MDGS and PHD research priorities, with a non-significant increase in the production of theses addressing the Faculty RPs. The present study is a practical model for policy makers within the universities to develop and implement a reliable monitoring and evaluation system for assessment of research output.

  3. Identifying Liver Cancer and Its Relations with Diseases, Drugs, and Genes: A Literature-Based Approach

    Science.gov (United States)

    Song, Min

    2016-01-01

    In biomedicine, scientific literature is a valuable source for knowledge discovery. Mining knowledge from textual data has become an ever important task as the volume of scientific literature is growing unprecedentedly. In this paper, we propose a framework for examining a certain disease based on existing information provided by scientific literature. Disease-related entities that include diseases, drugs, and genes are systematically extracted and analyzed using a three-level network-based approach. A paper-entity network and an entity co-occurrence network (macro-level) are explored and used to construct six entity specific networks (meso-level). Important diseases, drugs, and genes as well as salient entity relations (micro-level) are identified from these networks. Results obtained from the literature-based literature mining can serve to assist clinical applications. PMID:27195695

  4. Toward an efficient approach to identify molecular scaffolds possessing selective or promiscuous compounds.

    Science.gov (United States)

    Yongye, Austin B; Medina-Franco, José L

    2013-10-01

    The concept of a recurrent scaffold present in a series of structures is common in medicinal drug discovery. We present a scaffold analysis of compounds screened across 100 sequence-unrelated proteins to identify scaffolds that drive promiscuity or selectivity. Selectivity and promiscuity play a major role in traditional and poly-pharmacological drug design considerations. The collection employed here is the first publicly available data set containing the complete screening profiles of more than 15 000 compounds from different sources. In addition, no scaffold analysis of this data set has been reported. The protocol described here employs the Molecular Equivalence Index tool to facilitate the selection of Bemis-Murcko frameworks in the data set, which contain at least five compounds and Scaffold Hunter to generate a hierarchical tree of scaffolds. The annotation of the scaffold tree with protein-binding profile data enabled the successful identification of mostly highly specific compounds, due to data set constraints. We also applied this approach to a public set of 1497 small molecules screened non-uniformly across a panel of 172 protein kinases. The approach is general and can be applied to any other data sets and activity readout.

  5. Chemical proteomics approaches for identifying the cellular targets of natural products.

    Science.gov (United States)

    Wright, M H; Sieber, S A

    2016-05-01

    Covering: 2010 up to 2016Deconvoluting the mode of action of natural products and drugs remains one of the biggest challenges in chemistry and biology today. Chemical proteomics is a growing area of chemical biology that seeks to design small molecule probes to understand protein function. In the context of natural products, chemical proteomics can be used to identify the protein binding partners or targets of small molecules in live cells. Here, we highlight recent examples of chemical probes based on natural products and their application for target identification. The review focuses on probes that can be covalently linked to their target proteins (either via intrinsic chemical reactivity or via the introduction of photocrosslinkers), and can be applied "in situ" - in living systems rather than cell lysates. We also focus here on strategies that employ a click reaction, the copper-catalysed azide-alkyne cycloaddition reaction (CuAAC), to allow minimal functionalisation of natural product scaffolds with an alkyne or azide tag. We also discuss 'competitive mode' approaches that screen for natural products that compete with a well-characterised chemical probe for binding to a particular set of protein targets. Fuelled by advances in mass spectrometry instrumentation and bioinformatics, many modern strategies are now embracing quantitative proteomics to help define the true interacting partners of probes, and we highlight the opportunities this rapidly evolving technology provides in chemical proteomics. Finally, some of the limitations and challenges of chemical proteomics approaches are discussed.

  6. New approach for identifying the zero-order fringe in variable wavelength interferometry

    Science.gov (United States)

    Galas, Jacek; Litwin, Dariusz; Daszkiewicz, Marek

    2016-12-01

    The family of VAWI techniques (for transmitted and reflected light) is especially efficient for characterizing objects, when in the interference system the optical path difference exceeds a few wavelengths. The classical approach that consists in measuring the deflection of interference fringes fails because of strong edge effects. Broken continuity of interference fringes prevents from correct identification of the zero order fringe, which leads to significant errors. The family of these methods has been proposed originally by Professor Pluta in the 1980s but that time image processing facilities and computers were hardly available. Automated devices unfold a completely new approach to the classical measurement procedures. The Institute team has taken that new opportunity and transformed the technique into fully automated measurement devices offering commercial readiness of industry-grade quality. The method itself has been modified and new solutions and algorithms simultaneously have extended the field of application. This has concerned both construction aspects of the systems and software development in context of creating computerized instruments. The VAWI collection of instruments constitutes now the core of the Institute commercial offer. It is now practically applicable in industrial environment for measuring textile and optical fibers, strips of thin films, testing of wave plates and nonlinear affects in different materials. This paper describes new algorithms for identifying the zero order fringe, which increases the performance of the system as a whole and presents some examples of measurements of optical elements.

  7. The waveform similarity approach to identify dependent events in instrumental seismic catalogues

    Science.gov (United States)

    Barani, S.; Ferretti, G.; Massa, M.; Spallarossa, D.

    2007-01-01

    In this paper, waveform similarity analysis is adapted and implemented in a declustering procedure to identify foreshocks and aftershocks, to obtain instrumental catalogues that are cleaned of dependent events and to perform an independent check of the results of traditional declustering techniques. Unlike other traditional declustering methods (i.e. windowing techniques), the application of cross-correlation analysis allows definition of groups of dependent events (multiplets) characterized by similar location, fault mechanism and propagation pattern. In this way the chain of intervening related events is led by the seismogenetic features of earthquakes. Furthermore, a time-selection criterion is used to define time-independent seismic episodes eventually joined (on the basis of waveform similarity) into a single multiplet. The results, obtained applying our procedure to a test data set, show that the declustered catalogue is drawn by the Poisson distribution with a degree of confidence higher than using the Gardner and Knopoff method. The declustered catalogues, applying these two approaches, are similar with respect to the frequency-magnitude distribution and the number of earthquakes. Nevertheless, the application of our approach leads to declustered catalogues properly related to the seismotectonic background and the reology of the investigated area and the success of the procedure is ensured by the independence of the results on estimated location errors of the events collected in the raw catalogue.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-01-01

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

  9. Hermeneutics as Research Approach: A Reappraisal

    Directory of Open Access Journals (Sweden)

    Graham McCaffrey RN, PhD

    2012-07-01

    Full Text Available Hermeneutics as a research practice, if it is to remain true to its philosophical origins, involves reappraisal and reinterpretation in relation to its cultural contexts. Among the threads of connection affecting hermeneutic practice are the exigencies of academic institutions and evolving cross-cultural perspectives. This article addresses these issues from the perspective of exploring hermeneutics for a research study of nurses' relational practice on acute care mental health units from Buddhist perspectives. The exploration is, as hermeneutics must be, both a review and a refashioning, a looking back in order to look forward.

  10. Grounded Theory Approach in Social Research

    Directory of Open Access Journals (Sweden)

    Dr Venkat Pulla

    2014-11-01

    Full Text Available This paper discusses Grounded Theory, which is one of the newer methodologies becoming popular with social researchers since its evolution in the late 1960s. The paper discusses the principles and processes of the Grounded Theory and then explores the nature of codes, coding process and the concept of saturation. It then goes on to discuss the pros and cons, arguments for and against the use of Grounded Theory methodology in social research and explores the applicability of this methodology in producing sound theoretical basis for practice. Selected narratives from the author’s recent studies are used to explain the processes of Grounded Theory methodology.

  11. An integrated approach for identifying wrongly labelled samples when performing classification in microarray data.

    Directory of Open Access Journals (Sweden)

    Yuk Yee Leung

    Full Text Available BACKGROUND: Using hybrid approach for gene selection and classification is common as results obtained are generally better than performing the two tasks independently. Yet, for some microarray datasets, both classification accuracy and stability of gene sets obtained still have rooms for improvement. This may be due to the presence of samples with wrong class labels (i.e. outliers. Outlier detection algorithms proposed so far are either not suitable for microarray data, or only solve the outlier detection problem on their own. RESULTS: We tackle the outlier detection problem based on a previously proposed Multiple-Filter-Multiple-Wrapper (MFMW model, which was demonstrated to yield promising results when compared to other hybrid approaches (Leung and Hung, 2010. To incorporate outlier detection and overcome limitations of the existing MFMW model, three new features are introduced in our proposed MFMW-outlier approach: 1 an unbiased external Leave-One-Out Cross-Validation framework is developed to replace internal cross-validation in the previous MFMW model; 2 wrongly labeled samples are identified within the MFMW-outlier model; and 3 a stable set of genes is selected using an L1-norm SVM that removes any redundant genes present. Six binary-class microarray datasets were tested. Comparing with outlier detection studies on the same datasets, MFMW-outlier could detect all the outliers found in the original paper (for which the data was provided for analysis, and the genes selected after outlier removal were proven to have biological relevance. We also compared MFMW-outlier with PRAPIV (Zhang et al., 2006 based on same synthetic datasets. MFMW-outlier gave better average precision and recall values on three different settings. Lastly, artificially flipped microarray datasets were created by removing our detected outliers and flipping some of the remaining samples' labels. Almost all the 'wrong' (artificially flipped samples were detected, suggesting

  12. Multi-compartment approach to identify minimal flow and maximal recreational use of a lowland river

    Science.gov (United States)

    Pusch, Martin; Lorenz, Stefan

    2013-04-01

    Most approaches to establish a minimum flow rate for river sections subjected to water abstraction focus on flow requirements of fish and benthic invertebrates. However, artificial reduction of river flow will always affect additional key ecosystem features, as sediment properties and the metabolism of matter in these ecosystems as well, and may even influence adjacent floodplains. Thus, significant effects e.g. on the dissolved oxygen content of river water, on habitat conditions in the benthic zone, and on water levels in the floodplain are to be expected. Thus, we chose a multiple compartment method to identify minimum flow requirements in a lowland River in northern Germany (Spree River), selecting the minimal required flow level out of all compartments studied. Results showed that minimal flow levels necessary to keep key ecosystem features at a 'good' state depended significantly on actual water quality and on river channel morphology. Thereby, water quality of the Spree is potentially influenced by recreational boating activity, which causes mussels to stop filter-feeding, and thus impedes self-purification. Disturbance of mussel feeding was shown to directly depend on boat type and speed, with substantial differences among mussel species. Thus, a maximal recreational boating intensity could be derived that does not significantly affect self purification. We conclude that minimal flow levels should be identified not only based on flow preferences of target species, but also considering channel morphology, ecological functions, and the intensity of other human uses of the river section.

  13. SU-E-J-212: Identifying Bones From MRI: A Dictionary Learnign and Sparse Regression Approach

    Energy Technology Data Exchange (ETDEWEB)

    Ruan, D; Yang, Y; Cao, M; Hu, P; Low, D [UCLA, Los Angeles, CA (United States)

    2014-06-01

    Purpose: To develop an efficient and robust scheme to identify bony anatomy based on MRI-only simulation images. Methods: MRI offers important soft tissue contrast and functional information, yet its lack of correlation to electron-density has placed it as an auxiliary modality to CT in radiotherapy simulation and adaptation. An effective scheme to identify bony anatomy is an important first step towards MR-only simulation/treatment paradigm and would satisfy most practical purposes. We utilize a UTE acquisition sequence to achieve visibility of the bone. By contrast to manual + bulk or registration-to identify bones, we propose a novel learning-based approach for improved robustness to MR artefacts and environmental changes. Specifically, local information is encoded with MR image patch, and the corresponding label is extracted (during training) from simulation CT aligned to the UTE. Within each class (bone vs. nonbone), an overcomplete dictionary is learned so that typical patches within the proper class can be represented as a sparse combination of the dictionary entries. For testing, an acquired UTE-MRI is divided to patches using a sliding scheme, where each patch is sparsely regressed against both bone and nonbone dictionaries, and subsequently claimed to be associated with the class with the smaller residual. Results: The proposed method has been applied to the pilot site of brain imaging and it has showed general good performance, with dice similarity coefficient of greater than 0.9 in a crossvalidation study using 4 datasets. Importantly, it is robust towards consistent foreign objects (e.g., headset) and the artefacts relates to Gibbs and field heterogeneity. Conclusion: A learning perspective has been developed for inferring bone structures based on UTE MRI. The imaging setting is subject to minimal motion effects and the post-processing is efficient. The improved efficiency and robustness enables a first translation to MR-only routine. The scheme

  14. A novel approach identifying hybrid sterility QTL on the autosomes of Drosophila simulans and D. mauritiana.

    Science.gov (United States)

    Dickman, Christopher T D; Moehring, Amanda J

    2013-01-01

    When species interbreed, the hybrid offspring that are produced are often sterile. If only one hybrid sex is sterile, it is almost always the heterogametic (XY or ZW) sex. Taking this trend into account, the predominant model used to explain the genetic basis of F1 sterility involves a deleterious interaction between recessive sex-linked loci from one species and dominant autosomal loci from the other species. This model is difficult to evaluate, however, as only a handful of loci influencing interspecies hybrid sterility have been identified, and their autosomal genetic interactors have remained elusive. One hindrance to their identification has been the overwhelming effect of the sex chromosome in mapping studies, which could 'mask' the ability to accurately map autosomal factors. Here, we use a novel approach employing attached-X chromosomes to create reciprocal backcross interspecies hybrid males that have a non-recombinant sex chromosome and recombinant autosomes. The heritable variation in phenotype is thus solely caused by differences in the autosomes, thereby allowing us to accurately identify the number and location of autosomal sterility loci. In one direction of backcross, all males were sterile, indicating that sterility could be entirely induced by the sex chromosome complement in these males. In the other direction, we identified nine quantitative trait loci that account for a surprisingly large amount (56%) of the autosome-induced phenotypic variance in sterility, with a large contribution of autosome-autosome epistatic interactions. These loci are capable of acting dominantly, and thus could contribute to F1 hybrid sterility.

  15. Identifying genetic risk variants for coronary heart disease in familial hypercholesterolemia: an extreme genetics approach

    Science.gov (United States)

    Versmissen, Jorie; Oosterveer, Daniëlla M; Yazdanpanah, Mojgan; Dehghan, Abbas; Hólm, Hilma; Erdman, Jeanette; Aulchenko, Yurii S; Thorleifsson, Gudmar; Schunkert, Heribert; Huijgen, Roeland; Vongpromek, Ranitha; Uitterlinden, André G; Defesche, Joep C; van Duijn, Cornelia M; Mulder, Monique; Dadd, Tony; Karlsson, Hróbjartur D; Ordovas, Jose; Kindt, Iris; Jarman, Amelia; Hofman, Albert; van Vark-van der Zee, Leonie; Blommesteijn-Touw, Adriana C; Kwekkeboom, Jaap; Liem, Anho H; van der Ouderaa, Frans J; Calandra, Sebastiano; Bertolini, Stefano; Averna, Maurizio; Langslet, Gisle; Ose, Leiv; Ros, Emilio; Almagro, Fátima; de Leeuw, Peter W; Civeira, Fernando; Masana, Luis; Pintó, Xavier; Simoons, Maarten L; Schinkel, Arend FL; Green, Martin R; Zwinderman, Aeilko H; Johnson, Keith J; Schaefer, Arne; Neil, Andrew; Witteman, Jacqueline CM; Humphries, Steve E; Kastelein, John JP; Sijbrands, Eric JG

    2015-01-01

    Mutations in the low-density lipoprotein receptor (LDLR) gene cause familial hypercholesterolemia (FH), a disorder characterized by coronary heart disease (CHD) at young age. We aimed to apply an extreme sampling method to enhance the statistical power to identify novel genetic risk variants for CHD in individuals with FH. We selected cases and controls with an extreme contrast in CHD risk from 17 000 FH patients from the Netherlands, whose functional LDLR mutation was unequivocally established. The genome-wide association (GWA) study was performed on 249 very young FH cases with CHD and 217 old FH controls without CHD (above 65 years for males and 70 years of age for females) using the Illumina HumanHap550K chip. In the next stage, two independent samples (one from the Netherlands and one from Italy, Norway, Spain, and the United Kingdom) of FH patients were used as replication samples. In the initial GWA analysis, we identified 29 independent single nucleotide polymorphisms (SNPs) with suggestive associations with premature CHD (P<1 × 10−4). We examined the association of these SNPs with CHD risk in the replication samples. After Bonferroni correction, none of the SNPs either replicated or reached genome-wide significance after combining the discovery and replication samples. Therefore, we conclude that the genetics of CHD risk in FH is complex and even applying an ‘extreme genetics' approach we did not identify new genetic risk variants. Most likely, this method is not as effective in leveraging effect size as anticipated, and may, therefore, not lead to significant gains in statistical power. PMID:24916650

  16. A phase coherence approach to identifying co-located earthquakes and tremor

    Science.gov (United States)

    Hawthorne, J. C.; Ampuero, J.-P.

    2017-01-01

    We present and use a phase coherence approach to identify seismic signals that have similar path effects but different source time functions: co-located earthquakes and tremor. The method used is a phase coherence-based implementation of empirical matched field processing, modified to suit tremor analysis. It works by comparing the frequency-domain phases of waveforms generated by two sources recorded at multiple stations. We first cross-correlate the records of the two sources at a single station. If the sources are co-located, this cross-correlation eliminates the phases of the Green's function. It leaves the relative phases of the source time functions, which should be the same across all stations so long as the spatial extent of the sources are small compared with the seismic wavelength. We therefore search for cross-correlation phases that are consistent across stations as an indication of co-located sources. We also introduce a method to obtain relative locations between the two sources, based on back-projection of inter-station phase coherence. We apply this technique to analyze two tremor-like signals that are thought to be composed of a number of earthquakes. First, we analyze a 20-second-long seismic precursor to a M 3.9 earthquake in central Alaska. The analysis locates the precursor to within 2 km of the mainshock, and it identifies several bursts of energy-potentially foreshocks or groups of foreshocks-within the precursor. Second, we examine several minutes of volcanic tremor prior to an eruption at Redoubt Volcano. We confirm that the tremor source is located close to repeating earthquakes identified earlier in the tremor sequence. The amplitude of the tremor diminishes about 30 seconds before the eruption, but the phase coherence results suggest that the tremor may persist at some level through this final interval.

  17. A systems biology approach identifies molecular networks defining skeletal muscle abnormalities in chronic obstructive pulmonary disease.

    Directory of Open Access Journals (Sweden)

    Nil Turan

    2011-09-01

    Full Text Available Chronic Obstructive Pulmonary Disease (COPD is an inflammatory process of the lung inducing persistent airflow limitation. Extensive systemic effects, such as skeletal muscle dysfunction, often characterize these patients and severely limit life expectancy. Despite considerable research efforts, the molecular basis of muscle degeneration in COPD is still a matter of intense debate. In this study, we have applied a network biology approach to model the relationship between muscle molecular and physiological response to training and systemic inflammatory mediators. Our model shows that failure to co-ordinately activate expression of several tissue remodelling and bioenergetics pathways is a specific landmark of COPD diseased muscles. Our findings also suggest that this phenomenon may be linked to an abnormal expression of a number of histone modifiers, which we discovered correlate with oxygen utilization. These observations raised the interesting possibility that cell hypoxia may be a key factor driving skeletal muscle degeneration in COPD patients.

  18. A dynamic discourse approach to classroom research

    NARCIS (Netherlands)

    Bannink, A.; Van Dam, J.

    2006-01-01

    In this paper we propose a theoretical reassessment of the discourse-analytic tools that are used in classroom research and of the data that are addressed. To that end we present in-depth analyses of 1) an IRE structure in a first English (EFL) lesson in a Dutch secondary school; 2) episodes from Du

  19. Identifying and Investigating Difficult Concepts in Engineering Mechanics and Electric Circuits. Research Brief

    Science.gov (United States)

    Streveler, Ruth; Geist, Monica; Ammerman, Ravel; Sulzbach, Candace; Miller, Ronald; Olds, Barbara; Nelson, Mary

    2007-01-01

    This study extends ongoing work to identify difficult concepts in thermal and transport science and measure students' understanding of those concepts via a concept inventory. Two research questions provided the focal point: "What important concepts in electric circuits and engineering mechanics do students find difficult to learn?" and…

  20. Molecular approaches to identify cryptic species and polymorphic species within a complex community of fig wasps.

    Directory of Open Access Journals (Sweden)

    Jin-Hua Xiao

    Full Text Available Cryptic and polymorphic species can complicate traditional taxonomic research and both of these concerns are common in fig wasp communities. Species identification is very difficult, despite great effort and the ecological importance of fig wasps. Herein, we try to identify all chalcidoid wasp species hosted by one species of fig, using both morphological and molecular methods. We compare the efficiency of four different DNA regions and find that ITS2 is highly effective for species identification, while mitochondrial COI and Cytb regions appear less reliable, possibly due to the interference signals from either nuclear copies of mtDNA, i.e. NUMTs, or the effects of Wolbachia infections. The analyses suggest that combining multiple markers is the best choice for inferring species identifications as any one marker may be unsuitable in a given case.

  1. Identifying emotional and behavioral risk among gifted and nongifted children: A multi-gate, multi-informant approach.

    Science.gov (United States)

    Eklund, Katie; Tanner, Nick; Stoll, Katie; Anway, Leslie

    2015-06-01

    The purpose of the current investigation was to compare 1,206 gifted and nongifted elementary students on the identification of emotional and behavioral risk (EBR) as rated by teachers and parents using a multigate, multi-informant approach to assessment. The Parent and Teacher Behavioral Assessment System for Children, Second Edition (BASC-2) and the Behavioral and Emotional Screening System were used to assess behavioral functioning as rated by teachers and parents. There were significant differences between the number of gifted and nongifted children demonstrating emotional and behavioral risk, with parents and teachers identifying a higher number of boys and nongifted children as at risk. Among children demonstrating EBR, gifted children demonstrated elevated internalizing behaviors as rated by parents. Gifted students demonstrated higher academic performance regardless of risk level, suggesting higher cognitive abilities may be one of several protective factors that serve to attenuate the development of other social, emotional, or behavioral concerns. Implications for practice and future research needs are discussed.

  2. Strategies to design clinical studies to identify predictive biomarkers in cancer research.

    Science.gov (United States)

    Perez-Gracia, Jose Luis; Sanmamed, Miguel F; Bosch, Ana; Patiño-Garcia, Ana; Schalper, Kurt A; Segura, Victor; Bellmunt, Joaquim; Tabernero, Josep; Sweeney, Christopher J; Choueiri, Toni K; Martín, Miguel; Fusco, Juan Pablo; Rodriguez-Ruiz, Maria Esperanza; Calvo, Alfonso; Prior, Celia; Paz-Ares, Luis; Pio, Ruben; Gonzalez-Billalabeitia, Enrique; Gonzalez Hernandez, Alvaro; Páez, David; Piulats, Jose María; Gurpide, Alfonso; Andueza, Mapi; de Velasco, Guillermo; Pazo, Roberto; Grande, Enrique; Nicolas, Pilar; Abad-Santos, Francisco; Garcia-Donas, Jesus; Castellano, Daniel; Pajares, María J; Suarez, Cristina; Colomer, Ramon; Montuenga, Luis M; Melero, Ignacio

    2017-02-01

    The discovery of reliable biomarkers to predict efficacy and toxicity of anticancer drugs remains one of the key challenges in cancer research. Despite its relevance, no efficient study designs to identify promising candidate biomarkers have been established. This has led to the proliferation of a myriad of exploratory studies using dissimilar strategies, most of which fail to identify any promising targets and are seldom validated. The lack of a proper methodology also determines that many anti-cancer drugs are developed below their potential, due to failure to identify predictive biomarkers. While some drugs will be systematically administered to many patients who will not benefit from them, leading to unnecessary toxicities and costs, others will never reach registration due to our inability to identify the specific patient population in which they are active. Despite these drawbacks, a limited number of outstanding predictive biomarkers have been successfully identified and validated, and have changed the standard practice of oncology. In this manuscript, a multidisciplinary panel reviews how those key biomarkers were identified and, based on those experiences, proposes a methodological framework-the DESIGN guidelines-to standardize the clinical design of biomarker identification studies and to develop future research in this pivotal field.

  3. Developing a matrix to identify and prioritise research recommendations in HIV Prevention

    Directory of Open Access Journals (Sweden)

    Coates Bob

    2011-05-01

    Full Text Available Abstract Background HIV prevention continues to be problematic in the UK, as it does globally. The UK Department of Health has a strategic direction with greater focus on prevention as part of its World Class Commissioning Programme. There is a need for targeted evidence-based prevention initiatives. This is an exploratory study to develop an evidence mapping tool in the form of a matrix: this will be used to identify important gaps in contemporary HIV prevention evidence relevant to the UK. It has the potential to aid prioritisation in future research. Methods Categories for prevention and risk groups were developed for HIV prevention in consultation with external experts. These were used as axes on a matrix tool to map evidence. Systematic searches for publications on HIV prevention were undertaken using electronic databases for primary and secondary research undertaken mainly in UK, USA, Canada, Australia and New Zealand, 2006-9. Each publication was screened for inclusion then coded. The risk groups and prevention areas in each paper were counted: several publications addressed multiple risk groups. The counts were exported to the matrix and clearly illustrate the concentrations and gaps of literature in HIV prevention. Results 716 systematic reviews, randomised control trials and other primary research met the inclusion criteria for HIV prevention. The matrix identified several under researched areas in HIV prevention. Conclusions This is the first categorisation system for HIV prevention and the matrix is a novel tool for evidence mapping. Some important yet under-researched areas have been identified in HIV prevention evidence: identifying the undiagnosed population; international adaptation; education; intervention combinations; transgender; sex-workers; heterosexuals and older age groups. Other research recommendations: develop the classification system further and investigate transferability of the matrix to other prevention areas

  4. Identifying "social smoking" U.S. young adults using an empirically-driven approach.

    Science.gov (United States)

    Villanti, Andrea C; Johnson, Amanda L; Rath, Jessica M; Williams, Valerie; Vallone, Donna M; Abrams, David B; Hedeker, Donald; Mermelstein, Robin J

    2017-07-01

    The phenomenon of "social smoking" emerged in the past decade as an important area of research, largely due to its high prevalence in young adults. The purpose of this study was to identify classes of young adult ever smokers based on measures of social and contextual influences on tobacco use. Latent class models were developed using social smoking measures, and not the frequency or quantity of tobacco use. Data come from a national sample of young adult ever smokers aged 18-24 (Truth Initiative Young Adult Cohort Study, N=1564). The optimal models identified three latent classes: Class 1 - nonsmokers (52%); Class 2 - social smokers (18%); and Class 3 - smokers (30%). Nearly 60% of the "social smoker" class self-identified as a social smoker, 30% as an ex-smoker/tried smoking, and 12% as a non-smoker. The "social smoker" class was most likely to report using tobacco mainly or only with others. Past 30-day cigarette use was highest in the "smoker" class. Hookah use was highest in the "social smoker" class. Other tobacco and e-cigarette use was similar in the "social smoker" and "smoker" classes. Past 30-day tobacco and e-cigarette use was present for all products in the "non-smoker" class. Young adult social smokers emerge empirically as a sizable, distinct class from other smokers, even without accounting for tobacco use frequency or intensity. The prevalence of hookah use in "social smokers" indicates a group for which the social aspect of tobacco use could drive experimentation and progression to regular use.

  5. Dutch research on organic agriculture: approaches and characteristics

    NARCIS (Netherlands)

    Wijnands, F.G.; Koopmans, C.J.; Sukkel, W.; Hommes, M.

    2009-01-01

    Dutch research on organic agriculture began in the late 1970s. Key characteristics of this research were the systems approach and the strong participation of farmers and stakeholders. The ambitions for a fully sustainable organic agriculture as formulated by the Dutch organic sector set the research

  6. Theoretical approaches to e-book research

    Directory of Open Access Journals (Sweden)

    Tom D Wilson

    2016-12-01

    Full Text Available The adoption and continued use of innovations by societies, organisations and individuals has been a subject of research since before the 1930s. A variety of different theories have been developed to account for the different speeds at which innovations are adopted and the factors that affect the adoption process. This paper reviews theories of the adoption of innovations with particular reference to the recent phenomenon of the e-book as a cultural innovation that is having an impact on individuals, organizations and national policy makers. The paper will suggest which theories are most appropriate for the different levels at which the innovation is employed.

  7. Hybrid soft computing approaches research and applications

    CERN Document Server

    Dutta, Paramartha; Chakraborty, Susanta

    2016-01-01

    The book provides a platform for dealing with the flaws and failings of the soft computing paradigm through different manifestations. The different chapters highlight the necessity of the hybrid soft computing methodology in general with emphasis on several application perspectives in particular. Typical examples include (a) Study of Economic Load Dispatch by Various Hybrid Optimization Techniques, (b) An Application of Color Magnetic Resonance Brain Image Segmentation by ParaOptiMUSIG activation Function, (c) Hybrid Rough-PSO Approach in Remote Sensing Imagery Analysis,  (d) A Study and Analysis of Hybrid Intelligent Techniques for Breast Cancer Detection using Breast Thermograms, and (e) Hybridization of 2D-3D Images for Human Face Recognition. The elaborate findings of the chapters enhance the exhibition of the hybrid soft computing paradigm in the field of intelligent computing.

  8. (Post-)genomics approaches in fungal research.

    Science.gov (United States)

    Aguilar-Pontes, María Victoria; de Vries, Ronald P; Zhou, Miaomiao

    2014-11-01

    To date, hundreds of fungal genomes have been sequenced and many more are in progress. This wealth of genomic information has provided new directions to study fungal biodiversity. However, to further dissect and understand the complicated biological mechanisms involved in fungal life styles, functional studies beyond genomes are required. Thanks to the developments of current -omics techniques, it is possible to produce large amounts of fungal functional data in a high-throughput fashion (e.g. transcriptome, proteome, etc.). The increasing ease of creating -omics data has also created a major challenge for downstream data handling and analysis. Numerous databases, tools and software have been created to meet this challenge. Facing such a richness of techniques and information, hereby we provide a brief roadmap on current wet-lab and bioinformatics approaches to study functional genomics in fungi.

  9. Action Research and Organisational Learning: A Norwegian Approach to Doing Action Research in Complex Organisations

    Science.gov (United States)

    Eikeland, Olav

    2012-01-01

    The purpose of this article is to present a specific approach to the practice of action research "in complex organisations". Clearly, there are many approaches to the challenge of doing action research in organisations; approaches that are, and also must be, quite context dependent and specific. But my purpose is neither to give an overview nor a…

  10. Novel phenotypes and loci identified through clinical genomics approaches to pediatric cataract.

    Science.gov (United States)

    Patel, Nisha; Anand, Deepti; Monies, Dorota; Maddirevula, Sateesh; Khan, Arif O; Algoufi, Talal; Alowain, Mohammed; Faqeih, Eissa; Alshammari, Muneera; Qudair, Ahmed; Alsharif, Hadeel; Aljubran, Fatimah; Alsaif, Hessa S; Ibrahim, Niema; Abdulwahab, Firdous M; Hashem, Mais; Alsedairy, Haifa; Aldahmesh, Mohammed A; Lachke, Salil A; Alkuraya, Fowzan S

    2017-02-01

    Pediatric cataract is highly heterogeneous clinically and etiologically. While mostly isolated, cataract can be part of many multisystem disorders, further complicating the diagnostic process. In this study, we applied genomic tools in the form of a multi-gene panel as well as whole-exome sequencing on unselected cohort of pediatric cataract (166 patients from 74 families). Mutations in previously reported cataract genes were identified in 58% for a total of 43 mutations, including 15 that are novel. GEMIN4 was independently mutated in families with a syndrome of cataract, global developmental delay with or without renal involvement. We also highlight a recognizable syndrome that resembles galactosemia (a fulminant infantile liver disease with cataract) caused by biallelic mutations in CYP51A1. A founder mutation in RIC1 (KIAA1432) was identified in patients with cataract, brain atrophy, microcephaly with or without cleft lip and palate. For non-syndromic pediatric cataract, we map a novel locus in a multiplex consanguineous family on 4p15.32 where exome sequencing revealed a homozygous truncating mutation in TAPT1. We report two further candidates that are biallelically inactivated each in a single cataract family: TAF1A (cataract with global developmental delay) and WDR87 (non-syndromic cataract). In addition to positional mapping data, we use iSyTE developmental lens expression and gene-network analysis to corroborate the proposed link between the novel candidate genes and cataract. Our study expands the phenotypic, allelic and locus heterogeneity of pediatric cataract. The high diagnostic yield of clinical genomics supports the adoption of this approach in this patient group.

  11. Building persistent identifier systems for geoscience research - Technical solutions and community governance

    Science.gov (United States)

    Klump, J. F.; Lehnert, K. A.; Huber, R.

    2015-12-01

    The emergence of the Internet gave rise to the expectation that the internet would lead to greater accessibility, transparency and reproducibility of research results. New communication technologies enabled far easier and faster collaboration in larger, geographically more distributed networks. However, the distributed and disorganised nature of the internet not only allowed new technologies to emerge, it also made it difficult to maintain a persistent record of science. Persistent identifiers were invented to allow unambiguous identification of resources on the net. At first, these resources referred to scholarly literature and related resources. The concept of using persistent identifiers has since been expanded to other, non-textual resources, like datasets and geological specimens, and more recently to authors and contributors of scholarly works, and to software and instruments.Setting up identifier systems is technically trivial. The real challenge lies in creating a governance system for the respective identifiers. While Digital Object Identifiers (DOI) were originally invented by the publishing industry, they quickly became an established way for the identification of research resources. Other identifier systems, some of them using DOI as an example, were developed as grass-roots efforts by the scientific community.Together with semantic technologies and linked data, unambiguous identification allows us to harness information at large scales beyond human comprehension. The technical possibilities offered by technology challenge some of the norms of scholarly cooperation, such as using and sharing resources beyond the emulation of paper-based publications.This presentation will discuss the development of persistent identification of research resources as a community effort, using the technical and governance patterns developed for DOI and for IGSN for data as an example.

  12. Using a Person-Oriented Approach in Nursing Research.

    Science.gov (United States)

    Knisely, Mitchell R; Draucker, Claire Burke

    2016-04-01

    The purpose of this article was to provide an overview of the person-oriented approach, describe empirical examples of its use, and discuss how the approach may be used in nursing research. The person-oriented approach consists of theoretical and methodological components and provides a way to explore the heterogeneity of populations related to phenomena of interest. For analytic purposes, the person-oriented approach views the person as a holistic unit rather than a sum of his or her characteristics, and thus, it provides an alternative or complementary approach to the more traditional, variable-oriented approaches most commonly used to study health phenomena. Although the person-oriented approach has not been used extensively in nursing research, it offers promise for nursing scholars who study complex problems within heterogeneous populations and who seek to develop targeted interventions to more effectively promote desired health outcomes.

  13. An observation-based approach to identify local natural dust events from routine aerosol ground monitoring

    Directory of Open Access Journals (Sweden)

    D. Q. Tong

    2012-02-01

    Full Text Available Dust is a major component of atmospheric aerosols in many parts of the world. Although there exist many routine aerosol monitoring networks, it is often difficult to obtain dust records from these networks, because these monitors are either deployed far away from dust active regions (most likely collocated with dense population or contaminated by anthropogenic sources and other natural sources, such as wildfires and vegetation detritus. Here we propose a new approach to identify local dust events relying solely on aerosol mass and composition from general-purpose aerosol measurements. Through analyzing the chemical and physical characteristics of aerosol observations during satellite-detected dust episodes, we select five indicators to be used to identify local dust records: (1 high PM10 concentrations; (2 low PM2.5/PM10 ratio; (3 higher concentrations and percentage of crustal elements; (4 lower percentage of anthropogenic pollutants; and (5 low enrichment factors of anthropogenic elements. After establishing these identification criteria, we conduct hierarchical cluster analysis for all validated aerosol measurement data over 68 IMPROVE sites in the Western United States. A total of 182 local dust events were identified over 30 of the 68 locations from 2000 to 2007. These locations are either close to the four US Deserts, namely the Great Basin Desert, the Mojave Desert, the Sonoran Desert, and the Chihuahuan Desert, or in the high wind power region (Colorado. During the eight-year study period, the total number of dust events displays an interesting four-year activity cycle (one in 2000–2003 and the other in 2004–2007. The years of 2003, 2002 and 2007 are the three most active dust periods, with 46, 31 and 24 recorded dust events, respectively, while the years of 2000, 2004 and 2005 are the calmest periods, all with single digit dust records. Among these deserts, the Chihuahua Desert (59 cases and the

  14. A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells.

    Directory of Open Access Journals (Sweden)

    Victor Trevino

    2016-04-01

    Full Text Available The advent of functional genomics has enabled the genome-wide characterization of the molecular state of cells and tissues, virtually at every level of biological organization. The difficulty in organizing and mining this unprecedented amount of information has stimulated the development of computational methods designed to infer the underlying structure of regulatory networks from observational data. These important developments had a profound impact in biological sciences since they triggered the development of a novel data-driven investigative approach. In cancer research, this strategy has been particularly successful. It has contributed to the identification of novel biomarkers, to a better characterization of disease heterogeneity and to a more in depth understanding of cancer pathophysiology. However, so far these approaches have not explicitly addressed the challenge of identifying networks representing the interaction of different cell types in a complex tissue. Since these interactions represent an essential part of the biology of both diseased and healthy tissues, it is of paramount importance that this challenge is addressed. Here we report the definition of a network reverse engineering strategy designed to infer directional signals linking adjacent cell types within a complex tissue. The application of this inference strategy to prostate cancer genome-wide expression profiling data validated the approach and revealed that normal epithelial cells exert an anti-tumour activity on prostate carcinoma cells. Moreover, by using a Bayesian hierarchical model integrating genetics and gene expression data and combining this with survival analysis, we show that the expression of putative cell communication genes related to focal adhesion and secretion is affected by epistatic gene copy number variation and it is predictive of patient survival. Ultimately, this study represents a generalizable approach to the challenge of deciphering cell

  15. A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells.

    Science.gov (United States)

    Trevino, Victor; Cassese, Alberto; Nagy, Zsuzsanna; Zhuang, Xiaodong; Herbert, John; Antczak, Philipp; Clarke, Kim; Davies, Nicholas; Rahman, Ayesha; Campbell, Moray J; Guindani, Michele; Bicknell, Roy; Vannucci, Marina; Falciani, Francesco

    2016-04-01

    The advent of functional genomics has enabled the genome-wide characterization of the molecular state of cells and tissues, virtually at every level of biological organization. The difficulty in organizing and mining this unprecedented amount of information has stimulated the development of computational methods designed to infer the underlying structure of regulatory networks from observational data. These important developments had a profound impact in biological sciences since they triggered the development of a novel data-driven investigative approach. In cancer research, this strategy has been particularly successful. It has contributed to the identification of novel biomarkers, to a better characterization of disease heterogeneity and to a more in depth understanding of cancer pathophysiology. However, so far these approaches have not explicitly addressed the challenge of identifying networks representing the interaction of different cell types in a complex tissue. Since these interactions represent an essential part of the biology of both diseased and healthy tissues, it is of paramount importance that this challenge is addressed. Here we report the definition of a network reverse engineering strategy designed to infer directional signals linking adjacent cell types within a complex tissue. The application of this inference strategy to prostate cancer genome-wide expression profiling data validated the approach and revealed that normal epithelial cells exert an anti-tumour activity on prostate carcinoma cells. Moreover, by using a Bayesian hierarchical model integrating genetics and gene expression data and combining this with survival analysis, we show that the expression of putative cell communication genes related to focal adhesion and secretion is affected by epistatic gene copy number variation and it is predictive of patient survival. Ultimately, this study represents a generalizable approach to the challenge of deciphering cell communication networks

  16. A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells

    Science.gov (United States)

    Trevino, Victor; Cassese, Alberto; Nagy, Zsuzsanna; Zhuang, Xiaodong; Herbert, John; Antzack, Philipp; Clarke, Kim; Davies, Nicholas; Rahman, Ayesha; Campbell, Moray J.; Bicknell, Roy; Vannucci, Marina; Falciani, Francesco

    2016-01-01

    Abstract The advent of functional genomics has enabled the genome-wide characterization of the molecular state of cells and tissues, virtually at every level of biological organization. The difficulty in organizing and mining this unprecedented amount of information has stimulated the development of computational methods designed to infer the underlying structure of regulatory networks from observational data. These important developments had a profound impact in biological sciences since they triggered the development of a novel data-driven investigative approach. In cancer research, this strategy has been particularly successful. It has contributed to the identification of novel biomarkers, to a better characterization of disease heterogeneity and to a more in depth understanding of cancer pathophysiology. However, so far these approaches have not explicitly addressed the challenge of identifying networks representing the interaction of different cell types in a complex tissue. Since these interactions represent an essential part of the biology of both diseased and healthy tissues, it is of paramount importance that this challenge is addressed. Here we report the definition of a network reverse engineering strategy designed to infer directional signals linking adjacent cell types within a complex tissue. The application of this inference strategy to prostate cancer genome-wide expression profiling data validated the approach and revealed that normal epithelial cells exert an anti-tumour activity on prostate carcinoma cells. Moreover, by using a Bayesian hierarchical model integrating genetics and gene expression data and combining this with survival analysis, we show that the expression of putative cell communication genes related to focal adhesion and secretion is affected by epistatic gene copy number variation and it is predictive of patient survival. Ultimately, this study represents a generalizable approach to the challenge of deciphering cell communication

  17. Research and Collaboration Overview of Institut Pasteur International Network: A Bibliometric Approach toward Research Funding Decisions

    Directory of Open Access Journals (Sweden)

    Ehsan Mostafavi

    2014-01-01

    Full Text Available Background Institut Pasteur International Network (IPIN, which includes 32 research institutes around the world, is a network of research and expertise to fight against infectious diseases. A scientometric approach was applied to describe research and collaboration activities of IPIN. Methods Publications were identified using a manual search of IPIN member addresses in Science Citation Index Expanded (SCIE between 2006 and 2011. Total publications were then subcategorized by geographic regions. Several scientometric indicators and the H-index were employed to estimate the scientific production of each IPIN member. Subject and geographical overlay maps were also applied to visualize the network activities of the IPIN members. Results A total number of 12667 publications originated from IPIN members. Each author produced an average number of 2.18 papers and each publication received an average of 13.40 citations. European Pasteur Institutes had the largest amount of publications, authored papers, and H-index values. Biochemistry and molecular biology, microbiology, immunology and infectious diseases were the most important research topics, respectively. Geographic mapping of IPIN publications showed wide international collaboration among IPIN members around the world. Conclusion IPIN has strong ties with national and international authorities and organizations to investigate the current and future health issues. It is recommended to use scientometric and collaboration indicators as measures of research performance in IPIN future policies and investment decisions.

  18. Seeking Constructive Synergy: Design Science and the Constructive Research Approach

    DEFF Research Database (Denmark)

    Piirainen, Kalle; Gonzalez, Rafael A.

    2013-01-01

    Information systems research and management science create knowledge which can be applied in organizations. Design science specifically aims at applying existing knowledge to solve interesting and relevant business problems and has been steadily gaining support in information systems research....... However, design science is not the only design-oriented framework. Accordingly, this raises the question of whether it is possible to compare the results obtained from different brands of design-oriented research. This paper contributes to answering this question by comparing two research approaches......, enabling mutual learning possibilities and suggesting improvements in transparency and rigor. The objective of this paper is to compare design science research with the constructive research approach. The conclusion is that the two approaches are compatible, save for details in practical requirements...

  19. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

    Science.gov (United States)

    Delmont, Tom O.

    2016-01-01

    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes. PMID:27069789

  20. A Novel Approach for Identifying the Heme-Binding Proteins from Mouse Tissues

    Institute of Scientific and Technical Information of China (English)

    Xiaolei Li; Rong Wang; Zhongsheng Sun; Zuyuan Xu; Jingyue Bao; Xiuqing Zhang; Xiaoli Feng; Siqi Liu; Xiaoshan Wang; Kang Zhao; Zhengfeng Zhou; Caifeng Zhao; Ren Yan; Liang Lin; Tingting Lei; Jianning Yin

    2003-01-01

    Heme is a key cofactor in aerobic life, both in eukaryotes and prokaryotes. Because of the high reactivity of ferrous protoporphyrin IX, the reactions of heme in cells are often carried out through heme-protein complexes. Traditionally studies of hemebinding proteins have been approached on a case by case basis, thus there is a limited global view of the distribution of heme-binding proteins in different cells or tissues. The procedure described here is aimed at profiling hemne-binding proteins in mouse tissues sequentially by 1) purification of heme-binding proteins by hemeagarose, an affinity chromatographic resin; 2) isolation of heme-binding proteins by SDS-PAGE or two-dimensional electrophoresis; 3) identification of heme-binding proteins by mass spectrometry. In five mouse tissues, over 600 protein spots were visualized on 2DE gel stained by Commassie blue and 154 proteins were identified by MALDI-TOF, in which most proteins belong to heme related. This methodology makes it possible to globally characterize the heme-binding proteins in a biological system.

  1. A Novel Approach for Identifying the Heme—Binding Proteins from Mouse Tissues

    Institute of Scientific and Technical Information of China (English)

    XiaoleiLi; XiaoshanWang; KangZhao; ZhengfengZhou; CaifengZhao; RenYan; LiangLin; TingtingLei; JianningYin; RongWang; ZhongshengSun; ZuyuanXu; JingyueBao; XiugingZhang; XiaoliFeng; SiqiLiu

    2003-01-01

    Heme is a key cofactor in aerobic life,both in eukaryotes and prokaryotes.Because of the high reactivity of ferrous protoporphyrin IX,the reactions of heme in cells are often carried out through heme-protein complexes.Traditionally studies of hemebinding proteins have been approached on a case by case basis,thus there is a limited global view of the distribution of heme-binding proteins in different cells or tissues.The procedure described here is aimed at profiling heme-binding proteins in mouse tissues sequentially by 1)purification of heme-binding proteins by hemeagarose,an affinity chromatographic resin;2)isolation of heme-binding proteins by SDS-PAGE or two-dimensional electrophoresis;3)identification of heme-binding proteins by mass spectrometry.In five mouse tissues,over 600 protein spots were visualized on 2DE gel stained by Commassie blue and 154 proteins were identified by MALDI-TOF,in which most proteins belong to heme related.This methodology makes it possible to globally characterize the heme-binding proteins in a biological system.

  2. Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast.

    Science.gov (United States)

    Poos, Alexandra M; Maicher, André; Dieckmann, Anna K; Oswald, Marcus; Eils, Roland; Kupiec, Martin; Luke, Brian; König, Rainer

    2016-06-02

    Understanding telomere length maintenance mechanisms is central in cancer biology as their dysregulation is one of the hallmarks for immortalization of cancer cells. Important for this well-balanced control is the transcriptional regulation of the telomerase genes. We integrated Mixed Integer Linear Programming models into a comparative machine learning based approach to identify regulatory interactions that best explain the discrepancy of telomerase transcript levels in yeast mutants with deleted regulators showing aberrant telomere length, when compared to mutants with normal telomere length. We uncover novel regulators of telomerase expression, several of which affect histone levels or modifications. In particular, our results point to the transcription factors Sum1, Hst1 and Srb2 as being important for the regulation of EST1 transcription, and we validated the effect of Sum1 experimentally. We compiled our machine learning method leading to a user friendly package for R which can straightforwardly be applied to similar problems integrating gene regulator binding information and expression profiles of samples of e.g. different phenotypes, diseases or treatments.

  3. Mixed Integer Linear Programming based machine learning approach identifies regulators of telomerase in yeast

    Science.gov (United States)

    Poos, Alexandra M.; Maicher, André; Dieckmann, Anna K.; Oswald, Marcus; Eils, Roland; Kupiec, Martin; Luke, Brian; König, Rainer

    2016-01-01

    Understanding telomere length maintenance mechanisms is central in cancer biology as their dysregulation is one of the hallmarks for immortalization of cancer cells. Important for this well-balanced control is the transcriptional regulation of the telomerase genes. We integrated Mixed Integer Linear Programming models into a comparative machine learning based approach to identify regulatory interactions that best explain the discrepancy of telomerase transcript levels in yeast mutants with deleted regulators showing aberrant telomere length, when compared to mutants with normal telomere length. We uncover novel regulators of telomerase expression, several of which affect histone levels or modifications. In particular, our results point to the transcription factors Sum1, Hst1 and Srb2 as being important for the regulation of EST1 transcription, and we validated the effect of Sum1 experimentally. We compiled our machine learning method leading to a user friendly package for R which can straightforwardly be applied to similar problems integrating gene regulator binding information and expression profiles of samples of e.g. different phenotypes, diseases or treatments. PMID:26908654

  4. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

    Directory of Open Access Journals (Sweden)

    Tom O. Delmont

    2016-03-01

    Full Text Available High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today’s microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

  5. A statistical approach for identifying nuclear waste glass compositions that will meet quality and processability requirements

    Energy Technology Data Exchange (ETDEWEB)

    Piepel, G.F.

    1990-09-01

    Borosilicate glass provides a solid, stable medium for the disposal of high-level radioactive wastes resulting from the production of nuclear materials for United States defense needs. The glass must satisfy various quality and processability requirements on properties such as chemical durability, viscosity, and electrical conductivity. These properties depend on the composition of the waste glass, which will vary during production due to variations in nuclear waste composition and variations in the glass-making process. This paper discusses the experimentally-based statistical approach being used in the Hanford Waste Vitrification Plant (HWVP) Composition Variability Study (CVS). The overall goal of the CVS is to identify the composition region of potential HWVP waste glasses that satisfy with high confidence the applicable quality and processability requirements. This is being accomplished by melting and obtaining property data for simulated nuclear waste glasses of various compositions, and then statistically developing models and other tools needed to meet the goal. 6 refs., 1 fig., 5 tabs.

  6. Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies.

    Science.gov (United States)

    Delmont, Tom O; Eren, A Murat

    2016-01-01

    High-throughput sequencing provides a fast and cost-effective mean to recover genomes of organisms from all domains of life. However, adequate curation of the assembly results against potential contamination of non-target organisms requires advanced bioinformatics approaches and practices. Here, we re-analyzed the sequencing data generated for the tardigrade Hypsibius dujardini, and created a holistic display of the eukaryotic genome assembly using DNA data originating from two groups and eleven sequencing libraries. By using bacterial single-copy genes, k-mer frequencies, and coverage values of scaffolds we could identify and characterize multiple near-complete bacterial genomes from the raw assembly, and curate a 182 Mbp draft genome for H. dujardini supported by RNA-Seq data. Our results indicate that most contaminant scaffolds were assembled from Moleculo long-read libraries, and most of these contaminants have differed between library preparations. Our re-analysis shows that visualization and curation of eukaryotic genome assemblies can benefit from tools designed to address the needs of today's microbiologists, who are constantly challenged by the difficulties associated with the identification of distinct microbial genomes in complex environmental metagenomes.

  7. Gene networks associated with conditional fear in mice identified using a systems genetics approach

    Directory of Open Access Journals (Sweden)

    Eskin Eleazar

    2011-03-01

    Full Text Available Abstract Background Our understanding of the genetic basis of learning and memory remains shrouded in mystery. To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP with high mapping resolution. Results A total of 27 behavioral quantitative trait loci were mapped with a false discovery rate of 5%. By integrating fear phenotypes, transcript profiling data from hippocampus and striatum and also genotype information, two gene co-expression networks correlated with context-dependent immobility were identified. We prioritized the key markers and genes in these pathways using intramodular connectivity measures and structural equation modeling. Highly connected genes in the context fear modules included Psmd6, Ube2a and Usp33, suggesting an important role for ubiquitination in learning and memory. In addition, we surveyed the architecture of brain transcript regulation and demonstrated preservation of gene co-expression modules in hippocampus and striatum, while also highlighting important differences. Rps15a, Kif3a, Stard7, 6330503K22RIK, and Plvap were among the individual genes whose transcript abundance were strongly associated with fear phenotypes. Conclusion Application of our multi-faceted mapping strategy permits an increasingly detailed characterization of the genetic networks underlying behavior.

  8. Identifying an appropriate measurement modeling approach for the Mini-Mental State Examination.

    Science.gov (United States)

    Rubright, Jonathan D; Nandakumar, Ratna; Karlawish, Jason

    2016-02-01

    The Mini-Mental State Examination (MMSE) is a 30-item, dichotomously scored test of general cognition. A number of benefits could be gained by modeling the MMSE in an item response theory (IRT) framework, as opposed to the currently used classical additive approach. However, the test, which is built from groups of items related to separate cognitive subdomains, may violate a key assumption of IRT: local item independence. This study aimed to identify the most appropriate measurement model for the MMSE: a unidimensional IRT model, a testlet response theory model, or a bifactor model. Local dependence analysis using nationally representative data showed a meaningful violation of the local item independence assumption, indicating multidimensionality. In addition, the testlet and bifactor models displayed superior fit indices over a unidimensional IRT model. Statistical comparisons showed that the bifactor model fit MMSE respondent data significantly better than the other models considered. These results suggest that application of a traditional unidimensional IRT model is inappropriate in this context. Instead, a bifactor model is suggested for future modeling of MMSE data as it more accurately represents the multidimensional nature of the scale. (PsycINFO Database Record

  9. A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas

    Institute of Scientific and Technical Information of China (English)

    Antti Ylip(a)(a); Olli Yli-Harja; Wei Zhang; Matti Nykter

    2011-01-01

    Identification of genetic signatures is the main objective for many computational oncology studies. The signature usually consists of numerous genes that are differentially expressed between two clinically distinct groups of samples, such as tumor subtypes. Prospectively, many signatures have been found to generalize poorly to other datasets and, thus, have rarely been accepted into clinical use. Recognizing the limited success of traditionally generated signatures, we developed a systems biology-based framework for robust identification of key transcription factors and their genomic regulatory neighborhoods. Application of the framework to study the differences between gastrointestinal stromal tumor (GIST) and leiomyosarcoma (LMS) resulted in the identification of nine transcription factors (SRF, NKX2-5, CCDC6, LEF1, VDR, ZNF250, TRIM63, MAF, and MYC). Functional annotations of the obtained neighborhoods identified the biological processes which the key transcription factors regulate differently between the tumor types. Analyzing the differences in the expression patterns using our approach resulted in a more robust genetic signature and more biological insight into the diseases compared to a traditional genetic signature.

  10. Machine learning approach identifies new pathways associated with demyelination in a viral model of multiple sclerosis

    Science.gov (United States)

    Ulrich, Reiner; Kalkuhl, Arno; Deschl, Ulrich; Baumgärtner, Wolfgang

    2010-01-01

    Abstract Theiler’s murine encephalomyelitis is an experimentally virus-induced inflammatory demyelinating disease of the spinal cord, displaying clinical and pathological similarities to chronic progressive multiple sclerosis. The aim of this study was to identify pathways associated with chronic demyelination using an assumption-free combined microarray and immunohistology approach. Movement control as determined by rotarod assay significantly worsened in Theiler’s murine encephalomyelitis -virus-infected SJL/J mice from 42 to 196 days after infection (dpi). In the spinal cords, inflammatory changes were detected 14 to 196 dpi, and demyelination progressively increased from 42 to 196 dpi. Microarray analysis revealed 1001 differentially expressed genes over the study period. The dominating changes as revealed by k-means and functional annotation clustering included up-regulations related to intrathecal antibody production and antigen processing and presentation via major histocompatibility class II molecules. A random forest machine learning algorithm revealed that down-regulated lipid and cholesterol biosynthesis, differentially expressed neurite morphogenesis and up-regulated toll-like receptor-4-induced pathways were intimately associated with demyelination as measured by immunohistology. Conclusively, although transcriptional changes were dominated by the adaptive immune response, the main pathways associated with demyelination included up-regulation of toll-like receptor 4 and down-regulation of cholesterol biosynthesis. Cholesterol biosynthesis is a rate limiting step of myelination and its down-regulation is suggested to be involved in chronic demyelination by an inhibition of remyelination. PMID:19183246

  11. Identifying Local Determinants Of Research Commercialization Strategies In Iranian Biotechnology Sector

    Directory of Open Access Journals (Sweden)

    Jahangir Yadollahi Fars

    2012-06-01

    Full Text Available Biotechnology industry has a special place among novel industries. The majority of biotech companies are start-ups or small companies that have been working for several years yet are not profitable. Evidences showed that firms and researchers have problems in turning academic findings to commercial revenue and there is problem in commercialization process and choosing method of the exploitation academic opportunities or choosing proper commercialization strategy in this industry. In this study, firstly, the local determinants of commercialization strategy in 41 Iranian young biotechnology companies were identified through interview and then a questionnaire was prepared integrating these determinants and the rest of them exist in literature and was distributed among a larger sample in order to obtain the integrity. Finally, after analyzing the questionnaires, the local determinants of commercialization strategies for Iranian researcher in biotechnology sector were identified.

  12. Biomechanical approaches to identify and quantify injury mechanisms and risk factors in women's artistic gymnastics.

    Science.gov (United States)

    Bradshaw, Elizabeth J; Hume, Patria A

    2012-09-01

    Targeted injury prevention strategies, based on biomechanical analyses, have the potential to help reduce the incidence and severity of gymnastics injuries. This review outlines the potential benefits of biomechanics research to contribute to injury prevention strategies for women's artistic gymnastics by identification of mechanisms of injury and quantification of the effects of injury risk factors. One hundred and twenty-three articles were retained for review after searching electronic databases using key words, including 'gymnastic', 'biomech*', and 'inj*', and delimiting by language and relevance to the paper aim. Impact load can be measured biomechanically by the use of instrumented equipment (e.g. beatboard), instrumentation on the gymnast (accelerometers), or by landings on force plates. We need further information on injury mechanisms and risk factors in gymnastics and practical methods of monitoring training loads. We have not yet shown, beyond a theoretical approach, how biomechanical analysis of gymnastics can help reduce injury risk through injury prevention interventions. Given the high magnitude of impact load, both acute and accumulative, coaches should monitor impact loads per training session, taking into consideration training quality and quantity such as the control of rotation and the height from which the landings are executed.

  13. Using a community-driven approach to identify local forest and climate change priorities in Teslin, Yukon

    Directory of Open Access Journals (Sweden)

    Joleen Timko

    2015-12-01

    Full Text Available The likelihood of addressing the complex environmental, economic, and social/cultural issues associated with local climate change impacts is enhanced when collaborative partnerships with local people are established. Using a community-centered approach in the Teslin region of Canada’s Yukon Territory, we utilized our research skills to respond to local needs for information by facilitating both an internal community process to clarify traditional and local knowledge, values, and perceptions on locally identified priorities, while gathering external information to enable local people to make sound decisions. Specifically, we sought to clarify local perceptions surrounding climate change impacts on fire risk and wildlife habitat, and the potential adaptation strategies appropriate and feasible within the Teslin Tlingit Traditional Territory. This paper provides a characterization of the study region and our project team; provides background on the interview and data collection process; presents our key results; and discusses the importance of our findings and charts a way forward for our continued work with the people in the Teslin region. This approach presents an excellent opportunity to help people holistically connect a range of local values, including fire risk mitigation, habitat enhancement, economic development, and enhanced social health.

  14. Identifying differences in the experience of (in)authenticity: a latent class analysis approach.

    Science.gov (United States)

    Lenton, Alison P; Slabu, Letitia; Bruder, Martin; Sedikides, Constantine

    2014-01-01

    Generally, psychologists consider state authenticity - that is, the subjective sense of being one's true self - to be a unitary and unidimensional construct, such that (a) the phenomenological experience of authenticity is thought to be similar no matter its trigger, and (b) inauthenticity is thought to be simply the opposing pole (on the same underlying construct) of authenticity. Using latent class analysis, we put this conceptualization to a test. In order to avoid over-reliance on a Western conceptualization of authenticity, we used a cross-cultural sample (N = 543), comprising participants from Western, South-Asian, East-Asian, and South-East Asian cultures. Participants provided either a narrative in which the described when they felt most like being themselves or one in which they described when they felt least like being themselves. The analysis identified six distinct classes of experiences: two authenticity classes ("everyday" and "extraordinary"), three inauthenticity classes ("self-conscious," "deflated," and "extraordinary"), and a class representing convergence between authenticity and inauthenticity. The classes were phenomenologically distinct, especially with respect to negative affect, private and public self-consciousness, and self-esteem. Furthermore, relatively more interdependent cultures were less likely to report experiences of extraordinary (in)authenticity than relatively more independent cultures. Understanding the many facets of (in)authenticity may enable researchers to connect different findings and explain why the attainment of authenticity can be difficult.

  15. A systems biology approach identifies a regulatory network in parotid acinar cell terminal differentiation.

    Directory of Open Access Journals (Sweden)

    Melissa A Metzler

    Full Text Available The transcription factor networks that drive parotid salivary gland progenitor cells to terminally differentiate, remain largely unknown and are vital to understanding the regeneration process.A systems biology approach was taken to measure mRNA and microRNA expression in vivo across acinar cell terminal differentiation in the rat parotid salivary gland. Laser capture microdissection (LCM was used to specifically isolate acinar cell RNA at times spanning the month-long period of parotid differentiation.Clustering of microarray measurements suggests that expression occurs in four stages. mRNA expression patterns suggest a novel role for Pparg which is transiently increased during mid postnatal differentiation in concert with several target gene mRNAs. 79 microRNAs are significantly differentially expressed across time. Profiles of statistically significant changes of mRNA expression, combined with reciprocal correlations of microRNAs and their target mRNAs, suggest a putative network involving Klf4, a differentiation inhibiting transcription factor, which decreases as several targeting microRNAs increase late in differentiation. The network suggests a molecular switch (involving Prdm1, Sox11, Pax5, miR-200a, and miR-30a progressively decreases repression of Xbp1 gene transcription, in concert with decreased translational repression by miR-214. The transcription factor Xbp1 mRNA is initially low, increases progressively, and may be maintained by a positive feedback loop with Atf6. Transfection studies show that Xbp1 activates the Mist1 promoter [corrected]. In addition, Xbp1 and Mist1 each activate the parotid secretory protein (Psp gene, which encodes an abundant salivary protein, and is a marker of terminal differentiation.This study identifies novel expression patterns of Pparg, Klf4, and Sox11 during parotid acinar cell differentiation, as well as numerous differentially expressed microRNAs. Network analysis identifies a novel stemness arm, a

  16. A meta-composite software development approach for translational research.

    Science.gov (United States)

    Sadasivam, Rajani S; Tanik, Murat M

    2013-06-01

    Translational researchers conduct research in a highly data-intensive and continuously changing environment and need to use multiple, disparate tools to achieve their goals. These researchers would greatly benefit from meta-composite software development or the ability to continuously compose and recompose tools together in response to their ever-changing needs. However, the available tools are largely disconnected, and current software approaches are inefficient and ineffective in their support for meta-composite software development. Building on the composite services development approach, the de facto standard for developing integrated software systems, we propose a concept-map and agent-based meta-composite software development approach. A crucial step in composite services development is the modeling of users' needs as processes, which can then be specified in an executable format for system composition. We have two key innovations. First, our approach allows researchers (who understand their needs best) instead of technicians to take a leadership role in the development of process models, reducing inefficiencies and errors. A second innovation is that our approach also allows for modeling of complex user interactions as part of the process, overcoming the technical limitations of current tools. We demonstrate the feasibility of our approach using a real-world translational research use case. We also present results of usability studies evaluating our approach for future refinements.

  17. Selection effects in identifying magnetic clouds and the importance of the closest approach parameter

    Directory of Open Access Journals (Sweden)

    R. P. Lepping

    2010-08-01

    Full Text Available This study is motivated by the unusually low number of magnetic clouds (MCs that are strictly identified within interplanetary coronal mass ejections (ICMEs, as observed at 1 AU; this is usually estimated to be around 30% or lower. But a looser definition of MCs may significantly increase this percentage. Another motivation is the unexpected shape of the occurrence distribution of the observers' "closest approach distances" (measured from a MC's axis, and called CA which drops off somewhat rapidly as |CA| (in % of MC radius approaches 100%, based on earlier studies. We suggest, for various geometrical and physical reasons, that the |CA|-distribution should be somewhere between a uniform one and the one actually observed, and therefore the 30% estimate should be higher. So we ask, When there is a failure to identify a MC within an ICME, is it occasionally due to a large |CA| passage, making MC identification more difficult, i.e., is it due to an event selection effect? In attempting to answer this question we examine WIND data to obtain an accurate distribution of the number of MCs vs. |CA| distance, whether the event is ICME-related or not, where initially a large number of cases (N=98 are considered. This gives a frequence distribution that is far from uniform, confirming earlier studies. This along with the fact that there are many ICME identification-parameters that do not depend on |CA| suggest that, indeed an MC event selection effect may explain at least part of the low ratio of (No. MCs/(No. ICMEs. We also show that there is an acceptable geometrical and physical consistency in the relationships for both average "normalized" magnetic field intensity change and field direction change vs. |CA| within a MC, suggesting that our estimates of |CA|, BO (magnetic field intensity on the axis, and choice of a proper "cloud coordinate" system (all needed in the analysis are acceptably accurate. Therefore, the MC

  18. Compare and Contrast Inductive and Deductive Research Approaches

    Science.gov (United States)

    Soiferman, L. Karen

    2010-01-01

    This discussion paper compares and contrasts "inductive" and "deductive" research approaches as described by Trochim (2006) and Plano Clark and Creswell (2007). It also examines the "exploratory" and "confirmatory" approaches by Onwueghuzie and Leech (2005) with respect to the assumption each holds about the nature of knowledge. The paper starts…

  19. Propensity Score Analysis: An Alternative Statistical Approach for HRD Researchers

    Science.gov (United States)

    Keiffer, Greggory L.; Lane, Forrest C.

    2016-01-01

    Purpose: This paper aims to introduce matching in propensity score analysis (PSA) as an alternative statistical approach for researchers looking to make causal inferences using intact groups. Design/methodology/approach: An illustrative example demonstrated the varying results of analysis of variance, analysis of covariance and PSA on a heuristic…

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

    Science.gov (United States)

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

    2011-10-01

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

  1. Innovative new technologies to identify and treat traumatic brain injuries: crossover technologies and approaches between military and civilian applications.

    Science.gov (United States)

    Doarn, Charles R; McVeigh, Francis; Poropatich, Ronald

    2010-04-01

    Traumatic brain injury (TBI) has become the signature injury of Operation Iraqi Freedom and Operation Enduring Freedom. The use of improvised explosive devices has seen an exponential increase in both Iraq and Afghanistan. In previous conflicts prior to Iraq, survivability of such an injury was far less. Today, technological improvements in trauma care have increased an injured warfighter's chance of survival. A reduction in severe TBI has been achieved but an increase in mild or moderate TBI has been observed. The consequences of this kind of injury can be both physical and mental and can often be hidden or even misdiagnosed. The U.S. Army is interested in pursuing technological solutions for early detection and treatment of TBI to reduce its lasting impact on the warfighter. Such technological breakthroughs have benefit beyond the military, as TBI is a high probable event in nonmilitary settings as well. To gauge what technologies or methods are currently available, the U.S. Army's Telemedicine and Advanced Technology Research Center partnered with the American Telemedicine Association to organize and conduct a discipline-specific symposium entitled "Innovative New Technologies to Identify and Treat Traumatic Brain Injuries: Crossover Technologies and Approaches Between Military and Civilian Applications." This symposium was held in Palm Springs, CA, in September 2009. The purpose of the meeting was to provide a unique opportunity for leaders from disparate organizations involved in telemedicine and related other activities to meet and explore opportunities to collaborate in new partnership models. The meeting was designed to help Telemedicine and Advanced Technology Research Center identify opportunities to expand strategic operations and form new alliances. This report summarizes this symposium while raising awareness for collaboration into better ways of adapting and adopting technologies to address this growing health issue.

  2. A Proteomics Approach to Identify New Putative Cardiac Intercalated Disk Proteins.

    Directory of Open Access Journals (Sweden)

    Siddarth Soni

    Full Text Available Synchronous beating of the heart is dependent on the efficient functioning of the cardiac intercalated disk (ID. The ID is composed of a complex protein network enabling electrical continuity and chemical communication between individual cardiomyocytes. Recently, several different studies have shed light on increasingly prevalent cardiac diseases involving the ID. Insufficient knowledge of its composition makes it difficult to study these disease mechanisms in more detail and therefore here we aim expand the ID proteome. Here, using a combination of general membrane enrichment, in-depth quantitative proteomics and an intracellular location driven bioinformatics approach, we aim to discover new putative ID proteins in rat ventricular tissue.General membrane isolation, enriched amongst others also with ID proteins as based on presence of the established markers connexin-43 and n-cadherin, was performed using centrifugation. By mass spectrometry, we quantitatively evaluated the level of 3455 proteins in the enriched membrane fraction (EMF and its counterpart, the soluble cytoplasmic fraction. These data were stringently filtered to generate a final set of 97 enriched, putative ID proteins. These included Cx43 and n-cadherin, but also many interesting novel candidates. We selected 4 candidates (Flotillin-2 (FLOT2, Nexilin (NEXN, Popeye-domain-containg-protein 2 (POPDC2 and thioredoxin-related-transmembrane-protein 2 (TMX2 and confirmed their co-localization with n-cadherin in the ID of human and rat heart cryo-sections, and isolated dog cardiomyocytes.The presented proteomics dataset of putative new ID proteins is a valuable resource for future research into this important molecular intersection of the heart.

  3. Recasting Communication Theory and Research: A Cybernetic Approach.

    Science.gov (United States)

    Hill, Gary A.

    The author's main concern is to provide a research format which will supply a unitary conception of communication. The wide range of complex topics and variety of concepts embraced by communication theory and the rather disparate set of phenomena encompassed by communication research create this need for a unitary study approach capable of linking…

  4. Conjecture Mapping: An Approach to Systematic Educational Design Research

    Science.gov (United States)

    Sandoval, William

    2014-01-01

    Design research is strongly associated with the learning sciences community, and in the 2 decades since its conception it has become broadly accepted. Yet within and without the learning sciences there remains confusion about how to do design research, with most scholarship on the approach describing what it is rather than how to do it. This…

  5. Estranged Familiars: A Deweyan Approach to Philosophy and Qualitative Research

    Science.gov (United States)

    Shuffelton, Amy

    2015-01-01

    This essay argues that philosophy can be combined with qualitative research without sacrificing the aims of either approach. Philosophers and qualitative researchers have articulated and supported the idea that human meaning-constructions are appropriately grasped through close attention to "consequences incurred in action," in…

  6. Interdisciplinarity of Nano Research Fields : A Keyword Mining Approach

    NARCIS (Netherlands)

    Wang, L.; Notten, A.; Surpatean, A.

    2012-01-01

    Using a keyword mining approach, this paper explores the interdisciplinary and integrative dynamics in five nano research fields. We argue that the general trend of integration in nano research fields is converging in the long run, although the degree of this convergence depends greatly on the indic

  7. Book Review: Comparative Education Research: Approaches and Methods

    Directory of Open Access Journals (Sweden)

    Noel Mcginn

    2014-10-01

    Full Text Available Book Review Comparative Education Research: Approaches and Methods (2nd edition By Mark Bray, Bob Adamson and Mark Mason (Eds. (2014, 453p ISBN: 978-988-17852-8-2, Hong Kong: Comparative Education Research Centre and Springer

  8. Focus Groups: A Practical and Applied Research Approach for Counselors

    Science.gov (United States)

    Kress, Victoria E.; Shoffner, Marie F.

    2007-01-01

    Focus groups are becoming a popular research approach that counselors can use as an efficient, practical, and applied method of gathering information to better serve clients. In this article, the authors describe focus groups and their potential usefulness to professional counselors and researchers. Practical implications related to the use of…

  9. A team approach to recruitment in hospice research: engaging patients, close people and health professionals.

    Science.gov (United States)

    L Campbell, Cathy; Bailey, Cara; Armour, Kathy; Perry, Rachel; Orlando, Rosanna; Kinghorn, Philip; Jones, Louise; Coast, Joanna

    2016-07-02

    Research is vital to the future development of hospice care. However, research in hospice settings is very challenging. This paper describes a case study of a successful multidisciplinary research team approach (MDRT) to the recruitment of participants (hospice patients, family members and health professionals) for a study in a hospice setting on the economic evaluation of end-of-life care. A successful recruitment plan includes three key strategies: identifying key members of the MDRT early in the research process; having a clear and constant communication stream; and creating an environment where all team members have a shared commitment to the research, all voices are heard and valued, and everyone contributes to the research aims. An MDRT approach will be helpful to guide the development of successful recruitment plans for academic-community research partnerships in the hospice setting.

  10. A Bayesian Approach to Identifying New Risk Factors for Dementia: A Nationwide Population-Based Study.

    Science.gov (United States)

    Wen, Yen-Hsia; Wu, Shihn-Sheng; Lin, Chun-Hung Richard; Tsai, Jui-Hsiu; Yang, Pinchen; Chang, Yang-Pei; Tseng, Kuan-Hua

    2016-05-01

    Dementia is one of the most disabling and burdensome health conditions worldwide. In this study, we identified new potential risk factors for dementia from nationwide longitudinal population-based data by using Bayesian statistics.We first tested the consistency of the results obtained using Bayesian statistics with those obtained using classical frequentist probability for 4 recognized risk factors for dementia, namely severe head injury, depression, diabetes mellitus, and vascular diseases. Then, we used Bayesian statistics to verify 2 new potential risk factors for dementia, namely hearing loss and senile cataract, determined from the Taiwan's National Health Insurance Research Database.We included a total of 6546 (6.0%) patients diagnosed with dementia. We observed older age, female sex, and lower income as independent risk factors for dementia. Moreover, we verified the 4 recognized risk factors for dementia in the older Taiwanese population; their odds ratios (ORs) ranged from 3.469 to 1.207. Furthermore, we observed that hearing loss (OR = 1.577) and senile cataract (OR = 1.549) were associated with an increased risk of dementia.We found that the results obtained using Bayesian statistics for assessing risk factors for dementia, such as head injury, depression, DM, and vascular diseases, were consistent with those obtained using classical frequentist probability. Moreover, hearing loss and senile cataract were found to be potential risk factors for dementia in the older Taiwanese population. Bayesian statistics could help clinicians explore other potential risk factors for dementia and for developing appropriate treatment strategies for these patients.

  11. A systematic approach to instruction in research ethics.

    Science.gov (United States)

    Antes, Alison L

    2014-01-01

    This article describes a systematic approach for developing instructional programs that emphasizes defining learning needs, planning the learning environment, and evaluating learning to ensure continuous course improvement. This review outlines the nature of these interrelated components of instructional development and draws attention to issues specific to instruction in research ethics. Guiding questions summarize key, practical considerations, and the discussion suggests future steps in the pursuit of effective instruction in research ethics. Overall, the variety of approaches to instruction and mixed findings regarding its effectiveness underscore the need to apply a systematic framework to instruction in research ethics.

  12. Improving product development practice: An action-research based approach

    DEFF Research Database (Denmark)

    Harmsen, Hanne

    the widely published normative advice. While there may be several reasons for discrepancies between research results and prac-tice this paper focuses on problems of implementation of the identified success factors. Within the research area of NPD-management there has been numerous surveys as well as case...

  13. A multivariate and stochastic approach to identify key variables to rank dairy farms on profitability.

    Science.gov (United States)

    Atzori, A S; Tedeschi, L O; Cannas, A

    2013-05-01

    The economic efficiency of dairy farms is the main goal of farmers. The objective of this work was to use routinely available information at the dairy farm level to develop an index of profitability to rank dairy farms and to assist the decision-making process of farmers to increase the economic efficiency of the entire system. A stochastic modeling approach was used to study the relationships between inputs and profitability (i.e., income over feed cost; IOFC) of dairy cattle farms. The IOFC was calculated as: milk revenue + value of male calves + culling revenue - herd feed costs. Two databases were created. The first one was a development database, which was created from technical and economic variables collected in 135 dairy farms. The second one was a synthetic database (sDB) created from 5,000 synthetic dairy farms using the Monte Carlo technique and based on the characteristics of the development database data. The sDB was used to develop a ranking index as follows: (1) principal component analysis (PCA), excluding IOFC, was used to identify principal components (sPC); and (2) coefficient estimates of a multiple regression of the IOFC on the sPC were obtained. Then, the eigenvectors of the sPC were used to compute the principal component values for the original 135 dairy farms that were used with the multiple regression coefficient estimates to predict IOFC (dRI; ranking index from development database). The dRI was used to rank the original 135 dairy farms. The PCA explained 77.6% of the sDB variability and 4 sPC were selected. The sPC were associated with herd profile, milk quality and payment, poor management, and reproduction based on the significant variables of the sPC. The mean IOFC in the sDB was 0.1377 ± 0.0162 euros per liter of milk (€/L). The dRI explained 81% of the variability of the IOFC calculated for the 135 original farms. When the number of farms below and above 1 standard deviation (SD) of the dRI were calculated, we found that 21

  14. Evaluation of different approaches for identifying optimal sites to predict mean hillslope soil moisture content

    Science.gov (United States)

    Liao, Kaihua; Zhou, Zhiwen; Lai, Xiaoming; Zhu, Qing; Feng, Huihui

    2017-04-01

    The identification of representative soil moisture sampling sites is important for the validation of remotely sensed mean soil moisture in a certain area and ground-based soil moisture measurements in catchment or hillslope hydrological studies. Numerous approaches have been developed to identify optimal sites for predicting mean soil moisture. Each method has certain advantages and disadvantages, but they have rarely been evaluated and compared. In our study, surface (0-20 cm) soil moisture data from January 2013 to March 2016 (a total of 43 sampling days) were collected at 77 sampling sites on a mixed land-use (tea and bamboo) hillslope in the hilly area of Taihu Lake Basin, China. A total of 10 methods (temporal stability (TS) analyses based on 2 indices, K-means clustering based on 6 kinds of inputs and 2 random sampling strategies) were evaluated for determining optimal sampling sites for mean soil moisture estimation. They were TS analyses based on the smallest index of temporal stability (ITS, a combination of the mean relative difference and standard deviation of relative difference (SDRD)) and based on the smallest SDRD, K-means clustering based on soil properties and terrain indices (EFs), repeated soil moisture measurements (Theta), EFs plus one-time soil moisture data (EFsTheta), and the principal components derived from EFs (EFs-PCA), Theta (Theta-PCA), and EFsTheta (EFsTheta-PCA), and global and stratified random sampling strategies. Results showed that the TS based on the smallest ITS was better (RMSE = 0.023 m3 m-3) than that based on the smallest SDRD (RMSE = 0.034 m3 m-3). The K-means clustering based on EFsTheta (-PCA) was better (RMSE sampling design stratified by the land use was more efficient than the global random method. Forty and 60 sampling sites are needed for stratified sampling and global sampling respectively to make their performances comparable to the best K-means method (EFsTheta-PCA). Overall, TS required only one site, but its

  15. An Implementation Research Approach to Evaluating Health Insurance Programs: Insights from India

    Directory of Open Access Journals (Sweden)

    Krishna D. Rao

    2016-05-01

    Full Text Available One of the distinguishing features of implementation research is the importance given to involve implementers in all aspects of research, and as users of research. We report on a recent implementation research effort in India, in which researchers worked together with program implementers from one of the longest serving government funded insurance schemes in India, the Rajiv Aarogyasri Scheme (RAS in the state of undivided Andhra Pradesh, that covers around 70 million people. This paper aims to both inform on the process of the collaborative research, as well as, how the nature of questions that emerged out of the collaborative exercise differed in scope from those typically asked of insurance program evaluations. Starting in 2012, and over the course of a year, staff from the Aarogyasri Health Care Trust (AHCT, and researchers held a series of meetings to identify research questions that could serve as a guide for an evaluation of the RAS. The research questions were derived from the application of a Logical Framework Approach (“log frame” to the RAS. The types of questions that emerged from this collaborative effort were compared with those seen in the published literature on evaluations of insurance programs in low- and middle-income countries (LMICs. In the published literature, 60% of the questions pertained to output/outcome of the program and the remaining 40%, relate to processes and inputs. In contrast, questions generated from the RAS participatory research process between implementers and researchers had a remarkably different distribution – 81% of questions looked at program input/processes, and 19% on outputs and outcomes. An implementation research approach can lead to a substantively different emphasis of research questions. While there are several challenges in collaborative research between implementers and researchers, an implementation research approach can lead to incorporating tacit knowledge of program implementers

  16. Interdisciplinarity, Qualitative Research, and the Complex Phenomenon: Toward an Integrative Approach to Intercultural Research

    Science.gov (United States)

    Ryan, Phillip; Kurtz, Jill Sornsen; Carter, Deanne; Pester, Danielle

    2014-01-01

    This article is a collaboration by the lead faculty member in a Masters program in Intercultural Studies and students who completed the program under his aegis. This article presents the program's approach to its research course sequence, an approach involving the integration of interdisciplinary and qualitative research. The authors first provide…

  17. Research Methods Identifying Correlation Between Physical Environment of Schools and Educational Paradigms

    Directory of Open Access Journals (Sweden)

    Grėtė Brukštutė

    2016-04-01

    Full Text Available The article is analysing the research that was already carried out in order to determine correlation between a physical environment of schools and educational paradigms. While selecting materials for the analysis, the attention was focused on studies conducted in the USA and European countries. Based on these studies the methodological attitudes towards coherence of the education and spatial structures were tried to identify. Homogeneity and conformity of an educational character and a physical learning environment became especially important during changes of educational conceptions. The issue how educational paradigms affect the architecture of school buildings is not yet analysed in Lithuania, therefore the results of this research could actualize a theme on correlation between educational paradigms and the architecture of school buildings and form initial guidelines for the development of the modern physical learning environment.

  18. CURRENT APPROACHES FOR RESEARCH OF MULTIPLE SCLEROSIS BIOMARKERS

    Directory of Open Access Journals (Sweden)

    Kolyada T.I

    2016-12-01

    severity, progression, pathogenetic type and treatment efficacy are based on transcriptomics, proteomics and metabolomics technologies. Transcriptomics includes genome-wide research of RNA sequences based on the results obtained with comparative genomic hybridization on biochips, massive parallel RNA sequencing, and measuring the amount of mRNA by real-time PCR. This technology is actively used in studies of gene expression profile of peripheral blood mononuclear cells from MS patients aimed at identifying molecular markers of disease status suitable for clinical use. Proteomics is a large-scale expression and protein distribution studies in patients with MS based on the results obtained via microarray and mass spectrometry, liquid and gas chromatography methods. In recent years, a growing number of MS proteomic studies using 2DE-MS method (two-dimensional electrophoresis coupled with mass spectrometry. Metabolomics studies of low-molecular-weight metabolic profiles based on the results obtained by mass spectrometry, liquid and gas chromatography, nuclear magnetic resonance. However, unlike other «-omics»-technologies, in metabolomics microarray-techniques are not used. Conclusion. Search, verification and clinical application of biomarkers for multiple sclerosis are one of the most challenging medical and biological problems. Its solution requires an interdisciplinary approach, organization of large-scale research and engagement of new research methods. In recent years, a significant amount of data received allowed to reveal hundreds of candidate biomarkers. Some of these biomarkers have significant potential for the monitoring of disease activity and assessment of therapy efficiency. However, the verification is required for a widespread clinical application; it implies further large-scale studies in different countries. The development of personalized medicine in Ukraine, the application of its principles to the management of multiple sclerosis patients, along with

  19. Identifying Creatively Gifted Students: Necessity of a Multi-Method Approach

    Science.gov (United States)

    Ambrose, Laura; Machek, Greg R.

    2015-01-01

    The process of identifying students as creatively gifted provides numerous challenges for educators. Although many schools assess for creativity in identifying students for gifted and talented services, the relationship between creativity and giftedness is often not fully understood. This article reviews commonly used methods of creativity…

  20. On becoming multicultural in a monocultural research world: A conceptual approach to studying ethnocultural diversity.

    Science.gov (United States)

    Hall, Gordon C Nagayama; Yip, Tiffany; Zárate, Michael A

    2016-01-01

    Race, culture, and ethnicity are critical components of the human experience, yet they are often treated as nuisance variables or as post hoc explanations for poorly predicted results. Mandates to pay attention to ethnocultural diversity in research have largely been ignored. Here, we affirm some basic principles of multicultural psychology in conceptually grounded research. We first identify the importance of clear and conceptually guided ethnocultural research, and describe multiple perspectives in the field. The first perspective, a generalizability approach, seeks to find similarities and universalities across diverse groups. The second perspective, a group differences approach, attempts to determine the generalizability and limits to generalizability across different groups that are assumed to represent different cultures. The third perspective, multicultural psychology, involves specifying and measuring the mechanisms of cultural influences on behavior in ethnocultural groups underrepresented in research. In contrast to conventional approaches to culture that apply existing models to other groups, we propose an "inside-out" model that prizes the perspectives of those in ethnocultural communities that are underrepresented in research and places a secondary emphasis on generalizability. We follow with examples and new directions for multicultural psychology research. This approach has the potential to enhance researchers' ability to answer conceptually derived research questions and in combination with the other approaches promises to enhance the advancement of psychological science generally. (PsycINFO Database Record

  1. Scenario development as a basis for formulating a research program on future agriculture: a methodological approach.

    Science.gov (United States)

    Oborn, Ingrid; Bengtsson, Jan; Hedenus, Fredrik; Rydhmer, Lotta; Stenström, Maria; Vrede, Katarina; Westin, Charles; Magnusson, Ulf

    2013-11-01

    To increase the awareness of society to the challenges of global food security, we developed five contrasting global and European scenarios for 2050 and used these to identify important issues for future agricultural research. Using a scenario development method known as morphological analysis, scenarios were constructed that took economic, political, technical, and environmental factors into account. With the scenarios as a starting point future challenges were discussed and research issues and questions were identified in an interactive process with stakeholders and researchers. Based on the outcome of this process, six socioeconomic and biophysical overarching challenges for future agricultural were formulated and related research issues identified. The outcome was compared with research priorities generated in five other research programs. In comparison, our research questions focus more on societal values and the role of consumers in influencing agricultural production, as well as on policy formulation and resolving conflicting goals, areas that are presently under-represented in agricultural research. The partly new and more interdisciplinary research priorities identified in Future Agriculture compared to other programs analyzed are likely a result of the methodological approach used, combining scenarios and interaction between stakeholders and researchers.

  2. Myths, Artifacts, and Fatal Flaws: Identifying Limitations and Opportunities in Vitamin C Research

    Directory of Open Access Journals (Sweden)

    Alexander J. Michels

    2013-12-01

    Full Text Available Research progress to understand the role of vitamin C (ascorbic acid in human health has been slow in coming. This is predominantly the result of several flawed approaches to study design, often lacking a full appreciation of the redox chemistry and biology of ascorbic acid. In this review, we summarize our knowledge surrounding the limitations of common approaches used in vitamin C research. In human cell culture, the primary issues are the high oxygen environment, presence of redox-active transition metal ions in culture media, and the use of immortalized cell lines grown in the absence of supplemental ascorbic acid. Studies in animal models are also limited due to the presence of endogenous ascorbic acid synthesis. Despite the use of genetically altered rodent strains lacking synthesis capacity, there are additional concerns that these models do not adequately recapitulate the effects of vitamin C deprivation and supplementation observed in humans. Lastly, several flaws in study design endemic to randomized controlled trials and other human studies greatly limit their conclusions and impact. There also is anecdotal evidence of positive and negative health effects of vitamin C that are widely accepted but have not been substantiated. Only with careful attention to study design and experimental detail can we further our understanding of the possible roles of vitamin C in promoting human health and preventing or treating disease.

  3. To Be or Not to Be Associated: Power study of four statistical modeling approaches to identify parasite associations in cross-sectional studies

    Directory of Open Access Journals (Sweden)

    Elise eVaumourin

    2014-05-01

    Full Text Available A growing number of studies are reporting simultaneous infections by parasites in many different hosts. The detection of whether these parasites are significantly associated is important in medicine and epidemiology. Numerous approaches to detect associations are available, but only a few provide statistical tests. Furthermore, they generally test for an overall detection of association and do not identify which parasite is associated with which other one. Here, we developed a new approach, the association screening approach, to detect the overall and the detail of multi-parasite associations. We studied the power of this new approach and of three other known ones (i.e. the generalized chi-square, the network and the multinomial GLM approaches to identify parasite associations either due to parasite interactions or to confounding factors. We applied these four approaches to detect associations within two populations of multi-infected hosts: 1 rodents infected with Bartonella sp., Babesia microti and Anaplasma phagocytophilum and 2 bovine population infected with Theileria sp. and Babesia sp.. We found that the best power is obtained with the screening model and the generalized chi-square test. The differentiation between associations, which are due to confounding factors and parasite interactions was not possible. The screening approach significantly identified associations between Bartonella doshiae and B. microti, and between T. parva, T. mutans and T. velifera. Thus, the screening approach was relevant to test the overall presence of parasite associations and identify the parasite combinations that are significantly over- or under-represented. Unravelling whether the associations are due to real biological interactions or confounding factors should be further investigated. Nevertheless, in the age of genomics and the advent of new technologies, it is a considerable asset to speed up researches focusing on the mechanisms driving interactions

  4. Automated Research Impact Assessment: A New Bibliometrics Approach.

    Science.gov (United States)

    Drew, Christina H; Pettibone, Kristianna G; Finch, Fallis Owen; Giles, Douglas; Jordan, Paul

    2016-03-01

    As federal programs are held more accountable for their research investments, The National Institute of Environmental Health Sciences (NIEHS) has developed a new method to quantify the impact of our funded research on the scientific and broader communities. In this article we review traditional bibliometric analyses, address challenges associated with them, and describe a new bibliometric analysis method, the Automated Research Impact Assessment (ARIA). ARIA taps into a resource that has only rarely been used for bibliometric analyses: references cited in "important" research artifacts, such as policies, regulations, clinical guidelines, and expert panel reports. The approach includes new statistics that science managers can use to benchmark contributions to research by funding source. This new method provides the ability to conduct automated impact analyses of federal research that can be incorporated in program evaluations. We apply this method to several case studies to examine the impact of NIEHS funded research.

  5. Action Research – A New Approach for Environmental RD

    Directory of Open Access Journals (Sweden)

    Danubianu Mirela

    2015-05-01

    Full Text Available High efficiency research, development and innovation (RD&I constitute an answer to the ever growing importance that EU states give to knowledge-based development (a central idea in the Europe 2020 Strategy, directed toward finding comprehensive solutions to concerns connected to the Europe’s resource depletion, energy future, climate changes, etc. The "Action Research" paradigm appeared in the late 1940s but its systematic application is the attribute of recent years. It keeps researchers in the real world, requires teamwork, collaboration with communities and other stakeholders. Action Research is especially suitable in projects for reducing anthropic footprint / environmental aggression and in waste management. In essence, Action Research (for the first time systematically applied in Romania is the research approach that lets the problem studied to conduct the analysis and generate appropriate solutions; it constitutes a flexible, versatile technique to generate new knowledge through iterative interaction with the domain studied - namely the environment - researchers and communities.

  6. A Proteomic Approach to Identify Phosphorylation-Dependent Targets of BRCT Domains

    Science.gov (United States)

    2008-03-01

    targets To develop the BiFC technology for screening for BRCT- BRCA1 interacting proteins in mammalian cells, we constructed expression...domain To screen for BRCA1-BRCT interacting proteins using BiFC, we undertook several approaches. In the last report, we described a reduction approach...candidate BRCT- interacting proteins . Indeed, we obtained many cell clones that exhibited either strong or weak fluorescence, indicating that these

  7. Quantitative and Qualitative Approaches to Identifying Migration Chronology in a Continental Migrant

    OpenAIRE

    Beatty, William S.; Dylan C Kesler; Elisabeth B Webb; Andrew H Raedeke; Naylor, Luke W.; Humburg, Dale D.

    2013-01-01

    The degree to which extrinsic factors influence migration chronology in North American waterfowl has not been quantified, particularly for dabbling ducks. Previous studies have examined waterfowl migration using various methods, however, quantitative approaches to define avian migration chronology over broad spatio-temporal scales are limited, and the implications for using different approaches have not been assessed. We used movement data from 19 female adult mallards (Anas platyrhynchos) eq...

  8. Identifying regime shifts in Indian stock market: A Markov switching approach

    OpenAIRE

    Wasim, Ahmad; Bandi, Kamaiah

    2011-01-01

    Seeking for the existence of bull and bear regimes in the Indian stock market, a two state Markov switching autoregressive model (MS (2)-AR (2)) is used to identify bull and bear market regimes. The model predicts that Indian stock market will remain under bull regime with very high probability compared to bear regime. The results also identify the bear phases during all major global economic crises including recent US sub-prime (2008) and European debt crisis (2010). The paper concludes that...

  9. Public Private Partnerships: Identifying Practical Issues for an Accounting Research Agenda

    Directory of Open Access Journals (Sweden)

    Nick Sciulli

    2014-09-01

    Full Text Available This article provides a structured framework for research into the accounting implications of Public Private Partnerships (PPPs. PPPs worldwide have taken on increasing significance as a tool that governments can use to develop infrastructure and for the delivery of services. Given the minimal coverage in the literature of the Victorian State Government experience to date regarding the efficacy of PPPs, this report establishes a number of parameters from which academics can conduct research into this strategy and, moreover, make policy recommendations based on those findings. Accounting principles are used to identify whether a PPP will lead to value for money. Consequently, a model is developed to define potential areas of investigation, from which a series of research questions are posed. This is important because, public sector managers need to be aware of the failures and the success stories of particular PPP projects so that lessons can be learned from these experiences. This would inform government officials of any necessary reforms that need to be undertaken for future PPPs.

  10. Translational research-the need of a new bioethics approach.

    Science.gov (United States)

    Hostiuc, Sorin; Moldoveanu, Alin; Dascălu, Maria-Iuliana; Unnthorsson, Runar; Jóhannesson, Ómar I; Marcus, Ioan

    2016-01-15

    Translational research tries to apply findings from basic science to enhance human health and well-being. Many phases of the translational research may include non-medical tasks (information technology, engineering, nanotechnology, biochemistry, animal research, economy, sociology, psychology, politics, and so on). Using common bioethics principles to these areas might sometimes be not feasible, or even impossible. However, the whole process must respect some fundamental, moral principles. The purpose of this paper is to argument the need for a different approach to the morality in translational bioethics, and to suggest some directions that might be followed when constructing such a bioethics. We will show that a new approach is needed and present a few ethical issues that are specific to the translational research.

  11. Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Cindy

    2015-07-17

    The interactions among different microbial populations in a community could play more important roles in determining ecosystem functioning than species numbers and their abundances, but very little is known about such network interactions at a community level. The goal of this project is to develop novel framework approaches and associated software tools to characterize the network interactions in microbial communities based on high throughput, large scale high-throughput metagenomics data and apply these approaches to understand the impacts of environmental changes (e.g., climate change, contamination) on network interactions among different nitrifying populations and associated microbial communities.

  12. Identifying target groups for environmentally sustainable transport: assessment of different segmentation approaches

    DEFF Research Database (Denmark)

    Haustein, Sonja; Hunecke, Marcel

    2013-01-01

    Recently, the use of attitude-based market segmentation to promote environmentally sustainable transport has significantly increased. The segmentation of the population into meaningful groups sharing similar attitudes and preferences provides valuable information about how green measures should...... be designed and promoted in order to attract different user groups. This review highlights advances in the understanding of mode choice from a psychological perspective, taking into account behavioural theories of car use and car-use reduction. In this contribution, attitudinal, sociodemographic, geographical...... and behavioural segmentations are compared regarding marketing criteria. Although none of the different approaches can claim absolute superiority, attitudinal approaches show advantages in providing startingpoints for interventions to reduce car use....

  13. Exploring a new narrative inquiry approach: "narrative as research (nar)"

    OpenAIRE

    Young, Allan Buddy

    2012-01-01

    Narrative is an ancient practice still woven throughout our modern society in a myriad forms ranging from novels to computer games, yet the field of narrative inquiry is among the youngest of research approaches, and hence among the most swiftly evolving. This dissertation explores a newly emerging form of narrative inquiry in an education context, “Narrative as Research (NAR).” The dissertation first examines the familiar form of narrative inquiry in an education context, which draws upon st...

  14. Candidate gene linkage approach to identify DNA variants that predispose to preterm birth

    DEFF Research Database (Denmark)

    Bream, Elise N A; Leppellere, Cara R; Cooper, Margaret E;

    2013-01-01

    genes with evidence of linkage: ENPP1 (P = 0.003), IGFBP3 (P = 0.006), DHCR7 (P = 0.009), and TRAF2 (P = 0.01). DNA sequence analysis of the coding exons and splice sites for CRHR1 and TRAF2 identified no new likely etiologic variants.Conclusion:These findings suggest the involvement of six genes acting...... used. Premature infants and mothers of premature infants were defined as affected cases in independent analyses.Results:Analyses with the infant as the case identified two genes with evidence of linkage: CRHR1 (P = 0.0012) and CYP2E1 (P = 0.0011). Analyses with the mother as the case identified four...

  15. A Novel Approach to Identifying a Neuroimaging Biomarker for Patients With Serious Mental Illness.

    Science.gov (United States)

    Madan, Alok; Fowler, J Christopher; Patriquin, Michelle A; Salas, Ramiro; Baldwin, Philip R; Velasquez, Kenia M; Viswanath, Humsini; Molfese, David L; Sharp, Carla; Allen, Jon G; Hardesty, Susan; Oldham, John M; Frueh, B Christopher

    2017-02-27

    Serious mental illness (SMI) is disabling, and current interventions are ineffective for many. This exploratory study sought to demonstrate the feasibility of applying topological data analysis (TDA) to resting-state functional connectivity data obtained from a heterogeneous sample of 235 adult inpatients to identify a biomarker of treatment response. TDA identified two groups based on connectivity between the prefrontal cortex and striatal regions: patients admitted with greater functional connectivity between these regions evidenced less improvement from admission to discharge than patients with lesser connectivity between them. TDA identified a potential biomarker of an attenuated treatment response among inpatients with SMI. Insofar as the observed pattern of resting-state functional connectivity collected early during treatment is replicable, this potential biomarker may indicate the need to modify standard of care for a small, albeit meaningful, percentage of patients.

  16. A novel reverse-genetic approach (SIMF) identifies Mutator insertions in new Myb genes.

    Science.gov (United States)

    Rabinowicz, P D; Grotewold, E

    2000-11-01

    We have developed a new strategy designated SIMF (Systematic Insertional Mutagenesis of Families), to identify DNA insertions in many members of a gene family simultaneously. This method requires only a short amino acid sequence conserved in all members of the family to make a degenerate oligonucleotide, and a sequence from the end of the DNA insertion. The SIMF strategy was successfully applied to the large maize R2R3 Myb family of regulatory genes, and Mutator insertions in several novel Myb genes were identified. Application of this technique to identify insertions in other large gene families could significantly decrease the effort involved in screening at the same time for insertions in all members of groups of genes that share a limited sequence identity.

  17. Particle Swarm Based Approach of a Real-Time Discrete Neural Identifier for Linear Induction Motors

    Directory of Open Access Journals (Sweden)

    Alma Y. Alanis

    2013-01-01

    Full Text Available This paper focusses on a discrete-time neural identifier applied to a linear induction motor (LIM model, whose model is assumed to be unknown. This neural identifier is robust in presence of external and internal uncertainties. The proposed scheme is based on a discrete-time recurrent high-order neural network (RHONN trained with a novel algorithm based on extended Kalman filter (EKF and particle swarm optimization (PSO, using an online series-parallel con…figuration. Real-time results are included in order to illustrate the applicability of the proposed scheme.

  18. Numerical and Experimental Approach for Identifying Elastic Parameters in Sandwich Plates

    Directory of Open Access Journals (Sweden)

    Sergio Ferreira Bastos

    2002-01-01

    Full Text Available This article deals with the identification of elastic parameters (engineering constants in sandwich honeycomb orthotropic rectangular plates. A non-destructive method is introduced to identify the elastic parameters through the experimental measurements of natural frequencies of a plate undergoing free vibrations. Four elastic constant are identified. The estimation of the elastic parameter problem is solved by minimizing the differences between the measured and the calculated natural frequencies. The numerical method to calculate the natural frequencies involves the formulation of Rayleigh-Ritz using a series of characteristic orthogonal polynomials to properly model the free edge boundary conditions. The analysis of the results indicates the efficiency of the method.

  19. Applying the community partnership approach to human biology research.

    Science.gov (United States)

    Ravenscroft, Julia; Schell, Lawrence M; Cole, Tewentahawih'tha'

    2015-01-01

    Contemporary human biology research employs a unique skillset for biocultural analysis. This skillset is highly appropriate for the study of health disparities because disparities result from the interaction of social and biological factors over one or more generations. Health disparities research almost always involves disadvantaged communities owing to the relationship between social position and health in stratified societies. Successful research with disadvantaged communities involves a specific approach, the community partnership model, which creates a relationship beneficial for researcher and community. Paramount is the need for trust between partners. With trust established, partners share research goals, agree on research methods and produce results of interest and importance to all partners. Results are shared with the community as they are developed; community partners also provide input on analyses and interpretation of findings. This article describes a partnership-based, 20 year relationship between community members of the Akwesasne Mohawk Nation and researchers at the University at Albany. As with many communities facing health disparity issues, research with Native Americans and indigenous peoples generally is inherently politicized. For Akwesasne, the contamination of their lands and waters is an environmental justice issue in which the community has faced unequal exposure to, and harm by environmental toxicants. As human biologists engage in more partnership-type research, it is important to understand the long term goals of the community and what is at stake so the research circle can be closed and 'helicopter' style research avoided.

  20. Applying Hybrid Heuristic Approach to Identify Contaminant Source Information in Transient Groundwater Flow Systems

    Directory of Open Access Journals (Sweden)

    Hund-Der Yeh

    2014-01-01

    Full Text Available Simultaneous identification of the source location and release history in aquifers is complicated and time-consuming if the release of groundwater contaminant source varies in time. This paper presents an approach called SATSO-GWT to solve complicated source release problems which contain the unknowns of three location coordinates and several irregular release periods and concentrations. The SATSO-GWT combines with ordinal optimization algorithm (OOA, roulette wheel approach, and a source identification algorithm called SATS-GWT. The SATS-GWT was developed based on simulated annealing, tabu search, and three-dimensional groundwater flow and solute transport model MD2K-GWT. The OOA and roulette wheel method are utilized mainly to reduce the size of feasible solution domain and accelerate the identification of the source information. A hypothetic site with one contaminant source location and two release periods is designed to assess the applicability of the present approach. The results indicate that the performance of SATSO-GWT is superior to that of SATS-GWT. In addition, the present approach works very effectively in dealing with the cases which have different initial guesses of source location and measurement errors in the monitoring points as well as problems with large suspicious areas and several source release periods and concentrations.

  1. Protocol for a thematic synthesis to identify key themes and messages from a palliative care research network.

    LENUS (Irish Health Repository)

    Nicholson, Emma

    2016-10-21

    Research networks that facilitate collaborative research are increasing both regionally and globally and such collaborations contribute greatly to knowledge transfer particularly in health research. The Palliative Care Research Network is an Irish-based network that seeks to create opportunities and engender a collaborative environment to encourage innovative research that is relevant for policy and practice. The current review outlines a methodology to identify cross-cutting messages to identify how dissemination outputs can be optimized to ensure that key messages from this research reaches all knowledge users.

  2. The basis for improving and reforming long-term care. Part 4: identifying meaningful improvement approaches (segment 2).

    Science.gov (United States)

    Levenson, Steven A

    2010-03-01

    While many aspects of nursing home care have improved over time, numerous issues persist. Presently, a potpourri of approaches and a push to "fix" the problem have overshadowed efforts to correctly define the problems and identify their diverse causes. This fourth and final article in the series (divided between last month's issue and this one) recommends strategies to make sense of improvement and reform efforts. This month's concluding segment covers additional proposed approaches. Despite the challenges of the current environment, all of the proposed strategies could potentially be applied with little or no delay. Despite having brought vast increases in knowledge, the research effort may be losing its traction as a formidable force for meaningful change. It is necessary to rethink the questions being asked and the scope of answers being sought. A shift to overcoming implementation challenges is needed. In addition, it is essential to address issues of jurisdiction (the apparent "ownership" of assessment and decision making over patient problems or body parts) and reductionism (the excessive management of these issues and problems without proper context) that result in fragmented and problematic care. Issues of knowledge and skill also need to be addressed, with greater emphasis on key generic and technical competencies of staff and practitioners, in addition to factual knowledge. There is a need to rethink the approach to measuring performance and trying to improve quality of care and services. There are significant limits to trying to use quality measures to improve outcomes and performance. Ultimately, vast improvement is needed in applying care principles and practices, independent of regulatory sources. Reimbursement needs to be revamped so that it helps promote care that is consistent with human biology and other key concepts. Finally, improving long-term care will require a coordinated societal effort. All social institutions and health care settings need

  3. Combining phenotypic and proteomic approaches to identify membrane targets in a ‘triple negative’ breast cancer cell type

    Directory of Open Access Journals (Sweden)

    Rust Steven

    2013-02-01

    Full Text Available Abstract Background The continued discovery of therapeutic antibodies, which address unmet medical needs, requires the continued discovery of tractable antibody targets. Multiple protein-level target discovery approaches are available and these can be used in combination to extensively survey relevant cell membranomes. In this study, the MDA-MB-231 cell line was selected for membranome survey as it is a ‘triple negative’ breast cancer cell line, which represents a cancer subtype that is aggressive and has few treatment options. Methods The MDA-MB-231 breast carcinoma cell line was used to explore three membranome target discovery approaches, which were used in parallel to cross-validate the significance of identified antigens. A proteomic approach, which used membrane protein enrichment followed by protein identification by mass spectrometry, was used alongside two phenotypic antibody screening approaches. The first phenotypic screening approach was based on hybridoma technology and the second was based on phage display technology. Antibodies isolated by the phenotypic approaches were tested for cell specificity as well as internalisation and the targets identified were compared to each other as well as those identified by the proteomic approach. An anti-CD73 antibody derived from the phage display-based phenotypic approach was tested for binding to other ‘triple negative’ breast cancer cell lines and tested for tumour growth inhibitory activity in a MDA-MB-231 xenograft model. Results All of the approaches identified multiple cell surface markers, including integrins, CD44, EGFR, CD71, galectin-3, CD73 and BCAM, some of which had been previously confirmed as being tractable to antibody therapy. In total, 40 cell surface markers were identified for further study. In addition to cell surface marker identification, the phenotypic antibody screening approaches provided reagent antibodies for target validation studies. This is illustrated

  4. Constructing New Theory for Identifying Students with Emotional Disturbance: A Grounded Theory Approach

    Science.gov (United States)

    Barnett, Dori A.

    2010-01-01

    The problem area explored by this study is the identification of students with emotional and behavioral difficulties for special education supports and services under the criteria for emotional disturbance (ED). A review of the literature indicated that the problem of identifying students with ED was compounded by subjectivity and ambiguity…

  5. A library screening approach identifies naturally occurring RNA sequences for a G-quadruplex binding ligand.

    Science.gov (United States)

    Mirihana Arachchilage, Gayan; Morris, Mark J; Basu, Soumitra

    2014-02-07

    An RNA G-quadruplex library was synthesised and screened against kanamycin A as the ligand. Naturally occurring G-quadruplex forming sequences that differentially bind to kanamycin A were identified and characterized. This provides a simple and effective strategy for identification of potential intracellular G-quadruplex targets for a ligand.

  6. Enhanced approaches for identifying Amadori products:application to peanut allergens

    Science.gov (United States)

    The dry roasting of peanuts is suggested to influence allergenic sensitization due to formation of advanced glycation end products (AGE) on peanut proteins. Identifying AGEs is technically challenging. The AGE composition of peanut proteins was probed with nanoLC-ESI-MS and MS/MS analyses. Amadori ...

  7. A complementary bioinformatics approach to identify potential plant cell wall glycosytransferase encoding genes

    DEFF Research Database (Denmark)

    Egelund, Jack; Skjøt, Michael; Geshi, Naomi;

    2004-01-01

    . Although much is known with regard to composition and fine structures of the plant CW, only a handful of CW biosynthetic GT genes-all classified in the CAZy system-have been characterized. In an effort to identify CW GTs that have not yet been classified in the CAZy database, a simple bioinformatics...

  8. Thermal management in heavy vehicles : a review identifying issues and research requirements.

    Energy Technology Data Exchange (ETDEWEB)

    Wambsganss, M. W.

    1999-01-15

    Thermal management in heavy vehicles is cross-cutting because it directly or indirectly affects engine performance, fuel economy, safety and reliability, engine/component life, driver comfort, materials selection, emissions, maintenance, and aerodynamics. It follows that thermal management is critical to the design of large (class 6-8) trucks, especially in optimizing for energy efficiency and emissions reduction. Heat rejection requirements are expected to increase, and it is industry's goal to develop new, innovative, high-performance cooling systems that occupy less space and are lightweight and cost-competitive. The state of the art in heavy vehicle thermal management is reviewed, and issues and research areas are identified.

  9. Concept for linking de-identified biomedical research data using a study participant management system.

    Science.gov (United States)

    Stahmann, Alexander; Bauer, Christian R K D; Schwanke, Jens

    2014-01-01

    Biomedical research projects show an increasing demand of large numbers of participants from different recruiting centers to achieve statistically significant results. The collected types of data are stored in distributed databases and are linked to the participant by different non-resolvable identifiers (layered pseudonyms) for de-identification. To ensure the quality of the gathered data, regular quality assurance analyses are required at each local center. Because of the distributed databases and layered pseudonyms the analyses can only be achieved manually. Therefore, the process is error-prone and laborious. The objective of this paper is to propose a solution concept to automate the manual process by using a local study participant management system. It orchestrates the process and enables the quality assurance analyses within a clinical data warehouse.

  10. Managing Cybersecurity Research and Experimental Development: The REVO Approach

    Directory of Open Access Journals (Sweden)

    Dan Craigen

    2013-07-01

    Full Text Available We present a systematic approach for managing a research and experimental development cybersecurity program that must be responsive to continuously evolving cybersecurity, and other, operational concerns. The approach will be of interest to research-program managers, academe, corporate leads, government leads, chief information officers, chief technology officers, and social and technology policy analysts. The approach is compatible with international standards and procedures published by the Organisation for Economic Co-operation and Development (OECD and the Treasury Board of Canada Secretariat (TBS. The key benefits of the approach are the following: i the breadth of the overall (cybersecurity space is described; ii depth statements about specific (cybersecurity challenges are articulated and mapped to the breadth of the problem; iii specific (cybersecurity initiatives that have been resourced through funding or personnel are tracked and linked to specific challenges; and iv progress is assessed through key performance indicators. Although we present examples from cybersecurity, the method may be transferred to other domains. We have found the approach to be rigorous yet adaptive to change; it challenges an organization to be explicit about the nature of its research and experimental development in a manner that fosters alignment with evolving business priorities, knowledge transfer, and partner engagement.

  11. Research Student and Supervisor. An Approach to Good Supervisory Practice.

    Science.gov (United States)

    Council of Graduate Schools in the U.S., Washington, DC.

    The lack of a planned, disciplined, and well-supervised approach to research which frustrates a student's timely completion of a Ph.D. program is addressed. Some practices are discussed which, if adopted, could lead many more students to complete their Ph.D. expeditiously. A framework is presented that is intended to help the student and the…

  12. Capitalising on multiplicity: an transdisciplinary systems approach to landscape research

    NARCIS (Netherlands)

    Tress, B.; Tress, G.

    2001-01-01

    Different disciplines have landscape as the focal point of their research. They are successful in presenting new findings about landscapes within their specialization, but collaboration - and thus, transfer of knowledge across disciplinary boundaries - is seldom realized because a common approach th

  13. FEATURES OF AN ECONOMIC APPROACH AT RESEARCH OF CORRUPTION PHENOMENON

    Directory of Open Access Journals (Sweden)

    M.O. Izotov

    2012-08-01

    Full Text Available In article features of an economic approach are considered when developing the anti-corruption measures directed on restriction of possibilities of any discretion and excessive intervention of civil servants in economic activity, including through differentiation of functions and specification of competences. The special urgency of researches of a problem of corruption as special social phenomenon is noted.

  14. A Learning Progressions Approach to Early Algebra Research and Practice

    Science.gov (United States)

    Fonger, Nicole L.; Stephens, Ana; Blanton, Maria; Knuth, Eric

    2015-01-01

    We detail a learning progressions approach to early algebra research and how existing work around learning progressions and trajectories in mathematics and science education has informed our development of a four-component theoretical framework consisting of: a curricular progression of learning goals across big algebraic ideas; an instructional…

  15. Medical Researchers' Ancillary Care Obligations: The Relationship-Based Approach.

    Science.gov (United States)

    Olson, Nate W

    2016-06-01

    In this article, I provide a new account of the basis of medical researchers' ancillary care obligations. Ancillary care in medical research, or medical care that research participants need but that is not required for the validity or safety of a study or to redress research injuries, is a topic that has drawn increasing attention in research ethics over the last ten years. My view, the relationship-based approach, improves on the main existing theory, Richardson and Belsky's 'partial-entrustment model', by avoiding its problematic restriction on the scope of health needs for which researchers could be obligated to provide ancillary care. Instead, it grounds ancillary care obligations in a wide range of morally relevant features of the researcher-participant relationship, including the level of engagement between researchers and participants, and weighs these factors against each other. I argue that the level of engagement, that is, the duration and intensity of interactions, between researchers and participants matters for ancillary care because of its connection to the meaningfulness of a relationship, and I suggest that other morally relevant features can be grounded in researchers' role obligations.

  16. NASA Research For Instrument Approaches To Closely Spaced Parallel Runways

    Science.gov (United States)

    Elliott, Dawn M.; Perry, R. Brad

    2000-01-01

    Within the NASA Aviation Systems Capacity Program, the Terminal Area Productivity (TAP) Project is addressing airport capacity enhancements during instrument meteorological condition (IMC). The Airborne Information for Lateral Spacing (AILS) research within TAP has focused on an airborne centered approach for independent instrument approaches to closely spaced parallel runways using Differential Global Positioning System (DGPS) and Automatic Dependent Surveillance-Broadcast (ADS-B) technologies. NASA Langley Research Center (LaRC), working in partnership with Honeywell, Inc., completed in AILS simulation study, flight test, and demonstration in 1999 examining normal approaches and potential collision scenarios to runways with separation distances of 3,400 and 2,500 feet. The results of the flight test and demonstration validate the simulation study.

  17. Case Studies Approach in Tourism Destination Branding Research

    Directory of Open Access Journals (Sweden)

    Adeyinka-Ojo S.F.

    2014-01-01

    Full Text Available A review of literature indicates that there are different types of qualitative research methods such as action research, content analysis, ethnography, grounded theory, historical analysis, phenomenology and case study. However, which approach is to be used depends on several factors such as the nature and objectives of the research. The aim of this paper is to focus on the research methodology aspects of applying case study as a research approach and its relevance in tourism destination branding research specifically on a single case study (SCS context. There are arguments that the SCS is a weak research strategy. Some of the potentials or shortcomings highlighted in the literature include the primitive nature of SCS, flexibility of sample technique, data collection method and data analysis. Others include lack of rigour, reliability, validity, credibility of findings and generalisation. This paper has adopted content analysis of the literature on tourism destination branding. Findings indicate that the quality of SCS can be verified using specific case study tactics for four design tests such as validity (construct, internal and external; and reliability using the case study protocol. Theoretical implication suggests that SCS is an empirical enquiry use to understand complex phenomena and favoured by practitioners.

  18. Identifying functional modules in protein-protein interaction networks: An integrated exact approach

    NARCIS (Netherlands)

    Dittrich, M.; Klau, G.W.; Rosenwald, A.; Dandekar, T.; et al, not CWI

    2008-01-01

    Motivation: With the exponential growth of expression and protein-protein interaction (PPI) data, the frontier of research in system biology shifts more and more to the integrated analysis of these large datasets. Of particular interest is the identification of functional modules in PPI networks, sh

  19. An Achievement Degree Analysis Approach to Identifying Learning Problems in Object-Oriented Programming

    Science.gov (United States)

    Allinjawi, Arwa A.; Al-Nuaim, Hana A.; Krause, Paul

    2014-01-01

    Students often face difficulties while learning object-oriented programming (OOP) concepts. Many papers have presented various assessment methods for diagnosing learning problems to improve the teaching of programming in computer science (CS) higher education. The research presented in this article illustrates that although max-min composition is…

  20. Identifying a Core Set of Science Teaching Practices: A Delphi Expert Panel Approach

    Science.gov (United States)

    Kloser, Matthew

    2014-01-01

    The "Framework for K-12 Science Education" details ambitious goals for students' learning of science content and practices. However, this document provides science teachers little guidance about instructional practices that are central to helping students achieve these goals. Research indicates that a teacher's instructional…

  1. A DNA barcoding approach to identify plant species in multiflower honey.

    Science.gov (United States)

    Bruni, I; Galimberti, A; Caridi, L; Scaccabarozzi, D; De Mattia, F; Casiraghi, M; Labra, M

    2015-03-01

    The purpose of this study was to test the ability of DNA barcoding to identify the plant origins of processed honey. Four multifloral honeys produced at different sites in a floristically rich area in the northern Italian Alps were examined by using the rbcL and trnH-psbA plastid regions as barcode markers. An extensive reference database of barcode sequences was generated for the local flora to determine the taxonomic composition of honey. Thirty-nine plant species were identified in the four honey samples, each of which originated from a mix of common plants belonging to Castanea, Quercus, Fagus and several herbaceous taxa. Interestingly, at least one endemic plant was found in all four honey samples, providing a clear signature for the geographic identity of these products. DNA of the toxic plant Atropa belladonna was detected in one sample, illustrating the usefulness of DNA barcoding for evaluating the safety of honey.

  2. A systems genetics approach identifies genes and pathways for type 2 diabetes in human islets

    DEFF Research Database (Denmark)

    Taneera, Jalal; Lang, Stefan; Sharma, Amitabh;

    2012-01-01

    Close to 50 genetic loci have been associated with type 2 diabetes (T2D), but they explain only 15% of the heritability. In an attempt to identify additional T2D genes, we analyzed global gene expression in human islets from 63 donors. Using 48 genes located near T2D risk variants, we identified...... gene coexpression and protein-protein interaction networks that were strongly associated with islet insulin secretion and HbA(1c). We integrated our data to form a rank list of putative T2D genes, of which CHL1, LRFN2, RASGRP1, and PPM1K were validated in INS-1 cells to influence insulin secretion...... of genes potentially involved in T2D....

  3. Comparison of four molecular approaches to identify Candida parapsilosis complex species

    Science.gov (United States)

    Barbedo, Leonardo Silva; Figueiredo-Carvalho, Maria Helena Galdino; Muniz, Mauro de Medeiros; Zancopé-Oliveira, Rosely Maria

    2017-01-01

    Since the description of Candida orthopsilosis and C. metapsilosis in 2005, several methods have been proposed to identify and differentiate these species from C. parapsilosis sensu stricto. Species-specific uniplex polymerase chain reaction (PCR) was performed and compared with sequencing of the D1/D2 region of the LSU 28S rDNA gene, microsatellite typing of C. parapsilosis sensu stricto, and PCR-restriction fragment length polymorphism patterns in the ITS1-5.8S-ITS2 region of the rDNA gene. There was agreement between results of testing of 98 clinical isolates with the four PCR-based methods, with 59 isolates identified as C. parapsilosis sensu stricto, 37 as C. orthopsilosis, and two as C. metapsilosis. PMID:28225905

  4. Astronomy and big data a data clustering approach to identifying uncertain galaxy morphology

    CERN Document Server

    Edwards, Kieran Jay

    2014-01-01

    With the onset of massive cosmological data collection through media such as the Sloan Digital Sky Survey (SDSS), galaxy classification has been accomplished for the most part with the help of citizen science communities like Galaxy Zoo. Seeking the wisdom of the crowd for such Big Data processing has proved extremely beneficial. However, an analysis of one of the Galaxy Zoo morphological classification data sets has shown that a significant majority of all classified galaxies are labelled as “Uncertain”. This book reports on how to use data mining, more specifically clustering, to identify galaxies that the public has shown some degree of uncertainty for as to whether they belong to one morphology type or another. The book shows the importance of transitions between different data mining techniques in an insightful workflow. It demonstrates that Clustering enables to identify discriminating features in the analysed data sets, adopting a novel feature selection algorithms called Incremental Feature Select...

  5. Knowledge-Assisted Approach to Identify Pathways with Differential Dependencies | Office of Cancer Genomics

    Science.gov (United States)

    We have previously developed a statistical method to identify gene sets enriched with condition-specific genetic dependencies. The method constructs gene dependency networks from bootstrapped samples in one condition and computes the divergence between distributions of network likelihood scores from different conditions. It was shown to be capable of sensitive and specific identification of pathways with phenotype-specific dysregulation, i.e., rewiring of dependencies between genes in different conditions.

  6. A proteomic approach to identify proteins from Trichuris trichiura extract with immunomodulatory effects.

    Science.gov (United States)

    Santos, L N; Gallo, M B C; Silva, E S; Figueiredo, C A V; Cooper, P J; Barreto, M L; Loureiro, S; Pontes-de-Carvalho, L C; Alcantara-Neves, N M

    2013-01-01

    Infections with Trichuris trichiura and other trichurid nematodes have been reported to display protective effects against atopy, allergic and autoimmune diseases. The aims of the present study were to investigate the immunomodulatory properties of T. trichiura adult worm extract (TtE) and its fractions (TtEFs) on the production of cytokines by peripheral blood mononuclear cells and to identify their proteinaceous components. Fourteen TtEFs were obtained by ion exchange chromatography and tested for effects on cytokine production by peripheral blood mononuclear cells. The molecular constituents of the six most active fractions were evaluated using nano-LC/mass spectrometry. The homology between T. trichiura and the related nematode Trichinella spiralis was used to identify 12 proteins in TtEFs. Among those identified, fructose biphosphate aldolase, a homologue of macrophage migration inhibitory factor and heat-shock protein 70 may contribute to the immunomodulatory effects of TtEFs. The identification of such proteins could lead to the development of novel drugs for the therapy of allergic and other inflammatory diseases.

  7. A target based approach identifies genomic predictors of breast cancer patient response to chemotherapy

    Directory of Open Access Journals (Sweden)

    Hallett Robin M

    2012-05-01

    Full Text Available Abstract Background The efficacy of chemotherapy regimens in breast cancer patients is variable and unpredictable. Whether individual patients either achieve long-term remission or suffer recurrence after therapy may be dictated by intrinsic properties of their breast tumors including genetic lesions and consequent aberrant transcriptional programs. Global gene expression profiling provides a powerful tool to identify such tumor-intrinsic transcriptional programs, whose analyses provide insight into the underlying biology of individual patient tumors. For example, multi-gene expression signatures have been identified that can predict the likelihood of disease reccurrence, and thus guide patient prognosis. Whereas such prognostic signatures are being introduced in the clinical setting, similar signatures that predict sensitivity or resistance to chemotherapy are not currently clinically available. Methods We used gene expression profiling to identify genes that were co-expressed with genes whose transcripts encode the protein targets of commonly used chemotherapeutic agents. Results Here, we present target based expression indices that predict breast tumor response to anthracycline and taxane based chemotherapy. Indeed, these signatures were independently predictive of chemotherapy response after adjusting for standard clinic-pathological variables such as age, grade, and estrogen receptor status in a cohort of 488 breast cancer patients treated with adriamycin and taxotere/taxol. Conclusions Importantly, our findings suggest the practicality of developing target based indices that predict response to therapeutics, as well as highlight the possibility of using gene signatures to guide the use of chemotherapy during treatment of breast cancer patients.

  8. A New Approach to Identifying the Most Powerful Gravitational Lensing Telescopes

    CERN Document Server

    Wong, Kenneth C; Ammons, S Mark; Keeton, Charles R; Hogg, David W; Gonzalez, Anthony H

    2013-01-01

    The best gravitational lenses for detecting distant galaxies are those with the largest mass concentrations and the most advantageous configurations of that mass along the line of sight. Our new method for finding such gravitational telescopes uses optical data to identify projected concentrations of luminous red galaxies (LRGs). LRGs are biased tracers of the underlying mass distribution, so lines of sight with the highest total luminosity in LRGs are likely to contain the largest total mass. We apply this selection technique to the Sloan Digital Sky Survey and identify the 200 fields with the highest total LRG luminosities projected within a 3.5' radius over the redshift range 0.1 < z < 0.7. The redshift and angular distributions of LRGs in these fields trace the concentrations of non-LRG galaxies. These fields are diverse; 22.5% contain one known galaxy cluster and 56% contain multiple known clusters previously identified in the literature. Thus, our results confirm that these LRGs trace massive stru...

  9. Stress and inflammation: a biobehavioral approach for nursing research.

    Science.gov (United States)

    Kang, Duck-Hee; Rice, Marti; Park, Na-Jin; Turner-Henson, Anne; Downs, Charles

    2010-10-01

    Despite known advantages, the use of biobehavioral approaches in nursing research remains limited. The purposes of this article are to (1) present applications of stress and inflammation in various health conditions as examples of biobehavioral concepts and (2) stimulate similar applications of biobehavioral concepts in future nursing research. Under a biobehavioral conceptual framework, studies on stress and selective inflammatory biomarkers in cardiovascular, cancer, and pulmonary health are reviewed and summarized. Inflammation underlies many diseases, and stress is a significant source of increased inflammation. Biobehavioral concepts of stress and inflammation are highly relevant to nursing research concerned with health-related issues. Diverse biobehavioral concepts are readily applicable and should be utilized in nursing research with children and adults. To stimulate further biobehavioral research, more training and resources for nurse scientists, more unified conceptual definitions and biobehavioral conceptual frameworks, rigorous and expanded methodologies, and more collaboration are essential.

  10. Constructive Synergy in Design Science Research: A Comparative Analysis of Design Science Research and the Constructive Research Approach

    DEFF Research Database (Denmark)

    Piirainen, Kalle; Gonzalez, Rafael A.

    2014-01-01

    Information systems research is focused on creating knowledge which can be applied in organizations. Design science research, which specifically aims at applying existing knowledge to solve interesting and relevant business problems, has been steadily gaining support in information systems research....... However, design science research is not the only design-oriented research framework available. Accordingly, this raises the question of whether there is something to learn between the different approaches. This paper contributes to answering this question by comparing design science research...... with the constructive research approach. The conclusion is that the two approaches are similar and compatible, save for details in practical requirements and partly underlying philosophical assumptions. The main finding that arises from the comparison is, however, that there is a potential problem in claiming knowledge...

  11. Supervisors’ approaches to supervision and how these relate to conceptions of research

    DEFF Research Database (Denmark)

    Kobayashi, Sofie

    how supervision is different or similar to research. Møller Madsen and Winsløw (2009) have investigated researchers' understanding of relations between research and teaching in two disciplines: Mathematics and Physical Geography using Chevallard's anthropological theory of didactics (Chevallard 2006...... of research have also been studied by various authors (e.g. Kiley and Mullins 2005), leading to discipline-neutral conceptual frameworks. Supervisors can use these frameworks in their communication about research with students as a common conceptual language to avoid miscommunication. To my knowledge we...... are short of empirical studies that can shed light on the relations between supervisors' conceptions of research and their approaches to supervision. This work which lies in the research-teaching nexus arena of doctoral supervision has the potential to provide new insights into supervision by identifying...

  12. Toward an integrated approach to nutritional quality, environmental sustainability, and economic viability: research and measurement gaps.

    Science.gov (United States)

    Herforth, Anna; Frongillo, Edward A; Sassi, Franco; Mclean, Mireille Seneclauze; Arabi, Mandana; Tirado, Cristina; Remans, Roseline; Mantilla, Gilma; Thomson, Madeleine; Pingali, Prabhu

    2014-12-01

    Nutrition is affected by numerous environmental and societal causes. This paper starts with a simple framework based on three domains: nutritional quality, economic viability, and environmental sustainability, and calls for an integrated approach in research to simultaneously account for all three. It highlights limitations in the current understanding of each domain, and how they influence one another. Five research topics are identified: measuring the three domains (nutritional quality, economic viability, environmental sustainability); modeling across disciplines; furthering the analysis of food systems in relation to the three domains; connecting climate change and variability to nutritional quality; and increasing attention to inequities among population groups in relation to the three domains. For an integrated approach to be developed, there is a need to identify and disseminate available metrics, modeling techniques, and tools to researchers, practitioners, and policy makers. This is a first step so that a systems approach that takes into account potential environmental and economic trade-offs becomes the norm in analyzing nutrition and food-security patterns. Such an approach will help fill critical knowledge gaps and will guide researchers seeking to define and address specific research questions in nutrition in their wider socioeconomic and environmental contexts.

  13. Exome-first approach identified a novel gloss deletion associated with Lowe syndrome.

    Science.gov (United States)

    Watanabe, Miki; Nakagawa, Ryuji; Kohmoto, Tomohiro; Naruto, Takuya; Suga, Ken-Ichi; Goji, Aya; Horikawa, Hideaki; Masuda, Kiyoshi; Kagami, Shoji; Imoto, Issei

    2016-01-01

    Lowe syndrome (LS) is an X-linked disorder affecting the eyes, nervous system and kidneys, typically caused by missense or nonsense/frameshift OCRL mutations. We report a 6-month-old male clinically suspected to have LS, but without the Fanconi-type renal dysfunction. Using a targeted-exome sequencing-first approach, LS was diagnosed by the identification of a deletion involving 1.7 Mb at Xq25-q26.1, encompassing the entire OCRL gene and neighboring loci.

  14. A competence approach to adult continuing education for identify and classifying living organisms

    Directory of Open Access Journals (Sweden)

    Julio César Rifa Téllez

    2015-09-01

    Full Text Available A competence approach to the systematic identification and classification of vegetal organisms is described in connection with the training of Biology professors for integrating citizens’ attitude to plants, with strictly professional methods. Several theoretical methods were used to construct a general framework together with the application of surveys to experts. The findings include three units of competence together with its components, essential knowledge and performance indicators; patterns of achievement were set in three levels: 1 empirical distinction of the phytodiversity; 2 characterization in the context of wise range use and 3 systematization of systematic botany contents involved in leading the educational process characterized by protagonist strategic actions in management.

  15. Application of a PCR-based approach to identify sex in Hawaiian honeycreepers (Drepanidinae)

    Science.gov (United States)

    Jarvi, S.I.; Banko, P.C.

    2000-01-01

    The application of molecular techniques to conservation genetics issues can provide important guidance criteria for management of endangered species. The results from this study establish that PCR-based approaches for sex determination developed in other bird species (Griffiths and Tiwari 1995; Griffiths et al. 1996, 1998; Ellegren 1996) can be applied with a high degree of confidence to at least four species of Hawaiian honeycreepers. This provides a rapid, reliable method with which population managers can optimize sex ratios within populations of endangered species that are subject to artificial manipulation through captive breeding programmes or geographic translocation.

  16. A stable isotope approach and its application for identifying nitrate source and transformation process in water.

    Science.gov (United States)

    Xu, Shiguo; Kang, Pingping; Sun, Ya

    2016-01-01

    Nitrate contamination of water is a worldwide environmental problem. Recent studies have demonstrated that the nitrogen (N) and oxygen (O) isotopes of nitrate (NO3(-)) can be used to trace nitrogen dynamics including identifying nitrate sources and nitrogen transformation processes. This paper analyzes the current state of identifying nitrate sources and nitrogen transformation processes using N and O isotopes of nitrate. With regard to nitrate sources, δ(15)N-NO3(-) and δ(18)O-NO3(-) values typically vary between sources, allowing the sources to be isotopically fingerprinted. δ(15)N-NO3(-) is often effective at tracing NO(-)3 sources from areas with different land use. δ(18)O-NO3(-) is more useful to identify NO3(-) from atmospheric sources. Isotopic data can be combined with statistical mixing models to quantify the relative contributions of NO3(-) from multiple delineated sources. With regard to N transformation processes, N and O isotopes of nitrate can be used to decipher the degree of nitrogen transformation by such processes as nitrification, assimilation, and denitrification. In some cases, however, isotopic fractionation may alter the isotopic fingerprint associated with the delineated NO3(-) source(s). This problem may be addressed by combining the N and O isotopic data with other types of, including the concentration of selected conservative elements, e.g., chloride (Cl(-)), boron isotope (δ(11)B), and sulfur isotope (δ(35)S) data. Future studies should focus on improving stable isotope mixing models and furthering our understanding of isotopic fractionation by conducting laboratory and field experiments in different environments.

  17. Validation of a Non-Targeted LC-MS Approach for Identifying Ancient Proteins: Method Development on Bone to Improve Artifact Residue Analysis

    Directory of Open Access Journals (Sweden)

    Andrew Barker

    2015-09-01

    Full Text Available Identification of protein residues from prehistoric cooking pottery using mass spectrometry is challenging because proteins are removed from original tissues, are degraded from cooking, may be poorly preserved due to diagenesis, and occur in a palimpsest of exogenous soil proteins. In contrast, bone proteins are abundant and well preserved. This research is part of a larger method-development project for innovation and improvement of liquid chromatography – mass spectrometry analysis of protein residues from cooking pottery; here we validate the potential of our extraction and characterization approach via application to ancient bone proteins. Because of its preservation potential for proteins and given that our approach is destructive, ancient bone identified via skeletal morphology represents an appropriate verification target. Proteins were identified from zooarchaeological turkey (Meleagris gallopavo Linnaeus Phasianidae, rabbit (Lagomorpha, and squirrel (Sciuridae remains excavated from ancient pueblo archaeological sites in southwestern Colorado using a non-targeted LC-MS/MS approach. The data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD002440. Improvement of highly sensitive targeted LC-MS/MS approaches is an avenue for future method development related to the study of protein residues from artifacts such as stone tools and pottery.

  18. Metabolomics: a novel approach to identify potential diagnostic biomarkers and pathogenesis in Alzheimer's disease

    Institute of Scientific and Technical Information of China (English)

    Xu-Hua Xu; Yue Huang; Gang Wang; Sheng-Di Chen

    2012-01-01

    Although the pathogenesis of Alzheimer's disease (AD) is still not fully understood,it is acknowledged that intervention should be made at the early stage.Therefore,identifying biomarkers for the clinical diagnosis is critical.Metabolomics,a novel "omics",uses methods based on low-molecular-weight molecules,with high-throughput evaluation of a large number of metabolites that may lead to the identification of new disease-specific biomarkers and the elucidation of pathophysiological mechanisms.This review discusses metabolomics investigations of AD and potential future developments in this field.

  19. A Data Mining Approach to Identify Sexuality Patterns in a Brazilian University Population.

    Science.gov (United States)

    Waleska Simões, Priscyla; Cesconetto, Samuel; Toniazzo de Abreu, Larissa Letieli; Côrtes de Mattos Garcia, Merisandra; Cassettari Junior, José Márcio; Comunello, Eros; Bisognin Ceretta, Luciane; Aparecida Manenti, Sandra

    2015-01-01

    This paper presents the profile and experience of sexuality generated from a data mining classification task. We used a database about sexuality and gender violence performed on a university population in southern Brazil. The data mining task identified two relationships between the variables, which enabled the distinction of subgroups that better detail the profile and experience of sexuality. The identification of the relationships between the variables define behavioral models and factors of risk that will help define the algorithms being implemented in the data mining classification task.

  20. Identifying patterns in treatment response profiles in acute bipolar mania: a cluster analysis approach

    Directory of Open Access Journals (Sweden)

    Houston John P

    2008-07-01

    Full Text Available Abstract Background Patients with acute mania respond differentially to treatment and, in many cases, fail to obtain or sustain symptom remission. The objective of this exploratory analysis was to characterize response in bipolar disorder by identifying groups of patients with similar manic symptom response profiles. Methods Patients (n = 222 were selected from a randomized, double-blind study of treatment with olanzapine or divalproex in bipolar I disorder, manic or mixed episode, with or without psychotic features. Hierarchical clustering based on Ward's distance was used to identify groups of patients based on Young-Mania Rating Scale (YMRS total scores at each of 5 assessments over 7 weeks. Logistic regression was used to identify baseline predictors for clusters of interest. Results Four distinct clusters of patients were identified: Cluster 1 (n = 64: patients did not maintain a response (YMRS total scores ≤ 12; Cluster 2 (n = 92: patients responded rapidly (within less than a week and response was maintained; Cluster 3 (n = 36: patients responded rapidly but relapsed soon afterwards (YMRS ≥ 15; Cluster 4 (n = 30: patients responded slowly (≥ 2 weeks and response was maintained. Predictive models using baseline variables found YMRS Item 10 (Appearance, and psychosis to be significant predictors for Clusters 1 and 4 vs. Clusters 2 and 3, but none of the baseline characteristics allowed discriminating between Clusters 1 vs. 4. Experiencing a mixed episode at baseline predicted membership in Clusters 2 and 3 vs. Clusters 1 and 4. Treatment with divalproex, larger number of previous manic episodes, lack of disruptive-aggressive behavior, and more prominent depressive symptoms at baseline were predictors for Cluster 3 vs. 2. Conclusion Distinct treatment response profiles can be predicted by clinical features at baseline. The presence of these features as potential risk factors for relapse in patients who have responded to treatment

  1. A phenotypic screening approach to identify anticancer compounds derived from marine fungi.

    Science.gov (United States)

    Ellinger, Bernhard; Silber, Johanna; Prashar, Anjali; Landskron, Johannes; Weber, Jonas; Rehermann, Sarah; Müller, Franz-Josef; Smith, Stephen; Wrigley, Stephen; Taskén, Kjetil; Gribbon, Philip; Labes, Antje; Imhoff, Johannes F

    2014-04-01

    This study covers the isolation, testing, and identification of natural products with anticancer properties. Secondary metabolites were isolated from fungal strains originating from a variety of marine habitats. Strain culture protocols were optimized with respect to growth media composition and fermentation conditions. From these producers, isolated compounds were screened for their effect on the viability and proliferation of a subset of the NCI60 panel of cancer cell lines. Active compounds of interest were identified and selected for detailed assessments and structural elucidation using nuclear magnetic resonance. This revealed the majority of fungal-derived compounds represented known anticancer chemotypes, confirming the integrity of the process and the ability to identify suitable compounds. Examination of effects of selected compounds on cancer-associated cell signaling pathways used phospho flow cytometry in combination with 3D fluorescent cell barcoding. In parallel, the study addressed the logistical aspects of maintaining multiple cancer cell lines in culture simultaneously. A potential solution involving microbead-based cell culture was investigated (BioLevitator, Hamilton). Selected cell lines were cultured in microbead and 2D methods and cell viability tests showed comparable compound inhibition in both methods (R2=0.95). In a further technology assessment, an image-based assay system was investigated for its utility as a possible complement to ATP-based detection for quantifying cell growth and viability in a label-free manner.

  2. A Systematic Approach to Identify Markers of Distinctly Activated Human Macrophages

    Directory of Open Access Journals (Sweden)

    Bayan eSudan

    2015-05-01

    Full Text Available Polarization has been a useful concept for describing activated macrophage phenotypes and gene expression profiles. However, macrophage activation status within tumors and other settings are often inferred based on only a few markers. Complicating matters for relevance to human biology, many of the best studied macrophage activation markers have been best characterized in mice and sometimes are not similarly regulated in human macrophages. To identify novel markers of activated human macrophages, gene expression profiles for human macrophages of a single donor subjected to 33 distinct activating conditions were obtained and a set of putative activation markers were subsequently evaluated in macrophages from multiple donors using integrated fluidic circuit (IFC-based RT-PCR. Using unsupervised hierarchical clustering of the microarray screen, highly-altered transcripts (>4-fold change in expression sorted the macrophage transcription profiles into two major and 13 minor clusters. Among the 1874 highly-altered transcripts, over 100 were uniquely altered in one major or two related minor clusters. IFC PCR-derived data confirmed the microarray results and to show the kinetics of expression of potential macrophage activation markers. Transcripts encoding chemokines, cytokines, and cell surface were prominent in our analyses. The activation markers identified by this study could be used to better characterize tumor-associated macrophages from biopsies as well as other macrophage populations collected from human clinical samples.

  3. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci.

    Science.gov (United States)

    Shen, Changbing; Gao, Jing; Sheng, Yujun; Dou, Jinfa; Zhou, Fusheng; Zheng, Xiaodong; Ko, Randy; Tang, Xianfa; Zhu, Caihong; Yin, Xianyong; Sun, Liangdan; Cui, Yong; Zhang, Xuejun

    2016-01-01

    Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association study (GWAS). More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWAS. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo. Many susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in the development of vitiligo.

  4. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci

    Directory of Open Access Journals (Sweden)

    Chang eShen

    2016-02-01

    Full Text Available Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association studies (GWASs. More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWASs. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo, such as immunoregulatory function, melanocyte regulation and so on. A number of susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in vitiligo development.

  5. Identifying structures, processes, resources and needs of research ethics committees in Egypt

    Directory of Open Access Journals (Sweden)

    Sleem Hany

    2010-06-01

    Full Text Available Abstract Background Concerns have been expressed regarding the adequacy of ethics review systems in developing countries. Limited data are available regarding the structural and functional status of Research Ethics Committees (RECs in the Middle East. The purpose of this study was to survey the existing RECs in Egypt to better understand their functioning status, perceived resource needs, and challenges. Methods We distributed a self-administered survey tool to Egyptian RECs to collect information on the following domains: general characteristics of the REC, membership composition, ethics training, workload, process of ethics review, perceived challenges to effective functioning, and financial and material resources. We used basic descriptive statistics to evaluate the quantitative data. Results We obtained responses from 67% (12/18 of the identified RECs. Most RECs (10/12 have standard operating procedures and many (7/12 have established policies to manage conflicts of interests. The average membership was 10.3 with a range from 7-19. The predominant member type was physicians (69.5% of all of the REC members with little lay representation (13.7%. Most RECs met at least once/month and the average number of protocols reviewed per meeting was 3.8 with a range from 1-10. Almost three-quarters of the members from all of the 12 RECs indicated they received some formal training in ethics. Regarding resources, roughly half of the RECs have dedicated capital equipment (e.g., meeting room, computers, office furniture, etc; none of the RECs have a formal operating budget. Perceived challenges included the absence of national research ethics guidelines and national standards for RECs and lack of ongoing training of its members in research ethics. Conclusion Our study documents several areas of strengths and areas for improvements in the operations of Egyptian RECs. Regarding strengths, many of the existing RECs meet frequently, have a majority of members

  6. Approaches of researches in medical geography in Poland and Ukraine

    Science.gov (United States)

    Pantylej, Wiktoria

    2008-01-01

    This paper deals with the historical review of medical geography in the world, in Poland and in Ukraine. There are different approaches in medical geography: according to the research subject (ecological and economic approaches) and according to the current affairs of research (approach concerns sexuality, the age of the population and accordingly, accessibility of health care services to the population). To the author's mind, the most perspective approaches in medical geography in Poland and Ukraine are as follows: - integrative - dedicated to the health status of the population in connection with the quality and life level; - mathematical-statistical - connected with the problem of synthetic indexes of health status of the populations and factors influencing it, and with the problem of economic value of health and life of the population; - social-economic - the analysis of the influence of socioeconomic factors (such as wealth measure, rate of unemployment, work conditions and others) on public health; - ecological - connected with the researches dedicated to the analysis of environmental impact on public health status of the population; - demographical - the analysis of demographical factors of forming public health status; - social-psychological - health culture of the population, perception of the own health/morbidity and health care systems existing in different countries.

  7. Practice-Based Interdisciplinary Approach and Environmental Research

    Directory of Open Access Journals (Sweden)

    Ranjan Kumar Datta

    2017-03-01

    Full Text Available Interdisciplinary researchers and educators, as community members, creators of knowledge, and environmental activists and practitioners, have a responsibility to build a bridge between community practice, academic scholarship, and professional contributions aimed at establishing environmental sustainability. In this paper, I focus on an undervalued area of environmental politics, practices, and often unarticulated assumptions which underlie human–environmental relations. This article challenges interdisciplinary studies that are not connected with practice by reconfiguring the meaning of a community-based, interdisciplinary approach. Drawing from works by Foucault, Latour, and Haraway, this paper first shows how to reconfigure the meaning of an interdisciplinary approach. Second, using Bourdieu and Brightman’s ethnographic studies as a framework, the paper situates practice as central to our efforts to deconstruct and replace current interdisciplinary initiatives with a practice-based approach. Through a practice-based interdisciplinary approach (PIA, environmental educators and researchers gain an awareness of and learn to make an investment in sustainable communities. As teams of environmental researchers practising in the local community, they are meaningfully involved with the community, with each other, and with the environment.

  8. Novel in vivo targets of ΔNp63 in keratinocytes identified by a modified chromatin immunoprecipitation approach

    Directory of Open Access Journals (Sweden)

    Ortt Kori

    2007-05-01

    Full Text Available Abstract Background p63 is a transcription factor that plays an important role in skin epidermal development and differentiation. The p63 gene encodes for two major protein isoforms, those containing an amino-terminal trans-activation domain (TAp63 and those lacking this domain (ΔNp63. Both the TA and ΔN transcripts are also alternatively spliced at the 3' end producing proteins with unique C-termini that are designated as α, β and γ isoforms. Recent research has suggested that ΔNp63 is the predominant isoform expressed and active in keratinocytes. Results To better elucidate the biological role of p63 in regulating gene expression in keratinocytes we performed chromatin immunoprecipitation (ChIP experiments with ΔNp63-specific antibodies. We included an additional step in the ChIP procedure to enrich for ΔNp63 targets by screening the library of immunoprecipitated DNA for its ability to bind recombinant GST-ΔNp63. Cloning of ΔNp63-ChIP-derived DNA fragments identified more than 60 potential ΔNp63 target loci that were located close to or embedded within known or predicted genes. Identity of these target genes suggests that they may participate in a myriad of cellular processes including transcriptional regulation, signaling and metabolism. Here we confirm the binding of ΔNp63 to several of these genomic loci both by EMSA and replicate ChIP assays. Finally we show that the expression of many of these target genes is altered when ΔNp63 levels in keratinocytes are reduced by siRNA, further confirming that these are bona fide targets. Conclusion This unbiased genomic approach has allowed us to uncover functional targets of ΔNp63 and serves as the initial step in further analysis of the transcriptional regulatory mechanisms that are governed by p63 in keratinocytes.

  9. A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

    Directory of Open Access Journals (Sweden)

    Ana C. D’Alessio

    2015-11-01

    Full Text Available Hundreds of transcription factors (TFs are expressed in each cell type, but cell identity can be induced through the activity of just a small number of core TFs. Systematic identification of these core TFs for a wide variety of cell types is currently lacking and would establish a foundation for understanding the transcriptional control of cell identity in development, disease, and cell-based therapy. Here, we describe a computational approach that generates an atlas of candidate core TFs for a broad spectrum of human cells. The potential impact of the atlas was demonstrated via cellular reprogramming efforts where candidate core TFs proved capable of converting human fibroblasts to retinal pigment epithelial-like cells. These results suggest that candidate core TFs from the atlas will prove a useful starting point for studying transcriptional control of cell identity and reprogramming in many human cell types.

  10. Utilizing Soize's Approach to Identify Parameter and Model Uncertainties

    Energy Technology Data Exchange (ETDEWEB)

    Bonney, Matthew S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Univ. of Wisconsin, Madison, WI (United States); Brake, Matthew Robert [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2014-10-01

    Quantifying uncertainty in model parameters is a challenging task for analysts. Soize has derived a method that is able to characterize both model and parameter uncertainty independently. This method is explained with the assumption that some experimental data is available, and is divided into seven steps. Monte Carlo analyses are performed to select the optimal dispersion variable to match the experimental data. Along with the nominal approach, an alternative distribution can be used along with corrections that can be utilized to expand the scope of this method. This method is one of a very few methods that can quantify uncertainty in the model form independently of the input parameters. Two examples are provided to illustrate the methodology, and example code is provided in the Appendix.

  11. Identifying the optimal supply temperature in district heating networks - A modelling approach

    DEFF Research Database (Denmark)

    Mohammadi, Soma; Bojesen, Carsten

    2014-01-01

    dynamically while the flow and pressure are calculated on the basis of steady state conditions. The implicit finite element method is applied to simulate the transient temperature behaviour in the network. Pipe network heat losses, pressure drop in the network and return temperature to the plant...... of this study is to develop a model for thermo-hydraulic calculation of low temperature DH system. The modelling is performed with emphasis on transient heat transfer in pipe networks. The pseudo-dynamic approach is adopted to model the District Heating Network [DHN] behaviour which estimates the temperature...... are calculated in the developed model. The model will serve eventually as a basis to find out the optimal supply temperature in an existing DHN in later work. The modelling results are used as decision support for existing DHN; proposing possible modifications to operate at optimal supply temperature....

  12. Identifying Silence Climate in Organizations in the Framework of Contemporary Management Approaches

    Directory of Open Access Journals (Sweden)

    Mustafa Emre Civelek

    2015-10-01

    Full Text Available Dynamic competition conditions in present day, bring about the consequence for businesses to face varied problems with each passing day. At this point, current management approaches include studies that would shed light on the new problems of businesses. Organizational Silence, a concept that has recently been being voiced in business world, has come up in such context. Organizational silence could be expressed as the employee behavior of keeping silent about certain negativities due to various reasons in an organization. Since knowledge sharing in modern organizations is of capital importance in terms of responding hastily to the changes in a competitive environment, spread of this behavior of employees to organization culture and climate presents a threat of indifference. In this study, the concept of Organizational Silence is defined and the effects of conceived silence climate on management of organizations are discussed.

  13. The ethics of pharmaceutical research funding: a social organization approach.

    Science.gov (United States)

    Gray, Garry C

    2013-01-01

    This paper advances a social organization approach to examining unethical behavior. While unethical behaviors may stem in part from failures in individual morality or psychological blind spots, they are both generated and performed through social interactions among individuals and groups. To illustrate the value of a social organization approach, a case study of a medical school professor's first experience with pharmaceutical-company-sponsored research is provided in order to examine how funding arrangements can constrain research integrity. The case illustrates three significant ways that institutional corruption can occur in the research process. First, conflicts of norms between pharmaceutical companies, universities, and affiliated teaching hospitals can result in compromises and self-censorship. Second, normal behavior is shaped through routine interactions. Unethical behaviors can be (or can become) normal behaviors when they are produced and reproduced through a network of social interactions. Third, funding arrangements can create networks of dependency that structurally distort the independence of the academic researcher in favor of the funder's interests. More broadly, the case study demonstrates how the social organization approach deepens our understanding of the practice of ethics.

  14. Identifying dominant controls on hydrologic parameter transfer from gauged to ungauged catchments: a comparative hydrology approach

    Science.gov (United States)

    Singh, R.; Archfield, S.A.; Wagener, T.

    2014-01-01

    Daily streamflow information is critical for solving various hydrologic problems, though observations of continuous streamflow for model calibration are available at only a small fraction of the world’s rivers. One approach to estimate daily streamflow at an ungauged location is to transfer rainfall–runoff model parameters calibrated at a gauged (donor) catchment to an ungauged (receiver) catchment of interest. Central to this approach is the selection of a hydrologically similar donor. No single metric or set of metrics of hydrologic similarity have been demonstrated to consistently select a suitable donor catchment. We design an experiment to diagnose the dominant controls on successful hydrologic model parameter transfer. We calibrate a lumped rainfall–runoff model to 83 stream gauges across the United States. All locations are USGS reference gauges with minimal human influence. Parameter sets from the calibrated models are then transferred to each of the other catchments and the performance of the transferred parameters is assessed. This transfer experiment is carried out both at the scale of the entire US and then for six geographic regions. We use classification and regression tree (CART) analysis to determine the relationship between catchment similarity and performance of transferred parameters. Similarity is defined using physical/climatic catchment characteristics, as well as streamflow response characteristics (signatures such as baseflow index and runoff ratio). Across the entire US, successful parameter transfer is governed by similarity in elevation and climate, and high similarity in streamflow signatures. Controls vary for different geographic regions though. Geology followed by drainage, topography and climate constitute the dominant similarity metrics in forested eastern mountains and plateaus, whereas agricultural land use relates most strongly with successful parameter transfer in the humid plains.

  15. Pharmacophore-based virtual screening and density functional theory approach to identifying novel butyrylcholinesterase inhibitors

    Institute of Scientific and Technical Information of China (English)

    Sugunadevi SAKKIAH; Keun Woo LEE

    2012-01-01

    Aim:To identify the critical chemical features,with reliable geometric constraints,that contributes to the inhibition of butyrylcholinesterase (BChE) function.Methods:Ligand-based pharmacophore modeling was used to identify the critical chemical features of BChE inhibitors.The generated pharmacophore model was validated using various techniques,such as Fischer's randomization method,test set,and decoy set.The best pharmacophore model was used as a query in virtual screening to identify novel scaffolds that inhibit BChE.Compounds selected by the best hypothesis in the virtual screening were tested for drug-like properties,and molecular docking study was applied to determine the optimal orientation of the hit compounds in the BChE active site.To find the reactivity of the hit compounds,frontier orbital analysis was carried out using density functional theory.Results:Based on its correlation coefficient (0.96),root mean square (RMS) deviation (1.01),and total cost (105.72),the quantitative hypothesis Hypo1 consisting of 2 HBA,1 Hy-Ali,and 1 Hy-Ar was selected as the best hypothesis.Thus,Hypo1 was used as a 3D query in virtual screening of the Maybridge and Chembridge databases.The hit compounds were filtered using ADMET,Lipinski's Rule of Five,and molecular docking to reduce the number of false positive results.Finally,33 compounds were selected based on their critical interactions with the significant amino acids in BChE's active site.To confirm the inhibitors' potencies,the orbital energies,such as HOMO and LUMO,of the hit compounds and 7 training set compounds were calculated.Among the 33 hit compounds,10 compounds with the highest HOMO values were selected,and this set was further culled to 5 compounds based on their energy gaps important for stability and energy transfer.From the overall results,5 hit compounds were confirmed to be potential BChE inhibitors that satisfied all the pharmacophoric features in Hypo1.Conclusion:This study pinpoints important chemical

  16. Ovarian serous adenocarcinoma identified during IVF: diagnostic approach, surgical management, and reproductive outcome

    Directory of Open Access Journals (Sweden)

    Gleeson Noreen C

    2009-05-01

    Full Text Available Abstract Background To present a diagnostic evaluation and treatment strategy for serous adenocarcinoma of the ovary discovered during an in vitro fertilisation (IVF sequence, and report on reproductive outcome after tumour resection and embryo transfer. Case presentation Cycle monitoring in IVF identified an abnormal ovarian lesion which was subjected to ultrasound-guided needle aspiration. Cytology suggested malignancy, and unilateral oophorectomy was performed after formal staging. After surgery, the patient underwent an anonymous donor oocyte IVF cycle which established a viable twin intrauterine pregnancy. No recurrence of cancer has been detected in the >72 month follow-up interval; mother and twin daughters continue to do well. Conclusion Suspicious adnexal structures noted during controlled ovarian hyperstimulation for IVF warrant assessment, and this report confirms the role of aspiration cytology in such cases. If uterine conservation is possible, successful livebirth can be achieved from IVF if donor oocyes are utilised, as described here.

  17. A high-throughput approach to identify compounds that impair envelope integrity in Escherichia coli

    DEFF Research Database (Denmark)

    Baker, Kristin Renee; Jana, Bimal; Franzyk, Henrik

    2016-01-01

    was to develop and validate an assay for identifying compounds that increase envelope permeability, thereby conferring antimicrobial susceptibility by weakening of the cell envelope barrier in Gram-negative bacteria. A high-throughput whole-cell screening platform was developed to measure Escherichia coli...... sequence type 131 clone. Notably, in the presence of 0.25 μM of this peptide, both strains were susceptible to rifampin according to the resistance breakpoints (R > 0.5 μg/ml) for Gram-positive bacterial pathogens. The high-throughput screening platform developed in this study can be applied to accelerate...... the discovery of antimicrobial helper drug candidates and targets that enhance the delivery of existing antibiotics by impairing envelope integrity in Gram-negative bacteria....

  18. A new system identification approach to identify genetic variants in sequencing studies for a binary phenotype.

    Science.gov (United States)

    Kang, Guolian; Bi, Wenjian; Zhao, Yanlong; Zhang, Ji-Feng; Yang, Jun J; Xu, Heng; Loh, Mignon L; Hunger, Stephen P; Relling, Mary V; Pounds, Stanley; Cheng, Cheng

    2014-01-01

    We propose in this paper a set-valued (SV) system model, which is a generalized form of logistic (LG) and Probit (Probit) regression, to be considered as a method for discovering genetic variants, especially rare genetic variants in next-generation sequencing studies, for a binary phenotype. We propose a new SV system identification method to estimate all underlying key system parameters for the Probit model and compare it with the LG model in the setting of genetic association studies. Across an extensive series of simulation studies, the Probit method maintained type I error control and had similar or greater power than the LG method, which is robust to different distributions of noise: logistic, normal, or t distributions. Additionally, the Probit association parameter estimate was 2.7-46.8-fold less variable than the LG log-odds ratio association parameter estimate. Less variability in the association parameter estimate translates to greater power and robustness across the spectrum of minor allele frequencies (MAFs), and these advantages are the most pronounced for rare variants. For instance, in a simulation that generated data from an additive logistic model with an odds ratio of 7.4 for a rare single nucleotide polymorphism with a MAF of 0.005 and a sample size of 2,300, the Probit method had 60% power whereas the LG method had 25% power at the α = 10(-6) level. Consistent with these simulation results, the set of variants identified by the LG method was a subset of those identified by the Probit method in two example analyses. Thus, we suggest the Probit method may be a competitive alternative to the LG method in genetic association studies such as candidate gene, genome-wide, or next-generation sequencing studies for a binary phenotype.

  19. PREDICT‐PD: An online approach to prospectively identify risk indicators of Parkinson's disease

    Science.gov (United States)

    Noyce, Alastair J.; R'Bibo, Lea; Peress, Luisa; Bestwick, Jonathan P.; Adams‐Carr, Kerala L.; Mencacci, Niccolo E.; Hawkes, Christopher H.; Masters, Joseph M.; Wood, Nicholas; Hardy, John; Giovannoni, Gavin; Lees, Andrew J.

    2017-01-01

    Background A number of early features can precede the diagnosis of Parkinson's disease (PD). Objective To test an online, evidence‐based algorithm to identify risk indicators of PD in the UK population. Methods Participants aged 60 to 80 years without PD completed an online survey and keyboard‐tapping task annually over 3 years, and underwent smell tests and genotyping for glucocerebrosidase (GBA) and leucine‐rich repeat kinase 2 (LRRK2) mutations. Risk scores were calculated based on the results of a systematic review of risk factors and early features of PD, and individuals were grouped into higher (above 15th centile), medium, and lower risk groups (below 85th centile). Previously defined indicators of increased risk of PD (“intermediate markers”), including smell loss, rapid eye movement–sleep behavior disorder, and finger‐tapping speed, and incident PD were used as outcomes. The correlation of risk scores with intermediate markers and movement of individuals between risk groups was assessed each year and prospectively. Exploratory Cox regression analyses with incident PD as the dependent variable were performed. Results A total of 1323 participants were recruited at baseline and >79% completed assessments each year. Annual risk scores were correlated with intermediate markers of PD each year and baseline scores were correlated with intermediate markers during follow‐up (all P values power for incident PD was improved by the addition of genetic variants to risk scores. Conclusions The online PREDICT‐PD algorithm is a unique and simple method to identify indicators of PD risk. © 2017 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society. PMID:28090684

  20. A New System Identification Approach to Identifying Genetic Variants in Sequencing Studies for A Binary Phenotype

    Science.gov (United States)

    Kang, Guolian; Bi, Wenjian; Zhao, Yanlong; Zhang, Ji-Feng; Yang, Jun J.; Xu, Heng; Loh, Mignon L.; Hunger, Stephen P.; Relling, Mary V.; Pounds, Stanley; Cheng, Cheng

    2014-01-01

    We propose in this paper a set-valued (SV) system model, which is a generalized form of Logistic (LG) and Probit (Probit) regression, to be considered as a method for discovering genetic variants, especially rare genetic variants in next generation sequencing studies, for a binary phenotype. We propose a new set-valued system identification method to estimate all the underlying key system parameters for the Probit model and compare it with the LG model in the setting of genetic association studies. Across an extensive series of simulation studies, the Probit method maintained Type I error control and had similar or greater power than the LG method which is robust to different distributions of noise: logistic, normal or t distributions. Additionally, the Probit association parameter estimate was 2.7–46.8 fold less variable than the LG log-odds ratio association parameter estimate. Less variability in the association parameter estimate translates to greater power and robustness across the spectrum of minor allele frequencies (MAFs), and these advantages are the most pronounced for rare variants. For instance, in a simulation that generated data from an additive logistic model with odds ratio of 7.4 for a rare single nucleotide polymorphism with a MAF of 0.005 and a sample size of 2300, the Probit method had 60% power whereas the LG method had 25% power at the α=10−6 level. Consistent with these simulation results, the set of variants identified by the LG method was a subset of those identified by the Probit method in two example analyses. Thus, we suggest the Probit method may be a competitive alternative to the LG method in genetic association studies such as candidate gene, genome-wide, or next generation sequencing studies for a binary phenotype. PMID:25096228

  1. Identifying Where REDD+ Financially Out-Competes Oil Palm in Floodplain Landscapes Using a Fine-Scale Approach

    Science.gov (United States)

    MacMillan, Douglas C.; Xofis, Panteleimon; Ancrenaz, Marc; Tzanopoulos, Joseph; Ong, Robert; Goossens, Benoit; Koh, Lian Pin; Del Valle, Christian; Peter, Lucy; Morel, Alexandra C.; Lackman, Isabelle; Chung, Robin; Kler, Harjinder; Ambu, Laurentius; Baya, William; Knight, Andrew T.

    2016-01-01

    Reducing Emissions from Deforestation and forest Degradation (REDD+) aims to avoid forest conversion to alternative land-uses through financial incentives. Oil-palm has high opportunity costs, which according to current literature questions the financial competitiveness of REDD+ in tropical lowlands. To understand this more, we undertook regional fine-scale and coarse-scale analyses (through carbon mapping and economic modelling) to assess the financial viability of REDD+ in safeguarding unprotected forest (30,173 ha) in the Lower Kinabatangan floodplain in Malaysian Borneo. Results estimate 4.7 million metric tons of carbon (MgC) in unprotected forest, with 64% allocated for oil-palm cultivations. Through fine-scale mapping and carbon accounting, we demonstrated that REDD+ can outcompete oil-palm in regions with low suitability, with low carbon prices and low carbon stock. In areas with medium oil-palm suitability, REDD+ could outcompete oil palm in areas with: very high carbon and lower carbon price; medium carbon price and average carbon stock; or, low carbon stock and high carbon price. Areas with high oil palm suitability, REDD+ could only outcompete with higher carbon price and higher carbon stock. In the coarse-scale model, oil-palm outcompeted REDD+ in all cases. For the fine-scale models at the landscape level, low carbon offset prices (US $3 MgCO2e) would enable REDD+ to outcompete oil-palm in 55% of the unprotected forests requiring US $27 million to secure these areas for 25 years. Higher carbon offset price (US $30 MgCO2e) would increase the competitiveness of REDD+ within the landscape but would still only capture between 69%-74% of the unprotected forest, requiring US $380–416 million in carbon financing. REDD+ has been identified as a strategy to mitigate climate change by many countries (including Malaysia). Although REDD+ in certain scenarios cannot outcompete oil palm, this research contributes to the global REDD+ debate by: highlighting REDD

  2. Identifying Where REDD+ Financially Out-Competes Oil Palm in Floodplain Landscapes Using a Fine-Scale Approach.

    Directory of Open Access Journals (Sweden)

    Nicola K Abram

    Full Text Available Reducing Emissions from Deforestation and forest Degradation (REDD+ aims to avoid forest conversion to alternative land-uses through financial incentives. Oil-palm has high opportunity costs, which according to current literature questions the financial competitiveness of REDD+ in tropical lowlands. To understand this more, we undertook regional fine-scale and coarse-scale analyses (through carbon mapping and economic modelling to assess the financial viability of REDD+ in safeguarding unprotected forest (30,173 ha in the Lower Kinabatangan floodplain in Malaysian Borneo. Results estimate 4.7 million metric tons of carbon (MgC in unprotected forest, with 64% allocated for oil-palm cultivations. Through fine-scale mapping and carbon accounting, we demonstrated that REDD+ can outcompete oil-palm in regions with low suitability, with low carbon prices and low carbon stock. In areas with medium oil-palm suitability, REDD+ could outcompete oil palm in areas with: very high carbon and lower carbon price; medium carbon price and average carbon stock; or, low carbon stock and high carbon price. Areas with high oil palm suitability, REDD+ could only outcompete with higher carbon price and higher carbon stock. In the coarse-scale model, oil-palm outcompeted REDD+ in all cases. For the fine-scale models at the landscape level, low carbon offset prices (US $3 MgCO2e would enable REDD+ to outcompete oil-palm in 55% of the unprotected forests requiring US $27 million to secure these areas for 25 years. Higher carbon offset price (US $30 MgCO2e would increase the competitiveness of REDD+ within the landscape but would still only capture between 69%-74% of the unprotected forest, requiring US $380-416 million in carbon financing. REDD+ has been identified as a strategy to mitigate climate change by many countries (including Malaysia. Although REDD+ in certain scenarios cannot outcompete oil palm, this research contributes to the global REDD+ debate by

  3. A microarray approach to identify genes involved in seed-pericarp cross-talk and development in peach

    Directory of Open Access Journals (Sweden)

    Zaffalon Valerio

    2011-06-01

    Full Text Available Abstract Background Field observations and a few physiological studies have demonstrated that peach embryogenesis and fruit development are tightly coupled. In fact, attempts to stimulate parthenocarpic fruit development by means of external tools have failed. Moreover, physiological disturbances during early embryo development lead to seed abortion and fruitlet abscission. Later in embryo development, the interactions between seed and fruit development become less strict. As there is limited genetic and molecular information about seed-pericarp cross-talk and development in peach, a massive gene approach based on the use of the μPEACH 1.0 array platform and quantitative real time RT-PCR (qRT-PCR was used to study this process. Results A comparative analysis of the transcription profiles conducted in seed and mesocarp (cv Fantasia throughout different developmental stages (S1, S2, S3 and S4 evidenced that 455 genes are differentially expressed in seed and fruit. Among differentially expressed genes some were validated as markers in two subsequent years and in three different genotypes. Seed markers were a LTP1 (lipid transfer protein, a PR (pathogenesis-related protein, a prunin and LEA (Late Embryogenesis Abundant protein, for S1, S2, S3 and S4, respectively. Mesocarp markers were a RD22-like protein, a serin-carboxypeptidase, a senescence related protein and an Aux/IAA, for S1, S2, S3 and S4, respectively. The microarray data, analyzed by using the HORMONOMETER platform, allowed the identification of hormone-responsive genes, some of them putatively involved in seed-pericarp crosstalk. Results indicated that auxin, cytokinins, and gibberellins are good candidates, acting either directly (auxin or indirectly as signals during early development, when the cross-talk is more active and vital for fruit set, whereas abscisic acid and ethylene may be involved later on. Conclusions In this research, genes were identified marking different phases of

  4. Identifying Where REDD+ Financially Out-Competes Oil Palm in Floodplain Landscapes Using a Fine-Scale Approach.

    Science.gov (United States)

    Abram, Nicola K; MacMillan, Douglas C; Xofis, Panteleimon; Ancrenaz, Marc; Tzanopoulos, Joseph; Ong, Robert; Goossens, Benoit; Koh, Lian Pin; Del Valle, Christian; Peter, Lucy; Morel, Alexandra C; Lackman, Isabelle; Chung, Robin; Kler, Harjinder; Ambu, Laurentius; Baya, William; Knight, Andrew T

    2016-01-01

    Reducing Emissions from Deforestation and forest Degradation (REDD+) aims to avoid forest conversion to alternative land-uses through financial incentives. Oil-palm has high opportunity costs, which according to current literature questions the financial competitiveness of REDD+ in tropical lowlands. To understand this more, we undertook regional fine-scale and coarse-scale analyses (through carbon mapping and economic modelling) to assess the financial viability of REDD+ in safeguarding unprotected forest (30,173 ha) in the Lower Kinabatangan floodplain in Malaysian Borneo. Results estimate 4.7 million metric tons of carbon (MgC) in unprotected forest, with 64% allocated for oil-palm cultivations. Through fine-scale mapping and carbon accounting, we demonstrated that REDD+ can outcompete oil-palm in regions with low suitability, with low carbon prices and low carbon stock. In areas with medium oil-palm suitability, REDD+ could outcompete oil palm in areas with: very high carbon and lower carbon price; medium carbon price and average carbon stock; or, low carbon stock and high carbon price. Areas with high oil palm suitability, REDD+ could only outcompete with higher carbon price and higher carbon stock. In the coarse-scale model, oil-palm outcompeted REDD+ in all cases. For the fine-scale models at the landscape level, low carbon offset prices (US $3 MgCO2e) would enable REDD+ to outcompete oil-palm in 55% of the unprotected forests requiring US $27 million to secure these areas for 25 years. Higher carbon offset price (US $30 MgCO2e) would increase the competitiveness of REDD+ within the landscape but would still only capture between 69%-74% of the unprotected forest, requiring US $380-416 million in carbon financing. REDD+ has been identified as a strategy to mitigate climate change by many countries (including Malaysia). Although REDD+ in certain scenarios cannot outcompete oil palm, this research contributes to the global REDD+ debate by: highlighting REDD

  5. Research on international terrorism: orthodox approach or critical study?

    Directory of Open Access Journals (Sweden)

    Cristina Aboboaie

    2011-10-01

    Full Text Available This study examines the epistemological, ontological, methodological and ethical challenges that the researchers of the new current of critical study on terrorism, put to the traditional research on this phenomenon. The study begins with the presentation of the orthodox theory of terrorism and its weaknesses, as they are captured by the critical theory that stresses the need for a new research agenda. Further, we intend to present "solutions" made by the researchers of critical study on terrorism and "commitments" that they take to the discipline. Finally, this study recognizes that each approach has valuable ideas and the controversies presented are nothing but a source of progress in the real and profound knowledge of the phenomenon of international terrorism.

  6. Integrating relationship- and research-based approaches in Australian health promotion practice.

    Science.gov (United States)

    Klinner, Christiane; Carter, Stacy M; Rychetnik, Lucie; Li, Vincy; Daley, Michelle; Zask, Avigdor; Lloyd, Beverly

    2015-12-01

    We examine the perspectives of health promotion practitioners on their approaches to determining health promotion practice, in particular on the role of research and relationships in this process. Using Grounded Theory methods, we analysed 58 semi-structured interviews with 54 health promotion practitioners in New South Wales, Australia. Practitioners differentiated between relationship-based and research-based approaches as two sources of knowledge to guide health promotion practice. We identify several tensions in seeking to combine these approaches in practice and describe the strategies that participants adopted to manage these tensions. The strategies included working in an evidence-informed rather than evidence-based way, creating new evidence about relationship-based processes and outcomes, adopting 'relationship-based' research and evaluation methods, making research and evaluation useful for communities, building research and evaluation skills and improving collaboration between research and evaluation and programme implementation staff. We conclude by highlighting three systemic factors which could further support the integration of research-based and relationship-based health promotion practices: (i) expanding conceptions of health promotion evidence, (ii) developing 'relationship-based' research methods that enable practitioners to measure complex social processes and outcomes and to facilitate community participation and benefit, and (iii) developing organizational capacity.

  7. Utilizing a logic model to identify clinical research problems: a lesson from philosophy of science

    Directory of Open Access Journals (Sweden)

    Collins CR

    2016-10-01

    Full Text Available Cynthia R Collins School of Nursing, College of Social Sciences, Loyola University, New Orleans, LA, USA Abstract: Communication and decision making in the health care workplace often involve finding solutions to ill-structured problems in uncertain, dynamic environments influenced by the competing interests of multiple stakeholders. In this environment, doctoral-prepared nurses who practice as administrators, policy makers, or advanced practice practitioners are often compelled to make important decisions based upon evaluating the merit of colleagues’ proposals against some desired organizational or population outcome. Of equal importance is the nurse leader’s own capacity to construct a compelling argument or proposal that will drive the organization forward to meet the evolving needs for quality health care. Where do we learn the skills necessary to foster this kind of critical thinking in our professional communications? The author suggests that one teaching–learning approach can be found through the thoughtful application of the work of British philosopher Steven Toulmin. Toulmin defined a model for both the analysis and derivation of logical arguments or proposals that can be readily learned and applied for use in health care systems. This model posits that a substantive argument or claim can be evaluated based on the assumptions it presumes (warrants and the strength of the evidence base (backing. Several of the social science professions have adapted Toulmin’s model to generate analysis and creative solutions to complex or emergent problems. The author proposes that an application of this model be included in the pedagogy of doctoral level Philosophy of Science or Nursing Theory courses. The Toulmin process often provides the doctoral student or novice researcher with their first real learning experience in defining the scope and inherent challenges of framing a clinical issue to be the focus of their scholarly translational

  8. Have We Identified Effective Teachers? Validating Measures of Effective Teaching Using Random Assignment. Research Paper. MET Project

    Science.gov (United States)

    Kane, Thomas J.; McCaffrey, Daniel F.; Miller, Trey; Staiger, Douglas O.

    2013-01-01

    To develop, reward, and retain great teachers, school systems first must know how to identify them. The authors designed the Measures of Effective Teaching (MET) project to test replicable methods for identifying effective teachers. In past reports, the authors described three approaches to measuring different aspects of teaching: student surveys,…

  9. Security of the distributed electronic patient record: a case-based approach to identifying policy issues.

    Science.gov (United States)

    Anderson, J G

    2000-11-01

    The growth of managed care and integrated delivery systems has created a new commodity, health information and the technology that it requires. Surveys by Deloitte and Touche indicate that over half of the hospitals in the US are in the process of implementing electronic patient record (EPR) systems. The National Research Council has established that industry spends as much as $15 billion on information technology (IT), an amount that is expanding by 20% per year. The importance of collecting, electronically storing, and using the information is undisputed. This information is needed by consumers to make informed choices; by physicians to provide appropriate quality clinical care: and by health plans to assess outcomes, control costs and monitor quality. The collection, storage and communication of a large variety of personal patient data, however, present a major dilemma. How can we provide the data required by the new forms of health care delivery and at the same time protect the personal privacy of patients? Recent debates concerning medical privacy legislation, software regulation, and telemedicine suggest that this dilemma will not be easily resolved. The problem is systemic and arises out of the routine use and flow of information throughout the health industry. Health care information is primarily transferred among authorized users. Not only is the information used for patient care and financial reimbursement, secondary users of the information include medical, nursing, and allied health education, research, social services, public health, regulation, litigation, and commercial purposes such as the development of new medical technology and marketing. The main threats to privacy and confidentiality arise from within the institutions that provide patient care as well as institutions that have access to patient data for secondary purposes.

  10. Identifying Microphone from Noisy Recordings by Using Representative Instance One Class-Classification Approach

    Directory of Open Access Journals (Sweden)

    Huy Quan Vu

    2012-06-01

    Full Text Available Rapid growth of technical developments has created huge challenges for microphone forensics - a sub-category of audio forensic science, because of the availability of numerous digital recording devices and massive amount of recording data. Demand for fast and efficient methods to assure integrity and authenticity of information is becoming more and more important in criminal investigation nowadays. Machine learning has emerged as an important technique to support audio analysis processes of microphone forensic practitioners. However, its application to real life situations using supervised learning is still facing great challenges due to expensiveness in collecting data and updating system. In this paper, we introduce a new machine learning approach which is called One-class Classification (OCC to be applied to microphone forensics; we demonstrate its capability on a corpus of audio samples collected from several microphones. In addition, we propose a representative instance classification framework (RICF that can effectively improve performance of OCC algorithms for recording signal with noise. Experiment results and analysis indicate that OCC has the potential to benefit microphone forensic practitioners in developing new tools and techniques for effective and efficient analysis.

  11. Candidiasis drug discovery and development: new approaches targeting virulence for discovering and identifying new drugs

    Science.gov (United States)

    Pierce, Christopher G.; Lopez-Ribot, Jose L.

    2014-01-01

    Introduction Targeting pathogenetic mechanisms rather than essential processes represents a very attractive alternative for the development of new antibiotics. This may be particularly important in the case of antimycotics, due to the urgent need for novel antifungal drugs and the paucity of selective fungal targets. The opportunistic pathogenic fungus Candida albicans is the main etiological agent of candidiasis, the most common human fungal infection. These infections carry unacceptably high mortality rates, a clear reflection of the many shortcomings of current antifungal therapy, including the limited armamentarium of antifungal agents, their toxicity, and the emergence of resistance. Moreover the antifungal pipeline is mostly dry. Areas covered This review covers some of the most recent progress towards understanding C. albicans pathogenetic processes and how to harness this information for the development of anti-virulence agents. The two principal areas covered are filamentation and biofilm formation, as C. albicans pathogenicity is intimately linked to its ability to undergo morphogenetic conversions between yeast and filamentous morphologies and to its ability to form biofilms. Expert opinion We argue that filamentation and biofilm formation represent high value targets, yet clinically unexploited, for the development of novel anti-virulence approaches against candidiasis. Although this has proved a difficult task despite increasing understanding at the molecular level of C. albicans virulence, we highlight new opportunities and prospects for antifungal drug development targeting these two important biological processes. PMID:23738751

  12. Multi-omics approach identifies molecular mechanisms of plant-fungus mycorrhizal interaction

    Directory of Open Access Journals (Sweden)

    Peter E Larsen

    2016-01-01

    Full Text Available In mycorrhizal symbiosis, plant roots form close, mutually beneficial interactions with soil fungi. Before this mycorrhizal interaction can be established however, plant roots must be capable of detecting potential beneficial fungal partners and initiating the gene expression patterns necessary to begin symbiosis. To predict a plant root – mycorrhizal fungi sensor systems, we analyzed in vitro experiments of Populus tremuloides (aspen tree and Laccaria bicolor (mycorrhizal fungi interaction and leveraged over 200 previously published transcriptomic experimental data sets, 159 experimentally validated plant transcription factor binding motifs, and more than 120-thousand experimentally validated protein-protein interactions to generate models of pre-mycorrhizal sensor systems in aspen root. These sensor mechanisms link extracellular signaling molecules with gene regulation through a network comprised of membrane receptors, signal cascade proteins, transcription factors, and transcription factor biding DNA motifs. Modeling predicted four pre-mycorrhizal sensor complexes in aspen that interact with fifteen transcription factors to regulate the expression of 1184 genes in response to extracellular signals synthesized by Laccaria. Predicted extracellular signaling molecules include common signaling molecules such as phenylpropanoids, salicylate, and, jasmonic acid. This multi-omic computational modeling approach for predicting the complex sensory networks yielded specific, testable biological hypotheses for mycorrhizal interaction signaling compounds, sensor complexes, and mechanisms of gene regulation.

  13. A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint

    Science.gov (United States)

    Rios-Estepa, Rigoberto; Turner, Glenn W.; Lee, James M.; Croteau, Rodney B.; Lange, B. Markus

    2008-01-01

    The integration of mathematical modeling and experimental testing is emerging as a powerful approach for improving our understanding of the regulation of metabolic pathways. In this study, we report on the development of a kinetic mathematical model that accurately simulates the developmental patterns of monoterpenoid essential oil accumulation in peppermint (Mentha × piperita). This model was then used to evaluate the biochemical processes underlying experimentally determined changes in the monoterpene pathway under low ambient-light intensities, which led to an accumulation of the branchpoint intermediate (+)-pulegone and the side product (+)-menthofuran. Our simulations indicated that the environmentally regulated changes in monoterpene profiles could only be explained when, in addition to effects on biosynthetic enzyme activities, as yet unidentified inhibitory effects of (+)-menthofuran on the branchpoint enzyme pulegone reductase (PR) were assumed. Subsequent in vitro analyses with recombinant protein confirmed that (+)-menthofuran acts as a weak competitive inhibitor of PR (Ki = 300 μM). To evaluate whether the intracellular concentration of (+)-menthofuran was high enough for PR inhibition in vivo, we isolated essential oil-synthesizing secretory cells from peppermint leaves and subjected them to steam distillations. When peppermint plants were grown under low-light conditions, (+)-menthofuran was selectively retained in secretory cells and accumulated to very high levels (up to 20 mM), whereas under regular growth conditions, (+)-menthofuran levels remained very low (<400 μM). These results illustrate the utility of iterative cycles of mathematical modeling and experimental testing to elucidate the mechanisms controlling flux through metabolic pathways. PMID:18287058

  14. An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates.

    Science.gov (United States)

    Hawley, Robert G; Chen, Yuzhong; Riz, Irene; Zeng, Chen

    2012-05-04

    In this study, we utilized an integrated bioinformatics and computational biology approach in search of new BH3-only proteins belonging to the BCL2 family of apoptotic regulators. The BH3 (BCL2 homology 3) domain mediates specific binding interactions among various BCL2 family members. It is composed of an amphipathic α-helical region of approximately 13 residues that has only a few amino acids that are highly conserved across all members. Using a generalized motif, we performed a genome-wide search for novel BH3-containing proteins in the NCBI Consensus Coding Sequence (CCDS) database. In addition to known pro-apoptotic BH3-only proteins, 197 proteins were recovered that satisfied the search criteria. These were categorized according to α-helical content and predictive binding to BCL-xL (encoded by BCL2L1) and MCL-1, two representative anti-apoptotic BCL2 family members, using position-specific scoring matrix models. Notably, the list is enriched for proteins associated with autophagy as well as a broad spectrum of cellular stress responses such as endoplasmic reticulum stress, oxidative stress, antiviral defense, and the DNA damage response. Several potential novel BH3-containing proteins are highlighted. In particular, the analysis strongly suggests that the apoptosis inhibitor and DNA damage response regulator, AVEN, which was originally isolated as a BCL-xL-interacting protein, is a functional BH3-only protein representing a distinct subclass of BCL2 family members.

  15. A Systems Approach Identifies Essential FOXO3 Functions at Key Steps of Terminal Erythropoiesis.

    Directory of Open Access Journals (Sweden)

    Raymond Liang

    2015-10-01

    Full Text Available Circulating red blood cells (RBCs are essential for tissue oxygenation and homeostasis. Defective terminal erythropoiesis contributes to decreased generation of RBCs in many disorders. Specifically, ineffective nuclear expulsion (enucleation during terminal maturation is an obstacle to therapeutic RBC production in vitro. To obtain mechanistic insights into terminal erythropoiesis we focused on FOXO3, a transcription factor implicated in erythroid disorders. Using an integrated computational and experimental systems biology approach, we show that FOXO3 is essential for the correct temporal gene expression during terminal erythropoiesis. We demonstrate that the FOXO3-dependent genetic network has critical physiological functions at key steps of terminal erythropoiesis including enucleation and mitochondrial clearance processes. FOXO3 loss deregulated transcription of genes implicated in cell polarity, nucleosome assembly and DNA packaging-related processes and compromised erythroid enucleation. Using high-resolution confocal microscopy and imaging flow cytometry we show that cell polarization is impaired leading to multilobulated Foxo3-/- erythroblasts defective in nuclear expulsion. Ectopic FOXO3 expression rescued Foxo3-/- erythroblast enucleation-related gene transcription, enucleation defects and terminal maturation. Remarkably, FOXO3 ectopic expression increased wild type erythroblast maturation and enucleation suggesting that enhancing FOXO3 activity may improve RBCs production. Altogether these studies uncover FOXO3 as a novel regulator of erythroblast enucleation and terminal maturation suggesting FOXO3 modulation might be therapeutic in disorders with defective erythroid maturation.

  16. A macroepigenetic approach to identify factors responsible for the autism epidemic in the United States

    Directory of Open Access Journals (Sweden)

    Dufault Renee

    2012-04-01

    Full Text Available Abstract The number of children ages 6 to 21 in the United States receiving special education services under the autism disability category increased 91% between 2005 to 2010 while the number of children receiving special education services overall declined by 5%. The demand for special education services continues to rise in disability categories associated with pervasive developmental disorders. Neurodevelopment can be adversely impacted when gene expression is altered by dietary transcription factors, such as zinc insufficiency or deficiency, or by exposure to toxic substances found in our environment, such as mercury or organophosphate pesticides. Gene expression patterns differ geographically between populations and within populations. Gene variants of paraoxonase-1 are associated with autism in North America, but not in Italy, indicating regional specificity in gene-environment interactions. In the current review, we utilize a novel macroepigenetic approach to compare variations in diet and toxic substance exposure between these two geographical populations to determine the likely factors responsible for the autism epidemic in the United States.

  17. Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model

    Directory of Open Access Journals (Sweden)

    Zhai Chengxiang

    2010-05-01

    Full Text Available Abstract Background Large-scale genomic studies often identify large gene lists, for example, the genes sharing the same expression patterns. The interpretation of these gene lists is generally achieved by extracting concepts overrepresented in the gene lists. This analysis often depends on manual annotation of genes based on controlled vocabularies, in particular, Gene Ontology (GO. However, the annotation of genes is a labor-intensive process; and the vocabularies are generally incomplete, leaving some important biological domains inadequately covered. Results We propose a statistical method that uses the primary literature, i.e. free-text, as the source to perform overrepresentation analysis. The method is based on a statistical framework of mixture model and addresses the methodological flaws in several existing programs. We implemented this method within a literature mining system, BeeSpace, taking advantage of its analysis environment and added features that facilitate the interactive analysis of gene sets. Through experimentation with several datasets, we showed that our program can effectively summarize the important conceptual themes of large gene sets, even when traditional GO-based analysis does not yield informative results. Conclusions We conclude that the current work will provide biologists with a tool that effectively complements the existing ones for overrepresentation analysis from genomic experiments. Our program, Genelist Analyzer, is freely available at: http://workerbee.igb.uiuc.edu:8080/BeeSpace/Search.jsp

  18. Refinement of the ECETOC approach to identify endocrine disrupting properties of chemicals in ecotoxicology.

    Science.gov (United States)

    Weltje, Lennart; Wheeler, James R; Weyers, Arnd; Galay-Burgos, Malyka

    2013-12-16

    To use and implement an assessment scheme for the evaluation of endocrine disrupting properties of chemicals in ecotoxicology, the types of effect need to be agreed. Effects that merit further consideration in this context should fulfil the following three criteria: caused by an endocrine mode of action, be adverse, and be relevant at the population level to reflect the protection goal of ecotoxicological assessments. Thereafter, a comparison of effect values, regardless of the causative mechanisms, should be made, firstly to determine if endocrine toxicity generates the lowest endpoint within a taxon, and secondly if it is the lowest endpoint compared to that of other taxa living in the same compartment. These comparisons inform on two levels of specificity and determine if endocrine-mediated side-effects determine the ecotoxicological profile of a chemical. Various quantitative measures for the assessment of potency are also presented, which could assist in determining how to handle substances in the risk assessment when a regulatory concern is identified. Finally, derogation criteria should be defined for compounds that were designed as endocrine disruptors for non-vertebrates and those for which there is 'negligible exposure'. This paper discusses and provides proposals on how to apply these concepts for assessment of substances.

  19. An improved approach to identify irradiated spices using electronic nose, FTIR, and EPR spectroscopy.

    Science.gov (United States)

    Sanyal, Bhaskar; Ahn, Jae-Jun; Maeng, Jeong-Hwan; Kyung, Hyun-Kyu; Lim, Ha-Kyeong; Sharma, Arun; Kwon, Joong-Ho

    2014-09-01

    Changes in cumin and chili powder from India resulting from electron-beam irradiation were investigated using 3 analytical methods: electronic nose (E-nose), Fourier transform infrared (FTIR) spectroscopy, and electron paramagnetic resonance (EPR) spectroscopy. The spices had been exposed to 6 to 14 kGy doses recommended for microbial decontamination. E-nose measured a clear difference in flavor patterns of the irradiated spices in comparison with the nonirradiated samples. Principal component analysis further showed a dose-dependent variation. FTIR spectra of the samples showed strong absorption bands at 3425, 3007 to 2854, and 1746 cm(-1). However, both nonirradiated and irradiated spice samples had comparable patterns without any noteworthy changes in functional groups. EPR spectroscopy of the irradiated samples showed a radiation-specific triplet signal at g = 2.006 with a hyper-fine coupling constant of 3 mT confirming the results obtained with the E-nose technique. Thus, E-nose was found to be a potential tool to identify irradiated spices.

  20. Proteomic Approaches Identify Members of Cofilin Pathway Involved in Oral Tumorigenesis

    Science.gov (United States)

    Polachini, Giovana M.; Sobral, Lays M.; Mercante, Ana M. C.; Paes-Leme, Adriana F.; Xavier, Flávia C. A.; Henrique, Tiago; Guimarães, Douglas M.; Vidotto, Alessandra; Fukuyama, Erica E.; Góis-Filho, José F.; Cury, Patricia M.; Curioni, Otávio A.; Michaluart Jr, Pedro; Silva, Adriana M. A.; Wünsch-Filho, Victor; Nunes, Fabio D.; Leopoldino, Andréia M.; Tajara, Eloiza H.

    2012-01-01

    The prediction of tumor behavior for patients with oral carcinomas remains a challenge for clinicians. The presence of lymph node metastasis is the most important prognostic factor but it is limited in predicting local relapse or survival. This highlights the need for identifying biomarkers that may effectively contribute to prediction of recurrence and tumor spread. In this study, we used one- and two-dimensional gel electrophoresis, mass spectrometry and immunodetection methods to analyze protein expression in oral squamous cell carcinomas. Using a refinement for classifying oral carcinomas in regard to prognosis, we analyzed small but lymph node metastasis-positive versus large, lymph node metastasis-negative tumors in order to contribute to the molecular characterization of subgroups with risk of dissemination. Specific protein patterns favoring metastasis were observed in the “more-aggressive” group defined by the present study. This group displayed upregulation of proteins involved in migration, adhesion, angiogenesis, cell cycle regulation, anti-apoptosis and epithelial to mesenchymal transition, whereas the “less-aggressive” group was engaged in keratinocyte differentiation, epidermis development, inflammation and immune response. Besides the identification of several proteins not yet described as deregulated in oral carcinomas, the present study demonstrated for the first time the role of cofilin-1 in modulating cell invasion in oral carcinomas. PMID:23227181

  1. A Genetic Algorithm Based Approach for Segmentingand Identifying Defects in Glass Bottles

    Directory of Open Access Journals (Sweden)

    George Mathew

    2016-07-01

    Full Text Available This work mainly aims at designing and developing a suitable tool for identifying defects in glass bottles through visual inspection based on Segmentation algorithm. The defect identification is done in three stages. These are Image acquisition, Pre-processing and filtering and Segmentation. In the Image acquisition stage, samples of real time images are taken and are converted into 512x512 monochrome images. In the Preprocessing and filtering stage, the image acquired is passed through median filters. The Proposed filter is Modified Decision Based Unsymmetric Trimmed Median Filter (MDBUTMF because it produces a high value of Peak to Signal Ratio (PSNR of 60-75db.The de-noised images is further sent to the third stage which is Segmentation. In this work, Segmentation is done using Genetic Algorithm (GA. The defects in the images are segmented and highlighted. Thus the areas of defects are spotted out. The Genetic segmentation has produced high Sensitivity, high Specificity and high Accuracy of 92%, 93% and 93% respectively. Thus the Proposed work produced effective results and hence this tool shall be useful for food processing industries for the Quality Inspection of the glass bottles

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

    Science.gov (United States)

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

    2009-12-01

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

  3. A Neural Network Approach for Identifying Relativistic Electron Pitch Angle Distributions in Van Allen Probes Data

    Science.gov (United States)

    Souza, V. M. C. E. S.; Vieira, L.; Alves, L. R.; Da Silva, L. A.; Koga, D.; Sibeck, D. G.; Walsh, B.; Kanekal, S. G.; Silveira, M. D.; Medeiros, C.; Mendes, O., Jr.; Marchezi, J.; Rockenbach, M.; Jauer, P. R.; Gonzalez, W.; Baker, D. N.

    2015-12-01

    A myriad of physical phenomena occur in the inner magnetosphere, in particular at the Earth's radiation belts, which can be a result of the combination of both internal and external processes. However, the connection between physical processes occurring deep within the magnetosphere and external interplanetary drivers it is not yet well understood. In this work we investigate whether a selected set of interplanetary structures affect the local time distribution of three different classes of high energy electron pitch angle distributions (PADs), namely normal, isotropic, and butterfly. We split this work into two parts: initially we focus on the methodology used which employs a Self-Organized Feature Map (SOFM) neural network for identifying different classes of electron PAD shapes in the Van Allen Probes' Relativistic Electron Proton Telescope (REPT) data. The algorithm can categorize the input data into an arbitrary number of classes from which three of them appears the most: normal, isotropic and butterfly. Other classes which are related with these three also emerge and deserve to be addressed in detail in future works. We also discuss the uncertainties of the algorithm. Then, we move to the second part where we describe in details the criteria used for selecting the interplanetary events, and also try to investigate the relation between key parameters characterizing such interplanetary structures and the local time distributions of electron PAD shapes.

  4. Ab initio Thermodynamic Approach to Identify Mixed Solid Sorbents for CO2 Capture Technology

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    Yuhua eDuan

    2015-10-01

    Full Text Available Because the current technologies for capturing CO2 are still too energy intensive, new materials must be developed that can capture CO2 reversibly with acceptable energy costs. At a given CO2 pressure, the turnover temperature (Tt of the reaction of an individual solid that can capture CO2 is fixed. Such Tt may be outside the operating temperature range (ΔTo for a practical capture technology. To adjust Tt to fit the practical ΔTo, in this study, three scenarios of mixing schemes are explored by combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations. Our calculated results demonstrate that by mixing different types of solids, it’s possible to shift Tt to the range of practical operating temperature conditions. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO2 capture reactions by the mixed solids of interest, we were able to identify the mixing ratios of two or more solids to form new sorbent materials for which lower capture energy costs are expected at the desired pressure and temperature conditions.

  5. IDENTIFYING THE INDUSTRY BUSINESS CYCLE USING THE MARKOV SWITCHING APPROACH IN CENTRAL AND EASTERN EUROPE

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    Cristi SPULBĂR

    2012-01-01

    Full Text Available In this article we use a Markov Switching model with two lags to identify and to compare the business cycle in Romania, Czech Republic, Hungary and Poland using data on industrial production for the 1991-2011 period. We use a model with two regimes that reflect the economic expansions and contractions. The Markov Switching models have been widely used in order to detect and to date the business cycle turning points. However, it should be pointed out that the industrial production may have a little bit different dynamics than the quarterly gross domestic product which is the main measure of economic activity. Based on the smoothed regime probabilities the model track three recessionary periods of the Romanian economy in 1991, 1997 and 2009 and two recessionary periods for the other countries in 1991 and 2009. Mean yoy growth of IPI is 5.01% during expansion periods, while it switches to -18.6% during contraction periods for the Romanian economy. In comparison, mean yoy growth of IPI is 7.25% during expansion periods, while it switches to -13.4% during contraction periods for the Poland economy. Furthermore, in Romania, the duration of the three recessions in months was 25, 25 and 9 months. In Poland, the duration of the two recessions was 16 and 10 months. The results of the study may be used in order to compare the business cycle in Central and Eastern European countries with the Euro Area business cycle.

  6. Know Your Monkey: Identifying Primate Conservation Challenges in an Indigenous Kichwa Community Using an Ethnoprimatological Approach.

    Science.gov (United States)

    Stafford, Ciara A; Alarcon-Valenzuela, Javiera; Patiño, Javier; Preziosi, Richard F; Sellers, William I

    2016-01-01

    Increasing pressure on tropical forests is continually highlighting the need to find new solutions that mitigate the impact of human populations on biodiversity. However, developing solutions that can tackle the drivers of anthropogenic pressure, or at least take them into account, hinges upon building a good understanding of the culture and perceptions of local people. This study aims to provide an overview of the ethnoprimatology of an indigenous Kichwa community in the Ecuadorian Amazon that maintains a traditional lifestyle but also has good access to markets. We examine whether primates are seen as a distinctive group and their relative importance as sources of bushmeat and as household pets. Pile-sorting exercises revealed that although locals generally group members of the order Primates together, tree-dwelling non-primates including sloths, coatis, kinkajous and tamanduas are also frequently classified as 'monkeys'. The perceived importance of primates to the forest and the community lay more in their potential as bushmeat, and only 1 respondent identified an ecological role for the group in terms of seed dispersal. Gaining a better understanding of local perceptions will allow for better-informed conservation decisions that are more aware of potential impacts and are more likely to gain community support.

  7. Evaluating the impact of interdisciplinary research: a multilayer network approach

    CERN Document Server

    Omodei, Elisa; Arenas, Alex

    2016-01-01

    Nowadays, scientific challenges usually require approaches that cross traditional boundaries between academic disciplines, driving many researchers towards interdisciplinarity. Despite its obvious importance, there is a lack of studies on how to quantify the influence of interdisciplinarity on the research impact, posing uncertainty in a proper evaluation for hiring and funding purposes. Here we propose a method based on the analysis of bipartite interconnected multilayer networks of citations and disciplines, to assess scholars, institutions and countries interdisciplinary importance. Using data about physics publications and US patents, we show that our method allows to reveal, using a quantitative approach, that being more interdisciplinary causes -- in the Granger sense -- benefits in scientific productivity and impact. The proposed method could be used by funding agencies, universities and scientific policy decision makers for hiring and funding purposes, and to complement existing methods to rank univer...

  8. Ecosystem approach to inland fisheries: research needs and implementation strategies

    Science.gov (United States)

    Beard, T. Douglas; Arlinghaus, Robert; Cooke, Steven J.; McIntyre, Peter B.; De Silva, Sena; Bartley, Devin M.; Cowx, Ian G.

    2011-01-01

    Inland fisheries are a vital component in the livelihoods and food security of people throughout the world, as well as contributing huge recreational and economic benefits. These valuable assets are jeopardized by lack of research-based understanding of the impacts of fisheries on inland ecosystems, and similarly the impact of human activities associated with inland waters on fisheries and aquatic biodiversity. To explore this topic, an international workshop was organized in order to examine strategies to incorporate fisheries into ecosystem approaches for management of inland waters. To achieve this goal, a new research agenda is needed that focuses on: quantifying the ecosystem services provided by fresh waters; quantifying the economic, social and nutritional benefits of inland fisheries; improving assessments designed to evaluate fisheries exploitation potential; and examining feedbacks between fisheries, ecosystem productivity and aquatic biodiversity. Accomplishing these objectives will require merging natural and social science approaches to address coupled social–ecological system dynamics.

  9. A zone-based approach to identifying urban land uses using nationally-available data

    Science.gov (United States)

    Falcone, James A.

    Accurate identification of urban land use is essential for many applications in environmental study, ecological assessment, and urban planning, among other fields. However, because physical surfaces of land cover types are not necessarily related to their use and economic function, differentiating among thematically-detailed urban land uses (single-family residential, multi-family residential, commercial, industrial, etc.) using remotely-sensed imagery is a challenging task, particularly over large areas. Because the process requires an interpretation of tone/color, size, shape, pattern, and neighborhood association elements within a scene, it has traditionally been accomplished via manual interpretation of aerial photography or high-resolution satellite imagery. Although success has been achieved for localized areas using various automated techniques based on high-spatial or high-spectral resolution data, few detailed (Anderson Level II equivalent or greater) urban land use mapping products have successfully been created via automated means for broad (multi-county or larger) areas, and no such product exists today for the United States. In this study I argue that by employing a zone-based approach it is feasible to map thematically-detailed urban land use classes over large areas using appropriate combinations of non-image based predictor data which are nationally and publicly available. The approach presented here uses U.S. Census block groups as the basic unit of geography, and predicts the percent of each of ten land use types---nine of them urban---for each block group based on a number of data sources, to include census data, nationally-available point locations of features from the USGS Geographic Names Information System, historical land cover, and metrics which characterize spatial pattern, context (e.g. distance to city centers or other features), and measures of spatial autocorrelation. The method was demonstrated over a four-county area surrounding the

  10. Repurposing Approach Identifies Auranofin with Broad Spectrum Antifungal Activity That Targets Mia40-Erv1 Pathway

    Science.gov (United States)

    Thangamani, Shankar; Maland, Matthew; Mohammad, Haroon; Pascuzzi, Pete E.; Avramova, Larisa; Koehler, Carla M.; Hazbun, Tony R.; Seleem, Mohamed N.

    2017-01-01

    Current antifungal therapies have limited effectiveness in treating invasive fungal infections. Furthermore, the development of new antifungal is currently unable to keep pace with the urgent demand for safe and effective new drugs. Auranofin, an FDA-approved drug for the treatment of rheumatoid arthritis, inhibits growth of a diverse array of clinical isolates of fungi and represents a new antifungal agent with a previously unexploited mechanism of action. In addition to auranofin's potent antifungal activity against planktonic fungi, this drug significantly reduces the metabolic activity of Candida cells encased in a biofilm. Unbiased chemogenomic profiling, using heterozygous S. cerevisiae deletion strains, combined with growth assays revealed three probable targets for auranofin's antifungal activity—mia40, acn9, and coa4. Mia40 is of particular interest given its essential role in oxidation of cysteine rich proteins imported into the mitochondria. Biochemical analysis confirmed auranofin targets the Mia40-Erv1 pathway as the drug inhibited Mia40 from interacting with its substrate, Cmc1, in a dose-dependent manner similar to the control, MB-7. Furthermore, yeast mitochondria overexpressing Erv1 were shown to exhibit resistance to auranofin as an increase in Cmc1 import was observed compared to wild-type yeast. Further in vivo antifungal activity of auranofin was examined in a Caenorhabditis elegans animal model of Cryptococcus neoformans infection. Auranofin significantly reduced the fungal load in infected C. elegans. Collectively, the present study provides valuable evidence that auranofin has significant promise to be repurposed as a novel antifungal agent and may offer a safe, effective, and quick supplement to current approaches for treating fungal infections. PMID:28149831

  11. Considerations on a data-driven approach to identify plant's imprint on ecosystem functioning

    Science.gov (United States)

    Musavi, Talie; Kattge, Jens; Mahecha, Miguel; Reichstein, Markus; Van de Weg, Martine Janet; Van Bodegom, Peter; Bahn, Michael; Migliavacca, Mirco; Wirth, Christian; Reich, Peter

    2015-04-01

    Terrestrial ecosystems strongly determine the exchange of carbon, water and energy between the biosphere and atmosphere. These exchanges are influenced and partly driven by environmental conditions (e.g. local meteorology, soils), but generally mediated by organisms. In commonly used terrestrial biosphere models, this principle is implemented by process-based descriptions of plant functioning at the organ level. In order to validate these model formulations, we need an independent empirical approach to understand the plant's imprint on ecosystem functioning. We use land-atmosphere exchange of fluxes of CO2, H2O and energy in tandem with environmental controls available in FLUXNET to quantify "ecosystem functional properties" (EFPs). The latter are generally time-invariant ecosystem specific properties, for instance process sensitivities or efficiencies that shape ecosystem scale responses. Our crucial question is if plant traits measured at the organ level (available e.g. in the TRY database) can elucidate the characteristics of EFPs. In this study we follow this new avenue and link the two global databases FLUXNET and TRY to study the role of plants for biogeochemical cycles across a large number of different globally distributed ecosystem types. We aim to address emerging difficulties and possible solutions. For instance, we show that using average values of plant traits from TRY that are not necessarily measured at the fluxnet sites is of use but has clear limitations. However having information on the amount of vegetation at the sites derived from remote sensing is needed for weighting the plant traits. In addition, we have to consider that EFPs are not really time-invariant and subject to alterations after disturbance, meteorological extremes, management etc. Overall, we provide an outlook on perspectives and applications of empirical analyses of plants' imprint on ecosystem functioning by combining remote sensing, in situ measured plant traits and ecosystem

  12. Identifying Opportunities for Decision Support Systems in Support of Regional Resource Use Planning: An Approach Through Soft Systems Methodology.

    Science.gov (United States)

    Zhu; Dale

    2000-10-01

    / Regional resource use planning relies on key regional stakeholder groups using and having equitable access to appropriate social, economic, and environmental information and assessment tools. Decision support systems (DSS) can improve stakeholder access to such information and analysis tools. Regional resource use planning, however, is a complex process involving multiple issues, multiple assessment criteria, multiple stakeholders, and multiple values. There is a need for an approach to DSS development that can assist in understanding and modeling complex problem situations in regional resource use so that areas where DSSs could provide effective support can be identified, and the user requirements can be well established. This paper presents an approach based on the soft systems methodology for identifying DSS opportunities for regional resource use planning, taking the Central Highlands Region of Queensland, Australia, as a case study.

  13. Integrative approach to pain genetics identifies pain sensitivity loci across diseases.

    Directory of Open Access Journals (Sweden)

    David Ruau

    Full Text Available Identifying human genes relevant for the processing of pain requires difficult-to-conduct and expensive large-scale clinical trials. Here, we examine a novel integrative paradigm for data-driven discovery of pain gene candidates, taking advantage of the vast amount of existing disease-related clinical literature and gene expression microarray data stored in large international repositories. First, thousands of diseases were ranked according to a disease-specific pain index (DSPI, derived from Medical Subject Heading (MESH annotations in MEDLINE. Second, gene expression profiles of 121 of these human diseases were obtained from public sources. Third, genes with expression variation significantly correlated with DSPI across diseases were selected as candidate pain genes. Finally, selected candidate pain genes were genotyped in an independent human cohort and prospectively evaluated for significant association between variants and measures of pain sensitivity. The strongest signal was with rs4512126 (5q32, ABLIM3, P = 1.3×10⁻¹⁰ for the sensitivity to cold pressor pain in males, but not in females. Significant associations were also observed with rs12548828, rs7826700 and rs1075791 on 8q22.2 within NCALD (P = 1.7×10⁻⁴, 1.8×10⁻⁴, and 2.2×10⁻⁴ respectively. Our results demonstrate the utility of a novel paradigm that integrates publicly available disease-specific gene expression data with clinical data curated from MEDLINE to facilitate the discovery of pain-relevant genes. This data-derived list of pain gene candidates enables additional focused and efficient biological studies validating additional candidates.

  14. An evolutionary genomic approach to identify genes involved in human birth timing.

    Directory of Open Access Journals (Sweden)

    Jevon Plunkett

    2011-04-01

    Full Text Available Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have remained elusive, due to divergence in physiological mechanisms between humans and model organisms typically studied. Because of relatively large human head size and narrow birth canal cross-sectional area compared to other primates, we hypothesized that genes involved in parturition would display accelerated evolution along the human and/or higher primate phylogenetic lineages to decrease the length of gestation and promote delivery of a smaller fetus that transits the birth canal more readily. Further, we tested whether current variation in such accelerated genes contributes to preterm birth risk. Evidence from allometric scaling of gestational age suggests human gestation has been shortened relative to other primates. Consistent with our hypothesis, many genes involved in reproduction show human acceleration in their coding or adjacent noncoding regions. We screened >8,400 SNPs in 150 human accelerated genes in 165 Finnish preterm and 163 control mothers for association with preterm birth. In this cohort, the most significant association was in FSHR, and 8 of the 10 most significant SNPs were in this gene. Further evidence for association of a linkage disequilibrium block of SNPs in FSHR, rs11686474, rs11680730, rs12473870, and rs1247381 was found in African Americans. By considering human acceleration, we identified a novel gene that may be associated with preterm birth, FSHR. We anticipate other human accelerated genes will similarly be associated with preterm birth risk and elucidate essential pathways for human parturition.

  15. A combined approach to data mining of textual and structured data to identify cancer-related targets

    OpenAIRE

    Adelstein S James; Iyer Lakshmanan K; Pospisil Pavel; Kassis Amin I

    2006-01-01

    Abstract Background We present an effective, rapid, systematic data mining approach for identifying genes or proteins related to a particular interest. A selected combination of programs exploring PubMed abstracts, universal gene/protein databases (UniProt, InterPro, NCBI Entrez), and state-of-the-art pathway knowledge bases (LSGraph and Ingenuity Pathway Analysis) was assembled to distinguish enzymes with hydrolytic activities that are expressed in the extracellular space of cancer cells. Pr...

  16. Macrophage polarisation: an immunohistochemical approach for identifying M1 and M2 macrophages.

    Directory of Open Access Journals (Sweden)

    Mário Henrique M Barros

    Full Text Available Macrophage polarization is increasingly recognised as an important pathogenetic factor in inflammatory and neoplastic diseases. Proinflammatory M1 macrophages promote T helper (Th 1 responses and show tumoricidal activity. M2 macrophages contribute to tissue repair and promote Th2 responses. CD68 and CD163 are used to identify macrophages in tissue sections. However, characterisation of polarised macrophages in situ has remained difficult. Macrophage polarisation is regulated by transcription factors, pSTAT1 and RBP-J for M1, and CMAF for M2. We reasoned that double-labelling immunohistochemistry for the detection of macrophage markers together with transcription factors may be suitable to characterise macrophage polarisation in situ. To test this hypothesis, we have studied conditions associated with Th1- and Th2-predominant immune responses: infectious mononucleosis and Crohn's disease for Th1 and allergic nasal polyps, oxyuriasis, wound healing and foreign body granulomas for predominant Th2 response. In all situations, CD163+ cells usually outnumbered CD68+ cells. Moreover, CD163+ cells, usually considered as M2 macrophages, co-expressing pSTAT1 and RBP-J were found in all conditions examined. The numbers of putative M1 macrophages were higher in Th1- than in Th2-associated diseases, while more M2 macrophages were seen in Th2- than in Th1 related disorders. In most Th1-related diseases, the balance of M1 over M2 cells was shifted towards M1 cells, while the reverse was observed for Th2-related conditions. Hierarchical cluster analysis revealed two distinct clusters: cluster I included Th1 diseases together with cases with high numbers of CD163+pSTAT1+, CD68+pSTAT1+, CD163+RBP-J+ and CD68+RBP-J+ macrophages; cluster II comprised Th2 conditions together with cases displaying high numbers of CD163+CMAF+ and CD68+CMAF+ macrophages. These results suggest that the detection of pSTAT1, RBP-J, and CMAF in the context of CD68 or CD163 expression is a

  17. Social and behavioral research in genomic sequencing: approaches from the Clinical Sequencing Exploratory Research Consortium Outcomes and Measures Working Group.

    Science.gov (United States)

    Gray, Stacy W; Martins, Yolanda; Feuerman, Lindsay Z; Bernhardt, Barbara A; Biesecker, Barbara B; Christensen, Kurt D; Joffe, Steven; Rini, Christine; Veenstra, David; McGuire, Amy L

    2014-10-01

    The routine use of genomic sequencing in clinical medicine has the potential to dramatically alter patient care and medical outcomes. To fully understand the psychosocial and behavioral impact of sequencing integration into clinical practice, it is imperative that we identify the factors that influence sequencing-related decision making and patient outcomes. In an effort to develop a collaborative and conceptually grounded approach to studying sequencing adoption, members of the National Human Genome Research Institute's Clinical Sequencing Exploratory Research Consortium formed the Outcomes and Measures Working Group. Here we highlight the priority areas of investigation and psychosocial and behavioral outcomes identified by the Working Group. We also review some of the anticipated challenges to measurement in social and behavioral research related to genomic sequencing; opportunities for instrument development; and the importance of qualitative, quantitative, and mixed-method approaches. This work represents the early, shared efforts of multiple research teams as we strive to understand individuals' experiences with genomic sequencing. The resulting body of knowledge will guide recommendations for the optimal use of sequencing in clinical practice.

  18. A systems biology approach to identify the signalling network regulated by Rho-GDI-γ during neural stem cell differentiation.

    Science.gov (United States)

    Wang, Jiao; Hu, Fuyan; Cheng, Hua; Zhao, Xing-Ming; Wen, Tieqiao

    2012-11-01

    Understanding the molecular mechanism that underlies the differentiation of neural stem cells (NSCs) is vital to develop regenerative medicines for neurological disorders. In our previous work, Rho-GDI-γ was found to be able to prompt neuronal differentiation when it was down regulated. However, it is unclear how Rho-GDI-γ regulates this differentiation process. Therefore, a novel systems biology approach is presented here to identify putative signalling pathways regulated by Rho-GDI-γ during NSC differentiation, and these pathways can provide insights into the NSC differentiation mechanisms. In particular, our proposed approach combines the predictive power of computational biology and molecular experiments. With different biological experiments, the genes in the computationally identified signalling network were validated to be indeed regulated by Rho-GDI-γ during the differentiation of NSCs. In particular, one randomly selected pathway involving Vcp, Mapk8, Ywhae and Ywhah was experimentally verified to be regulated by Rho-GDI-γ. These promising results demonstrate the effectiveness of our proposed systems biology approach, indicating the potential predictive power of integrating computational and experimental approaches.

  19. A general model-based design of experiments approach to achieve practical identifiability of pharmacokinetic and pharmacodynamic models.

    Science.gov (United States)

    Galvanin, Federico; Ballan, Carlo C; Barolo, Massimiliano; Bezzo, Fabrizio

    2013-08-01

    The use of pharmacokinetic (PK) and pharmacodynamic (PD) models is a common and widespread practice in the preliminary stages of drug development. However, PK-PD models may be affected by structural identifiability issues intrinsically related to their mathematical formulation. A preliminary structural identifiability analysis is usually carried out to check if the set of model parameters can be uniquely determined from experimental observations under the ideal assumptions of noise-free data and no model uncertainty. However, even for structurally identifiable models, real-life experimental conditions and model uncertainty may strongly affect the practical possibility to estimate the model parameters in a statistically sound way. A systematic procedure coupling the numerical assessment of structural identifiability with advanced model-based design of experiments formulations is presented in this paper. The objective is to propose a general approach to design experiments in an optimal way, detecting a proper set of experimental settings that ensure the practical identifiability of PK-PD models. Two simulated case studies based on in vitro bacterial growth and killing models are presented to demonstrate the applicability and generality of the methodology to tackle model identifiability issues effectively, through the design of feasible and highly informative experiments.

  20. The Arts-Based Research’ approach: hints for educational research

    Directory of Open Access Journals (Sweden)

    Monica Pentassuglia

    2017-01-01

    Full Text Available The last two decades have seen a growing interest on the different ways of knowing in all the fields. Although some research has highlights the importance of this topic, there is still very little scientific understanding about this process. The first serious discussions and analyses of the construction of knowledge emerged during the 1900s. In Humanities field, questions have been raised about the use of traditional research paradigm considered unable for the understanding of these complex subjects. In this perspective, this article provided an important opportunity to advance the understanding of new research paths that not only overturn the classical perspective of research, but also allow us to reformulate and reinvent strategies, tools, and forms of representations of research findings. This article considers the implications of the approach of Arts-Based Research (ABR and deeply of dance-based methods for educational research.L’approccio dell’Arts-Based Research: quali spunti per la ricerca educativa?Tra i temi che più si sono imposti, negli ultimi anni, all’attenzione dei ricercatori, è il problema dei processi di costruzione della conoscenza ad aver catalizzato su di sé la maggior parte degli studi; è soprattutto in ambito umanistico che cresce l’idea secondo cui i classici paradigmi di ricerca non siano in grado di comprendere ed indagare la complessità dei fenomeni esplorati. Sulla scia di tali necessità, il presente contributo intende approfondire l’approccio dell’Arts-Based Research (ABR ed in particolare dei dance-based methods nel campo della ricerca educativa che negli ultimi anni sta contribuendo a capovolgere l’impostazione classica del processo di ricerca a favore di nuovi percorsi in grado di utilizzare le potenzialità dell’Arte secondo nuove prospettive.

  1. An evaluation of the 'Designated Research Team' approach to building research capacity in primary care

    Directory of Open Access Journals (Sweden)

    Dyas Jane

    2008-06-01

    Full Text Available Abstract Background This paper describes an evaluation of an initiative to increase the research capability of clinical groups in primary and community care settings in a region of the United Kingdom. The 'designated research team' (DRT approach was evaluated using indicators derived from a framework of six principles for research capacity building (RCB which include: building skills and confidence, relevance to practice, dissemination, linkages and collaborations, sustainability and infrastructure development. Methods Information was collated on the context, activities, experiences, outputs and impacts of six clinical research teams supported by Trent Research Development Support Unit (RDSU as DRTs. Process and outcome data from each of the teams was used to evaluate the extent to which the DRT approach was effective in building research capacity in each of the six principles (as evidenced by twenty possible indicators of research capacity development. Results The DRT approach was found to be well aligned to the principles of RCB and generally effective in developing research capabilities. It proved particularly effective in developing linkages, collaborations and skills. Where research capacity was slow to develop, this was reflected in poor alignment between the principles of RCB and the characteristics of the team, their activities or environment. One team was unable to develop a research project and the funding was withdrawn at an early stage. For at least one individual in each of the remaining five teams, research activity was sustained beyond the funding period through research partnerships and funding successes. An enabling infrastructure, including being freed from clinical duties to undertake research, and support from senior management were found to be important determinants of successful DRT development. Research questions of DRTs were derived from practice issues and several projects generated outputs with potential to change daily

  2. Research on runoff forecast approaches to the Aksu River basin

    Institute of Scientific and Technical Information of China (English)

    OUYANG RuLin; CHENG WeiMing; WANG WeiSheng; JIANG Yan; ZHANG YiChi; WANG YongQin

    2007-01-01

    The Aksu River (the international river between China and Kirghiz) has become the main water source for the Tarim River. It significantly influences the Tarim River's formation, development and evolution.Along with the western region development strategy and the Tarim River basin comprehensive development and implementation, the research is now focused on the Aksu River basin hydrologic characteristic and hydrologic forecast. Moreover, the Aksu River is representative of rivers supplied with glacier and snow melt in middle-high altitude arid district. As a result, the research on predicting the river flow of the Aksu River basin has theoretical and practical significance. In this paper, considering the limited hydrometeorological data for the Aksu River basin, we have constructed four hydrologic forecast approaches using the daily scale to simulate and forecast daily runoff of two big branches of the Aksu River basin. The four approaches are the upper air temperature and the daily runoff correlation method, AR(p) runoff forecast model, temperature and precipitation revised AR(p) model and the NAM rainfall-runoff model. After comparatively analyzing the simulation results of the four approaches, we discovered that the temperature and precipitation revised AR(p) model, which needs less hydrological and meteorological data and is more predictive, is suitable for the short-term runoff forecast of the Aksu River basin. This research not only offers a foundation for the Aksu River and Tarim Rivers' hydrologic forecast, flood prevention, control and the entire basin water collocation, but also provides the hydrologic forecast reference approach for other arid ungauged basins.

  3. Graduate Education to Facilitate Interdisciplinary Research Collaboration: Identifying Individual Competencies and Developmental Activities

    Science.gov (United States)

    Holt, Valerie Ciocca

    2013-01-01

    Interdisciplinary research collaborations (IDRC) are considered essential for addressing the most complex global community problems concerning science, health, education, energy, the environment, and society. In spite of technological advances, supportive funding, and even researcher proclivity to collaborate, these complex interdisciplinary…

  4. Q methodology and a Delphi poll: a useful approach to researching a narrative approach to therapy

    OpenAIRE

    2009-01-01

    Q methodology and a Delphi poll combined qualitative and quantitative methods to explore definitions of White and Epston's (1990) narrative approach to therapy among a group of UK practitioners. A Delphi poll was used to generate statements about narrative therapy. The piloting of statements by the Delphi panel identified agreement about theoretical ideas underpinning narrative therapy and certain key practices. A wider group of practitioners ranked the statements in a Q sort and made qualita...

  5. Non-gay-identifying men who have sex with men: formative research results from Seattle, Washington.

    OpenAIRE

    Goldbaum, G; Perdue, T R; Higgins, D.

    1996-01-01

    Non-gay-identifying men who have sex with men are at risk for human immunodeficiency virus (HIV) infection. To understand these men and to develop interventions to reduce their HIV risks, the authors interviewed staff at agencies that serve non-gay-identifying men who have sex with men, business people who interact with them, and the men themselves. Interviews were augmented with focus groups of non-gay-identifying men who have sex with men and field observations at sites identified as places...

  6. Knowledge Mobilization in Canadian Educational Research: Identifying Current Developments and Future Directions

    Directory of Open Access Journals (Sweden)

    Snezana Ratkovic

    2016-06-01

    Full Text Available In this special issue of Brock Education: Journal for Educational Research and Practice, we build on the knowledge mobilization (KMb discourses initiated by the Ontario Ministry of Education (MOE, Social Sciences and Humanities Research Council of Canada (SSHRC, Knowledge Network for Applied Education Research (KNAER, Canadian Society for the Study of Education (CSSE, and School District-University Research Exchange (SURE network. We feature five journal articles and a book review addressing the three main KMb questions: How to assess KMb efforts across educational systems?  To what extent do educators use research to inform their praxis? How to make KMb work?

  7. Spatial extent in demographic research - approach and problems

    Directory of Open Access Journals (Sweden)

    Knežević Aleksandar

    2015-01-01

    Full Text Available One of the starting methodological problems in demographic research is the definition of spatial extent, which mostly doesn’t correspond to spatial extent already defined by different levels of administrative-territorial unitsthat are used for distribution of usable statistical data. That’s why determining the spatial extent of a demographic research is closely tied with administrative-territorial division of the territory that is being researched, wherein the fact that differentiation of demographic phenomena and processes cannot be the only basis of setting the principles of regionalization must be strictly acknowledged. This problem is particularly common in historical demographic analyses of geographically determined wholes, which are in administratively-territorial sense represented by one or more smaller territorial units, with their borders changing through the history, which directly affects comparability of the statistical data, and makes it considerably more difficult to track demographic change through longer time intervals. The result of these efforts is usually a solution based on a compromise which enables us to examine the dynamics of population change with little deviation from already defined borders of regional geographic wholes. For that reason in this paper the problem of defining spatial extent in demographic research is examined trough several different approaches in case of Eastern Serbia, as a geographically determined region, a historic area, a spatially functioning whole and as a statistical unit for demographic research, with no judgment calls in regard to any of the regionalization principles. [Projekat Ministarstva nauke Republike Srbije, br. III 47006

  8. Sniffer dogs as part of a bimodal bionic research approach to develop a lung cancer screening.

    Science.gov (United States)

    Boedeker, Enole; Friedel, Godehard; Walles, Thorsten

    2012-05-01

    Lung cancer (LC) continues to represent a heavy burden for health care systems worldwide. Epidemiological studies predict that its role will increase in the near future. While patient prognosis is strongly associated with tumour stage and early detection of disease, no screening test exists so far. It has been suggested that electronic sensor devices, commonly referred to as 'electronic noses', may be applicable to identify cancer-specific volatile organic compounds in the breath of patients and therefore may represent promising screening technologies. However, three decades of research did not bring forward a clinically applicable device. Here, we propose a new research approach by involving specially trained sniffer dogs into research strategies by making use of their ability to identify LC in the breath sample of patients.

  9. New approaches to social and economic research on schistosomiasis in TDR

    Directory of Open Access Journals (Sweden)

    Carol Vlassoff

    1992-01-01

    Full Text Available This paper describes new approaches to social and economic research being developed by the Social and Economic Research component of the Special Programme for Research and Trainning in Tropical Diseases of the World Health Organization. One of these is a study to acess the possibility of identifying high risk communities for urinary schistosomiasis through a "mailed"questionaire approach distributed through an existing administrative system, thereby eliminating the need for face-to-face interviews by the research or disease control team. This approach, developed by the Swiss Tropical Institute in Ifakara, Tanzania, i s currently being tested in seven other African countries. The paper also describes a change of emphasis of economic research on schistosomiasis, focusing on the intra-household effects of the disease on rural households, rather than, as previously done, studying the impact of the disease on the productivity of individual wage labourers. Other priorities involve the identification of epidemiological information neede for improoved decision-making regarding acceptable treatment strategies in endemic areas with limited financial capacity, as well as research on how the adverse effects of economic development projects can be alleviated.

  10. A weight-of-evidence approach to identify nanomaterials in consumer products: a case study of nanoparticles in commercial sunscreens.

    Science.gov (United States)

    Cuddy, Michael F; Poda, Aimee R; Moser, Robert D; Weiss, Charles A; Cairns, Carolyn; Steevens, Jeffery A

    2016-01-01

    Nanoscale ingredients in commercial products represent a point of emerging environmental concern due to recent findings that correlate toxicity with small particle size. A weight-of-evidence (WOE) approach based upon multiple lines of evidence (LOE) is developed here to assess nanomaterials as they exist in consumer product formulations, providing a qualitative assessment regarding the presence of nanomaterials, along with a baseline estimate of nanoparticle concentration if nanomaterials do exist. Electron microscopy, analytical separations, and X-ray detection methods were used to identify and characterize nanomaterials in sunscreen formulations. The WOE/LOE approach as applied to four commercial sunscreen products indicated that all four contained at least 10% dispersed primary particles having at least one dimension <100 nm in size. Analytical analyses confirmed that these constituents were comprised of zinc oxide (ZnO) or titanium dioxide (TiO2). The screening approaches developed herein offer a streamlined, facile means to identify potentially hazardous nanomaterial constituents with minimal abrasive processing of the raw material.

  11. Approaches to identifying reservoir heterogeneity and reserve growth opportunities from subsurface data: The Oficina Formation, Budare field, Venezuela

    Energy Technology Data Exchange (ETDEWEB)

    Hamilton, D.S.; Raeuchle, S.K.; Holtz, M.H. [Bureau of Economic Geology, Austin, TX (United States)] [and others

    1997-08-01

    We applied an integrated geologic, geophysical, and engineering approach devised to identify heterogeneities in the subsurface that might lead to reserve growth opportunities in our analysis of the Oficina Formation at Budare field, Venezuela. The approach involves 4 key steps: (1) Determine geologic reservoir architecture; (2) Investigate trends in reservoir fluid flow; (3) Integrate fluid flow trends with reservoir architecture; and (4) Estimate original oil-in-place, residual oil saturation, and remaining mobile oil, to identify opportunities for reserve growth. There are three main oil-producing reservoirs in the Oficina Formation that were deposited in a bed-load fluvial system, an incised valley-fill, and a barrier-strandplain system. Reservoir continuity is complex because, in addition to lateral facies variability, the major Oficina depositional systems were internally subdivided by high-frequency stratigraphic surfaces. These surfaces define times of intermittent lacustrine and marine flooding events that punctuated the fluvial and marginal marine sedimentation, respectively. Syn and post depositional faulting further disrupted reservoir continuity. Trends in fluid flow established from initial fluid levels, response to recompletion workovers, and pressure depletion data demonstrated barriers to lateral and vertical fluid flow caused by a combination of reservoir facies pinchout, flooding shale markers, and the faults. Considerable reserve growth potential exists at Budare field because the reservoir units are highly compartment by the depositional heterogeneity and structural complexity. Numerous reserve growth opportunities were identified in attics updip of existing production, in untapped or incompletely drained compartments, and in field extensions.

  12. Who’s Who at the Border? A rights-based approach to identifying human trafficking at international borders

    Directory of Open Access Journals (Sweden)

    Marika McAdam

    2013-11-01

    Full Text Available International borders are widely touted as bastions in the fight against trafficking in persons. This article acknowledges the important role border officials play in preventing human trafficking, but calls for expectations to be tempered by deference to the conceptual complexity of cross-border trafficking and the migration processes involved. The fact that many trafficked victims begin their journeys as irregular or smuggled migrants highlights the challenge posed to border officials in identifying trafficked persons among the people they encounter. Indicators of trafficking generally relate to the exploitation phase, leaving border officials with little guidance as to how persons vulnerable to trafficking can be accurately identified before any exploitation has occurred. Ultimately, this paper advocates a pragmatic rights-based approach in designating anti-trafficking functions to border officials. A rights-based approach to border control acknowledges the core work of border officials as being to uphold border integrity, while ensuring that their performance of this role does not jeopardise the rights of those they intercept nor result in missed opportunities for specialists to identify trafficked persons and other vulnerable people among them.

  13. A GENERAL APPROACH TO THE TOURISM RESEARCH IN SINALOA

    Directory of Open Access Journals (Sweden)

    Luis Miguel Flores-Campaña

    2015-01-01

    Full Text Available The historical development of tourism research is described, analyzing trends in the short term and the role they have played some government agencies to support tourism and training of human resources in Sinaloa. He was elected to Mazatlan, main tourist destination in the state, to establish the development of tourism research in Sinaloa, using cognitive arguments to analyze its scientific nature also epistemological and scientific level compared from the academic production two units of higher education in the centennial Autonomous University of Sinaloa. 40 educational training and human resource development for the tourism sector in seven municipalities of the state territory, both in public institutions (20 and private (20, four of them in training, a similar number in the high school level were identified , two higher technical college, 27 undergraduate and graduate in only three. This type of provision begins in the early 1970s and today, 12 schools have closed or changed programs, while 28 are active. Limited articulation between management and tourism policy, whose pillars are academic institutions aimed at tourism research in sight. The creation of a government agency dedicated to tourism research to determine, monitor and implement plans to adverse situations emerging in tourist destinations in Sinaloa, under consistent, rigorous and systematic processes, as required by all scientific research is recommended.

  14. Strategic approach to information security and assurance in health research.

    Science.gov (United States)

    Akazawa, Shunichi; Igarashi, Manabu; Sawa, Hirofumi; Tamashiro, Hiko

    2005-09-01

    and certification, risk assessment and audit, monitoring and incident response, awareness and training, and modern protection method and architecture. Governments should enforce a comprehensive scheme, and international health research communities should adopt standardized innovative methods and approaches.

  15. An evaluation approach for research project pilot technological applications

    Science.gov (United States)

    Marcelino-Jesus, Elsa; Sarraipa, Joao; Jardim-Goncalves, Ricardo

    2013-10-01

    In a world increasingly more competitive and in a constantly development and growth it's important that companies have economic tools, like frameworks to help them to evaluate and validate the technology development to better fits in each company particular needs. The paper presents an evaluation approach for research project pilot applications to stimulate its implementation and deployment, increasing its adequacy and acceptance to their stakeholders and consequently providing new business profit and opportunities. Authors used the DECIDE evaluation framework as a major guide to this approach, which was tested in the iSURF project to support the implementation of an interoperability service utility for collaborative supply chain planning across multiple domains supported by RFID devices.

  16. Research on teacher education programs: logic model approach.

    Science.gov (United States)

    Newton, Xiaoxia A; Poon, Rebecca C; Nunes, Nicole L; Stone, Elisa M

    2013-02-01

    Teacher education programs in the United States face increasing pressure to demonstrate their effectiveness through pupils' learning gains in classrooms where program graduates teach. The link between teacher candidates' learning in teacher education programs and pupils' learning in K-12 classrooms implicit in the policy discourse suggests a one-to-one correspondence. However, the logical steps leading from what teacher candidates have learned in their programs to what they are doing in classrooms that may contribute to their pupils' learning are anything but straightforward. In this paper, we argue that the logic model approach from scholarship on evaluation can enhance research on teacher education by making explicit the logical links between program processes and intended outcomes. We demonstrate the usefulness of the logic model approach through our own work on designing a longitudinal study that focuses on examining the process and impact of an undergraduate mathematics and science teacher education program.

  17. Research gaps identified during systematic reviews of clinical trials: glass-ionomer cements

    OpenAIRE

    Mickenautsch Steffen

    2012-01-01

    Abstract Background To report the results of an audit concerning research gaps in clinical trials that were accepted for appraisal in authored and published systematic reviews regarding the application of glass-ionomer cements (GIC) in dental practice Methods Information concerning research gaps in trial precision was extracted, following a framework that included classification of the research gap reasons: ‘imprecision of information (results)’, ‘biased information’, ‘inconsistency or unknow...

  18. The personnel economics approach to public workforce research.

    Science.gov (United States)

    Gibbs, Michael

    2009-11-01

    This article argues that the relatively new field of personnel economics (PE) holds strong potential as a tool for studying public sector workforces. This subfield of labor economics is based on a strong foundation of microeconomics, which provides a robust theoretical foundation for studying workforce and organizational design issues. PE has evolved on this foundation to a strong practical emphasis, with theoretical insights designed for practical use and with strong focus on empirical research. The field is also characterized by creative data entrepreneurship. The types of datasets that personnel economists use are described. If similar datasets can be obtained for public sector workforces, PE should be a very useful approach for studying them.

  19. An Institutional Approach to Developing Research Data Management Infrastructure

    Directory of Open Access Journals (Sweden)

    James A. J. Wilson

    2011-10-01

    Full Text Available This article outlines the work that the University of Oxford is undertaking to implement a coordinated data management infrastructure. The rationale for the approach being taken by Oxford is presented, with particular attention paid to the role of each service division. This is followed by a consideration of the relative advantages and disadvantages of institutional data repositories, as opposed to national or international data centres. The article then focuses on two ongoing JISC-funded projects, ‘Embedding Institutional Data Curation Services in Research’ (Eidcsr and ‘Supporting Data Management Infrastructure for the Humanities’ (Sudamih. Both projects are intra-institutional collaborations and involve working with researchers to develop particular aspects of infrastructure, including: University policy, systems for the preservation and documentation of research data, training and support, software tools for the visualisation of large images, and creating and sharing databases via the Web (Database as a Service.

  20. A Participatory Research Approach to develop an Arabic Symbol Dictionary.

    Science.gov (United States)

    Draffan, E A; Kadous, Amatullah; Idris, Amal; Banes, David; Zeinoun, Nadine; Wald, Mike; Halabi, Nawar

    2015-01-01

    The purpose of the Arabic Symbol Dictionary research discussed in this paper, is to provide a resource of culturally, environmentally and linguistically suitable symbols to aid communication and literacy skills. A participatory approach with the use of online social media and a bespoke symbol management system has been established to enhance the process of matching a user based Arabic and English core vocabulary with appropriate imagery. Participants including AAC users, their families, carers, teachers and therapists who have been involved in the research from the outset, collating the vocabularies, debating cultural nuances for symbols and critiquing the design of technologies for selection procedures. The positive reaction of those who have voted on the symbols with requests for early use have justified the iterative nature of the methodologies used for this part of the project. However, constant re-evaluation will be necessary and in depth analysis of all the data received has yet to be completed.

  1. Research studies on patients' illness experience using the Narrative Medicine approach: a systematic review

    Science.gov (United States)

    Fioretti, Chiara; Mazzocco, Ketti; Oliveri, Serena; Masiero, Marianna; Pravettoni, Gabriella

    2016-01-01

    Objective Since its birth about 30 years ago, Narrative Medicine approach has increased in popularity in the medical context as well as in other disciplines. This paper aims to review Narrative Medicine research studies on patients' and their caregivers' illness experience. Setting and participants MEDLINE, Psycinfo, EBSCO Psychological and Behavioural Science, The Cochrane Library and CINAHL databases were searched to identify all the research studies which focused on the Narrative Medicine approach reported in the title, in the abstract and in the keywords the words ‘Narrative Medicine’ or ‘Narrative-based Medicine’. Primary and secondary outcome measures: number of participants, type of disease, race and age of participants, type of study, dependent variables, intervention methods, assessment. Results Of the 325 titles screened, we identified 10 research articles fitting the inclusion criteria. Our systematic review showed that research on Narrative Medicine has no common specific methodology: narrative in Medicine is used as an intervention protocol as well as an assessment tool. Patients' characteristics, types of disease and data analysis procedures differ among the screened studies. Conclusions Narrative Medicine research in medical practice needs to find clear and specific protocols to deepen the impact of narrative on medical practice and on patients' lives. PMID:27417197

  2. Comparison of two model approaches in the Zambezi river basin with regard to model reliability and identifiability

    Directory of Open Access Journals (Sweden)

    H. C. Winsemius

    2006-01-01

    Full Text Available Variations of water stocks in the upper Zambezi river basin have been determined by 2 different hydrological modelling approaches. The purpose was to provide preliminary terrestrial storage estimates in the upper Zambezi, which will be compared with estimates derived from the Gravity Recovery And Climate Experiment (GRACE in a future study. The first modelling approach is GIS-based, distributed and conceptual (STREAM. The second approach uses Lumped Elementary Watersheds identified and modelled conceptually (LEW. The STREAM model structure has been assessed using GLUE (Generalized Likelihood Uncertainty Estimation a posteriori to determine parameter identifiability. The LEW approach could, in addition, be tested for model structure, because computational efforts of LEW are low. Both models are threshold models, where the non-linear behaviour of the Zambezi river basin is explained by a combination of thresholds and linear reservoirs. The models were forced by time series of gauged and interpolated rainfall. Where available, runoff station data was used to calibrate the models. Ungauged watersheds were generally given the same parameter sets as their neighbouring calibrated watersheds. It appeared that the LEW model structure could be improved by applying GLUE iteratively. Eventually, it led to better identifiability of parameters and consequently a better model structure than the STREAM model. Hence, the final model structure obtained better represents the true hydrology. After calibration, both models show a comparable efficiency in representing discharge. However the LEW model shows a far greater storage amplitude than the STREAM model. This emphasizes the storage uncertainty related to hydrological modelling in data-scarce environments such as the Zambezi river basin. It underlines the need and potential for independent observations of terrestrial storage to enhance our understanding and modelling capacity of the hydrological processes. GRACE

  3. CONDITIONAL PROBABILITY ANALYSIS APPROACH FOR IDENTIFYING BIOLOGICAL THRESHOLD OF IMPACT FOR SEDIMENTATION: APPICATION TO FRESHWATER STREAMS IN OREGON COAST RANGE ECOREGION

    Science.gov (United States)

    A conditional probability analysis (CPA) approach has been developed for identifying biological thresholds of impact for use in the development of geographic-specific water quality criteria for protection of aquatic life. This approach expresses the threshold as the likelihood ...

  4. Research Information System in Health Domain: Comparative Approach

    Directory of Open Access Journals (Sweden)

    Ramezan Ghorbani Nahid

    2015-07-01

    Full Text Available Objective: In recent decades, in low-income developing countries, management has faced serious challenges due to deficient information. An increasing number of dispersed data, concepts, observation of poor outputs, and separate software applications aggravated the situation, too. In order to promote and balance the research environment in the field of health, developing a platform for appropriate interactions is essential. Thus, the basic question is what requirements must be considered for suitable health research information system in Iran? Materials and Methods: The present study is a descriptive-comparative approach conducted in Iran in the years 2010-2011. System requirements of research information in Iran, United States, Australia, Japan and Netherland were reviewed and compared. Checklist was used for data collection. Data was collected from conference and journals papers and relevant manuals/guidelines from websites on their systems. Finally, data collected in the comparative tables were compared and described. Results: The requirement for national health research information system were determined based on the following central axis: structure, content, methods of gathering information, services and capabilities and methods of disseminating information which were assigned base on common and diverse components in countries’ systems. Conclusion: In order to achieve this national system, it is important that there should be a common serious determination for its development, change in attitude and culture of the researcher’s society in the domain of health and also improvement in the country’s information and communications technology (ICT infrastructure.

  5. Integrated pathway-based approach identifies association between genomic regions at CTCF and CACNB2 and schizophrenia.

    Directory of Open Access Journals (Sweden)

    Dilafruz Juraeva

    2014-06-01

    Full Text Available In the present study, an integrated hierarchical approach was applied to: (1 identify pathways associated with susceptibility to schizophrenia; (2 detect genes that may be potentially affected in these pathways since they contain an associated polymorphism; and (3 annotate the functional consequences of such single-nucleotide polymorphisms (SNPs in the affected genes or their regulatory regions. The Global Test was applied to detect schizophrenia-associated pathways using discovery and replication datasets comprising 5,040 and 5,082 individuals of European ancestry, respectively. Information concerning functional gene-sets was retrieved from the Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and the Molecular Signatures Database. Fourteen of the gene-sets or pathways identified in the discovery dataset were confirmed in the replication dataset. These include functional processes involved in transcriptional regulation and gene expression, synapse organization, cell adhesion, and apoptosis. For two genes, i.e. CTCF and CACNB2, evidence for association with schizophrenia was available (at the gene-level in both the discovery study and published data from the Psychiatric Genomics Consortium schizophrenia study. Furthermore, these genes mapped to four of the 14 presently identified pathways. Several of the SNPs assigned to CTCF and CACNB2 have potential functional consequences, and a gene in close proximity to CACNB2, i.e. ARL5B, was identified as a potential gene of interest. Application of the present hierarchical approach thus allowed: (1 identification of novel biological gene-sets or pathways with potential involvement in the etiology of schizophrenia, as well as replication of these findings in an independent cohort; (2 detection of genes of interest for future follow-up studies; and (3 the highlighting of novel genes in previously reported candidate regions for schizophrenia.

  6. The promoter competition assay (PCA): a new approach to identify motifs involved in the transcriptional activity of reporter genes.

    Science.gov (United States)

    Hube, Florent; Myal, Yvonne; Leygue, Etienne

    2006-05-01

    Identifying particular motifs responsible for promoter activity is a crucial step toward the development of new gene-based preventive and therapeutic strategies. However, to date, experimental methods to study promoter activity remain limited. We present in this report a promoter competition assay designed to identify, within a given promoter region, motifs critical for its activity. This assay consists in co-transfecting the promoter to be analyzed and double-stranded oligonucleotides which will compete for the binding of transcription factors. Using the recently characterized SBEM promoter as model, we first delineated the feasibility of the method and optimized the experimental conditions. We then identified, within an 87-bp region responsible for a strong expression of the reporter gene, an octamer-binding site essential for its transcriptional regulation. The importance of this motif has been confirmed by site-directed mutagenesis. The promoter competition assay appears to be a fast and efficient approach to identify, within a given promoter sequence, sites critical for its activity.

  7. A combined approach to data mining of textual and structured data to identify cancer-related targets

    Directory of Open Access Journals (Sweden)

    Adelstein S James

    2006-07-01

    Full Text Available Abstract Background We present an effective, rapid, systematic data mining approach for identifying genes or proteins related to a particular interest. A selected combination of programs exploring PubMed abstracts, universal gene/protein databases (UniProt, InterPro, NCBI Entrez, and state-of-the-art pathway knowledge bases (LSGraph and Ingenuity Pathway Analysis was assembled to distinguish enzymes with hydrolytic activities that are expressed in the extracellular space of cancer cells. Proteins were identified with respect to six types of cancer occurring in the prostate, breast, lung, colon, ovary, and pancreas. Results The data mining method identified previously undetected targets. Our combined strategy applied to each cancer type identified a minimum of 375 proteins expressed within the extracellular space and/or attached to the plasma membrane. The method led to the recognition of human cancer-related hydrolases (on average, ~35 per cancer type, among which were prostatic acid phosphatase, prostate-specific antigen, and sulfatase 1. Conclusion The combined data mining of several databases overcame many of the limitations of querying a single database and enabled the facile identification of gene products. In the case of cancer-related targets, it produced a list of putative extracellular, hydrolytic enzymes that merit additional study as candidates for cancer radioimaging and radiotherapy. The proposed data mining strategy is of a general nature and can be applied to other biological databases for understanding biological functions and diseases.

  8. Identifying Faculty Types Using Peer Ratings of Teaching, Research, and Service.

    Science.gov (United States)

    Kremer, John

    1991-01-01

    A study classified 90 full-time tenure-track faculty in 1 university into 5 discrete types based on teaching, research, and service. Types include all-stars, teachers and good citizens, researchers, teachers, and uninvolved. This mix of types is seen as resulting from past administrative decisions and helps shape future decisions. (Author/MSE)

  9. Identifying and Intervening with Substance-Using Women Exposed to Intimate Partner Violence: Phenomenology, Comorbidities, and Integrated Approaches Within Primary Care and Other Agency Settings

    Science.gov (United States)

    Gilbert, Louisa; El-Bassel, Nabila; Resnick, Heidi S.; Noursi, Samia

    2015-01-01

    Abstract Substance use and/or disorders (SUDs) have been identified as a significant correlate of intimate partner violence (IPV) exposure and present complex issues that intersect with the topography of IPV, attendant mental health, and physical co-morbidities and may pose barriers to primary care- and other agency-based screening and intervention efforts. Despite substantial research indicating significantly higher rates of all types and severity of IPV victimization among women with SUDs and bidirectional associations between partner or self-use of drugs or alcohol and IPV victimization, effective screening, brief interventions, coordinated systems of care, and treatment approaches to address these co-occurring problems remain very limited. We integrated select research examining the intersection of IPV victimization and SUDs and several comorbidities that have significant public health impact and provided recommendations for scaling up targeted interventions to redress these co-occurring problems among women in primary, emergency, and other care settings. PMID:25554915

  10. Evaluating international research ethics capacity development: an empirical approach.

    Science.gov (United States)

    Ali, Joseph; Kass, Nancy E; Sewankambo, Nelson K; White, Tara D; Hyder, Adnan A

    2014-04-01

    The US national institutes of health, Fogarty International Center (NIH-FIC) has, for the past 13 years, been a leading funder of international research ethics education for resource-limited settings. Nearly half of the NIH-FIC funding in this area has gone to training programs that train individuals from sub-Saharan Africa. Identifying the impact of training investments, as well as the potential predictors of post-training success, can support curricular decisionmaking, help establish funding priorities, and recognize the ultimate outcomes of trainees and training programs. Comprehensive evaluation frameworks and targeted evaluation tools for bioethics training programs generally, and for international research ethics programs in particular, are largely absent from published literature. This paper shares an original conceptual framework, data collection tool, and detailed methods for evaluating the inputs, processes, outputs, and outcomes of research ethics training programs serving individuals in resource-limited settings. This paper is part of a collection of papers analyzing the Fogarty International Center's International Research Ethics Education and Curriculum Development program.

  11. Identifying Ethical Issues in Mental Health Research with Minors Adolescents: Results of a Delphi Study

    Directory of Open Access Journals (Sweden)

    Elisabeta Ioana Hiriscau

    2016-05-01

    Full Text Available Research with minors, especially for preventive purposes, e.g., suicide prevention, investigating risk or self-destructive behaviors such as deviance, drug abuse, or suicidal behavior, is ethically sensitive. We present a Delphi study exploring the ethical implications of the needs formulated by researchers in an international pre-conference who would benefit from ethics support and guidance in conducting Mental Health Research with minors. The resulting List of Ethical Issues (LEI was submitted to a 2-rounds Delphi process via the Internet, including 34 multidisciplinary experts. In the first round, the experts reviewed the LEI and completed a questionnaire. Results from this round were analyzed and grouped in nine categories comprising 40 items. In the second round, the experts had to agree/disagree with the needs expressed in the LEI leading to a final list of 25 ethical issues considered relevant for Mental Health Research with minors such as: confidentiality of the sensitive data, competence for consenting alone and risk of harm and stigma related to the methodology used in research. It was shown that studies like SEYLE (Saving and Empowering Young Lives in Europe trigger among researchers wishes to obtain specific recommendations helping to comply with standards for good practice in conducting research with minors.

  12. A new approach in cross-domain collaborative research

    Science.gov (United States)

    Diviacco, Paolo; Fox, Peter; Busato, Alessandro

    2016-04-01

    Scientific research commonly faces the study of complex systems where multiple skills and competences are needed at the same time. Effective collaboration among researchers then becomes of paramount importance. Multidisciplinary studies imply the use of information and knowledge from domains that can be rather far from each other. Notwithstanding this, researchers, need to understand: what they handle, how to extract what they need and eventually produce something that can be used also by others. The management of information and knowledge in this perspective is not trivial. To develop methods and tools able to support such activities we need to analyze how collaborative research takes place. Besides the standard view that picture scientists committed to their endeavour to achieve solid and undebatable results, modern epistemology and sociology of science added a more fluid perspective where science can be considered mostly a social construct conditioned also by cognitive issues. These aspects cannot be obliterated; on the contrary they need to be carefully taken into consideration. Information is to be built from different perspectives and ways of thinking by actors with different point of views, approaches and aims, and in this, data should be understandable by all the designated community. In fact different communities develop their own ways of thinking, language and even myths, in other words they can be considered such as different cultures. To address these issues we invoke two strategies: (I) to formalize all the knowledge relevant for the study. This will means resolving all conflicting models among actors; something that is theoretically and has been demonstrated practically, very difficult to achieve. (II) Exploit the results of ethnographic studies conducted in the 1990's that explained how the introduction of representative artifacts allow different cultures to understand and use the same concepts in a different way. Both approaches have limitations and

  13. SMpred: a support vector machine approach to identify structural motifs in protein structure without using evolutionary information.

    Science.gov (United States)

    Pugalenthi, Ganesan; Kandaswamy, Krishna Kumar; Suganthan, P N; Sowdhamini, R; Martinetz, Thomas; Kolatkar, Prasanna R

    2010-12-01

    Knowledge of three dimensional structure is essential to understand the function of a protein. Although the overall fold is made from the whole details of its sequence, a small group of residues, often called as structural motifs, play a crucial role in determining the protein fold and its stability. Identification of such structural motifs requires sufficient number of sequence and structural homologs to define conservation and evolutionary information. Unfortunately, there are many structures in the protein structure databases have no homologous structures or sequences. In this work, we report an SVM method, SMpred, to identify structural motifs from single protein structure without using sequence and structural homologs. SMpred method was trained and tested using 132 proteins domains containing 581 motifs. SMpred method achieved 78.79% accuracy with 79.06% sensitivity and 78.53% specificity. The performance of SMpred was evaluated with MegaMotifBase using 188 proteins containing 1161 motifs. Out of 1161 motifs, SMpred correctly identified 1503 structural motifs reported in MegaMotifBase. Further, we showed that SMpred is useful approach for the length deviant superfamilies and single member superfamilies. This result suggests the usefulness of our approach for facilitating the identification of structural motifs in protein structure in the absence of sequence and structural homologs. The dataset and executable for the SMpred algorithm is available at http://www3.ntu.edu.sg/home/EPNSugan/index_files/SMpred.htm.

  14. Chemical genetic approach identifies microtubule affinity-regulating kinase 1 as a leucine-rich repeat kinase 2 substrate.

    Science.gov (United States)

    Krumova, Petranka; Reyniers, Lauran; Meyer, Marc; Lobbestael, Evy; Stauffer, Daniela; Gerrits, Bertran; Muller, Lionel; Hoving, Sjouke; Kaupmann, Klemens; Voshol, Johannes; Fabbro, Doriano; Bauer, Andreas; Rovelli, Giorgio; Taymans, Jean-Marc; Bouwmeester, Tewis; Baekelandt, Veerle

    2015-07-01

    Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of autosomal-dominant forms of Parkinson's disease. LRRK2 is a modular, multidomain protein containing 2 enzymatic domains, including a kinase domain, as well as several protein-protein interaction domains, pointing to a role in cellular signaling. Although enormous efforts have been made, the exact pathophysiologic mechanisms of LRRK2 are still not completely known. In this study, we used a chemical genetics approach to identify LRRK2 substrates from mouse brain. This approach allows the identification of substrates of 1 particular kinase in a complex cellular environment. Several of the identified peptides are involved in the regulation of microtubule (MT) dynamics, including microtubule-associating protein (MAP)/microtubule affinity-regulating kinase 1 (MARK1). MARK1 is a serine/threonine kinase known to phosphorylate MT-binding proteins such as Tau, MAP2, and MAP4 at KXGS motifs leading to MT destabilization. In vitro kinase assays and metabolic-labeling experiments in living cells confirmed MARK1 as an LRRK2 substrate. Moreover, we also showed that LRRK2 and MARK1 are interacting in eukaryotic cells. Our findings contribute to the identification of physiologic LRRK2 substrates and point to a potential mechanism explaining the reported effects of LRRK2 on neurite morphology.

  15. Disease-Specific Regions Outperform Whole-Brain Approaches in Identifying Progressive Supranuclear Palsy: A Multicentric MRI Study

    Science.gov (United States)

    Mueller, Karsten; Jech, Robert; Bonnet, Cecilia; Tintěra, Jaroslav; Hanuška, Jaromir; Möller, Harald E.; Fassbender, Klaus; Ludolph, Albert; Kassubek, Jan; Otto, Markus; Růžička, Evžen; Schroeter, Matthias L.

    2017-01-01

    To identify progressive supranuclear palsy (PSP), we combined voxel-based morphometry (VBM) and support vector machine (SVM) classification using disease-specific features in multicentric magnetic resonance imaging (MRI) data. Structural brain differences were investigated at four centers between 20 patients with PSP and 20 age-matched healthy controls with T1-weighted MRI at 3T. To pave the way for future application in personalized medicine, we applied SVM classification to identify PSP on an individual level besides group analyses based on VBM. We found a major decline in gray matter density in the brainstem, insula, and striatum, and also in frontomedian regions, which is in line with current literature. Moreover, SVM classification yielded high accuracy rates above 80% for disease identification in imaging data. Focusing analyses on disease-specific regions-of-interest (ROI) led to higher accuracy rates compared to a whole-brain approach. Using a polynomial kernel (instead of a linear kernel) led to an increased sensitivity and a higher specificity of disease detection. Our study supports the application of MRI for individual diagnosis of PSP, if combined with SVM approaches. We demonstrate that SVM classification provides high accuracy rates in multicentric data—a prerequisite for potential application in diagnostic routine. PMID:28326008

  16. Identifying Indicators of Progress in Thermal Spray Research Using Bibliometrics Analysis

    Science.gov (United States)

    Li, R.-T.; Khor, K. A.; Yu, L.-G.

    2016-08-01

    We investigated the research publications on thermal spray in the period of 1985-2015 using the data from Web of Science, Scopus and SciVal®. Bibliometrics analysis was employed to elucidate the country and institution distribution in various thermal spray research areas and to characterize the trends of topic change and technology progress. Results show that China, USA, Japan, Germany, India and France were the top countries in thermal spray research, and Xi'an Jiaotong University, Universite de Technologie Belfort-Montbeliard, Shanghai Institute of Ceramics, ETH Zurich, National Research Council of Canada, University of Limoges were among the top institutions that had high scholarly research output during 2005-2015. The terms of the titles, keywords and abstracts of the publications were analyzed by the Latent Dirichlet Allocation model and visually mapped using the VOSviewer software to reveal the progress of thermal spray technology. It is found that thermal barrier coating was consistently the main research area in thermal spray, and high-velocity oxy-fuel spray and cold spray developed rapidly in the last 10 years.

  17. Philosophy of Science: How to Identify the Potential Research for the Day after Tomorrow?

    Directory of Open Access Journals (Sweden)

    Søren Ventegodt

    2004-01-01

    Full Text Available We were asked to participate in a workshop to assist the European Commission on how to choose financial support for high-potential, basic research projects that can give new scientific breakthroughs and thus contribute significantly to the positive development of society, industry, and economy for the day after tomorrow. At this workshop, we analyzed the problem in some detail using experience from our own research on the global quality of life. We would suggest that the most promising projects have the following characteristics: (1 they are led by a brilliant researcher who considers his/her research to be “sweet science”, who wants to explain the anomalies of his/her field of science, and who lives in a nonmainstream scientific paradigm; (2 they are deeply engaged in the philosophical problems of their research field, they are searching eagerly for a new understanding and a new theory, giving new tools for measurement and creating change, and results are taken as feedback on all levels from tool to theory and philosophy; (3 they are focused on the key point(s, which is an essential feature of the universe that creates global change if intervened upon. At the NEST Pathfinder 2005 Topic Identification Workshop, Brussels 28 May 2004 entitled “Measuring the Impossible”, we advised the European Commission Research Directorate to allocate funds for projects focusing on the state of consciousness — how to understand it, how to map it, and how to develop it.

  18. Identifying Indicators of Progress in Thermal Spray Research Using Bibliometrics Analysis

    Science.gov (United States)

    Li, R.-T.; Khor, K. A.; Yu, L.-G.

    2016-12-01

    We investigated the research publications on thermal spray in the period of 1985-2015 using the data from Web of Science, Scopus and SciVal®. Bibliometrics analysis was employed to elucidate the country and institution distribution in various thermal spray research areas and to characterize the trends of topic change and technology progress. Results show that China, USA, Japan, Germany, India and France were the top countries in thermal spray research, and Xi'an Jiaotong University, Universite de Technologie Belfort-Montbeliard, Shanghai Institute of Ceramics, ETH Zurich, National Research Council of Canada, University of Limoges were among the top institutions that had high scholarly research output during 2005-2015. The terms of the titles, keywords and abstracts of the publications were analyzed by the Latent Dirichlet Allocation model and visually mapped using the VOSviewer software to reveal the progress of thermal spray technology. It is found that thermal barrier coating was consistently the main research area in thermal spray, and high-velocity oxy-fuel spray and cold spray developed rapidly in the last 10 years.

  19. The benefits of using a mixed methods approach--quantitative with qualitative--to identify client satisfaction and unmet needs in an HIV healthcare centre.

    Science.gov (United States)

    Chow, M Y K; Quine, S; Li, M

    2010-04-01

    Research into patient satisfaction with HIV ambulatory healthcare facilities is limited due to confidentiality restraints, the short history of the condition and the stigma attached. Furthermore, most satisfaction studies of this client group have not used mixed methods (quantitative with qualitative) despite its increasing use since the 1990s in healthcare research. This cross-sectional study demonstrates how a mixed methods approach is beneficial in assessing HIV client satisfaction and in identifying unmet needs in HIV healthcare. Conducted at the largest ambulatory HIV healthcare centre in Australia, this study consisted of two phases conducted sequentially: Phase One, a quantitative self-administered questionnaire survey, provided an overall statistical picture of satisfaction levels. This was followed by Phase Two, qualitative semi-structured face-to-face interviews, which enabled in-depth investigation of the reasons for satisfaction/dissatisfaction. Phase One had 166 respondents, giving a high response rate of 71%, while Phase Two had 22 participants. The study demonstrates the three advantages of using a mixed methods approach. Firstly, it increased the comprehensiveness of overall findings, by showing how qualitative data (Phase Two) provided explanations for statistical data (Phase One). Secondly, it expanded the dimensions of the research topic, as Phase Two enabled investigation of the determinants of satisfaction/dissatisfaction more broadly after assessing the client satisfaction levels in Phase One. Thirdly, it increased the methodological rigour as findings in both phases could be checked for consistency. Thus using a mixed methods approach can greatly enhance our understanding of client satisfaction in HIV/AIDS research.

  20. Modeling and Analysis of Multidiscipline Research Teams at NASA Langley Research Center: A Systems Thinking Approach

    Science.gov (United States)

    Waszak, Martin R.; Barthelemy, Jean-Francois; Jones, Kenneth M.; Silcox, Richard J.; Silva, Walter A.; Nowaczyk, Ronald H.

    1998-01-01

    Multidisciplinary analysis and design is inherently a team activity due to the variety of required expertise and knowledge. As a team activity, multidisciplinary research cannot escape the issues that affect all teams. The level of technical diversity required to perform multidisciplinary analysis and design makes the teaming aspects even more important. A study was conducted at the NASA Langley Research Center to develop a model of multidiscipline teams that can be used to help understand their dynamics and identify key factors that influence their effectiveness. The study sought to apply the elements of systems thinking to better understand the factors, both generic and Langley-specific, that influence the effectiveness of multidiscipline teams. The model of multidiscipline research teams developed during this study has been valuable in identifying means to enhance team effectiveness, recognize and avoid problem behaviors, and provide guidance for forming and coordinating multidiscipline teams.

  1. Identifying potential selective fluorescent probes for cancer-associated protein carbonic anhydrase IX using a computational approach.

    Science.gov (United States)

    Kamstra, Rhiannon L; Floriano, Wely B

    2014-11-01

    Carbonic anhydrase IX (CAIX) is a biomarker for tumor hypoxia. Fluorescent inhibitors of CAIX have been used to study hypoxic tumor cell lines. However, these inhibitor-based fluorescent probes may have a therapeutic effect that is not appropriate for monitoring treatment efficacy. In the search for novel fluorescent probes that are not based on known inhibitors, a database of 20,860 fluorescent compounds was virtually screened against CAIX using hierarchical virtual ligand screening (HierVLS). The screening database contained 14,862 compounds tagged with the ATTO680 fluorophore plus an additional 5998 intrinsically fluorescent compounds. Overall ranking of compounds to identify hit molecular probe candidates utilized a principal component analysis (PCA) approach. Four potential binding sites, including the catalytic site, were identified within the structure of the protein and targeted for virtual screening. Available sequence information for 23 carbonic anhydrase isoforms was used to prioritize the four sites based on the estimated "uniqueness" of each site in CAIX relative to the other isoforms. A database of 32 known inhibitors and 478 decoy compounds was used to validate the methodology. A receiver-operating characteristic (ROC) analysis using the first principal component (PC1) as predictive score for the validation database yielded an area under the curve (AUC) of 0.92. AUC is interpreted as the probability that a binder will have a better score than a non-binder. The use of first component analysis of binding energies for multiple sites is a novel approach for hit selection. The very high prediction power for this approach increases confidence in the outcome from the fluorescent library screening. Ten of the top scoring candidates for isoform-selective putative binding sites are suggested for future testing as fluorescent molecular probe candidates.

  2. A Systems Genetic Approach to Identify Low Dose Radiation-Induced Lymphoma Susceptibility/DOE2013FinalReport

    Energy Technology Data Exchange (ETDEWEB)

    Balmain, Allan [University of California, San Francisco; Song, Ihn Young [University of California, San Francisco

    2013-05-15

    The ultimate goal of this project is to identify the combinations of genetic variants that confer an individual's susceptibility to the effects of low dose (0.1 Gy) gamma-radiation, in particular with regard to tumor development. In contrast to the known effects of high dose radiation in cancer induction, the responses to low dose radiation (defined as 0.1 Gy or less) are much less well understood, and have been proposed to involve a protective anti-tumor effect in some in vivo scientific models. These conflicting results confound attempts to develop predictive models of the risk of exposure to low dose radiation, particularly when combined with the strong effects of inherited genetic variants on both radiation effects and cancer susceptibility. We have used a Systems Genetics approach in mice that combines genetic background analysis with responses to low and high dose radiation, in order to develop insights that will allow us to reconcile these disparate observations. Using this comprehensive approach we have analyzed normal tissue gene expression (in this case the skin and thymus), together with the changes that take place in this gene expression architecture a) in response to low or high- dose radiation and b) during tumor development. Additionally, we have demonstrated that using our expression analysis approach in our genetically heterogeneous/defined radiation-induced tumor mouse models can uniquely identify genes and pathways relevant to human T-ALL, and uncover interactions between common genetic variants of genes which may lead to tumor susceptibility.

  3. Research on identifying the dynamic error model of strapdown gyro on 3-axis turntable

    Institute of Scientific and Technical Information of China (English)

    WANG Hai; REN Shun-qing; WANG Chang-hong

    2005-01-01

    The dynamic errors of gyros are the important error sources of a strapdown inertial navigation system.In order to identify the dynamic error model coefficients accurately, the static erTor model coefficients which lay a foundation for compensating while identifying the dynamic error model are identified in the gravity acceleration fields by using angular position function of the three-axis turntable. The angular acceleration and angular velocity are excited on the input, output and spin axis of the gyros when the outer axis and the middle axis of a threeaxis turntable are in the uniform angular velocity state simultaneously, while the inner axis of the turntable is in different static angular positions. 8 groups of data are sampled when the inner axis is in 8 different angular positions. These data are the function of the middle axis positions and the inner axis positions. For these data, harmonic analysis method is applied two times versus the middle axis positions and inner axis positions respectively so that the dynamic error model coefficients are finally identified through the least square method. In the meantime the optimal angular velocity of the outer axis and the middle axis are selected by computing the determination value of the information matrix.

  4. Identifying robust communities and multi-community nodes by combining top-down and bottom-up approaches to clustering.

    Science.gov (United States)

    Gaiteri, Chris; Chen, Mingming; Szymanski, Boleslaw; Kuzmin, Konstantin; Xie, Jierui; Lee, Changkyu; Blanche, Timothy; Chaibub Neto, Elias; Huang, Su-Chun; Grabowski, Thomas; Madhyastha, Tara; Komashko, Vitalina

    2015-11-09

    Biological functions are carried out by groups of interacting molecules, cells or tissues, known as communities. Membership in these communities may overlap when biological components are involved in multiple functions. However, traditional clustering methods detect non-overlapping communities. These detected communities may also be unstable and difficult to replicate, because traditional methods are sensitive to noise and parameter settings. These aspects of traditional clustering methods limit our ability to detect biological communities, and therefore our ability to understand biological functions. To address these limitations and detect robust overlapping biological communities, we propose an unorthodox clustering method called SpeakEasy which identifies communities using top-down and bottom-up approaches simultaneously. Specifically, nodes join communities based on their local connections, as well as global information about the network structure. This method can quantify the stability of each community, automatically identify the number of communities, and quickly cluster networks with hundreds of thousands of nodes. SpeakEasy shows top performance on synthetic clustering benchmarks and accurately identifies meaningful biological communities in a range of datasets, including: gene microarrays, protein interactions, sorted cell populations, electrophysiology and fMRI brain imaging.

  5. PATE, a gene expressed in prostate cancer, normal prostate, and testis, identified by a functional genomic approach

    Science.gov (United States)

    Bera, Tapan K.; Maitra, Rangan; Iavarone, Carlo; Salvatore, Giuliana; Kumar, Vasantha; Vincent, James J.; Sathyanarayana, B. K.; Duray, Paul; Lee, B. K.; Pastan, Ira

    2002-03-01

    To identify target antigens for prostate cancer therapy, we have combined computer-based screening of the human expressed sequence tag database and experimental expression analysis to identify genes that are expressed in normal prostate and prostate cancer but not in essential human tissues. Using this approach, we identified a gene that is expressed specifically in prostate cancer, normal prostate, and testis. The gene has a 1.5-kb transcript that encodes a protein of 14 kDa. We named this gene PATE (expressed in prostate and testis). In situ hybridization shows that PATE mRNA is expressed in the epithelial cells of prostate cancers and in normal prostate. Transfection of the PATE cDNA with a Myc epitope tag into NIH 3T3 cells and subsequent cell fractionation analysis shows that the PATE protein is localized in the membrane fraction of the cell. Analysis of the amino acid sequence of PATE shows that it has structural similarities to a group of proteins known as three-finger toxins, which includes the extracellular domain of the type transforming growth factor receptor. Restricted expression of PATE makes it a potential candidate for the immunotherapy of prostate cancer.

  6. How desertification research is addressed in Spain? Land versus Soil approaches

    Science.gov (United States)

    Barbero Sierra, Celia; Marques, María Jose; Ruiz, Manuel; Escadafal, Richard; Exbrayat, Williams; Akthar-Schuster, Mariam; El Haddadi, Anass

    2013-04-01

    This study intend to understand how desertification research is organised in a south Mediterranean country, as is Spain. It is part of a larger work addressing soil and land research and its relationships with stakeholders. This wider work aims to explain the weakness of the United Nation Convention to Combat Desertification (UNCCD), which devoid of a scientific advisory panel. Within this framework, we assume that a fitting coordination between scientific knowledge and a better flow of information between researchers and policy makers is needed in order to slow down and reverse the impacts of land degradation on drylands. With this purpose we conducted an in-depth study at national level in Spain. The initial work focused on a small sample of published references in scientific journals indexed in the Web of Science. It allowed us to identify the most common thematic approaches and working issues, as well as the corresponding institutions and research teams and the relationships between them. The preliminary results of this study pointed out that two prevalent approaches at this national level could be identified. The first one is related to applied science being sensitive to socio-economic issues, and the second one is related to basic science studying the soil in depth, but it is often disconnected from socio-economic factors. We also noticed that the Spanish research teams acknowledge the other Spanish teams in this subject, as frequent co-citations are found in their papers, nevertheless, they do not collaborate. We also realised that the Web of Science database does not collect the wide spectrum of sociology, economics and the human implications of land degradation which use to be included in books or reports related to desertification. A new wider database was built compiling references of Web of Science related to "desertification", "land", "soil", "development" and "Spain" adding references from other socioeconomic databases. In a second stage we used

  7. Oil palm research in context: identifying the need for biodiversity assessment.

    Directory of Open Access Journals (Sweden)

    Edgar C Turner

    Full Text Available Oil palm cultivation is frequently cited as a major threat to tropical biodiversity as it is centered on some of the world's most biodiverse regions. In this report, Web of Science was used to find papers on oil palm published since 1970, which were assigned to different subject categories to visualize their research focus. Recent years have seen a broadening in the scope of research, with a slight growth in publications on the environment and a dramatic increase in those on biofuel. Despite this, less than 1% of publications are related to biodiversity and species conservation. In the context of global vegetable oil markets, palm oil and soyabean account for over 60% of production but are the subject of less than 10% of research. Much more work must be done to establish the impacts of habitat conversion to oil palm plantation on biodiversity. Results from such studies are crucial for informing conservation strategies and ensuring sustainable management of plantations.

  8. A network biology approach evaluating the anticancer effects of bortezomib identifies SPARC as a therapeutic target in adult T-cell leukemia cells

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2008-10-01

    Full Text Available Junko H Ohyashiki1, Ryoko Hamamura2, Chiaki Kobayashi2, Yu Zhang2, Kazuma Ohyashiki21Intractable Immune System Disease Research Center, Tokyo Medical University, Tokyo, Japan; 2First Department of Internal Medicine, Tokyo Medical University, Tokyo, JapanAbstract: There is a need to identify the regulatory gene interaction of anticancer drugs on target cancer cells. Whole genome expression profiling offers promise in this regard, but can be complicated by the challenge of identifying the genes affected by hundreds to thousands of genes that induce changes in expression. A proteasome inhibitor, bortezomib, could be a potential therapeutic agent in treating adult T-cell leukemia (ATL patients, however, the underlying mechanism by which bortezomib induces cell death in ATL cells via gene regulatory network has not been fully elucidated. Here we show that a Bayesian statistical framework by VoyaGene® identified a secreted protein acidic and rich in cysteine (SPARC gene, a tumor-invasiveness related gene, as a possible modulator of bortezomib-induced cell death in ATL cells. Functional analysis using RNAi experiments revealed that inhibition of the expression SPARC by siRNA enhanced the apoptotic effect of bortezomib on ATL cells in accordance with an increase of cleaved caspase 3. Targeting SPARC may help to treat ATL patients in combination with bortezomib. This work shows that a network biology approach can be used advantageously to identify the genetic interaction related to anticancer effects.Keywords: network biology, adult T cell leukemia, bortezomib, SPARC

  9. California Levee Risk, Now and in the Future:Identifying Research and Tool Development Needs

    Energy Technology Data Exchange (ETDEWEB)

    Newmark, R L; Hanemann, M; Farber, D

    2006-11-28

    The Center for Catastrophic Risk Management (CCRM) and the California Center for Environmental Law and Policy (CCELP) at UC Berkeley and the Lawrence Livermore National Laboratory (LLNL) joined together to cosponsor a workshop to define research requirements to mitigate the hazards facing the Sacramento-San Joaquin Delta Levee system. The Workshop was intended to provide a forum to (1) Report assessments of current vulnerabilities facing the levees, such as structural failure, seismic loading, flooding, terrorism; (2) Consider longer term challenges such as climate change, sea level rise; and (3) Define research requirements to fill gaps in knowledge and reduce uncertainties in hazard assessments.

  10. A New Approach to Commercialization of NASA's Human Research Program Technologies Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This Phase I SBIR proposal describes, "A New Approach to Commercialization of NASA's Human Research Program Technologies." NASA has a powerful research...

  11. Research Area 7.4: Identifying a Path Towards Rapid Discrimination of Infection Disease Outbreaks

    Science.gov (United States)

    2014-07-15

    a sophisticated analysis identified the source, many countries acted proactively to remove cucumbers and tomatoes from store shelves, Russia issued...Eisenstein, M. (2012). Oxford Nanopore announcement sets sequencing sector abuzz. Nature Biotechnology , 30(4), 295–6. doi:10.1038/nbt0412-295... Biotechnology , 29(7). Grad, Y. H., Lipsitch, M., Feldgarden, M., Arachchi, H. M., Cerqueira, G. C., Fitzgerald, M., .. . Hanage, W. P. (2012). Genomic

  12. Approaches in Synesthesia Research: Neurocognitive Aspects and Diagnostic Criteria

    Directory of Open Access Journals (Sweden)

    Nina Mikus

    2013-10-01

    Full Text Available Synesthesia is a fairly rare phenomenon in which the subject in contact with certain stimulus in one modality experiences unusual extra sensations in other modalities, such as seeing or feeling colours while listening to music or personifying of letters and numbers. The phenomenon was long perceived to be merely a product of imagination and associations. Latest research, however, is based on a multidisciplinary approach, which includes first-hand synesthetic reports, neuroimaging and behavioural tests used in confirming and explaining the phenomenon’s presence as well as its neurophysiological foundations. This article presents an overview of such investigations through the lens of cognitive and psychophysical paradigms, neural models and genetic studies of synesthesia.

  13. A hybrid approach identifies metabolic signatures of high-producers for chinese hamster ovary clone selection and process optimization.

    Science.gov (United States)

    Popp, Oliver; Müller, Dirk; Didzus, Katharina; Paul, Wolfgang; Lipsmeier, Florian; Kirchner, Florian; Niklas, Jens; Mauch, Klaus; Beaucamp, Nicola

    2016-09-01

    In-depth characterization of high-producer cell lines and bioprocesses is vital to ensure robust and consistent production of recombinant therapeutic proteins in high quantity and quality for clinical applications. This requires applying appropriate methods during bioprocess development to enable meaningful characterization of CHO clones and processes. Here, we present a novel hybrid approach for supporting comprehensive characterization of metabolic clone performance. The approach combines metabolite profiling with multivariate data analysis and fluxomics to enable a data-driven mechanistic analysis of key metabolic traits associated with desired cell phenotypes. We applied the methodology to quantify and compare metabolic performance in a set of 10 recombinant CHO-K1 producer clones and a host cell line. The comprehensive characterization enabled us to derive an extended set of clone performance criteria that not only captured growth and product formation, but also incorporated information on intracellular clone physiology and on metabolic changes during the process. These criteria served to establish a quantitative clone ranking and allowed us to identify metabolic differences between high-producing CHO-K1 clones yielding comparably high product titers. Through multivariate data analysis of the combined metabolite and flux data we uncovered common metabolic traits characteristic of high-producer clones in the screening setup. This included high intracellular rates of glutamine synthesis, low cysteine uptake, reduced excretion of aspartate and glutamate, and low intracellular degradation rates of branched-chain amino acids and of histidine. Finally, the above approach was integrated into a workflow that enables standardized high-content selection of CHO producer clones in a high-throughput fashion. In conclusion, the combination of quantitative metabolite profiling, multivariate data analysis, and mechanistic network model simulations can identify metabolic

  14. Antimicrobial Approaches for Textiles: From Research to Market

    Directory of Open Access Journals (Sweden)

    Diana Santos Morais

    2016-06-01

    Full Text Available The large surface area and ability to retain moisture of textile structures enable microorganisms’ growth, which causes a range of undesirable effects, not only on the textile itself, but also on the user. Due to the public health awareness of the pathogenic effects on personal hygiene and associated health risks, over the last few years, intensive research has been promoted in order to minimize microbes’ growth on textiles. Therefore, to impart an antimicrobial ability to textiles, different approaches have been studied, being mainly divided into the inclusion of antimicrobial agents in the textile polymeric fibers or their grafting onto the polymer surface. Regarding the antimicrobial agents, different types have been used, such as quaternary ammonium compounds, triclosan, metal salts, polybiguanides or even natural polymers. Any antimicrobial treatment performed on a textile, besides being efficient against microorganisms, must be non-toxic to the consumer and to the environment. This review mainly intends to provide an overview of antimicrobial agents and treatments that can be performed to produce antimicrobial textiles, using chemical or physical approaches, which are under development or already commercially available in the form of isolated agents or textile fibers or fabrics.

  15. Approaches to the utilization of space for CO2 research

    Science.gov (United States)

    Glaser, P.; Aronson, J.; Brecher, A.; Csigi, K.; Mcarthur, R.

    1985-01-01

    A system study of the potential of space technology to monitor climate changes and improve the understanding of the coupling beteen CO2 and cloud cover is summarized. The basis for the study is scientific data requirements pertinent to the U.S. Department of Energy's CO2 Research Program. The capabilities of space-based sensor systems are matched to meet these requirements. New sensor system concepts are identified, including a Space Shuttle-launched recalibration package to provide for continuity of measurement and recalibration between satellites, a high-orbit radiation budget satellite, or parallax sensor to measure cloud altitude, a passive method for the direct measurements of CO2 and a high-altitude powered platform to monitor select regional parameters. Space-based sensor systems that could be the development focus for the time frames of 0-5, 5-10 and 10-20 years are recommended.

  16. Learning in context: identifying gaps in research on the transfer of medical communication skills to the clinical workplace.

    NARCIS (Netherlands)

    Eertwegh, V. van den; Dulmen, S. van; Dalen, J. van; Scherpbier, A.J.J.A.; Vleuten, C.P.M. van der

    2013-01-01

    Objective: In order to reduce the inconsistencies of findings and the apparent low transfer of communication skills from training to medical practice, this narrative review identifies some main gaps in research on medical communication skills training and presents insights from theories on learning

  17. Learning in context: identifying gaps in research on the transfer of medical communication skills to the clinical workplace

    NARCIS (Netherlands)

    Eertwegh, V. van den; Dulmen, S. van; Dalen, J. Van; Scherpbier, A.J.J.A.; Vleuten, C.P.M. van der

    2013-01-01

    OBJECTIVE: In order to reduce the inconsistencies of findings and the apparent low transfer of communication skills from training to medical practice, this narrative review identifies some main gaps in research on medical communication skills training and presents insights from theories on learning

  18. IDENTIFYING NETWORK LOAD BALANCING REQUIREMENTS ON HISTORICAL TRAFFIC FLOW USING MACHINE LEARNING APPROACH FOR FLEXIBLE MULTIPATH NETWORKS

    Directory of Open Access Journals (Sweden)

    K BALAMURUGAN

    2010-08-01

    Full Text Available Multipath routing uses several paths to distribute traffic from a source to destination. This not only improves network performance but also achieves load balancing and fault tolerance. Though multipath routing is not deployed widely in the internet, current systems chooses the paths with the same lowest cost to the destination and the same administrative distance.In this paper we propose a flexible multipath network wherein multipath routing algorithm is invoked when the quality of service is affected. Our proposal provides a method to gradually shift from a single path existing network to a reliable multipath network in the future.We have used machine learning approach to identify the instance when network load balancing is required with good results.

  19. A Kriging surrogate model coupled in simulation-optimization approach for identifying release history of groundwater sources

    Science.gov (United States)

    Zhao, Ying; Lu, Wenxi; Xiao, Chuanning

    2016-02-01

    As the incidence frequency of groundwater pollution increases, many methods that identify source characteristics of pollutants are being developed. In this study, a simulation-optimization approach was applied to determine the duration and magnitude of pollutant sources. Such problems are time consuming because thousands of simulation models are required to run the optimization model. To address this challenge, the Kriging surrogate model was proposed to increase computational efficiency. Accuracy, time consumption, and the robustness of the Kriging model were tested on both homogenous and non-uniform media, as well as steady-state and transient flow and transport conditions. The results of three hypothetical cases demonstrate that the Kriging model has the ability to solve groundwater contaminant source problems that could occur during field site source identification problems with a high degree of accuracy and short computation times and is thus very robust.

  20. Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach

    Science.gov (United States)

    Yuan, Fei; Zhou, You; Wang, Meng; Yang, Jing; Wu, Kai; Lu, Changhong; Kong, Xiangyin; Cai, Yu-Dong

    2015-01-01

    Prostate cancer is a type of cancer that occurs in the male prostate, a gland in the male reproductive system. Because prostate cancer cells may spread to other parts of the body and can influence human reproduction, understanding the mechanisms underlying this disease is critical for designing effective treatments. The identification of as many genes and chemicals related to prostate cancer as possible will enhance our understanding of this disease. In this study, we proposed a computational method to identify new candidate genes and chemicals based on currently known genes and chemicals related to prostate cancer by applying a shortest path approach in a hybrid network. The hybrid network was constructed according to information concerning chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions. Many of the obtained genes and chemicals are associated with prostate cancer. PMID:26504486

  1. A Dynamic Combinatorial Approach for Identifying Side Groups that Stabilize DNA-Templated Supramolecular Self-Assemblies

    Directory of Open Access Journals (Sweden)

    Delphine Paolantoni

    2015-02-01

    Full Text Available DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.

  2. Drivers of occupational human capital: identifying and developing research productivity in the globalized business school Industry

    OpenAIRE

    Ryazanova, Olga

    2015-01-01

    This thesis looks at the antecedents of research productivity in business schools as part of a wider conversation on the development of occupational human capital in knowledge-intensive industries. Building upon the social capital and sociology of science literatures, the present study seeks to advance this conversation in two ways. First, it focuses on the consequences of academic researchers’ early-career and mid-career choices by exploring the interplay between organizational scripts and i...

  3. Mechanisms of change in psychotherapy for depression: An empirical update and evaluation of research aimed at identifying psychological mediators.

    Science.gov (United States)

    Lemmens, Lotte H J M; Müller, Viola N L S; Arntz, Arnoud; Huibers, Marcus J H

    2016-12-01

    We present a systematic empirical update and critical evaluation of the current status of research aimed at identifying a variety of psychological mediators in various forms of psychotherapy for depression. We summarize study characteristics and results of 35 relevant studies, and discuss the extent to which these studies meet several important requirements for mechanism research. Our review indicates that in spite of increased attention for the topic, advances in theoretical consensus about necessities for mechanism research, and sophistication of study designs, research in this field is still heterogeneous and unsatisfactory in methodological respect. Probably the biggest challenge in the field is demonstrating the causal relation between change in the mediator and change in depressive symptoms. The field would benefit from a further refinement of research methods to identify processes of therapeutic change. Recommendations for future research are discussed. However, even in the most optimal research designs, explaining psychotherapeutic change remains a challenge. Psychotherapy is a multi-dimensional phenomenon that might work through interplay of multiple mechanisms at several levels. As a result, it might be too complex to be explained in relatively simple causal models of psychological change.

  4. A Bayesian Approach for Analysis of Whole-Genome Bisulphite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation.

    Science.gov (United States)

    Rackham, Owen J L; Langley, Sarah R; Oates, Thomas; Vradi, Eleni; Harmston, Nathan; Srivastava, Prashant K; Behmoaras, Jacques; Dellaportas, Petros; Bottolo, Leonardo; Petretto, Enrico

    2017-02-17

    DNA methylation is a key epigenetic modification involved in gene regulation whose contribution to disease susceptibility remains to be fully understood. Here, we present a novel Bayesian smoothing approach (called ABBA) to detect differentially methylated regions (DMRs) from whole-genome bisulphite sequencing (WGBS). We also show how this approach can be leveraged to identify disease-associated changes in DNA methylation, suggesting mechanisms through which these alterations might affect disease. From a data modeling perspective, ABBA has the distinctive feature of automatically adapting to different correlation structures in CpG methylation levels across the genome whilst taking into account the distance between CpG sites as a covariate. Our simulation study shows that ABBA has greater power to detect DMRs than existing methods, providing an accurate identification of DMRs in the large majority of simulated cases. To empirically demonstrate the method's efficacy in generating biological hypotheses, we performed WGBS of primary macrophages derived from an experimental rat system of glomerulonephritis and used ABBA to identify >1,000 disease-associated DMRs. Investigation of these DMRs revealed differential DNA methylation localized to a 600bp region in the promoter of the Ifitm3 gene. This was confirmed by ChIP-seq and RNA-seq analyses, showing differential transcription factor binding at the Ifitm3 promoter by JunD (an established determinant of glomerulonephritis) and a consistent change in Ifitm3 expression. Our ABBA analysis allowed us to propose a new role for Ifitm3 in the pathogenesis of glomerulonephritis via a mechanism involving promoter hypermethylation that is associated with Ifitm3 repression in the rat strain susceptible to glomerulonephritis.

  5. Security approaches in using tablet computers for primary data collection in clinical research.

    Science.gov (United States)

    Wilcox, Adam B; Gallagher, Kathleen; Bakken, Suzanne

    2013-01-01

    Next-generation tablets (iPads and Android tablets) may potentially improve the collection and management of clinical research data. The widespread adoption of tablets, coupled with decreased software and hardware costs, has led to increased consideration of tablets for primary research data collection. When using tablets for the Washington Heights/Inwood Infrastructure for Comparative Effectiveness Research (WICER) project, we found that the devices give rise to inherent security issues associated with the potential use of cloud-based data storage approaches. This paper identifies and describes major security considerations for primary data collection with tablets; proposes a set of architectural strategies for implementing data collection forms with tablet computers; and discusses the security, cost, and workflow of each strategy. The paper briefly reviews the strategies with respect to their implementation for three primary data collection activities for the WICER project.

  6. Immunogenic and invasive properties of Brucella melitensis 16M outer membrane protein vaccine candidates identified via a reverse vaccinology approach.

    Directory of Open Access Journals (Sweden)

    Gabriel Gomez

    Full Text Available Brucella is the etiologic agent of brucellosis, one of the most common and widely distributed zoonotic diseases. Its highly infectious nature, the insidious, systemic, chronic, debilitating aspects of the disease and the lack of an approved vaccine for human use in the United States are features that make Brucella a viable threat to public health. One of the main impediments to vaccine development is identification of suitable antigens. In order to identify antigens that could potentially be used in a vaccine formulation, we describe a multi-step antigen selection approach. We initially used an algorithm (Vaxign to predict ORF encoding outer membrane proteins with antigenic determinants. Differential gene expression during acute infection and published evidence for a role in virulence were used as criteria for down-selection of the candidate antigens that resulted from in silico prediction. This approach resulted in the identification of nine Brucella melitensis outer membrane proteins, 5 of which were recombinantly expressed and used for validation. Omp22 and Hia had the highest in silico scores for adhesin probability and also conferred invasive capacity to E. coli overexpressing recombinant proteins. With the exception of FlgK in the goat, all proteins reacted to pooled sera from exposed goats, mice, and humans. BtuB, Hia and FlgK stimulated a mixed Th1-Th2 response in splenocytes from immunized mice while BtuB and Hia elicited NO release from splenocytes of S19 immunized mice. The results support the applicability of the current approach to the identification of antigens with immunogenic and invasive properties. Studies to assess immunogenicity and protective efficacy of individual proteins in the mouse are currently underway.

  7. Immunogenic and invasive properties of Brucella melitensis 16M outer membrane protein vaccine candidates identified via a reverse vaccinology approach.

    Science.gov (United States)

    Gomez, Gabriel; Pei, Jianwu; Mwangi, Waithaka; Adams, L Garry; Rice-Ficht, Allison; Ficht, Thomas A

    2013-01-01

    Brucella is the etiologic agent of brucellosis, one of the most common and widely distributed zoonotic diseases. Its highly infectious nature, the insidious, systemic, chronic, debilitating aspects of the disease and the lack of an approved vaccine for human use in the United States are features that make Brucella a viable threat to public health. One of the main impediments to vaccine development is identification of suitable antigens. In order to identify antigens that could potentially be used in a vaccine formulation, we describe a multi-step antigen selection approach. We initially used an algorithm (Vaxign) to predict ORF encoding outer membrane proteins with antigenic determinants. Differential gene expression during acute infection and published evidence for a role in virulence were used as criteria for down-selection of the candidate antigens that resulted from in silico prediction. This approach resulted in the identification of nine Brucella melitensis outer membrane proteins, 5 of which were recombinantly expressed and used for validation. Omp22 and Hia had the highest in silico scores for adhesin probability and also conferred invasive capacity to E. coli overexpressing recombinant proteins. With the exception of FlgK in the goat, all proteins reacted to pooled sera from exposed goats, mice, and humans. BtuB, Hia and FlgK stimulated a mixed Th1-Th2 response in splenocytes from immunized mice while BtuB and Hia elicited NO release from splenocytes of S19 immunized mice. The results support the applicability of the current approach to the identification of antigens with immunogenic and invasive properties. Studies to assess immunogenicity and protective efficacy of individual proteins in the mouse are currently underway.

  8. A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network.

    Science.gov (United States)

    Unnikrishnan, Ashwin; Guan, Yi F; Huang, Yizhou; Beck, Dominik; Thoms, Julie A I; Peirs, Sofie; Knezevic, Kathy; Ma, Shiyong; de Walle, Inge V; de Jong, Ineke; Ali, Zara; Zhong, Ling; Raftery, Mark J; Taghon, Tom; Larsson, Jonas; MacKenzie, Karen L; Van Vlierberghe, Pieter; Wong, Jason W H; Pimanda, John E

    2016-12-15

    Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34(+) haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.

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

    Directory of Open Access Journals (Sweden)

    Deodutta Roy

    2015-10-01

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

  10. What, who or where? Rejoinder to "identifying research topic development in Business and Management education research using legitimation code theory"

    OpenAIRE

    Anne-Wil HARZING

    2016-01-01

    Arbaugh, Fornaciari and Hwang (2016) use citation analysis – with Google Scholar as their source of citation data – to track the development of Business and Management Education research by studying the field’s 100 most highly cited articles. In their article, the authors distinguish several factors that might impact on an article’s level of citations: the topic it addresses, the profile of the author(s) who wrote it and the prominence of the journal that the article is published in. Alth...

  11. Identifying Unique Neighborhood Characteristics to Guide Health Planning for Stroke and Heart Attack: Fuzzy Cluster and Discriminant Analyses Approaches

    Science.gov (United States)

    Pedigo, Ashley; Seaver, William; Odoi, Agricola

    2011-01-01

    Background Socioeconomic, demographic, and geographic factors are known determinants of stroke and myocardial infarction (MI) risk. Clustering of these factors in neighborhoods needs to be taken into consideration during planning, prioritization and implementation of health programs intended to reduce disparities. Given the complex and multidimensional nature of these factors, multivariate methods are needed to identify neighborhood clusters of these determinants so as to better understand the unique neighborhood profiles. This information is critical for evidence-based health planning and service provision. Therefore, this study used a robust multivariate approach to classify neighborhoods and identify their socio-demographic characteristics so as to provide information for evidence-based neighborhood health planning for stroke and MI. Methods and Findings The study was performed in East Tennessee Appalachia, an area with one of the highest stroke and MI risks in USA. Robust principal component analysis was performed on neighborhood (census tract) socioeconomic and demographic characteristics, obtained from the US Census, to reduce the dimensionality and influence of outliers in the data. Fuzzy cluster analysis was used to classify neighborhoods into Peer Neighborhoods (PNs) based on their socioeconomic and demographic characteristics. Nearest neighbor discriminant analysis and decision trees were used to validate PNs and determine the characteristics important for discrimination. Stroke and MI mortality risks were compared across PNs. Four distinct PNs were identified and their unique characteristics and potential health needs described. The highest risk of stroke and MI mortality tended to occur in less affluent PNs located in urban areas, while the suburban most affluent PNs had the lowest risk. Conclusions Implementation of this multivariate strategy provides health planners useful information to better understand and effectively plan for the unique

  12. EFSA’s approach to identifying emerging risks in food and feed: taking stock and looking forward

    Directory of Open Access Journals (Sweden)

    Robinson T

    2012-10-01

    Full Text Available

    The Emerging Risks Unit has the responsibility for coordinating EFSA’s activities to establish a capacity for the identification of emerging risks. A process was trialled and further developed during a pilot period of 18 months from 2010-2012. This included the implementation of an operational procedure for emerging risks identification, the assessment of selected data sources, the testing of tools for collecting information, the consolidation of knowledge networks for sharing information and the development of a methodological framework. Specific issues were identified for follow-up activities using an expert judgment approach. These include a study on climate change and the emergence of aflatoxins in cereal crops in the European Union (EU, a European-wide survey on the consumption of energy drinks, a task force on human risk assessment of chemical mixtures, an internal task force on bee health, and a foresight study on the potential impact of omics technologies on food and feed safety risk assessment. These follow-up activities will contribute to the determination of whether the issues identified can indeed give rise to emerging risks. Overall, our experience shows that emerging risks identification requires a high level of expertise due to major data gaps and uncertainties in the evaluation process. Effective networking has proven to be essential for exchanging methods, data and evaluations of emerging risks. The system piloted has shown some potential for the identification of issues that may give rise to emerging risks. Useful knowledge has been gained in the area of gathering and filtering large amounts of information and building knowledge networks on emerging risks. Next steps include the establishment of a standing Working Group (WG on Emerging Risks, the reinforcement of the engagement with Member States and Stakeholders, the fine tuning of the revised methodological framework, and the completion of the projects on the issues

  13. Identifiability of sorption parameters in stirred flow-through reactor experiments and their identification with a Bayesian approach.

    Science.gov (United States)

    Nicoulaud-Gouin, V; Garcia-Sanchez, L; Giacalone, M; Attard, J C; Martin-Garin, A; Bois, F Y

    2016-10-01

    This paper addresses the methodological conditions -particularly experimental design and statistical inference- ensuring the identifiability of sorption parameters from breakthrough curves measured during stirred flow-through reactor experiments also known as continuous flow stirred-tank reactor (CSTR) experiments. The equilibrium-kinetic (EK) sorption model was selected as nonequilibrium parameterization embedding the Kd approach. Parameter identifiability was studied formally on the equations governing outlet concentrations. It was also studied numerically on 6 simulated CSTR experiments on a soil with known equilibrium-kinetic sorption parameters. EK sorption parameters can not be identified from a single breakthrough curve of a CSTR experiment, because Kd,1 and k(-) were diagnosed collinear. For pairs of CSTR experiments, Bayesian inference allowed to select the correct models of sorption and error among sorption alternatives. Bayesian inference was conducted with SAMCAT software (Sensitivity Analysis and Markov Chain simulations Applied to Transfer models) which launched the simulations through the embedded simulation engine GNU-MCSim, and automated their configuration and post-processing. Experimental designs consisting in varying flow rates between experiments reaching equilibrium at contamination stage were found optimal, because they simultaneously gave accurate sorption parameters and predictions. Bayesian results were comparable to maximum likehood method but they avoided convergence problems, the marginal likelihood allowed to compare all models, and credible interval gave directly the uncertainty of sorption parameters θ. Although these findings are limited to the specific conditions studied here, in particular the considered sorption model, the chosen parameter values and error structure, they help in the conception and analysis of future CSTR experiments with radionuclides whose kinetic behaviour is suspected.

  14. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    Directory of Open Access Journals (Sweden)

    Nickerson Cheryl A

    2006-01-01

    Full Text Available Abstract Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level using computer software or hybridization analysis to compare different bacterial genomic sequences. We describe here a novel experimental approach to study the evolution of species-specific bacterial genomic islands that identifies island genes that have evolved in such a way that they are differentially-expressed depending on the bacterial host background into which they are transferred. Results We demonstrate this approach by using a "test" genomic island that we have cloned from the Salmonella typhimurium genome (island 4305 and transferred to a range of Gram negative bacterial hosts of differing evolutionary relationships to S. typhimurium. Systematic analysis of the expression of the island genes in the different hosts compared to proper controls allowed identification of genes with genera-specific expression patterns. The data from the analysis can be arranged in a matrix to give an expression "array" of the island genes in the different bacterial backgrounds. A conserved 19-bp DNA site was found upstream of at least two of the differentially-expressed island genes. To our knowledge, this is the first systematic analysis of horizontally-transferred genomic island gene expression in a broad range of Gram negative hosts. We also present evidence in this study that the IS200 element found in island 4305 in S. typhimurium strain LT2 was inserted after the island had already been acquired by the S. typhimurium lineage and that this element is likely not

  15. Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

    Directory of Open Access Journals (Sweden)

    Dimitrios Iliopoulos

    Full Text Available BACKGROUND: Osteoarthritis is a multifactorial disease characterized by destruction of the articular cartilage due to genetic, mechanical and environmental components affecting more than 100 million individuals all over the world. Despite the high prevalence of the disease, the absence of large-scale molecular studies limits our ability to understand the molecular pathobiology of osteoathritis and identify targets for drug development. METHODOLOGY/PRINCIPAL FINDINGS: In this study we integrated genetic, bioinformatic and proteomic approaches in order to identify new genes and their collaborative networks involved in osteoarthritis pathogenesis. MicroRNA profiling of patient-derived osteoarthritic cartilage in comparison to normal cartilage, revealed a 16 microRNA osteoarthritis gene signature. Using reverse-phase protein arrays in the same tissues we detected 76 differentially expressed proteins between osteoarthritic and normal chondrocytes. Proteins such as SOX11, FGF23, KLF6, WWOX and GDF15 not implicated previously in the genesis of osteoarthritis were identified. Integration of microRNA and proteomic data with microRNA gene-target prediction algorithms, generated a potential "interactome" network consisting of 11 microRNAs and 58 proteins linked by 414 potential functional associations. Comparison of the molecular and clinical data, revealed specific microRNAs (miR-22, miR-103 and proteins (PPARA, BMP7, IL1B to be highly correlated with Body Mass Index (BMI. Experimental validation revealed that miR-22 regulated PPARA and BMP7 expression and its inhibition blocked inflammatory and catabolic changes in osteoarthritic chondrocytes. CONCLUSIONS/SIGNIFICANCE: Our findings indicate that obesity and inflammation are related to osteoarthritis, a metabolic disease affected by microRNA deregulation. Gene network approaches provide new insights for elucidating the complexity of diseases such as osteoarthritis. The integration of microRNA, proteomic

  16. Identifying key research objectives to make European forests greener for bats

    Directory of Open Access Journals (Sweden)

    Danilo Russo

    2016-07-01

    Full Text Available Bats are a biodiverse mammal order providing key ecosystem services such as pest suppression, pollination and seed dispersal. Bats are also very sensitive to human actions, and significant declines in many bat populations have been recorded consequently. Many bat species find crucial roosting and foraging opportunities in European forests. Such forests have historically been exploited by humans and are still influenced by harvesting. One of the consequences of this pressure is the loss of key habitat resources, often making forests inhospitable to bats. Despite the legal protection granted to bats across Europe, the impacts of forestry on bats are still often neglected. Because forest exploitation influences forest structure at several spatial scales, economically viable forestry could become more sustainable and even favour bats. We highlight that a positive future for bat conservation that simultaneously benefits forestry is foreseeable, although more applied research is needed to develop sound management. Key future research topics include the detection of factors influencing the carrying capacity of forests, and determining the impacts of forest management and the economic importance of bats in forests. Predictive tools to inform forest managers are much needed, together with greater synergies between forest managers and bat conservationists.

  17. Qualitative research to identify racialist discourse: towards equity in nursing curricula.

    Science.gov (United States)

    Hagey, R; MacKay, R W

    2000-02-01

    Professional curriculum planning is beginning to address issues of equity. The authors report on findings from a research initiative to begin to integrate antiracism into an undergraduate curriculum. Theory and methods of Essed, Fanon, Frankenberg, Hall, van Dijk and Woodward are synthesized for interpreting racialist discourse. The findings support the principle of normalizing accountability for discourse practices which construct whiteness and otherness in their representations. Essentialist discourse practices are implicated in the perpetuation of racism, ableism, heterosexism, ageism, etc. Hence, the ideal of equity is expanded to include the enactment of non-essentialist discourse. The logic is revealed as either/or; either equity or dominance through normalized perpetuation of essential categories assigning negative value to others constructing difference, marginalization, problematization, exclusion and containment. The confused, middle or neutral position is one of condoning racism and other forms of dominance.

  18. Identified research directions for using manufacturing knowledge earlier in the product lifecycle.

    Science.gov (United States)

    Hedberg, Thomas D; Hartman, Nathan W; Rosche, Phil; Fischer, Kevin

    2017-01-01

    Design for Manufacturing (DFM), especially the use of manufacturing knowledge to support design decisions, has received attention in the academic domain. However, industry practice has not been studied enough to provide solutions that are mature for industry. The current state of the art for DFM is often rule-based functionality within Computer-Aided Design (CAD) systems that enforce specific design requirements. That rule-based functionality may or may not dynamically affect geometry definition. And, if rule-based functionality exists in the CAD system, it is typically a customization on a case-by-case basis. Manufacturing knowledge is a phrase with vast meanings, which may include knowledge on the effects of material properties decisions, machine and process capabilities, or understanding the unintended consequences of design decisions on manufacturing. One of the DFM questions to answer is how can manufacturing knowledge, depending on its definition, be used earlier in the product lifecycle to enable a more collaborative development environment? This paper will discuss the results of a workshop on manufacturing knowledge that highlights several research questions needing more study. This paper proposes recommendations for investigating the relationship of manufacturing knowledge with shape, behavior, and context characteristics of product to produce a better understanding of what knowledge is most important. In addition, the proposal includes recommendations for investigating the system-level barriers to reusing manufacturing knowledge and how model-based manufacturing may ease the burden of knowledge sharing. Lastly, the proposal addresses the direction of future research for holistic solutions of using manufacturing knowledge earlier in the product lifecycle.

  19. EMBASE search strategies for identifying methodologically sound diagnostic studies for use by clinicians and researchers

    Directory of Open Access Journals (Sweden)

    Haynes R Brian

    2005-03-01

    Full Text Available Abstract Background Accurate diagnosis by clinicians is the cornerstone of decision making for recommending clinical interventions. The current best evidence from research concerning diagnostic tests changes unpredictably as science advances. Both clinicians and researchers need dependable access to published evidence concerning diagnostic accuracy. Bibliographic databases such as EMBASE provide the most widely available entrée to this literature. The objective of this study was to develop search strategies that optimize the retrieval of methodologically sound diagnostic studies from EMBASE for use by clinicians. Methods An analytic survey was conducted, comparing hand searches of 55 journals with retrievals from EMBASE for 4,843 candidate search terms and 6,574 combinations. All articles were rated using purpose and quality indicators, and clinically relevant diagnostic accuracy articles were categorized as 'pass' or 'fail' according to explicit criteria for scientific merit. Candidate search strategies were run in EMBASE, the retrievals being compared with the hand search data. The proposed search strategies were treated as "diagnostic tests" for sound studies and the manual review of the literature was treated as the "gold standard." The sensitivity, specificity, precision and accuracy of the search strategies were calculated. Results Of the 433 articles about diagnostic tests, 97 (22.4% met basic criteria for scientific merit. Combinations of search terms reached peak sensitivities of 100% with specificity at 70.4%. Compared with best single terms, best multiple terms increased sensitivity for sound studies by 8.2% (absolute increase, but decreased specificity (absolute decrease 6% when sensitivity was maximized. When terms were combined to maximize specificity, the single term "specificity.tw." (specificity of 98.2% outperformed combinations of terms. Conclusion Empirically derived search strategies combining indexing terms and textwords

  20. Molecular approaches identify known species, reveal cryptic species and verify host specificity of Chinese Philotrypesis (Hymenoptera: Pteromalidae).

    Science.gov (United States)

    Zhou, Mei-Jiao; Xiao, Jin-Hua; Bian, Sheng-Nan; Li, Yan-Wei; Niu, Li-Ming; Hu, Hao-Yuan; Wu, Wen-Shan; Murphy, Robert W; Huang, Da-Wei

    2012-07-01

    Philotrypesis, a major component of the fig wasp community (Hymenoptera: Pteromalidae), is a model taxon for studying male fighting and mating behaviour. Its extreme sexual dimorphism and male polymorphism render species identification uncertain and in-depth research on its ecology, behaviour and other evolutionary topics challenging. The fig wasps' enclosed habitat within the syconia makes their mating behaviour inaccessible, to the extent of matching conspecific females and males. In this study, we combine morphological and molecular analyses to identify species of Philotrypesis sampled from south China and to associate their extraordinarily dimorphic genders and labile male morphologies. Morphological evaluations of females identify 22 species and 28 male morphs. The mitochondrial cytochrome c oxidase I and nuclear internal transcribed spacer 2 data detect 21 species using females, and 15 species among the males. Most of the males match the species as delimited by females. Both markers reveal cryptic species in P. quadrisetosa on Ficus vasculosa. Most species of wasps live on one species of fig but three species co-occur in two hosts (F. microcarpa and F. benjamina), which indicates host switching.

  1. Identifying and prioritizing factors that influence reapeted patronage of Etka chain-stores customers: a neural network approach

    Directory of Open Access Journals (Sweden)

    Behrouz Jahandideh

    2013-03-01

    Full Text Available Nowadays, chain stores are experiencing a severe competitive environment. In such an environment, a growing number of customers are equipped by high volumes of information and are more risk-taking. As they tend to switch their store based on the higher value that they might receive elsewhere, as customers switching behavior has become so commonplace and has become a challenge for retailers. Thus, factors that influence the willingness of customers to repurchase will play a critical role in the performance and success of chain stores. This paper aimed to identify and prioritize the determinative factors that cause customers repeat patronage in Etka chain stores. Factors were extracted based on a thorough literature review and then these factors were modified using pre-test and interview methods. In this study, questionnaires were used for data collection. Respectively, to identify and prioritize determinative factors, correlation analysis and artificial neural networks were used. Results showed that in order of importance, quality, price loyalty program, number of service counters, store staff, shelf labels, product selection, parking facilities, home delivery, store brand, and store atmosphere are factors that determine customers’ repeat patronage of Etka chain stores. Meanwhile, young, educated and wealthy customers showed lower store repeat patronage. Finally, the paper concludes with suggestions for increasing consumer repeat-patronage of Etka chain-stores and directions for future research.

  2. Novel approach to improve molecular imaging research: Correlation between macroscopic and molecular pathological findings in patients

    Energy Technology Data Exchange (ETDEWEB)

    Boehm, Ingrid, E-mail: i.boehm@uni-bonn.de [Department of Diagnostic Radiology, ZARF Project, Center for Molecular Imaging Research MBMB, Philipps University of Marburg, Baldingerstrasse, 35039 Marburg (Germany)

    2011-09-15

    Purpose: Currently, clinical research approaches are sparse in molecular imaging studies. Moreover, possible links between imaging features and pathological laboratory parameters are unknown, so far. Therefore, the goal was to find a possible relationship between imaging features and peripheral blood cell apoptosis, and thereby to present a novel way to complement molecular imaging research. Materials and methods: The investigation has been done in systemic lupus erythematosus (SLE), a prototype of an autoimmune disease characterized by multiorgan involvement, autoantibody production, and disturbed apoptosis. Retrospectively, radiological findings have been compared to both autoantibody findings and percentage apoptotic blood cells. Results: Two SLE groups could be identified: patients with normal (annexin V binding < 20%), and with increased apoptosis (annexin V binding > 20%) of peripheral blood cells. The frequency of radiological examinations in SLE patients significantly correlated with an increased percentage of apoptotic cells (p < 0.005). In patients with characteristic imaging findings (e.g. lymph node swelling, pleural effusion) an elevated percentage of apoptotic cells was present. In contrast SLE-patients with normal imaging findings or uncharacteristic results of minimal severity had normal percentages of apoptotic blood cells. Conclusion: This correlation between radiographic findings and percentage of apoptotic blood cells provides (1) further insight into pathological mechanisms of SLE, (2) will offer the possibility to introduce apoptotic biomarkers as molecular probes for clinical molecular imaging approaches in future to early diagnose organ complaints in patients with SLE, and (3) is a plea to complement molecular imaging research by this clinical approach.

  3. 76 FR 52954 - Workshop: Advancing Research on Mixtures; New Perspectives and Approaches for Predicting Adverse...

    Science.gov (United States)

    2011-08-24

    ... HUMAN SERVICES Workshop: Advancing Research on Mixtures; New Perspectives and Approaches for Predicting... ``Advancing Research on Mixtures: New Perspectives and Approaches for Predicting Adverse Human Health Effects... Research and Training, NIEHS, P.O. Box 12233, MD K3-04, Research Triangle Park, NC 27709, (telephone)...

  4. A COMBINED FUZZY MCDM APPROACH FOR IDENTIFYING THE SUITABLE LANDS FOR URBAN DEVELOPMENT: AN EXAMPLE FROM BANDAR ABBS, IRAN

    Directory of Open Access Journals (Sweden)

    Mohsen Dadras

    2014-01-01

    Full Text Available This study aims at identifying the suitable lands for urban dev elopment in Bandar Abbas city based on its real world use regarding specific crite ria and sub-criteria. The city of Bandar Abbas is considered as the most important commer cial and economic city of Iran. It is also considered as one of the major cities of Iran which has played a pivotal role in the country's development and progress in recen t years especially after the end of Iran-Iraq war owing to its embracing the country's m ain commercial ports. This process has caused the immigration rate into the city to rise significantly over the past 20 years. Thus, the development of the city is meanwhile c onsidered as a high priority. Bandar Abbas city does not have a rich capacity for g rowth and development due to its special geographical situation being located in coastal border. Among the limitations placed in the city's development way, natural limit ations (heights and sea shore in the northern and southern parts of the city and struc tural limitations (military centers in the east and west sides of the city may be referred . Therefore, identifying the suitable lands for urban development within Bandar Abbas city l imits is becoming an essential priority. Therefore, d ifferent quantitative and quali tative criteria have been studied in order to select and identify these lands. The struct ures of qualitative criteria for most parts involve ambiguities and vagueness. This leads us to use Fuzzy logic in this study as a natural method for determining the solutions fo r problems of Multi- criteria decision making (MCDM. In the current research, a com bination of MCDM methods has been presented for analysis. To assignee weights of the criteria Fuzzy AHP (analytic hierarchy process is used for land selection and Fuzzy TOPSIS (method for order priority by similarity to ideal solution is utilized to choose the alternative that is the most appropriate through these criteria weights. The

  5. Adopting a farming systems research approach to carry out an economic and environmental analysis of food supply chains

    DEFF Research Database (Denmark)

    Tavella, Elena; Pedersen, Søren Marcus; Gylling, Morten

    2012-01-01

    as to structure and manage research projects. The aim of this paper is to suggest and present a guideline for agricultural researchers to carry out an economic and environmental analysis of food supply chains with a FSR approach. We describe how participants of the EU-project SOLIBAM (Strategies for Organic...... and Low-input Integrated Breeding and Management) used the guideline to structure, manage and carry out an economic and environmental analysis of the food supply chains of concern. The FSR approach enabled the participants to jointly define and model the structure of the supply chains, identify......Agricultural systems are complex, because managers need to cope with interlinked and dynamic ecological, social, political and economic aspects. Understanding and analysing such systems requires researchers to adopt a holistic approach to grasp the links between those aspects. Holistic approaches...

  6. Structure and Evolution of Mediterranean Forest Research: A Science Mapping Approach.

    Directory of Open Access Journals (Sweden)

    Pierfrancesco Nardi

    Full Text Available This study aims at conducting the first science mapping analysis of the Mediterranean forest research in order to elucidate its research structure and evolution. We applied a science mapping approach based on co-term and citation analyses to a set of scientific publications retrieved from the Elsevier's Scopus database over the period 1980-2014. The Scopus search retrieved 2,698 research papers and reviews published by 159 peer-reviewed journals. The total number of publications was around 1% (N = 17 during the period 1980-1989 and they reached 3% (N = 69 in the time slice 1990-1994. Since 1995, the number of publications increased exponentially, thus reaching 55% (N = 1,476 during the period 2010-2014. Within the thirty-four years considered, the retrieved publications were published by 88 countries. Among them, Spain was the most productive country, publishing 44% (N = 1,178 of total publications followed by Italy (18%, N = 482 and France (12%, N = 336. These countries also host the ten most productive scientific institutions in terms of number of publications in Mediterranean forest subjects. Forest Ecology and Management and Annals of Forest Science were the most active journals in publishing research in Mediterranean forest. During the period 1980-1994, the research topics were poorly characterized, but they become better defined during the time slice 1995-1999. Since 2000s, the clusters become well defined by research topics. Current status of Mediterranean forest research (20092014 was represented by four clusters, in which different research topics such as biodiversity and conservation, land-use and degradation, climate change effects on ecophysiological responses and soil were identified. Basic research in Mediterranean forest ecosystems is mainly conducted by ecophysiological research. Applied research was mainly represented by land-use and degradation, biodiversity and conservation and fire research topics. The citation analyses

  7. Advances in the Kepler Transit Search Engine and Automated Approaches to Identifying Likely Planet Candidates in Transit Surveys

    Science.gov (United States)

    Jenkins, Jon Michael

    2015-08-01

    Twenty years ago, no planets were known outside our own solar system. Since then, the discoveries of ~1500 exoplanets have radically altered our views of planets and planetary systems. This revolution is due in no small part to the Kepler Mission, which has discovered >1000 of these planets and >4000 planet candidates. While Kepler has shown that small rocky planets and planetary systems are quite common, the quest to find Earth’s closest cousins and characterize their atmospheres presses forward with missions such as NASA Explorer Program’s Transiting Exoplanet Survey Satellite (TESS) slated for launch in 2017 and ESA’s PLATO mission scheduled for launch in 2024.These future missions pose daunting data processing challenges in terms of the number of stars, the amount of data, and the difficulties in detecting weak signatures of transiting small planets against a roaring background. These complications include instrument noise and systematic effects as well as the intrinsic stellar variability of the subjects under scrutiny. In this paper we review recent developments in the Kepler transit search pipeline improving both the yield and reliability of detected transit signatures.Many of the phenomena in light curves that represent noise can also trigger transit detection algorithms. The Kepler Mission has expended great effort in suppressing false positives from its planetary candidate catalogs. While over 18,000 transit-like signatures can be identified for a search across 4 years of data, most of these signatures are artifacts, not planets. Vetting all such signatures historically takes several months’ effort by many individuals. We describe the application of machine learning approaches for the automated vetting and production of planet candidate catalogs. These algorithms can improve the efficiency of the human vetting effort as well as quantifying the likelihood that each candidate is truly a planet. This information is crucial for obtaining valid planet

  8. Identifying postpartum intervention approaches to prevent type 2 diabetes in women with a history of gestational diabetes

    Directory of Open Access Journals (Sweden)

    Abdul-Rahim Zainab S

    2011-03-01

    Full Text Available Abstract Background Women who develop gestational diabetes mellitus (GDM have an increased risk for the development of type 2 diabetes. Despite this "window of opportunity," few intervention studies have targeted postpartum women with a history of GDM. We sought perspectives of women with a history of GDM to identify a barriers and facilitators to healthy lifestyle changes postpartum, and b specific intervention approaches that would facilitate participation in a postpartum lifestyle intervention program. Methods We used mixed methods to gather data from women with a prior history of GDM, including focus groups and informant interviews. Analysis of focus groups relied on grounded theory and used open-coding to categorize data by themes, while frequency distributions were used for the informant interviews. Results Of 38 women eligible to participate in focus groups, only ten women were able to accommodate their schedules to attend a focus group and 15 completed informant interviews by phone. We analyzed data from 25 women (mean age 35, mean pre-pregnancy BMI 28, 52% Caucasian, 20% African American, 12% Asian, 8% American Indian, 8% refused to specify. Themes from the focus groups included concern about developing type 2 diabetes, barriers to changing diet, and barriers to increasing physical activity. In one focus group, women expressed frustration about feeling judged by their physicians during their GDM pregnancy. Cited barriers to lifestyle change were identified from both methods, and included time and financial constraints, childcare duties, lack of motivation, fatigue, and obstacles at work. Informants suggested facilitators for lifestyle change, including nutrition education, accountability, exercise partners/groups, access to gyms with childcare, and home exercise equipment. All focus group and informant interview participants reported access to the internet, and the majority expressed interest in an intervention program delivered

  9. Flow cytometric and laser scanning microscopic approaches in epigenetics research.

    Science.gov (United States)

    Szekvolgyi, Lorant; Imre, Laszlo; Minh, Doan Xuan Quang; Hegedus, Eva; Bacso, Zsolt; Szabo, Gabor

    2009-01-01

    Our understanding of epigenetics has been transformed in recent years by the advance of technological possibilities based primarily on a powerful tool, chromatin immunoprecipitation (ChIP). However, in many cases, the detection of epigenetic changes requires methods providing a high-throughput (HTP) platform. Cytometry has opened a novel approach for the quantitative measurement of molecules, including PCR products, anchored to appropriately addressed microbeads (Pataki et al. 2005. Cytometry 68, 45-52). Here we show selected examples for the utility of two different cytometry-based platforms of epigenetic analysis: ChIP-on-beads, a flow-cytometric test of local histone modifications (Szekvolgyi et al. 2006. Cytometry 69, 1086-1091), and the laser scanning cytometry-based measurement of global epigenetic modifications that might help predict clinical behavior in different pathological conditions. We anticipate that such alternative tools may shortly become indispensable in clinical practice, translating the systematic screening of epigenetic tags from basic research into routine diagnostics of HTP demand.

  10. Integrative genome-wide approaches in embryonic stem cell research.

    Science.gov (United States)

    Zhang, Xinyue; Huang, Jing

    2010-10-01

    Embryonic stem (ES) cells are derived from blastocysts. They can differentiate into the three embryonic germ layers and essentially any type of somatic cells. They therefore hold great potential in tissue regeneration therapy. The ethical issues associated with the use of human embryonic stem cells are resolved by the technical break-through of generating induced pluripotent stem (iPS) cells from various types of somatic cells. However, how ES and iPS cells self-renew and maintain their pluripotency is still largely unknown in spite of the great progress that has been made in the last two decades. Integrative genome-wide approaches, such as the gene expression microarray, chromatin immunoprecipitation based microarray (ChIP-chip) and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) offer unprecedented opportunities to elucidate the mechanism of the pluripotency, reprogramming and DNA damage response of ES and iPS cells. This frontier article summarizes the fundamental biological questions about ES and iPS cells and reviews the recent advances in ES and iPS cell research using genome-wide technologies. To this end, we offer our perspectives on the future of genome-wide studies on stem cells.

  11. Identifying tree crown delineation shapes and need for remediation on high resolution imagery using an evidence based approach

    Science.gov (United States)

    Leckie, Donald G.; Walsworth, Nicholas; Gougeon, François A.

    2016-04-01

    In order to fully realize the benefits of automated individual tree mapping for tree species, health, forest inventory attribution and forest management decision making, the tree delineations should be as good as possible. The concept of identifying poorly delineated tree crowns and suggesting likely types of remediation was investigated. Delineations (isolations or isols) were classified into shape types reflecting whether they were realistic tree shapes and the likely kind of remediation needed. Shape type was classified by an evidence based rules approach using primitives based on isol size, shape indices, morphology, the presence of local maxima, and matches with template models representing trees of different sizes. A test set containing 50,000 isols based on an automated tree delineation of 40 cm multispectral airborne imagery of a diverse temperate-boreal forest site was used. Isolations representing single trees or several trees were the focus, as opposed to cases where a tree is split into several isols. For eight shape classes from regular through to convolute, shape classification accuracy was in the order of 62%; simplifying to six classes accuracy was 83%. Shape type did give an indication of the type of remediation and there were 6% false alarms (i.e., isols classed as needing remediation but did not). Alternately, there were 5% omissions (i.e., isols of regular shape and not earmarked for remediation that did need remediation). The usefulness of the concept of identifying poor delineations in need of remediation was demonstrated and one suite of methods developed and shown to be effective.

  12. FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs.

    Science.gov (United States)

    Zhou, Hongyi; Skolnick, Jeffrey

    2012-06-01

    We have developed FINDSITE(X), an extension of FINDSITE, a protein threading based algorithm for the inference of protein binding sites, biochemical function and virtual ligand screening, that removes the limitation that holo protein structures (those containing bound ligands) of a sufficiently large set of distant evolutionarily related proteins to the target be solved; rather, predicted protein structures and experimental ligand binding information are employed. To provide the predicted protein structures, a fast and accurate version of our recently developed TASSER(VMT), TASSER(VMT)-lite, for template-based protein structural modeling applicable up to 1000 residues is developed and tested, with comparable performance to the top CASP9 servers. Then, a hybrid approach that combines structure alignments with an evolutionary similarity score for identifying functional relationships between target and proteins with binding data has been developed. By way of illustration, FINDSITE(X) is applied to 998 identified human G-protein coupled receptors (GPCRs). First, TASSER(VMT)-lite provides updates of all human GPCR structures previously modeled in our lab. We then use these structures and the new function similarity detection algorithm to screen all human GPCRs against the ZINC8 nonredundant (TC identity > 30% to the target from the binding data library) on a 168 human GPCR set with known binding data, the average enrichment factor in the top 1% of the compound library (EF(0.01)) is 22.7, whereas EF(0.01) by FINDSITE is 7.1. For virtual screening when just the target and its native ligands are excluded, the average EF(0.01) reaches 41.4. We also analyze off-target interactions for the 168 protein test set. All predicted structures, virtual screening data and off-target interactions for the 998 human GPCRs are available at http://cssb.biology.gatech.edu/skolnick/webservice/gpcr/index.html .

  13. Multipronged approach to identify and validate a novel upstream regulator of Sncg in mouse retinal ganglion cells.

    Science.gov (United States)

    Chintalapudi, Sumana R; Morales-Tirado, Vanessa M; Williams, Robert W; Jablonski, Monica M

    2016-02-01

    Loss of retinal ganglion cells (RGCs) is one of the hallmarks of retinal neurodegenerative diseases, glaucoma being one of the most common. Mechanistic studies on RGCs are hindered by the lack of sufficient primary cells and consensus regarding their signature markers. Recently, γ-synuclein (SNCG) has been shown to be highly expressed in the somas and axons of RGCs. In various mouse models of glaucoma, downregulation of Sncg gene expression correlates with RGC loss. To investigate the role of Sncg in RGCs, we used a novel systems genetics approach to identify a gene that modulates Sncg expression, followed by confirmatory studies in both healthy and diseased retinae. We found that chromosome 1 harbors an expression quantitative trait locus that modulates Sncg expression in the mouse retina, and identified the prefoldin-2 (PFDN2) gene as the candidate upstream modulator of Sncg expression. Our immunohistochemical analyses revealed similar expression patterns in both mouse and human healthy retinae, with PFDN2 colocalizing with SNCG in RGCs and their axons. In contrast, in retinae from glaucoma subjects, SNCG levels were significantly reduced, although PFDN2 levels were maintained. Using a novel flow cytometry-based RGC isolation method, we obtained viable populations of murine RGCs. Knocking down Pfdn2 expression in primary murine RGCs significantly reduced Sncg expression, confirming that Pfdn2 regulates Sncg expression in murine RGCs. Gene Ontology analysis indicated shared mitochondrial function associated with Sncg and Pfdn2. These data solidify the relationship between Sncg and Pfdn2 in RGCs, and provide a novel mechanism for maintaining RGC health.

  14. A genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants.

    Directory of Open Access Journals (Sweden)

    Dong Wang

    2006-11-01

    Full Text Available Many biological processes are controlled by intricate networks of transcriptional regulators. With the development of microarray technology, transcriptional changes can be examined at the whole-genome level. However, such analysis often lacks information on the hierarchical relationship between components of a given system. Systemic acquired resistance (SAR is an inducible plant defense response involving a cascade of transcriptional events induced by salicylic acid through the transcription cofactor NPR1. To identify additional regulatory nodes in the SAR network, we performed microarray analysis on Arabidopsis plants expressing the NPR1-GR (glucocorticoid receptor fusion protein. Since nuclear translocation of NPR1-GR requires dexamethasone, we were able to control NPR1-dependent transcription and identify direct transcriptional targets of NPR1. We show that NPR1 directly upregulates the expression of eight WRKY transcription factor genes. This large family of 74 transcription factors has been implicated in various defense responses, but no specific WRKY factor has been placed in the SAR network. Identification of NPR1-regulated WRKY factors allowed us to perform in-depth genetic analysis on a small number of WRKY factors and test well-defined phenotypes of single and double mutants associated with NPR1. Among these WRKY factors we found both positive and negative regulators of SAR. This genomics-directed approach unambiguously positioned five WRKY factors in the complex transcriptional regulatory network of SAR. Our work not only discovered new transcription regulatory components in the signaling network of SAR but also demonstrated that functional studies of large gene families have to take into consideration sequence similarity as well as the expression patterns of the candidates.

  15. Use of a Machine Learning-Based High Content Analysis Approach to Identify Photoreceptor Neurite Promoting Molecules.

    Science.gov (United States)

    Fuller, John A; Berlinicke, Cynthia A; Inglese, James; Zack, Donald J

    2016-01-01

    High content analysis (HCA) has become a leading methodology in phenotypic drug discovery efforts. Typical HCA workflows include imaging cells using an automated microscope and analyzing the data using algorithms designed to quantify one or more specific phenotypes of interest. Due to the richness of high content data, unappreciated phenotypic changes may be discovered in existing image sets using interactive machine-learning based software systems. Primary postnatal day four retinal cells from the photoreceptor (PR) labeled QRX-EGFP reporter mice were isolated, seeded, treated with a set of 234 profiled kinase inhibitors and then cultured for 1 week. The cells were imaged with an Acumen plate-based laser cytometer to determine the number and intensity of GFP-expressing, i.e. PR, cells. Wells displaying intensities and counts above threshold values of interest were re-imaged at a higher resolution with an INCell2000 automated microscope. The images were analyzed with an open source HCA analysis tool, PhenoRipper (Rajaram et al., Nat Methods 9:635-637, 2012), to identify the high GFP-inducing treatments that additionally resulted in diverse phenotypes compared to the vehicle control samples. The pyrimidinopyrimidone kinase inhibitor CHEMBL-1766490, a pan kinase inhibitor whose major known targets are p38α and the Src family member lck, was identified as an inducer of photoreceptor neuritogenesis by using the open-source HCA program PhenoRipper. This finding was corroborated using a cell-based method of image analysis that measures quantitative differences in the mean neurite length in GFP expressing cells. Interacting with data using machine learning algorithms may complement traditional HCA approaches by leading to the discovery of small molecule-induced cellular phenotypes in addition to those upon which the investigator is initially focusing.

  16. A Coordinated Approach to Curricular Review and Development in Undergraduate Geoscience Programs: Using a Matrix to Identify and Track Skills and Skill Development

    Science.gov (United States)

    MacDonald, R.; Savina, M. E.

    2003-12-01

    One approach to curriculum review and development is to construct a matrix of the desired skills versus courses in the departmental curriculum. The matrix approach requires faculty to articulate their goals, identify specific skills, and assess where in the curriculum students will learn and practice these skills and where there are major skills gaps. Faculty members in the Geology Department at Carleton College developed a matrix of skills covered in geology courses with the following objectives: 1) Geology majors should begin their "senior integrative exercise" having practiced multiple times all of the formal steps in the research process (recognizing problems, writing proposals, carrying out a project, reporting a project in several ways); 2) Geology majors should learn and practice a variety of professional and life skills life (e.g. computer skills, field skills, lab skills, and interpretive skills).The matrix was used to identify where in the curriculum various research methods and skills were addressed and to map potential student experiences to the objectives. In Carleton's non-hierarchical curriculum, the matrix was used to verify that students have many opportunities to practice research and life skills regardless of the path they take to completion of the major. In William and Mary's more structured curriculum, the matrix was used to ensure that skills build upon each other from course to course. Faculty members in the Geology Department at the College of William and Mary first used this approach to focus on teaching quantitative skills across the geology curriculum, and later used it in terms of teaching research, communication, and information literacy skills. After articulating goals and skills, faculty members in both departments developed more specific skill lists within each category of skills, then described the current assignments and activities in each course relative to the specific components of the matrix and discussed whether to add

  17. Exploring teacher's perceptions of concept mapping as a teaching strategy in science: An action research approach

    Science.gov (United States)

    Marks Krpan, Catherine Anne

    In order to promote science literacy in the classroom, students need opportunities in which they can personalize their understanding of the concepts they are learning. Current literature supports the use of concept maps in enabling students to make personal connections in their learning of science. Because they involve creating explicit connections between concepts, concept maps can assist students in developing metacognitive strategies and assist educators in identifying misconceptions in students' thinking. The literature also notes that concept maps can improve student achievement and recall. Much of the current literature focuses primarily on concept mapping at the secondary and university levels, with limited focus on the elementary panel. The research rarely considers teachers' thoughts and ideas about the concept mapping process. In order to effectively explore concept mapping from the perspective of elementary teachers, I felt that an action research approach would be appropriate. Action research enabled educators to debate issues about concept mapping and test out ideas in their classrooms. It also afforded the participants opportunities to explore their own thinking, reflect on their personal journeys as educators and play an active role in their professional development. In an effort to explore concept mapping from the perspective of elementary educators, an action research group of 5 educators and myself was established and met regularly from September 1999 until June 2000. All of the educators taught in the Toronto area. These teachers were interested in exploring how concept mapping could be used as a learning tool in their science classrooms. In summary, this study explores the journey of five educators and myself as we engaged in collaborative action research. This study sets out to: (1) Explore how educators believe concept mapping can facilitate teaching and student learning in the science classroom. (2) Explore how educators implement concept

  18. A System-Wide Approach to Identify the Mechanisms of Barnacle Attachment: Toward the Discovery of New Antifouling Compounds

    KAUST Repository

    Al-Aqeel, Sarah

    2015-11-01

    Biofouling is a significant economic problem, particularly for marine and offshore oil industries. The acorn barnacle (Amphibalanus (Balanus) amphitrite) is the main biofouling organism in marine environments. Environmental conditions, the physiology of the biofouling organism, the surrounding microbial community, and the properties of the substratum can all influence the attachment of biofouling organisms to substrates. My dissertation investigated the biological processes involved in B. amphitrite development and attachment in the unique environment of the Red Sea, where the average water surface temperature is 34°C and the salinity reaches 41‰. I profiled the transcriptome and proteome of B. amphitrite at different life stages (nauplius II, nauplius VI, and cyprid) and identified 65,784 expressed contigs and 1387 expressed proteins by quantitative proteomics. During the planktonic stage, genes related to osmotic stress, salt stress, the hyperosmotic response, and the Wnt signaling pathway were strongly up-regulated, hereas genes related to the MAPK pathway, lipid metabolism, and cuticle development were down-regulated. In the transition from the nauplius VI to cyprid stages, there was up-regulation of genes involved in blood coagulation, cuticle development, and eggshell formation, and down-regulation of genes in the nitric oxide pathway, which stimulates the swimming and feeding responses of marine invertebrates. This system-wide integrated approach elucidated the development and attachment pathways important in B. amphitrite. Enzymes and metabolites in these pathways are potential molecular targets for the development of new antifouling compounds.

  19. Ethics in Violence and Abuse Research - a Positive Empowerment Approach

    OpenAIRE

    Julia Downes; Liz Kelly; Nicole Westmarland

    2014-01-01

    Research governance, including research ethics committees and data protection legislation, is invested in protecting the individual rights of participants in social care and health research. Increasingly funders expect evidence of outcomes that engage with 'service users', making research critical in supporting social interventions to compete for scant resources in an economic climate marked by 'austerity' (Sullivan 2011). This article focuses on the tensions that can arise from the research ...

  20. OBJECT-ORIENTED APPROACH TO IDENTIFYING THE RELEVANCE OF IT-EDUCATION TO THE LABOR MARKET DEMAND

    Directory of Open Access Journals (Sweden)

    Masuma H. Mamedova

    2014-01-01

    Full Text Available The paper deals with the issues of human resources development and IT-staff training. The authors put a special emphasis on bringing the IT-staff training system in line with the labor market demands both in quantitative and qualitative terms. Based on the object-oriented approach, the authors explore the reasons behind the existing imbalance between the markets of IT-education services and IT-specialists in Azerbaijan, the challenges facing the IT education and specificity of the IT-specialists market being described.For overcoming the above gap between the IT labor market supply and demand, the authors put forward a model of professional competences, reflecting the real-life requirements for a specialist’s quality. Additionally, the paper outlines the recommended trends of IT-sector development in Azerbaijan, which include organization of innovative research and education centers for specialists’ training and retraining, legislative and institutional coordination of the IT industry and education, development of new educational standards, increase in the number of IT-profile students.

  1. An international eDelphi study identifying the research and education priorities in wound management and tissue repair.

    LENUS (Irish Health Repository)

    2012-02-01

    Aim. To incorporate an international and multidisciplinary consensus in the determination of the research and education priorities for wound healing and tissue repair. Background. A compelling reason for the study is the lack of an agreed list of priorities for wound care research and education. Furthermore, there is a growth in the prevalence of chronic wounds, a growth in wound care products and marketing, and an increase in clinician attendance at conferences and education programmes. Design. The study used a survey method. Methods. A four-round eDelphi technique was used to collect responses from an international population of health professionals across 24 countries. Results. Responses were obtained from 360 professionals representing many health care settings. The top education priorities related to the standardisation of all foundation education programmes in wound care, the inclusion of wound care in all professional undergraduate and postgraduate education programmes, selecting dressings and the prevention of pressure ulcers. The top research priorities related to the dressing selection, pressure ulcer prevention and wound infection. Conclusion. Professionals from different backgrounds and countries who are engaged in wound management share a common set of priorities for research and education. Most notably, the priorities identified relate to long-established clinical challenges in wound care and underpin the principles of good patient care practices. The priorities are closely allied to an ageing population and identify many challenges ahead for practitioners engaged in wound management services. Relevance to clinical practice. The provision of wound care is a major investment of health service resources and remains a clinical challenge today. Research is essential to building evidence-based practice and fundamental to development of quality in standards of practice; education is central to achieving competence to deliver effective care. The

  2. Approaches to Mixed Methods Dissemination and Implementation Research: Methods, Strengths, Caveats, and Opportunities

    OpenAIRE

    Green, Carla A.; Duan, Naihua; Gibbons, Robert D.; Hoagwood, Kimberly E; Palinkas, Lawrence A.; Wisdom, Jennifer P.

    2015-01-01

    Limited translation of research into practice has prompted study of diffusion and implementation, and development of effective methods of encouraging adoption, dissemination and implementation. Mixed methods techniques offer approaches for assessing and addressing processes affecting implementation of evidence-based interventions. We describe common mixed methods approaches used in dissemination and implementation research, discuss strengths and limitations of mixed methods approaches to data...

  3. Identifying users of traditional and Internet-based resources for meal ideas: An association rule learning approach.

    Science.gov (United States)

    Doub, Allison E; Small, Meg L; Levin, Aron; LeVangie, Kristie; Brick, Timothy R

    2016-08-01

    Increasing home cooking while decreasing the consumption of food prepared away from home is a commonly recommended weight management strategy, however research on where individuals obtain ideas about meals to cook at home is limited. This study examined the characteristics of individuals who reported using traditional and Internet-based resources for meal ideas. 583 participants who were ≥50% responsible for household meal planning were recruited to approximate the 2014 United States Census distribution on sex, age, race/ethnicity, and household income. Participants reported demographic characteristics, home cooking frequency, and their use of 4 traditional resources for meal ideas (e.g., cookbooks), and 7 Internet-based resources for meal ideas (e.g., Pinterest) in an online survey. Independent samples t-tests compared home cooking frequency by resource use. Association rule learning identified those demographic characteristics that were significantly associated with resource use. Family and friends (71%), food community websites (45%), and cookbooks (41%) were the most common resources reported. Cookbook users reported preparing more meals at home per week (M = 9.65, SD = 5.28) compared to non-cookbook users (M = 8.11, SD = 4.93; t = -3.55, p Resource use was generally higher among parents and varied systematically with demographic characteristics. Findings suggest that home cooking interventions may benefit by modifying resources used by their target population.

  4. A multi-criteria approach to identify favorable areas for goat production systems in Veracruz, México.

    Science.gov (United States)

    Ramírez-Rivera, Emmanuel de Jesús; Lopez-Collado, Jose; Díaz-Rivera, Pablo; Ortega-Jiménez, Eusebio; Torres-Hernández, Glafiro; Jacinto-Padilla, Jazmín; Herman-Lara, Erasmo

    2017-02-09

    This research identifies favorable areas for goat production systems in the state of Veracruz, Mexico. Through the use of the analytic hierarchy process, layers of biophysical and soil information were combined to generate a model of favorability. Model validation was performed by calculating the area under the curve, the true skill statistic, and a qualitative comparison with census records. The results showed the existence of regions with high (4494.3 km(2)) and moderate (2985.8 km(2)) favorability, and these areas correspond to 6.25 and 4.15%, respectively, of the state territory and are located in the regions of Sierra de Huayacocotla, Perote, and Orizaba. These regions are characterized as mountainous and having predominantly temperate-wet or cold climates, and having montane mesophilic forests, containing pine, fir, and desert scrub. The reliability of the distribution model was supported by the area under the curve value (0.96), the true skill statistic (0.86), and consistency with census records.

  5. A Cost Benefit Analysis Approach to Identify Improvements in Merchant Navy Deck Officers’ HELM (Human Element Leadership and Management Training

    Directory of Open Access Journals (Sweden)

    Farhan Saeed

    2016-12-01

    Full Text Available A review of maritime accidents conducted over the last decade confirms that human error is the main contributing factor in these incidents. Well-developed Non-Technical Skills (NTS can reduce the effects of human error. NTS include both interpersonal and cognitive skills such as situation awareness, teamwork, decision-making, leadership, managerial skills, communication and language skills. In a crisis situation good NTS allow a deck officer to recognise the problem quickly, take action to manage the situation, and utilise the available team members safely and effectively. This paper identifies the importance of NTS training for merchant navy deck officers. It also highlights room for improvement in the existing HELM training. Research has shown that at present the structure of HELM training is not very effective. The other safety critical domains’ efforts into NTS developments are investigated and examples of best practice are adapted into the maritime domain’s NTS training. Suggestions are given for improvements to the HELM course based on proven successful methods in other safety critical domains (aviation and anaesthesia. A subsequent Cost Benefit Analysis for improving deck officers’ NTS is also carried out through the use of Bayesian Networks and Decision Tree Modelling.

  6. Neuroproteomics and Systems Biology Approach to Identify Temporal Biomarker Changes Post Experimental Traumatic Brain Injury in Rats

    Directory of Open Access Journals (Sweden)

    Firas H Kobeissy

    2016-11-01

    Full Text Available Traumatic brain injury (TBI represents a critical health problem of which diagnosis, management and treatment remain challenging. TBI is a contributing factor in approximately 1/3 of all injury-related deaths in the United States. The Centers for Disease Control and Prevention (CDC estimate that 1.7 million TBI people suffer a TBI in the United States annually. Efforts continue to focus on elucidating the complex molecular mechanisms underlying TBI pathophysiology and defining sensitive and specific biomarkers that can aid in improving patient management and care. Recently, the area of neuroproteomics-systems biology is proving to be a prominent tool in biomarker discovery for central nervous system (CNS injury and other neurological diseases. In this work, we employed the controlled cortical impact (CCI model of experimental TBI in rat model to assess the temporal-global proteome changes after acute (1 day and for the first time, subacute (7 days, post-injury time frame using the established CAX-PAGE LC-MS/MS platform for protein separation combined with discrete systems biology analyses to identify temporal biomarker changes related to this rat TBI model. Rather than focusing on any one individual molecular entities, we used in silico systems biology approach to understand the global dynamics that govern proteins that are differentially altered post-injury. In addition, gene ontology analysis of the proteomic data was conducted in order to categorize the proteins by molecular function, biological process, and cellular localization. Results show alterations in several proteins related to inflammatory responses and oxidative stress in both acute (1 day and subacute (7 days periods post TBI. Moreover, results suggest a differential upregulation of neuroprotective proteins at 7-days post-CCI involved in cellular functions such as neurite growth, regeneration, and axonal guidance. Our study is amongst the first to assess temporal neuroproteome

  7. A Mixed Methods Approach to Equity and Justice Research: Insights from Research on Children's Reasoning About Economic Inequality.

    Science.gov (United States)

    Mistry, Rashmita S; White, Elizabeth S; Chow, Kirby A; Griffin, Katherine M; Nenadal, Lindsey

    2016-01-01

    Mixed methods research approaches are gaining traction across various social science disciplines, including among developmental scientists. In this chapter, we discuss the utility of a mixed methods research approach in examining issues related to equity and justice. We incorporate a brief overview of quantitative and qualitative monomethod research approaches in our larger discussion of the advantages, procedures, and considerations of employing a mixed methods design to advance developmental science from an equity and justice perspective. To better illustrate the theoretical and practical significance of a mixed methods research approach, we include examples of research conducted on children and adolescents' conceptions of economic inequality as one example of developmental science research with an equity and justice frame.

  8. Policy, Research and Residents’ Perspectives on Built Environments Implicated in Heart Disease: A Concept Mapping Approach

    Directory of Open Access Journals (Sweden)

    Ivana Stankov

    2017-02-01

    Full Text Available An underrepresentation of stakeholder perspectives within urban health research arguably limits our understanding of what is a multi-dimensional and complex relationship between the built environment and health. By engaging a wide range of stakeholders using a participatory concept mapping approach, this study aimed to achieve a more holistic and nuanced understanding of the built environments shaping disease risk, specifically cardiometabolic risk (CMR. Moreover, this study aimed to ascertain the importance and changeability of identified environments through government action. Through the concept mapping process, community members, researchers, government and non-government stakeholders collectively identified eleven clusters encompassing 102 built environmental domains related to CMR, a number of which are underrepresented within the literature. Among the identified built environments, open space, public transportation and pedestrian environments were highlighted as key targets for policy intervention. Whilst there was substantive convergence in stakeholder groups’ perspectives concerning the built environment and CMR, there were disparities in the level of importance government stakeholders and community members respectively assigned to pedestrian environments and street connectivity. These findings support the role of participatory methods in strengthening how urban health issues are understood and in affording novel insights into points of action for public health and policy intervention.

  9. The Impact of a Multifaceted Approach to Teaching Research Methods on Students' Attitudes

    Science.gov (United States)

    Ciarocco, Natalie J.; Lewandowski, Gary W., Jr.; Van Volkom, Michele

    2013-01-01

    A multifaceted approach to teaching five experimental designs in a research methodology course was tested. Participants included 70 students enrolled in an experimental research methods course in the semester both before and after the implementation of instructional change. When using a multifaceted approach to teaching research methods that…

  10. The Impact of a Multifaceted Approach to Teaching Research Methods on Students' Attitudes

    Science.gov (United States)

    Ciarocco, Natalie J.; Lewandowski, Gary W., Jr.; Van Volkom, Michele

    2013-01-01

    A multifaceted approach to teaching five experimental designs in a research methodology course was tested. Participants included 70 students enrolled in an experimental research methods course in the semester both before and after the implementation of instructional change. When using a multifaceted approach to teaching research methods that…

  11. 76 FR 45268 - Center for Drug Evaluation and Research, Approach to Addressing Drug Shortage; Public Workshop

    Science.gov (United States)

    2011-07-28

    ... HUMAN SERVICES Food and Drug Administration Center for Drug Evaluation and Research, Approach to... approach of the Center for Drug Evaluation and Research (CDER) to addressing drug shortages. This public... Benner, Center for Drug Evaluation and Research, Food and Drug Administration, 10903 New Hampshire...

  12. The Participatory Research Approach in Non-Western Countries: Practical Experiences from Central Asia and Zambia

    Science.gov (United States)

    Katsui, Hisayo; Koistinen, Mari

    2008-01-01

    This paper focuses on the application of the participatory research approach in non-Western contexts. The aim is to provide critical insights into the participatory research discourse through an examination of its theory and practice based on our own experiences of using this approach in our doctoral research in five Central Asian countries and…

  13. Genetics in psychosomatic medicine : research designs and statistical approaches

    NARCIS (Netherlands)

    McCaffery, Jeanne M.; Snieder, Harold; Dong, Yanbin; de Geus, Eco

    2007-01-01

    It has become increasingly clear that genetic factors influence many of the behaviors and disease endpoints of interest to psychosomatic medicine researchers. There has been increasing interest in incorporating genetic variation markers into psychosomatic research. In this Statistical Corner article

  14. Engendering Change within a Water Infrastructure Client Organisation: A Participatory Action Research Approach

    Directory of Open Access Journals (Sweden)

    Michael Potts

    2015-07-01

    Full Text Available Continuing demands by stakeholders for improved service delivery has caused Infrastructure Client Organisations (ICO in the UK to embark upon organisational restructuring. It is expected that such restructuring would enhance cost-effectiveness and quality in asset management and service delivery. However, this change, if not properly managed and sustained, could result in the inability of the ICO to achieve these targets. This study outlines the use of systemic thinking and Participatory Action Research (PAR in driving and managing such change within a UK-based Water and Wastewater ICO (UK WASC. Besides highlighting the context for change in response to policy, austerity and regulatory pressures, this study portrays how the PAR approach can assist in the management of change within ICOs. Furthermore, it provides an insight into the evolution of an external researcher, from novice to expert within the ICO, imbued with the required knowledge to encourage other stakeholders to participate in driving the change management process. Preliminary findings indicate the usefulness of this phased approach toward PAR. This study provides a platform for researchers wishing to engage with ICOs to improve service delivery, identifying the value of engagement, change and systemic thinking.

  15. HEDIS Research Identifiable Files

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Healthcare Effectiveness Data and Information Set (HEDIS) is a tool used by more than 90 percent of Americas health plans to measure performance on important...

  16. Consilient research approaches in studying gene x environment interactions in alcohol research.

    Science.gov (United States)

    Sher, Kenneth J; Dick, Danielle M; Crabbe, John C; Hutchison, Kent E; O'Malley, Stephanie S; Heath, Andrew C

    2010-04-01

    This review article discusses the importance of identifying gene-environment interactions for understanding the etiology and course of alcohol use disorders and related conditions. A number of critical challenges are discussed, including the fact that there is no organizing typology for classifying different types of environmental exposures, many key human environmental risk factors for alcohol dependence have no clear equivalents in other species, much of the genetic variance of alcohol dependence in human is not 'alcohol specific', and the potential range of gene-environment interactions that could be considered is so vast that maintaining statistical control of Type 1 errors is a daunting task. Despite these and other challenges, there appears to be a number of promising approaches that could be taken in order to achieve consilience and ecologically valid translation between human alcohol dependence and animal models. Foremost among these is to distinguish environmental exposures that are thought to have enduring effects on alcohol use motivation (and self-regulation) from situational environmental exposures that facilitate the expression of such motivations but do not, by themselves, have enduring effects. In order to enhance consilience, various domains of human approach motivation should be considered so that relevant environmental exposures can be sampled, as well as the appropriate species to study them in (i.e. where such motivations are ecologically relevant). Foremost among these are social environments, which are central to the initiation and escalation of human alcohol consumption. The value of twin studies, human laboratory studies and pharmacogenetic studies is also highlighted.

  17. Framing design research for service orientation through PSS approaches

    DEFF Research Database (Denmark)

    Sakao, Tomohiko; Sandström, Gunilla Ölundh; Matzen, Detlef

    2009-01-01

    , as a first step, proposes a way to frame such design research. First, an extensive literature review is performed of over 100 articles on not only PSS-design research but also on related research in fields as PSS in general, service design, innovation, and business models in a broad view. Based......In order to respond to the industrial trend towards service design and delivery, design research must address a vast area partially related to value creation, marketing and network theories. However, compared to the space to be explored, there is little insight available. Thus, this paper...... on the literature analysis, the authors present three crucial dimensions for service oriented design research, i.e. an offer dimension representing products and services, a provider dimension, and a customer/user dimension. In addition, three research targets are proposed; PSS-offer modelling, PSS development...

  18. Faculty research productivity in allied health settings: a TQM approach.

    Science.gov (United States)

    Paterson, M; Baker, D; Gable, C; Michael, S; Wintch, K

    1993-01-01

    Faculty research productivity in colleges of allied health has often been discussed in the literature over the last five years. Articles have focused on the problem of faculty research productivity from various viewpoints, but none have used a theoretical framework to analyze the problem. The total quality management (TQM) framework is currently being used in health care to improve quality and productivity. This article uses the TQM framework to synthesize literature concerning faculty research productivity and verifies the current relevance of synthesis findings using an allied health faculty survey. These analyses show that the TQM framework is useful in suggesting ways to increase faculty research productivity in colleges of allied health.

  19. Operations Research Approaches to Asset Management in Freight Rail

    DEFF Research Database (Denmark)

    Gorman, Michael F.; Harrod, Steven

    2011-01-01

    This article describes operations research methodologies as they apply to asset management in freight rail. We describe state-of-the-art methods for locomotive, crew, railcar, line and yard planning and management. We conclude with emerging areas of research in rail.......This article describes operations research methodologies as they apply to asset management in freight rail. We describe state-of-the-art methods for locomotive, crew, railcar, line and yard planning and management. We conclude with emerging areas of research in rail....

  20. Assessing quality in European educational research indicators and approaches

    CERN Document Server

    Åström, Fredrik; Hansen, Antje

    2014-01-01

    Competition-based models for research policy and management have an increasing influence throughout the research process, from attracting funding to publishing results. The introduction of quality control methods utilizing various forms of performance indicators is part of this development. The authors presented in this volume deal with the following questions: What counts as ‘quality’ and how can this be assessed? What are the possible side effects of current quality control systems on research conducted in the European Research Area, especially in the social sciences and the humanities?